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A

a - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Implicit curve parameter a.
A - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Optimization matrix A, to be modified by snake energies in each iteration.
Abl_X(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Calculate the x-derivative of the gradient image.
Abl_Y(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Calculate the y-derivative of the gradient image.
abs(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Absolute values of the image elements.
abs(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Absolute values of the image elements.
abs_diff(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Absolute difference of the elements of two images
absDiff(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Absolute difference of two images.
AbsenceDetectionMethod() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.AbsenceDetectionMethod
 
AbstractAssociationDistribution<S extends Copyable<?>,T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class for association distributions that allow sampling of the association variables for a set of observations in a multi-target tracking framework.
AbstractAssociationDistribution(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, DataAssociationFactory) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
Constructor
AbstractMultiObservationDistribution<S extends Copyable<?>,T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class for multi target observation distributions.
AbstractMultiObservationDistribution(AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<S>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
Constructor to set the condition conditionX, and the factories of multi state and multi observation variables
AbstractMultiObservationDistributionIndep<S extends Copyable<?>,T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class for multi target observation distributions.
AbstractMultiObservationDistributionIndep(AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<S>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Constructor to set the condition conditionX, and the factories of multi state and multi observation variables
AbstractMultiState<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts
Abstract class to hold the states of multiple targets.
AbstractMultiState(AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Constructor that assigns a factory
AbstractMultiStateFactory<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts
Factory class for creating new multi state objects
AbstractMultiStateFactory(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Constructor with specification of the variables of a single state
AbstractMultiStateTransitionDistribution<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class for multi-target state transition distributions.
AbstractMultiStateTransitionDistribution(AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
Constructor to set the condition X, and the factories of multi state and multi observation variables
AbstractMultiStateTransitionDistributionIndep<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class of multi-target state transition distribution with independent targets.
AbstractMultiStateTransitionDistributionIndep(AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistributionIndep
 
accept(File) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow.DataTabFileFilter
 
accept(File) - Method in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
acceptStacks(File) - Method in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
accuracy - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Local accuracy for comparisons of values against zero.
acot(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Return the arcus cotangens of value in radian.
ActinAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton
Operator for analyzing actin filament structures in 2D images.
ActinAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Default constructor.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
Fires a PropertyChangeEvent with property CheckBoxPanel.CHECK_CHANGED_PROPERTY if a checkbox value was changed
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Assigns the reader options to the option variables when a file selection is approved by the file chooser.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Assigns the writer options to the option variables when a file selection is approved by the file chooser.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Assigns the selected radio button string and fires a PropertyChangeEvent with property RadioButtonPanel.SELECTION_CHANGED_PROPERTY
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
 
activeImage - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Image currently under processing.
activePlus - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Reference to currently active image.
activeProcessor - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Reference to processor of currently active image LabelImageEditor.activePlus.
activeSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Array with active snakes.
activityArray - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Vector tagging regions as active or not during presegmentation phase.
activityArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Array of active snakes, suitable for masking snakes in optimization.
actualSliceOnly - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
adaptedGamma - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
The new and adapted gamma values for all snake points.
adapter - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
Adapter object to be iterated over.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Gamma adaptation using fixed decreasing factor for all gamma values.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
No gamma adaptation is made.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
Gamma adaptation using a point wise adaptation, depending on the current snake and the external energy force.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Method for gamma adaptation.
add(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
add(MTBBorder2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Append a border (at the end) to the set of borders.
add(MTBContour2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Append a contour (at the end) to the set of contours.
add(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
add histogram data to this MTBHistogram object.
add(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Append a new segment (at the end) to the set of line segments.
add(Point2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
add(MTBPolygon2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Append a polygon (at the end) to the set of polygons.
add(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Append a region (at the end) to the set of regions.
add(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Add a region set to this bag
add(MTBRegion3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Append a region (at the end) to the set of regions.
add(MTBSurface3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Append a region (at the end) to the set of regions
add(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Appends the specified element to the end of this list.
add(MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Appends the specified element to the end of this list.
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Method to add two images.
add(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Add a constant to each image value
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Add the elements of two images
add(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Add a constant to each image value
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Add the elements two images
add(TrackEvaluator.TrackEvaluatorResult) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
addActionListenerToButtons(ActionListener) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Adds external action listeners to buttons.
addAll(MTBPoint2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
addBordersToRoiManager(MTBBorder2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds a set of 2D borders to the ROI manager.
addChild(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Add a new child to the node.
addCloseButtonPanel() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Adds set of control buttons to the main panel.
addContoursToRoiManager(MTBContour2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds a set of 2D contours to the ROI manager.
addCurrentInfo(double, DataAssociation, AbstractMultiState<T>, Set<Short>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Add sample info of the current time step
addData(Vector<Vector<Point2D.Double>>, Vector<Vector<Line2D.Double>>, int[], Vector<Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Add data to the current neurite object.
addEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Add a edge to MTBGraph.
addElementAt(int, MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Inserts the specified element at the specified position in this list.
addElementAt(int, MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Inserts the specified element at the specified position in this list.
addEnergy(T, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Append another energy to the list.
addEnergy(T) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Append another energy to the list with default weight 1.0.
addEnergy(MTBLevelsetEnergyDerivable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Append another energy to the list.
addEnergy(MTBLevelsetEnergyDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Append another energy to the list with default weight 1.0.
addEnergy(MTBSnakeEnergyComputable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Append another energy to the list.
addEnergy(MTBSnakeEnergyComputable) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Append another energy to the list with default weight 1.0.
addEnergy(MTBSnakeEnergyDerivable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Append another energy to the list.
addEnergy(MTBSnakeEnergyDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Append another energy to the list with default weight 1.0.
addEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Add button for energies.
addFeatures(double, double[]) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
add the given patterns (feature arrays) together with their corresponding label to the existing patterns used to train the SVM
addFile(String) - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Adds a file to the list of the node.
addFirst(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Inserts the specified element at the beginning of this list.
addImage(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
addIndentationSegments(LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment>) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Add list of indentation segments to object.
addIndepGaussian(GaussianDistribution, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Add an independent Gaussian state distribution
addInEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Add a incoming MTBGraphEdge to the MTBGraphNode
addInflectionPoints(LinkedList<MorphologyAnalyzer2DInProData.InflectionPoint>) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Add list of inflection points to object.
addInner(MTBBorder2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Add an inner border to the existing border object.
addInner(MTBBorder2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Add a inner contour to the existing contour object.
addInnerContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Adding the possible inner contours to the outer contour of a region.
additionalResultsWanted - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Flag to activate calculation of additional result images.
addLast(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Appends the specified element to the end of this list.
addMarker(CellCntrMarker) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Adds a marker to the vector.
addNewResult(SegResult_Complete) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
 
addNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Add a node to MTBGraph.
addOutEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Add a outgoing MTBGraphEdge to the MTBGraphNode
addParameterInputFields(JPanel) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Adds the input fields for all relevant parameters.
addPixel(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Add a 2D point to the existing border.
addPixel(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Append a point to the region from the given coordinates.
addPixel(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Append a point to the region from the given point object.
addPoint(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
addPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Appends a new point to the end of the polygon.
addPoint(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Append a 3D point to the region.
addPoint(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Append a point to the region from the given coordinates.
addPoint(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
Append a 3D point to the region.
addPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Overwrites Polygon2D method.
addPolygonsToRoiManager(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds a set of polygons to the ROI manager.
addPolygonToRoiManager(MTBPolygon2D) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds the given polygon to the ROI manager.
addProtrusionSegments(LinkedList<MorphologyAnalyzer2DInProData.InProContourSegment>) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Add list of protrusion segments to object.
addRegionsToRoiManager(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds a set of 2D regions to the ROI manager.
addResult(FeatureCalculatorResult[]) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Adds result data to the object.
addResultImages - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Vector of additional result images.
addResultImages(FeatureCalculatorResult[]) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Generates a visual representation of the tile data and stores it.
addSegmentationResult(SegResult_Particles) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Method is to be called for cleaning-up the operator resources.
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
addSubgraph(MTBGraph, Color) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Specify a subgraph that is to be painted in the given color.
addSubgraphAdjaceny(AdjacencyMatrix<T>, Color) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Specify a subgraph that is to be painted in the given color.
AdjacencyMatrix<T extends Comparable<?>> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
Interface for the adjacency matrix of a graph.
adjmatrix - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
adjMatrix - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
adoptSliceLabels(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Copy slice labels from src to this
algorithm - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
The algorithm used for estimating the curvature.
Algorithm() - Constructor for enum de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator.Algorithm
 
alpha - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
alpha - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Weighting factor for snake length term.
alphaDecrease - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
Value by which alpha is decreased in each iteration.
alphaInitial - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Initial weighting factor for the length term, should be > 0.
alphas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Vector of point-specific alpha values.
alphaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Update function for alpha values.
alphaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
alphaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
Update function for alphas.
analysisDisplayImg - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Image illustrating analysis results.
analyzedImages - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Vector with all analyzed image files.
analyzeIntensities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
analyzeIntensities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeIntensities(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeLocalCurvatures() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Calculates and analyses pixel-wise local curvatures.
analyzeProtrusionsIndentations - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Flag to turn on/off analysis of protrusions and indentations.
analyzerList - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Set of feature calculator identifiers.
analyzeShapes - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
analyzeShapes - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeShapes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeTrajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
analyzeTrajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeTrajectories(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
and(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Bitwise logical AND of two images.
and(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Bitwise logical AND of two images.
angle(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
angle - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Orientation of the filter.
angleDiff360(double, double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
 
angleDiff360(double, double) - Static method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Compute angle difference of two angles in interval 0 up to 360 degree
angleDiffPM180(double, double) - Static method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Compute angle difference of two angles in interval -180 up to 180 degree
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Angular sampling step size.
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Angular sampling interval.
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Sampling step size for orientations.
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Sampling step size for orientations considered.
angularSecondMoment - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
apicalLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Apical length of the segment, from equator to top.
ApplicationMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D.ApplicationMode
 
applyComponentWise - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Flag to activate component-wise application, yields a binary result image.
applyMask(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Invokes dilation.
applyMask(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Invokes erosion.
applyMaskBinary(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Applies a dilation mask to the given binary image.
applyMaskBinary(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Applies an erosion mask to the given binary image.
applyMaskGray(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Applies a dilation mask to the given intensity image.
applyMaskGray(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Applies an erosion mask to the given intensity image.
applyNiblackThreshold(MTBImage, int, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
This function implements the conventional (enhanced) Niblack binarization.
applyNiblackThreshold_withLocalVarCheck(MTBImage, int, double, double, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
This function implements the conventional Niblack binarization, enhanced with a local variance check.
applyNiblackThresholdMaskwise(MTBImage, int, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Enhanced Niblack binarization applied maskwise to the image, i.e. all pixels inside the mask get the same threshold.
applyNiblackThresholdWholeImage(ImageProcessor, double, double, ImagePlus) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Deprecated.
applyNiblackThresholdWholeImage(MTBImage, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
This function implements the conventional (enhanced) Niblack binarization.
applyRamerDouglasPeuckerAlgorithm(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
Algorithm idea: - Urs Ramer, "An iterative procedure for the polygonal approximation of plane curves", Computer Graphics and Image Processing, 1(3), 244–256 (1972) doi:10.1016/S0146-664X(72)80017-0 - David Douglas & Thomas Peucker, "Algorithms for the reduction of the number of points required to represent a digitized line or its caricature", The Canadian Cartographer 10(2), 112–122 (1973) doi:10.3138/FM57-6770-U75U-7727 Implementation according to: https://www.namekdev.net/2014/06/iterative-version-of-ramer-douglas-peucker-line-simplification-algorithm/
applyRamerDouglasPeuckerAlgorithm(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
Calls MTBPoint2DSet.applyRamerDouglasPeuckerAlgorithm(int, int, double) with the first and last point of the point list.
applyVesselnessFilter(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Gaussian smoothing and vesselness enhancement filtering.
approxFunction - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Helper to calculate values of approximated Dirac impulse function.
ApproxVersion() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper.ApproxVersion
 
area - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Size of region in pixels.
areaFraction - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Area fraction factor.
areaFraction - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Area fraction factor.
ArealParameterExtractor - Class in de.unihalle.informatik.MiToBo.apps.biofilms
operator for calculating areal parameters from biofilm images as described in Yang et al., Quantifying biofilm structure using image analysis.
ArealParameterExtractor() - Constructor for class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
ArealParameterExtractor(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
arealPorosity - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
areas - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
areas - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
areas - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Region sizes, entry with index 0 is assumed to refer to background.
areas - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Region sizes.
areas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
areAssociated(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
Determine if target and observation are associated.
areAssociated(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Ask if the specified target and observation are associated
areRegionsInManagerAvailable() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Returns true if there are regions available in ROI manager.
arithmeticOp - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
ArithOp() - Constructor for enum de.unihalle.informatik.MiToBo.math.images.ImageArithmetics.ArithOp
 
ArrayFilterDouble1D - Class in de.unihalle.informatik.MiToBo.math.arrays.filter
This class defines a superclass for filters for 1D arrays.
ArrayFilterDouble1D() - Constructor for class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D
Default constructor.
ArrayToColorMapImage - Class in de.unihalle.informatik.MiToBo.visualization.colormappings
This operator visualizes a 2D array using a specified color mapping.
ArrayToColorMapImage() - Constructor for class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Default constructor.
ArrayToColorMapImage(double[][]) - Constructor for class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Constructor.
ArrayToColorMapImage.RangeColor - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings
Possible colors to colorize value ranges.
assign(MTBRegion2DSet, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
assign regions from one frame to regions from another frame
assignStructsToCell_com(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Assigns the given set of structure regions to individual cells.
assignStructsToCell_overlap(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Assigns the given set of structure regions to individual cells.
assocDistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
assocfactory - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
factory for the data association object
AssociationDistribution<S extends TargetID,T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
Association distribution to sample association variables for a set of observations based on a model of how observations are formed.
AssociationDistribution(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Constructor.
AssociationDistribution(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Constructor where the maximum number of observations in the time series is specified to avoid some re-computations.
AssociationDistributionNN<S extends TargetID,T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
Association distribution to sample association variables for a set of observations based on a model of how observations are formed.
AssociationDistributionNN(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double, int, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Constructor.
AssociationDistributionNN(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double, int, int, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Constructor where the maximum number of observations in the time series is specified to avoid some re-computations.
AssociationDistributionNN.AType - Enum in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
 
AssociationDistributionNN.ObsDistance - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
 
AssociationDistributionNN.ProbTreeData - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
 
assocObs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
aTrousDWT(MTBImage, int, MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
A trous DWT
AType() - Constructor for enum de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.AType
 
auto - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
availableClasses - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
List of available energies.
availableCodecs(Class<? extends IFormatWriter>) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Get available codecs of a specific writer class.
availableQualities(Class<? extends IFormatWriter>) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Get available qualities of a specific writer class.
averageDeltas(double[], int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Return the averaged deltas, i.e.
averageRegionIntensities - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Vector of average region intensities.
avgApicalIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average of apical indentations lengths.
avgApicalIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgApicalProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average of apical protrusion lengths.
avgApicalProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgBasalIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average of basal indentation lengths.
avgBasalIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgBasalProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average of basal protrusion lengths.
avgBasalProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgBaselineIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average length of indentations baselines.
avgBaselineIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgBaselineProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average length of protrusion baselines.
avgBaselineProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgBranchLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgConcavities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgDiffusionDist - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
avgEndpointDistances - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgEquatorIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average length of indentation equators.
avgEquatorIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgEquatorProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average length of protrusion equators.
avgEquatorProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgFactor - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
avgHorizontalRunLength - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
avgIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average length of indentations.
avgIndentationLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgIntensity - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape
Average intensity of all shape pixels.
avgLobeDepths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgNeckDepths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgNeuriteWidths - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Vector of neurite widths, containing 3 elements. 1. average width of whole neurite, 2. average width of neurite shaft, and 3. average width of growth cone.
avgProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Average length of protrusions.
avgProtrusionLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgsize_cells - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Average size of cells.
avgsize_nuclei - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Average size of nuclei.
avgsize_particles - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Average size of particles.
avgVerticalRunLength - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
AwtColorDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Data I/O provider for Cmdline-OpRunner for java.awt.Color objects.
AwtColorDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
 
AwtColorDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Data I/O provider for GUI-OpRunner for java.awt.Color objects.
AwtColorDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
AwtColorDataIOSwing.ColorChooserPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Panel with configuration elements.
AwtColorDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Xmlbeans provider for java.awt.Color objects.
AwtColorDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
 
AwtPoint2dDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Data I/O provider for Cmdline-OpRunner for java.awt.geom.Point2D.Double objects.
AwtPoint2dDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtPoint2dDataIOCmdline
 
AwtPoint2dDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Xmlbeans provider for java.awt.Color objects.
AwtPoint2dDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtPoint2dDataIOXmlbeans
 

B

b - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Implicit curve parameter b.
B - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
External energy vector, to be modified by snake energies.
background_color - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
 
BACKGROUND_PIXEL - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
backgroundLabel - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
backwardDifferencing_X(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
backwardDifferencing_X(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
backwardDifferencing_Y(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
backwardDifferencing_Y(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
backwardDifferencing_Z(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
backwardDifferencing_Z(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
basalLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Basal length of the segment, from baseline to equator.
baselineConstant - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Baseline constant.
baselineLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Length of segment baseline.
BasicMorphology - Class in de.unihalle.informatik.MiToBo.morphology
class implementing basic morphological operations (for use with grayscale as well as with binary images)
BasicMorphology() - Constructor for class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
BasicMorphology(MTBImage, MTBStructuringElement) - Constructor for class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
BasicMorphology(Integer, BasicMorphology.opMode, BasicMorphology.maskShape) - Constructor for class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
Constructor to create new BasicMorphology object with mask size, mode and shape of the structuring element.
BasicMorphology.maskShape - Enum in de.unihalle.informatik.MiToBo.morphology
 
BasicMorphology.opMode - Enum in de.unihalle.informatik.MiToBo.morphology
 
beta - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
beta - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Weighting factor for snake curvature term.
betaDecrease - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
Value by which beta is decreased in each iteration.
betaInitial - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Weighting factor for the curvature term, should always be > 0.
betas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Vector of point-specific beta values.
betaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Update function for beta values.
betaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
betaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
Update function for betas.
BG_PHASE - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Level set function value to represent the background phase
bg_value - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
bgLabel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
bgLabel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
bgLabel - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
bgLabel - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
bgValue - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
binaryCorrelationImages - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Stack of binarized correlation images.
binaryImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
BinaryImageEndpointTools - Class in de.unihalle.informatik.MiToBo.morphology
Tool functions for extracting endpoints and branches from binary images, particularly images of skeletons.
BinaryImageEndpointTools() - Constructor for class de.unihalle.informatik.MiToBo.morphology.BinaryImageEndpointTools
 
binaryMasks - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
(Optinal) stack with binary segmentation masks.
binFilteredImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Intermediate result: binarized vesselness image after filtering.
binMask - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Binary segmentation mask.
binMask - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Binary segmentation mask.
binning(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
change the binning of the histogram
binomial(int, int) - Static method in class de.unihalle.informatik.MiToBo.math.MathX
Binomial coefficient of n over k
binVesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Intermediate result: binarized vesselness image.
blacklist - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
blackTophat(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
calculates the black tophat transform, i.e. difference of the closing of the image and the image
(also called closing tophat)
blue - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Definition of blue color.
BLUE_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
BorderBackgroundContrast() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.BorderBackgroundContrast
 
BorderBackgroundContrast() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.BorderBackgroundContrast
 
BorderConnectivity() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D.BorderConnectivity
 
borderContrast - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Border to background relation.
borderContrast - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Border to background relation.
borderDist - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Safety distance along image borders.
borderSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
The set of borders represented as a Vector.
borderSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Set of 2D borders.
borderSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Set of borders of the 2D regions.
BordersOnLabeledComponents - Class in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
Class to extract borders from connected components.
BordersOnLabeledComponents() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Standard constructor.
BordersOnLabeledComponents(MTBImage, MTBRegion2DSet, MTBBorder2D.BorderConnectivity, BordersOnLabeledComponents.BorderType, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Constructor.
BordersOnLabeledComponents.BorderType - Enum in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
Possible types of borders to be extracted.
borderType - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Type of borders to be extracted.
BorderType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents.BorderType
 
boundaryChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Channel of input image containing stained cell boundaries.
BoundaryPadding() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow.BoundaryPadding
 
boundaryPadding - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
boundaryPadding - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
boundaryPadding - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
BoundEnsure(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Test the image boundary.
BoundExpand(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Expand the image boundary.
BoundShrink(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Shrink the image boundary.
boxLinksImagePlus - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Associative list for links between ImagePlus and associated image boxes.
boxLinksMTBImage - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Associative list for links between MTBImages and associated image boxes.
boxWhiskerChart - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Resulting box-whisker chart.
BoxWhiskerChartPlotter - Class in de.unihalle.informatik.MiToBo.visualization.plots
Operator that generates box-whisker plots using JFreeChart.
BoxWhiskerChartPlotter() - Constructor for class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Default constructor.
boxWhiskerCharts - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Box-whisker plot of the group-wise cluster distributions.
boxWhiskerCharts - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Box-whisker plot of the group-wise cluster distributions.
branchCounts - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
bthImage - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Black top-hat image.
bthMaskSize - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
 
build(int, int, MTBImageByte, MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Internal method to create the graph from the skeleton image.
buildMainPanel(Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Build the main panel for configuring the list of energies.
buildMainPanel() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Build the main panel for configuring the list of energies.
buildSkeletonGraph(int, int, int, int, MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Build the skeleton graph from a given binary skeleton image and a given starting point to build up the graph.
button - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
button - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowPanel
Button associated with the panel.
button - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowPanel
Button associated with the panel.
buttonEdit - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Button to edit loaded data or insert data manually.
buttonLoad - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
Button to load data, e.g., from file or ROI manager.
buttonLoad - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Button to load data, e.g., from file or ROI manager.
buttonReset - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
Button to delete currently loaded data.
buttonReset - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Button to delete currently loaded data.
buttonShow - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
BWImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
BYTE_TO_DEGREE - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Constants to convert from [0-255] to [0-359] and vice versa.

C

C - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
c - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
c - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Implicit curve parameter c.
C - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Covariance matrix calculated from mean-free data.
c - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
array to hold means of phases, starting with MTBLevelsetMembership.BG_PHASE
c - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
C2DtoMTB(C2DPolygon) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Converts a C2D polygon to the MiToBo polygon data type.
calcAngularSecondMoment(Double[][]) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
calcArea - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcArea() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcArealPorosity(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcASM - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
calcAverageDiffusionDistance(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcAverageSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Calculates the average size of the set.
calcAvgDiffusionDistance - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcAvgHorizontalRunLength - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcAvgHorizontalRunLength(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcAvgVerticalRunLength - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcAvgVerticalRunLength(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcBranchLength(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Calculates the lenght of the given branch.
calcCentre(Vector<MTBPoint3D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculate the centroid (not yet normalized by volume) of a given vector of points.
calcCircularity - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcCircularity() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcCompactness - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
calcCompactness() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
calcConcavityData - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Flag to turn on/off analysis of concavities.
calcContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get all inner- and outer-contours for the given regions.
calcConvexHullMeasures - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Flag to turn on/off analysis of convex hull.
calcDilationAreas - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcDilationAreas(MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcDM() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Method to calculate the distance map of the given binary image using the Chamfer-algorithm.
calcEccentricity - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcEccentricity() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcEllipseParameters() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Calculate concrete ellipse parameters from implicit equation.
calcEnergy(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Calculates the absolute energy value for the given segmentation.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Calculates normalized snake energy.
calcEnergy(SnakeOptimizerSingle, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Calculates length term of snake energy at a certain position for the current snake.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Calculates snake energy (non-normalized!).
calcEnergy(SnakeOptimizerSingle, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Calculates energy at a certain position for the current snake.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Calculates the current energy of the snake.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
calcEnergy(SnakeOptimizerSingle, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Calculates energy at a certain snake point.
calcEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Calculates the energy of the current snake.
calcEnhancedImage(MTBImage, double, int, boolean) - Static method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Calculates the new image intensity values of the image.
calcEntropy - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
calcEntropy(MTBImageHistogram) - Static method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Calculates the Shannon entropy for the given (normalized!)
calcFeatureFlagChanged() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Callback routine to change parameters on change of flag for enable/disable feature calculation.
calcFeatureFlagChanged() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Callback routine to change parameters on change of flag for enable/disable feature calculation.
calcFeatures(double[][]) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Extracts Haralick features from given matrix.
CalcGlobalThreshOtsu - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds
This class implements Otsu's method for calculating an optimal threshold for a given grayscale images.
CalcGlobalThreshOtsu() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Default constructor.
CalcGlobalThreshOtsu(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Default constructor with input image as argument.
CalcGlobalThreshOtsu(MTBImageHistogram) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Default constructor with input histogram as argument.
CalcGlobalThreshOtsu.InputType - Enum in de.unihalle.informatik.MiToBo.segmentation.thresholds
Type of input to work on.
calcGVF() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Calculate the GVF field with the given number of iterations on the given input image.
calcIDM - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
calcInteriorEnergy(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Calculates the interior part of energy value for the given segmentation.
calcInverseDifferenceMoment(Double[][]) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
calcLengthWidth - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcLengthWidth() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcMarginRoughness - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Flag to turn on/off calculation of margin roughness.
calcMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Function calculating actual matching, to be implemented by subclasses.
calcMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
 
calcMatching_mainTest() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Checks whether a valid solution has been found.
calcMatching_stageOne() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Implements stage one: searching for new candidate matches.
calcMatching_stageThree() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Implements stage three: decrease scores to generate new zero entries.
calcMatching_stageTwo(int, int) - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Implements stage two: extracting exchange chain.
calcMatrix(FeatureCalculatorHaralickMeasures.HaralickDirection) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Extracts the co-occurence matrix for the given distance and direction.
calcMaxDiffusionDistance - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcMaximumDiffusionDistance(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcMaxSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Calculates the maximum size of the set.
calcMean(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Return the mean value of an array of double.
calcMedian(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Returns the median value of an array of double.
calcMinMax(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Returns the min and max value.
calcMinSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Calculates the minimum size of the set.
calcMode - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
 
calcNormSpatialDependenceMatrix(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
calcPerimeter - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcPerimeter() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcPorosity - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
calcPotential_approxLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Calculates an approximation of the potential of the field by gradient descent.
calcPotential_exactLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Calculates the potential of the field by solving a LSE with least squares.
calcPotential_exactLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Exact least squares reconstruction of the potential.
calcPotential_gradientDescent(boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Reconstruct potential via gradient descent.
calcPotential_incrementalLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Reconstructs the potential of the vector field incrementally.
calcPotential_incrLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Calculates a rough approximation of the potential of the field in linear time.
calcPrecision(int, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures
Calculates the precision from given true and false positives.
calcProfile() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
CalcQualityMeasures - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation
Helper class for calculating precision and recall values.
CalcQualityMeasures() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures
 
CalcQualityMeasures.PrecisionCalc - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation
Internal operator for precision calculation.
CalcQualityMeasures.RecallCalc - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation
Internal operator for recall calculation.
calcRadiusImage - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Flag to enable calculation and display of radius image (only in non-component mode).
calcRecall(int, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures
Calculates the recall value from given true positives and false negatives.
calcRegionAverageIntensities() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Calculates the average region intensities.
CalcSegmentationStatistics - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Operator for doing statistical calculations on segmentations of images.
CalcSegmentationStatistics() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Default constructor without arguments.
CalcSegmentationStatistics(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Default constructor.
CalcSegmentationStatistics(MTBImage, MTBSegmentationInterface) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Default constructor.
CalcSegmentationStatistics(MTBImage, MTBSegmentationInterface, Vector<CalcSegmentationStatistics.CalcTargets>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Default constructor.
CalcSegmentationStatistics.CalcTargets - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Statistical numbers provided by this class.
calcSkeletonBranchFeatures - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Flag to turn on/off calculation of skeleton branch features.
calcSnakeDomain() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Calculates snake bounding box (in non-normalized coordinates!).
calcSnakeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Calculates total snake energy.
calcSnakeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Calculates total snake energy.
calcSolidity - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Flag to turn on/off calculation of solidity.
CalcStructureStatistics - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation
Extracts statistics from cell and structure segmentation results.
CalcStructureStatistics() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Default constructor.
CalcStructureStatistics(MTBImageByte, MTBImageByte, MTBImageByte, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Deprecated.
CalcStructureStatistics(MTBImageByte, MTBImageByte, MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Default constructor.
CalcStructureStatistics.StructureCountMode - Enum in de.unihalle.informatik.MiToBo.segmentation.evaluation
Mode how to assign structures to cell regions.
calcSurfArea - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
calcSurfArea() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
CalcTargets() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics.CalcTargets
 
calcTexturalEntropy(Double[][]) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
calcThreshold(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Calculate Otsu threshold on given image.
calcThreshold(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Calculate Otsu threshold on given histogram.
calcTStD(double, double) - Static method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Calculates the threshold for the local standard daviation.
calculateConcavityData() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Extracts average concavity and standard deviation of concavities.
calculateConvexHullMeasures() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Calculates convex hull convexities and roundnesses.
calculateConvexHulls() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Calculates convex hull areas and perimeters.
calculateCovarianceMatrixAndEigenstuff() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Calculates covariance matrix and eigenvalues and -vectors.
calculateCurvatureBeusTiu(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
calculateCurvatureModifiedFreemanDavis(Vector<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Calculates the curvatures by a modified version of the Freeman and Davis curvature estimation algorithm.
calculateDistanceMatrices() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Calculates pairwise distance matrices and similarity network data.
calculateFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Performs the feature calculation.
calculateFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures
 
calculateFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorTiles
 
calculateMeanFreeData() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Computes the average data vector and makes data mean-free.
calculatePairwiseDistances() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Calculates pairwise Euclidean distances between all feature vectors.
calculatePointLineDistance(double, double, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
Calculates the distance between a point and a line.
calculateRegionFeatures(MTBRegion2DSet, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Extracts features for all detected and valid cell regions.
calculateSolidityValues() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Calculates solidity values.
calcVariance(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Returns the variance of an array of double.
calcVolume - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
calcVolume() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
calibration - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
calibration object (from ImageJ)
callbackArea() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Callback function called in case of changes of parameter MorphologyAnalyzer2D.calcArea.
callbackConcavity() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Callback function called in case of changes of parameter MorphologyAnalyzer2D.calcConcavityData.
callbackCurvature() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Callback function called in case of changes of parameters MorphologyAnalyzer2D.analyzeProtrusionsIndentations or MorphologyAnalyzer2D.calcMarginRoughness.
callbackInputDir() - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Callback function called in case of changes of parameter LabelImageEditor.inputDir.
callbackSolidity() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Callback function called in case of changes of parameter MorphologyAnalyzer2D.calcSolidity.
callBackUpdateSigmaThresholds() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
calledFirstTime - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Flag to ensure that callback only works once the operator has been called.
callingOperator - Variable in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
 
callNeuriteScript(String, String) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Call a specified R script for neurite calculations.
callNeuriteSrcipt(Rengine, String, String[]) - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Call a specified R script for neurite calculations.
calStDI(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Calculates the standard deviation of the given image.
candidateRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
List of stromule candidate regions.
candidates - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
canvas - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
Canvas used by ImageJ to display the image.
categoryColors - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Color map for category colors in plot.
categoryColors - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Color map for category colors in plot.
categoryCount - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Local variable to store number of categories.
cb - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
cbbox - Variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
container for arrangement of checkboxes
cbs - Variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
checkbox components
cdf - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
cumulative distribution function, used for sampling
cDOF - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
degrees of freedom of the continuous variables of a single state
CellBoundaryExtractor2D - Class in de.unihalle.informatik.MiToBo.apps.cells2D
Operator for segmenting cell boundaries in microtubuli experiments.
CellBoundaryExtractor2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Default constructor.
CellBoundaryExtractor2D.BorderBackgroundContrast - Enum in de.unihalle.informatik.MiToBo.apps.cells2D
Border color.
CellBoundaryExtractor2D.OperationMode - Enum in de.unihalle.informatik.MiToBo.apps.cells2D
Operation mode of the operator.
cellChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Channel for cell boundary detection.
CellCntrMarker - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Class to represent a single marker in the image.
CellCntrMarker() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Creates a new instance of marker class.
CellCntrMarker(int, int, int, CellCntrMarkerShape) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Constructor with given coordinates and shape.
CellCntrMarkerShape - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Class to represent the geometric shape of a single marker in the image.
CellCntrMarkerShape() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape
 
CellCntrMarkerShapeCurve - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Class using a parametric curve as shape for markers.
CellCntrMarkerShapeCurve() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeCurve
Default constructor, it's protected to avoid constructing objects without curve data.
CellCntrMarkerShapeCurve(MTBQuadraticCurve2D) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeCurve
Default constructor with parametric curve object.
CellCntrMarkerShapeLine - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Class using a line segment as shape for markers.
CellCntrMarkerShapeLine() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine
Default constructor, it's protected to avoid constructing objects without curve data.
CellCntrMarkerShapeLine(Point2D.Double, Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine
Default constructor.
CellCntrMarkerShapePolygon - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Class using a polygon as shape for markers.
CellCntrMarkerShapePolygon() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon
Default constructor, it's protected to avoid constructing objects without polygon data.
CellCntrMarkerShapePolygon(MTBPolygon2D) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon
Default constructor with region object.
CellCntrMarkerShapeRegion - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Class using a region as shape for markers.
CellCntrMarkerShapeRegion() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion
Default constructor, it's protected to avoid constructing objects without region data.
CellCntrMarkerShapeRegion(MTBRegion2D) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion
Default constructor with region object.
CellCntrMarkerShapeRegion(MTBRegion2D, MTBBorder2D) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion
Constructor with region and border object.
CellCntrMarkerVector - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Class to represent a set of markers of a single type.
CellCntrMarkerVector(int) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Creates a new instance of MarkerVector.
CellCntrSegResult - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Base class representing results of MTB_CellCounter presegmentation stage(s).
CellCntrSegResult(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Default constructor.
CellCntrSegResultCurves - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Class representing results of MTB_CellCounter presegmentation stage(s).
CellCntrSegResultCurves(MTBImage, Vector<MTBQuadraticCurve2D>) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves
Constructor.
CellCntrSegResultRegions - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
Class representing region-based results of MTB_CellCounter presegmentation stage(s).
CellCntrSegResultRegions(MTBImage, MTBRegion2DSet, MTBBorder2DSet, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Constructor.
CellCntrSegResultRegions(MTBImage, MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Constructor.
cellContours - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Set of extracted regions.
cellContours - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Set of detected cell boundaries.
CellCounterDetectOperator - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators
Container base class for all detectors used in the cell counter.
CellCounterDetectOperator() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Constructor.
CellCounterDetectOperatorConfigWin - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators
Deprecated.
CellCounterDetectOperatorConfigWin(ALDOperator) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Constructs a control frame for an operator object.
CellCounterDetectOperatorParticlesUWT - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators
Cell counter detector for detecting plastids.
CellCounterDetectOperatorParticlesUWT() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
Constructor.
CellCounterDetectOperatorStromules - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators
Detector wrapper for detection of stromules from given plastid regions.
CellCounterDetectOperatorStromules() - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Constructor.
cellGroupNames - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
List of group names, filled in ActinAnalyzer2D.clusterFeatures().
cellGroupNames - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
List of group names, filled in CytoskeletonAnalyzer2D.clusterFeatures().
cellGroups - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Group-wise cell distribution data, for each group the vector contains a hash map with the following structure: - the keys of the map are given by the cell IDs of the different cells (without basename which is equal to the group name) - the values are represented again as a hash map where the keys are given by the cluster IDs and the values by the relative frequency of the corresponding cluster in the cell Example: --------- cellGroups.get(0) = < 001-01, < [c1, vc1], ..., [c6, vc6] > > ,
cellGroups - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Group-wise cell distribution data, for each group the vector contains a hash map with the following structure: - the keys of the map are given by the cell IDs of the different cells (without basename which is equal to the group name) - the values are represented again as a hash map where the keys are given by the cluster IDs and the values by the relative frequency of the corresponding cluster in the cell Example: --------- cellGroups.get(0) = < 001-01, < [c1, vc1], ..., [c6, vc6] > > ,
cellLabelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Label image of extracted cell regions.
cellLabelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Label image of cell areas.
CellMaskFormat() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor.CellMaskFormat
 
CellMigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
Operator for segmenting, tracking and analyzing 2D image sequences of fluorescently labeled cells
CellMigrationAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
CellMigrationAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
CellSegmentationPostprocessing - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
operator for doing common postprocessing tasks on already segmented cell images
CellSegmentationPostprocessing() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
CellSegmentationPostprocessing(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
CellSegmenter - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
base class for cell segmentation
CellSegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
CellSegmenter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
cellSizes - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Array indexed with snake IDs containing region sizes of snake interiors.
cellsResult - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Result for cell/cytoplasm channel.
CellTrackerBipartite - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
This operator assigns unique labels to regions representing individual cells in the input binary image sequence
CellTrackerBipartite() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
CellTrackerBipartite(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
cellwiseDistroKeys - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Sorted list of keys in CytoskeletonAnalyzer2D.cellwiseDistros once it is filled.
cellwiseDistros - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Map of cluster distributions per cell, filled in ActinAnalyzer2D.clusterFeatures().
cellwiseDistros - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Map of cluster distributions per cell, filled in CytoskeletonAnalyzer2D.clusterFeatures().
centerX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Ellipse center in x-direction.
centerX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
centerY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Ellipse center in x-direction.
centerY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
centroid - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
The centroid of the region (not normalised by volume!)
centroids - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
chainMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Helper matrix for exchange chain extraction: 0 = unselected, 1 = selected.
changePhase(int, int, int, short) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Change a pixel/voxel to a new phase.
changePhase(int, int, short) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Change a pixel to a new phase.
channel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
channel - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
channelIdx - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
channelsAreRGB - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
channelsToCopy - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set of image channels to copy into result stack.
chart - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
JFreeChart object associated with the button.
chartFrame - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
Frame to display the chart.
ChartShowButton(Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
Constructor.
ChartShowPanel(MTBJFreeChartDataIOSwing.ChartShowButton, String) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowPanel
Constructor.
chartTitle - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Title of the chart.
chartTitle - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Title of the chart.
ChaudhuriMatchedFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
2D Matched filter.
ChaudhuriMatchedFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Default constructor.
CHECK_CHANGED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
property string that is fired when the state of any checkbox is changed
CheckBoxPanel - Class in de.unihalle.informatik.MiToBo.gui
A panel with a titled border and a set of checkboxes that can be reconfigured easily.
CheckBoxPanel(String) - Constructor for class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
Constructor
checkForIncrease() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
checkMethod - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
checkNeighbor(List<Point2D.Double>, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
Test if the given neighbor is to be added to the region.
checkSelectionConsistency() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Checks if a proper set of regions is selected in ImageJ ROI manager.
checkSelectionConsistencyForLineSegments() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Checks if a proper set of ROIs convertible to line segments is selected in ImageJ ROI manager.
chi - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
childs - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
List of nodes that are childs of the given node.
circularities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
circularities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
cl - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
classID - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Class identifier.
classID - Static variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Class identifier.
classID - Static variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Class identifier.
classify(MTBImage, MTBImage, String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
decide, whether the given entropy image contains an open scratch or not
classify(double[]) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
classifyLobes - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Flag to classify lobes into different type classes.
classLock - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Lock variable to make singleton thread-safe.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
2D map with class labels.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
2D map with class labels.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
2D map marking the region enclosed by the snake.
classNameMapping - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Mapping of short names to class objects.
cleanNeurites(MTBNeurite2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Method to clean up the extracted neurites, due to multiple features along a NSG path or feature shifts at the start point due to different NSG lengths.
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Remove all line segments from this set.
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Remove all regions from this set
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Remove all regions from this set
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Remove all regions from this set
clear() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Deletes all(!)
clearData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Clears all data.
clearData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves
Clears all data.
clearData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Clears all data.
clearPanel() - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
Remove all radiobuttons from the panel.
clearPanel() - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Remove all radiobuttons from the panel.
clearPanel() - Method in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
Remove all entries from the panel.
clearShapeData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Delete shape data during reset of vector.
clickedPoints - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
List of pixels the user selected.
clone() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree
 
clone() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Clone function.
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
 
clone() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
generate a clone of this object
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
cloneChild(MTBTreeNode, MTBTreeNode) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Helper function to recursively clone child nodes in a deep fashion.
cloneTargetImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Flag to enable/disable cloning of target image.
close() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Close the displayed ImagePlus
close(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
closeButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Close button.
closeButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Close button.
closeButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Button to close the configuration window.
closeGapsNativeLinks(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Method to close gaps by linking adjacent endpoints.
closeGapsNativeLinks(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Close gaps by native linkage.
closeGapsWatershed(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Method to close gaps by watershed transformation.
closestObjectPixelMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Map of closest object pixels for each background location.
closeWindows() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Close all windows openened by this operator (for clean-up).
closeWindows() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
closeWindows() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
closingMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
clusterFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Performs the feature clustering via Weka's kMeans algorithm.
clusterFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Performs the feature clustering via Weka's kMeans algorithm.
clusterLabels - Variable in class de.unihalle.informatik.MiToBo.clustering.KMeans
List of assigned cluster indices, starting with 1.
clusterNum - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Number of clusters to be used in feature clustering.
clusterNum - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Number of clusters to be used in feature clustering.
clusterNum - Variable in class de.unihalle.informatik.MiToBo.clustering.KMeans
Number of clusters to be used.
clutterdistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
spatial clutter distribution
cmdTools.cellAnalysis - package cmdTools.cellAnalysis
 
cmdTools.mtb_imagetools - package cmdTools.mtb_imagetools
 
cmdTools.tracking.multitarget - package cmdTools.tracking.multitarget
 
cmdTools.visualization - package cmdTools.visualization
 
codeArrayRI - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Array containing rotation invariant LBP codes.
codeArrayRIU - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Array containing uniform rotation invariant LBP codes.
codeArrayRIU - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU
Rotation invariant uniform LBP code array.
codec - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
codec - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
codeDistributionRI - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Distribution of codes.
codeStack - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Additional code stack.
codpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
coffset - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
 
CollectContoursStageOne(MTBImage, ArrayList<Integer>) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
This method collects all contour pixels for a region in a given MTBImage.
CollectContoursStageTwo(MTBImage, ArrayList<Integer>, ArrayList<ArrayList<Point>>, boolean[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
This method implements the final stage of the contour detection.
colMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Array containing column marks.
color - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Current color selected.
color - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Color of markers.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Color to be used.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Color or gray value to use.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
 
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
Color for mask, default is white.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Color to be used, known colors are: red, green, blue, yellow, white
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Color value used, e.g., for color and transparent images.
color - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
Color to use.
color2int(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Transforms color to integer value.
color_blue - Static variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
color_graphEdge - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of graph edge points.
color_graphNode - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of graph node points.
color_red - Static variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
color_skelBranch - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of pre-detected branch points.
color_skelSpecial - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of pre-detected special points, for example a 2x2 skeleton region.
color_skelVisitB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of visited graph branch points.
color_skelVisitE - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of visited graph edge points.
colorArray - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Array with colors for visualization.
colorArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Array containing pseudo-colors for snake visualization.
ColorChannel(int, int, int) - Constructor for enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
 
ColorChooserPanel(Color, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Default constructor for panel without reset button.
ColorChooserPanel(Color, ALDParameterDescriptor, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Default constructor.
colorFG - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
colorImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Image of regions in random colors.
ColorMapperDataIOFileInPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
Default constructor.
ColorMapperInputDirectoryIOPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Default constructor.
colorNegative - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Color for negative values.
colorPlot() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Plots the field in colored image.
colorPositive - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Color for positive values.
colors - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
 
cols - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Number of columns of the table.
columnIDs - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData
Indices of selected column.
columnNameToIDMap - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
columnSelection - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
columnSelectionItems - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
com_x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Center of mass in x (just sum, not normalized by area!).
com_y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Center of mass in y (just sum, not normalized by area!).
compactFactor - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
factors needed for compactness calculation
compactnesses - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
compactnessTreshold - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Compactness threshold for components.
compare(GraphNodeID, GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
 
compare(GraphNodeID, GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
 
compare(TrackEvaluator.TrackObservation, TrackEvaluator.TrackObservation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
compare(TrackEvaluator.TrackSegment, TrackEvaluator.TrackSegment) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
compareTo(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
 
compareTo(GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
 
compareTo(GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
 
compareTo(AssociationDistributionNN<S, T>.ObsDistance) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
 
compareTo(TrackEvaluator.TrackObservation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
compareTo(TrackEvaluator.TrackSegment) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
componentNum - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Number of sub-space components in mode ReductionMode.NUMBER_COMPONENTS.
ComponentPostprocess - Class in de.unihalle.informatik.MiToBo.morphology
Methods for post-processing components/pixels in binary images.
ComponentPostprocess() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Default constructor.
ComponentPostprocess(MTBImage, ComponentPostprocess.ProcessMode) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Default constructor.
ComponentPostprocess(MTBImage, ComponentPostprocess.ProcessMode, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Deprecated. 
ComponentPostprocess(MTBImage, ComponentPostprocess.ProcessMode, int, int, int, double) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Deprecated. 
ComponentPostprocess.ProcessMode - Enum in de.unihalle.informatik.MiToBo.morphology
Processing mode identifiers.
comppanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
compression - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
compression - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
compute(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit
This method implements the PRA itself for two given contours.
compute_pczAhead(MTBTreeNode, Vector<Integer>, Stack<Integer>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Compute probability of all possible associations of neighboring observations including their likelihood
compute_qAhead(int, int, int, int, double, MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Compute tree of data association prior probabilities depending on previous associations.
computeDeltas(double[]) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Return the centered angles (named delta).
ComputeDetectionErrors() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors
This method is the implementation of the Detection Errors.
computeESS() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Compute effective sample size (ESS).
computeN() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Derive N_n^k from X, see Han et al.
computeN() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN4
 
computeN() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN8
 
ComputeOdetsCriteria() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria
This method is the implementation of Odet's criteria.
computeSigmaScales() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Compute scaling factors of noise sigma for wavelet scales (these scaling factors are estimated using a gaussian noise image with sigma=1 to measure noise in the wavelet scales)
computeSubgraphs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Compute subgraphs with greedyGourmet algorithm.
computeThetas(Vector<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Calculate the theta angle for all contour pixels provided.
comXs - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
List of x-coordinates of centers of mass of plastid regions.
comYs - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
List of y-coordinates of centers of mass of plastid regions.
concaveness(int, int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
concavenessValues - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
concavityMaskSize - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Masksize for concavity calculations.
ConditionalDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for conditional densities, e.g. p(x|y)
condX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
multi state condition on the density
condX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
multi state condition on the density
confButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Button to display configuration window.
confEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Config button for energies.
configButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Configuration button.
configGUIModeLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Enable GUI components for label mode.
configGUIModeMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Enable GUI components for mask mode.
configGUIModeRegion() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Enable GUI components for region mode.
configGUIModeShape() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Enable GUI components for shape mode.
configGUIModeThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Enable GUI components for threshold mode.
configPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Panel containing configuration buttons.
ConfigureSegmentationButton(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Constructor.
configureSnakes(double, int, double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Configures basic snake parameters.
confObj - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
The object instance.
confWin - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Configuration window to show/edit loaded data.
confWin - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
confWin - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Collection configuration window.
confWin - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Configuration window.
connectivity - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Connectivity of border pixels.
connectivity - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Connectivity within resulting borders.
connectNodesCase1(MTBGraphNode<PartitGraphNodeID>, MTBGraphNode<PartitGraphNodeID>, MTBGraphNode<PartitGraphNodeID>, MTBGraphNode<PartitGraphNodeID>, boolean) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Connect nodes if case 1
connectorIDs - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
List of connectors the corresponding treeline is attached to.class Note: usually a treeline should only be member of one connector, only in case of conflicts there could be more.
contains(double, double, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Determines if a point lies inside a polygon or on its boundary.
contains(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Test if a point is inside the region or not.
containsImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Checks if the box contains an ImagePlus.
containsMTBImage() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Checks if the box contains a MTBImage.
containsPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Checks if a given point is part of the segment.
containsPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Checks if given point lies inside of the polygon.
containsPoint(MTBPolygon2D, double, double) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if a point lies inside of the polygon.
contour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Analyzed region contour.
Contour2DConcavityCalculator - Class in de.unihalle.informatik.MiToBo.features.contours
class for calculating concaveness of contour pixels according to the method proposed in: Fernandez, G., Kunt, M. & Zryd, J.P. (1995) A new plant image segmentation algorithm.
Contour2DConcavityCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
Contour2DConcavityCalculator(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
Contour2DConcavityCalculator(MTBImage, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
Contour2DConcavityCalculator(MTBImage, MTBContour2DSet, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
Contour2DCurvatureCalculator - Class in de.unihalle.informatik.MiToBo.features.contours
Implementation of curvature estimating algorithm's for discrete curved lines in a 2D space.
Contour2DCurvatureCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Default empty constructor.
Contour2DCurvatureCalculator(MTBContour2DSet) - Constructor for class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
Contour2DCurvatureCalculator.Algorithm - Enum in de.unihalle.informatik.MiToBo.features.contours
 
ContourConverter(MTBContour2D) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
Default constructor.
contourID - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
ID of the contour.
ContourOnLabeledComponents - Class in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
Class to segment contours from a binary image using the contour following algorithm.
ContourOnLabeledComponents() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Standard constructor.
ContourOnLabeledComponents(MTBImageByte, MTBRegion2DSet, ContourOnLabeledComponents.ContourType, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Constructor.
ContourOnLabeledComponents(MTBRegion2DSet, ContourOnLabeledComponents.ContourType, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Constructor.
ContourOnLabeledComponents.ContourType - Enum in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
The possible type of contours for segmentation.
contours - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
contourSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
The set of contours represented as a Vector.
contourSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Set of 2D contours.
contourType - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Special type of contours to calculate.
ContourType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents.ContourType
 
contourWorkSet - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
contrastEnhancer - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
 
conv(MTBImage, MTBImage[], int) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Convolve input image with an 'a trous' kernel (zeros inserted) given the original kernel and scale j
convert(Object, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
convertContourToSnake(MTBContour2D) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Converts a contour into a snake.
convertLabelImages() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Converts input images to short pixel format and optionally inverts them.
convertRangeColorToHue(ArrayToColorMapImage.RangeColor) - Static method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Converts given color to hue value.
convertRegionsToSnakes(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Converts the regions of a label/binary image into a set of snakes.
convertRegionToSnake(MTBRegion2D) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Converts a region into a snake.
convertToImageJRoi() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.interfaces.MTBDataExportableToImageJROI
Function to convert object to ImageJ ROI or set of ROIs.
convertToImageJRoi() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
 
convertToImageJRoi() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
 
convertToImageJRoi() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
 
convertToImageJRoi() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
 
convertType(MTBImage.MTBImageType, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Create an image of given type from this image's values.
convertType(MTBOperator, MTBImage.MTBImageType, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Create an image of given type from this image's values.
convertType(MTBImage, MTBImage.MTBImageType, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Create an image of given type from this image's values.
convexHullAreas - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
convexHullConvexities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
ConvexHullExtraction - Class in de.unihalle.informatik.MiToBo.morphology
operator for calculating the convex hulls of binary connected components
in a given image or of a set of regions using the Jarvis march algorithm
ConvexHullExtraction() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
ConvexHullExtraction(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
ConvexHullExtraction(MTBImage, boolean, boolean) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
ConvexHullExtraction.InputType - Enum in de.unihalle.informatik.MiToBo.morphology
Type of input to work on.
convexHullPerimeters - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
convexHullRoundnessValues - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
convexHulls - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
convolve(MTBImage, MTBImage, int[], boolean, MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Convolve an image with a specified kernel.
coordinatesNeighborNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
For each neighbor in the neighborhood this collection holds coordinates of all other pixels in the neighborhood which are connected to the neighbor under consideration with regard the the neighborhood definition.
coordinatesNeighborNeighborsByCoord - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
As this array gives for each neighbor in the neighborhood coordinates of its neighbors (i.e. neighborneighbors).
coordinatesNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
For each neighbor in the neighborhood this gives their coordinates in a 3x3x3 array center around the current pixel (of which the neighborhood is represented).
CoordInt3D(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
 
copy() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
copy() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
copy() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilterIndep
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
Not implemented, always returns null
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Copy this multi-state
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
 
copy() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.Copyable
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
Copyable<T> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
Interface for objects that can be copied (deep copy is assumed).
copyInputImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Flag to enable/disable plotting directly into input image.
copyPhysicalProperties(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Copy physical properties like stepsizes and units from {#sourceImg} to this.
copyTo(MTBLevelsetFunctionPDE) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
copy this object to another one
correctDirectness(MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Method to correct the direction of every edge inside the skeleton graph from a given root node.
correctGamma - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
correctGamma(MTBImage, double, int) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Perform gamma correction to the specified channel of the input image, using the given gamma value.
correctGammaAuto(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Perform gamma correction to the specified channel of the input image.
correctPosition - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Correct the line position if it has different contrast on each side of it.
correlationImages - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Stack of correlation images for different scale combinations.
corrThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Threshold for correlation images.
corrThreshold - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
Threshold for correlation images.
cost - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Cost of the MTBGraphEdge.
cot(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Return the cotangens of value.
count - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
 
counterClockwiseSnakePointOrderRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag to indicate if snakes are required to be sorted counter-clockwise.
countInner() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get the number of inner borders included.
countMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Mode for assigning structures to regions.
cov - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
covariance matrix
covs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
cparticles - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
create2DTrajectoryImage(boolean, boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
create3DTrajectoryImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
createChart(CategoryDataset) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Creates the chart.
createChart(CategoryDataset) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Creates the chart.
createCircularElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
createColor(int) - Static method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Returns a marker color according to given type ID.
createColorImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Flag to enable/disable creation of region image in random colors.
createContourOverlay - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
 
createCurvatureInfoImage - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Flag to enable drawing curvature information to info image.
createDataAssociation() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusiveFactory
 
createDataAssociation(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusiveFactory
 
createDataAssociation() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociationFactory
Create a new data association object
createDataAssociation(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociationFactory
Create a new data association object for given number of targets/states and observations
createDataset() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Create the dataset from the given input data.
createDataset() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Create the dataset from input data.
createDynamicModels() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
createEmptyMultiState() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Create an empty multi state object
createEmptyMultiState() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
 
createEnergy(MTBLevelsetMembership, double) - Static method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
Create a proper length energy asked for by the level set function.
createEnergy(MTBImage, MTBLevelsetMembership, double) - Static method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
Create a proper length energy asked for by the level set function.
createFloatImage - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Create byte or float image
createGaussianNoiseImage(double, double, double, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Create an image with Gaussian noise
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
Generic reading of table models.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
GUI element for reading sets of snake energies.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
Generic reading of segmentation objects.
createHorizontalLineElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
createIDImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Flag to enable/disable creation of gray-scale image with region IDs.
createImageFromWindow() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
 
createInitBar(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
create rectangular shaped bar as initialization for the scratch
createInitialStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
createLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Flag to enable/disable creation of gray-scale label image.
createMasks - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Flag to enable binary mask creation.
createMTBImage(ImagePlus) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Factory method to create MTBImage objects.
createMTBImage(int, int, int, int, int, MTBImage.MTBImageType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Factory method to create MTBImage objects with value 0 at each coordinate.
createMTBImageByte(int, int, int, int, int, byte[][]) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Creates an image of type MTBImage.MTBImageType.MTB_BYTE from the given data array.
createMultiState(double[][], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Create a multi state object initialized by the specified data
createMultiState(Matrix[], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Create a multi state object initialized by the specified data
createMultiState(double[][], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
 
createMultiState(Matrix[], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
 
createObservationModel() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
createOverlay() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
 
createOverlayImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
createProgressionImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
createQuadraticElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
createRandomRegion2D(int, int, int, Random) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Create a random connected 2D region of size maxArea in a hypothetical image of a random size between 1 and maxArea.
createRectangularElement(int, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
createRengine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Method to generate a R thread inside the java application.
createRengine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Method to generate a R thread inside the java application.
createResultDir(String) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Create directory where all results will be stored.
createResultTable(Vector<Vector<Integer>>) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Create result table with statistics about nuclei and particles.
createResultTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
This method prepares the result table for the solution.
createSeedRegions(MTBImageByte, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Create seed regions from the intial segmentation.
createSkeletonInfoImage - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Flag to enable drawing skeleton information to info image.
createSwapResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Create result table with statistics about nuclei and particles.
createVerticalLineElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
CropImage - Class in de.unihalle.informatik.MiToBo.tools.image
Crop an image part.
CropImage() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.CropImage
Constructor.
cSize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Size of input image in c dimension.
cSnakeOpt - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Reference to a coupled snake optimizer.
cSnakeOpt - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Reference to a coupled snake optimizer.
csvFile - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter
Output file name.
ctrPoints - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
cumulate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
calculate the cumulative histogram
cumulatedObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
cumulated number of previous observations for each time step, required to determine the individual array sizes in the adjacency matrix
cumulateOnly() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
calculate the cumulative histogram without changing the sum of absolute frequencies (normalizing factor), because cumulate() calls initialize() and thus destroys this normalizing factor
CURRENT_TYPE - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
currentFile - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Full path name of currently active image file.
currentIndex - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
Index of iterator in set.
currentIndexCol - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
Index of iterator in set.
currentIndexRow - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
Index of iterator in set.
currentInput - Static variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get initial directory from environment configuration.
currentInput - Static variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get initial directory from environment configuration.
currentMaskShape - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
shape of mask if mask !
currentMaskSize - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
mask size of mask if mask !
currentMax - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
currentOverlapMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Overlap mask of current snake configuration, updated in each iteration.
currentSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Current set of snakes.
currentSnk - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Current snake the energy is based on.
curvatureInfoImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Info image for curvature analysis.
curve - Variable in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet
Estimated curve.
curve - Variable in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet
Estimated curve.
curveType - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Type of curve.
CurveType() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.CurveType
 
cweights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
cytoChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Channel of input image containing stained cytoskeleton.
cytoDetector - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Cytoplasma detection operator.
CytoplasmAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.cytoplasm2D
Operator to segment cell contours from a given single-layer image.
CytoplasmAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Default constructor.
CytoplasmAnalyzer2D(MTBImage, MTBPolygon2DSet, SnakeOptimizerCoupled, CytoplasmAnalyzer2D.DetectMode, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Default constructor.
CytoplasmAnalyzer2D.DetectMode - Enum in de.unihalle.informatik.MiToBo.apps.cytoplasm2D
Operator mode.
cytoSkelChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Channel of input image containing stained cytoskeleton.
CytoskeletonAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton
Operator for extracting quantative global features of the cytoskeleton.
CytoskeletonAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Default constructor.
CytoskeletonFeatureExtractor - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton
Operator for extracting features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractor() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Default constructor.
CytoskeletonFeatureExtractor.CellMaskFormat - Enum in de.unihalle.informatik.MiToBo.apps.cytoskeleton
Format of cell segmentation data.
CytoskeletonFeatureExtractorEigenStructures - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton
Operator for extracting Eigen structures as features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorEigenStructures() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures
Default constructor.
CytoskeletonFeatureExtractorHaralickMeasures - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton
Operator for extracting Haralick texture measures from co-occurrence matrices as features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorHaralickMeasures() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
Default constructor.
CytoskeletonFeatureExtractorLBPs - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton
Operator for extracting LBP features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorLBPs() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs
Default constructor.
CytoskeletonFeatureExtractorLBPsRIU - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton
Operator for extracting LBP RIU features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorLBPsRIU() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU
Default constructor.
CytoskeletonFeatureExtractorTiles - Class in de.unihalle.informatik.MiToBo.apps.cytoskeleton
Operator for extracting features for the ActinAnalyzer2D.
CytoskeletonFeatureExtractorTiles() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorTiles
Default constructor.

D

d - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Implicit curve parameter d.
darkLine - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
If true, dark lines on bright background are extracted.
data - Variable in class de.unihalle.informatik.MiToBo.clustering.KMeans
Data to be clustered.
data - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Currently loaded data set.
data - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton
Data to be displayed.
data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
MTBGraphNode data.
data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
Array holding the histogram data
data - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
Data to save to file.
data - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
The data contained in the table.
data - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Data to display.
data - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Data to display.
DataAssociation - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
Interface for data association objects.
DataAssociationExclusive - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A class that represents exlusive data association.
DataAssociationExclusive() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
Constructor
DataAssociationExclusiveFactory - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
Factory class for exclusive data association objects
DataAssociationExclusiveFactory() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusiveFactory
 
DataAssociationFactory - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
Interface for data association object factories
DataConverter<S,T> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatools
An operator class to convert between data types.
DataConverter() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
 
dataDim - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Dimensionality of the input data.
dataIsPeriodic - Variable in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D
Flag to indicate if data is periodic.
dataObject - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Data object associated with the given node.
dataset - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Input data with each column containing a data vector.
DataTabFileFilter() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow.DataTabFileFilter
 
DatatypeExceptionType() - Constructor for enum de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException.DatatypeExceptionType
 
db - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
dbf - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
DE - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Check if you want to compute the Detection Errors
de.unihalle.informatik.MiToBo.apps.biofilms - package de.unihalle.informatik.MiToBo.apps.biofilms
 
de.unihalle.informatik.MiToBo.apps.cellMorphology - package de.unihalle.informatik.MiToBo.apps.cellMorphology
 
de.unihalle.informatik.MiToBo.apps.cells2D - package de.unihalle.informatik.MiToBo.apps.cells2D
 
de.unihalle.informatik.MiToBo.apps.cytoplasm2D - package de.unihalle.informatik.MiToBo.apps.cytoplasm2D
 
de.unihalle.informatik.MiToBo.apps.cytoskeleton - package de.unihalle.informatik.MiToBo.apps.cytoskeleton
Provides tools and applications for quantifying actin filament structures in microscopy images of cells.
de.unihalle.informatik.MiToBo.apps.datatypes.cellImages - package de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
 
de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes - package de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes
 
de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation - package de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation
 
de.unihalle.informatik.MiToBo.apps.minirhizotron.utils - package de.unihalle.informatik.MiToBo.apps.minirhizotron.utils
 
de.unihalle.informatik.MiToBo.apps.neurites2D - package de.unihalle.informatik.MiToBo.apps.neurites2D
 
de.unihalle.informatik.MiToBo.apps.neurons2D - package de.unihalle.informatik.MiToBo.apps.neurons2D
 
de.unihalle.informatik.MiToBo.apps.nuclei2D - package de.unihalle.informatik.MiToBo.apps.nuclei2D
 
de.unihalle.informatik.MiToBo.apps.particles2D - package de.unihalle.informatik.MiToBo.apps.particles2D
 
de.unihalle.informatik.MiToBo.apps.plantCells.plastids - package de.unihalle.informatik.MiToBo.apps.plantCells.plastids
 
de.unihalle.informatik.MiToBo.apps.plantCells.stromules - package de.unihalle.informatik.MiToBo.apps.plantCells.stromules
 
de.unihalle.informatik.MiToBo.apps.scratchAssay - package de.unihalle.informatik.MiToBo.apps.scratchAssay
 
de.unihalle.informatik.MiToBo.apps.singleCellTracking2D - package de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
de.unihalle.informatik.MiToBo.apps.xylem - package de.unihalle.informatik.MiToBo.apps.xylem
 
de.unihalle.informatik.MiToBo.clustering - package de.unihalle.informatik.MiToBo.clustering
 
de.unihalle.informatik.MiToBo.color.conversion - package de.unihalle.informatik.MiToBo.color.conversion
 
de.unihalle.informatik.MiToBo.color.tools - package de.unihalle.informatik.MiToBo.color.tools
 
de.unihalle.informatik.MiToBo.core.batch.provider.input.swing - package de.unihalle.informatik.MiToBo.core.batch.provider.input.swing
 
de.unihalle.informatik.MiToBo.core.batch.provider.output.swing - package de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
 
de.unihalle.informatik.MiToBo.core.dataconverter - package de.unihalle.informatik.MiToBo.core.dataconverter
 
de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline - package de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
 
de.unihalle.informatik.MiToBo.core.dataio.provider.swing - package de.unihalle.informatik.MiToBo.core.dataio.provider.swing
 
de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components - package de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components
 
de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans - package de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
 
de.unihalle.informatik.MiToBo.core.datatypes - package de.unihalle.informatik.MiToBo.core.datatypes
Provides basic datatypes for MiToBo.
de.unihalle.informatik.MiToBo.core.datatypes.defines - package de.unihalle.informatik.MiToBo.core.datatypes.defines
 
de.unihalle.informatik.MiToBo.core.datatypes.images - package de.unihalle.informatik.MiToBo.core.datatypes.images
Contains MiToBo image data types.
de.unihalle.informatik.MiToBo.core.datatypes.interfaces - package de.unihalle.informatik.MiToBo.core.datatypes.interfaces
 
de.unihalle.informatik.MiToBo.core.datatypes.neurites - package de.unihalle.informatik.MiToBo.core.datatypes.neurites
 
de.unihalle.informatik.MiToBo.core.datatypes.wrapper - package de.unihalle.informatik.MiToBo.core.datatypes.wrapper
Provides wrapper for for input and output datatypes for MiToBo operators.
de.unihalle.informatik.MiToBo.core.exceptions - package de.unihalle.informatik.MiToBo.core.exceptions
Defines MiToBo exceptions.
de.unihalle.informatik.MiToBo.core.grappa - package de.unihalle.informatik.MiToBo.core.grappa
 
de.unihalle.informatik.MiToBo.core.gui - package de.unihalle.informatik.MiToBo.core.gui
 
de.unihalle.informatik.MiToBo.core.helpers - package de.unihalle.informatik.MiToBo.core.helpers
 
de.unihalle.informatik.MiToBo.core.imageJ - package de.unihalle.informatik.MiToBo.core.imageJ
Provides convenience classes for interaction with ImageJ system.
de.unihalle.informatik.MiToBo.core.operator - package de.unihalle.informatik.MiToBo.core.operator
Provides basis classes for MiToBo operator concept.
de.unihalle.informatik.MiToBo.enhance - package de.unihalle.informatik.MiToBo.enhance
Provides classes for image preprocessing and improvement (no filters!).
de.unihalle.informatik.MiToBo.features - package de.unihalle.informatik.MiToBo.features
Provides operators for calculating features from given images, e.g., statistical indicators or texture measures.
de.unihalle.informatik.MiToBo.features.contours - package de.unihalle.informatik.MiToBo.features.contours
 
de.unihalle.informatik.MiToBo.features.regions - package de.unihalle.informatik.MiToBo.features.regions
 
de.unihalle.informatik.MiToBo.features.statistical - package de.unihalle.informatik.MiToBo.features.statistical
Provides operators for calculating statistical image features, e.g., average intensities or variances, or moments of the intensity distribution.
de.unihalle.informatik.MiToBo.features.texture - package de.unihalle.informatik.MiToBo.features.texture
Provides operators for calculating texture features from given images, e.g., Haralick measures.
de.unihalle.informatik.MiToBo.features.texture.lbp - package de.unihalle.informatik.MiToBo.features.texture.lbp
 
de.unihalle.informatik.MiToBo.fields - package de.unihalle.informatik.MiToBo.fields
Provides classes for calculating gradient vector flow fields, image gradient fields, potential fields and other possible fields from different data sources.
de.unihalle.informatik.MiToBo.filters.linear - package de.unihalle.informatik.MiToBo.filters.linear
Provides classes implementing linear systems.
de.unihalle.informatik.MiToBo.filters.linear.anisotropic - package de.unihalle.informatik.MiToBo.filters.linear.anisotropic
 
de.unihalle.informatik.MiToBo.filters.nonlinear - package de.unihalle.informatik.MiToBo.filters.nonlinear
Provides classes implementing nonlinear image filters.
de.unihalle.informatik.MiToBo.filters.vesselness - package de.unihalle.informatik.MiToBo.filters.vesselness
Provides various operators for enhancing vessel-like structures in images.
de.unihalle.informatik.MiToBo.gui - package de.unihalle.informatik.MiToBo.gui
 
de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes - package de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes
 
de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators - package de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators
 
de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml - package de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml
 
de.unihalle.informatik.MiToBo.io.dirs - package de.unihalle.informatik.MiToBo.io.dirs
Provides classes for dealing with directories.
de.unihalle.informatik.MiToBo.io.files - package de.unihalle.informatik.MiToBo.io.files
Provides classes for handling (non-)image files.
de.unihalle.informatik.MiToBo.io.images - package de.unihalle.informatik.MiToBo.io.images
Provides classes for handling image files.
de.unihalle.informatik.MiToBo.io.importer - package de.unihalle.informatik.MiToBo.io.importer
 
de.unihalle.informatik.MiToBo.io.tools - package de.unihalle.informatik.MiToBo.io.tools
Contains helper classes for image I/O.
de.unihalle.informatik.MiToBo.math - package de.unihalle.informatik.MiToBo.math
Provides mathematical functionality.
de.unihalle.informatik.MiToBo.math.arrays.filter - package de.unihalle.informatik.MiToBo.math.arrays.filter
 
de.unihalle.informatik.MiToBo.math.distributions.impl - package de.unihalle.informatik.MiToBo.math.distributions.impl
 
de.unihalle.informatik.MiToBo.math.distributions.interfaces - package de.unihalle.informatik.MiToBo.math.distributions.interfaces
 
de.unihalle.informatik.MiToBo.math.fitting - package de.unihalle.informatik.MiToBo.math.fitting
 
de.unihalle.informatik.MiToBo.math.graphs - package de.unihalle.informatik.MiToBo.math.graphs
 
de.unihalle.informatik.MiToBo.math.images - package de.unihalle.informatik.MiToBo.math.images
Provides mathematical operations on images.
de.unihalle.informatik.MiToBo.math.optimization - package de.unihalle.informatik.MiToBo.math.optimization
 
de.unihalle.informatik.MiToBo.math.statistics - package de.unihalle.informatik.MiToBo.math.statistics
This package contains oeprators for performing statistical analysis of data sets.
de.unihalle.informatik.MiToBo.morphology - package de.unihalle.informatik.MiToBo.morphology
Provides classes for morphological processing of binary images.
de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes - package de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
 
de.unihalle.informatik.MiToBo.segmentation.activecontours.energies - package de.unihalle.informatik.MiToBo.segmentation.activecontours.energies
 
de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions - package de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
 
de.unihalle.informatik.MiToBo.segmentation.basics - package de.unihalle.informatik.MiToBo.segmentation.basics
 
de.unihalle.informatik.MiToBo.segmentation.contours.extraction - package de.unihalle.informatik.MiToBo.segmentation.contours.extraction
Provides classes for performing contour extractions from regions or other image elements.
de.unihalle.informatik.MiToBo.segmentation.evaluation - package de.unihalle.informatik.MiToBo.segmentation.evaluation
 
de.unihalle.informatik.MiToBo.segmentation.evaluation.measures - package de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
 
de.unihalle.informatik.MiToBo.segmentation.helpers - package de.unihalle.informatik.MiToBo.segmentation.helpers
 
de.unihalle.informatik.MiToBo.segmentation.levelset.core - package de.unihalle.informatik.MiToBo.segmentation.levelset.core
 
de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable - package de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
 
de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE - package de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
 
de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes - package de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
 
de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver - package de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver
 
de.unihalle.informatik.MiToBo.segmentation.regions.convert - package de.unihalle.informatik.MiToBo.segmentation.regions.convert
 
de.unihalle.informatik.MiToBo.segmentation.regions.filling - package de.unihalle.informatik.MiToBo.segmentation.regions.filling
Provides operators for filling wholes in binary 2D/3D regions.
de.unihalle.informatik.MiToBo.segmentation.regions.labeling - package de.unihalle.informatik.MiToBo.segmentation.regions.labeling
Provides classes to perform region labeling to find connected components in binarized images.
de.unihalle.informatik.MiToBo.segmentation.regions.mser - package de.unihalle.informatik.MiToBo.segmentation.regions.mser
 
de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes - package de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Provides basic datatypes for MiToBo explicit active contours (snakes).
de.unihalle.informatik.MiToBo.segmentation.snakes.energies - package de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Provides classes with energies to be used with MiToBo snakes.
de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt - package de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Provides classes with parameter adaptation for energies to be used with MiToBo snakes.
de.unihalle.informatik.MiToBo.segmentation.snakes.optimize - package de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Provides classes for performing snake-based segmentation on images.
de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize - package de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Provides classes for calculating several update strategies of the snake step size gamma.
de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination - package de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Provides classes for calculating several termination strategies of the snake optimization.
de.unihalle.informatik.MiToBo.segmentation.thresholds - package de.unihalle.informatik.MiToBo.segmentation.thresholds
Provides classes for thresholding grayscale and color images.
de.unihalle.informatik.MiToBo.tools - package de.unihalle.informatik.MiToBo.tools
 
de.unihalle.informatik.MiToBo.tools.image - package de.unihalle.informatik.MiToBo.tools.image
 
de.unihalle.informatik.MiToBo.tools.interactive - package de.unihalle.informatik.MiToBo.tools.interactive
 
de.unihalle.informatik.MiToBo.tools.strings - package de.unihalle.informatik.MiToBo.tools.strings
 
de.unihalle.informatik.MiToBo.tools.system - package de.unihalle.informatik.MiToBo.tools.system
 
de.unihalle.informatik.MiToBo.topology - package de.unihalle.informatik.MiToBo.topology
 
de.unihalle.informatik.MiToBo.tracking.multitarget.algo - package de.unihalle.informatik.MiToBo.tracking.multitarget.algo
 
de.unihalle.informatik.MiToBo.tracking.multitarget.datatools - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatools
 
de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts
 
de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
 
de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
 
de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts - package de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
 
de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl - package de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
 
de.unihalle.informatik.MiToBo.tracking.multitarget.eval - package de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
de.unihalle.informatik.MiToBo.transforms - package de.unihalle.informatik.MiToBo.transforms
 
de.unihalle.informatik.MiToBo.visualization.colormappings - package de.unihalle.informatik.MiToBo.visualization.colormappings
 
de.unihalle.informatik.MiToBo.visualization.drawing - package de.unihalle.informatik.MiToBo.visualization.drawing
Provides operators to visualize data types.
de.unihalle.informatik.MiToBo.visualization.plots - package de.unihalle.informatik.MiToBo.visualization.plots
 
debug - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
debug - Variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
debug - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Debug flag for internal use only.
debug - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
debug - Variable in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
Debug flag (not accessible from outside).
debug - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Local flag for debug output.
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
Debugging output
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Bit mask for debug output on System.out.
debug - Static variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
For internal use.
debug - Static variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
debug flag
debugInfoImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Debug image to visualize analysis results.
debugReport(String) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
decrease - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Fixed decrease factor for adaptation of all gamma values.
DEFAULT_ALPHA - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
DEFAULT_erodeSize - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default size of the structuring element to erode the image
DEFAULT_FALL_BACK - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
DEFAULT_hueThresh - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default hue threshold
DEFAULT_KAPPA - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
DEFAULT_LAMBDA_BG - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
DEFAULT_LAMBDA_FG - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
DEFAULT_linkageMode - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default linkage mode for growing
DEFAULT_MAXITER - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
DEFAULT_minAreaAfterOpening - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
DEFAULT_minAreaPostProcessing - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Minimum area of a region in post processing.
DEFAULT_minAreaSeedRegions - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default minimum area for a region to be further eroded
DEFAULT_minCompactness - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
DEFAULT_MU - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
DEFAULT_neighbourhood - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default neighborhood for growing
DEFAULT_NU - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
DEFAULT_openingSESize - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default size of structuring element for opening (post processing)
DEFAULT_satThresh - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default saturation threshold
DEFAULT_seOpeningSize - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
DEFAULT_SIGMA - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
DEFAULT_xThresh - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default intensity threshold
defaultDirections - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
Default directions for Haralick features.
defaultfps - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
degree - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
DEGREE_TO_BYTE - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
degSampling - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Sampling step size for vesselness enhancement filtering.
deleteRegionFromImage(MTBImageByte, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set pixels of the points contained in the given region to 0(zero).
delim - Variable in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles
Delimiter in xSV files.
delimiter - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Delimiter to be used when exporting the model.
delta - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
X- and Y-coordinate differences of the 8-way neighbors.
delta - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Difference between threshold levels to compare.
delta_t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
delta_t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
delta_t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
DeltaApproxHelper - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Class calculating approximations to the Dirac impulse function.
DeltaApproxHelper(double, DeltaApproxHelper.ApproxVersion) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper
Default constructor.
DeltaApproxHelper.ApproxVersion - Enum in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Available approximations for the Heaviside function and its derivatives.
deltaApproximator - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Helper to calculate approximated values for the Dirac function.
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Calculate differences of energy if the pixel/voxel (x,y,z) is changed from its current phase in the level set function phi supplied from current phase to newPhase.
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Calculate differences of energy if the pixel/voxel (x,y,z) changes its phase in the levelest function phi supplied as argument and assumed to be associated with this energy object.
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
 
deltaE(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
 
deltaHelper - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
Helper object for calculating approximated values of Heaviside function.
deltaHelper - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
Helper object to calculate values of approximated function.
deltaHelper - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
Helper object for calculating approximated values of Heaviside function.
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
deltaT - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Time step size in iterative optimization.
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
deltaX - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
deltaXY - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
deltaXY - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Physical pixel resolution.
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
deltaZ - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
deltaZ - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
denoise - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
denoise(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Denoise wavelet coefficients using Jeffrey's noninformative prior for a given sigma of noise
denoiseDWTJeffreys(MTBImage[], double, double[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Denoise wavelet coefficients using Jeffrey's noninformative prior [..]
denormalize() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Denormalizes the snake coordinates.
depth - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Depth of segmentation domain.
depth - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Depth of the input image and levelset function.
depth - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Depth of the input image.
depthFirstSearch(Vector<Point2D.Double>, Vector<Integer>, MTBNeuriteSkelGraphNode<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Depth-first-search to collect data from the neurite skeleton graph in a SWC file like format.
desiredImageClass - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Class of image to be returned.
destinationImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
detectedBorders - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Set of pre-segmented borders.
detectedNeurites - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Vector of detected neurite sets for each image.
detectedNeuritesSet - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Final set of detected neurites.
detectedParticles - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
 
detectedRegions - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Set of pre-segmented regions.
detectedRegions - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
detectedStomata - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves
Set of pre-segmented regions.
detectionChannel - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
detectionChannel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
detectionMode - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Operator mode to run.
detectionResultTable - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
detectionResultTable - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
DetectMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D.DetectMode
 
DetectMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D.DetectMode
 
DetectMSERs - Class in de.unihalle.informatik.MiToBo.segmentation.regions.mser
Implementation of maximally stable extremal regions based on ImgLib2.
DetectMSERs() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Default constructor.
DetectMSERs.Thresholding_Direction - Enum in de.unihalle.informatik.MiToBo.segmentation.regions.mser
Modes for direction of intensity thresholding.
DetectorExternalEnergy() - Constructor for enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos.DetectorExternalEnergy
 
detectorMode - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
detectProtrusionsIndentations(MTBContour2D, MorphologyAnalyzer2DInProData, double[], int, int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Method to detect significant indentations and protrusions along contour.
detectResults - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Detection result.
detectStromuliRidgeModel(MTBImageShort, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Detect stromule candidates applying Steger operator.
detectStromuliStatisticalModel(MTBImageShort, MTBImage, double[], double[], double[]) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Detect stromules applying a statistical model.
detectWithLocalContrastEnhancement() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detect nuclei by first improving image contrast.
detectWithNiblack() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detects nuclei based on Niblack thresholding.
detectWithOtsu_erodedilate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detects nuclei based on Otsu thresholding and a combination of erosion/ dilation.
detectWithOtsu_openclose() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detects nuclei based on Otsu thresholding and a combination of opening and closing.
detectZSlice - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Index of input image slice if z-stack is provided as input.
determineGatingDistance() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
automatic gating distance determination according to:

"Automated and semi-automated cell tracking: addressing portability challenges"
KAN, A. and CHAKRAVORTY, R. and BAILEY, J. and LECKIE, C. and MARKHAM, J. and DOWLING, M.R.
determineSubspaceDimension() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Determines desired sub-space dimensionality according to selected mode.
determineTypeOfCurve() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Figure out which kind of curve we have.
diagonalNeighbors - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Flag for using 8-neighborhood.
diagonalNeighbors - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Flag to define 4-/8-neighborhood in components.
diameter - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
DijkstraShortestPixelPathFinder - Class in de.unihalle.informatik.MiToBo.math.graphs
Search shortest path between two pixels in an image using Dijkstra.
DijkstraShortestPixelPathFinder() - Constructor for class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Default constructor.
DijkstraShortestPixelPathFinder.GraphNode - Class in de.unihalle.informatik.MiToBo.math.graphs
Local class to represent the nodes of the graph.
DijkstraShortestPixelPathFinder.WeightModel - Enum in de.unihalle.informatik.MiToBo.math.graphs
Modes how to set the weights.
dilate(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
dilate1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
dilateComponentsTopologyPreserving(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Perform a dilation of the given image with given masksize, but preserve topology.
dilateMaskSize - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Mask size for topology-preserving dilation.
dilationAreas - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
dimension - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Dimension of image
dirac_v1(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper
Implements version 1 of approximation.
dirac_v2(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper
Implements version 2 of approximation.
directed - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
True if MTBGraph is directed.
directed - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
directions - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
Directions for calculating cooccurrence matrices.
directions - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Directions.
directoryDefault - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Default directory to be used initially.
DirectoryTree - Class in de.unihalle.informatik.MiToBo.io.dirs
This class implements a data structure for representing directory trees.
DirectoryTree(String) - Constructor for class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Standard constructor.
DirectoryTree(String, boolean) - Constructor for class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Constructor.
DirectoryTreeNodeData - Class in de.unihalle.informatik.MiToBo.io.dirs
Implements class MTBTreeNodeData for the tree sub-class DirectoryTree.
DirectoryTreeNodeData(String) - Constructor for class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Default constructor.
dirLoaderPanel - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
Panel containing elements for selecting input directory.
dirPath - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData
Name of directory including full path.
dirProvider - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Provider to read input directory.
dirSelection - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
Directory chooser.
disableComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Disables graphical elements to prohibit value changes.
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Deactivates the configuration window to prohibit value changes.
disabledColor - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
disableEnergyCalculation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Disable energy calculations completely.
disableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Disable kernel normalization.
disableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Disable kernel normalization.
disableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Disable kernel normalization.
disableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Do not save intermediate results.
disableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Deactivates writing of intermediate results.
disableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Disable display of intermediate results.
disableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Deactivates display of intermediate results.
DISAPPEARED - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
discardShortTracks() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
delete trajectories whose length is too short
discardShortTracks() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
delete trajectories whose length is too short
dispImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Image for displaying intermediate/final results.
dispImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Image for showing/saving intermediate results.
display - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.HistogramFrame
 
displayColor - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
displayEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Config button for energies.
DisplayImage - Class in cmdTools.visualization
A simple commandline tool to display image files using MiToBo's image reader.
DisplayImage() - Constructor for class cmdTools.visualization.DisplayImage
 
displayThres - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
displayWin - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayButton
Collection display window.
dispose() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
dispose() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
 
dispose() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
 
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
 
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
 
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
dispose() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
 
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
 
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Releases all graphical components associcated with this provider.
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Disposes this window and all sub-components.
dist(MTBTopologicalNumber.Point3D) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
Euclidean distance to pt
dist - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
 
distance - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
Distance.
distance(Point2D.Double, Point2D.Double, double, double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
distance(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Compute the Euclidean distance between this 3D point object and the given 3D point object.
distance(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Compute the Euclidean distance between this 3D point object and the given location.
distance - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Distance.
distanceImg - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
The distance field as MTBImage.
distanceMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
The distance field as two-dimensional double array.
distanceMetric - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Distance metric to apply.
DistanceMetric() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric
 
DistanceTargetFunction(Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction
Default constructor.
DistanceTransform - Class in de.unihalle.informatik.MiToBo.morphology
Calculate Champfer distance transform with optional precursor infos.
DistanceTransform() - Constructor for class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Standard constructor.
DistanceTransform(MTBImageByte, DistanceTransform.DistanceMetric, DistanceTransform.ForegroundColor) - Constructor for class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Constructor to create a new DistanceTransform object.
DistanceTransform.DistanceMetric - Enum in de.unihalle.informatik.MiToBo.morphology
Several distance metrics.
DistanceTransform.ForegroundColor - Enum in de.unihalle.informatik.MiToBo.morphology
Color of binary image foreground.
distField - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
The calculated 2D vector field from the distance map.
distImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Calculated distance map.
DistinctColorListGenerator - Class in de.unihalle.informatik.MiToBo.color.tools
Operator generating a list of N colors with subsequent colors being significantly different to each other.
DistinctColorListGenerator() - Constructor for class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator
Default constructor.
distmet - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Metric for distance map calculation.
distMetric - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
The used distance metric for the distance map calculation.
distroData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Cluster distribution data, rows refer to clusters and columns to cells.
distroData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Cluster distribution data, rows refer to clusters and columns to cells.
distroDataGroups - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Group names linked to entries in CytoskeletonAnalyzer2D.distroData.
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Method to divide two images.
div(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Divide each image value by a constant.
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Divide the elements of two images (img1/img2)
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Divide the elements of two images (img1/img2)
doc - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
doClustering(Instances) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Does the actual clustering.
doDimensionReduction() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Does the actual dimension reduction by data projection into sub-space.
doErosion - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Calculates evaluation measures.
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Method to overwrite that does actual calculations.
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors
 
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance
 
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria
This method does the actual work.
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit
 
doEvaluation() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_RecallPrecisionF
 
DOF - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
doFeatureCalculation - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Flag for calculating features.
doFeatureCalculation - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Flag for calculating features.
doFillHoles - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Flag to enable hole filling.
doGauss - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Preprocess cytoplasm channel by Gaussian smoothing.
doHS(MTBImageDouble) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
Does the hysteresis thresholding.
doHysteresisThresholding - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
Flag to enable/disable additional hysteresis thresholding.
doIsotropicCalcutations(boolean) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Set flag for isotropic calculations.
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Here the main work should be done.
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Performs one single optimization step, i.e. iterates once over all points.
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Performs one single optimization step.
domainXmax - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Maximal x coordinate of user-specified domain.
domainXmin - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Minimal x coordinate of user-specified domain.
domainYmax - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Maximal y coordinate of user-specified domain.
domainYmin - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Minimal y coordinate of user-specified domain.
doMorphOps - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Flag to enable/disable morphological pre-/postprocessing.
doNMS() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
Applies non-maximum-suppression to the input data.
doNormalization - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
do normalization?
doNucleiSeparation - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Flag to enable separation of merged nuclei regions.
doPCA - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Perform PCA in second stage?
doPCA() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Performs a Karhunen-Loeve transformation on the cluster distribution data.
doPCA - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Perform PCA in second stage?
doPCA() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Performs a Karhunen-Loeve transformation on the cluster distribution data.
doProtrusionIndentationAnalysis(MTBContour2DSet, Vector<double[]>, int, int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Method to perform analysis of intrusions/protrusions along contours.
doRemoveSpines(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Enable/disable removal of spines.
doResampleSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns true if snake should be resampled during optimization.
doResampling - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Flag to enable/disable snake resampling.
dotGlobalAttributes - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
dotGraphFilename - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
doUseSpecifiedDomain(boolean) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Enable/disable use of domain specified by the user.
draw(MTBXMLRootImageAnnotationType, MTBImage, Drawing.DrawType, EnumSet<Drawing.ROOTSEGMENT_STATUS>) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
 
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Called method to temporary view the selected set of borders from the Roi-Manager into the current image.
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Called method to temporary view the selected set of contours from the Roi-Manager into the current image.
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Called method to temporary view the selected set of polygons from the Roi-Manager into the current image.
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Called method to temporary view the selected set of regions from the Roi-Manager into the current image.
draw(Point2D.Double[]) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
drawBordersToImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Draws result contours to an image.
drawCircle2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Draws a circle at the given position into the x-y-plane.
drawContour(MTBImage, Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Draw a contour into an image.
DrawContour2DSet - Class in de.unihalle.informatik.MiToBo.visualization.drawing
A class to visualize 2D contours.
DrawContour2DSet() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Default constructor.
DrawContour2DSet(MTBContour2DSet) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Simple constructor with contour set.
DrawContour2DSet(MTBContour2DSet, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Constructor with contour set and image.
drawContours(MTBImage, MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Draw contours of resultImg and if non null initLabelImg into inIMg and return this result in a new image
DrawEllipse - Class in de.unihalle.informatik.MiToBo.visualization.drawing
Operator to draw an ellipse to a given image.
DrawEllipse() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Default constructor.
drawEllipse() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Draw ellipse to image.
drawFilledCircle(ImagePlus, int, int, float, int) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
Draws a filled circle at position ('x', 'y') with radius 'radius'.
drawFilledCircle2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Draws a 2D circle at the given z position into the x-y-plane.
Drawing - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.utils
Created by Andreas Lange on 8/30/17.
Drawing() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
 
Drawing.DrawType - Enum in de.unihalle.informatik.MiToBo.apps.minirhizotron.utils
 
Drawing.ROOTSEGMENT_STATUS - Enum in de.unihalle.informatik.MiToBo.apps.minirhizotron.utils
 
DrawLine - Class in de.unihalle.informatik.MiToBo.visualization.drawing
Implementation of the Bresenham line drawing algorithm according to Wikipedia.
DrawLine() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
 
DrawLine(MTBImage, Point2D.Double, Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
 
drawLine2D(Line2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Draws a 2D line into the neuron image.
drawLine2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Draws a 2D line into the current slice of the image.
drawLine2D(int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Draws a 2D line into the given slice of the image.
drawLine2D(Line2D.Double, Point2D.Double, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Draws a 2D line into the neuron image.
DrawMask2D - Class in de.unihalle.informatik.MiToBo.visualization.drawing
Operator for drawing a mask into an image.
DrawMask2D() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
Default constructor.
DrawMask2D(MTBImage, MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
Constructor.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Called method to draw the selected entry from the Roi-Manager into the current image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Called method to draw the selected entry from the Roi-Manager into the current image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Called method to draw the selected entry from the Roi-Manager into the current image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Called method to draw the selected entry from the Roi-Manager into the current image.
drawPoint2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Draws a point at given position into the x-y-plane.
drawPolygon(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Draw a polygon into an image (in red color).
drawPolygon(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Draw a polygon into an image.
drawPolygon(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Draw snake into an image.
DrawPolygon2DSet - Class in de.unihalle.informatik.MiToBo.visualization.drawing
A class to visualize 2D polygons.
DrawPolygon2DSet() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Default constructor.
DrawPolygon2DSet(MTBPolygon2DSet) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Simple constructor with polygon set.
DrawPolygon2DSet(MTBPolygon2DSet, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Constructor with polygon set and image.
drawPolygonPoints(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Draw polygon points into an image (in red color and as crosses).
drawPolygonPoints(MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Draw polygon points into an image.
drawPolygonPoints(MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Draw snake points into an image (as crosses).
DrawRegion2DSet - Class in de.unihalle.informatik.MiToBo.visualization.drawing
A class to visualize 2D regions.
DrawRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Default constructor where no parameters are set.
DrawRegion2DSet(DrawRegion2DSet.DrawType, MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Simple constructor to create the most common region image types.
DrawRegion2DSet(DrawRegion2DSet.DrawType, MTBRegion2DSet, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Simple constructor to draw the most common region image types to a given image.
DrawRegion2DSet.DrawType - Enum in de.unihalle.informatik.MiToBo.visualization.drawing
Type of image to be drawn.
drawRegionIDsToOutputImages - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Flag to enable/disable drawing region IDs.
drawRegions(MTBRegion2DSet, int, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
draw regions to the output image
drawRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
drawResultsToImage(MTBImageRGB, Lines, Junctions, boolean, boolean) - Static method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Draw results to given image.
drawRootIDs(MTBXMLRootType[], MTBImage, Color) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
drawSample(int, T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.IndependentSamplingDistribution
Generate a new sample from this density by drawing only one independent variable for a given realization x.
drawSample() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.SamplingDistribution
Generate a new sample from this density.
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
 
drawSample(int, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistributionIndep
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistributionIndep
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
drawSample(int, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
drawSample(int, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
drawSampleDebug(DataAssociation, OutputStream) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
 
drawSampleDebug(DataAssociation, OutputStream) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
drawSampleDebug(DataAssociation, OutputStream) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
 
drawSegment(ImagePlus, int, int, int, int, int, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
Draws a filled rectangle.
drawSpot(MTBImage, MTBRegion2D, int, int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
Draw region to an image at time=t and channel=c with specified color.
drawSpots - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
drawSqare(MTBImage, MTBRegion2D, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
Draw square to an image at time=t and channel=c with specified color and size=2*radius+1.
drawStringToImage(MTBImageRGB, String, int, int, int, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Draws string at given position into image.
drawStringToImage(MTBImageShort, String, int, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Draws string at given position into image.
drawStringToImage(MTBImage, String, int, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Draws string at given position into image.
DrawStringToImage - Class in de.unihalle.informatik.MiToBo.visualization.drawing
Operator to draw a given string into a given image.
DrawStringToImage() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
Default constructor.
DrawTracks2D - Class in de.unihalle.informatik.MiToBo.visualization.drawing
Draw trajectories of tracked observations over time.
DrawTracks2D() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
Constructor.
drawTrajectories - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
drawTrajectories(Matrix, Matrix, int, int, int, MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
Draw trajectory between two points at the given and all later timepoints until t_last
DrawType() - Constructor for enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.DrawType
 
drawType - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Type of image to be created.
DrawType() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet.DrawType
 
duplicate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Duplicates the object.
duplicate(ALDOperator.HidingMode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Duplicates the object.
duplicate(MTBOperator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Deprecated.
duplicate(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
duplicate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
duplicateImageJType(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
duplicateNonImageJType(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
DynamicColorLUT - Class in de.unihalle.informatik.MiToBo.visualization.drawing
A color lookup table that generates colors dynamically and randomly for indices that do not exist.
DynamicColorLUT() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Constructor with a (seeded) random generator and channel offset = 20.
DynamicColorLUT(Random) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Constructor for a specific random generator and channel offset = 20..
DynamicColorLUT(Random, int) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Constructor for a specific random generator and a given channel offset

E

e - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Implicit curve parameter e.
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Return the complete energy for the level set function phi.
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
 
E(int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
Get energy term a pixel (x,y) for phi. 2D only
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
 
E(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
Get energy term a voxel (x,y,z) for phi.
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
 
e_x - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
x coordinate of displacement vector defining neighbor hood
e_y - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
x coordinate of displacement vector defining neighbor hood
eccentricities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
eccentricities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
edgeData - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Data of the MTBGraphEdge, included in a vector object.
edges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Vector of included graph edges.
eigenVals - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Set of computed eigenvalues.
eigenVects - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Matrix of eigenvectors, each column containing a vector.
eightconnected - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
eightconnected - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Use 8-connectedness in component labeling (only active if ConvexHullExtraction.inType is InputType.IMAGE).
elemCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get a border by index.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get a contour by index.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Get a specific line segment by index including a safety check.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Get a polygon by index.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Get a region by index
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Get a region by index
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Get a region by index
elementMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Matrix for elements markers: 0 = no mark, 1 = starred, 2 = primed
ellipse - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Ellipse to draw.
ellipseDistThresh - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Ellipse distance threshold.
ellipseDistThresh - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Maximal distance between contact points along ellipse contour.
ellipsoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Function to extract elliptical snake primers.
enableComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Enables graphical elements to allow for value changes.
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Reactivates the configuration window to allow for value changes.
enableEnergyCalculation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Enable energy calculation in each iteration.
enableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Enable kernel normalization.
enableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Enable kernel normalization.
enableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Enable kernel normalization.
enableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Save intermediate results.
enableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Activates writing of intermediate results to disc.
enableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Enable display of intermediate results.
enableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Activates display of intermediate results.
end - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
 
endPoint - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
End pixel of the path.
endPointHash - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
 
endPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Index of segment end pixel on contour.
energies - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
List of snake energies.
energies - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
energies - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
energy - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Current energy of the snake.
energyCalculationRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Flag for invoking energy calculations.
energyConfWins - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Mapping of short names to configuration windows.
energyConfWins - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Mapping of short names to configuration windows.
energyData - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
energyLabel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Label of available external snake energies, which are usable by the detector.
EnergyNormalizationMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.EnergyNormalizationMode
 
energyPotential - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Potential field reconstructed from GVF.
energyRange - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Interval boundaries of adapted energy interval.
energySelection - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Combobox for selecting energies.
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Set of energies to apply.
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Set of energies.
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
 
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
 
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
List of snake energies to be used in segmentation.
energySetFields - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
Fields of a EnergySet we parse
energyTab - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
List of selected energies.
energyTab - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
List of selected energies.
energyTabModel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Model for the energy table.
energyTabModel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Model for the energy table.
energyWeights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Individual energy weights.
energyWeights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Individual energy weights.
energyWeightsNormed - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
List of normalized energy weights.
energyWeightsNormed - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
List of normalized energy weights.
enhanceBoundaries(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Enhance cell boundaries by applying a vesselness enhancement filter.
enhanceR - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Niblack factor R.
entireTargetIDs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
The targetIDs of all targets that have ever existed up to current time
entriespanel - Variable in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
panel to hold all the entries
entropyFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
entropyFilterSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
entropyFilterSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
entropyFilterSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
entropyImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
ep - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine
End point of segment.
epsilon - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.defines.MTBConstants
Accuracy for numerical calculations.
epsilon - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper
Epsilon value to configure scale to use.
epsilon - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Epsilon value for approximation of Heaviside function.
equalizeImageHisto(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Apply histogram equalization to the given image.
equals(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Test if this object and img are of same type, have same size and same values
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D.IntersectionPoint2D
Checks if two intersection points are equal.
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
 
equals(MTBLevelsetFunctionPDE) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
are these two LevelSets equal?
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
equalSize(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Test if this object and img have the same size in x-, y-, z-, t- and c-dimension
equalWeights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
equalWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Returns true if all particle weights are equal
equatorLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Length of the equator in pixels.
EraseLargeComponents(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function to remove large components from a binary image.
eraseNonCompactComponents(MTBImageByte, double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function to remove all non compact/circular components of a binary image.
EraseRoundComponents(MTBImageByte, double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Remove components with small eccentricity.
EraseSmallComponents(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function to remove small components from a binary image.
erode(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
erode1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
erodeComponent(int, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
erode one component with given label
erodeImageWithCircle(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Erode an image of type MTBImageByte.
erodeSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
erodeSize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The size of the structuring element for erosion to compute seed regions.
erodeSize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The size of the structuring element for erosion to compute seed regions.
error - Variable in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
 
error - Variable in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
 
error - Variable in exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
 
error - Variable in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
 
error - Variable in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException
Exception error message.
error_msg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
essPercentage - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
esspercentage - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
estimateMean(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Suche nach bestem Mittelpunkt des Embryos: ueberpruefe kreisfoermige Raster (8 Punkte +Mittelpunkt des Bildes) um Bildmittelpunkt aus Kriterium: max. min.
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Estimate internal parameters (if any) for the level set function phi assumed to be associated with this energy object.
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
estimateWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
If true the widths of the lines are estimated.
euklidDist(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Hilfsmethode zur Bestimmung der euklidischen Distanz zw. 2 Punkten
evalData - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Result data.
evalData - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.MTBGroundtruthEvaluationData
Result data object.
evaltime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
time that elapsed for evaluation
EvalTracks - Class in cmdTools.tracking.multitarget
Commandline tools to compare observation-files, i.e. the target-IDs of the individual observation, to evaluate the quality of target-association in one file with respect to the other that is interpreted as groundtruth.
EvalTracks() - Constructor for class cmdTools.tracking.multitarget.EvalTracks
 
EvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for distributions that can be evaluated for each realization x of its random variable X.
evaluateFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction
 
evaluateFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
 
evaluateGradientOfFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction
 
evaluateGradientOfFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
 
EvaluationMeasure - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
Base class for evaluation measures comparing a segmentation result against a groundtruth segmentation.
EvaluationMeasure(MTBImageShort, MTBImageShort) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Constructor.
EvaluationMeasure() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Default constructor.
EvaluationMeasureContours - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
Class implements the super class for contour detection evaluation operators.
EvaluationMeasureContours() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours
Default constructor.
examineDataset() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Extracts number of samples and their dimension from dataset.
ExceptionType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException.ExceptionType
 
exclude - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
excludeBackground - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
If true all background pixels, defined as pixels with label equals backgroundLabel are excluded
excludeBorderRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
exclude regions that are adjacent to the image borders
excluded - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
excludeLargeRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
exclude regions that are larger than the predefined (Parameter maxArea) maximum
excludeList - Variable in class de.unihalle.informatik.MiToBo.clustering.KMeans
Exclude list with indices of attributes to ignore.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Optional mask to exclude particles in certain regions.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Optional mask to exclude particles in certain regions.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Global exclude mask for image to be segmented.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Mask to exclude image pixels from calculations.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
excludeParticlesInNuclei - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Flag to ignore particle in nuclei regions.
excludeSmallRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
exclude regions that are smaller than the predefined (Parameter minArea) minimum
executeOperator(ALDOperatorLocation) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
 
existingTargetIDs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
The targetIDs of the existing target at the specific time
expectedWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Expected width of vessels.
ExponentialDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
Exponential distribution.
ExponentialDistribution(double) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
Constructor for exponential distribution lambda*exp(-lambda*x) if x >= 0.
ext - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
extendLine - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
If true lines are extended.
extensions - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
extract(File[], double) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
segment the given images and extract their features for classification
extract(Vector<File>, double) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
segment the given images and extract their features for classification
extractBorders() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Extract requested borders for given input data.
extractCentroids() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
extract centroids from labeled regions
extractCentroids(MTBImage, boolean, double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
extractedNeurites - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
extractFeatures() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Method to extract code histogram from the given image.
extractHullsOnRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
extractLabelsSizesOverlaps() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Extracts evaluation data in terms of overlaps and missed pixels.
extractLocalComponents() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Extracts list of connected components from Otsu thresholded input image.
extractMolProf(MTBImage, MTBNeurite2DSet, String, String) - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Extraction of molecular profiles along the detected neurites.
extractMSERs(Img<T>) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Method to calculate MSERs from given image.
extractParticles - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
extractParticles(MTBImage, MTBNeurite2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Extraction of molecular particles along the detected neurites.
extractPointVectorPolygon(MTBXMLPolygon2DType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Extract the list of polygon points for a polygon.
extractPointVectorSnake(MTBXMLPolygon2DType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Extract the list of polygon points for a snake.
extractPrecursorInfos - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Flag to enable/disable extraction of precursor infos.
extractProfiles - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
extractRegionBorders() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves
Extract borders of detected ellipses.
extractRegionBorders() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Extract borders of detected regions.
extractTrajectoriesWithOffsets() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
extract Hashtables containing the centroid locations of each trajectory
and the offsets for the starting time of each trajectory

F

f - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Implicit curve parameter f.
F - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
state-transition matrix
factor - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
factorial(int) - Static method in class de.unihalle.informatik.MiToBo.math.MathX
Calculates the factorial of the given natural number.
factorialVals - Static variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Pre-computed factorial values.
factory - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
factory that holds information how a target's state is composed
FactoryMethod() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.FactoryMethod
 
factoryMethod - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
factoryX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
factoryX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
multi state factory for condition variable, used for validity checks
factoryX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
multi state factory for condition variable, used for validity checks
factoryZ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
factoryZ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
multi state factory for observation variable, used for validity checks
falseFileNames - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
falseNegativeFileNames - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
falsePositiveFileNames - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
featureCalcResults - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Tile-wise result data of the different calculators.
FeatureCalculator - Class in de.unihalle.informatik.MiToBo.features
Super class for operators calculating features on images.
FeatureCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Default constructor.
FeatureCalculatorHaralickMeasures - Class in de.unihalle.informatik.MiToBo.features.texture
Calculates set of Haralick co-occurrence texture features from an image.
FeatureCalculatorHaralickMeasures() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Default constructor.
FeatureCalculatorHaralickMeasures.HaralickDirection - Enum in de.unihalle.informatik.MiToBo.features.texture
Directions available for matrix calculations.
FeatureCalculatorHaralickMeasuresResult - Class in de.unihalle.informatik.MiToBo.features.texture
Class representing the result of statistical feature calculations.
FeatureCalculatorHaralickMeasuresResult(double[]) - Constructor for class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
Default constructor.
FeatureCalculatorIntensityStats - Class in de.unihalle.informatik.MiToBo.features.statistical
Calculates statistical features on images tile-wise, based on FeatureCalculator.
FeatureCalculatorIntensityStats() - Constructor for class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
Default constructor.
FeatureCalculatorIntensityStatsResult - Class in de.unihalle.informatik.MiToBo.features.statistical
Class representing the result of statistical feature calculations.
FeatureCalculatorIntensityStatsResult(ImageStatistics.StatValue, double) - Constructor for class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
Default constructor.
FeatureCalculatorLBP - Class in de.unihalle.informatik.MiToBo.features.texture.lbp
Implements an extended version of local binary patterns (LBPs).
FeatureCalculatorLBP() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBP
Default constructor.
FeatureCalculatorLBPJFeatureLib - Class in de.unihalle.informatik.MiToBo.features.texture.lbp
Abstract super class for LBP operators building on the JFeatureLib.
FeatureCalculatorLBPJFeatureLib() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Default constructor.
FeatureCalculatorLBPJFeatureLib.FeatureType - Enum in de.unihalle.informatik.MiToBo.features.texture.lbp
Type of feature to be extracted.
FeatureCalculatorLBPOriginal - Class in de.unihalle.informatik.MiToBo.features.texture.lbp
Operator for extracting Local Binary Patterns (LBPs).
FeatureCalculatorLBPOriginal() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Default constructor.
FeatureCalculatorLBPOriginal.NeighborhoodSelection - Enum in de.unihalle.informatik.MiToBo.features.texture.lbp
Kind of neighborhood to be considered for code calculation.
FeatureCalculatorLBPResult - Class in de.unihalle.informatik.MiToBo.features.texture.lbp
Class representing the LBP features.
FeatureCalculatorLBPResult(double[]) - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
Default constructor.
FeatureCalculatorLBPRIU - Class in de.unihalle.informatik.MiToBo.features.texture.lbp
Implements rotation invariant uniform local binary patterns (LBP-RIU).
FeatureCalculatorLBPRIU() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIU
Default constructor.
FeatureCalculatorLBPRIULUTs - Class in de.unihalle.informatik.MiToBo.features.texture.lbp
Class keeping look-up tables for rotation invariant LBP codes.
FeatureCalculatorLBPRIULUTs() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
 
FeatureCalculatorResult - Interface in de.unihalle.informatik.MiToBo.features
Interface for result data returned from classes extending FeatureCalculator.
FeatureColorMapper - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology
This operator maps numerical feature values to objects in an indexed image.
FeatureColorMapper() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Default constructor.
featureDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Feature directory.
featureExtractor - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Feature extractor to apply.
featureExtractor - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Feature extractor to apply.
featureLines - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Borderlines that separate the neurite from the soma and additionally separate the neurite from its growth cone.
featureNameMapper - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
 
FeatureNames() - Constructor for enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D.FeatureNames
 
FeatureNames() - Constructor for enum de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer.FeatureNames
 
featureOps - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
List of feature calculators to apply.
featureParameters - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
List of parameters relevant for feature extraction phase.
featurePoints - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Vector of detected feature points for each neurite.
featurePoints - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Features of the single neurite branches.
FeatureType() - Constructor for enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib.FeatureType
 
fg_value - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
fgValue - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
field - Variable in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Vector field the potential is reconstructed for.
fieldMap - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
used to work around generics
FieldOperation() - Constructor for enum de.unihalle.informatik.MiToBo.fields.FieldOperations2D.FieldOperation
 
FieldOperations2D - Class in de.unihalle.informatik.MiToBo.fields
Class implements several operations on a 2D vector field.
FieldOperations2D() - Constructor for class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Standard constructor.
FieldOperations2D(MTBVectorField2D, MTBImageDouble, FieldOperations2D.FieldOperation) - Constructor for class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Constructor to create a new field operation operator.
FieldOperations2D(MTBVectorField2D, FieldOperations2D.FieldOperation) - Constructor for class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Constructor to create a new field operation operator.
FieldOperations2D.FieldOperation - Enum in de.unihalle.informatik.MiToBo.fields
Several operation types on a 2D vector field.
fieldSizeX - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Vector field size in x-direction.
fieldSizeY - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Vector field size in y-direction.
file - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
File name for optionally saving the image.
file_name_noExtension - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Current image name without file extension.
fileName - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
File name of the current multichannel fluorescence image.
fileName - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Name of input image file.
filename - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
fileName - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
fileName - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
fileName - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
FilenameGenerator - Class in de.unihalle.informatik.MiToBo.tools
Utility operator to generate a filename from a given filename.
FilenameGenerator() - Constructor for class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
fileNameOut - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
FileOptionsRefresher(ImageReaderOptionsPane, File[]) - Constructor for class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
 
filePath - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Textfile with mapping.
FilePathManipulator - Class in de.unihalle.informatik.MiToBo.io.tools
Class providing helpers to manipulate file and directory paths.
FilePathManipulator() - Constructor for class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
 
files - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
 
files - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
List of files (no subdirectories!)
fileSep - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
File separator character, operating system dependent.
fill(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
fill(MTBImage, Color) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
fillBlack() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set all pixels of the image to black, i.e. the minimal available value.
fillHoles(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
FillHoles2D - Class in de.unihalle.informatik.MiToBo.segmentation.regions.filling
Operator to fill holes in connected components of binary or label images.
FillHoles2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Default constructor.
FillHoles2D(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Constructor with input image.
fillImage(MTBImage, double, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Fill the specified image with a gray value.
fillImage(MTBImage, Color, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Fill the image with a RGB color value.
fillPanel(String[], boolean[]) - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
Adds checkboxes to the panel according the entries array.
fillPanel(String[], String) - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Adds radio buttons to the panel according the choices array.
fillPanel(HashMap<String, Component>) - Method in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
Add the components in the HashMap to the panel.
fillResultTable(HashMap<String, HashMap<Integer, Double>>) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Method to fill the result table.
fillWhite() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set all pixels of the image to white, i.e. the maximal available value.
fillWhite() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
 
filter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
The current state distribution of targets in this sample estimated by a prediction filter
filterImage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
filterMethod - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
FilterMethod() - Constructor for enum de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter.FilterMethod
 
filterMode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
FilterMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D.FilterMode
 
filterRegions(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Checks region sizes and average intensities against specified intervals.
filterValidCellRegions(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Postprocesses cell regions and applies some filtering.
findEndpointBranches(MTBImageByte) - Static method in class de.unihalle.informatik.MiToBo.morphology.BinaryImageEndpointTools
Extracts set of endpoint branches from a given binary image.
findEndpoints(MTBImageByte) - Static method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Detect end-points in binary image.
findEndpoints(MTBImageByte) - Static method in class de.unihalle.informatik.MiToBo.morphology.BinaryImageEndpointTools
Extracts set of endpoints from a given binary image.
findMiddleScale(double, double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Numerically finds the middle scale between to given scales.
findNextPoint(Point2D.Double, int, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Find direction to next pixel in specific direction from the last pixel.
findPrefixes(Vector<String>) - Static method in class de.unihalle.informatik.MiToBo.tools.strings.StringAnalysis
Helper to recursively extract common prefixes.
finished - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Flag to indicate if operations are finished.
firstOneImageOneConstOrdinal - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
firstOneImageOnlyOrdinal - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
FirstOrderMoment<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for classes that provide a first order moment.
FitEllipseToPointSet - Class in de.unihalle.informatik.MiToBo.math.fitting
Operator that fits an ellipse to a given set of 2D points.
FitEllipseToPointSet() - Constructor for class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet
Default constructor.
FitQuadraticCurveToPointSet - Class in de.unihalle.informatik.MiToBo.math.fitting
Operator that fits a quadratic curve or conic to a given set of 2D points.
FitQuadraticCurveToPointSet() - Constructor for class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet
Default constructor.
fittingEnergy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
five_thirds - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
 
FLAG_LENGTH - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
Bit mask for length energies for debugging purposes.
FLAG_SOLVER - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
FLAG_SOLVER2 - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
FluorescentCellSegmenter - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
This operator is for segmenting images or image sequences containing fluorescently labeled cells
FluorescentCellSegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
FluorescentCellSegmenter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
fn - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
fn - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc
False negatives.
FNclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FNtrackend - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FNtracksegment - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FNtrackstart - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
foreground - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Foreground color of the foreground object.
ForegroundColor() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.ForegroundColor
 
foregroundToBackground(Vector<Point2D.Double>, MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set the pixel value containing in a java.util.Vector of java.awt.geom.Points2D to 0.
format - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Target format.
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
Converts an java.awt.Color object to a string-representation in the format "rINT:bINT:gINT:aINT".
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtPoint2dDataIOCmdline
Converts an java.awt.geom.Point2D.Double object to a string-representation in the format (x;y).
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
 
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline
Format the given object value to a string
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
Get a string representing the seed of the specified Random generator.
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
 
forwardDifferencing_X(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
forwardDifferencing_Y(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
forwardDifferencing_Z(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
fp - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
fp - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc
False negatives.
FPclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
fps - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
fps - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
fpsfield - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
FPtrackend - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FPtracksegment - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FPtrackstart - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
fracDigits - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
fracDigits - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
frameHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Fixed height of window.
frameHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Fixed height of window.
frameHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Fixed height of window.
frameWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Fixed width of window.
frameWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Fixed width of window.
frameWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Fixed width of window.
frequency - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Filter frequency.
fromMaxVal - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
fromMinVal - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
fromXMLType(MTBXMLMatrixType) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Obtain a JAMA matrix from its xml-beans type
fromXMLType(MTBXMLMultiStateMMIDType) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Obtain a MultiState object from its xml-beans representation
fromXMLType(MTBXMLMultiStateMMIDVectorType) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Obtain a Vector> object from its xml-beans representation

G

GaborFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
2D Gabor filter.
GaborFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Default constructor.
GaborFilter2D.KernelPart - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Allows to request kernel masks for real and complex parts independently.
GaborFilter2D.ResultType - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Reponse mode.
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Step-size in iterative snake optimization.
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
gamma - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
gammaAdaptive - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Vector containing the current gamma values (step sizes).
GammaCorrection2D - Class in de.unihalle.informatik.MiToBo.enhance
Gamma correction on a 8- oder 16-bit image for one- or multi-channel images.
GammaCorrection2D() - Constructor for class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Standard constructor.
GammaCorrection2D(MTBImage, Double, Integer) - Constructor for class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Constructor to create a new gamma correction 2D operator.
GammaCorrection2D(MTBImage, Integer) - Constructor for class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
No gamma value is set.
gammaUpdater - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Gamma update strategy.
GapCloseMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.GapCloseMode
 
gapMode - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Mode for closing gaps.
gauss2poisson(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Transforms image with gaussian noise to image with poisson noise J.
GaussFilter - Class in de.unihalle.informatik.MiToBo.filters.linear
Multidimensional Gauss filter class.
GaussFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Constructor with default parameters sigmaX=1, sigmaY=1, sigmaZ=0, sigmaT=0, sigmaC=0, kernelTruncation=3, sigmaInterpretation=PHYSICALSIZE.
GaussFilter(MTBImage, double, double) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Constructor for Gaussian filtering in x- and y-dimension.
GaussFilter(MTBImage, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Constructor for Gaussian filtering in x-, y- and z-dimension.
GaussFilter(MTBImage, double, double, double, double, double, MTBImageWindow.BoundaryPadding, double, GaussFilter.SigmaInterpretation) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Constructor for Gaussian filtering.
gaussFilter() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
compute the Gaussian filter
GaussFilter.SigmaInterpretation - Enum in de.unihalle.informatik.MiToBo.filters.linear
Indicator how to interpret the specified standard deviations: - PIXEL: Sigma is given in pixels - PHYSICALSIZE: Sigma is given in terms of the physical pixel size (see MTBImage.getStepsizeX/Y/Z/T, in c-dimension always pixel interpretation is used)
GaussFilterDouble1D - Class in de.unihalle.informatik.MiToBo.math.arrays.filter
This class implements a Gaussian filter for 1D arrays.
GaussFilterDouble1D() - Constructor for class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D
Default constructor.
gaussFilterImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Gauss filtered input image (for internal use only).
gaussian - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
multivariate gaussian density object for evaluation
gaussian - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
multivariate gaussian density object for evaluation
GaussianDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A multivariate Gaussian distribution.
GaussianDistribution(int) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Constructor for a Gaussian distribution of dimension DOF with the zero vector as mean, the unity matrix as covariance matrix and a new random generator for sampling
GaussianDistribution(int, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Constructor for a Gaussian distribution of dimension DOF with the zero vector as mean, the unity matrix as covariance matrix and a given random generator for sampling
GaussianDistribution(Matrix, Matrix) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Gaussian distribution with given mean, covariance and a new random generator for sampling
GaussianDistribution(Matrix, Matrix, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Gaussian distribution with given mean, covariance and random generator for sampling
gaussians - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
gaussianSigma - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Standard deviation of Gaussian kernel in curvature smoothing.
GaussMixDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A multivariate Gaussian mixture distribution.
GaussMixDistribution(GaussianDistribution[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
Constructor with equally weighted Gaussian components
GaussMixDistribution(GaussianDistribution[], double[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
Constructor for weighted Gaussian components
gaussmixtures - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
gaussnoise - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
GaussPDxFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
2D linear filter implementing first partial derivative of a Gaussian in x.
GaussPDxFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Default constructor.
GaussPDxxFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
2D filter implementing second partial derivative of Gaussian in x.
GaussPDxxFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Default constructor.
gaussSigma - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Sigma for Gaussian smoothing.
gaussStdDev - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Standard deviation of the Gaussian.
gaussStdDev - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Standard deviation of the Gaussian.
gaussStdDev - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Standard deviation of the Gaussian.
gaussStdDevX - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Standard deviation of the Gaussian in x.
gaussStdDevY - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Standard deviation of the Gaussian in x.
generateCoarseSoma() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Compute a coarse neuron cell body region (soma).
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
 
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
 
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
 
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Set up the help menu.
generateNeuriteRegions(Vector<Vector<Vector<Line2D.Double>>>, Vector<Vector<Vector<Point2D.Double>>>) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Generate neurite region from calculated features.
generateNextStates(MultiState<MotionModelID>, LinearTransformGaussNoise[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
generateObservations(MultiState<MotionModelID>, LinearTransformGaussNoise, MultiStateFactory<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
generateSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates segmentation objects given specified data.
generateSkelGraph() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Compute the skeleton graph for the complete neuron region.
generateStackWithIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Generates a stack with intermediate results.
generateStructuringElement() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
GeneratorInfo() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
GenericDiscreteDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A generic discrete distribution
GenericDiscreteDistribution(double[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
Constructor.
GenericDiscreteDistribution(double[], Random, boolean) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
Constructor.
genInfo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Get a specific line segment by index.
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Get a region by index
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
 
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Get a region by index
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Get a region by index
get(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Get the function value at position (x,y,z).
get(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
get the value of this function at the position of the predecessor of ( x, y, z )
get2DInterface(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates 2D segmentation.
get2DMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates a synthetic 2D mask according to given specification.
get3DInterface(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates 3D segmentation.
get3DMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates a synthetic 3D mask according to given specification.
get3SigClippedStdDev(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get the standard deviation (sigma) of an image only using values clipped by 3*sigma from a first estimate of sigma
get8NeighborsPhase(int, int, short[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Compute phases of 8 neighbors of (x,y) and store these in the array nb.
getActivityArray() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Get reference to activity array.
getActivityArray() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Returns current activity array.
getActualSliceOnly() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get flag for thresholding only the actual slice (true) or the whole image (false)
getAlgorithm() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
getAllEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get all edges of the node.
getAllInner() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Get all inner contours from the contour object.
getAllInnerBorders() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get all inner borders from the border object.
getAllInputImages() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Getter for all input images.
getAllInputTreelines() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Getter for the input treelines of the specified layer.
getAllNodesDepthFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Get all nodes in a depth-first sorting.
getAllPaths(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the pixels of all paths of the neurite skeleton graph.
getAllPixels(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get all pixels of the neurite skeleton graph from the nodes and edges.
getAllPixels(Vector<Point2D.Double>, MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get all pixels of the neurite skeleton graph from the nodes and edges.
getAllResultTreelines() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Getter for all result treelines.
getAllSubtreeNodesDepthFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Recursively collect all nodes of the subtree below this node.
getAllTiles() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Generates and returns array of all tiles.
getAlpha() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get snake length term weight alpha.
getAlpha() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get weighting factor for snake length term.
getAlphaDecrease() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
Get the fix alpha decrease value.
getAnalysisImage() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Get image with visualized analysis results.
getAnalyzedImages() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get vector of analyzed images.
getApicalLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Get apical length.
getAPIText() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame
 
getAPIURL() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame
 
getApplicationMode() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Get application mode.
getArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return the area of the region in pixels.
getArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
 
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape
Get area of the shape.
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeCurve
 
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine
 
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon
 
getArea() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion
 
getAreaFracMatrix(MTBRegion2DSet, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
getAreaFraction(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
getAreaFraction() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Get area fraction.
getAreaFraction() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Get area fraction.
getAreaFractions(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
getArithmeticOperation() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getAssociatedObservations(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
getAssociatedObservations(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the indices of all observations that are associated with the specified state.
getAssociatedTargets(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
getAssociatedTargets(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the indices of all targets that are associated with the specified observation.
getAvailableCodecs() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Return available codecs for movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap.
getAvailableCompression() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the available compression methods for the specified file format.
getAvailableQualities() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Return available qualities for quicktime movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap.
getAverageIntensities() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Get average intensities of regions.
getAverageMean(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getAverageStdDev(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getAvgConeWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get average widths of each neurite growth cone.
getAvgIntensity() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape
Get average intensity.
getAvgNeuriteWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get average widths of each complete neurite branch.
getAvgShaftWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get average widths of each neurite shaft.
getBackground(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
 
getBasalLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Get basal length.
getBaselineLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Get baseline length.
getBeta() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get snake curvature term weight beta.
getBeta() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get weighting factor for snake curvature term.
getBetaDecrease() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
Get the fix beta decrease value.
getBGValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get background value
getBhattacharyyaCoefficient(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getBinaryImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the image for binary mode.
getBinaryMask(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Generates binary mask for inside part of the polygon.
getBinaryMask(int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Generates binary mask for inside part of the polygon.
getBinaryMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get a binary mask of the represented segmentation.
getBinaryMask(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Generates binary mask for inside part of the snake.
getBinaryMask(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Generates binary mask for inside part of the snake.
getBinaryPattern(int, int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU
 
getBinaryResultMap() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Returns the final binary map.
getBinIndex(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
determines the index of the histogram bin, to which a value is assigned, if histogram value range and binning were specified at creation
getBinMidpoint(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
determines the value midpoint of a histogram bin for given bin index, if
histogram value range and binning were specified at creation
getBinValue(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getBorder() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to get the border object from the current 2D region, for example to visualize the regions.
getBorderCount() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Get number of borders in set.
getBorderLine(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get borderlines between soma/neurite shaft and neurite shaft/growth cone.
getBorders() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Get set of region borders.
getBorderSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Get 2D border set from Roi.
getBorderSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads a ROI manager selection into a set of borders.
getBoundaryPadding() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get value of Parameter argument boundaryPadding.
getBoundaryPadding() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get value of Parameter argument boundaryPadding.
getBoundaryPadding() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get value of Parameter argument boundaryPadding.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Calculates the axes-parallel bounding box of the contour.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Calculates the axes-parallel bounding box of the snake.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates the axes-parallel bounding box of the region.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculates the axes-parallel bounding box of the region.
getBrancheCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get number of neurite branches.
getBranchLengths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get lengths of neurite branches along the complete neurite skeleton graph.
getBranchNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get all branch nodes of the MTBNeuriteSkelGraph.
getBthImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get black top-hat image.
getBthMaskSize() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get mask size of black top-hat.
getC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getCalibration() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
getCalibration() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
getCalibration() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
getCalibration() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the calibration object.
getCalibration() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
getCalibration() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
getCandidates() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns set of detected candidate peaks.
getCConditionalProb(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the probability of the associations at time t conditional on the previous associations and all observations up to time t.
getCellAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns average size of detected cells.
getCellCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns number of detected cells.
getCellSizes() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns sizes of snake interiors.
getCenterOfMass_X() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return x-coordinate of the center of mass.
getCenterOfMass_Y() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return y-coordinate of the center of mass.
getCenterX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get coordinate of center in x.
getCenterX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getCenterY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get coordinate of center in y.
getCenterY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getCentralMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculate central moment of the region of order p,q.
getCentralMoment(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
 
getCentre() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the center of the region as 3D point.
getCentreX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the x-coordinate of the center of the region.
getCentreY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the y-coordinate of the center of the region.
getCentreZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the z-coordinate of the center of the region.
getCentroid(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
auxiliary method to determine the centroid (x,y) and width/heigth of compoment with label in a double array of length 4 (should go in class/record)
getChaincode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Calculates chaincode from the outer contour.
getChannel() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get the image channel.
getChannelB() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get a reference to the blue channel image.
getChannelG() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get a reference to the green channel image.
getChannelR() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get a reference to the red channel image.
getChannelsAreRGBFlag() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get flag if RGB color channels are interpreted as real image channels.
getChart() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Get reference to resulting chart.
getChart() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Get reference to resulting chart.
getChartObject() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
Returns the chart object associated with the button.
getChartShowButton() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowPanel
Returns the button object associated with the panel.
getChildNodes(Element) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
getChilds() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Returns Vector with child nodes.
getChosenColor() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Read currently selected color.
getCircularity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates circularity of given region.
getCJointProb() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the joint probability of all associations up to 'current time' (see getCurrentTime) conditional on all observations up to that time.
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getClass(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the class label of position (x,y).
getClass(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the class label of position (x,y,z).
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getClickedPoints() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
Get a reference to the list of clicked points.
getCLogConditionalProb(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the log of probability of the associations at time t conditional on the previous associations and all observations up to time t.
getCLogJointProb() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the natural log of joint probability of all associations up to 'current time' (see getCurrentTime) conditional on all observations up to that time.
getClosestObjectPixelMap() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the calculated map of closest object pixels.
getClosestPointOnEllipse(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Returns the point on ellipse closest to given point.
getCodec() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Get codec option
getCodec() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the codec (quicktime only)
getCodeDistributionRI(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Get array with LBP-RI code distributions.
getColor() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Get color of markers.
getColor() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the uniform color of the regions in a color image (COLOR_IMAGE only).
getColor(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Get the color for a given key.
getColorImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get image of randomly colored regions, if the create-color-image-flag was set to true.
getColorList() - Method in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator
Returns color list.
getColumnCount() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
getColumnIDs() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData
Returns index of currently selected column(s).
getColumnName(int) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
getCompactness() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
calculates compactness value according to
Carlos Martinez-Ortiz. "2D and 3D Shape Descriptors".
getCompactnessThreshold() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the actual value of compactness threshold.
getComplexKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Generates the sinus filter mask of the complex part of the Gabor filter.
getCompression() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Get compression option
getCompression() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the compression type
getCOMx() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the center of mass of the snake in x-direction.
getCOMy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the center of mass of the snake in y-direction.
getConcaveness(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
getConcavenessValues() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
getCondition() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
getCondition() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.ConditionalDistribution
Get conditional variable
getCondition() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
 
getCondition() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
 
getConeAreas() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get areas of growth cone regions.
getConeLengths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get length of the growth cone region along the neurite skeleton graph without neurite shaft areas.
getConeRoundness() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get roundness of growth cone regions, 1 means a perfect circle.
getConeSpineCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get number of spines (filopodia-like protrusions) per growth cones.
getConfigValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This function reads out the value of a given environment property.
getConfigWin(ALDOperator, ALDOpParameterUpdateEventListener) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorCollection
 
getConnectivity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Query the connectivity of pixels within border.
getConnectorIDs() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Get connector IDs.
getContinuousDOF() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get continuous dimensions of target state in continuous
getContinuousDOF() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Get number of continuous state variables
getContour() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Get a Contour2D copy of this object.
getContour() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to get the contour object from the current 2D region.
getContour() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Get a reference to the contour.
getContour2DAsXml(MTBContour2D, MTBXMLContour2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Copy the information of contour into the corresponding xml element xmlContour.
getContour2DFromXml(MTBXMLContour2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get a new MTBContour2D from the information of the xmlContour.
getContourID() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Get the contour ID.
getContourImg(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Create a new image where all contour pixels of img are set to 1, all other pixels to 0.
getContourLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Calculates the length of the outer contour using it's chaincode.
getContourPoints(int, int, int, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
Computes both points perpendicular to the vector x1,x2 with distance 'distance'.
getContours() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns extracted contours.
getContourSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Get 2D contour set from Roi.
getContourSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads a ROI manager selection into a set of contours.
getContourType() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the current contour type.
getCoordinatesNeighborNeighbors(int, int, int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
 
getCorrCircularity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates corrected circularity of given region.
getCorrectGamma() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get flag to use gamma correction.
getCorrelationImages() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Compute the correlation images as specified by the parameters.
getCorrelationThreshold() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get threshold for thresholding wavelet correlation images
getCost() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Get edge cost as double value.
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Returns the covariance matrix
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
getCovariance() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.SecondOrderCentralMoment
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
getCreateColorImageFlag() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get the flag that determines the creation of an image with randomly colored regions.
getCreateLabelImageFlag() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get the flag that determines the creation of an image with region labels.
getCurGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Returns current gamma vector.
getCurrentMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Extracts currently selected mode, i.e. data source.
getCurrentOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Get the current overlap mask.
getCurrentSlice() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of the current slice.
getCurrentSlice(MTBOperator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of the current slice.
getCurrentSliceCoords() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the current slice coordinates (z,t,c) (for functions that work on a slice only, this has nothing to do with the ij.ImageStack's current slice)
getCurrentSliceIndex() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the current slice index (for functions that work on a slice only, this has nothing to do with the ij.ImageStack's current slice)
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the slice label of the slice specified by the current slice index
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the slice label of the slice specified by the actual slice index
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the slice label of the slice specified by the actual slice index
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the slice label of the slice specified by the actual slice index
getCurrentSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns a copy of the current snake.
getCurrentSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns a copy of the current snake(s).
getCurrentSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Returns a copy of the set of current snakes.
getCurrentSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns a set with current snake(!).
getCurrentTime() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the current time index, i.e. the time index that was assigned to the latest added information
getCurrentZStackCoords() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the current z-stack coordinates. [0]=t-coordinate, [1]=c-coordinate.
getCurvature(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Curvature at point (x,y,z).
getCurvature(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
compute the curvature at at nearest contourpoint to (x,y,z) if x or y are not in the boundaries it returns 0 if z is not in the boundaries it returns the 2d cuvature
getCurvatureInfoImage() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Access info image about curvature analysis.
getCytoplasmResult() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns reference to cytoplasm/cell boundary detection result.
getData() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
Returns the data read from GUI or file.
getData(Class<?>) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
getData() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Returns the data read from GUI or file.
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Get data for current MTBGraphEdge.
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get data of MTBGraphNode.
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Returns a reference to the data associated with the node.
getDataLabels() - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Get assigned labels.
getDate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get current date for result dirs.
getDebug() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of debug.
getDebug() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of debug.
getDebug() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of debug.
getDefinedSpineLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get length to define a neurite branch as spine (filopodia-like protrusions).
getDelimiter() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Returns the currently chosen delimiter.
getDeltaApproximator() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get reference to delta function approximator.
getDeltaT() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get step size.
getDeltaX() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
getDeltaXY() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
getDeltaY() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
getDeltaZ() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
getDenoise() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get the denoising flag. true if denoising is activated.
getDerivative(MTBSegmentationInterface, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Returns the energy derivative value at position (x,y,z).
getDerivative(MTBSegmentationInterface, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Returns the energy derivative value at position (x,y,z).
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Get the energy derivative value, i.e. velocity, for position (x,y,z).
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Updates the fitting term based on new region average values.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Updates matrix A given weights for the internal energy term.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Updates matrix A given weights for the internal energy term.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Updates the region coupling energy term in matrix A.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Returns the linear matrix part of this energy for snake optimization.
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Returns the vector part of this energy for snake optimization.
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Get the energy derivative value, i.e. velocity, for position (x,y,z).
getDerivativeX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Partial derivative in x direction at position (x,y,z).
getDerivativeX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Get x-derivative of the distance map at given position using central differences.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Get x-derivative of negative absolute gradient value to the power of two (external energy) at given position using central differences.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Get x-derivative of external snake energy at given position.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Get x-derivative of external snake energy at given position using central differences.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get x-derivative of external snake energy at given position.
getDerivativeX_norm(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get x-derivative of external snake energy at given position on a normalizes image coordinates in range [width*scale, height*scale].
getDerivativeXX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in x direction at position (x,y,z).
getDerivativeXX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in x direction 2 times at nearest contourpoint to (x,y,z)
getDerivativeXY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in x-y direction at position (x,y,z).
getDerivativeXY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in x and y direction at nearest contourpoint to (x,y,z)
getDerivativeXZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in x-z direction at position (x,y,z).
getDerivativeXZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in x and z direction at nearest contourpoint to (x,y,z)
getDerivativeY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Partial derivative in y direction at position (x,y,z).
getDerivativeY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Get y-derivative of the distance map at given position using central differences.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Get y-derivative of negative absolute gradient value to the power of two (external energy) at given position using central differences.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Get y-derivative of external snake energy at given position.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Get y-derivative of external snake energy at given position using central differences.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get y-derivative of external snake energy at given position.
getDerivativeY_norm(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get y-derivative of external snake energy at given position on a normalizes image coordinates in range [width*scale, height*scale].
getDerivativeYY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in y direction at position (x,y,z).
getDerivativeYY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in y direction 2 times at nearest contourpoint to (x,y,z)
getDerivativeYZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in y-z direction at position (x,y,z).
getDerivativeYZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in y and z direction at nearest contourpoint to (x,y,z)
getDerivativeZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Partial derivative in z direction at position (x,y,z).
getDerivativeZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
getDerivativeZZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in z direction at position (x,y,z).
getDerivativeZZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in z direction 2 times at nearest contourpoint to (x,y,z)
getDescription() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow.DataTabFileFilter
 
getDescription() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU
 
getDescription() - Method in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
getDestinationImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get value of Input argument DestinationImage.
getDetailedInProResults() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Access detailed information on indentations and protrusions.
getDetectedNeurites() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get vector of detected neurite sets for each image.
getDetectedNeuritesSet() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get set of detected neurites.
getDetectedParticles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Get regions of detected particles.
getDetectionResults() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Get the detection results.
getDetectionResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get the result table of the detected neurites.
getDetectorMode() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get current detector mode.
getDetectors() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Get a reference to configured detectors' vector.
getDiagonalNeighbors() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Get value of Parameter argument DiagonalNeighbors.
getDiagonalNeighborsFlag() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get the neighborhood flag.
getDiameter() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
getDiffX_image() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Calculate the image from the first order partial derivative in x-direction from the vectors U.
getDiffY_image() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Calculate the image from the first order partial derivative in y-direction from the vectors V.
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Returns the dimension of the given membership.
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Returns the dimension of the given membership.
getDimension() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the dimension of the segmentation.
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the dimension of the given membership.
getDimensionality() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Returns the dimension of the result object.
getDimensionality() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getDimensionality() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getDimensionality() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
 
getDimensionOfScope() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction
 
getDimensionOfScope() - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
 
getDirDialog - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
File/directory chooser dialogue.
getDirection(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get direction of the vector at position (x,y) in the vector field.
getDirectionalDifferences(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getDirectionalities(Hashtable<Integer, Vector<Double>>, Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getDirections() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getDirectoryName() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData
Returns current name of directory.
getDirName() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Get directory for processing.
getDistance(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
getDistanceAlgebraic(Collection<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Returns the algebraic distance of the given point set.
getDistanceEuclideanPointToEllipse(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Returns the Euclidean distance of a point to an ellipse.
getDistanceImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
getDistanceImage() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the calculated distance map image.
getDistanceMap() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the calculated distance map.
getDistances() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getDistImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns calculated distance map.
getDistMatrix(MTBRegion2DSet, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
getDistMetric() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the used distance metric.
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
 
getDocumentation() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
 
getDoErosion() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of doErosion.
getDomainXMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal x coordinate represented in class map.
getDomainXMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal x coordinate represented in class map.
getDomainYMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal y coordinate represented in visibility map.
getDomainYMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal y coordinate represented in class map.
getDrawType() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the kind of region image drawn by the operator
getEccentricity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates eccentricity of the region in the range of [0,1].
getEdgeNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get number of included MTBGraphEdges.
getEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get all edges of the MTBGraph.
getEigenvalueDecompositionAt(int, int) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get eigenvalue decomposition of of the Hessian matrix to get largest eigenvalue at pixel (x,y) to get the vector perpendicular to the vessel path and eigenvalues.
getEigenvalues() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Get calculated eigenvalues in ascending order.
getEigenvects() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Get calculated eigenvectors, one vector per column, in ascending order.
getElapsedTime() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Returns the elapsed time since last reset (or invoking the constructor) in seconds
getElement(NodeList, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
getElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns the element at the specified position in this list.
getElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Returns the element at the specified position in this list.
getEllipsoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns set of initial snake ellipses.
getEndCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get number of end points.
getEndNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get all end nodes of the MTBNeuriteSkelGraph.
getEndPoint() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine
Get the end point of the line segment.
getEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Returns a reference to the list of energies.
getEnergy() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get external snake energy label.
getEnergy(int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Returns the energy with given index.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Returns element i of the energy list.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns element i of the energy list.
getEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of energy.
getEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of energy.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns element i of the energy list.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Returns element i of the energy list.
getEnergyDerivativeMaxVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Returns the maximum possible derivative value this energy may yield.
getEnergyDerivativeMaxVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Returns the maximum possible derivative value this energy may yield.
getEnergyDerivativeMinVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Returns the minimum possible derivative value this energy may yield.
getEnergyDerivativeMinVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Returns the minimum possible derivative value this energy may yield.
getEnergyLabel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get energy label for external energy, used for optimization.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Returns the list of energies.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns the list of level set energies.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns list of energies with actual type.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
 
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get set of energies.
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns a reference to the set of energies.
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
getEnergyValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Get current energy value for the snake.
getEntireTargetIDs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the targetIDs of all targets that ever existed up to current time.
getEntropyImage() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getEntropyMeanDifference(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getEnvVarValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This function reads out the value of a given environment variable.
getEpsilon() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get epsilon for Heaviside function approximation.
getEquatorLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Get equator length.
getErodeSize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of erodeSize.
getErodeSize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The size of the eroding element.
getError() - Method in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
 
getError() - Method in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
 
getError() - Method in exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
 
getError() - Method in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
 
getError() - Method in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException
Returns the complete exception message as string.
getESSPercentage() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
If this percentage of number of samples is below the current effective sample size (ESS), the samples are resampled.
getEstimatedCurve() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet
Get estimated curve.
getEstimatedCurve() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet
Get estimated curve.
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException
 
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBException
 
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException
 
getExcluded() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getExcluded() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
getExcludeMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns the current exclude mask.
getExcludeMask() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
getExistingTargetIDs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
getExistingTargetIDs(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the targetIDs of all targets existing at time t.
getExtEnergyInit() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Calculate the initial image for the external energy of the snake.
getExtension(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
Get extension from filename if any.
getExtractedNeurites() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get extracted neurites as result of the NeuriteExtraction2D operator.
getFactory() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get associated factory
getFactoryMethod() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getFeatureLines() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite corresponding feature lines of borders between soma and neurite shafts and neurite shafts and growth cones.
getFeatureOp() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBP
Get instance of actual feature calculator.
getFeatureOp() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Get instance of actual feature calculator.
getFeatureOp() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIU
 
getFeatureOps() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
 
getFeatureOps() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs
 
getFeatureOps() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU
 
getFeatureOps() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorTiles
Method to request operators for feature extraction to be applied.
getFeaturePoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite corresponding feature points of borders between soma and neurite shafts and neurite shafts and growth cones.
getFGValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get foreground value
getFieldSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
 
getFieldSizeX() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the field size in x-direction.
getFieldSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
 
getFieldSizeY() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the field size in y-direction.
getFileList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Collect all files in the directory tree including their complete paths.
getFileList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Get the list of all files inside the directory.
getFileName() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the filename of the image that has to be read.
getFileName() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get image filename
getFileName(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
Returns the file name without leading directories or file description (extension).
getFilterImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get flag to use gaussian filter.
getFilterMode() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get filter mode to define relation of foreground to background.
getFilterResponseStack() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Get individual filter responses.
getFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns the first element in this list.
getfirstFeatureAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get first feature of neurite corresponding feature points from borders between soma and neurite shafts.
getForeground() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the used foreground color.
getForegroundSum() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getFps() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the frames per second for movie writers (*.avi,*.mov).
getFramesPerSecond() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Get fps option
getGamma() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get gamma correction value.
getGamma() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get the gamma value.
getGammaToAuto() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get if gamma should be calculated automatically or not.
getGaussianKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Generates the Gaussian part of the Gabor kernel for a given orientation.
getGaussKernel() - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D
Get normalized Gaussian kernel for given parameters.
getGaussKernelC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in c-dimension for given parameters, null if sigma is zero in c-dimension
getGaussKernelT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in t-dimension for given parameters, null if sigma is zero in t-dimension
getGaussKernelX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in x-dimension for given parameters, null if sigma is zero in x-dimension
getGaussKernelY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in y-dimension for given parameters, null if sigma is zero in y-dimension
getGaussKernelZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in z-dimension for given parameters, null if sigma is zero in z-dimension
getGaussMixture(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
getGenericEnergyList() - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Returns list of energies converted to generic type.
getGenericEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns the list of energies.
getGenericEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns the list of energies.
getGenericEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Returns the list of energies.
getGradientMode() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get the used gradient mode for field calculation.
getGraphCost() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get total amount of the graph costs.
getGraphNode(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Get the graph node from partition 'partitionID' in subgraph 'subgraphID'.
getGrayValue() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getGrayValue() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the gray value of the regions in a mask image (MASK_IMAGE only).
getGrownRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Returns a MTBImageByte image after growing.
getGrowthConeRegions() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get regions of the separated growth cones.
getGtContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
Get list of groundtruth contours.
getGVF() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Get the calculated Gradient Vector Flow field.
getH() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Get current h-parameter (max height of the h-domes).
getHeatmapImage() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Returns the result color heat map.
getHeight() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get skeleton graph image size in y direction.
getHeight() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get height of level set function.
getHistogram() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
getHistoryLink(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Gets the port to which the object is currently linked in history.
getHueMTBImg() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Get the hue channel image.
getHueThresh() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Return the treshold for the hue channel.
getIcon() - Method in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon
Get reference to the icon.
getID() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
getID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return the ID of the region.
getID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the ID of the region.
getID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
Return the ID of the region.
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException
 
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException
 
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException
 
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBLevelsetException
 
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBSnakeException
 
getIDImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get image of region ID (of type MTB_BYTE).
getIgnoreInvalidStackSpecification() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the flag to ignore an invalid stack specification.
getImageBox(Object) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Gets the image container associated with the given image object.
getImageCount() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the number of (multi-dimensional) images stored in the specified file.
getImageDerivatives() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Calculate second partial derivatives of the input image to generate Hessian matrix at each pixel position and getting the vector perpendicular to the vessel path.
getImageFiles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get vector of all image files included in the experiment folder for detection.
getImageID(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the ID of the imageIdx-th image in the file, if available
getImageJPropValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This function reads out the value of a given ImageJ preference.
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
 
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
 
getImageName() - Method in interface de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Interface
Returns the name of the processed image.
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
 
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Note: Returned string might be null if the result is associated with a single cell rather than a complete image!
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Note: Returned string might be null if the result is associated with a single cell rather than a complete image!
getImageName(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the name of the imageIdx-th image in the file, if available
getImageObject() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton
Returns the image object associated with the button.
getImagePart(int, int, int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of a part of this image as new MTBImage.
getImagePart(MTBOperator, int, int, int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of a part of this image as new MTBImage.
getImagePart(MTBImage, int, int, int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Get a copy of a part of this image as new MTBImage
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Gets the stored ImagePlus.
getImageShowButton() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowPanel
Returns the button object associated with the panel.
getImageSizeX() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the image size in x-direction.
getImageSizeY() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the image size in y-direction.
getImageType() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Get output image type.
getImageType() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the datatype of the resulting image.
getImg() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get reference to the (input) image.
getInConst() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getIndentationSegments() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Get list of indentation segments.
getIndex() - Method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
The index of this channel.
getIndexMap() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Get map of indices of maximal responses.
getIndexOfImageToRead() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the index of the image that has to be read from the file.
getInEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get input edges for node.
getInflectionPoints() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Get list of inflection points.
getInfo() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Get info string.
getInfo() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getInfoImage() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Get the info image with analysis data visualized.
getInImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getInImg() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Input argument inImg.
getInImg() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the input image.
getInImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of inImg.
getInImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Get input image.
getInImg1() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getInImg2() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getInitAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Get the initial alpha value.
getInitBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Get the initial beta value.
getInitBinImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of initBinImg.
getInitialGUIValue(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
 
getInitialGUIValue(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
 
getInitialSegmentation() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getInitialSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Get initial segmentation.
getInitialSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns initial snake.
getInitLabelImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of initLabelImg.
getInitSegImageByte() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Return the resulting initial segmentation image.
getInner(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get a specific inner border.
getInner(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Get a specific inner contour from the contour object.
getInnerContourLengthMin() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get the minimum number of pixels in the inner contour (length of the contour).
getInnerCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Get the number of inner contours including in the contour object.
getInputDir() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get directory of input images.
getInputImage(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Getter for the input image of specified layer.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get multichannel fluorescence input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get input image
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get the input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Get uneven illuminated input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get low contrast input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get the underlying input image of the gradient field..
getInputImage() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
getInputImage() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose
Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Get value of inImg.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor
Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get input image
getInputImage() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getInputImagePlus() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get ImagePlus that has to be stored to disk
getInputImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get input image
getInputMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get input mode.
getInputMTBImage() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get MTBImage that has to be stored to disk
getInputMTBImgRGB() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Returns the input image, null if not set.
getInputRegions() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the input regions.
getInputRegions() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the regions that have to be drawn
getInputRegs() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Get set of input regions.
getInputTreelines(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Getter for the input treelines of the specified layer.
getInstance() - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon
Get singleton instance.
getInstance() - Static method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Single access point for singleton functionality.
getInstance() - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Single access point for singleton functionality.
getIntensityMeans() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
getIntensityNormalizationMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Request mode for normalizing image intensities.
getIntensityReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
getIntensityStdDevs(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
getIntermediateLS() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
getIntermediateLS() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of intermediateLS.
getIntersection(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Calculates the point of intersection between the segments.
getInvalidImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of invalidImage.
getInvalidImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of invalidImg.
getInvalidTilesNum() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Get number of invalid tiles.
getInverseCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
getIterationCount() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns the current iteration count.
getIterationsPerSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Returns the total number of iterations per snake.
getJComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
getJmax() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get Jmax
getJmax() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get Jmax (maximum scale 2^Jmax - 1)
getJmin() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get Jmin
getJVMPropValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This function reads out the value of a given JVM property.
getK() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Calculates kernel for given angle and pre-defined sigma and length.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Calculates kernel for given angle and pre-defined sigmas.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Calculates Gaussian derivative kernel for given parameters.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Calculates Gaussian derivative kernel for given parameters.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Calculates kernel for the given orientation.
getKernelImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get convolution kernel (image).
getKernelMask() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Get mask of valid kernel elements.
getKernelNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get value of Parameter argument kernelNormalization.
getKernelOrigin() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get value of Parameter argument kernelOrigin.
getKernels() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get smoothing kernels
getKernelTruncation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get kernel truncation factor.
getKey(HashMap<Integer, String>, String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Obtain the key for a given value of a HashMap, if available.
getKLower() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
getKolmogorovSmirnovStatistic(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getKUpper() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
getLabel(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
returns the value of labelImg at position (x,y).
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns label mask with segmentation result.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns label image of detected nuclei.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns gray-scale label image with nuclei regions.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Get the label image.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Returns a label image visualizing the segmentation.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the label image.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Get reference to the current Label image.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get image of region labels (of type MTB_INT).
getLabelImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of labelImg.
getLabelImg() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
getLabelMostInRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
getLabelsInRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
getLambda() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
getLambdaArray() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
getLambdaArray() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
getLargestNonEmptyBin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getLast() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns the last element in this list.
getLayer() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Get the layer where the node is located.
getLayerSubsetForInputImages() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Request the set of layers from which to provide images to the operator.
getLayerSubsetForInputTreelines() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Request the set of layers from which to provide treelines to the operator.
getLBPCodeArrayRI(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Get array with LBP rotation invariant codes.
getLBPCodeArrayRIU(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Get array with LBP rotation invariant uniform codes.
getLBPHistogram(int, int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapter
Calculate the histogram of LBP codes in the neighborhood of the specified pixel.
getLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Get the length of the polygon.
getLevel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Return the tree level (level identifier).
getLineSegmentSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads ROI manager selections into a set of line segments.
getLinkageMode() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getLogFaculty(int) - Method in class de.unihalle.informatik.MiToBo.math.LogFaculty
log(n!)
getLogFacultyFraction(int, int) - Method in class de.unihalle.informatik.MiToBo.math.LogFaculty
log(n1!
getLongestCommonPrefixes(Vector<String>) - Static method in class de.unihalle.informatik.MiToBo.tools.strings.StringAnalysis
Extracts the set of all prefixes shared by at least two strings in the given set.
getLongestPath(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the pixels of the longest path of the neurite skeleton graph.
getLowerBound() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Get lower bound of the normalization to range [lowerBound, upperBound].
getLPB16(int, int, double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Extract codes for 16-pixel neighborhood with r=2.
getLPB24(int, int, double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Extract codes for 24-pixel neighborhood with r=3.
getLPB8(int, int, double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Extract codes for 8-pixel neighborhood with r=1.
getMagImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Calculate the gradient magnitude image from the vectors U and V.
getMagnitude(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get magnitude of the vector at position (x,y) in the vector field.
getMajorAxisLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates length of the major axis of the ellipse best fitting.
getMarker(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Returns a marker from the vector.
getMarkerFromPosition(Point, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Get marker closest to given point position in given slice.
getMask() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns binary mask with segmentation result.
getMask() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns binary mask with segmentation result.
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getMask(int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Gets the mask of the specified class (0 Background, 255 Foreground)
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getMaskFromNuclei(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
getMaskRadiusC() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusC.
getMaskRadiusT() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusT.
getMaskRadiusX() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusX.
getMaskRadiusY() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusY.
getMaskRadiusZ() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusZ.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose
Returns the given mask size, 0 if not set.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Get value of masksize.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Returns the given mask size, 0 if not set.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Returns the given mask size, 0 if not set.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Get current masksize.
getMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Returns result matrix with matching result.
getMax() - Method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
The maximum value of this channel.
getMaxAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Get the maximum value for parameter alpha.
getMaxAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
getMaxAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
 
getMaxBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Get the maximum value for parameter beta.
getMaxBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
getMaxBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
 
getMaxBinaryPattern() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU
 
getMaxDist() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
 
getMaxFragmentDistance() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get maximum neuron fragment distance in pixel.
getMaxFragmentDistance() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get maximum fragment distance , in pixel.
getMaximalComponentDist() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the maximal component distance for linking.
getMaximalComponentSize() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the maximal valid component size for component removal.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of maxIter.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Get maximum iteration count.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Get maximum iteration count.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Get maximum iteration count.
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get maximum number of iterations to stop detection.
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get maximum number of iterations to finish snake optimization,
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of maxIterations.
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get maximal number of iterations.
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Returns the maximal label used in the membership representation.
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Returns the maximal label used in the membership representation.
getMaxLabel() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the maximal label used in the segmentation representation.
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the maximal label used in the membership representation.
getMaxLevels() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Returns maximum number of levels in iterative mode.
getMaxN() - Method in class de.unihalle.informatik.MiToBo.math.LogFaculty
 
getMaxSpineLength() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get maximum length of a spine (filopodia-like protrusion) in pixel.
getMaxSpineLength() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get maximum length of a spine, in pixel.
getMaxSpineLength() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get maximum length of a spine (filopodia-like protrusion) in pixel.
getMaxValue() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getMaxValueBin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getMaxVoronoiExpandDist() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the maximal distance of pixels considered in Voronoi expansion.
getMaxWeight() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getMean() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Returns the mean vector.
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
getMean() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.FirstOrderMoment
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
getMeanBackgroundIntensity() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
getMeanKernelC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in c-dimension for given parameters, null if size is zero in c-dimension
getMeanKernelT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in t-dimension for given parameters, null if size is zero in t-dimension
getMeanKernelX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in x-dimension for given parameters, null if size is zero in x-dimension
getMeanKernelY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in y-dimension for given parameters, null if size is zero in y-dimension
getMeanKernelZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in z-dimension for given parameters, null if size is zero in z-dimension
getMeans() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Returns the average region intensities last calculated.
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
 
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
 
getMeasurementUnit() - Method in interface de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Interface
Returns the unit of measurements.
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
 
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
 
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
 
getMemorizedMatrixA() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Returns matrix carrying always the values of the last iteration, or null before first run.
getMin() - Method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
The minimum value of this channel.
getMinAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Get the minimum value for parameter alpha.
getMinAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
getMinAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
 
getMinAreaAfterErosion() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getMinAreaAfterOpening() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getminAreaSeedRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getMinBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Get the minimum value for parameter beta.
getMinBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
getMinBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
 
getMinCompactness() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getMinimalComponentSize() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the minimal valid component size for component removal.
getMinMaxCoordinates() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Extracts the extreme coordinates of the region in each dimension.
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get minimum and maximum value of the image (all channels) as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get minimum and maximum value of the image as double
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get minimum and maximum value of the image as int
getMinorAxisLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates length of the minor axis of the ellipse best fitting.
getMinRegionArea() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getMinRegionSize() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get the minimum size of detected regions.
getMinSize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of minSize.
getMinSizeFraction() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of minSizeFraction.
getMinWeight() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getMode() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Get the desired operator mode.
getModification() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getMoelculeImg() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the input image with the fluorescence labeled molecules.
getMoleculeChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get molecule channels, used for extraction.
getMoleculeChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get molecule channels, used for molecular profile extraction.
getMolecules() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get names of molecules for each image channel.
getMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculate moment of the region of order p,q.
getMoment(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
 
getMorphOp() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Get morphological operation for illumination correction, default is closing.
getMotionFraction() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get minimum fraction of point motion to stop detection.
getMotionFraction() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get minimum motion fraction of snake control points, to finish snake optimization.
getMotionFraction() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Get motion fraction.
getMSERs() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Returns set of detected MSERs.
GetMTBContour2DSetFromXSVFiles - Class in de.unihalle.informatik.MiToBo.io.importer
Read a MTBContour2DSet from a list of ASCII xSV files.
GetMTBContour2DSetFromXSVFiles() - Constructor for class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles
Default constructor.
getMTBImage() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Gets the stored MTBImage.
getMTBImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Creates a bi-level MTBImageShort of the level set function.
getMTBImageLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Creates a MTBImageShort of the level set function.
getMultiphase() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of multiphase.
getNarrowBandWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get width of narrow band.
getNarrowIterator() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
get an iterator through narrow band
getNeighbors() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get all neighbors of the current node.
getNeighbourhood() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getNetDirections() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getNetDistances() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getNeurite() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
getNeuriteColor() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get neurite region color (RGB) for result image.
getNeuriteColor() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get neurite region color (RGB) for result image.
getNeuriteDetector() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get current neurite detector.
getNeuriteFeatures(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Method to calculate the neurite features from the neurite width profile.
getNeuriteGraph() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite corresponding skeleton graph.
getNeuriteImage(Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Visualize the neurites skeleton graphs and regions.
getNeuriteMaskSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get neurite mask size in pixel.
getNeuriteMaskSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get maximum neurite mask size, in pixel.
getNeuriteMaskSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get neurite mask size in pixel.
getNeuriteRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite corresponding region.
getNeuriteSet() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the input set of neurites.
getNeuriteSet() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Get the input set of neurites.
getNeuriteShaftArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get area of neurite shaft region (without growth cone).
getNeuriteShaftRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite shaft region (without growth cone).
getNeuriteStack(Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Visualize the neurites skeleton graphs and regions.
getNeuriteWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get average widths of each neurite branch, including the average widths of the whole branches, the shafts and the growth cones.
getNeuronChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get neuron channels, used for detection.
getNeuronChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get neuron channels, used for detection.
getNeuronColor() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get binary neuron color.
getNeuronImage() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get input image of the binary neuron.
getNewConfigWin(ALDOperator, ALDGrappaWorkbenchTab.ParameterUpdateListener) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
 
getNewConfigWin(ALDOperator) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorGUIExecutionProxy
 
getNewIndent(String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Return a new indentation string.
getNiblackConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get niblack constant.
getNiblackConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get Niblack thresholding constant.
getNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
Return the node object containing the data.
getNodeListFromTag(Document, String) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
getNodeNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get number of included MTBGraphNodes.
getNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get all nodes of the MTBGraph.
getNodes() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getNodes() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Get graph nodes
getNodeType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
 
getNoiseCovariance() - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
getNorm() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Calculates the Euclidean norm of the segment.
getNormal(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get normal vector between two points.
getNormalCentralMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculate normalized central moment of the region of order p,q.
getNormalizationFactor(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
getNormalizationFactor(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
getNormalizationMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns energy normalization mode.
getNormalizedCumulativeHistogram(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Create a normalized cumulative histogram from an image
getNormalizedImageHisto() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
Extracts the normalized image histogram with 256 bins.
getNormedMagImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Normalize the gradient magnitude values into a range of [0,1].
getNRSCandidates() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns possible peak locations from NucleusRegionSeperator.
getNRSDistImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns distance image calculated intermediately.
getNRSEllipsoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Creates and returns a set of polygons as starting regions for snake analysis based on hypothesized ellipses from nucleus information
getNRSResultAreas() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns set of result regions from region separator.
getNRSResultCenters() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns set of detected region centers from region separator.
getNRSVoronoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Creates and returns a set of polygons as starting regions for the snakes.
getNucDetector() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get detector for nuclei.
getNucleiAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns average size of detected nuclei.
getNucleiChannel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get image channel of nuclei.
getNucleiChannel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get channel number, including the labeled nuclei.
getNucleiChannel() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get nuclei channel number.
getNucleiCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns number of detected nuclei.
getNucleiRegions() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns set of detected regions.
getNucleiRegions() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get detected nuclei regions.
getNucleiResult() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns nuclei detection result.
getNucleusRatio() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get ratio of nucleus pixels which should be included in an intact neuron region
getNucleusRatio() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get ratio of nucleus pixels which should be included in an intact neuron region
getNucleusSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get minimum nucleus size of nuclei regions
getNucleusSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get minimum nucleus size of nuclei regions
getNumberChannels() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns the number of image channels available.
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Returns the number of classes represented in the membership.
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Returns the number of classes represented in the membership.
getNumberOfClasses() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the number of classes represented by the segmentation.
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the number of classes represented in the membership.
getNumberOfFrames() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getNumberOfInEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get number of incoming edges for MTBGraphNode.
getNumberOfMSERs() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Returns number of detected MSERs.
getNumberOfOutEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get number of outgoing edges for MTBGraphNode.
getNumberOfStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get number of states
getNumberOfStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
getNumEntries() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getNumericalValue(int) - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Returns a numerical value representing the requested result component.
getNumericalValue(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getNumericalValue(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getNumericalValue(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
 
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get number of iterations for the GVF field.
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of numIterations Explanation: Number of iterations performed
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of numIterations Explanation: Number of iterations performed
getNumOfComponents() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
getNumOfImages() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
getNumOfIndeps() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
 
getNumOfIndeps() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
getNumOfIndeps() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
getNumOfParticles() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get number of particles
getNumPhases() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return .e. number phases.
getNx() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
 
getNx() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
getNy() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
 
getNy() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
getObjectsMeans(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getObjectsStdDevs(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getObservationDistribution() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
getObservationDistribution() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilterIndep
 
getObservationMatrices() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
getObservations() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
getObservations(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the observations of time t.
getOldId() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Get previous index of snake point from the previous snake.
getOnlySelectedTreelines() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Ask operator if only selected or all treelines should be provided.
getOpeningSESize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getOperation() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Return UserTime or RealTime depending on mode of operation
getOperationType() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the operation type which should be applied to the input vector field.
getOperatorWorkingMode() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Request working mode of the operator, i.e., how the operator deals with treelines.
getOpIdentifier() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Method returns an identifier characterizing the operator.
getOpIdentifier() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getOpIdentifier() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getOpIdentifier() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
 
getOpMode() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of opMode.
getOptimalNeighbor(MTBGraphNode<PartitGraphNodeID>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Get node of partition 'partitionID' which is connected to current node and has optimal weight
getOrientation(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Deprecated.
getOrientation() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get orientation.
getOrientation() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates the orientation of the principal axis of the MTBRegion2D.
getOtsuRegs() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns set of regions resulting from Otsu thresholding.
getOtsuThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Get the resulting threshold.
getOutEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get outgoing edges for node.
getOuterContours(MTBRegion2DSet, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Calculate the outer contours of the given regions in a image.
getOutImageType() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the type of image object that is created as result image.
getOutline() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape
Get outline of shape.
getOutputDir() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get directory of output results.
getOutputImage() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get medialness filter image.
getOutputObservations() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get a copy of the input observations with IDs set corresponding to the tracking results after GreedyGourmetPartitioning of the track graph constructed from the RBMCDA samples.
getOutputSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
Get cloned snake object.
getOutputType() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get output image type
getOverlaps() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
getOverwrite() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the overwrite permission flag
getParameterA() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get value of implicit parameter a.
getParameterB() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get value of implicit parameter b.
getParameterC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get value of implicit parameter c.
getParameterD() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get value of implicit parameter d.
getParameterE() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get value of implicit parameter e.
getParameterF() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get value of implicit parameter f.
getParent() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Get the parent of this node.
getParentID() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
getPartChannel() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get particle channel number.
getPartDetector() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get detector for particles.
getPartialDiffX() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in x-direction using central differences.
getPartialDiffX(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get approximation of partial derivative in x-direction at point with given index.
getPartialDiffX_forward() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in x-direction using forward differences.
getPartialDiffX_sobel() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in x-direction using Sobel.
getPartialDiffY() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in y-direction using central differences.
getPartialDiffY(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get approximation of partial derivative in y-direction at point with given index.
getPartialDiffY_forward() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in y-direction using forward differences.
getPartialDiffY_sobel() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in y-direction using Sobel.
getParticle(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get idx-th particle
getParticleAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns average size of detected particles.
getParticleChannel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Get image channel including particles.
getParticleCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns number of detected particles.
getParticleDetector() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Get particle detector.
getParticleDetector2D() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
getParticleRegions() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get detected particle regions.
getParticleResult(int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns number of detected particles per channel.
getParticles() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get particles
getPath(Vector<Point2D.Double>, MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Internal method to traverse the path and return the pixel list.
getPath() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Request path associated with the node.
getPdf(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
getPerCellAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns detected particle average size per cell.
getPerCellCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns detected particles per cell.
getPersistences(Hashtable<Integer, Vector<Double>>, Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getPhase(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return phase for a pixel/voxel
getPhase(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return phase for a pixel/voxel, z coordinate defaults to zero
getPhaseCheckXY(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return phase for a pixel checking limits of all coordinates.
getPhaseCheckXYZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return phase for a pixel/voxel checking limits of all coordinates.
getPhi() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get current level set function.
getPhi() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of phi.
getPhiColorImage2D(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get visualization of current level set function in red-blue color map.
getPhiImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get visualization of current level set function.
getPixelInside() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return number of pixels of all object phases.
getPixelOutside() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return number of pixels of background phase.
getPixelsAlongSegment() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Calculates the set of integer pixel positions along the a segment.
getPlastidRegions() - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
Access detected plastid regions.
getPointAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get a specific 2D point belonging to the border object.
getPointDist(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Deprecated.
getPointNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get the number of points of the border object.
getPointNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Get the number of points from the polygon.
getPoints() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get all points belonging to the border object.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Get polygon points.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return all points of the region.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the points which are included in the 3D region.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
Return the points which are included in the 3D region.
getPoisson2Gauss() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get flag if input image with poisson noise is to be transformed to image with gaussian noise following J.
getPolygon() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Get a Polygon2D copy of this object.
getPolygon() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon
Get polygon representing the shape.
getPolygon2DFromXml(MTBXMLPolygon2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
* Get a new Polygon2D from the information of the xmlPolygon .
getPolygonSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Get 2D polygon set from Roi.
getPolygonSetFromRoiFile(String, boolean) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads an ImageJ roi file into a set of polygons/snakes.
getPolygonSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads ROI manager selections into a set of polygons/snakes.
getPolySet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Get the polygon set.
getPortHashAccessObject() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Returns access object for port hash.
getPotential() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Returns a copy of the potential field (for faster access!).
getPotential() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Get the energy potential field from this external energy.
getPotentialNewPhases2D(boolean, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
getPrecision() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc
Returns calculated precision.
getPrecisionClutter() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getPrecisionTrackEnd() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getPrecisionTrackSegment() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getPrecisionTrackStart() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getPrecursorMap() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the calculated precursor map.
getPrecursorSegment() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Get preceeding segment along contour.
getPredecessor() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
getPredecessorOnContour(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
gets the value of the nearest contourpoint to point (x,y,z)
getPreferredSize() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
getPreserveTopology() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of preserveTopology.
getPreserveTopology() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of preserveTopology.
getPreviousEnergyValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Get old energy value for the snake at last iteration.
getPreviousSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns the previous snake.
getProcessedChannel() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Get the processed channel.
getProcessMode() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Get current process mode.
getProfile() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Get profile data of the neurite region.
getProfilePoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
getProfiles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the resulting set of neurite profiles.
getProfileSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
getProtrusionSegments() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Get list of protrusion segments.
getQuality() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Get quality option
getQuality() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the quality (quicktime only)
getRadius() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Get the radius of the node.
getRadiusImage() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Returns supplemental radius image, null if not generated.
getRandom() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
getRandom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the random number generator which is responsable to draw each region in a random color (COLOR_IMAGE only).
getRankOpMode() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument rankOpMode.
getRealKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Generates the cosine filter mask of the complex part of the Gabor filter.
getRecall() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc
Returns calculated recall.
getRecallClutter() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getRecallTrackEnd() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getRecallTrackSegment() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getRecallTrackStart() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getRegCenters() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns the centers of the nuclei sorted to their original regions.
getRegion(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Method to get the included region in a 2D contour as Region2D object.
getRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Get a Region2D copy of this object.
getRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Return the 2D region.
getRegion() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion
Get region representing the shape.
getRegionCount() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Get number of regions in set.
getRegionID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the region id.
getRegionMeans() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get average intensity array indexed with class labels for first channel.
getRegionMeansAllChannels() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get average intensity array indexed with class labels for all channels.
getRegions() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Get set of segmented regions.
getRegions(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
 
getRegions(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
 
getRegions3D(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
 
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Get 2D region set from Roi.
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Get the region set.
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the region set.
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
getRegionSetFromRoiFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads an ImageJ roi file into a set of regions.
getRegionSetFromRoiFile(String, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads an ImageJ roi file into a set of regions.
getRegionSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads a ROI manager selection into a set of regions.
getRegionSizes() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get array of region areas indexed with class labels for first channel.
getRegionsTree(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Build a tree of regions from binarized images.
getRegionVars() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get intensity variance array indexed with class labels for first channel.
getRegionVarsAllChannels() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get intensity variance array indexed with class labels for all channels.
getREngine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get JRI R engine to run R as a single thread.
getREngine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get R engine.
getReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getRepositoryTag(String) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Returns the tag/release of the current jar.
getRepositoryTag() - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Returns the tag/release of the current checkout, as specified in a given info file.
getResampleConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get snake point resampling constant.
getResampleConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get constant for snake point resampling.
getResponseStack() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Returns stack with intermediate (non-binary) results.
getResult() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Returns the result data object of the calculator.
getResult() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getResult() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getResult() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
 
getResult() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Get result data.
getResult() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Returns evaluation result data.
getResultAreas() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns separated regions sorted according to original regions.
getResultArray() - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D
Returns result array.
getResultBinaryCorrelationStack() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get resulting binarized correlation image stack.
getResultBorders() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Get result borders.
getResultCellImg() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns (optional) result image with cell contours.
getResultCenters() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns centers of result regions.
getResultContourImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of ResultContourImage.
getResultContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the calculated contours.
getResultCorrelationStack() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get resulting correlation image stack.
getResultCosts() - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Returns the costs of the shortest path.
getResultData() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Returns result data object.
getResultData() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Returns result data object.
getResultData() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Get the result data, i.e. mask and related quantitative data.
getResultData() - Method in class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Returns result data object.
getResultData() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Get the transformed dataset.
getResultData() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.MTBGroundtruthEvaluationData
Returns result data.
getResultDataAreaFractions() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with area fractions per cell.
getResultDataArray() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Returns extracted result data.
getResultDataAvgSize() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with average size per cell.
getResultDataCellSizes() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with areas per cell.
getResultDataCounts() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with counts per cell.
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Helper method to allow for requesting invalid dummy results.
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
 
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
 
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
 
getResultDataObjectInvalid(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
 
getResultDataTotalSize() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with total structure size per cell.
getResultDir() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get directory of intermediate and final results.
getResultIdentifier(int) - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Method returns an identifier characterizing the related component of the result.
getResultIdentifier(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getResultIdentifier(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getResultIdentifier(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
Returns postprocessed skeleton image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Get the result label image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Returns result image, i.e. the segmentation mask.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns RGB color image overlayed with nuclei contours.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Returns result image, i.e. the segmentation mask.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get the gamma corrected image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching
Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Get illumination corrected result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Returns result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get contrast enhanced result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Get image with result data.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get result image of the operation on the vector field.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Get result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Get result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Returns the result image with path overlay.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Get the result image after applying operator.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Get the resulting h-dome image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose
Returns the opened image, null if not available.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Get value of resultImg.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Returns the eroded image, null if not available.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Returns the opened image, null if not available.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Get the result image after applying the operator.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor
Returns the skeleton image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Returns post-processed skeleton image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.WatershedBinary
Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Get result image with extracted borders.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the binary image with the calculated contours.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of ResultImage.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of resultImage.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get image with segmentation result overlay.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Get the resulting image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Returns the generated image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Returns image with plotted snakes.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get the result image
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Get the resulting thresholded image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Returns the result color image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Get the resulting region image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Get result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Get the resulting region image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the resulting region image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
Get result image.
getResultImagePlus() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get resulting image that was read from disk.
getResultImageStack() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns stack with result segmentation images.
getResultImageType() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
getResultImageType() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
getResultImageType() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
getResultImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Get value of resultImg.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get resulting image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get resulting image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get resulting image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Output argument resultImg.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getResultImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Get result image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get result image
getResultImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Get result image.
getResultingConvexHulls() - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Get set of extracted convex hulls.
getResultingHullImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Get image with convex hulls plotted.
getResultingRegions() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get the resulting regions.
getResultingRegionsets() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
getResultJunctions() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Get detected junctions.
getResultLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter
Returns result label image.
getResultLines() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Get detected lines.
getResultMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get binary mask of segmentation result.
getResultMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Returns generated mask.
getResultMTBImage() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Returns the converted image, null if not available.
getResultMTBImage() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get resulting image that was read from disk.
getResultPath() - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Returns the extracted shortest path as point list.
getResultRGB() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Returns the result RGB color.
getResults() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get resulting regions (each detetection corresponds to a region)
getResultSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
Returns resulting snake object.
getResultSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
Returns resulting snake object.
getResultSnakeImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns image with snakes contours.
getResultSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Returns resulting snake objects.
getResultSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns the set of result snakes.
getResultsTable() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get the result table of the detected neurites.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get final result table of morphology measurements.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get particle statistics.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Get table of calculated features.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Get result table.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Get evaluation results.
getResultTreelines(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Getter for the result treelines of a specific layer.
getResultValue() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
Get result value;
getResultVec() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
 
getResultVectorOfCurvatures() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Get calculated curvatures.
getResultVesselMap() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Get result.
getResultXylemRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Return the binary image after the post processing of the grown region image.
getRevisionFile() - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Request name of the revision file.
getRGBImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
Flag to request a RGB image in any case.
getRGBResult() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
Get RGB values.
getRGBResult() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Get RGB values.
getRGBValue() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getRoot() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Access the root node.
getRoundnessThreshold() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the currently active roundness threshold.
getRowCount() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
getRuntime() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getSample(double[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Returns a sample in the range [0, 1] from a cumulative distribution given by the array cdf
getSample(double[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Returns a sample in the range [0, 1] from a cumulative distribution given by the array cdf
getSampleConditionalProb(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get the probability of the associations of i-th sample at the time t conditional on previous associations and all observations up to time t.
getSampleInfo(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get the sample info object of the i-th sample.
getSampleInfo() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
Get the info object of this RBMCDA-sample
getSampleJointProb(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get the joint probability of all associations of the i-th sample conditional on all observations, normalized by all samples' probabilities.
getSampleJointProbs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get the joint probability of all associations of all samples conditional on all observations, normalized by all samples' probabilities.
getSampleObservations(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get a copy of the observations with IDs set corresponding to the i-th sample's tracking results.
getSatMTBImg() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Get the saturation channel image.
getSatTresh() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getSaveIntermediateResultPath() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Returns path where to save intermediate results.
getScaleDown() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get the scaling factor of the snake.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get scaling factor.
getScaleFactor() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Get scaling factor.
getScaleFactor() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Get scaling factor.
getScaleIntervalSize() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get the size of the scale interval for correlation images
getScaleMax() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get maximum of scales.
getScaleMin() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get minimum of scales.
getScaleNum() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get number of scales.
getScratchArea() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getScratchFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getsecondFeatureAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get second feature of neurite corresponding feature points from borders between neurite shafts and growth cones.
getSeedPoints(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
coarse segementation of input frame to localize cells
getSeedPoints(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
coarse segmentation of input frame to localize cells
getSeedRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getSeErosionSize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getSegContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
Get list of segmentation contours.
getSegDim() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get target dimension.
getSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the generated segmentation object.
getSegmentationMode() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns mode activated during segmentation.
getSegmentLength() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns desired segment length for resampling.
getSelection() - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Get the currently selected radio button string
getSelections() - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
 
getSelections() - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Returns a hash map with the absolute filename as key and the indices of images selected from the corresponding file.
getSemiLengthAxisA() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get half-length of axis A.
getSemiLengthAxisB() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Get half-length of axis B.
getSeOpeningSize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getSettings() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getShaftLengths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite shaft lengths of all branches without growth cone areas.
getShape() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Get shape of marker.
getShape() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the selected shape.
getShapeDimX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get extent of shape in x dimension.
getShapeDimY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get extent of shape in y dimension.
getShapeDimZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get extent of shape in z dimension.
getShapeFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
calculate several shape features in one method
getShapeFeatures() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
getShapeForErosion() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getShapeForOpening() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getShapeMaskSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get size of shape mask in x dimension.
getShapeMaskSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get size of shape mask in y dimension.
getShapeMaskSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get size of shape mask in z dimension.
getShapePosX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get position of shape in x dimension.
getShapePosY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get position of shape in y dimension.
getShapePosZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get position of shape in z dimension.
getShapeReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
getShortestPath(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the pixels of the shortest path of the neurite skeleton graph.
getShortName() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Get common short name of operator for GUI.
getShortName() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
 
getShortName() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
 
getSigmaC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in c-dimension.
getSigmaInterpretation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get the mode of how sigmas are interpreted.
getSigmaT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in t-dimension.
getSigmaX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in x-dimension.
getSigmaY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in y-dimension.
getSigmaZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in z-dimension.
getSignedArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Calculates the signed area of simple (!)
getSimpleShapeFeatures() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
calculate several shape features in one method
getSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
getSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getSize() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
count number of elements
getSizeC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of c(hannel)-dimension
getSizeC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeC() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of c(hannel)-dimension
getSizeC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in c-dimension
getSizeC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in c-dimension.
getSizeDilation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of sizeDilation.
getSizeNeighborhood() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
 
getSizeOpening() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of sizeOpening.
getSizePhase(short) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return the size, i.e. number of pixel/voxels of a phase.
getSizeStack() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of the underlying (ImageJ) stack which corresponds to the number of slices
getSizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of t(ime)-dimension
getSizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeT() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of t(ime)-dimension
getSizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in t-dimension
getSizeT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in t-dimension.
getSizeTH() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of sizeTH.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of x-dimension
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeX() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of x-dimension
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in x-dimension
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculate the expansion in x-direction of the region.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getSizeX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in x-dimension.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getSizeX() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the size of the segmentation domain in x direction.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return X size of the level set function.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get width of level set function.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of y-dimension
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeY() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of y-dimension
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in y-dimension
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculate the expansion in y-direction of the region.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getSizeY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in y-dimension.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getSizeY() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the size of the segmentation domain in y direction.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return Y size of the level set function.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get height of level set function.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of z-dimension
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeZ() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of z-dimension
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in z-dimension
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculate the expansion in z-direction of the region.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in z-dimension.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getSizeZ() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the size of the segmentation domain in z direction.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return Z size of the level set function.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get depth of level set function.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getSkeletonGraphNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get all nodes of the MTBNeuriteSkelGraph as MTBNeuriteSkelGraphNodes.
getSkeletonInfoImage() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Access info image about skeleton analysis.
getSlice(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of the specified slice.
getSlice(MTBOperator, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of the specified slice.
getSlice(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Get a copy of the specified slice
getSliceLabel(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the slice label of the slice specified by (z,t,c)
getSmallestNonEmptyBin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getSnakeControlPoints(MTBContour2D) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Method to get each 7th point of the initial contour as snake control point.
getSnakeIterCount() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get number snake iteration counts, used for optimization.
getSnakeNumber() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns the number of snakes currently managed.
getSnakePoints() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get snake points as vector of SnakePoint2D objects.
getSnakeRegion(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get the region which is included in the snake contour.
getSnakes() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns the result snakes.
getSndPartialDiffX(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get approximation of 2nd order partial derivative in x-direction.
getSndPartialDiffY(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get approximation of 2nd order partial derivative in y-direction.
getSpacing() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of spacing.
getSpacingIntermediate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of spacingIntermediate.
getSpeeds(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getSpineCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get number of spines (filopodia-like protrusions).
getSpinePaths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the pixels of all spine paths of the neurite skeleton graph.
getSrcNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Get source node of the MTBGraphEdge.
getStackWithIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns a stack with intermediate segmentation results.
getStartFrame() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
getStartNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the start node of the MTBNeuriteSkelGraph.
getStartPoint() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine
Get the start point of the line segment.
getStartPoints() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get the skeleton start points of every single neurite from the inside of the coarse cell body region.
getStateContinuous(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get the continuous part of the idx-th state (indices start from 0)
getStateContinuous(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
getStateDiscrete(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get the discrete part of the idx-th state (indices start from 0)
getStateDiscrete(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
getStatus() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Get the status of the node (segment).
getStdDev() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getStdDev(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get standard deviation of the image
getStdDevBackgroundIntensity(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
getStepSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get step size of snake movement.
getStepSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get step size of snake point movement.
getStepsizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the stepsize in t-dimension (timestep)
getStepsizeT() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the stepsize in t-dimension (timestep)
getStepsizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the stepsize in t-dimension (timestep)
getStepsizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the physical size of a voxel (stepsize) in x-dimension
getStepsizeX() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the physical size of a voxel (stepsize) in x-dimension
getStepsizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the physical size of a voxel (stepsize) in x-dimension
getStepsizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the physical size of a voxel (stepsize) in y-dimension
getStepsizeY() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the physical size of a voxel (stepsize) in y-dimension
getStepsizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the physical size of a voxel (stepsize) in y-dimension
getStepsizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the physical size of a voxel (stepsize) in z-dimension
getStepsizeZ() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the physical size of a voxel (stepsize) in z-dimension
getStepsizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the physical size of a voxel (stepsize) in z-dimension
getStomataCount() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves
Get number of stomata regions in set.
getString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData
 
getSubdirectoryList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Get a list of all subdirectories in the root folder.
getSubtreeDirList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Collects the list of all sub-directories of this directory.
getSubtreeFileList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Collects the list of all files inside this directory and also inside all subdirectories.
getSuccessorSegment() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Get subsequent segment along contour.
getSum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getSummary() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
getSurfaceImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
draw surfaces into an image with the surface ids as labels
getSurfaces() - Method in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
getSynthMask(SegmentationInitializer.SegmentationDimension) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generate synthetic mask.
getT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getTable() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
getTable() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
getTableEntry(int) - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Returns entry in requested field as string representation.
getTableEntry(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getTableEntry(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getTableEntry(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
 
getTangentOrientation(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Returns the orientation of the tangent at point p on the ellipse.
getTargetImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the target image to which the regions are drawn, if one was specified.
getTargetImageType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getTgtNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Get target node of the MTBGraphEdge.
getTheta() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get coefficient to relate vessel radius and scale.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get threshold to be applied to image.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of threshold.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get threshold.
getThresholdImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get image for thresholding
getThresTH() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of thresTH.
getTicks() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Declaration of native method for getting ticks.
getTile(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Returns tile with given indices.
getTileCenterX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Returns x-coordinate of tile center.
getTileCenterY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Returns x-coordinate of tile center.
getTileCols() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Returns number of tiles and colums, respectively, in x-dimension.
getTileCountX() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Get number of tiles in x-direction.
getTileCountY() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Get number of tiles in x-direction.
getTileRows() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Returns number of tiles and rows, respectively, in y-dimension.
getTitle() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the image's title
getTitle() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get title string
getTitle() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get title of underlying image
getTitleRunning(String) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Return a unique title for the copy of an image, i.e. a running number is appended/incremented.
getTotalDistances(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getTotalLength() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Get total length.
getTotalNumberOfEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get total number of edges for MTBGraphNode.
getTrack(short) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get track of target given by targetID up to current time, where targetID may be 0 to obtain the clutter observations (which do not form a track).
getTrackImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
getTrackReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
getTrajectories() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
 
getTrajectories() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
getTransferFunktion(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Get the discrete transfer function for the histogram.
getTransformMatrix() - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
getTransitionMatrices() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
getType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get MiToBo image type
getType() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get data type
getType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get underlying data type
getType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Returns the type of the curve.
getType() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get input image type.
getType() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Get type of markers.
getTypeMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Return the maximum value that the current type can handle
getTypeMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Return the minimum value that the current type can handle
getTypeName(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Deprecated.
getU() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get vector U of the field.
getUniqueClassIdentifier() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
 
getUniqueClassIdentifier() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
 
getUniqueName(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Generates a unique name for a new roi in the manager.
getUnitT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the unit of the t-dimension
getUnitT() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the unit of the t-dimension
getUnitT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the unit of the t-dimension
getUnitX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the unit of the x-dimension
getUnitX() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the unit of the x-dimension
getUnitX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the unit of the x-dimension
getUnitXY() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
getUnitXYZ() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
getUnitY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the unit of the y-dimension
getUnitY() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the unit of the y-dimension
getUnitY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the unit of the y-dimension
getUnitZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the unit of the z-dimension
getUnitZ() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the unit of the z-dimension
getUnitZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the unit of the z-dimension
getUpperBound() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Get upper bound of the normalization to range [lowerBound, upperBound].
getUserTime() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Declaration of native method for user time measurement.
getUseThresh() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get adaptive thresholding tag.
getUWT() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get the UWT coefficient images.
getV() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get vector V of the field.
getValue(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get RGB value from the specified position.
getValue(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get RGB value from the specified position in the actual slice.
getValue(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getValue() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
Returns the double value.
getValue() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
 
getValue(NodeList, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
getValue(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper
Calculate approximated value for given parameter value.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Returns the distance value from the distance map at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Returns the negative absolute gradient value to the power of 2 (the external energy) at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Returns the value of the external energy at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Returns the value of the external energy at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Returns the value of the external energy at the given position.
getValue_norm(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Returns the value of the external energy at the given position on a normalizes image coordinates in range [width*scale, height*scale].
getValueAt(int, int) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
getValueB(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get blue value from the specified position.
getValueB(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get blue value from the specified position in the actual slice.
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the current slice at coordinate (x,y,z) as an Double
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the current slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the value of the actual slice at coordinate (x,y) as a Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
getValueG(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get green value from the specified position.
getValueG(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get green value from the specified position in the actual slice.
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the current z-stack coordinate (x,y,z) as an Integer
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the current slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
getValuePotential(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Returns value of potential at specified position.
getValueR(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get red value from the specified position.
getValueR(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get red value from the specified position in the actual slice.
getValues() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get the double values of the given image.
getValueU(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get value from vector U at position (x,y).
getValueV(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get value from vector V at position (x,y).
getVariance() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getVectorField() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the operation based 2D vector field.
getVectorField() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get the resulting 2D vector field.
getVectorField() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get calculated GVF vector field..
getVectorFieldImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the operation based 2D vector field image.
getVectorFieldImage() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get the resulting 2D vector field image.
getVectorIndex(CellCntrMarker) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Returns the index of the given marker.
getVersion() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
 
getVersionProvider() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Returns version provider object.
getVisibilityMapHeight() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns height of the visibility map.
getVisibilityMapWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns width of the visibility map.
getVisibilityMapXMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal x coordinate represented in visibility map.
getVisibilityMapXMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal x coordinate represented in visibility map.
getVisibilityMapYMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal y coordinate represented in visibility map.
getVisibilityMapYMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal y coordinate represented in visibility map.
getVolume() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the volume of the 3D region (number of points within the region).
getVolume() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
Get volume of the hypercube where p(x) > 0
getVoronoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns set of snake polygons resulting from Voronoi tesselation.
getVoronoiImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Get voronoi tesselation image.
getVoronoiStack() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Get stack of voronoi tesselation images.
getVotesAdjacency(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getVotesClutter(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getVotesTarget(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get weight of idx-th particle
getWeight(double, double) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Return edge weight for edge between given nodes.
getWeight(int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Returns the weight of the energy with given index.
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Returns element i of the weight list.
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getWeight(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the pixel weight of position (x,y).
getWeight(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the pixel weight of position (x,y,z).
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns element i of the weight list.
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns element i of the weight list.
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Returns element i of the weight list.
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getWeight(PartitGraphNodeID, PartitGraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getWeight(T, T) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Get weight of edge from nodeSrc to nodeTgt.
getWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
getWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get particle weights
getWeights() - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Returns the list of weights.
getWeightsSum() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get sum of weights
getWidth() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Get the width associated with the segment.
getWidth() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get skeleton graph image size in x direction.
getWidth() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get width of level set function domain.
getWindowPosition() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the current window position
getWorkingImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns working image.
getWorkingImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
getWorkingImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
getWthImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get white top-hat image.
getWthMaskSize() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get mask size of white top-hat.
getX() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
getX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Return coordinate of x-dimension.
getX() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Get x-coordinate.
getX() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
getXMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the maximal x-coordinate of the domain of this border set.
getXMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the maximal x-coordinate of the domain of this contour set.
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Returns maximal x coordinate of the domain.
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
 
getXMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the minimal x-coordinate of the domain of this border set.
getXMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the minimal x-coordinate of the domain of this contour set.
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Returns minimal x coordinate of the domain.
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
 
getXML() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the XML file description string if one was available.
getXMTBImg() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Get the value channel image.
getXPos() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Get x-position of the node.
getXThresh() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The Intensity/Brighntness/Value-Parameter (depending on the used input image type).
getXylemImage() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Return the Hue/Saturation/{Intensity|Brightness|Value}-MTBImage.
getXylemImage() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Return the input xylem image.
getY() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
getY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Return coordinate of y-dimension.
getY() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Get y-coordinate.
getY() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
getYMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the maximal y-coordinate of the domain of this border set.
getYMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the maximal y-coordinate of the domain of this contour set.
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Returns maximal x coordinate of the domain.
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
 
getYMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the minimal y-coordinate of the domain of this border set.
getYMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the minimal y-coordinate of the domain of this contour set.
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Returns minimal y coordinate of the domain.
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
 
getYPos() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Get y-position of the node.
getZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Return coordinate of z-dimension.
getZ() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Get z-coordinate.
getZ() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
getZmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getZmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
 
getZmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getZmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
 
gif - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
GlobalContrastStretching - Class in de.unihalle.informatik.MiToBo.enhance
Global contrast stretching.
GlobalContrastStretching() - Constructor for class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching
Default constructor.
GlobalContrastStretching(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching
Constructor with default image.
gradField - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
GradientFieldCalculator2D - Class in de.unihalle.informatik.MiToBo.fields
Class to calculate a gradient vector field of a given image.
GradientFieldCalculator2D() - Constructor for class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Standard constructor.
GradientFieldCalculator2D(MTBImage, GradientFieldCalculator2D.GradientMode) - Constructor for class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Constructor.
GradientFieldCalculator2D.GradientMode - Enum in de.unihalle.informatik.MiToBo.fields
Provided calculation modes for calculation the gradient image.
GradientFieldNonMaxSuppression - Class in de.unihalle.informatik.MiToBo.fields
Non-Maximum-Suppression and (optional) hysteresis thresholding on gradient fields.
GradientFieldNonMaxSuppression() - Constructor for class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
Standard constructor.
gradientMode - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
The used gradient mode for field calculation.
GradientMode() - Constructor for enum de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D.GradientMode
 
gradMagHeaviside(double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE
calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one pixel
gradMagHeaviside(double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE
calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one pixel
gradMagHeaviside(double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one pixel
gradMagHeaviside(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
calculate the gradient magnitude of the forward difference of the heaviside function corresponding to the level set for one voxel
gradMagHeaviside(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DMPNonPDE
Calculate the gradient magnitude of the foreard difference of the heavyside function corresponding to the level set for one voxel
gradMagHeaviside(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one voxel
graph - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
GraphNode(int, int) - Constructor for class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.GraphNode
Default constructor.
GraphNodeID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A graph node object to hold a nodeID as well as a subgraphID
GraphNodeID(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
Constructor (subgraphID=0)
GraphNodeID(int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
Constructor to assign the node to a subgraph
GraphvizWriter<T extends Comparable<?> & Comparator<?>> - Class in de.unihalle.informatik.MiToBo.io.files
Write graph to file using the DOT-language for visualization using graphviz tools.
GraphvizWriter() - Constructor for class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Empty constructor
GraphvizWriter(AdjacencyMatrix<T>, String) - Constructor for class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Constructor for specifying the graph by an adjacency matrix
GraphvizWriter(MTBGraph, String) - Constructor for class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Constructor for specifying the graph by MTBGraph
gratwanderung(int, int, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Function to travers ridges.
GrayscaleImageToHeatmap - Class in de.unihalle.informatik.MiToBo.visualization.colormappings
This operator converts a gray-scale image to a heat map image.
GrayscaleImageToHeatmap() - Constructor for class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Default constructor.
GrayscaleImageToHeatmap.OperationMode - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings
Operation mode of the operator.
GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings
Available modes how to handle values out of range.
GrayscaleToGrayscaleMapping - Class in de.unihalle.informatik.MiToBo.visualization.colormappings
This operator transforms the intensity values of a gray-scale image according to a given intensity mapping.
GrayscaleToGrayscaleMapping() - Constructor for class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Default constructor.
GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings
Available modes how to handle ignored values.
GrayscaleToGrayscaleMapping.OperationMode - Enum in de.unihalle.informatik.MiToBo.visualization.colormappings
Operation mode of the operator.
grayValue - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
grayValue - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Gray value used, e.g., for mask or contour images.
GreedyGourmetPartitioning - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
greedyGourmet graph partitioning algorithm following:
J.
GreedyGourmetPartitioning(MatchingAdjacencyMatrix, boolean, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Constructor.
green - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Definition of green color.
GREEN_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
GroundtruthEvaluation - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation
Implementation of segmentation evaluation measures.
GroundtruthEvaluation() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Default constructor.
GroundtruthEvaluation(MTBImage, MTBImage, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Default constructor with parameters.
groundtruthObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
groundtruthToSampleTargetIDs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
GrowingMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingMode
 
growingRegion - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
GrowingRegion2D(MTBRegion2D, MTBImageByte, XylemGrower.Neighbourhood, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
grownRegionImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
grownRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Resulting regions from growing.
grownRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Resulting regions from growing.
growRandomRegion2D(int, int, int, int, int, MTBRegion2D, Random) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Grow a 2D region adding the pixel specified and potentially grow further
growRegion() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
Grow the region.
growthCones - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Neurite corresponding growth cone regions as MTBRegion2D objects.
GTC - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Check if you want to compute Recall and Precision
gtContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours
List of point-wise groundtruth contours.
gtContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
List of contours of groudtruth objects.
gtIDs - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Match list of set entries to original groundtruth labels.
gtIDs - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Match list of set entries to original groundtruth labels.
gtImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
Groundtruth labeling.
gtLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Preprocessed groundtruth label image with short pixel type.
gtLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Groundtruth labeling.
gtLabels - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
List of labels of groundtruth regions.
gtLabelsOrig - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Groundtruth labeling.
gtRegionLabels - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours
List of labels of groundtruth regions.
guiElements - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
 
gvf - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
The resulting gradient vector flow field.
GVFFieldCalculator2D - Class in de.unihalle.informatik.MiToBo.fields
Class to calculate a special 2D vector field, a Gradient Vector Flow Field (GVF) with its x- and y-flows from the given image.
GVFFieldCalculator2D() - Constructor for class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Standard constructor.
GVFFieldCalculator2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Constructor.

H

h - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
Array of hue values.
h - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Hue of HSV space.
h - Variable in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
 
h(ArrayList<Point>, ArrayList<Point>) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance
This methods computes for all points in a contour the maximum minimal distance to an other contour.
H - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
state-to-observation-space linear transform matrix
H - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
 
HaralickDirection() - Constructor for enum de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures.HaralickDirection
 
haralickMeasures - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
Result values.
hasEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Check if energies are given.
hasEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
hasEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
hasForeign26Neighbor(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
hasForeign4Neighbor(short, short[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Check whether there is a different/foreign phase (then phase) in the 4-neighborhood as represented in the 8 neighborhood nbPhases.
hasForeign6Neighbor(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
hashCode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
 
hashtableToString(Hashtable<Integer, Vector<Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
hashtableToString(Hashtable<Integer, Vector<Double>>, String, Hashtable<Integer, Integer>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
hasImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
 
hasOneCC() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Checks if the neighborhood represented in X has exactly one connected component of entries set to true using the neighborhood definition as as represented in the neighborhood arrays of the class.
HAU - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Check if you want to compute the Hausdorff-Distance
HAU() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance
This method is the implementation of the Hausdorff Distance
haveJNI - Static variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Were we able to load the JNI library?
HDomeTransform3D - Class in de.unihalle.informatik.MiToBo.morphology
H-dome transform in 3D (straightforward use with 2D-images).
HDomeTransform3D() - Constructor for class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Constructor
HDomeTransform3D(MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Constructor
head - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
 
header - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
Header defines.
headerStrings - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Header defines.
height - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Height of the input image.
height - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Height of the input image.
height - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
height - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Image size in y-direction, given in pixel.
height - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Height of the binary neuron image.
height - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
height - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Height of the processed image.
height - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Skeleton image size in y-direction.
height - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Height of the image where the vector field comes from.
height - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Height of currently processed image.
height - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Height of reference image domain.
height - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Height of input label image.
height - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Height of the image.
height - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Size of the image and the calculated gvf field in y-direction.
height - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Height of the filter mask.
height - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Height of the filter mask.
height - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Height of the filter mask.
height - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
 
height - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Height of the given image.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Height of segmentation domain.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Height of segmentation domain.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Image height.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Image height.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Height of label images.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Height of label images.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter
Input image height.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Height of the input image and levelset function.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Height of the input image.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Height of the given image for the energy.
helperArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
2D array of first two levelset dimension used for visualization
highBound - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
upper boundary of the last bin
highContrast - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Highest grayscale value of the line.
highContrast - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Highest grayscale value of the line.
higherThresholdRatio - Static variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Factor to choose higher threshold in hysteresis thresholding automatically.
highQualityData - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Flag to enable extraction of data with highest accuracy.
histBins - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs
Number of histogram bins.
histBins - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU
Number of histogram bins.
histBins - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Number of histogram bins.
histogram - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
Histogram() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
 
HistogramEqualization - Class in de.unihalle.informatik.MiToBo.enhance
Histogram linearization by entropy maximization.
HistogramEqualization() - Constructor for class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Default constructor.
HistogramEqualization(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Constructor with default image.
HistogramFrame(double[]) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.HistogramFrame
 
histoRegionSize - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Size of region for histogram binning.
hookPointsUpdated() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Function to update object state after setting new point list.
hookPointsUpdated() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Function to update object state after setting new point list.
hookPointsUpdated() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Function to update object state after setting new point list.
hsiInput - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Input HSI values.
HSIToRGBPixelConverter - Class in de.unihalle.informatik.MiToBo.color.conversion
Operator to convert a single HSI value to RGB.
HSIToRGBPixelConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Default constructor.
HSIToRGBPixelConverter(double[]) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Constructor.
HSVToRGBArrayConverter - Class in de.unihalle.informatik.MiToBo.color.conversion
Class to convert a whole array of values from HSV color space to RGB.
HSVToRGBArrayConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
Standard constructor.
HSVToRGBArrayConverter(double[], double[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
Constructor to create a HSVconverter object
HSVToRGBPixelConverter - Class in de.unihalle.informatik.MiToBo.color.conversion
Class to convert values from HSV color space into other color spaces like RGB or so.
HSVToRGBPixelConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Standard constructor.
HSVToRGBPixelConverter(double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Constructor to create a HSVconverter object
HUE_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
HUE_UNDEFINED - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
hueMeanDegree - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
hueMTBImg - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Hue channel image.
hueThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The hue threshold.
hueThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The hue threshold.
hullImage - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
hybridGrayscaleReconstruct(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Implements the fast hybrid grayscale reconstruction algo of [Vincent93].
HyperStackParticleDetectorUWT2D - Class in de.unihalle.informatik.MiToBo.apps.particles2D
A particle detector that runs the ParticleDetectorUWT2D given as input (with all parameters set) over all slices of the input image for a given channel.
HyperStackParticleDetectorUWT2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
HyperStackParticleDetectorUWT2D(MTBImage, ParticleDetectorUWT2D, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
HysteresisThresholding - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds
Hysteresis thresholding on gray-scale images.
HysteresisThresholding() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Standard constructor.

I

i - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.IntObject
Internal position counter.
ic - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Image canvas for displaying image and interacting.
iChannels - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Number of channels of the image.
iChannels - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Number of channels of working image.
iChannels - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image channels.
iconData - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
iconData - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
iconLabel - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
iconLabel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
iconNoData - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
iconNoData - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
icov - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
inverse covariance matrix
id - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
id - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Id of the region (uniqueness is not guaranteed nor checked!).
id - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
ID of the region (uniqueness is not guaranteed nor checked!)
id - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
ID of the region (uniqueness is not guaranteed nor checked!)
ID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
Target ID
identifiedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
List of validated plastid regions with stromules.
iDepth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Depth of working image.
iDepth - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Depth of working image.
iDepth - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Depth of input image, i.e. dimension in z or third axis.
idImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Gray-scale image with IDs printed to regions.
idxUntitled - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Index to number untitled images popped-up.
ignoreBorder - Variable in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
Flag to indicate how the border should be handled.
ignoreButtonPress - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Flag to ignore presses on either button.
ignoreButtonPress(boolean) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Enable/disable buttons.
IgnoredValuesHandlingMode() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode
 
ignoredValuesMode - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Mode how to handle ignored values.
ignoreInvalidStackSpec - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
ignoreMask - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Optional binary mask of additional pixels to ignore.
ignoreMask - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Optional binary mask of additional pixels to ignore.
ignoreStructsAtBorder - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Flag to ignore structures along border.
ignoreStructsInNuclei - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Height of working image.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Height of working image.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Height of input image, i.e. dimension in y or second axis.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Height of the image to be generated.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Height of working image.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image height.
IlluminationCorrection - Class in de.unihalle.informatik.MiToBo.enhance
This class corrects the uneven illumination (e.g. background gradient) of especially gray value bright filed or DIC images.
IlluminationCorrection() - Constructor for class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Standard constructor.
IlluminationCorrection(MTBImage, BasicMorphology, MTBImage.MTBImageType) - Constructor for class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Constructor to create a new IlluminationCorrection object.
image - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Reference to the image from which the segmentation data originates.
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Input image.
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
The given input image to calculate the external energy from it.
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
 
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
The given input image to calculate the external energy from it.
image - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
Image to split.
image - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
image_channel - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Channel of the image that was processed.
IMAGE_FILE_PATH - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Name of the image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Name of the analyzed image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Name of the analyzed image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Name of the analyzed image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Name of the analyzed image.
ImageArithmetics - Class in de.unihalle.informatik.MiToBo.math.images
Image arithmetics class for MTBImage objects.
ImageArithmetics() - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Create empty ImageArithmetics object.
ImageArithmetics(ImageArithmetics.ArithOp, MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Constructor for arithmetic operations considering two images.
ImageArithmetics(ImageArithmetics.ArithOp, MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Constructor for arithmetic operations considering one image and a constant.
ImageArithmetics.ArithOp - Enum in de.unihalle.informatik.MiToBo.math.images
Arithmetic operations:
ADD, SUB, MULT, DIV, MIN, MAX, AND, OR, ABS_DIFF require two input images,
ADD_CONST, MULT_CONST, DIV_CONST, POW_CONST require one input image and a constant
INV, ABS require one input image only
imageClasses - Static variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
all supported classes besides RGB
imageClosed(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
imageClosed(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
ImageContrastReducer - Class in de.unihalle.informatik.MiToBo.tools.image
Contrast-reduction of images by reducing number of gray-scale values.
ImageContrastReducer() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Default constructor.
ImageContrastReducer.ResultValueMode - Enum in de.unihalle.informatik.MiToBo.tools.image
Modes for choosing result values.
ImageContrastReducer.TargetContrast - Enum in de.unihalle.informatik.MiToBo.tools.image
Available target contrast modes.
ImageConvert - Class in cmdTools.mtb_imagetools
Commandline tool to convert image formats and datatypes.
ImageConvert() - Constructor for class cmdTools.mtb_imagetools.ImageConvert
 
ImageConverter - Class in de.unihalle.informatik.MiToBo.tools.image
Plugin to convert images that are represented by MTBImage.
ImageConverter() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Constructor.
ImageConverter(MTBImage, MTBImage.MTBImageType, boolean, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Constructor
ImageDimensionReducer - Class in de.unihalle.informatik.MiToBo.tools.image
Operator to reduce image dimension by projecting multi-dimensional images along selected dimensions.
ImageDimensionReducer() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Constructor.
ImageDimensionReducer(MTBImage, boolean, boolean, boolean, boolean, boolean, ImageDimensionReducer.ReducerMethod) - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Constructor with arguments.
ImageDimensionReducer.IntObject - Class in de.unihalle.informatik.MiToBo.tools.image
Internal helper class for iterating over an image dimension.
ImageDimensionReducer.ReducerMethod - Enum in de.unihalle.informatik.MiToBo.tools.image
Methods for dimension reduction/projection.
imageDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Input image directory.
imageDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Input image directory.
imageDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Input image directory.
imageFiles - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Vector with all image files included in the experiment folder for detection.
ImageFilter - Class in de.unihalle.informatik.MiToBo.io.tools
Class to filter the files by a file chooser.
ImageFilter() - Constructor for class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
ImageFilter(String[]) - Constructor for class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
imageHeight - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Height of the images taking first image as reference.
imageHeight - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Height of the images taking first image as reference.
imageHeight - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Height of the images, taking first image as reference.
imageIndex - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
ImageIOUtils - Class in de.unihalle.informatik.MiToBo.io.tools
A class of utility functions used by the MiToBo's image-IO classes
ImageIOUtils() - Constructor for class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
 
ImageMaker(MTBSnake, int, int, int, String, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Default constructor.
imageNormalized - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Normalized version of input image used in calculations.
imageNormalized - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Normalized version of input image used in calculations.
imageOpened(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
imageOpened(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
ImagePlusInteractionFrame - Class in de.unihalle.informatik.MiToBo.core.imageJ
Adapter for GUI interactions with ImageJ's ImagePlus.
ImagePlusInteractionFrame(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
Default constructor.
ImageReaderMTB - Class in de.unihalle.informatik.MiToBo.io.images
Image reader operator to create MTBImage or ImagePlus objects from image files while reading and restoring image history from corresponding history files (.mph).
ImageReaderMTB() - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
ImageReaderMTB(String) - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Constructor of an image reader instance by filename.
ImageReaderMTB.OutImageType - Enum in de.unihalle.informatik.MiToBo.io.images
Specifies the image object that is constructed by the reader
ImageReaderOptionsPane - Class in de.unihalle.informatik.MiToBo.gui
A panel for image reader options that is used as accessory in a JFileChooser
ImageReaderOptionsPane(JFileChooser) - Constructor for class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Constructor that will install this reader options panel to the specified JFileChooser
ImageReaderOptionsPane.FileOptionsRefresher - Class in de.unihalle.informatik.MiToBo.gui
 
images - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
 
images - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
images - Variable in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
imagesAsMasks - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
If flag is true, only masks are copied to result stack.
ImageShowButton(Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton
Constructor.
ImageShowPanel(MTBImageDataIOSwing.ImageShowButton, String) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowPanel
Constructor.
ImageStatistics - Class in de.unihalle.informatik.MiToBo.math.images
Class offering statistical calculations on objects of type MTBImage.
ImageStatistics() - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
Default constructor.
ImageStatistics(MTBImage, ImageStatistics.StatValue) - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
Constructor with image argument.
ImageStatistics.StatValue - Enum in de.unihalle.informatik.MiToBo.math.images
Statistical values that could be calculated.
ImageToTilesSplitter - Class in de.unihalle.informatik.MiToBo.tools.image
Operator to split an image into tiles and save them to disk.
ImageToTilesSplitter() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
Empty constructor.
ImageType() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.ImageType
 
imageType - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Desired type of output image.
imageTypeIsOk(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
imageUpdated(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
imageUpdated(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
ImageValueModification() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageValueTools.ImageValueModification
 
ImageValueTools - Class in de.unihalle.informatik.MiToBo.tools.image
An operator class for different simple operations on the values of an image like inversion, filling with a constant value, etc.
ImageValueTools() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
ImageValueTools(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Constructor.
ImageValueTools.ImageValueModification - Enum in de.unihalle.informatik.MiToBo.tools.image
Available image value modification methods.
imageWidth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Width of the images taking first image as reference.
imageWidth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Width of the images taking first image as reference.
imageWidth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Width of the images, taking first image as reference.
ImageWriterMTB - Class in de.unihalle.informatik.MiToBo.io.images
Image writer operator to store MTBImage or ImagePlus to disk along with the image history (.mph) file.
ImageWriterMTB() - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
ImageWriterMTB(MTBImage, String) - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Image file output operator for MTBImage objects.
ImageWriterMTB(ImagePlus, String) - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Image file output operator for ImagePlus objects.
ImageWriterOptionsPane - Class in de.unihalle.informatik.MiToBo.gui
A panel for image writer options that is used as accessory in a JFileChooser
ImageWriterOptionsPane(JFileChooser) - Constructor for class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Constructor that will install this writer options panel to the specified JFileChooser
ImageXX - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
ImageXY - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
ImageYX - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
ImageYY - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
img - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
Associated MiToBo image.
img - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
Image to be segmented
img - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Image to be segmented
img - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
Image to be segmented
img - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
ImgClose - Class in de.unihalle.informatik.MiToBo.morphology
This class implements morphological closing on 2D binary/grayscale images.
ImgClose() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgClose
Default constructor.
ImgClose(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgClose
Constructor.
ImgDilate - Class in de.unihalle.informatik.MiToBo.morphology
This class implements morphological dilation on 2D binary/grayscale images.
ImgDilate() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Default constructor.
ImgDilate(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Constructor.
ImgErode - Class in de.unihalle.informatik.MiToBo.morphology
This class implements morphological erosion on 2D binary/grayscale images.
ImgErode() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgErode
Default constructor.
ImgErode(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgErode
Constructor.
imgFile - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
File from where to load the image to split.
ImgOpen - Class in de.unihalle.informatik.MiToBo.morphology
This class implements morphological opening on 2D binary/grayscale images.
ImgOpen() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Default constructor.
ImgOpen(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Constructor.
imgPlusRef - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
ImagePlus object in container.
imgReadInfo(IFormatReader) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Create a string of image reading information
imgStatsOp - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Operator to calculate energy parameters, i.e., some statistical numbers on the regions of the segmentation.
imgStatsOp - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Operator to calculate energy parameters.
ImgThresh - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds
Image thresholding operator with lower threshold (threshold and upper threshold (upperThreshold.
ImgThresh(MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Constructor for thresholding using 255 as foreground and 0 as background value.
ImgThresh(MTBImage, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Constructor for thresholding using 'fgValue' as foreground and 'bgValue' as background value.
ImgThresh() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
ImgThreshNiblack - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds
Image binarization based on local Niblack thresholding.
ImgThreshNiblack() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Default constructor.
ImgThreshNiblack(MTBImage, ImgThreshNiblack.Mode, double, double, int, int, double, MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Constructor.
ImgThreshNiblack.Mode - Enum in de.unihalle.informatik.MiToBo.segmentation.thresholds
Niblack processing mode.
ImgTophat - Class in de.unihalle.informatik.MiToBo.morphology
This class implements the tophat operator.
ImgTophat() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Default constructor.
ImgTophat(MTBImage, ImgTophat.tophatMode, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Constructor with parameters.
ImgTophat.tophatMode - Enum in de.unihalle.informatik.MiToBo.morphology
Available operating modes.
imgWriteInfo(String, IFormatWriter, int) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Create a string of image writing information
imType - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Image type.
imType - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Type of the image to be generated.
include - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
include - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
includeMask(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
inConst - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
inContour - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
Input contour.
inContours - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Set of contours to compute curvatures for
incrPositionC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the c-dimension
incrPositionC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the c-dimension
incrPositionT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the t-dimension
incrPositionT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the t-dimension
incrPositionX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the x-dimension
incrPositionX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the x-dimension
incrPositionY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the y-dimension
incrPositionY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the y-dimension
incrPositionZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the z-dimension
incrPositionZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the z-dimension
inData - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Input data.
indentationSegs - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
List of indentation segments along the contour.
IndependentlyEvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for densities p(X) with independent variables in X, that can be evaluated for each element in the realization x of its random variable X.
IndependentSamplingDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for densities with independent variables, where components of a sample can be drawn independently.
index - Variable in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
 
indexOfLowestPoint(Point2D.Double[]) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
indexOfRightmostPoint(Point2D.Double[], Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
indexR1 - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Channel index of code image for R = 1.
indexR2 - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Channel index of code image for R = 2.
indexR3 - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Channel index of code image for R = 3.
inDir - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Input directory where to find the images to process.
inDir - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Input directory where to find the images to process in batch mode.
inDir - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Input directory.
inDir - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Input directory.
individually - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Process each component individually (only active if ConvexHullExtraction.inType is InputType.IMAGE).
inEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Vector of incoming edges of the MTBGraphNode.
inf - Static variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
inFile - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Input file name.
InflectionPoint(double, double, MorphologyAnalyzer2DInProData.SegmentType) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InflectionPoint
Default constructor.
inflectionPoints - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
List of inflection points along the contour.
info - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Information about this set of line segments.
info - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Information about this region set
inHisto - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Input histogram.
inImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Optional input image to be used for drawing.
inImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Input image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Input grayscale image/stack to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Multi-channel input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Single-layer input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Reference to original image, for internal use only
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Binary input image to be analyzed.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Multi-channel input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
Gray-scale input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Gray-scale input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
inImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
inImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching
Input grayscale image.
inImg - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Input image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
inImg - Variable in class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Input image to calculate features for.
inImg - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Label image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Input image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
inImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
inImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Input gray-scale image.
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
(Binary) Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgClose
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgErode
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor
Binary input image, pixels with value 0 are interpreted as background.
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.WatershedBinary
Binary input image to segment.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Image to work on.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Image to work on.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Input image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Input image to be segmented.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Multi-dimensional input image or input stack.
inImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Input image where to draw the ellipse into.
inImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
 
inImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
Input image to which the string is to be drawn.
inImg1 - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
inImg2 - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
inImgOrig - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Input image to process.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Initialization method.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Initialize detector.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Initialization method.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Initialization method.
init() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Initializes the operator, i.e. allocates memory.
init() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Method to properly initialize instances of this class.
init() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Method to properly initialize instances of this class.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
Initialize the energy object.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Initialize the energy object.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Initialization routine which is called once before the energy is actually used.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
 
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2P4NNonPDE
Here potentially anisotropic grids may be reflected setting weights accordingly
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
 
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
 
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
Initialize the energy object.
init(MTBSnakeEnergyCD_KassCurvature) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Initialize the updater according to associated energy object.
init(MTBSnakeEnergyCD_KassCurvature) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
init(MTBSnakeEnergyCD_KassCurvature) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
 
init(MTBSnakeEnergyCD_KassLength) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Initialize the updater according to associated energy object.
init(MTBSnakeEnergyCD_KassLength) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
init(MTBSnakeEnergyCD_KassLength) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
 
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
 
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
 
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
 
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Initializing routine which is called once before the gamma adaptation is actually used.
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
 
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Initializing routine which is called once before the termination is actually used.
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
 
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
 
initAlpha - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Initial alpha value of the internal Kass energy.
initArrayRI(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Initializes the array with rotation invariant and uniform codes.
initArrayRIU(int) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Initializes the array with rotation invariant and uniform codes.
initBeta - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Initial beta value of the Kass curvature energy.
initBinImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
initEnergy(LevelsetSolverDerivatives) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
initEnergy(LevelsetSolverDerivatives) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
initEnergy(LevelsetSolverDerivatives) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
initEnergy(LevelsetSolverDerivatives) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Initializes the energy object according to given solver settings.
initEnergy(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
initEnergy(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
initEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Init routine which is called once before the energy is actually used.
initEnergy(SnakeOptimizerCoupled) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled
Init routine which is called once before the energy is actually used.
initEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Init routine which is called once before the energy is actually used.
initFromDirectory() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Builds the directory tree by initiating the (recursive) parse procedure.
initFromLabels(MTBImage, MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Helper for constructors from a label image.
initGenerator - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Operator to generate initialization for the level set function.
initialGammas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Initial step size in snake optimization.
initialize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
initialize histogram, i.e. determine smallest non empty bin, largest non
empty bin, number of histogram entries and sum of the histogram
initialSegmentation - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Initial segmentation of xylem regions.
initialSegmentation - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Initial segmentation for initializing level set function.
initialSegmentationOut - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Initial segmentation of xylem regions computed of supplied
initialSegmentPoints - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Initial border points of the segment (before any shift takes place).
initialSigmaOneHalve - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Flag to use initial sigma = 0.5 for the wavelet transform
initialSkelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Intermediate result: initial contour skeleton.
initialSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Initial snakes for cells, e.g. nuclei contours.
initialSnakes - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Set of initial snake contours.
initLabelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
initLevelset(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Helper to initialize a two phase level set function of size as given by invalidImg with a circle/sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
initLevelset(MTBImage, int, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Initialize a two phase level set function by thresholding an image.
initLS() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Construct an initial level set function.
initMainFrame() - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Initialize the main window on opening the first image.
initMask - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
initNeighbors() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2D
This initializes all relevant arrays containing information on neighbors where maxDist defines the neighborhood, e.g.
initNewTab(ALDGrappaWorkbenchGraph) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
 
initNodeNames() - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
initOperator() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Initial setip of the operator.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Initializes the optimizer.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Initializes the optimizer.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Initializes the optimizer.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Initializes the optimizer.
initReader() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Initialize the reader (this method is called in the constructor)
initRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
initReloadedTab(mxGraph, ALDWorkflow) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
 
initReloadedWorkflow(mxGraph, ALDWorkflow) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
 
initSegImageByte - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
The resulting binary image after the initial segmentation.
initSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Runs initializer to calculate initial segmentation.
initSolver() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Create a parameter object and set/initialize all objects.
initWorkbench() - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaFrame
 
inLabelImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
inMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
inModes - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
inner - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Set of inner borders if available.
innerContourLengthMin - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Minimum number of pixels a inner contour must have (length of the contour).
InProContourSegment() - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
 
inProDetails - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Vector with detailed result data on indentations and protrusions.
inputArray - Variable in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D
Input data array.
inputArray - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Input array to visualize.
inputConts - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Set of contours of type MTBContour2D to draw.
inputData - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
 
inputDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Define detector parameters.
inputDir - Variable in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles
Input directory from where to read the xSV files.
inputDir - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Image directory to process.
inputEntropy - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Initial Shannon entropy of the input image.
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Multichannel fluorescence image of the labeled neuron.
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Input image to process.
inputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
The input image to get the gradient values and differences.
inputImage - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The input image as base for the GVF field calculation.
inputImage - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Input image to process.
inputImage - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Binary input image.
inputImage - Variable in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
(Optional) input image where the borders should be extracted from.
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
The binary input image where the contours should be calculated from.
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Input image to label.
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Input image into which the contours are to be drawn.
inputImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Input image into which the polygons are to be drawn.
inputImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
inputImagePlus - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
inputImages - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Input images.
inputImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
Input skeleton image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Input image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Input image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Input skeleton image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Image to segment.
inputImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Input image.
inputImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Input image.
InputMode() - Constructor for enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.InputMode
 
InputMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.InputMode
 
inputMTBImage - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
inputMTBImageRGB - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Input Image.
inputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
inputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
inputPolys - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Set of polygons of type MTBPolygon2D to draw.
inputRegExp - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Optional file filter.
inputRegions - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Optional set of pre-segmented input regions.
inputRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
(Optional) region set where the borders should be extracted from.
inputRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
The input regions where the contours should be calculated from.
inputRegions - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set of regions to draw.
inputSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
 
inputTreelines - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Input treelines to be improved and updated.
InputType() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction.InputType
 
InputType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu.InputType
 
inputTypeChanged() - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Callback routine to change parameters on change of input type.
inputTypeChanged() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Callback routine to change parameters on change of input type.
inRange - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Dynamic range of image intensities.
inRegion - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
Input region.
inRegions - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Input image to process.
inRegions - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
inRegions - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Set of input regions.
inRegs - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
insertData(Vector<Object[]>) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Appends a set of results to the table, i.e. adds a new row at the end.
insertState(Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Insert an additional state
insertState(Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
inSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Input snake.
inSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Input snake.
instance - Static variable in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon
Singleton reference.
int2Color(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Transforms integer value to Color object.
IntegrableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for distributions with distribution functions that can be evaluated for each realization x of its random variable X.
IntensityAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
IntensityAnalyzer(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
intensityImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
IntensityNormalizationMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.IntensityNormalizationMode
 
intermediateLS - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
intermediateLS - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
intermediatePhiColorImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Color image to visualize intermediate segmentation results.
intermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
List of intermediate result segmentations.
intermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Set of intermediate segmentation results, required for stack generation.
intermediateResultSamplingRate - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
intermediateResultStack - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
internalOutputDir - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Internal variable of output dir (to avoid modifying parameter).
IntersectionPoint2D(double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D.IntersectionPoint2D
Default constructor.
intImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
intNormMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Mode for normalizing image intensities.
IntObject() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.IntObject
Constructor.
intReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
intReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
inType - Variable in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Input type.
inType - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Input type.
inv(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Inverts the image.
inv(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Invert the image.
INVALID_PHASE - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Level set function value to represent invalid pixels
invalidColor - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
invalidImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
invalidImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
invalidTilesNum - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Number of invalid, i.e. background tiles.
inverseATrousDWT(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
inverseATrousDWT(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Inverse a trous DWT
inverseDifferenceMoment - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
invert() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
inverts the values of the structuring element
invert(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
invertGroundtrouth - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Flag to invert ground-truth image prior to evaluation.
invertImage(MTBImage, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Invert the specified image.
invertInputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Flag to invert input image.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Flag to invert filter mask.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Flag to invert filter mask.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Flag to invert filter mask.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Flag to invert filter mask.
invertPixelValues - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
If true image values are inverted, i.e., the algorithm seeks to find a path along bright pixels.
invisibleRegionSet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
invokeLaterRepaint(ImageReaderOptionsPane) - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
ioPanel - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Swing component to be integrated in GUI.
iRead - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Operator for reading image files from disk.
isActive - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Flag to indicate if marker is active, by default true.
isActive() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Check if marker is active.
isAppliedComponentwise() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Return operator mode.
isBGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Test if background pixels keep their original pixel values
isCellEditable(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
 
isCellEditable(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel
 
isClockwiseOriented(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if polygon is oriented counter-clockwise.
isClosed - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Indicates if the polygon is closed or not.
isClosed() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Returns true if the polygon forms a closed polygon.
isConvertableToNumericalData() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Indicates if result data can be 'condensed' to numerical values, e.g., for visualization purposes.
isConvertableToNumericalData() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
isConvertableToNumericalData() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
isConvertableToNumericalData() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
 
isConvex() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Check if polygon is convex.
isConvex(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if a polygon is convex.
isCounterClockwiseOriented(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if polygon is oriented counter-clockwise.
isDirected() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Directed or undirected graph?
isDirected() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
isDirected() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Returns true if graph has directed edges, false if undirected
isEmpty() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns true if this collection contains no elements.
isEmpty() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Returns true if this collection contains no elements.
isFGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Test if foreground pixels keep their original pixel values
isForwardTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Test if parameter object is set to (forward) transform (image to wavelet)
isFurther(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
isHorizontal - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
isHorizontal - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
isHorizontal - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
isHueUndefined(float) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Return true if the hue channel is undefined which is true is saturation is zero or undefined which in turn is encoded as zero.
isHueUndefined(int) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Return true if the hue channel is undefined which is true is saturation is zero or undefined which in turn is encoded as zero.
isInverseTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Test if parameter object is set to Inverse Transform (wavelet to image)
iSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Total area/volume of working image.
isLess(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
isMeanFree - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Flag for indicating if input data is already mean-free.
isOrderedClockwise() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Check if points are ordered clockwise.
isOrderedCounterClockwise() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Check if points are ordered counter-clockwise.
isotropicCalcs - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
Flag for isotropic calculations.
isotropicCalcs - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Flag for isotropic calculations.
isRegionBinaryMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Check for region input mode.
isRegistered(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Checks if an object is registered in the database.
isRegisteredImageBox(Object) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Checks if the given image object is already registered.
isSaturationUndefined(float) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Return true if the saturation channel is undefined which is true if the x channel is zero.
isSaturationUndefined(int) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Return true if the saturation channel is undefined which is true if the x channel is zero.
isScaleValues() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get flag if values are scaled to match the range of output type values if necessary
isSimple() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Check if polygon is simple, i.e. has no self-overlaps.
isSimple(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if a polygon is simple.
isValid(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
returns true, if pixel/voxel is valid.
isValidType(MTBImage.MTBImageType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Deprecated.
isVerbose() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
isVisible(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
True, if position (x,y) is visible.
isVisible(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
True, if position (x,y,z) is visible.
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
is this pixel visible?
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get visibility of a certain pixel position.
itCounter - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Iteration counter.
itemStateChanged(ItemEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
iteration - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Iteration counter.
iterationsPerSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Number of iterations done for each snake.
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
 
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
 
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
 
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
 
iterator() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Returns a iterator for the coordinatesNeighbors in the order as defined
iteratorOffsets() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Returns a iterator for the pixelOffsets in the order as defined
iTimeDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Time dimensionality of input image, i.e. dimension in t or time line.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Width of working image.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Width of working image.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Width of input image, i.e. dimension in x or first axis.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Width of the image to be generated.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Width of working image.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image width.

J

jarvisMarch(Point2D.Double[]) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Jarvis march convex hull computation
JComboBoxImage(String, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Default constructor.
jfc - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
jfc - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
JFeatureLibLBPAdapter - Class in de.unihalle.informatik.MiToBo.features.texture.lbp
Adapter for JFeatureLib's Local Binary Patterns.
JFeatureLibLBPAdapter() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapter
Default constructor.
JFeatureLibLBPAdapterRIU - Class in de.unihalle.informatik.MiToBo.features.texture.lbp
Implementation of rotation invariant uniform LBPs.
JFeatureLibLBPAdapterRIU(int) - Constructor for class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU
Default constructor.
Jmax - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Maximum scale to consider.
Jmax - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
Maximum scale to consider.
Jmax - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
Jmin - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Minimal scale to consider.
Jmin - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
Minimal scale to consider.
jMode - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Mode for joining results from different orientations.
join(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Join a region with this region.
JoinMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer.JoinMode
 
jpeg - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
jpg - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
junitTest - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Internal flag for interrupting recursive calls in unit testing.

K

k - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
k - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Used only for MODIFIED_FREEMAN_DAVIS
K_MIN - Static variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
in length of vector k as suggested by H.Freeman and L.S.Davis
keepLargestCC(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
remove all but the largest connected component with label
KERNEL_TYPE() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.KERNEL_TYPE
 
kernelImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
kernelMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Internal helper mask to mark valid/invalid kernel elements.
kernelNormalization - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
kernelOrigin - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
KernelPart() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.KernelPart
 
kernels - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
kernelSize - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Size of the (squared) kernel window.
kernelTrunctation - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
keyPressed(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
keyPressed(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
keyReleased(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
keyReleased(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
keyTyped(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
keyTyped(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
kLower - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Used only for BEUS_TIU
KMeans - Class in de.unihalle.informatik.MiToBo.clustering
Clustering of (feature) vectors with k-means based on Weka library.
KMeans() - Constructor for class de.unihalle.informatik.MiToBo.clustering.KMeans
Default constructor.
kNearestObs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Stores for each observation the k-nearest observations that will be associated after the corresponding observation.
kNearestObservations(int, double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Get the (k) nearest observations for each observation in this.Z, i.e. for each observation z_m all following observations z_{m:M} are sorted by Euklidean distance and stored in an array.
kPart - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Variable to configure which part of kernel mask is calculated.
kUpper - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Used only for BEUS_TIU
kurtosis(Vector<Double>, double, double) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
kurtosisFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 

L

L - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
label(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
LabelAreasToRegions - Class in de.unihalle.informatik.MiToBo.segmentation.regions.labeling
 
LabelAreasToRegions() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelAreasToRegions
 
labelComponents(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Sequential component labeling
labelComponentsOfImage(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Label a MTBImage.
LabelComponentsSequential - Class in de.unihalle.informatik.MiToBo.segmentation.regions.labeling
Sequential component labeling for binarized 2D images to find connected components.
LabelComponentsSequential() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Constructor.
LabelComponentsSequential(MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Constructor.
LABELHEIGHT - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
 
labelImage - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Label mask.
labelImage - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Gray-scale label image of nuclei regions.
labelImage(MTBImage, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
labelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
labelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Input image.
labelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Grayscale image of regions, gray values are identical to IDs.
labelImageColor - Variable in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter
Colored label image.
LabelImageConverter - Class in de.unihalle.informatik.MiToBo.segmentation.helpers
Converts (pseudo-) colored RGB labels to unique gray-scale labels.
LabelImageConverter() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter
Default constructor.
LabelImageConverter(MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter
Default constructor with parameters.
LabelImageEditor - Class in de.unihalle.informatik.MiToBo.tools.interactive
A small interactive tool for editing label images by mouse-clicks.
LabelImageEditor() - Constructor for class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Default constructor.
labelImageGray - Variable in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter
Output gray-scale image.
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Binary nuclei image to be processed.
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Input image to process.
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Input label image.
labelImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
labelInside - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Marker for label of enclosed area.
labelIO - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to read a label image.
labelListGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
List of groundtruth region labels.
labelListSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
List of labels found in segmentation.
labelNeighbors(MTBImage, MTBImage, int, int, double, double) - Static method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
Function for recursive labeling of contour pixels.
labelNeighbors(MTBImage, MTBImage, boolean[][], int, int, double, double) - Static method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Function for recursive labeling of foreground pixels.
labelResult - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
labels - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
labels - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
labelSetGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Set of available groundtruth labels.
labelsetGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Set of available groundtruth labels.
labelSetSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Set of available segmentation labels.
labelsetSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Set of available segmentation labels.
LABELWIDTH - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
 
lambda - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
lambda - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
mean=variance of the distribution
lambda_in - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Weighting factors for inner region fit, one for each channel.
lambda_out - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Weighting factors for outer region fit, one for each channel.
lambdaArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
An array of lambda values to be set in this energy object during initialization, i.e. the init() method.
lambdaArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
An array of lambda values to be set in this energy object during initialization, i.e. the init() method.
lambdaBg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
Lambda for background
lambdaBg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Lambda for background
lambdaBirth - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
lambdaBirth - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
lambdaClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
lambdaClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
lambdaDeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
lambdaDeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
lambdaFg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
Lambda for foreground
lambdaFg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Lambda for foreground
lambdaForOptimization - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
array to hold lambdas of phases, starting with MTBLevelsetMembership.BG_PHASE
largestNonEmptyBin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
largest intensity value contained in the input image
lastDir - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
For convenience: always open last directory for saving.
lastDirectory - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Last directory selected by user.
lastDirectory - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Last directory selected by user.
lastDirectory - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Last directory visited, initially it's user's home.
lastFile - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Last file selected by user.
lastFile - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Last file selected by user.
lastFile - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Last selected file.
lastLabel - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Stores the last clicked label for transfer in memory mode.
lastM - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Number of observations in last call of drawSample()
lastN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Number of targets in last call of drawSample()
lastPathPoint - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Local helper variable in drawing new boundaries, stores last point of current path.
lastProcessor - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Reference to last processor before last action.
lastSample - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Last sample that was sampled
layer - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Layer where the node is located.
LayerSubset() - Constructor for enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.LayerSubset
 
LE(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors
This method implements the localization error.
leaveOneOutCrossValidation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
leave-one-out cross validation, i.e. iteratively one sample is taken as test
sample whereas all others are used for training
leftBorderPoint - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Left boundary point of segment after potential shifts.
leftBorderPointPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Index of left boundary point of segment after potential shifts.
leftOutlierFraction - Variable in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching
Fraction of outlier pixels at left histogram margin.
length - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Expected length of vessel segments.
lengthEnergy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
lengths - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
lengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
letNewbornTargetIDsStartFrom(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Specify the starting target-ID for newborn targets
letTargetsDie() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Let targets die randomly using the specified distribution of target death and the internal random generator.
LevelsetIterator() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIterator
 
LevelsetIteratorContourPoints() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
LevelsetIteratorScan() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
LevelsetSegmentationNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Operator intended as user interface for level set segmentation using nonPDE optimization and optionally topology preserving.
LevelsetSegmentationNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Default constructor.
LevelsetSolveNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements a level set solver which may optionally perserve the topology using non PDE optimization.
LevelsetSolveNonPDE(MTBGenericEnergyNonPDE, MTBLevelsetMembership, int, int, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Constructor.
LevelsetSolveNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Constructor
LevelsetSolveNonPDE.CoordInt3D - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Just to hold 3D coordinate and nothing else
LevelsetSolveNonPDE.LevelsetIterator - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Abstract class for iterators of pixels/voxels of the level set function.
LevelsetSolveNonPDE.LevelsetIteratorContourPoints - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Iterator for all contour pixels/voxels of the level set function excluding invalid pixels/voxels.
LevelsetSolveNonPDE.LevelsetIteratorScan - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Iterator for all pixels/voxels of the level set function in scanline fashion excluding invalid pixels/voxels.
LevelsetSolver - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Generic super class for level set solvers.
LevelsetSolver() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Default constructor.
LevelsetSolverDerivatives - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Level set solver using variational calculus.
LevelsetSolverDerivatives() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Default constructor.
LevelsetSolverPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver
Solver for level set segmentation problems based on PDEs.
LevelsetSolverPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Default constructor.
LevelsetSolverPDE.VelocityExpansionMode - Enum in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver
Available modes for expanding zero level velocities.
lif - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
limit - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
line() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
Draw line into image.
LinearFilter - Class in de.unihalle.informatik.MiToBo.filters.linear
Generic linear filter operation class
LinearFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Empty constructor
LinearFilter(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Constructor
LinearFilter(MTBImage, MTBImage, int[], boolean, MTBImageWindow.BoundaryPadding) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Constructor
LinearTransformGaussNoise - Class in de.unihalle.informatik.MiToBo.math
A linear transform with additive Gaussian noise.
LinearTransformGaussNoise(Matrix, Matrix, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
lineSegmentSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
The set of line segments.
lineWidth - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Line width.
lineWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Line width.
LinkAdjacentComponents(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function for linking adjacent components/regions in a binary image.
LinkAdjacentPixels(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function for linking adjacent pixels in a binary image.
linkageMode - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The algorithm we use to link new pixels to the region.
linkageMode - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The algorithm we use to link new pixels to the region.
llimits - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
LobeTypes() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.LobeTypes
 
localBinaryPatternHist - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPResult
Result values.
LocallyAdaptiveContrastEnhancement - Class in de.unihalle.informatik.MiToBo.enhance
This class implements contrast enhancement for microscopy images.
LocallyAdaptiveContrastEnhancement() - Constructor for class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Default constructor.
LocallyAdaptiveContrastEnhancement(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Constructor with given image.
LocallyAdaptiveContrastEnhancement(MTBImage, double, int) - Constructor for class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Constructor with given image and parameters.
localVersion - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Local version information.
localXThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
LOG - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
Tells if the distribution is internally represented by the natural logarithm of the probability values
log_p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
log_p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
log_p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
log_p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
log_p - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
log_p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
log_p(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.LogEvaluatableDistribution
Evaluate natural logarithm of p(X) at location x. log(P(X=x))
log_p(T, int) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.LogIndependentlyEvaluatableDistribution
Evaluate log(p_i(X)) at x_i
log_p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
 
log_p(AbstractMultiState<S>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Evaluate the density independently for observation i in Z conditional on state j in X
log_p(AbstractMultiState<S>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Evaluate the density independently for observation i in Z conditional on state i in X
log_p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
 
log_p(DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
This method is here only valid for the latest DataAssociation sampled with drawSample().
log_p - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
log_p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
log_p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
log_p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
log_p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
log_p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
log_p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
log_pzc - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
storage for the log likelihood values of the observations for possible associations to avoid recomputation
logarithmize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
calculate the logarithmic (base e) histogram; entries smaller than one become zero!
logBinom - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Binomial distribution of number of observations associated to existing targets
LogEvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for distributions that can be evaluated for each realization x of its random variable X.
logfac - Variable in class de.unihalle.informatik.MiToBo.math.LogFaculty
array to store log(0!)
logFac - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
An object to compute and store log(n!)
logfactor - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
log of the normalization factor
LogFaculty - Class in de.unihalle.informatik.MiToBo.math
Class to compute the logarithm of the faculty of an integer n.
LogFaculty(int) - Constructor for class de.unihalle.informatik.MiToBo.math.LogFaculty
Constructor to precompute log(0!)
LogIndependentlyEvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for densities p(X) with independent variables in X, that can be evaluated (natural logarithm) for each element in the realization x of its random variable X.
logMuValues - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
(log) values of mu to avoid recomputation
logNuValues - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
(log) values of nu to avoid recomputation
logp(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
logP_C - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
(log) probability of the current set of association variables given observations and previous associations
logP_Ccond - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
The probability of the association set of any time step represented by this sample conditional on all previous associations in this sample and all observations up to the specific time step: P(C^t | C^{1:t-1}, Z^{1,t}) for all t
logP_Cjoint - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
The joint probability of the association sets of all time steps represented by this sample conditional on all observations: P(C^{1-t} | Z^{1,t})
logP_MN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
(log) propability of M observations given N existing targets and the current model configuration
logPofRegion(MTBRegion2D, MTBImage, MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
LogProbabilityDensityFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for multivariate distributions that allow evaluation of the natural logarithm of their probability density function.
LogProbabilityMassFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for univariate distributions based on log-probability mass functions
logSumP(double, double) - Static method in class de.unihalle.informatik.MiToBo.math.MathX
Natural logarithm of the sum of two values P1 and P2 when only their natural logarithms log(P1) and log(P2) are given.
longestPathLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
lowBound - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
lower boundary of the first bin.
lowContrast - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Lowest grayscale value of the line.
lowContrast - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Lowest grayscale value of the line.
lowerBound - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
lowerThresh - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Lower threshold for filter responses.

M

M - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
number of observations
m - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
m - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
m1 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
m2 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
m_currentC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
current c-coordinate, for 3D only access functions
m_currentSliceIdx - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Index of the current slice.
m_currentT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
current t-coordinate, for 3D only access functions
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
reference to the ImagePlus pixel data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
image data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
reference to the ImagePlus pixel data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
image data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
reference to the ImagePlus pixel data
m_dataB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the ImagePlus pixel data (blue channel)
m_dataG - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the ImagePlus pixel data (green channel)
m_dataR - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the ImagePlus pixel data (red channel)
m_height - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Height of input image.
m_idx - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
index of the minimum, median or maximum element in the sorted array
m_img - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
the underlying ImagePlus object
m_imgB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the red channel MTBImage
m_imgG - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the red channel MTBImage
m_imgR - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the red channel MTBImage
m_imgStack - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
reference to the ImageStack object of the underlying ImagePlus object
m_impulator - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
source image on which the window is applied
m_labelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Temporary label image.
m_level - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Tree level (level identifier).
M_max - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Maximum number of observations in the time series
m_padMode - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
padding mode for nonexistent values (outside the underlying image), see static finals
m_posC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current c-position of the window in the source image
m_posT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current t-position of the window in the source image
m_posX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current x-position of the window in the source image
m_posY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current y-position of the window in the source image
m_posZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current z-position of the window in the source image
m_rC - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_reg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
2D region object.
m_rT - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_rX - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_rY - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_rZ - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_sigmaScales - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
noise sigma scale factors for different wavelet scales
m_sizeC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of c-dimension
m_sizeC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in c-dimension
m_sizeC - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
m_sizeStack - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
stacksize
m_sizeT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of t-dimension
m_sizeT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in t-dimension
m_sizeT - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
m_sizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of x-dimension
m_sizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in x-dimension
m_sizeX - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
m_sizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of y-dimension
m_sizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in y-dimension
m_sizeY - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
m_sizeZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of z-dimension
m_sizeZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in z-dimension
m_sizeZ - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
m_sliceLabels - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
slice labels
m_sliceLabels - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
slice labels
m_sliceLabels - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
slice labels
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Vector of installed StatusListener objects.
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Vector of installed StatusListener objects.
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Vector of installed StatusListener objects.
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
vector of installed StatusListeners
m_title - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Image title This member is private to enforce access via the corresponding setter/getter only.
m_type - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
MiToBo image type
m_width - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Width of input image.
mad - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
mad - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Maximal allowed discrepancy.
mahalanobis(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
main(String[]) - Static method in class cmdTools.cellAnalysis.ParticleDetector2D
 
main(String[]) - Static method in class cmdTools.mtb_imagetools.ImageConvert
 
main(String[]) - Static method in class cmdTools.tracking.multitarget.EvalTracks
 
main(String[]) - Static method in class cmdTools.tracking.multitarget.ObservationSeriesGenerator
 
main(String[]) - Static method in class cmdTools.tracking.multitarget.ObservationsInfo
 
main(String[]) - Static method in class cmdTools.tracking.multitarget.RBMCDATracker
 
main(String[]) - Static method in class cmdTools.visualization.DisplayImage
 
main(String[]) - Static method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Test function.
main(String[]) - Static method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN4
Test
main(String[]) - Static method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN8
Test
mainFrame - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
The top level frame.
mainFrame - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Main window frame.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Main panel.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Main panel.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Main panel containing all graphical components.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
Main panel.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
The top level panel of this frame.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Main panel of main frame.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Main panel of main frame.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Main panel of main frame.
mainpath - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Root directory of the tree.
makeline(int, int, int, int, Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Draws a line between two points.
makePolySimple(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Simplifies the given polygon.
makeSimple() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Makes the polygon simple, i.e. removes self-overlaps.
makeSimple() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Create the result table and include the specific table header.
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
create results table
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
makeTable(MTBRegion2DSet, MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
create results table
makeTable() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
create result table
makeTable() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
create result table
ManualTrackingMigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
ManualTrackingMigrationAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
ManualTrackingMigrationAnalyzer(String) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
ManualTrackingTrajectoryExtraction - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
ManualTrackingTrajectoryExtraction(String, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
 
map - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Map for value mappings.
mapHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Height of class map.
mapIndexToValue(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
mapMaxX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Maximal x coordinate of class map.
mapMaxY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Maximal y coordinate of class map.
mapMinX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal x coordinate of class map.
mapMinY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal y coordinate of class map.
mapWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Width of class map.
MARGIN - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
 
marginRoughnessValues - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
markBranchPoints(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Mark branch/special points as first step before building up the whole skeleton graph.
markerVects - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Set of available marker vectors.
markov - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Markov matrix probability of dynamic model switching: A matrix with size (#dynamicmodels x #dynamicmodels).
mask - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
mask - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Mask to exclude image regions and tiles, respectively.
mask - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
mask - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Optional mask for excluding image regions from processing.
mask - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
Mask.
maskCenterX - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
maskCenterY - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
maskChannel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
maskDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Directory with (cell) masks.
maskDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
(Optional) directory with (cell) boundaries.
maskDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Directory with (cell) masks.
maskFormat - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Format of provided cell masks.
maskFormat - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Format of provided cell boundaries.
maskFormat - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Format of provided cell masks.
maskHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Height of the mask to be generated.
maskImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
maskImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
maskIO - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to read a binary image.
MaskMaker(MTBSnake, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Default constructor with zero offsets.
MaskMaker(MTBSnake, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Constructor with non-zero offsets.
maskRadiusC - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskRadiusT - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskRadiusX - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskRadiusY - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskRadiusZ - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskShape() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.maskShape
 
maskSize - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
maskSize - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgClose
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgErode
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
maskSizeX - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
maskSizeY - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
maskWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Width of the mask to be generated.
matchesRootSegmentStatusToDraw(EnumSet<Drawing.ROOTSEGMENT_STATUS>, MTBXMLRootSegmentStatusType.Enum) - Static method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing
 
MatchingAdjacencyMatrix - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts
Abstract class of an adjacency matrix for graph matching, i.e. graph nodes are associated to different partitions.
MatchingAdjacencyMatrix() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.MatchingAdjacencyMatrix
 
MatchingBipartite - Class in de.unihalle.informatik.MiToBo.math.optimization
Base class for bipartite matching algorithms.
MatchingBipartite() - Constructor for class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Default constructor.
MatchingBipartite_HungarianAlgorithm - Class in de.unihalle.informatik.MiToBo.math.optimization
Bipartite matching with Hungarian algorithm.
MatchingBipartite_HungarianAlgorithm() - Constructor for class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Default constructor.
MatchingBipartite_HungarianAlgorithm(double[][], MatchingBipartite_HungarianAlgorithm.ScoreInterpretation) - Constructor for class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Default constructor with parameters.
MatchingBipartite_HungarianAlgorithm.ScoreInterpretation - Enum in de.unihalle.informatik.MiToBo.math.optimization
Matrix scores interpretation.
matchingMatrix - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Matching matrix.
matchingMatrix - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Matching matrix.
matchParticles(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Match particle regions to nuclei regions.
MathHelper - Class in de.unihalle.informatik.MiToBo.apps.xylem
 
MathHelper() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
 
MathX - Class in de.unihalle.informatik.MiToBo.math
Math class with functions that are not provided by Java's Math class.
MathX() - Constructor for class de.unihalle.informatik.MiToBo.math.MathX
 
MathXGeom - Class in de.unihalle.informatik.MiToBo.math
Math class with helper functions for basic geometric operations.
MathXGeom() - Constructor for class de.unihalle.informatik.MiToBo.math.MathXGeom
 
matrixScore - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Score interpretation.
matrixSize - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Number of rows and columns, respectively.
max - Variable in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
 
max(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Pixelwise maximum
max(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Pixelwise maximum
MAX_ALLOWED_NUM_PHASES - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Maximal number of phases which may be represented including background phase.
max_d2c - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Maximum peak distance factor.
MAX_VALUE - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Constant used in SDF calculations.
maxAlpha - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Maximal possible value of alpha as can be provided by parameter updated.
maxAngle - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Maximal orientation where to end.
maxArea - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
maxAreaChange - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
maxAreaChange - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
maxAssociatedTargetID() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
maxAssociatedTargetID() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the maximum target id associated by this data association object
maxAxisLengths - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
List of maximal axis lengths of plastid regions.
maxBeta - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Maximal possible value of beta.
maxBitsSoFar - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIULUTs
Maximal bit number for which the class has already been initialized.
maxColor - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Color for maximal value.
maxColor - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Color for maximal value.
maxCompDist - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Maximal distance of adjacent components.
maxCompSize - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Minimal size of components in mode ERASE_SMALL_COMPS.
maxCoreRegionWidths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
maxDiffusionDist - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
maxDilMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
maxDist - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
maxDist - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
maxDist - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
maxDist - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Maximal distance of points within the neighborhood to current pixel, i.e. the pixel which neighborhood we are considering
maxDistNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
maxDistNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Maximum distance of neighboring observations
maxEnergyVal - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Maxmimum value of energy, dependent on number of snakes and rho.
maxExpansion - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Maximum expansion by Voronoi dilation.
maxFragmentDistance - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
maxFragmentDistance - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Maximum distance to connect a fragment to a detected neuron, given in pixel.
maximalCellSize - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Threshold for the maximal admissible cell size.
maximalCellSize - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Threshold for the maximal admissible cell size.
maxIncreaseFraction - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
maxIndexMap - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Map of indices of maximal responses.
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
maxIter - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
maxIterations - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
maxIterations - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Number of snake iterations.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Maximum number of iterations.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Maximum number of iterations.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Maximum number of iterations.
maxLabel - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Maximal label appearing in the label list.
maxLabel - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Maximal label appearing in the label list.
maxLevels - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Maximum number of levels to perform.
maxLineLength - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Maximal line length.
maxLineLength - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Maximal line length.
maxNumNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
maxNumNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Maximum number of neighboring observations
maxradius - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Maximal radius of region to be considered for intensity normalization.
maxRegionCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Maximum number of regions in groundtruth or segmented region set.
maxRegionCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Maximum number of regions in groundtruth or segmented region set.
maxScale - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.ResponseDifference
Upper vessel scale.
maxSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Maximum size of regions.
maxSizeValue - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Maximal value threshold.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
Maximal allowed length of a branch to be accepted as spine.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Maximum length to define a branch of a neurite as spine (filopodia-like protrusion) in pixel.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
 
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Given maximum lengths for definition of spines.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Maximal allowed length of a branch to be accepted as spine.
maxTargetID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
maxTargetID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
The maximum target ID that occurred in this sample up to the current time step
maxVal - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Maximal value of intensity range, depending on input image type.
maxValidNeighborCount - Static variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapterRIU
Maximal neighbor number for which array has been initialized so far.
maxVar - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Maximum instability score, should be in the interval of [0,1].
maxVoronoiExpDist - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Voronoi expansion distance.
maxWeight - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
maxWeights - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
maxWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Expected width of thick vessels.
mBorder - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape
Border of the object.
mCurve - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeCurve
Curve object representing the shape of the marker.
mean - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
mean vector
mean - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
mean - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Average vector of input dataset.
mean - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
mean - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
meanAndVariance(int[]) - Static method in class cmdTools.tracking.multitarget.ObservationsInfo
 
meanAreas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
MeanFilter - Class in de.unihalle.informatik.MiToBo.filters.linear
Multidimensional mean filter
MeanFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Constructor with default parameters sizeX=1, sizeY=1, sizeZ=0, sizeT=0, sizeC=0, kernelTruncation=3, sizeInterpretation=PHYSICALSIZE.
MeanFilter(MTBImage, Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Constructor for mean filtering in x- and y-dimension.
MeanFilter(MTBImage, Integer, Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Constructor for mean filtering in x-, y- and z-dimension.
MeanFilter(MTBImage, Integer, Integer, Integer, Integer, Integer, MTBImageWindow.BoundaryPadding) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Constructor for mean filtering.
meanFilter() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
compute the mean filter
meanFilterSize - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Size of mean filter for Gaussian derivative image.
meanfreeData - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Normalized, i.e., mean-free, dataset.
meanfreeDataMatrix - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Normalized, i.e., mean-free, data matrix.
meaningfulNodes(MTBTreeNode, MTBImage[], MTBImageHistogram[], int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get the most meaningful regions from a (sub)tree.
meanOfRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
means - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Average intensities per region, first index refers to channel.
means - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Average intensities.
meanX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
measure() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
measures the scratch area, i.e. number of pixels that don't have value 0
Measure_DetectionErrors - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
This class implements 3 detection errors for contour detection evaluation.
Measure_DetectionErrors() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors
Default constructor.
Measure_DetectionErrors(MTBImageShort, MTBImageShort, ArrayList<ArrayList<Point>>, ArrayList<ArrayList<Point>>, ArrayList<Integer>, ArrayList<Integer>, byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors
Constructor with arguments.
Measure_HausdorffDistance - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
The class implements the Hausdorff Distance for contour detection evaluation.
Measure_HausdorffDistance() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance
Default constructor.
Measure_HausdorffDistance(MTBImageShort, MTBImageShort, ArrayList<ArrayList<Point>>, ArrayList<ArrayList<Point>>, ArrayList<Integer>, ArrayList<Integer>, byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_HausdorffDistance
Constructor with arguments.
Measure_OdetsCriteria - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
This class implements Odet's contour detection evaluation criteria for oversegmentation (OCO) and undersegmentation (OCU).
Measure_OdetsCriteria() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria
Default constructor.
Measure_OdetsCriteria(MTBImageShort, MTBImageShort, ArrayList<ArrayList<Point>>, ArrayList<ArrayList<Point>>, ArrayList<Integer>, ArrayList<Integer>, byte[][], int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria
Constructor with arguments.
Measure_PrattsFigureOfMerit - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
This class implements Pratt's figure of merit for contour detection evaluation.
Measure_PrattsFigureOfMerit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit
Default constructor.
Measure_PrattsFigureOfMerit(MTBImageShort, MTBImageShort, ArrayList<ArrayList<Point>>, ArrayList<ArrayList<Point>>, ArrayList<Integer>, ArrayList<Integer>, byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit
Constructor with arguments.
Measure_RecallPrecisionF - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
Class for evaluating recalls, precisions, F1-scores and Jaccard indices.
Measure_RecallPrecisionF() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_RecallPrecisionF
Default constructor.
Measure_RecallPrecisionF(MTBImageShort, MTBImageShort, TreeSet<Integer>, TreeSet<Integer>, int[], int[], HashMap<Integer, Integer>, HashMap<Integer, Integer>, int, int, double[][], byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_RecallPrecisionF
Default constructor with parameters.
measureInfo - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Info string to structure GUI.
MeasurementUnits() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.MeasurementUnits
 
MeasureUnit() - Constructor for enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums.MeasureUnit
 
measureUnits - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Units to be used for measurements.
measureUnits - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Units for measurements.
MedialnessMultiScaleFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness
2D multi-scale medialness filter for vessel segmentation.
MedialnessMultiScaleFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Standard constructor.
MedialnessMultiScaleFilter2D(MTBImage, Integer, Double, Double, Double, MedialnessMultiScaleFilter2D.FilterMode, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Constructor to create a new 2D multi-scale medialness filter.
MedialnessMultiScaleFilter2D.FilterMode - Enum in de.unihalle.informatik.MiToBo.filters.vesselness
Settings.
memA - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Optimization matrix with values of last calculations.
memoryMode - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
In memory mode labels can be transferred from one region to another.
method - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
MFFDOGFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness
MF-FDOG filter for vessel segmentation.
MFFDOGFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Default constructor.
MFFDOGFilter2D.VesselMode - Enum in de.unihalle.informatik.MiToBo.filters.vesselness
Detection scenario mode.
MFFDOGMultiScaleFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness
MF-FDOG multi-scale filter for vessel segmentation.
MFFDOGMultiScaleFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Default constructor.
Mica2D - Class in de.unihalle.informatik.MiToBo.apps.cells2D
Operator for integrated cell image analysis.
Mica2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Default constructor.
Mica2D(MTBImage, int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Default constructor.
Mica2DTableModel - Class in de.unihalle.informatik.MiToBo.apps.cells2D
Implementation of a TableModel for the Granule Detector result table.
Mica2DTableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
Default constructor.
midPoint - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Median point of contour.
midPointPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Index of median segment pixel on contour.
MigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
Operator for analyzing the movement pattern of cells as well as changes in morphology and fluorescence intensity
MigrationAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
MigrationAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
MigrationAnalyzer(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
min - Variable in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
 
min(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Pixelwise minimum
min(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Pixelwise minimum
MIN_SE_SIZE - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Minimum size of an SE.
minAngle - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Minimal orientation from where to start.
minArea - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
minArea - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
minAreaAfterErosion - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
The minimum size of regions after the erosion to get preserved.
minAreaAfterOpening - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Minimal area (in pixels) of a region required after opening.
minAreaAfterOpeningInitSeg - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Minimal area (in pixels) of a region required after opening.
minAreaGrowth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Lower threshold for region growth.
minAreaPostProcessing - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The minimum size of a MTBRegion2D to not be removed (after opening the grown regions).
minAreaPostProcessing - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The minimum size of a MTBRegion2D to not be removed (after opening the grown regions).
minAreaSeedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The minimum size of a MTBRegion2D to further erode when computing seed regions.
minAreaSeedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The minimum size of a MTBRegion2D to further erode when computing seed regions.
minAxisLengths - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
List of minimal axis lengths of plastid regions.
minColor - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Color for minimal value.
minColor - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Color for minimal value.
minCompactness - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Minimal compactness of a region required after opening.
minCompactnessInitSeg - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Minimal compactness of a region required after opening.
minCompSize - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Minimal size of components in mode ERASE_SMALL_COMPS.
minCoreRegionWidths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
minDilMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
minDiversity - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Minimum diversity score, should be in the interval of [0,1].
minimalBorderLength - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Lower threshold for border length.
minimalCellSize - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Threshold for the minimal admissible cell size.
minimalCellSize - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Threshold for the minimal admissible cell size.
minimalCurvature - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Threshold for minimal curvature.
minIndentationLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Minimal number of pixels a valid indentation requires.
minIntensityVariance - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Minimum admissible variance in new snake interior fractions..
minLineLength - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Minimal line length.
minLineLength - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Minimal line length.
minMN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Minimum of number of observations and number of targets
minNucleusSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Minimal size of valid nuclei regions.
minProtrusionLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Minimal number of pixels a valid protrusion requires.
minRegionCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Minimum number of regions in groundtruth or segmented region set.
minRegionCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Minimum number of regions in groundtruth or segmented region set.
minRegionSize - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Minimal size of valid regions.
minRegionSize - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
Minimal size of valid regions.
minScale - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.ResponseDifference
Lower vessel scale.
minSeedSize - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
minSeedSize - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
minSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
minSize - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
minSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Minimum size of regions.
minSizeFraction - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
minSizeValue - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Minimal size threshold.
MinSnakePointNum - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Minimum number of points acceptable for snakes.
minStructureSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Minimal size of structure regions to be considered.
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
 
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
minW - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Estimated width of linear structures in vesselness enhancement filtering.
minWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Expected width of thin vessels.
mitoboIcon - Variable in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon
The icon by itself.
MixtureDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A distribution represented by a mixture of distributions
MixtureDistribution(ProbabilityDensityFunction[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
MixtureDistribution(ProbabilityDensityFunction[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
Constructor
mmID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
motion-model-ID
mode - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Detection mode.
mode - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Converter mode/algorithm
Mode() - Constructor for enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.Mode
 
mode - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Mode of application.
mode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Mode for detecting vessels.
mode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Scenario for detecting vessels.
mode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Scenario for detecting vessels, i.e. relation of foreground to background.
mode - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Mode for dimension reduction, i.e., how to determine the sub-space dimensionality.
mode - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
Mode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack.Mode
 
model - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
modelFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
modelTransition - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
modelTransition - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
modeSelection - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
modeSelection - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
modeSelectLabelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Button to select label image mode.
modeSelectMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Button to select binary mask mode.
modeSelectRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Button to select region set mode.
modeSelectShape - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Button to select shape mode.
modeSelectThreshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Button to select image thresholding mode.
modificationMode - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
moleculeChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
moleculeChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
moleculeImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
molecules - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
morphFeatureOp - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Operator to analyze morphology of cells.
morphGradient(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
morphMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Mask size to be used in morphological pre-/postprocessing.
MorphologyAnalyzer2D - Class in de.unihalle.informatik.MiToBo.features
Operator to extract shape and region features for given regions.
MorphologyAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
MorphologyAnalyzer2D(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
constructor
MorphologyAnalyzer2D(MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
MorphologyAnalyzer2D.FeatureNames - Enum in de.unihalle.informatik.MiToBo.features
Set of region features calculated from segmented cell regions.
MorphologyAnalyzer2DInProData - Class in de.unihalle.informatik.MiToBo.features
Data type for protrusion/indentation analysis of region contours.
MorphologyAnalyzer2DInProData(MTBContour2D, int) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Default constructor.
MorphologyAnalyzer2DInProData.InflectionPoint - Class in de.unihalle.informatik.MiToBo.features
Class to represent inflection points.
MorphologyAnalyzer2DInProData.InProContourSegment - Class in de.unihalle.informatik.MiToBo.features
Class to represent concave/convex segments along a contour.
MorphologyAnalyzer2DInProData.SegmentType - Enum in de.unihalle.informatik.MiToBo.features
Type of segment to distinguish between indentation and protrusions.
MorphologyAnalyzer2DInProHelper - Class in de.unihalle.informatik.MiToBo.features
Helper functions for analyzing protrusions and indentations along a contour.
MorphologyAnalyzer2DInProHelper(int, int, double, MTBImage, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Default constructor.
MorphologyAnalyzer3D - Class in de.unihalle.informatik.MiToBo.features
 
MorphologyAnalyzer3D() - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
MorphologyAnalyzer3D(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
MorphologyAnalyzer3D(MTBRegion3DSet, MTBSurface3DSet) - Constructor for class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
morphOp - Variable in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
 
motionFraction - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
motionFraction - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Minimum fraction of points which should have stooped to move until the snake optimization stops.
motionFraction - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Motion fraction factor.
MotionModelID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A target-ID class that additionally hold a "motion model"-ID.
MotionModelID(short, byte) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
Constructor.
MotionModelID(MTBXMLMotionModelIDType) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
Constructor with the corresponding XML-Type.
mouseClicked(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
 
mouseClicked(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
 
mouseDragged(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
 
mouseEntered(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
 
mouseEntered(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
 
mouseExited(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
 
mouseExited(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
 
mouseMoved(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
 
mousePressed(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
 
mousePressed(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
 
mouseReleased(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.ImagePlusInteractionFrame
 
mouseReleased(MouseEvent) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
 
MPH_EXTENSION - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Default extension of MiToBo processing history file.
MPMFFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness
Multiscale Production of the Matched Filter (MPMF) implementation.
MPMFFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Default constructor.
MPMFFilter2D.ResponseDifference - Class in de.unihalle.informatik.MiToBo.filters.vesselness
Function to find roots during middle scale calculation.
MPMFFilter2D.VesselMode - Enum in de.unihalle.informatik.MiToBo.filters.vesselness
Detection scenario mode.
mPolygon - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapePolygon
Region object representing the shape of the marker.
mRegion - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeRegion
Region object representing the shape of the marker.
mserCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Count of detected MSERs.
MTBActiveContourEnergy - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Common interface for active contour energies.
MTBActiveContourEnergy_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.energies
Active contour energy implementing Chan-Vese region fitting for gray-scale and vector-valued, i.e. multi-channel, images.
MTBActiveContourEnergy_CVRegionFit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Default constructor.
MTBActiveContourEnergy_CVRegionFit(MTBImage, double[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Default constructor with arguments.
MTBActiveContourEnergy_MeanSep - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.energies
Active contour energy based on region mean separation.
MTBActiveContourEnergy_MeanSep() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Default constructor.
MTBActiveContourEnergy_MeanSep(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Default constructor with parameter.
MTBActiveContourEnergyComputable - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Common interface for active contour energies used in non-PDE contexts.
MTBActiveContourEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Common interface for active contour energies used in PDE contexts.
MTBActiveContourException - Exception in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
MiToBo exception thrown in context of segmentation with active contours.
MTBActiveContourException(MTBActiveContourException.ExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException
Default constructor.
MTBActiveContourException.ExceptionType - Enum in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
Possible exception types.
MTBAwtPoint2DDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Data I/O class for Point2D.Double.
MTBAwtPoint2DDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
 
MTBAwtPoint2DDataIOSwing.PointConfigPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Panel to display and read 2D points.
MTBBatchInputImageDataIterator(String, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
Default constructor.
MTBBorder2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Datatype to represent borders of components.
MTBBorder2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Standard constructor.
MTBBorder2D(Vector<Point2D.Double>, MTBBorder2D.BorderConnectivity) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Constructor to create a 2D border object from a 2D point vector.
MTBBorder2D.BorderConnectivity - Enum in de.unihalle.informatik.MiToBo.core.datatypes
Kind of neighborhood to be applied to border pixels.
MTBBorder2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
A set of 2D borders.
MTBBorder2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Standard constructor.
MTBBorder2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Construct an empty set of borders with given extent of domain.
MTBBorder2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class to visualize and handle a MTBBorder2DSet in the ImageJ ROI-Manager.
MTBBorder2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Constructor of super class.
MTBBorder2DSetROI(MTBBorder2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Constructor to create a new Roi-Manager-Object, based on a MTBBorder2DSet.
MTBChanVeseEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
A class to implement the Chan-Vese energy for nonPDE level sets.
MTBChanVeseEnergyNonPDE(double, double, double[], double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
Construct an energy object realizing the Chan-Vese energy.
MTBChanVeseEnergyNonPDE(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
Construct an energy object realizing the Chan-Vese energy.
MTBChanVeseEnergyNonPDE(MTBImage, MTBLevelsetMembership, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
Construct an energy object realizing the Chan-Vese energy.
MTBChanVeseEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
Construct an energy object for the level set function realizing the Chan-Vese energy.
MTBChooseOpNameFrame - Class in de.unihalle.informatik.MiToBo.core.gui
Main window for selecting MiToBo annotated operators for running.
MTBChooseOpNameFrame() - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
Constructor.
MTBConstants - Class in de.unihalle.informatik.MiToBo.core.datatypes.defines
Constants globally defined for MiToBo.
MTBConstants() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.defines.MTBConstants
 
MTBContour2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to create 2D contour objects with a vector of points, belonging to the contour.
MTBContour2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Standard constructor.
MTBContour2D(Vector<Point2D.Double>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Constructor to create a 2D contour object from a 2D point vector.
MTBContour2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
A set of 2D contours living in a common domain which is a rectangular subset of R x R.
MTBContour2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Standard constructor.
MTBContour2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Construct an empty set of contours with given extent of domain.
MTBContour2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class to visualize and handle a MTBContour2DSet in the ImageJ ROI-Manager.
MTBContour2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Constructor of super class.
MTBContour2DSetROI(MTBContour2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Constructor to create a new Roi-Manager-Object, based on a MTBContour2DSet.
MTBCVFittingEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
A class to implement the fitting term of the Chan-Vese energy for level sets using a non PDE approach to optimization.
MTBCVFittingEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Construct an energy object for the level set function phi realizing the fitting term of the Chan-Vese energy.
MTBCVFittingEnergyNonPDE(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Construct an energy object realizing the fitting term of the Chan-Vese energy.
MTBCVFittingEnergyNonPDE(double, double, double[]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Construct an energy object realizing the fitting term of the Chan-Vese energy.
MTBCVFittingEnergyNonPDE(MTBImage, MTBLevelsetMembership, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Construct an energy object with the initial level set function phi realizing the fitting term of the Chan-Vese energy to segment img.
MTBDataExportableToImageJROI - Interface in de.unihalle.informatik.MiToBo.core.datatypes.interfaces
Interface for MiToBo data types which can be exported to ImageJ ROIs.
MTBDataIOFile - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
DataIO provider (for commandline-OpRunner) for classes that can only be read from and written to file.
MTBDataIOFile() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
 
MTBDataIOFile.MTBDataIOFileButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
 
MTBDataIOFileButton(Class<?>, Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
MTBDataIOFileInPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Default constructor.
MTBDataIOFileOutPanel(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
Default constructor.
MTBDataIOFileSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Data I/O provider for GUI-OpRunner supporting MiToBo container classes Provides data I/O for the following classes:
MTBRegion2DSetBag
MTBRegion2DSet
MTBRegion3DSet
MTBPolygon2DSet
MTBContour2DSet
MTBBorder2DSet
MTBLineSegment2DSet
Note that some of the classes allow for interaction with the ROI manager of ImageJ, i.e. the class MTBPolygon2DSet.
MTBDataIOFileSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
MTBDataIOFileSwing.InputMode - Enum in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Input mode for data.
MTBDataIOFileSwing.MTBDataIOFileInPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Panel for handling GUI I/O of MiToBo container classes.
MTBDataIOFileSwing.MTBDataIOFileOutPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Panel for displaying and saving MiToBo container classes.
MTBDataIOFileSwing.OutputMode - Enum in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Output mode for data.
MTBDataIOFileXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
DataIO provider for xmlbeans for classes that can only be read from and written to file.
MTBDataIOFileXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
 
MTBDatatypeException - Exception in de.unihalle.informatik.MiToBo.core.exceptions
MiToBo exception type related to problems with data types in general.
MTBDatatypeException(MTBDatatypeException.DatatypeExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException
Default constructor.
MTBDatatypeException.DatatypeExceptionType - Enum in de.unihalle.informatik.MiToBo.core.exceptions
Possible exception types.
MTBDoubleData - Class in de.unihalle.informatik.MiToBo.core.datatypes.wrapper
A double to be used as input or output for MTB operators.
MTBDoubleData(Double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
Construct an empty double data object from the given double value.
MTBEnergySumNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
 
MTBEnergySumNonPDE(String, Vector<MTBGenericEnergyNonPDE>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
Construct an energy object for a level set function realizing the sum of energies in the vector energies.
MTBEnergySumNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
Construct an energy object for a level set function realizing the sum of energies.
MTBEnvironmentConfig - Class in de.unihalle.informatik.MiToBo.core.helpers
This class extends the super class with routines to access ImageJ properties.
MTBEnvironmentConfig() - Constructor for class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
 
MTBException - Exception in de.unihalle.informatik.MiToBo.core.exceptions
MiToBo specific exception type.
MTBException() - Constructor for exception de.unihalle.informatik.MiToBo.core.exceptions.MTBException
 
MTBGammaFixed - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Class for gamma adaptation with a fixed decreasing factor for all gamma values.
MTBGammaFixed() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Default constructor.
MTBGammaFixed(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Constructor with fixed decreasing factor for adaptation.
MTBGammaNone - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Class which is not changing the gamma values.
MTBGammaNone() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
Standard constructor.
MTBGammaPtWiseExtEner - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Class for gamma adaptation depending on the external energy values for each snake control point.
MTBGammaPtWiseExtEner() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
Standardconstructor
MTBGammaUpdate - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Class for adaptive step size calculation of the snake step size gamma.
MTBGammaUpdate() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
 
MTBGenericEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
The base class for energies intended for a nonPDE level set approach.
MTBGenericEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
 
MTBGraph - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class implements an (un-) directed MTBGraph.
MTBGraph() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Standard constructor.
MTBGraph(boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Constructor to create an empty undirected or directed MTBGraph.
MTBGraph(Vector<MTBGraphNode<?>>, Vector<MTBGraphEdge>, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Constructor to create an undirected or directed MTBGraph with the given nodes and edges.
MTBGraphEdge - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class implements MTBGraphEdges for the MTBGraph.
MTBGraphEdge(MTBGraphNode<?>, MTBGraphNode<?>, Vector<?>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Constructor to create a new MTBGraphEdge.
MTBGraphEdge(MTBGraphNode<?>, MTBGraphNode<?>, Vector<?>, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Constructor to create a new MTBGraphEdge.
MTBGraphNode<T> - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class implements MTBGraphNodes for the MTBGraph.
MTBGraphNode(T) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Constructor to create a new MTBGraphNode object.
MTBGrappaFrame - Class in de.unihalle.informatik.MiToBo.core.grappa
Main frame of Grappa graphical editor for MiToBo.
MTBGrappaFrame(Collection<ALDOperatorLocation>, Collection<ALDOperatorLocation>) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaFrame
Default constructor
MTBGrappaWorkbench - Class in de.unihalle.informatik.MiToBo.core.grappa
Main frame of Grappa in MiToBo context.
MTBGrappaWorkbench(MTBGrappaFrame) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
Default constructor
MTBGrappaWorkbenchTab - Class in de.unihalle.informatik.MiToBo.core.grappa
Grappa workflow graph.
MTBGrappaWorkbenchTab(MTBGrappaWorkbench, ALDGrappaWorkbenchGraph) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
Default constructor
MTBGrappaWorkbenchTab(ALDGrappaWorkbench, mxGraph, ALDWorkflow) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
Constructor to setup tab from given (reloaded) workflow.
MTBGroundtruthEvaluationData - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation
Data object containing evaluation data from groundtruth comparison.
MTBGroundtruthEvaluationData(HashMap<String, HashMap<Integer, Double>>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.MTBGroundtruthEvaluationData
Default constructor.
MTBHistoryImageBox(MTBImage, ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Default constructor for an image pair.
MTBHistoryImageBox(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Default constructor for an MTBImage without associated ImagePlus.
MTBHistoryImageBox(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Default constructor for an ImagePlus without linked MTBImage.
MTBIcon - Class in de.unihalle.informatik.MiToBo.core.helpers
Singleton class to provide access to MiToBo icon in graphical environments.
MTBIcon() - Constructor for class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon
Default constructor.
MTBImage - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Abstract wrapper class for easy access to hyperstacks.
MTBImage(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Constructor.
MTBImage() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Constructor for initializing an empty image (dimension sizes = -1).
MTBImage.FactoryMethod - Enum in de.unihalle.informatik.MiToBo.core.datatypes.images
methods to create new image from an existing one. used in MTBImageFactory
MTBImage.MTBImageFactory - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
A class for creating MTBImages which implements the MTBOperator.
MTBImage.MTBImageType - Enum in de.unihalle.informatik.MiToBo.core.datatypes.images
MiToBo image types
MTBImageArithmetics - Class in de.unihalle.informatik.MiToBo.math.images
This class that provides convenience functions for the ImageArithmetics class.
MTBImageArithmetics() - Constructor for class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Constructor.
MTBImageArithmetics(MTBOperator) - Constructor for class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Constructor with calling operator.
MTBImageByte - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Wrapper class for easy access to Byte (hyper)stacks.
MTBImageByte(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Constructor
MTBImageByte(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Constructor
MTBImageByte(byte[][], int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Constructor
MTBImageConverter - Class in de.unihalle.informatik.MiToBo.core.dataconverter
Convert a MTBImage to any other image and any image type to a MTBImage.
MTBImageConverter() - Constructor for class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
MTBImageDataIO - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Implementation of ALDDataIOCmdline interface for MitoBo images.
MTBImageDataIO() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
 
MTBImageDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Implementation of ALDDataIOSwing interface for MiToBo images.
MTBImageDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Default constructor.
MTBImageDataIOSwing.ImageShowButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Button to display an image on demand.
MTBImageDataIOSwing.ImageShowPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Panel containing the button to display an image on demand.
MTBImageDataIOSwing.JComboBoxImage - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Class for handling images opened in GUI.
MTBImageDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Implementation of ALDDataIOCmdline interface for MitoBo images via xmlbeans provider.
MTBImageDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
 
MTBImageDouble - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Class for easy access to Double (hyper)stacks.
MTBImageDouble(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Constructor
MTBImageException - Exception in de.unihalle.informatik.MiToBo.core.exceptions
MiToBo exception type related to problems with its image data types.
MTBImageException(String) - Constructor for exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException
Default constructor.
MTBImageFactory() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
MTBImageFactory(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Duplicate constructor
MTBImageFactory(MTBImage, MTBImage.MTBImageType, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Convert constructor
MTBImageFactory(MTBImage, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Get slice constructor
MTBImageFactory(MTBImage, int, int, int, int, int, int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Create a new image from the specified image part
MTBImageFloat - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Wrapper class for easy access to Float (hyper)stacks.
MTBImageFloat(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Constructor
MTBImageFloat(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Constructor
MTBImageHistogram - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class for generating intensity histograms of objects from class MTBImage.
MTBImageHistogram() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
Default constructor.
MTBImageHistogram(MTBImage, int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a histogram for the given input image
with specification of binning and value range
all MTBImage types except RGB type are supported
MTBImageHistogram(MTBImage, MTBImage, int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a histogram for the given input image only for the pixels specified by a binary mask
all MTBImage types except RGB type are supported
with specification of binning and value range
MTBImageHistogram(MTBImage, MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a new MTBHistogram object from the given MTBImage
the histogram ranges from the smallest image value to the largest image value
MTBImageHistogram(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a new MTBHistogram object from the given MTBImage
the histogram ranges from the smallest image value to the largest image value
MTBImageHistogram(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a new MTBHistogram object from the given MTBImage
number of bins is 256 and the histogram ranges from the smallest
image value to the largest image value
MTBImageHistogram(double[], int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
Construct new histogram from array of values.
MTBImageHistogram(double[], double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a MTBImageHistogram from histogram data contained in an array
MTBImageInt - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Class for easy access to Int (hyper)stacks.
MTBImageInt(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Constructor
MTBImageIteratorImageDataPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Default constructor.
MTBImageManipulator - Interface in de.unihalle.informatik.MiToBo.core.datatypes.images
 
mtbImageRef - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
MTBImage object in container.
MTBImageRGB - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Class for easy access to RGB (hyper)stacks.
MTBImageRGB(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Constructor
MTBImageRGB(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Constructor
MTBImageSet - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
A set of MTBImages stored in a vector.
MTBImageSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
MTBImageSet(MTBImage[]) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
MTBImageShort - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Wrapper class for easy access to Short (hyper)stacks.
MTBImageShort(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Constructor
MTBImageShort(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Constructor
MTBImageTileAdapter - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Adapter class to support tile-wise processing of images.
MTBImageTileAdapter(MTBImage, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Default constructor.
MTBImageTileAdapter(MTBImage, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Default constructor.
MTBImageTileAdapter.TileIterator - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Iterates from top-left to bottom-right over the tiles of an image.
MTBImageType() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageType
 
MTBImageWindow - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Class for windowing a MTBImage.
MTBImageWindow(int, int, int, int, int, MTBImageManipulator, MTBImageWindow.BoundaryPadding) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Create a new window on a given source MTBImageManipulator (i.e.
MTBImageWindow.BoundaryPadding - Enum in de.unihalle.informatik.MiToBo.core.datatypes.images
Padding of image: Method of how to obtain pixel values outside the image domain
mtbImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
MTB input image to work on.
MTBIntegerData - Class in de.unihalle.informatik.MiToBo.core.datatypes.wrapper
an Integer wrapper class to be used as input or output for MTB operators
MTBIntegerData(Integer) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
 
MTBIteratorImageData - Class in de.unihalle.informatik.MiToBo.core.batch.provider.input.swing
Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBIteratorImageData() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
 
MTBIteratorImageData.MTBBatchInputImageDataIterator - Class in de.unihalle.informatik.MiToBo.core.batch.provider.input.swing
Polygon set iterator class.
MTBIteratorImageData.MTBImageIteratorImageDataPanel - Class in de.unihalle.informatik.MiToBo.core.batch.provider.input.swing
GUI element class for image batch iterator.
MTBJFreeChartDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Implementation of ALDDataIOSwing interface for JFreeChart objects.
MTBJFreeChartDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
Default constructor.
MTBJFreeChartDataIOSwing.ChartShowButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Button to display a chart on demand.
MTBJFreeChartDataIOSwing.ChartShowPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Panel containing the button to display an image on demand.
MTBLengthEnergyFW2D2PNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 2D images and a two phase level set function.
MTBLengthEnergyFW2D2PNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE
Constructor
MTBLengthEnergyFW2D2PNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE
Constructor
MTBLengthEnergyFW2DMPNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 2D images and a multi phase leve lset function.
MTBLengthEnergyFW2DMPNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE
constructor
MTBLengthEnergyFW2DMPNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE
constructor
MTBLengthEnergyFW2DNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 2D images.
MTBLengthEnergyFW2DNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
constructor
MTBLengthEnergyFW2DNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
constructor
MTBLengthEnergyFW3D2PNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 3D images and a two phase levelset function.
MTBLengthEnergyFW3D2PNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
constructor
MTBLengthEnergyFW3D2PNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
constructor
MTBLengthEnergyFW3DMPNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 3D images and a multi phase level set function.
MTBLengthEnergyFW3DMPNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DMPNonPDE
constructor
MTBLengthEnergyFW3DMPNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DMPNonPDE
constructor
MTBLengthEnergyFW3DNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 3D images.
MTBLengthEnergyFW3DNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
constructor
MTBLengthEnergyFW3DNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
constructor
MTBLengthEnergyFWNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Base class of length energies using forward differences.
MTBLengthEnergyFWNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
constructor
MTBLengthEnergyFWNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
constructor
MTBLengthEnergyKB2D2P4NNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using length approximation due to Kolmogorov/Boykov for tw0 phases and 4 neighborhood.
MTBLengthEnergyKB2D2P4NNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2P4NNonPDE
constructor
MTBLengthEnergyKB2D2P4NNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2P4NNonPDE
constructor
MTBLengthEnergyKB2D2PNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using length approximation due to Kolmogorov/Boykov for two phases.
MTBLengthEnergyKB2D2PNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
constructor
MTBLengthEnergyKB2D2PNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
constructor
MTBLengthEnergyKBNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Base class of length energies using forward differences.
MTBLengthEnergyKBNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
constructor
MTBLengthEnergyKBNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
constructor
MTBLengthEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
An class for energies for a nonPDF level set approach based on different length energies of the phases boundaries.
MTBLengthEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
Constructor
MTBLengthEnergyNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
Constructor
MTBLevelEnergyDerivable_Area - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
Level set energy minimizing area enclosed by the zero level.
MTBLevelEnergyDerivable_Area() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
Default constructor.
MTBLevelEnergyDerivable_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
Implementation of Chan-Vese energy for level set functions.
MTBLevelEnergyDerivable_CVRegionFit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
Default constructor.
MTBLevelEnergyDerivable_CVRegionFit(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
Constructor with given image.
MTBLevelEnergyDerivable_Length - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
Energy minimizing the length of a level set's isocontour.
MTBLevelEnergyDerivable_Length() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
Default constructor.
MTBLevelsetEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
Interface specifying level set energies to be used with techniques of the calculus of variations.
MTBLevelsetException - Exception in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
MiToBo exception thrown inside snake segmentation framework.
MTBLevelsetException(MTBActiveContourException.ExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBLevelsetException
Default constructor.
MTBLevelsetFunctionDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Level set function supporting optimization based on variational calculus.
MTBLevelsetFunctionDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
 
MTBLevelsetFunctionPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
Class representing a 3-dimensional level set function.
MTBLevelsetFunctionPDE(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Create a new levelset function.
MTBLevelsetFunctionPDE(int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Constructor to init empty function with safety border.
MTBLevelsetFunctionPDE(int, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
create a new levelsetfunction, setting a default handle for derivations on borders
MTBLevelsetFunctionPDE(boolean, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
create a new levelsetfunction, setting a default handle for derivations on borders
MTBLevelsetFunctionPDE(boolean, int, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
create a new levelsetfunction, setting a default handle for derivations on borders
MTBLevelsetFunctionPDE(int, int, int, MTBSegmentationInterface, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Constructor to build a level set function from a segmentation object.
MTBLevelsetFunctionPDE(int, int, int, MTBSegmentationInterface, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Constructor to build a level set function from a segmentation object.
MTBLevelsetFunctionPDE.SortedList<EType> - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
A genric class representing a sorted list
MTBLevelsetFunctionPDE.SortedListElement<EType> - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
internal representation of elements
MTBLevelsetMembership - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
A class to hold a level set function where only the membership to a phase is required and represented.
MTBLevelsetMembership(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructs a two phase level set function which is initialized with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
MTBLevelsetMembership(int, int, int, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructs a two phase level set function which is initialiazed with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
MTBLevelsetMembership(int, int, int, MTBImage, int, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Creates a two phase level set function from an image via thresholding.
MTBLevelsetMembership(MTBLevelsetMembership) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Creates a copy of phi.
MTBLevelsetMembership(int, int, Vector<MTBRegion2D>, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructor for given size which is initialized from a list of 2D regions for a 2D level set function.
MTBLevelsetMembership(int, int, MTBRegion2DSet, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructor for given size which is initialized from a MTBRegion2DSet for a 2D level set function.
MTBLevelsetMembership(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructor for a two phase level set function from a label image.
MTBLevelsetMembership(MTBImage, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructor for a level set function from a label image.
MTBLineSegment2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Enhanced 2D line segments.
MTBLineSegment2D(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Constructor.
MTBLineSegment2D(MTBLineSegment2D) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Copy constructor.
MTBLineSegment2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
A set of 2D line segments.
MTBLineSegment2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Standard constructor.
MTBMeijeringFittingEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
class that implements the energy functional introduced in O.
MTBMeijeringFittingEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
constructor
MTBMeijeringFittingEnergyNonPDE(MTBImage, MTBLevelsetMembership) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
constructor
MTBNeurite2D - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites
Class for neurite objects.
MTBNeurite2D(MTBNeuriteSkelGraph, Vector<Vector<Point2D.Double>>, Vector<Vector<Line2D.Double>>, MTBRegion2D, int, int[], Vector<Vector<Double>>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Constructor to generate a new neurite object.
MTBNeurite2DProfile - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites
Container class for storing neurite profile data and associated additional information for a single neurite region.
MTBNeurite2DProfile() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
MTBNeurite2DProfile(MTBNeurite2D, double[], Vector<Vector<Point2D.Double>>, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Constructor to create a new MTBNeuriteProfile object from the given MTBRegion2D.
MTBNeurite2DProfileSet - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites
A set of neurite profiles organized as linked list.
MTBNeurite2DProfileSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Constructor to create a new set of neurite profiles.
MTBNeurite2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites
Class to represent a set of MTBNeurite2D objects.
MTBNeurite2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Constructor to create a new set of neurites.
MTBNeuriteSkelGraph - Class in de.unihalle.informatik.MiToBo.core.datatypes
The class implements a neurite skeleton graph (NSG), based on the skeleton of a neurite region.
MTBNeuriteSkelGraph() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Standard constructor.
MTBNeuriteSkelGraph(int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Constructor that creates an empty directed MTBNeuriteSkelGraph with defined maximum spine length.
MTBNeuriteSkelGraph(Vector<MTBNeuriteSkelGraphNode<Point2D.Double>>, Vector<MTBGraphEdge>, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Constructor to create an directed MTBNeuriteSkelGraph with the given MTBSkeletonGraphNodes and MTBGraphEdges.
MTBNeuriteSkelGraphException - Exception in de.unihalle.informatik.MiToBo.core.datatypes
Exception handling for MTBSkeletonGraph.
MTBNeuriteSkelGraphException() - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
 
MTBNeuriteSkelGraphException(String) - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
 
MTBNeuriteSkelGraphNode<T> - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class implements a MTBSkeletonGraphNode, which is a type of the MTBGraphNode.
MTBNeuriteSkelGraphNode(T, MTBNeuriteSkelGraphNode.MTBSkeletonNodeType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
Constructor to create a new MTBGraphNode object.
MTBNeuriteSkelGraphNode.MTBSkeletonNodeType - Enum in de.unihalle.informatik.MiToBo.core.datatypes
Type of the MTBGraphNode
MTBOperator - Class in de.unihalle.informatik.MiToBo.core.operator
Abstract super class for all MiToBo operators.
MTBOperator() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperator
Default constructor.
MTBOperatorCollection<T extends de.unihalle.informatik.Alida.operator.ALDOperatorCollectionElement> - Class in de.unihalle.informatik.MiToBo.core.operator
Class to manage a set of operators.
MTBOperatorCollection(Class<T>) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorCollection
Default constructor.
MTBOperatorConfigTools - Class in de.unihalle.informatik.MiToBo.core.operator
Helper class for global `MiToBo` operator configuration.
MTBOperatorConfigTools() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Hidden constructor, never used outside of the class.
MTBOperatorConfigurationFrame - Class in de.unihalle.informatik.MiToBo.core.gui
Frame to configure an operator's parameters.
MTBOperatorConfigurationFrame(ALDOperator, ALDOpParameterUpdateEventListener) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
Constructs a control frame for an operator object.
MTBOperatorControlFrame - Class in de.unihalle.informatik.MiToBo.core.gui
This frame is used to display and modify the input parameters of an ALDOperator.
MTBOperatorControlFrame(ALDOperator, ALDOperatorGUIExecutionProxy, ALDOpParameterUpdateEventListener) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
Construct a JFrame to intantiate and configure an operator opName and use executeOperator to execute this operator if requested by the user.
MTBOperatorControllable - Class in de.unihalle.informatik.MiToBo.core.operator
Operator class with inherent event handling for execution control.
MTBOperatorControllable() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorControllable
Default constructor.
MTBOperatorDocumentationFrame - Class in de.unihalle.informatik.MiToBo.core.gui
Frame to show documentation for operators and tools.
MTBOperatorDocumentationFrame(String, String, String) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame
Constructor with title parameter.
MTBOperatorGUIExecutionProxy - Class in de.unihalle.informatik.MiToBo.core.gui
Manager for executing single MiToBo operator and workflow objects via GUI.
MTBOperatorGUIExecutionProxy(ALDOperatorLocation) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorGUIExecutionProxy
Default constructor.
MTBOperatorParameterPanel - Class in de.unihalle.informatik.MiToBo.core.gui
Implementation of panels for MiToBo operator parameters.
MTBOperatorParameterPanel(ALDOperator, Parameter.ExpertMode, boolean, ALDSwingValueChangeListener) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorParameterPanel
Default constructor.
MTBPlotHistogram - Class in de.unihalle.informatik.MiToBo.visualization.drawing
A class to visualize 2D polygons.
MTBPlotHistogram() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
Default constructor.
MTBPlotHistogram.Histogram - Class in de.unihalle.informatik.MiToBo.visualization.drawing
 
MTBPlotHistogram.HistogramFrame - Class in de.unihalle.informatik.MiToBo.visualization.drawing
 
MTBPoint2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
 
MTBPoint2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
Standard constructor.
MTBPoint2DSet(List<Point2D>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
Constructs a MTBPoint2DSet from a list of points.
MTBPoint3D - Class in de.unihalle.informatik.MiToBo.core.datatypes
The Point3D class defines a point representing a location in (x, y, z) coordinate space.
MTBPoint3D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Standardconstructor to create an new empty 3D point object.
MTBPoint3D(double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Construct a new 3D point with the given coordinates.
MTBPoint3D(MTBPoint3D) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Construct a new 3D point from the given 3D point.
MTBPoint3D(MTBXMLPoint3DType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Construct a new MTBPoint3D from a 3D-point object constructed from xml-representation.
MTBPolygon2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Polygon datatype with double precision.
MTBPolygon2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Default constructor.
MTBPolygon2D(double[], double[], boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Construct polygon from coordinate arrays.
MTBPolygon2D(Vector<Point2D.Double>, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Construct from point list.
MTBPolygon2D.IntersectionPoint2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Helper class for function simplify().
MTBPolygon2D_GeoPolygonsWrapper - Class in de.unihalle.informatik.MiToBo.core.datatypes
Wrapper class for C2DPolygon functions from GeoPolygons library.
MTBPolygon2D_GeoPolygonsWrapper() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
 
MTBPolygon2DException - Exception in de.unihalle.informatik.MiToBo.core.datatypes
Exception handling for Polygon2D object.
MTBPolygon2DException() - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException
Standardconstructor.
MTBPolygon2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException
Constructor for new MTBPolygon2DException with specific message output.
MTBPolygon2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
Data type to represent a set of MTBPolygon2D.
MTBPolygon2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Standard constructor
MTBPolygon2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Construct an empty set of polygons with given extent of domain.
MTBPolygon2DSet(Vector<MTBPolygon2D>, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Construct polygon set from given vector.
MTBPolygon2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class to visualize and handle a MTBPolygon2DSet in the ImageJ ROI-Manager.
MTBPolygon2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Constructor of super class.
MTBPolygon2DSetROI(MTBPolygon2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Constructor to create a new Roi-Manager-Object, based on a MTBPolygon2DSet.
MTBPortHashAccess - Class in de.unihalle.informatik.MiToBo.core.operator
Interface to the port database of the Alida / MiToBo operator history.
MTBPortHashAccess() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Constructor without function.
MTBPortHashAccess.MTBHistoryImageBox - Class in de.unihalle.informatik.MiToBo.core.operator
Database object boxing ImagePlus and MTBImage.
MTBQuadraticCurve2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
General quadratic curve.
MTBQuadraticCurve2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Default constructor.
MTBQuadraticCurve2D(double[], boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Constructor.
MTBQuadraticCurve2D.CurveType - Enum in de.unihalle.informatik.MiToBo.core.datatypes
Possible types of curve.
MTBQuadraticCurve2D.DistanceTargetFunction - Class in de.unihalle.informatik.MiToBo.core.datatypes
Distance function for a point's distance to an ellipse.
MTBRegion2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to implement a 2D region object. the region is stored in a vector of 2D double points with its x- and y-coordinate.
MTBRegion2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Construct a new empty MTBRegion2D object.
MTBRegion2D(Vector<Point2D.Double>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Construct a new MTBRegion2D from the given points.
MTBRegion2D(MTBXMLRegion2DType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Construct a new MTBRegion2D from a region object that was constructed from a xml-representation.
MTBRegion2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
A set of 2D regions living in a common domain which is a rectangular subset of R x R.
MTBRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Standard constructor.
MTBRegion2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct an empty set of regions with given extent of domain
MTBRegion2DSet(Vector<MTBRegion2D>, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct an empty set of regions with given extent of domain
MTBRegion2DSet(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct a set of regions from a xml-file that was written by the write method of this class.
MTBRegion2DSet(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct a set of regions from a label image.
MTBRegion2DSet(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct a set of regions from a label image.
MTBRegion2DSet(MTBXMLRegion2DSetType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct a new MTBRegion2DSet from a region set object that was constructed from a xml-representation.
MTBRegion2DSet.RegionSelector - Class in de.unihalle.informatik.MiToBo.core.datatypes
 
MTBRegion2DSetBag - Class in de.unihalle.informatik.MiToBo.core.datatypes
A datatype to store multiple MTBRegion2D sets
MTBRegion2DSetBag() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Constructor to create an empty bag of region sets
MTBRegion2DSetBag(int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Constructor to create an empty bag of region sets with the given capacity
MTBRegion2DSetBag(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Construct a bag of region sets from a xml-file that was written by the write method of this class.
MTBRegion2DSetBag(MTBXMLRegion2DSetBagType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Construct a bag of region sets from a xml-object created by the toXMLType method of this class.
MTBRegion2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class to visualize and handle a MTBRegion2DSet in the ImageJ ROI-Manager.
MTBRegion2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Constructor of super class.
MTBRegion2DSetROI(MTBRegion2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Constructor to create a new Roi-Manager-Object, based on a MTBRegion2DSet.
MTBRegion3D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to create a 3D region object.
MTBRegion3D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Construct a new MTBRegion3D object.
MTBRegion3D(Vector<MTBPoint3D>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Construct a new MTBRegion3D object from the given points.
MTBRegion3D(Vector<MTBPoint3D>, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Construct a new MTBRegion3D object from the given points and set its id
MTBRegion3D(MTBXMLRegion3DType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Construct a new MTBRegion3D from a 3D-region in xml-representation.
MTBRegion3DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
A set of 3D regions living in a common domain which is a rectangular subset of R x R.
MTBRegion3DSet(double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct an empty set of regions with given extent of domain
MTBRegion3DSet(int, double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct an empty set (with memory allocated for N elements) of regions with given extent of domain
MTBRegion3DSet(Vector<MTBRegion3D>, double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct an empty set of regions with given extent of domain
MTBRegion3DSet(MTBXMLRegion3DSetType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct set of 3D-regions from an xml-representation
MTBRegion3DSet(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct a set of 3D-regions from a xml-file that was written by the write method of this class.
MTBRegionInterface - Interface in de.unihalle.informatik.MiToBo.core.datatypes
Interface for regions in MiToBo to enable unified handling.
MTBRegionSetInterface - Interface in de.unihalle.informatik.MiToBo.core.datatypes
Interface for region sets in MiToBo to enable unified handling.
MTBRootTree - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes
Tree datatype to represent plant roots.
MTBRootTree() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree
Default constructor.
MTBRootTree(MTBRootTreeNodeData) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree
Constructor with given data.
MTBRootTree(MTBTreeNode) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree
Constructor with given root node.
MTBRootTree(MTBPoint2DSet) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTree
Constructor with given set of 2D points.
MTBRootTreeNodeData - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes
Node data object for MTBRootTree.
MTBRootTreeNodeData() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Default constructor, all members are initialized with zero.
MTBRootTreeNodeData(double, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Constructor with positional data.
MTBSegmentation2D - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Class for representing 2D segmentations of image data.
MTBSegmentation2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Default constructor with empty segmentation.
MTBSegmentation2D(int, int, int, int[][], boolean[][], double[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Constructor.
MTBSegmentation2D(int, int, int, byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Constructor.
MTBSegmentation3D - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Class for representing 3D segmentations of image data.
MTBSegmentation3D(int, int, int, int, int[][][], boolean[][][], double[][][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Constructor.
MTBSegmentationInterface - Interface in de.unihalle.informatik.MiToBo.segmentation.basics
Interface for representing 2D and 3D segmentations of image data.
MTBSegmentationInterface.SegmentationDimension - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Segmentation dimension datatype.
MTBSet_ActiveContourEnergy - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Common interface for sets of active contour energies.
MTBSet_ActiveContourEnergyConfigButton(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Constructor.
MTBSet_ActiveContourEnergyConfigWindow(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Default constructor.
MTBSet_ActiveContourEnergyDataIOCmdline - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Class for loading/saving sets of PDE energies for command line interfaces.
MTBSet_ActiveContourEnergyDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
Default constructor
MTBSet_ActiveContourEnergyDataIOSwing - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Class for loading/saving sets of PDE energies in GUI contexts.
MTBSet_ActiveContourEnergyDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
GUI element for configuring collections.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Collection configuration window.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Internal PDE snake energy GUI table model.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayButton - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
GUI element for showing energy collections.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Energy collection display window.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Internal GUI table model.
MTBSet_ActiveContourEnergyDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Class for loading/saving sets of PDE energies for command line interfaces.
MTBSet_ActiveContourEnergyDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
 
MTBSet_ActiveContourEnergyDisplayButton(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayButton
Constructor.
MTBSet_ActiveContourEnergyDisplayWindow(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Default constructor.
MTBSet_LevelEnergyDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Container data type for derivable level set energies.
MTBSet_LevelEnergyDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Default contructor for empty set.
MTBSet_LevelEnergyDerivable(Vector<MTBLevelsetEnergyDerivable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Constructor for a given vector of energies.
MTBSet_LevelEnergyDerivable(Vector<MTBLevelsetEnergyDerivable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Constructor with energies and weights.
MTBSet_SnakeEnergyComputable - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Container data type for snake energies in nonPDE approaches.
MTBSet_SnakeEnergyComputable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Default contructor for empty set.
MTBSet_SnakeEnergyComputable(Vector<MTBSnakeEnergyComputable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Constructor for a given vector of energies.
MTBSet_SnakeEnergyComputable(Vector<MTBSnakeEnergyComputable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Constructor with energies and weights.
MTBSet_SnakeEnergyDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Container data type for snake energies in PDE approaches.
MTBSet_SnakeEnergyDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Default contructor for empty set.
MTBSet_SnakeEnergyDerivable(Vector<MTBSnakeEnergyDerivable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Constructor for a given vector of energies.
MTBSet_SnakeEnergyDerivable(Vector<MTBSnakeEnergyDerivable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Constructor with energies and weights.
MTBSet_SnkEnergyPDEGUITableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
Default constructor.
MTBSet_SnkEnergyPDEGUITableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel
Default constructor.
MTBSetWeightedEnergy<T> - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Container data type for energies in PDE approaches.
MTBSetWeightedEnergy() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Default contructor for empty set.
MTBSetWeightedEnergy(Vector<T>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Constructor for a given vector of energies.
MTBSetWeightedEnergy(Vector<T>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Constructor with energies and weights.
MTBSizeEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
A class to implement the size energy of the Chan-Vese energy.
MTBSizeEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
Constructor for size energy with weight nu.
MTBSizeEnergyNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
Constructor for size energy with weight nu.
MTBSkeletonNodeType() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType
 
MTBSnake - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Active Contour (Snake) datatype.
MTBSnake() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Standard constructor to create a new and empty snake object.
MTBSnake(Vector<MTBSnakePoint2D>, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Constructor to create a new Snake object.
MTBSnake(Vector<MTBSnakePoint2D>, boolean, double, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Constructor to create a new Snake object.
MTBSnake.SnakeCloner - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to construct new snake object from a given one.
MTBSnakeEnergyCD_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Snake energy based on Chan-Vese region fitting.
MTBSnakeEnergyCD_CVRegionFit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Default constructor.
MTBSnakeEnergyCD_CVRegionFit(MTBImage, double[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Default constructor.
MTBSnakeEnergyCD_KassCurvature - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Curvature energy of the pioneering paper of Kass et al.
MTBSnakeEnergyCD_KassCurvature() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Default constructor.
MTBSnakeEnergyCD_KassCurvature(double, MTBSnakeEnergyCD_KassCurvature_ParamAdapt) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Constructor with dynamic parameter updater.
MTBSnakeEnergyCD_KassCurvature_ParamAdapt - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Parameter adaptation for Kass et al. curvature penalty.
MTBSnakeEnergyCD_KassCurvature_ParamAdapt() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
 
MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Fixed value parameter adaptation for Kass et al. curvature energy.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
Default constructor.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
Construct a new updater for the internal energy using a fixed value.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Dummy parameter adaptation for Kass et al. curvature energy.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
Default constructor.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
Construct a new updater.
MTBSnakeEnergyCD_KassLength - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Internal length penalty energy of the pioneering paper of Kass et al.
MTBSnakeEnergyCD_KassLength() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Default constructor.
MTBSnakeEnergyCD_KassLength(double, MTBSnakeEnergyCD_KassLength_ParamAdapt) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Constructor with dynamic parameter updater.
MTBSnakeEnergyCD_KassLength_ParamAdapt - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Parameter adaptation for Kass et al. length penalty.
MTBSnakeEnergyCD_KassLength_ParamAdapt() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
 
MTBSnakeEnergyCD_KassLength_ParamAdaptFix - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Parameter adaptation for Kass et al. length penalty energy by fixed value.
MTBSnakeEnergyCD_KassLength_ParamAdaptFix() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
Default constructor.
MTBSnakeEnergyCD_KassLength_ParamAdaptFix(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
Construct a new updater for the internal energy using a fixed value.
MTBSnakeEnergyCD_KassLength_ParamAdaptNone - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Dummy parameter adaptation for Kass et al. length penalty energy.
MTBSnakeEnergyCD_KassLength_ParamAdaptNone() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
Default constructor.
MTBSnakeEnergyCD_KassLength_ParamAdaptNone(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
Construct a new updater.
MTBSnakeEnergyCD_OverlapPenalty - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Energy to avoid overlaps of snakes in joint optimization of multiple snakes.
MTBSnakeEnergyCD_OverlapPenalty() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Default constructor.
MTBSnakeEnergyCD_OverlapPenalty(double, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Default constructor.
MTBSnakeEnergyCDIB_Distance - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Class for external energy from a distance transform (distance map / field).
MTBSnakeEnergyCDIB_Distance() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
MTBSnakeEnergyCDIB_Distance(MTBImageByte, DistanceTransform.DistanceMetric, DistanceTransform.ForegroundColor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Constructor to create a new SnakeExternalEnergyDistance object.
MTBSnakeEnergyCDIB_Gradient - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
External snake energy based on local intensity gradients.
MTBSnakeEnergyCDIB_Gradient() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Constructor to create a new SnakeExternalEnergyGradient object.
MTBSnakeEnergyCDIB_Gradient(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Constructor to create a new SnakeExternalEnergyGradient object.
MTBSnakeEnergyCDIB_GVF2D - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Class for external energy of a GVF field energy vector.
MTBSnakeEnergyCDIB_GVF2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Default constructor.
MTBSnakeEnergyCDIB_GVF2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Constructor to create a new SnakeExternalEnergyGVF2D object.
MTBSnakeEnergyCDIB_Intensity - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
External snake energy based on image intensities.
MTBSnakeEnergyCDIB_Intensity() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Default constructor.
MTBSnakeEnergyCDIB_Intensity(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Constructor to create a new SnakeExternalEnergyIntensity object.
MTBSnakeEnergyCDImageBased - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Interface class for snake energies that are purely image-based.
MTBSnakeEnergyCDImageBased() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
MTBSnakeEnergyComputable - Interface in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Super class for all energies to be used with greedy snakes in MiToBo.
MTBSnakeEnergyCoupled - Interface in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Super class for energies working simultaneously on multiple snakes.
MTBSnakeEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Super class for all energies to be used with PDE snakes in MiToBo.
MTBSnakeException - Exception in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
MiToBo exception thrown inside snake segmentation framework.
MTBSnakeException(MTBActiveContourException.ExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBSnakeException
Default constructor.
MTBSnakePoint2D - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Class to implement 2D snake points with a special structure: (snake points means control points of the snake, on which the snake energy is calculated and optimized) - every snake point has an old index (position) within the snake, if the point does not exists before, the old index is set to -1 by default - every snake point has a Point2D.Double object for point coordinates
MTBSnakePoint2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Standard constructor to create a new SnakePoint2D
MTBSnakePoint2D(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Constructor to create a new SnakePoint2D with x- and y-coordinates for the point.
MTBSnakePoint2D(Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Constructor to create a new SnakePoint2D from the specified Point2D.Double object.
MTBStringData - Class in de.unihalle.informatik.MiToBo.core.datatypes.wrapper
Class to implement string objects to be used as input or output to MTB operators.
MTBStringData(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData
Construct a new MTBStringData object from the given string.
MTBStructuringElement - Class in de.unihalle.informatik.MiToBo.core.datatypes
class representing a 2D flat (, i.e. without different gray values) structuring element
for the use with morphological operations
values are stored in a rectangular 2D array (rows: 1st dimension, columns: 2nd dimension)
whereas onValue represents set locations and 0 represents unset locations
MTBStructuringElement(int[][], int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
creates structuring element from given 2D-array
MTBStructuringElement(int[][]) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
creates structuring element from given 2D-array, center is assumed to be at the center of the array
MTBStructuringElement() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
create quadratic 3x3 structuring element
MTBSummarizerImageData - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBSummarizerImageData() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerImageData
 
MTBSummarizerRegion2DSet - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBSummarizerRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerRegion2DSet
 
MTBSummarizerSegResultParticlesMultiChannel - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBSummarizerSegResultParticlesMultiChannel() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerSegResultParticlesMultiChannel
 
MTBSummarizerTableModel - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
Implementation of ALDBatchInputIteratorSwing for MTBTableModel.
MTBSummarizerTableModel() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerTableModel
 
MTBSurface3D - Class in de.unihalle.informatik.MiToBo.core.datatypes
class representing the surface area of a 3D-object
points are not ordered!
MTBSurface3D(Vector<MTBPoint3D>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
 
MTBSurface3D(Vector<MTBPoint3D>, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
 
MTBSurface3DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
 
MTBSurface3DSet(double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Construct an empty set of regions with given extent of domain
MTBTableModel - Class in de.unihalle.informatik.MiToBo.gui
Table model for MiToBo data tables.
MTBTableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Default constructor.
MTBTableModel(int, int, Vector<String>) - Constructor for class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Constructor with given header strings.
MTBTableModelDataIO - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Class for loading/saving MTBTableModel data objects via commandline.
MTBTableModelDataIO() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
 
MTBTableModelDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Class for loading/saving MTBTableModel data objects.
MTBTableModelDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
 
MTBTableModelDataIOSwing.TableModelShowButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
GUI element for displaying table model data.
MTBTableModelDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Class for loading/saving MTBTableModel data objects via xmlbeans provider.
MTBTableModelDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
 
MTBTableWindow - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components
GUI window for displaying tables in MiToBo.
MTBTableWindow(MTBTableModel) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow
Default constructor.
MTBTableWindow.DataTabFileFilter - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components
Internal class that realizes a FileFilter for text files where MiToBo table data is stored.
MTBTermAreaDiff - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Check upon snake termination by the area within the snake.
MTBTermAreaDiff() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Default constructor.
MTBTermAreaDiff(double, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Constructor with area fraction below the snake iteration is terminated or if a maximum number of iterations is reached.
MTBTermAreaDiffSlidingOffset - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Check upon snake termination by area change within the snake.
MTBTermAreaDiffSlidingOffset() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Default constructor.
MTBTermAreaDiffSlidingOffset(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
MTBTermination - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Class for checking termination criteria of the current snake iteration.
MTBTermination() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
 
MTBTermMaxIterations - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Check upon snake termination by a given number of maximal iterations of the snake.
MTBTermMaxIterations() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Default constructor.
MTBTermMaxIterations(int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Constructor with maximum number of iterations on which the snake optimization is terminated.
MTBTermMotionDiff - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Check on snake termination by motion difference.
MTBTermMotionDiff() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Default constructor.
MTBTermMotionDiff(double, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Constructor with motion fraction factor and maximum iteration count.
MTBtoC2D(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Converts a MiToBo polygon to C2D data type.
MTBTopologicalNumber - Class in de.unihalle.informatik.MiToBo.topology
An abstract class to compute topological numbers given a neighborhood.
MTBTopologicalNumber() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
 
MTBTopologicalNumber.PixelIndexIterator - Class in de.unihalle.informatik.MiToBo.topology
 
MTBTopologicalNumber.PixelOffsetIterator - Class in de.unihalle.informatik.MiToBo.topology
 
MTBTopologicalNumber.Point3D - Class in de.unihalle.informatik.MiToBo.topology
This class is used as a light weight 3D point implementation
MTBTopologicalNumber2D - Class in de.unihalle.informatik.MiToBo.topology
An abstract class to compute topological numbers for the 2D case.
MTBTopologicalNumber2D() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2D
 
MTBTopologicalNumber2DN4 - Class in de.unihalle.informatik.MiToBo.topology
Class to compute topological numbers for the 2D case.
MTBTopologicalNumber2DN4() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN4
Construct a class for this neighborhood definitions
MTBTopologicalNumber2DN8 - Class in de.unihalle.informatik.MiToBo.topology
Class to compute topological numbers for the 2D case.
MTBTopologicalNumber2DN8() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN8
Construct a class for this neighborhood definition
MTBTree - Class in de.unihalle.informatik.MiToBo.core.datatypes
This class implements a simple tree data structure.
MTBTree(MTBTreeNodeData) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Constructor for the tree.
MTBTree(MTBTreeNode) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Constructor for the tree for a given root node.
MTBTreeNode - Class in de.unihalle.informatik.MiToBo.core.datatypes
This class implements the nodes of class 'Tree'.
MTBTreeNode(MTBTreeNodeData) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Constructor for a TreeNode.
MTBTreeNodeData - Class in de.unihalle.informatik.MiToBo.core.datatypes
Abstract class to define properties for data objects associated with TreeNodes.
MTBTreeNodeData() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
 
MTBTreeNodeRegion2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to create a TreeNodeData object for a 2D region (MTBRegion2D).
MTBTreeNodeRegion2D(MTBRegion2D) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Construct a new MTBTreeNodeRegion2D from the given 2D region object.
MTBVectorField2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to represent several kinds of vector fields.
MTBVectorField2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
 
MTBVectorField2D(double[], double[], int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
 
MTBVersionProviderReleaseFile - Class in de.unihalle.informatik.MiToBo.core.operator
Info class which provides MiToBo plugins with version information from release file in a jar archive.
MTBVersionProviderReleaseFile() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
 
MTBWrapperDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Class for loading/saving primitive datatypes in Alida.
MTBWrapperDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline
 
MTBWrapperDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Class for loading/saving wrapper datatypes in MiToBo.
MTBWrapperDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
 
MTBWrapperDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Class for loading/saving primitive datatypes in Alida.
MTBWrapperDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
 
mu - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
weight of the length term
mu - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
weight of the length term
mu - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Distribution of the number of clutter observations
mult(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Multiply each image value by a constant
mult(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Multiply the elements of two images
mult(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Multiply each image value by a constant
mult(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Multiply the elements of two images
MultiChannelParticleAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.particles2D
Operator for detecting sub-cellular structures in a given image.
MultiChannelParticleAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Empty constructor.
MultiChannelParticleAnalyzer2D(MTBImage, Vector<ParticleDetector>) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Default constructor.
MultiChannelParticleAnalyzer2D.ResultImageMode - Enum in de.unihalle.informatik.MiToBo.apps.particles2D
Display mode of the result image.
MultiObsDistributionIndepGaussians<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
A simple multi observation density, which assumes independence of the single observations with multivariate Gaussian noise.
MultiObsDistributionIndepGaussians(Random, Matrix, Matrix, AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix[], Matrix[], AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix, Matrix, MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix[], Matrix[], MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix, Matrix, MultiStateLinTransDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix[], Matrix[], MultiStateLinTransDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussMix<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
A simple multi observation density, which assumes independent Gaussian mixtures as the underlying distributions.
MultiObsDistributionIndepGaussMix(Random, Matrix, Vector<GaussMixDistribution>, AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
MultiObservationGenerator - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Operator to create a (time) series of observations which can be used for evaluation of multi target tracking algorithms.
MultiObservationGenerator() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
MultiObservationGenerator.GeneratorInfo - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
 
MultiObservationTrackerRBMCDAIMM - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Tracking of multiple targets using Rao-Blackwellized Monte Carlo Data Association (RBMCDA) for observation-to-target association and Interacting Multiple Models (IMM) filters for target state estimation.
MultiObservationTrackerRBMCDAIMM() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
multiphase - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
MultiState<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
Multi-target state implementation.
MultiState(MultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
MultiStateDistributionIndepGaussians<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
A simple multi state density, which assumes independence of the single states with multivariate Gaussian noise.
MultiStateDistributionIndepGaussians(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
MultiStateDistributionIndepGaussians(AbstractMultiState<T>, Matrix, Random) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Constructor with identical covariance matrices for all states
MultiStateDistributionIndepGaussians(AbstractMultiState<T>, Vector<Matrix>, Random) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Constructor with different covariance matrix for each state
MultiStateFactory<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
Multi-target state factory implementation.
MultiStateFactory(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
 
MultiStateIO - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatools
File-IO for (vectors of) MultiState objects.
MultiStateIO() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.MultiStateIO
 
MultiStateLinTransDistributionIndepGaussians<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
A simple multi state-transition density, which assumes independence of the single states and multivariate Gaussian process noise.
MultiStateLinTransDistributionIndepGaussians(Random, Matrix, Matrix, AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
MultiStateLinTransDistributionIndepGaussians(Random, Matrix[], Matrix[], AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
MultiStateLinTransDistributionIndepGaussians(Random, Matrix, Matrix, MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
MultiStateLinTransDistributionIndepGaussians(Random, Matrix[], Matrix[], MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
MultiTargetIMMFilter - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Multi-target Interacting Multiple Models (IMM) filter for varying number of targets.
MultiTargetIMMFilter(MultiTargetIMMFilter) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Copy constructor.
MultiTargetIMMFilter(Vector<GaussMixDistribution>, LinearTransformGaussNoise, LinearTransformGaussNoise[], Matrix, double, ExponentialDistribution, GaussMixDistribution, Matrix, AbstractMultiStateFactory<MotionModelID>, AbstractMultiStateFactory<MotionModelID>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Constructor that initializes the internal random generator with seed 1.
MultiTargetIMMFilter(Vector<GaussMixDistribution>, LinearTransformGaussNoise, LinearTransformGaussNoise[], Matrix, double, ExponentialDistribution, GaussMixDistribution, Matrix, AbstractMultiStateFactory<MotionModelID>, AbstractMultiStateFactory<MotionModelID>, Random) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Constructor.
MultiTargetPredictionFilter<T extends Copyable<?>> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Interface for multi-target prediction filters
MultiTargetPredictionFilterIndep<T extends Copyable<?>> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Interface for multi-target prediction filters with independent targets
MultiTargetRBMCDA<T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Rao-Blackwellized Monte Carlo Data Association following:
S.
MultiTargetRBMCDA(Random, RBMCDASample<T>, int, AssociationDistribution<T, T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
MultiTargetRBMCDA(Random, RBMCDASample<T>[], AssociationDistribution<T, T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
myClass - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
myClass - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Class associated with parameter.
myClass - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
myData - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
myDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
myDescriptor - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Descriptor associated with parameter.
myField - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
myField - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Field associated with parameter.
myField - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
myObject - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
(Default) object value associated with parameter.
myX - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The flows of the field in x- and y-direction.
myY - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The flows of the field in x- and y-direction.

N

n - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
For Odet's criteria only
n - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria
Exponent for calculations.
n - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
n - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
 
n - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
 
N - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
number of targets
naiveGapThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Maximal distance of gaps in naive mode to be closed.
name - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
name - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Name of the energy.
narrow - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Pixels in narrow-band.
narrowBandWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
naString - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
nbMode - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Neighborhood(s) to be considered.
nbPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
nbPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Phases of the 8-neighbors of the current pixel.
nbPhasesNonredundant - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Non redudant phases in the neighborhood of the current pixel.
nColors - Variable in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator
Number of colors to generate.
nearZero(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Checks if a pixel belongs to the zero level.
negDir - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
NeighborhoodSelection() - Constructor for enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal.NeighborhoodSelection
 
neighbourhood - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The neighbourhood mode to inspect new pixel.
neighbourhood - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
neighbourhood - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The neighbourhood mode to inspect new pixel.
Neighbourhood() - Constructor for enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.Neighbourhood
 
neurite - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
neuriteColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
neuriteColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Region color of detected neurites to view the neurites in the result image.
neuriteDetection(MTBContour2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Main method for 2D neurite detection.
neuriteDetector - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Define analyzer parameters.
NeuriteDetector2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
The Neurite Detector 2D application offers advanced functionality to detect neurites in 2D fluorescence microscope images of neurons.
NeuriteDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Standard constructor.
NeuriteDetector2D(String, Integer, int, double, Integer[], double, int, NeuriteDetector2D.NeuriteDetector2DMode, NeuriteDetector2DAlgos.DetectorExternalEnergy, double, double, double, double, int, int, int, int, Color, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Constructor
NeuriteDetector2D.NeuriteDetector2DMode - Enum in de.unihalle.informatik.MiToBo.apps.neurites2D
Different detection modes.
NeuriteDetector2DAlgos - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
The class implements the basic algorithm for neurite detection based on a 2D multichannel fluorescence image.
NeuriteDetector2DAlgos() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Standard constructor.
NeuriteDetector2DAlgos(MTBImage, int, int, double, int[], double, int, String, String, NeuriteDetector2DAlgos.DetectorExternalEnergy, double, double, double, double, int, int, int, int, Color, MTBTableModel, Boolean, Rengine) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Constructor.
NeuriteDetector2DAlgos.DetectorExternalEnergy - Enum in de.unihalle.informatik.MiToBo.apps.neurites2D
Label for different external energies of the snake which can be used by the detector.
NeuriteDetector2DException - Exception in de.unihalle.informatik.MiToBo.apps.neurites2D
Exception handling for 2D neurite detection.
NeuriteDetector2DException() - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
 
NeuriteDetector2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
 
NeuriteDetector2DMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D.NeuriteDetector2DMode
 
NeuriteExtractor2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
The Neurite Extractor 2D application offers advanced functionality to extract neurite regions in 2D binary neuron images of neurons.
NeuriteExtractor2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Standard constructor.
NeuriteExtractor2D(MTBImageByte, NeuriteExtractor2D.NeuronColor, int, int, Rengine, String) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Constructor to create a new neurite extraction object.
NeuriteExtractor2D.NeuronColor - Enum in de.unihalle.informatik.MiToBo.apps.neurites2D
Color of binary neuron image foreground.
NeuriteExtractor2DException - Exception in de.unihalle.informatik.MiToBo.apps.neurites2D
Exception handling for 2D neurite extraction.
NeuriteExtractor2DException() - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
 
NeuriteExtractor2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
 
neuriteGraph - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Neurite skeleton Graph (NSG) of the current neurite.
neuriteGraphs - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Vector of neurite graphs, one for each localized neurite.
neuriteMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
neuriteMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Mask size of average neurite with in pixel.
neuriteMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
NeuriteMolProfExtractor2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
The Neurite Molecular Profile Extractor 2D application offers advanced functionality to extract molecular intensity profiles of multichannel fluorescence images along detected neurite regions.
NeuriteMolProfExtractor2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Standard constructor
NeuriteMolProfExtractor2D(MTBImage, Integer[], MTBNeurite2DSet, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Constructor to create a new neurite profile extraction operator.
NeuriteParticleDetector2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
This operator detects particles of a neuron image, for example from FISH analysis.
NeuriteParticleDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Standardconstructor.
NeuriteParticleDetector2D(Integer, ParticleDetectorUWT2D, MTBNeurite2DSet, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Constructor.
neuriteProfiles - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
The current list of the neurite profiles.
neuriteRegion - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Neurite corresponding region as MTBRegion2D object.
neuriteSet - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
neuriteSet - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Set of neurite regions for detecting particle only inside these regions, an be null for detection all particles in the complete image
neuriteSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
The current set of neurites.
neuriteShaft - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Neurite corresponding neurite shaft region as MTBRegion2D object.
neuriteShaftLengths - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Array of detected lengths of the neurite shafts, without growth cone regions.
neuriteShaftLengths - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Lengths of the single branches of a neurite shaft.
neuriteWidths - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Average widths of the whole neurite, the neurite shaft and the growth cone.
NeuronAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.neurons2D
The Neuron Analyzer 2D application offers advanced functionality to analyze 2D fluorescence microscope images of neurons.
NeuronAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Standard constructor.
NeuronAnalyzer2D(NeuriteDetector2D, Boolean, String[], Integer[], Boolean, NeuriteParticleDetector2D, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Constructor.
NeuronAnalyzer2DException - Exception in de.unihalle.informatik.MiToBo.apps.neurons2D
Exception handling for 2D neuron analyzer.
NeuronAnalyzer2DException() - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
 
NeuronAnalyzer2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
 
neuronChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
neuronChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Channel numbers, including the neuron stains for detection of the neurons in the current multichannel fluorescence image.
neuronCoarseSoma - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
2D region of the coarse cell body region (soma).
neuronColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
NeuronColor() - Constructor for enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D.NeuronColor
 
neuronImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Define extractor parameters.
neuronMIP - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Maximum intensity projection (MIP) image of the neuron.
neuronSkelGraph - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
NSG of the whole neuron.
newborndistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
spatial distribution of observations from newborn targets
newbornStateDistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
newbornStateFromObs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
newtargetID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Target-ID to start from for newborn targets
next() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
 
next() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
 
next() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
next() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
next - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
next() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
 
next() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
 
nextSegment - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Reference to the subsequent segment along the contour.
nf - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
nf - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
nf - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
niblackConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
niblackConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Application based constant for Niblack thresholding.
niblackOperator - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Niblack operator, required if mode is 'NIBLACK'.
niblackVarianceThresh - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Niblack threshold.
nInitialTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
noCheck - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
Node - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation
 
Node() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
Node(double, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
Node(int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
Node(int, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
node - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
Reference to the associated node of the tree.
nodeID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
The node's ID
nodeIsSrc(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
 
nodeIsTgt(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
 
nodeNames - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
nodes - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Vector of included graph nodes.
nodes - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
nodeThreshold - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Threshold for nodes to be included, nodes with an intensity above the threshold are removed from the graph.
nodeType - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
MTBSkeletonNodeType of the MTBSkeletonGraphNode.
noiseCov - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
noNeighborsOldAlgo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
nonProtrusionArea - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Non-protrusion area in cell region.
nonProtrusionAreas - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
normalizationFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Normalization factor for scaling matrix entries.
normalizationFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Normalization factor for scaling matrix entries.
normalizationFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Normalization factor for scaling matrix entries.
normalize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
Normalize the histogram.
normalize(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Normalizes the snake coordinates.
normalizedFilterResponse(double, double) - Static method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Computes the (ideal) filter response to the Gaussian derivative kernel.
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Normalize the external energy in a range [0.0, 1.0].
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Normalization of the GVF field. !!!
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Normalize the external energy in a range [-1.0, 1.0].
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Normalize the external energy in a range [-1.0, 1.0].
normalizeImplicitParameters() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Normalizes the implicit parameters so that f=1.0.
normalizeInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Normalizes image intensities according to normalization mode of operator.
normalizeMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Flag to normalize sum of kernel elements to zero.
normalizeMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Flag to normalize sum of kernel elements to zero.
normalizeMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Flag to normalize sum of kernel elements to zero.
normalizePotentialToMin(double[], boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Function to normalize a potential to the minimum value of 0.
normalizeWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
Normalize weights
normalizeWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Normalize the particle weights to sum to 1.
normfactor - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
normalization factor
normFromTo(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
normImageFromTo(MTBImage, double, double, double, double, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Normalize the image values to range [lowerBound, upperBound].
normImageTo(MTBImage, double, double, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Normalize the image values to range [lowerBound, upperBound].
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Mode for normalizing energies.
normTo(MTBImage, double, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
normValues() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Normalize the values in the gvf field in a range of [-1,1].
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
nrs - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
nTimesteps - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
nu - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
weight of the size term
nu - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
weight for this energy
nu - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Distribution of the number of observations from newborn targets
nucChannel - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
nucDetector - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
nucImage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Part of the input image, representing the stained nuclei.
NuclDetectMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D.NuclDetectMode
 
NuclearParticleDetector2D - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
This class detects nuclei and particles inside these nuclei and gives some statistics about particles, like particle number per nuclei, particle size, sum of intensities, etc.
NuclearParticleDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Standard constructor.
NuclearParticleDetector2D(MTBImageByte, Integer, Integer, Boolean, Double, Boolean, NucleusDetector2D, ParticleDetectorUWT2D) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
nucleiChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Nuclei channel.
nucleiChannel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
nucleiChannel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Channel number, including the nuclei, in the current multichannel fluorescence image.
nucleiContours - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
(Optional) initial snake contours for nuclei.
nucleiDetector - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Operator for nucleus detection/separation.
nucleiMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Nuclei mask.
nucleiRegions - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Set of detected regions.
nucleiRegions - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
nucleus - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Fluorescence labeled nuclei image from the multichannel microscope image.
nucleusChannelID - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Index of the nucleus channel, if -1 it is unknown or image has only one.
NucleusDetector2D - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Operator for segmenting cell nuclei in 2D images.
NucleusDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Default constructor.
NucleusDetector2D(MTBImage, NucleusDetector2D.NuclDetectMode, ImgThreshNiblack, boolean, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Constructor.
NucleusDetector2D.NuclDetectMode - Enum in de.unihalle.informatik.MiToBo.apps.nuclei2D
Available modes for nuclei segmentation in 2D images.
nucleusRatio - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
nucleusRatio - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Ratio of nucleus pixels which should be included in a intact neuron region to specify the neuron region as active and use for detection.
nucleusResult - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Result for nucleus channel.
NucleusSeparator2D - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Class provides routines for separating conglomerates of cell nuclei in 2D.
NucleusSeparator2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Empty constructor.
NucleusSeparator2D(MTBImage, NucleusSeparator2DAlgos) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Default constructor.
NucleusSeparator2D.ResultImageMode - Enum in de.unihalle.informatik.MiToBo.apps.nuclei2D
Display mode of the result image.
NucleusSeparator2DAlgos - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Common super class for all nucleus separators.
NucleusSeparator2DAlgos() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Empty constructor.
NucleusSeparator2DBeamCut - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Class provides routines for separating conglomerates of cell nuclei in 2D.
NucleusSeparator2DBeamCut() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Default constructor
NucleusSeparator2DBeamCut(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Constructor.
NucleusSeparator2DBeamCut(MTBImage, NucleusSeparator2DBeamCut.NuclSeparateMode) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Constructor.
NucleusSeparator2DBeamCut.NuclSeparateMode - Enum in de.unihalle.informatik.MiToBo.apps.nuclei2D
Available modes for nuclei separation in 2D images.
NucleusSeparator2DPeakSearch - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Operator for separating merged nuclei regions in images.
NucleusSeparator2DPeakSearch() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Default constructor.
NucleusSeparator2DPeakSearch(MTBImageShort) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Constructor with input image.
NucleusSeparator2DPeakSearch(MTBImageShort, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Constructor with gray-scale and binary image.
NucleusSeparator2DPeakSearch_RegionSeparator - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Operator to analyze a given binary image or a set of nuclei regions.
NucleusSeparator2DPeakSearch_RegionSeparator() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Default constructor.
NucleusSeparator2DPeakSearch_RegionSeparator(MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Constructor with input image.
NucleusSeparator2DPeakSearch_RegionSeparator(MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Constructor with region set.
nucleusSepOp - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Operator to be applied for nuclei separation.
nucleusSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
nucleusSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Minimum size of nucleus region to set region as intact nucleus.
NuclSeparateMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut.NuclSeparateMode
 
nucSepOp - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Operation mode of the operator.
number_cells - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Count of detected cells.
number_channels - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Number of channels in the image.
number_nuclei - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Count of detected nuclei.
number_particles - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Count of detected particles.
numberNeighbors - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Number of neighboring pixels to consider for LBP codes.
numberOfBins - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
numberOfEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Number of edges in the MTBGraph.
numberOfNeighbors(MTBImage, int, int) - Static method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Counts the number of neighboring skeleton pixels.
numberOfNeighbors(MTBImage, int, int) - Static method in class de.unihalle.informatik.MiToBo.morphology.SkeletonAnalysisHelper
Counts the number of neighboring skeleton pixels.
numberOfNodes - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Number of nodes in the MTBGraph.
numberOfProtrusions - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
Number of detected protrusions along contour.
numberToString(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
numBlockChange(short[], int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Return number of connected components of different/foreign phase then r in the 8 neighborhood nbPhases, which are 4 connected to the current pixel.
numClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numClutterInput - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
number of clutter observations in input observations
numClutterTracker - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
number of clutter observations in tracking results
numDeadTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numEntries - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
number of histogram entries
numInitialTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numIterations - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
numIterations - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
numIterations - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Number of iterations for calculating the GVF field.
numIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
numIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
numIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
 
numNewbornTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
numOfConnectedNodes(PartitGraphNodeID, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Get number of nodes from partition 'partitionID' connected to current node
numOfDefinedHuePixel - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
numOfDefinedSaturationPixel - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
numOfNodes() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
numOfNodes() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Get number of graph nodes
numOfObservationAssocs(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
numOfObservationAssocs(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the number of observations that are associated with the specified target
numOfTargetAssocs(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
numOfTargetAssocs(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the number of targets that are associated with the specified observation
numOfXPixel - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
numPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
number of phases including background
numPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
numPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
numRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Number of represented regions.
numRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Number of represented regions.
numSamples - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
numTargetInput - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
number of target observations in input observations
numTargetTracker - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
number of target observations in tracker results
nx - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Used for drawing the estimated diameter during Ridge Detection.
nx - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
ny - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Used for drawing the estimated diameter during Ridge Detection.
ny - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 

O

obj - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton
Image object associated with the button.
objectLabels - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
objects26Connected - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
objects8Connected - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
objects8Connected - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
obsAssocAdjacency - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
obsConflict(Matrix, MultiState<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
ObsDistance(double, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
 
obsdistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
observation/measurement likelihood P(z_m^t | c_m, Z^{1:t-1}, c_{1:m-1}
obsDomainAreaRatio - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
ObservationAdjacency - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
An adjacency matrix for observations in a time series used for greedyGourmet-partitioning.
ObservationAdjacency(Vector<MultiState<MotionModelID>>, RBMCDASampleInfo<MotionModelID>[]) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
Constructor that initializes the adjacency matrix with the given observations and sets edge weights according to the information from RBMCDA-samples
ObservationAdjacency(Vector<MultiState<MotionModelID>>, DataAssociationExclusive[][]) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
Deprecated.
ObservationAdjacency(ObservationAdjacency) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
observations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
observations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
observations - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
ObservationSeriesGenerator - Class in cmdTools.tracking.multitarget
Commandline tool to create a (time) series of observations which can be used for evaluation of multi-target tracking algorithms.
ObservationSeriesGenerator() - Constructor for class cmdTools.tracking.multitarget.ObservationSeriesGenerator
 
ObservationsInfo - Class in cmdTools.tracking.multitarget
Commandline tool to print information about a (time) sequence of observations and optionally their association to targets/clutter.
ObservationsInfo() - Constructor for class cmdTools.tracking.multitarget.ObservationsInfo
 
observationsToRegions(boolean, Vector<MultiState<MotionModelID>>, double, double, double, double) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
Convert observations to regions.
observationsToTracks(Vector<MultiState<MotionModelID>>, HashMap<Integer, Vector<Integer>>) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
Obtain observations assigned to each target from observations with assigned target IDs
obsIdx - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
 
OCO(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria
This method implements Odet's oversegmentation error.
OCU(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_OdetsCriteria
This method implements Odet's undersegmentation error.
ODE(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors
This method computes the overdetection error.
Odet - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Check if you want to compute Odet's criteria
offer(EType, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
add an element to List
offsets - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
offsetsNeighborNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
As for the neighbors this collection is in analogy to coordinatesNeighborNeighbors and gives for each neighborneighbor the offset instead of coordinates.
offsetsNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
In analogy to coordinatesNeighbors this array hold the offsets of the neighbors.
oFilter - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Oriented filter to apply.
okOption - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Ok label to be used on button of Ok message boxes.
oldId - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Old index (position) of the point within the snake.
omemeta - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
omePixelType(MTBImage.MTBImageType) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Get the OME pixel type corresponding to the specified MTB image type
omexml - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
omitAssignment - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Flag to omit region assignment.
onValue - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
op - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
The operator associated with this frame.
opane - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
 
open(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
open1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
openByteImageWithCircle(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Open an image of type MTBImageByte.
openingSESize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The minimum size of a MTBRegion2D before erosion.
openingSESize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The minimum size of a MTBRegion2D before erosion.
openRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Gets an instance of the current ROI manager of ImageJ.
openRoiManagerFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Opens a zip file with ImageJ ROIs.
openWindow() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Displays configuration window.
openWindow() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Displays configuration window.
openWindows - Static variable in class cmdTools.visualization.DisplayImage
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Invokes analysis procedure on given image.
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetector
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector

operate() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower

operate() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
operate() - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Creates a MTBImage with three channels, the same size as the original one and converts each rgb pixel to a hsx pixel, where x stands for Inentsity or Brightness or Value depending on the mode set.
operate() - Method in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
operate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
operate() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
 
operate() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
 
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
 
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
 
operate() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
 
operate() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
This function calls the actual Gauss filtering method.
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
This function calls the actual mean filtering method.
operate() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
 
operate() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
 
operate() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
 
operate() - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
operate() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
operate() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
operate() - Method in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.WatershedBinary
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
This method initializes all required components.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
This function does the actual work, i.e. optimization of the energy.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Methode that runs the operator.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
 
operate() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
operate() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
operate() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
operate() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
 
OperationMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperationMode
 
OperationMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.OperationMode
 
OperationMode() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OperationMode
 
OperationMode() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.OperationMode
 
operationType - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
The operation which should be applied to the input vector field.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Identifier string for this operator class.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Identifier string for this operator class.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Identifier string for this operator class.
operatorID - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Identifier string for the operator class.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter
Identifier string for this operator.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
Identifier string for this operator.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Identifier string for this operator class.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Operator class identifier.
operatorID - Static variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Identifier string for this operator class.
operatorMode - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Mode of operation of the operator.
OperatorPhasesToRun() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperatorPhasesToRun
 
opID - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
Identifier string for this operator class.
opID - Static variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Identifier string for this operator class.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Identifier for outputs in verbose mode.
opIdentifier - Static variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Identifier for outputs in verbose mode.
opMode - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Mode of operation of the operator.
opMode - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detection mode.
opMode - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Operation mode of this separator.
opMode() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.opMode
 
opMode - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Mode of operation of the operator.
opMode - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Mode of operation of the operator.
opName - Variable in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame
Name of associated operator.
opPackage - Variable in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorDocumentationFrame
Package of associated operator/tool.
optimizeContrast(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Optimize visibility by shifting labels into upper part of gray-scale range.
optimizer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Current snake optimizer with all its parameters and fields like the current snake, old snake, gamma values and energies.
optimizer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Current snake optimizer with all its parameters and fields.
optimizeSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Optimization of the snakes (main snake and inner snakes) with its specified parameters and energies.
OpWorkingMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.OpWorkingMode
 
or(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Bitwise OR of the elements of two images
or(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Bitwise logical OR of two images.
ordinalToType(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Return the corresponding MTBImageType for its index in the enum.
orient - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
List of orientations of plastid regions.
orientation - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
orientation - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
orientation - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Ellipse orientation in degrees.
OrientedFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Base class for anisotropic linear filters in 2D.
OrientedFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Default constructor.
OrientedFilter2D.ApplicationMode - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Modes how to apply the filter to an image.
OrientedFilter2DBatchAnalyzer - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Base class for applying oriented filters in different orientations.
OrientedFilter2DBatchAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Default constructor.
OrientedFilter2DBatchAnalyzer.JoinMode - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Method for joining the results from the various orientations.
originalImage - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Original image currently under processing.
ostream - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
out - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML
 
outdata - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
outDigits - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
outDigits - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
outDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Output and working directory.
outDir - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Output and working directory.
outEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Vector of outgoing edges of the MTBGraphNode.
outFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
outFile - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
Output file name.
outImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Output image.
outImageType - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
OutImageType() - Constructor for enum de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB.OutImageType
 
outimg - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
outImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Binary result image.
outImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Result image.
outIntermediateResultsStack - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image stack with intermediate result images.
outIntermediateResultsStackInterval - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Interval for saving intermediate results in stack.
outIntermediateResultsStackWanted - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag to request a stack of intermediate result images.
outMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Generated mask.
outModes - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
outOfRangeValueMode - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Mode how to handle values out of range and masked pixels.
OutOfRangeValuesHandlingMode() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode
 
outpath - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Directory of output results.
outputArray - Variable in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D
Result data array.
outputData - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
 
outputDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Directory of output results.
outputDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
outputDir - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Optional output directory.
outputEntropy - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Final Shannon entropy of the output image.
outputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
 
outputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
 
outputImage - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
OutputMode() - Constructor for enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.OutputMode
 
outputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
outputPath - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
Path where to save the tile files.
outputSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
 
outputType - Variable in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
 
outputType - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
outRegs - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
outSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
Result snake.
outSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
Resulting snake.
outSnakes - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Result snakes.
outSnakes - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Result contours.
outSnakesImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image with final snake contours overlayed.
overlapMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Current overlap mask for joint optimization of multiple snakes.
overlapMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Mask to indicate overlap regions between snakes.
overlapMaskRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Flag to indicate if overlap mask is required by at least one energy.
overlapOpt - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Mode for how to resolve overlaps of lines.
overwrite - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
OverwriteException - Exception in de.unihalle.informatik.MiToBo.io.images
Special exception for the ImageWriterMTB operator.
OverwriteException(ALDOperatorException.OperatorExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.io.images.OverwriteException
 

P

P(Double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
p - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
p(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.EvaluatableDistribution
Evaluate p(X) at location x.
p(T, int) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.IndependentlyEvaluatableDistribution
Evaluate p_i(X) at x_i
P(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.IntegrableDistribution
Evaluate probability distribution function P(X <= x)
p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
 
p(AbstractMultiState<S>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Evaluate the density independently for observation i in Z conditional on state j in X
p(AbstractMultiState<S>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Evaluate the density independently for observation i in Z conditional on state i in X
p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
 
p(DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
This method is here only valid for the latest DataAssociation sampled with drawSample().
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
P_D - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Probability of target detection
p_obs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
P_t - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
The final transformation matrix to be used for dimension reduction.
PaCeQuant - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology
Operator for segmenting and analyzing pavement cell shape.
PaCeQuant() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Default constructor.
PaCeQuant.BorderBackgroundContrast - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology
Border color.
PaCeQuant.GapCloseMode - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology
Heuristic for closing border gaps.
PaCeQuant.ImageType - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology
Image type.
PaCeQuant.LobeTypes - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology
Different types of lobes.
PaCeQuant.MeasurementUnits - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology
Unit for measurements.
PaCeQuant.OperationMode - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology
Operation mode of the operator.
PaCeQuant.OperatorPhasesToRun - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology
Phases to run.
PaCeQuant.PixelCalibration - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology
Mode of calibrating pixel size.
PaCeQuant.SegmentationInputFormat - Enum in de.unihalle.informatik.MiToBo.apps.cellMorphology
Formats for input of external segmentation results.
PaCeQuant.SegmentationResult - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology
Internal class for representing the result data of segmenting an image.
PaCeQuant.SkeletonPostprocessor - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology
Helper operator to post-process border skeletons.
PaCeQuant_FeatureColorMapperInputData - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology
Datatype to handle input configurations for PaCeQuant_FeatureColorMapper.
PaCeQuant_FeatureColorMapperInputData(String, int[]) - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData
Default constructor.
PaCeQuant_FeatureColorMapperInputDataIOSwing - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology
Data I/O provider for input data of PaCeQuant_FeatureColorMapper.
PaCeQuant_FeatureColorMapperInputDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
 
PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology
Panel for handling GUI I/O of input directories for PaCeQuant_FeatureColorMapper.
PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel - Class in de.unihalle.informatik.MiToBo.apps.cellMorphology
 
paintComponent(Graphics) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
 
paintFilledRegion(MTBRegion2D, MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Draw a region without holes to an image.
paintFilledRegionsBinary(MTBImage, MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Close holes in binary image.
paintZeroWeightEdges - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
panelContainer - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
Main panel containing all graphical components.
param - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
paramDescr - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
 
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
(Operator) parameter descriptor associated with parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
(Operator) parameter descriptor of associated parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
(Operator) parameter descriptor of associated parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton
Descriptor of underlying parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
(Operator) parameter descriptor of associated parameter.
paramDescr - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
(Operator) parameter descriptor of associated parameter.
paramDescriptor - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Descriptor of the associated (operator) parameter.
parent - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Parent node
parentID - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
A java.awt.Color object is created from a string, which holds color information in the following format:

"rINT:bINT:gINT[:aINT]"

where INT is an integer value in the range [0,255].
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtPoint2dDataIOCmdline
A java.awt.geom.Point2D.Double object is created from a string, which holds coordinates in the following format:

"x;y" "rINT:bINT:gINT[:aINT]"

where INT is an integer value in the range [0,255].
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
 
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline
Method to parse MTB wrapper data from a string.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
Convert a string to a Random generator.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
 
partChannel - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
partDetector - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
particleChannel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Define extractor parameters.
particleDetector - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Particle detector.
particleDetector - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
 
particleDetector - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
ParticleDetector - Class in de.unihalle.informatik.MiToBo.apps.particles2D
Common super class for all particle detectors.
ParticleDetector() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetector
Empty constructor.
ParticleDetector2D - Class in cmdTools.cellAnalysis
Commandline tool for particle detection based on the undecimated wavelet transform.
ParticleDetector2D() - Constructor for class cmdTools.cellAnalysis.ParticleDetector2D
 
particleDetector_1 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
particleDetector_2 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
particleDetector_3 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
particleDetector_4 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
particleDetector_5 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
ParticleDetectorUWT2D - Class in de.unihalle.informatik.MiToBo.apps.particles2D
Detector for spotlike structures (bright on dark background) in 2D based on the undecimated wavelet transform.
ParticleDetectorUWT2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Constructor.
ParticleDetectorUWT2D(MTBImage, int, int, double, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Constructor with non-default parameters.
ParticleDetectorUWT2D(MTBImage, int, int, double, int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Constructor that sets the poisson2gauss flag to true
ParticleDetectorUWT2D.UWTRunner - Class in de.unihalle.informatik.MiToBo.apps.particles2D
Thread class to run UWT wavelet transformation threaded.
ParticleDistribution<G extends Copyable<? extends G>> - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A distribution represented by weighted particles
ParticleDistribution() - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Constructor where all fields are initialized by null.
ParticleDistribution(Random, G[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Constructor with equally weighted particles that must be specified.
ParticleDistribution(Random, G[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Constructor with equally weighted particles that must be specified.
ParticleDistribution(Random, SamplingDistribution<G>, int) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Constructor that samples numParticles from density.
particleOp - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
Particle detector object.
particleOp - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
Particle detector object.
particleRegions - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
List of detected regions.
particleRegions - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
particleResults - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Detection results for particles.
particles - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
partImage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Part of the input image, representing the stained particles.
PartitGraphNodeID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A graph node object for multipartite graphs to store a partitionID, a nodeID as well as a subgraphID.
PartitGraphNodeID(int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
Constructor to specify partitionID and nodeID (subgraphID=0)
PartitGraphNodeID(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
Constructor to specify partitionID, nodeID and subgraphID
partitionID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
The node's partitionID
partitions - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
path - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
path - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
 
path - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Absolute directory path associated with this node.
pathfield - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
PCA - Class in de.unihalle.informatik.MiToBo.math.statistics
This class implements the Karhunen-Loeve transformation, also known as PCA.
PCA() - Constructor for class de.unihalle.informatik.MiToBo.math.statistics.PCA
Default constructor.
PCA.ReductionMode - Enum in de.unihalle.informatik.MiToBo.math.statistics
Available modes for determining the sub-space dimensionality.
Pdeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
pdeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
pDetect - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
pDetect - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
pdetector - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
pdfs - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
peakdistance - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
perCellAvgSize - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Average particle size per cell (optional).
perCellCount - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Particle counts per cell (optional).
percentageVar - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Variance fraction for automatic dimension selection in mode ReductionMode.PERCENTAGE_VARIANCE.
perimeters - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
perimeters - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
pgm - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
phaseAInfo - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Info string for segmentation phase configuration parameters.
phaseBInfo - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Info string for segmentation phase configuration parameters.
phasesToRun - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Select with phases to run.
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Level set function.
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
The level set function.
phi_0 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
phi_1 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
phi_old - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Variable to store old level set function for comparison with new one.
physicalPixelSize_from_OME(Calibration, IMetadata, int) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Set the calibration of an image from the OME meta data of image of index imageIdx
physicalPixelSize_to_OME(Calibration, IMetadata, int) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Set OME meta data for image of index imageIdx using information from a Calibration object.
PI_HALF - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
 
pixCalibMode - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Mode for calibrating physical pixel size.
PixelCalibration() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.PixelCalibration
 
PixelIndexIterator() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
 
pixelLength - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Length of a pixel.
pixelLengthXY - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Physical size of a pixel.
pixelLengthXYinternal - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Pixel length only used internally.
PixelOffsetIterator() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
 
pixelUnitString - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Unit for pixel length.
PlastidDetector2DParticlesUWT - Class in de.unihalle.informatik.MiToBo.apps.plantCells.plastids
Operator to detect plastid regions in 2D microscope images.
PlastidDetector2DParticlesUWT() - Constructor for class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
Default constructor.
plastidMarkerType - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Type of plastid markers.
plastidMask - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Binary mask of pre-segmented plastid regions.
plastidRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
Set of detected plastid regions with stromuli.
plastidRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
(Optional) set of detected plastid regions.
plotImageToBackground() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Copies the input image as background into the output frame.
plotSnakesToImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns overlay of output snakes onto current input image.
plotSnakesToImage(MTBPolygon2DSet, MTBImage, int[]) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns overlay of given snakes onto given image.
plotSnakeToImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
pmf - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
probability mass function
png - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
pobs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
observation distribution: independent Gaussian mixtures for each target
point - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction
Point for which to calculate the distance to the ellipse.
point2DDiff(Point2D.Double, Point2D.Double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Substract two Point2D.Double .
point2DList - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
point2DSum(Point2D.Double, Point2D.Double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Sums up two Point2D.Double .
Point3D(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
PointConfigPanel(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Default constructor.
pointHashtableToString(Hashtable<Integer, Vector<Point2D.Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointHashtableToStringX(Hashtable<Integer, Vector<Point2D.Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointHashtableToStringY(Hashtable<Integer, Vector<Point2D.Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointNum - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
The number of border points.
pointOrderWasChanged(MTBPolygon2D, C2DPolygon) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if order of points was changed during initialization.
points - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Set of border pixels.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
List of polygon points.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Pixels belonging to region.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Points belonging to the region
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
Points belonging to the region
points - Variable in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet
Input set of points.
points - Variable in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet
Input set of points.
pointVectorToString(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointVectorToStringX(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointVectorToStringY(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
poisson2gauss - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Flag to activate Poisson-to-Gaussian noise transform.
poisson2gauss(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Transforms image with poisson noise to image with gaussian noise J.
PoissonDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
Poisson distribution.
PoissonDistribution(double, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
Constructor for Poisson distribution with parameter lambda (=mean=variance)
poll() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
retrieve element with highest priority
polygonSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
The set of polygons represented as a Vector.
polygonSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Set of 2D polygons.
polys - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Result polygon set, if target format are polygons or snakes.
popUpChart() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
Shows the chart to the user.
popUpImage(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Shows an image to the user.
portHashAccess - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Access object for port hash.
posDir - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
position - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
Position where to draw the string.
postProcessAfterGrowing(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Here we do some morphological operations to the shape of the regions from the region growing of XylemGrower.
postprocessedImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
Postprocessed skeleton image.
postprocessedImg - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Postprocessed skeleton image.
postProcessImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Post-process the vesselness filter result.
postprocessIndentationSegments(MorphologyAnalyzer2DInProData) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Post-process indentation segments to get more information on protrusions.
postprocessProtrusionSegments(MorphologyAnalyzer2DInProData) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Post-process protrusion segments to get more information on indentations.
potential - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Potential of the vector field.
PotentialFinderOptFunction(boolean) - Constructor for class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
Default constructor.
potentialNewPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Phases the current pixel is (topologically) allowed to change to.
potFinder - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Helper object for reconstructing potential from vector field.
pow(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Raise image values to the power of 'constant'
pow(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Raise image values to the power of 'exponent'
ppm - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
PRA - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Check if you want to compute Pratt's figure of merit
PRA() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_PrattsFigureOfMerit
This method is the implementation of Pratt's figure of merit.
precision - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc
Precision value.
PrecisionCalc() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc
Default constructor.
PrecisionCalc(Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc
Constructor with inputs.
precursorMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Map of precursor positions for each pixel in the background.
predecessor - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
predecessors - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Map of precursors on contour for each pixel in narrow-band.
predict() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
predict() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilter
Prediction step method
predict() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
predict(LinearTransformGaussNoise) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
predictIndep(int, LinearTransformGaussNoise) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
predictors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
dynamic models
prepareAdditionalResultDataStack(String) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
 
prepareFinalResultStack - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Flag for preparing final result image(s) stack.
prepareImageStack() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Puts all result images into a stack.
prepareMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Preprocess the matrix.
prepareResultImage(MTBImageShort) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Prepare visualization of result.
prepareResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Prepare visualization of result data by overlay on input image.
prepareResultImageStack() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Initialize result image stack.
prepareResultImageStack(Vector<MTBImage>) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Initialize result image stack.
prepareWekaData() - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Converts the given data set into Weka instances.
preprocess(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
preprocess(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
PreprocessLabelImages - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation.measures
Helper class to preprocess label images for segmentation evaluation.
PreprocessLabelImages() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
Default constructor.
PreprocessLabelImages(MTBImage, MTBImage, ArrayList<Integer>, ArrayList<Integer>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
Constructor.
preprocessPlastidRegions() - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Pre-filtering of plastid regions to find regions accidentally including already a stromule.
preSegmentation() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Method for pre-segmentation.
preserveTopology - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
preserveTopology - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
prev - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
previousEnergy - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Snake energy in previous iteration (for change assessment).
previousSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Old snake of previous iteration (for evolution assessment).
prevSegment - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Reference to the preceeding segment along the contour.
print() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Print the whole MTBGraph with all its nodes and edges.
print() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Print the neurite skeleton graph informations.
print() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Prints parameters of curve to standard output.
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Print this energy object - including the value of the energy for phi assumed to be associated with this energy object.
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
 
print() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Print information of this class to stdout
printData() - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
 
printData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Recursively prints the data contained in the nodes of the tree.
printData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
Method to print the data associated with the node.
printData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
 
printData() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
 
printData() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
printHelp() - Static method in class cmdTools.cellAnalysis.ParticleDetector2D
 
printHelp(String, String) - Static method in class cmdTools.mtb_imagetools.ImageConvert
 
printHelp() - Static method in class cmdTools.tracking.multitarget.EvalTracks
 
printHelp() - Static method in class cmdTools.tracking.multitarget.ObservationSeriesGenerator
 
printHelp() - Static method in class cmdTools.tracking.multitarget.ObservationsInfo
 
printHelp() - Static method in class cmdTools.tracking.multitarget.RBMCDATracker
 
printHelp() - Static method in class cmdTools.visualization.DisplayImage
 
printMatrix(Double[][]) - Method in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
printNbPhases(short[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Print current parameter settings to standard output device.
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Print important parameters to standard output stream.
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Print important parameters to standard output stream.
printPoints() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Prints points of snake to standard output stream.
printReadabeTimeInfo(long) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
printTiming - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Should time of processing be printed to stdout
printTree() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Prints tree data.
priority - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
prob - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
ProbabilityDensityFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for multivariate distributions that allow evaluation of their probability density function.
ProbabilityMassFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for univariate distributions based on probability mass functions
ProbTreeData() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
processedImage - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
processedRegionsToBinImage(MTBImage, MTBRegion2DSet, int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Create a binary image from given regions.
processImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Main image analysis routine.
processImage(MTBImage, double, double) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Convert a single image to a heatmap.
processImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Convert a single image.
processMode - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Processing mode.
ProcessMode() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess.ProcessMode
 
processMode - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
processMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Process mode.
profile - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Profile data along longest skeleton path.
profilePoints - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Points of the profile (neurite region) belonging to the longest path.
profileVector - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
projectAlongC - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enables/disables projection along c-dimension.
projectAlongT - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enables/disables projection along t-dimension.
projectAlongX - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enables/disables projection along x-dimension.
projectAlongY - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enables/disables projection along y-dimension.
projectAlongZ - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enables/disables projection along z-dimension.
projector - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
observation model
projMode - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Projection mode.
propertyChange(PropertyChangeEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Changes the available options of the reader option panel according to the selected files
propertyChange(PropertyChangeEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Changes the available options of the writer option panel according to the selected file filter of the file chooser
protrusionCounts - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
protrusionSegs - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData
List of protrusion segments along the contour.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerImageData
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerRegion2DSet
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerSegResultParticlesMultiChannel
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerTableModel
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtPoint2dDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Interface method to announce class for which IO is provided for
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
Interface method to announce class for which IO is provided for
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtPoint2dDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
Interface method to announce class for which IO is provided for.
providerClass - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Version provider class to be used in the current session.
psi - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
pstate - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
state distribution: independent Gaussian mixtures for each target
pUpdater - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Parameter update strategy.
pUpdater - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Parameter update strategy.
putValue(int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new RGB value at the specified position.
putValue(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new RGB value at the specified position in the actual slice.
putValueB(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new blue value at the specified position.
putValueB(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new blue value at the specified position in the actual slice.
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the current slice at coordinate (x,y,z) using a Double
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the current slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
putValueG(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new green value at the specified position.
putValueG(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new green value at the specified position in the actual slice.
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the current slice at coordinate (x,y,z) using an Integer
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the current slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
putValueR(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new red value at the specified position.
putValueR(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new red value at the specified position in the actual slice.

Q

Q - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
Gaussian process noise covariance matrix
qsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
qsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
quality - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
quality - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
qualpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
quit() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Clean-up on termination.
qxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
qxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
qxy_ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
qxy_ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 

R

R - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
Gaussian measurement noise covariance matrix
radiiMaxInscribedEmptyCircles - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
RadioButtonPanel - Class in de.unihalle.informatik.MiToBo.gui
A panel with a titled border and a set of radio buttons that can be reconfigured easily.
RadioButtonPanel(String) - Constructor for class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Constructor
radius - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Radius of the node
radius - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
radius - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Neighborhood radius for LBP code calculation.
radiusImg - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Optional radius image.
radiusScale - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU
Scale factor for radius.
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
random generator for sampling
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
random generator for sampling
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
rand - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
 
random - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Random generator for color sampling.
randomColor(Random) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Generates the next random color.
RandomGeneratorChooser(Random, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
RandomGeneratorDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Data I/O provider for ALDOpRunner (commandline) for java.util.Random objects.
RandomGeneratorDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
 
RandomGeneratorDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Data I/O provider for GUI-OpRunner for java.util.Random objects.
RandomGeneratorDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
 
RandomGeneratorDataIOSwing.RandomGeneratorChooser - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
 
RandomGeneratorDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Xmlbeans provider forjava.util.Random objects.
RandomGeneratorDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
 
randomSeed - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
randomSeed - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
RangeColor() - Constructor for enum de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage.RangeColor
 
rangeMax - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Maximum value of mapping range, will be mapped to second color.
rangeMin - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Minimum value of mapping range, will be mapped to first color.
rankedValueAt(int, int, int, int, int, MTBImage, double[]) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Compute rank operator value for coordinate (x,y,z,t,c) Treatment at boundaries: Image values are mirrored at the border element to determine values under the mask that are outside the image.
rankOp(MTBImage, RankOperator.RankOpMode, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Compute the rank operation of a gray-valued image, stack or hyperstack
RankOperator - Class in de.unihalle.informatik.MiToBo.filters.nonlinear
Rank operator class to compute Median, Minimum or Maximum filter for hyperstack, stack and plain images.
RankOperator() - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Constructor
RankOperator(MTBImage, RankOperator.RankOpMode, int) - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Constructor
RankOperator(MTBImage, RankOperator.RankOpMode, int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Constructor
RankOperator.RankOpMode - Enum in de.unihalle.informatik.MiToBo.filters.nonlinear
Defines the operation
rankOpMode - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
RankOpMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator.RankOpMode
 
rbbox - Variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
vertical box to place the radio buttons on the panel
rbgroup - Variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
the logical group of radio buttons
RBMCDASample<T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
Representation of a RBMCDA-sample.
RBMCDASample() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
Constructor.
RBMCDASample(MultiTargetPredictionFilterIndep<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
Constructor with an initial prediction filter.
RBMCDASampleInfo<T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
RBMCDA-sample info object.
RBMCDASampleInfo() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
RBMCDASampleInfo(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
RBMCDASampleInfo(RBMCDASampleInfo<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
RBMCDATracker - Class in cmdTools.tracking.multitarget
Commandline tool for multi-target tracking with RBMCDA-framework described in [Gress,Posch, "
RBMCDATracker() - Constructor for class cmdTools.tracking.multitarget.RBMCDATracker
 
read(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Read a contour set from an xml file filename and set the MTB polygon set accordingly.
read(MTBXMLContour2DSetType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Read a contour set from an xml object xmlContourSet and set the MTB polygon set accordingly.
read(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Read a polygon set from an xml file filename and set the MTB polygon set accordingly.
read(MTBXMLPolygon2DSetType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Read a polygon set from an xml object xmlPolygon2DSet and set the MTB polygon set accordingly.
readBorderFromASCIIFile(String, String, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Read a 2D border object from an ASCII file in xSV format.
readBordersFromASCIIFiles(String, String, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Read a set of 2D border objects from ASCII files in xSV format from the given directory.
readContourFromASCIIFile(String, String, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Read a 2D contour object from an ASCII file in xSV format.
readContoursFromASCIIFiles(String, String, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Read a set of 2D contours from ASCII files in xSV format from the given directory.
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Returns the contents of the text field.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
 
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
 
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
readData() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Gets the current coordinates.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Function to get selected image from GUI.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtPoint2dDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Gets the data from the configuration window.
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Extracts current collection data.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Gets the data from the configuration window.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Extracts current data.
reader - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
READER_OPTIONS_APPROVED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Property change when writer options are approved (i.e. when filechooser selection is approved)
readFromBinFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Reads a vector field from a file in binary format.
readImage(String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
readImagePlus(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Read image imageIdx from the specified file and return it as ImagePlus object.
readImgProperties(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
readInputImageMaxProjectChannel(String) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Read image from file, do optional max projection and extract selected cytoskeleton channel.
readMarker(NodeList, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
readMarkerData() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
readMaskImage(String, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Read mask data from disk if available.
readMaskImage(String, String, CytoskeletonFeatureExtractor.CellMaskFormat, double, double, double, double, boolean) - Static method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Read mask data from disk if available.
readMTBImage(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Read image imageIdx from the specified file and return it as MTBImage object.
readMultiStates(String) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.MultiStateIO
Read a vector of MultiState objects from a file with xml-beans representation.
readResolve() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperator
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Function for proper initialization of deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Function for proper initialization of deserialized objects.
readSingleValue(Document, String) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
readValue(NodeList, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
ReadXML - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml
Reads markers of an image from file in XML format.
ReadXML(String) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
Creates a new instance of ODReadXMLODD
recalcHueMean(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
Recalculate the mean including incrementing the number of pixels with define hue value, i.e. the number of pixels contributing to the hue sum.
recalcSatMean(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
Recalculate the saturation of the region including incrementing the number of pixels with define saturation value, i.e. the number of pixels contributing to the saturation sum.
recalcXMean(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
Recalculate the X(Intensity / Brightness / Value )-value of the region.
recall - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc
Recall value.
RecallCalc() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc
Default constructor.
RecallCalc(Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc
Constructor with inputs.
recursiveBox - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Flag to enable/disable recursive directory processing.
recursiveProcessing() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Query flag for recursive processing.
recursiveProcessing - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Flag for recursive processing of sub-directories.
red - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Definition of red color.
RED_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
reduce() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Method which implements the dimension reduction.
ReducerMethod() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.ReducerMethod
 
ReductionMode() - Constructor for enum de.unihalle.informatik.MiToBo.math.statistics.PCA.ReductionMode
 
refIndex - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
reflect() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
reflects the structuring element around its center
Region2DSetFromLabelimage - Class in de.unihalle.informatik.MiToBo.segmentation.regions.convert
Operator to convert 2D label image to a MTBRegionsSet2D.
Region2DSetFromLabelimage() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Default constructor.
Region2DSkeletonAnalyzer - Class in de.unihalle.informatik.MiToBo.features.regions
Operator to analyze skeletons of a given set of regions.
Region2DSkeletonAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Default constructor.
Region2DSkeletonAnalyzer.FeatureNames - Enum in de.unihalle.informatik.MiToBo.features.regions
Set of region features calculated from region skeletons.
regionBinaryMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
RegionConverter(MTBRegion2D) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
Default constructor.
regionID - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
regionID - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Region ID of the corresponding neurite region to this neurite skeleton graph.
RegionImageConverter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Default constructor with parameters.
regionIO - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to read a region set.
regionIObin - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to configure binary mode for region sets.
regionMeans - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
List of calculated region average values.
regions - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Result region set, if target format are regions.
regions - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
regions - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
RegionSelector() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
RegionSelector(MTBRegion2DSet, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
regionSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
The set of regions represented as a Vector.
regionSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
The set of regions represented as a Vector.
regionSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Set of 2D regions.
regionSet - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
regionSet - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Resulting region set.
regionsets - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
the container of the region sets
regionSizes - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
List of calculated region sizes.
regionsToBinImage(MTBImage, MTBImage, Vector<MTBRegion2D>) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Create binary image from a set of regions.
regionsToObservations(boolean, MTBRegion2DSetBag) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
Convert regions to observations
regionToFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Write the coordinates of the included 3D points into a text file.
regionTouchesBoundary(MTBRegion2D, int, int) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Test whether a region is located at, i.e. touches, the boundary of the image.
regionVars - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
List of calculated region variance values.
regionVoronoize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Function to perform Voronoi tesselation.
register(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Registers the object to the database.
registerImageBox(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Registers the given (image) object.
reinitOperator() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Re-initialize the operator just in case it was already run before.
relabel(byte[][], int, int, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
find and assign object labels to segmented objects in two frames
relabelRegion(MTBImageByte, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set the unique id of the given region to the pixel value found at the coordinate of the first pixel in the region on the pre labeled MTBImageByte.
relTo(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
 
remove() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
 
remove(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
remove() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
 
remove(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Delete the given lineobject from the set, if contained.
remove(Point2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
remove(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
remove(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Delete the given region object from the set, if contained.
remove(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Remove a region set from this bag
remove(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Remove a region set from this bag by its index
remove() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIterator
 
remove() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelIndexIterator
 
remove() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
 
removeBorderObjects - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
removeBorderObjects - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
removeChild(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Remove child node.
removeEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Remove the specified edge from the graph
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Delete the i-th border from the set.
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Delete the i-th contour from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Delete the i-th segment from the set.
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Delete the i-th region from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Delete the i-th region from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Delete the i-th region from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Removes the element at the specified position in this list.
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Removes the element at the specified position in this list.
removeEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Remove button for energies.
removeExcluded - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
removeExcluded - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
removeExcludedObjects(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
removeExtension(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
Remove extension from filename if any.
removeFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Removes and returns the first element from this list.
removeImage(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
removeIndepGaussian(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Remove independent Gaussian state distribution (at index i)
removeInEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Remove a incoming MTBGraphEdge from the MTBGraphNode.
removeItem(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Remove an item from the set.
removeItem(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves
Remove an item from the set.
removeItem(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Remove an item from the set.
removeLast() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Removes and returns the last element from this list.
removeLastItem() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResult
Removes the last data item.
removeLastItem() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultCurves
Removes the last data item.
removeLastItem() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrSegResultRegions
Removes the last data item.
removeLastMarker() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Removes the last marker from the vector.
removeLeadingDirectories(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
Remove all leading pathname components from a filename.
removeMarker(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Deletes marker with given index from vector.
removeNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Remove the specified node from the graph as well as the edges connected to it.
removeOutEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Remove a outgoing MTBGraphEdge from the MTBGraphNode.
removeShortRuns(int[], int, int) - Static method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Function to remove all sub-sequences of target shorter than the given minimum length by replacing them with negated target.
removeSmallComponents(MTBImageByte, int) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Remove small componentes from an image of type MTBImageByte.
removeSpines - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Flag to enable/disable spine removal.
removeState(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Remove the idx-th state (indices start from 0)
removeState(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
JRI R engine to run R as a single thread.
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
R engine to start R thread.
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
R engine to call R scripts.
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
JRI R engine to run R as a single thread.
replacementPattern - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
replacementString - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
report - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
report - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
ReportGenerator - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
ReportGenerator() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
requiresCounterClockwiseContourSorting() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Ask energy if contour points need to sorted counter-clockwise.
requiresCounterClockwiseContourSorting() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled
Ask energy if contour points need to sorted counter-clockwise.
requiresCounterClockwiseContourSorting() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Ask energy if contour points need to sorted counter-clockwise.
requiresNewlines() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
 
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
requiresOverlapMask() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Ask energy if an overlap mask for all snakes jointly optimized is required.
requiresOverlapMask() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled
Ask energy if an overlap mask for all snakes jointly optimized is required.
requiresOverlapMask() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Ask energy if an overlap mask for all snakes jointly optimized is required.
res_x - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
res_y - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
resample(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Method to re-sample the line segments of the polygon in a range of a given segment length.
resample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Resample this distribution and equalize weights
resample(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Method to re-sample the line segments of the snake in a range of a given segment length.
resampleConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
resampleConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Constant for resampling the snake control points.
resampleSegLength - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Target length of snake segments in resampling.
resampleSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Resamples the snake using the specified segment length.
reset() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Reset time
reset() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
resetButton - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Button to reset color to null.
resetLabel(int, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
resetPotential() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Resets the potential, next access to it will enforce recalculation.
resetShape() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Delete shape object, i.e. reset to null.
resizeMatrices() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Resize parameter matrices.
ResponseDifference(double, double) - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.ResponseDifference
Default constructor.
responseStack - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Stack with filter responses of all orientations.
responseStack - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Result stack with binary vessel maps for different scales and lengths.
responseStack - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Result stack with intermediate results.
restoreConfigWins() - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
 
result - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
result_energy - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result directory for snake energy results.
result_extraction - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result directory for neurite extraction results.
result_presegmentation - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result directory for pre-segmentation.
result_snakes - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result directory for snake results.
resultAdditionalImages - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Additional result images condensed into a single stack (only available if PaCeQuant.showAdditionalResultImages is true).
resultAreas - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
resultBinaryImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult
Binary image with segmented regions in foreground (white).
resultBinFilteredImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Filtered binary vesselness image.
resultBinVesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Binarized vesselness image.
resultBorders - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Set of extracted borders.
resultCellContours - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
ROI set of detected cell regions.
resultCellImg - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Input image with snake contours overlayed (optional).
resultCellLabelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Label image of detected cell regions.
resultCellLabelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Label image of detected cell regions.
resultCellOverlayImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Overlay of input image with pseudo-colored cell regions.
resultCellRegions - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Set of detected cell regions.
resultCenters - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Set of detected nuclei centers.
resultContourImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
resultContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
* The calculated contours, every contour can include several inner contours.
resultCosts - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Costs of the result path.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Result data object.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Result data object.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Result data object containing quantitative data and label images.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Vector of result data objects.
resultData - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Result of the calculation.
resultData - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Resulting data set with each column containing a data vector.
resultDataAreaFractions - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: area fractions.
resultDataAvgSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: average size.
resultDataCells - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Local container for cell cytoplasm segmentation result.
resultDataCellSizes - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: cell sizes.
resultDataCounts - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: counts.
resultDataTotalSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: total structure size per cell.
resultDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Main directory for result output.
resultDisplayMode - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Mode of how to display result image.
resultDisplayMode - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Mode of how to display result image.
resultFeatureStack - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Stack of individual feature images as heat maps (only available if PaCeQuant.showResultFeatureStack is true).
resultFeatureTable - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Table with region features.
resultFeatureTable - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Table with region skeleton features.
resultFile - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Optional file where to save the result table.
resultImage - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Result segmentation image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Optional stack of result visualizations, if result data suppports that.
resultImage - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Several result formats.
resultImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
Resulting thinned (and thresholded) magnitude image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Output image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Image of extracted borders.
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
* The binary image with the calculated contours and the contours as possible outputs from the operator.
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Resulting binarized image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Result image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Result image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Output image.
ResultImageMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D.ResultImageMode
 
ResultImageMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D.ResultImageMode
 
resultImagePlus - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
resultImages - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Local container for set of segmentation result and channel copy images.
resultImages - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Vector for collecting result images.
resultImageStack - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
(Optional) stack of result images with segmentation masks/overlays.
resultImageType - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
resultImageType - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
resultImageType - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Result label image of separated nuclei.
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Result label image of separated nuclei.
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Stack with result overlays corresponding to channels.
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching
Result image with stretched contrast.
resultImg - Variable in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Result image with improved contrast.
resultImg - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Enhanced or segmented result image, either of type double or binary.
resultImg - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Filtered image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Result image with path overlay, start pixel in green, end pixel in blue.
resultImg - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgClose
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgErode
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor
Binary result image, skeleton in white, background in black.
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.WatershedBinary
Segmented binary image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours
Result image showing the ground truth image and the segmented contours.
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Result image displaying the snakes as overlay.
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Result image (stack).
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Generated result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Generated result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Generated result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
Result image.
resultImgHeight - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Desired height of result image.
resultImgIntermediate - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Debug image with intermediate result data.
resultImgOffsetX - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Desired offset in x of result image.
resultImgOffsetY - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Desired offset in y of result image.
resultImgWidth - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Desired width of result image.
resultInfo - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Info string for segmentation phase configuration parameters.
resultingRegions - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set of detected particle regions.
resultingRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Resulting set of labeled regions.
resultingRegionsets - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
resultInitialSkeletonImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Initial skeleton image.
resultJunctions - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Detected junction points.
resultLabelImage - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
Label image of detected plastid regions with stromuli.
resultLabelImage - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Label image of detected plastid regions with stromuli.
resultLabelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult
Result image with labels of segmented regions.
resultLableImgWithoutIDs - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult
Label image without region ID strings.
resultLines - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Detected lines.
resultList - Variable in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator
Color list.
resultLobeFeatureTables - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
(Optional) set of tables with type information and features per lobe.
resultLobeTypeImage - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Image showing lobe classification.
resultMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
resultMaskBinary - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Binary mask of detected regions.
resultMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Result matrix containing final matching.
resultMaxRegionSizeThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Used threshold for maximal size of valid regions.
resultMinRegionSizeThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Used threshold for minimal size of valid regions.
resultMSERs - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set of detected MSER regions.
resultMTBImage - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
resultMTBImg - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Result Image.
resultObj - Variable in class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Result data object, e.g., an image, a histogram, a vector, ....
resultOverlay - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Detected regions plotted into input image.
resultOverlayImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult
Image overlay of detected regions over input image.
resultOverlayImgWithoutIDs - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult
Image overlay of detected regions over input image without ID strings.
resultPath - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Result path represented as point list.
resultRegCenters - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Nuclei centers sorted according to former regions.
resultRegionCount - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Number of detected regions.
resultRegs - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult
Set of segmented regions.
resultRGBimage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
RGB image overlay with result nuclei contours.
resultSet - Variable in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles
Resulting contour set.
resultSkelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Skeleton image (of cell boundaries).
resultSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.ArealParameterExtractor
 
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
A table containing information for each region
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
A table containing information for each region
resultStats - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Result data object.
resultTable - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result table showing the the detection and morphology measurements.
resultTable - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
resultTable - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Result table for visual result inspection.
resultTable - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Table with result data.
resultTreelines - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Resulting enhanced treeline annotations.
resultType - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Type of result features to be returned.
resultType - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Desired type of result.
ResultType() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.ResultType
 
resultValue - Variable in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
 
resultValueMode - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Result value mode.
ResultValueMode() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.ResultValueMode
 
resultVector - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Name of the analyzed image.
resultVesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Result of applying the vesselness filter to the input image.
resultVesselMap - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Final vessel map.
resultVesselMap - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Resulting binary vessel map.
resultVesselMap - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Resulting binary vessel map.
resultXylemRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Final xylem regions after postprocessing.
resultXylemRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Final xylem regions after post processing.
reversePolypoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Changes the ordering of the polygon points.
reversePolypoints() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Overwrite reversePolypoints method of Polygon2D.
revisionFile - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Name of revision file from where to read revision information.
rgbColor - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
Resulting RGB values.
rgbColor - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Resulting RGB values.
rgbOutput - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Output RGB values.
rgbToHSB_JRE(int[]) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Conversion from RGB into HSB color space.
rgbToHSI_Sonka(int[]) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Conversion from RGB to HSI color space according to Sonka et al.
rgbToHSV_EasyRGB(int[]) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Conversion from RGB into HSV color space.
RGBToHSXConverter - Class in de.unihalle.informatik.MiToBo.color.conversion
Converts an image of type MTBImageRGB ( RGB color space ) into an image with HSX( hue saturation intensity/brightness/value ) color space.
RGBToHSXConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Default constructor.
RGBToHSXConverter(MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Constructor.
RGBToHSXConverter.ColorChannel - Enum in de.unihalle.informatik.MiToBo.color.conversion
Supported Color Channels.
RGBToHSXConverter.Mode - Enum in de.unihalle.informatik.MiToBo.color.conversion
The way of converting an image from rgb to hsi.
rgbValue - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
rho - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Weighting factor and overlap penalty, respectively.
rightBorderPoint - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Right boundary point of segment after potential shifts.
rightBorderPointPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Index of right boundary point of segment after potential shifts.
rightOutlierFraction - Variable in class de.unihalle.informatik.MiToBo.enhance.GlobalContrastStretching
Fraction of outlier pixels at right histogram margin.
roiAdapt - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
The object instance.
roiFile - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter
Input ROI file or zip archive with ROIs.
RoiFileToCSVConverter - Class in de.unihalle.informatik.MiToBo.core.imageJ
Operator to convert contours of ImageJ ROIs to CSV format.
RoiFileToCSVConverter() - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter
Default constructor.
roiManager - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reference to the current ImageJ roi manager.
RoiManagerAdapter - Class in de.unihalle.informatik.MiToBo.core.imageJ
Convenience functions for interaction with ImageJ's ROI manager.
RoiManagerAdapter() - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Hidden constructor, never called from outside.
RoiManagerAdapter.RoiReader - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class for parsing ImageJ roi files and zip archives.
RoiManagerAdapter.RoiReader.TargetFormat - Enum in de.unihalle.informatik.MiToBo.core.imageJ
Format into which the ROIs should be converted.
roiManagerAdd - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
roiManagerChecker - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
RoiReader(String, RoiManagerAdapter.RoiReader.TargetFormat) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Default constructor.
roisAdded - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
roisAdded - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
roisAdded - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
roitable - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Helper hash table.
RoiWriter - Class in de.unihalle.informatik.MiToBo.core.imageJ
Operator to save data objects to native ImageJ ROIs.
RoiWriter() - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
Default constructor.
root - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Root node of the tree.
RootImageSegmentationOperator - Class in de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation
Abstract super class for operators segmenting roots from images.
RootImageSegmentationOperator() - Constructor for class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Default constructor.
RootImageSegmentationOperator.LayerSubset - Enum in de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation
 
RootImageSegmentationOperator.OpWorkingMode - Enum in de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation
 
ROOTSEGMENT_STATUS() - Constructor for enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.ROOTSEGMENT_STATUS
 
rotatePoint2D(Point2D.Double, double) - Static method in class de.unihalle.informatik.MiToBo.math.MathXGeom
Rotate a 2D point around the given angle.
rotatePoint2D(double, double, double) - Static method in class de.unihalle.informatik.MiToBo.math.MathXGeom
Rotate a 2D point around the given angle.
roundnessThreshold - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Roundness threshold for components.
rowMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Array containing row marks.
rows - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Number of rows of the table.
rsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
rsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
run() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D.UWTRunner
 
run() - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
 
runFeatureExtractionPhase(MTBImage, MTBRegion2DSet, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Extracts features from given set of regions and corresponding images
runIterativeMode() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Cell tissue segmentation in an iterative fashion.
runMeanVarMode() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Deprecated.
runOperation(MTBOperator, ImageArithmetics.ArithOp, MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Run an operation with one input image and one input constant
runOperation(MTBOperator, ImageArithmetics.ArithOp, MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Run an operation with two input images
runSegmentationPhase(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Method that processes a single image.
runtime - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
runtimes - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
rxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
rxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 

S

s - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
Array of saturation values.
s - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Saturation of HSV space.
s - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData
The string data to store.
sampleCount - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Number of data samples in input data.
sampleEnergyData - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
sampleInfo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
sampleinfo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
Properties represented by this sample.
sampleJointProb - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
SamplingDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for densities from which samples can be drawn.
satMean - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
satMTBImg - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Saturation channel image.
satSum - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
satThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The saturation threshold.
satThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The saturation threshold.
SATURATION_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
SATURATION_UNDEFINED - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
To cope with undefined saturation/hue-values, we use the following scheme.
save(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
write the histogram data into a text file
saveExtEnergy(String) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Save the gvf field in a MATLAB like file.
saveFile() - Method in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Saves the current processing result.
saveIntermediateResultPath - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Path where to save intermediate results.
saveIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Flag for saving intermediate results to a specified directory.
saveIntermediateResults(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set flag to save intermediate results.
saveIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Flag for saving intermediate results.
saveIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag to enable/disable saving of intermediate results.
saveIntermediateResultsPath - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Path where to save intermediate results.
saveIntermediateResultsPath - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Path to where intermediate results should be stored.
saveNeuriteWidthList(Vector<Double[]>, String) - Static method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Method to save the neurites width profile in a file.
savePolygon(PolygonRoi) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
Saves the given polygon to the specified output file.
savePolygonSet(PolygonRoi[]) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
Saves the set of polygons to the specified output file.
saveProfileSet(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Saves the given profile data list with N profiles to the given file.
saveRegionData(String, String, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Save region set to output file.
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Save intermediate results.
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Save intermediate results.
saveSnakeLoc - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Path where to save intermediate results.
saveSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Flag to enable/disable saving of intermediate snake results.
saveSVM() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
save resulting svm model file
saveTable(File) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Saves the contents of the table to given file, TSV format.
saveTilesToFiles(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Saves all tiles to the given path.
saveToBinFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Saves the vector field to a file in binary format.
SCALEBARWIDTH - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
 
scaleDown - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
Scaling factor for normalization Still experimental
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Scale factor of the snake for normalization.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Scaling factor for image coordinates.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Scaling factor for image coordinates.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Scale factor for snake normalization.
scaleIntervalSize - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Size of scale interval for calculating wavelet correlation images.
scaleIntervalSize - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorParticlesUWT
Size of scale interval for calculating wavelet correlation images.
scaleMax - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
scaleMin - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
scaleNormalizationFactor - Static variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Factor to normalize filter responses of different scales appropriately.
scaleNum - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
scaleValues(int, int, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Method to scale the intensity values (range [curMin, curMax]) of the image to a given range [scaleMin, scaleMax].
scaleValues - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
scalingK - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Niblack scaling parameter k.
scalprod(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Calculates the scalar product of the given segment to this one.
scanPath - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Local flag to indicate if we are currently tracing a path for a new piece of boundary.
schwelle - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Threshold to suppress peak analysis close to scraggy contours.
ScoreInterpretation() - Constructor for enum de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm.ScoreInterpretation
 
scoreMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Matrix containing pairwise scores of bipartite sets.
scoreMatrix - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Score matrix with pairwise overlaps.
scoreMatrix - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Score matrix with pairwise overlaps.
scratchArea - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
scratchAreas - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
ScratchAssayAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.scratchAssay
class for analyzing the scratch areas in a scratch assay/ gap closure/ wound closure assay
ScratchAssayAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
ScratchAssayAnalyzer(MTBImage, int, int, ScratchAssayAnalyzer.ScratchOrientation, boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
ScratchAssayAnalyzer.AbsenceDetectionMethod - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssayAnalyzer.ScratchOrientation - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssaySegmenter - Class in de.unihalle.informatik.MiToBo.apps.scratchAssay
class for segmenting the wound area of a scratch assay image

First the image is smoothed.
ScratchAssaySegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
ScratchAssaySegmenter(MTBImage, int, int, boolean, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
ScratchAssaySVMTrainer - Class in de.unihalle.informatik.MiToBo.apps.scratchAssay
class for training and cross validating a support vector machine for classification of scratch assay
images into images containing a scratch and those that don't
ScratchAssaySVMTrainer() - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
ScratchAssaySVMTrainer(String, String, int, int, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
ScratchAssaySVMTrainer.KERNEL_TYPE - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssaySVMTrainer.ScratchOrientation - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssaySVMTrainer.ValidationMethod - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
scratchFeatures - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
scratchFiles - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
ScratchOrientation() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.ScratchOrientation
 
ScratchOrientation() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ScratchOrientation
 
SecondOrderCentralMoment<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for classes that provide a second order central moment.
seedImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
seedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The seed regions as a binary image after the final erosion.
seedRegions - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The seed regions as a binary image after the final erosion.
seen - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
seErosionSize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Size of the structuring element for the erosion.
segContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours
List of point-wise segmented contours.
segContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
List of contours of segmented objects.
segDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
segImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
Label image of segmentation result.
segLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Preprocessed segmentation label image with short pixel type.
segLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Label image of segmentation result.
segLabels - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
List of labels of segmented regions.
segLabelsOrig - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Label image of segmentation result.
segLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Length of segment measured as number of pixels.
segment(MTBImage, String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
segment(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
segment cells in a single frame of the input image
segment(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
segmentation - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Segmentation object.
SegmentationConfigWin(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Default constructor.
SegmentationDimension() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface.SegmentationDimension
 
SegmentationDimension() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.SegmentationDimension
 
SegmentationInitializer - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Operator for initializing objects of type MTBSegmentationInterface.
SegmentationInitializer() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Default constructor.
SegmentationInitializer.InputMode - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Available data sources.
SegmentationInitializer.SegmentationDimension - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Available dimensions for segmentations.
SegmentationInitializer.ShapeType - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Available shape types.
SegmentationInitializerDataIOSwing - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Class for loading/saving objects of type SegmentationInitializer.
SegmentationInitializerDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
 
SegmentationInitializerDataIOSwing.ConfigureSegmentationButton - Class in de.unihalle.informatik.MiToBo.segmentation.basics
GUI element for configuring segmentations.
SegmentationInitializerDataIOSwing.SegmentationConfigWin - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Segmentation configuration window.
segmentationInputFormat - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Format of external segmentation input.
SegmentationInputFormat() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationInputFormat
 
SegmentationMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete.SegmentationMode
 
segmentationParameters - Static variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
List of parameters relevant for segmentation phase.
SegmentationResult() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationResult
 
segmentationResult - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
segmentInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Preprocessing and segmentation of input image.
segmentlength - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Snake segment length.
SegmentType() - Constructor for enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.SegmentType
 
segMode - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Mode how the channel of the image was treated during segmentation.
segObject - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
segRegionLabels - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours
List of labels of segmented regions.
SegResult_Complete - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Complete segmentation result from multi-channel image.
SegResult_Complete(String, int, SegResult_Complete.SegmentationMode, SegResult_Cytoplasm) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Default constructor.
SegResult_Complete.SegmentationMode - Enum in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Indicator for segmentation mode.
SegResult_Cytoplasm - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Cell boundary segmentation result from single-layer image.
SegResult_Cytoplasm(String, MTBPolygon2DSet, MTBImageByte, int, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Deprecated.
SegResult_Cytoplasm(String, MTBPolygon2DSet, MTBImageByte, int, int[], double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Default constructor.
SegResult_Interface - Interface in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Interface for unified handling of segmentation results extracted by particle, cell or nucleus detectors.
SegResult_Nuclei - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Nuclei segmentation result from a single image channel.
SegResult_Nuclei(String, int, MTBImageByte, MTBImage, MTBRegion2DSet, int, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Default constructor.
SegResult_Particles - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Particle detection result for a single channel of an image.
SegResult_Particles(String, int, MTBRegion2DSet, MTBImageByte, int, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Default constructor.
SegResult_ParticlesMultiChannel - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Particle detection result for a multi-channel image.
SegResult_ParticlesMultiChannel(String) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Default constructor.
SegResultEnums - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Defines of enumeration types used in conjunction with cell image analysis.
SegResultEnums() - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums
 
SegResultEnums.MeasureUnit - Enum in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Unit for measurements.
selectBox - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Combobox to select images.
selectButton - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Button to open selection window.
selectedEnergies - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
List of currently selected energies.
selectedEnergies - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
List of currently selected energies.
selectedImage - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Recently selected image.
selectFileDir - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Button to select via dialogue.
selection - Variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
string/label of the selected radio button
SELECTION_CHANGED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Property change of the panel when a selection is changed
selectLargeRegions(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
semiAxisLengthA - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Half-length of axis a.
semiAxisLengthB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Half-length of axis b.
seOpeningSize - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Size of the structuring element for Opening.
seOpeningSizeInitSeg - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Size of the structuring element for Opening.
separate(int, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
try to separate component with label 2.
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
 
serialVersionUID - Static variable in exception de.unihalle.informatik.MiToBo.io.images.OverwriteException
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
Default serial number.
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel
Default serial number.
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
 
seriesIndices - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
seriesnames - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
seriespanels - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
set(int, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
 
set(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
assign a value to the matrix at position ( x, y, z )
setActive() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Set marker active.
setActivityArray(boolean[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Specify set of active snakes.
setActualSliceOnly() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Only actual slice is thresholded, this will force the output image type to be of the same type as the input image (or destination image type)
setAdjacencyMatrix(AdjacencyMatrix<T>) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set the main graph's adjacency matrix
setAlgorithm(Contour2DCurvatureCalculator.Algorithm) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
setAnalyzeProtrusionsAndIndentations(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Turn on/off analysis of contour protrusions and indentations.
setAngle(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Set orientation of filter.
setAngleSampling(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Set angular sampling interval.
setArithmeticOperation(ImageArithmetics.ArithOp) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setAssociation(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
setAssociation(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Set an association between target and observation.
setAvgIntensity(double) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShape
Set average region intensity.
setBaselineConstant(double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Specify baseline constant for thresholding.
setBGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Tell the thresholder to use the original pixel value for background pixels
setBGValue(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set value of Parameter argument BGValue.
setBinaryImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set the binary image.
setBinValue(int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
set the bin value at i-th position
setBorderExclusion(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
should border touching objects be excluded
setBorderType(BordersOnLabeledComponents.BorderType) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Set border type to be extracted.
setBoundaryPadding(MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set value of Parameter argument boundaryPadding.
setBoundaryPadding(MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set value of Parameter argument boundaryPadding.
setBoundaryPadding(MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set value of Parameter argument boundaryPadding.
setBthMaskSize(Integer) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Set mask size of black top-hat.
setC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setCalcArea(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
setCalcCircularity(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Turn of/off calculation of circularity.
setCalcCompactness(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
setCalcConcavityData(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Turn on/off calculation of concavity information.
setCalcConvexHullMeasures(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Turn on/off calculation of convex hull measures.
setCalcEccentricity(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Turn of/off calculation of eccentricity.
setCalcLengthWidth(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Turn of/off calculation of region length and width.
setCalcMarginRoughness(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Turn on/off calculation of margin roughness values.
setCalcPerimeter(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
setCalcSkeletonBranchFeatures(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Turn on/off calculation of skeleton branch features.
setCalcSolidity(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Turn on/off calculation of solidities.
setCalcSurfArea(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
setCalcVolume(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
setCalibration(Calibration) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the calibration object (see getCalibration() for further information).
setCalibrationFromUnderlyingIJImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the MiToBo image calibration reference to underlying ImagePlus calibration.
setCategoryColors(Color[]) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Specify colors for different categories.
setCategoryColors(Color[]) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Specify colors for different categories.
setChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
setChannel(Integer) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Set the image channel.
setChannelsAreRGBFlag(Boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set flag if RGB color channels are interpreted as real image channels.
setChannelsToCopy(int[]) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify list of channels to copy to result stack.
setChosenColor(Color) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Select given color.
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setClass(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set the label of position (x,y) to c.
setClass(int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set the label of position (x,y,z) to c.
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Deprecated.
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Deprecated.
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Deprecated.
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Deprecated.
setCloneTargetImage(boolean) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Enable or disable cloning of target image.
setClosed() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Set polygon closed.
setClusterNum(int) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Specify number of clusters.
setCodec(Integer) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the codec (quicktime only).
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Set color of markers.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Specify color in which to draw the contours.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Specify color to use.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
Specify color to use for drawing.
setColor(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawMask2D
Specify color as integer value, right 24 bits are interpreted as R,G,B.
setColor(String) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Specify color in which to draw the snakes.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the uniform color of the regions in a color image.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
Specify color.
setColor(int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Set the color for given key.
setColorArray(int[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Specify pseudo-colors for snake visualization.
setColorImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Add the label image to the parameter object
setColorNumber(int) - Method in class de.unihalle.informatik.MiToBo.color.tools.DistinctColorListGenerator
Set number of colors.
setColorRangeMaximum(Color) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Color for range maximum.
setColorRangeMaximum(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Color for range maximum.
setColorRangeMinimum(Color) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Color for range minimum.
setColorRangeMinimum(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Color for range minimum.
setColumnName(int, String) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Sets the header of column to specified string.
setCompactnessThreshold(double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set the compactness threshold for eliminating non compact components.
setCompression(String) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the compression type
setConcavityMaskSize(int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Specify size of local mask for concavity calculations.
setCondition(Double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
setCondition(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.ConditionalDistribution
Set the conditional variable
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
 
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
 
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
setConnectivity(MTBBorder2D.BorderConnectivity) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Set the connectivity.
setConnectivity(MTBBorder2D.BorderConnectivity) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Specify connectivity for extracted border pixels.
setConnectorIDs(long[]) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Set connector IDs.
setContours(MTBContour2DSet) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
Specify optional input contours.
setContourType(ContourOnLabeledComponents.ContourType) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set reference to the contour type.
setCopyInputImage(boolean) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Enable/disable copy of input image.
setCorrectGamma(Boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set flag to use gamma correction.
setCorrectPosition(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify if to correct line positions.
setCorrelationThreshold(double) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set threshold for thresholding wavelet correlation images
setCountMode(CalcStructureStatistics.StructureCountMode) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Specify mode how to assign structures to cells.
setCovariance(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
setCreateBinaryMasks(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Enable/disable creation of binary masks.
setCreateColorImageFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set the flag that determines the creation of an image with randomly colored regions.
setCreateIDImageFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Enable/disable creation of ID image.
setCreateLabelImageFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set the flag that determines the creation of an image with region labels.
setCSVFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter
Specify the file where to save csv data.
setCurrentSlice(MTBImageManipulator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Copy the values of the source to the current slice
setCurrentSliceCoords(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the current slice for functions that work on a slice only (this has nothing to do with the ij.ImageStack's current slice)
setCurrentSliceIndex(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the current slice for functions that work on a slice only (this has nothing to do with the ij.ImageStack's current slice) Stack indices range from 0 to N-1 (unlike ImageJ, where stack indices range from 1 to N)
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the slice label of the slice specified by the current slice index
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the slice label of the slice specified by the actual slice index
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the slice label of the slice specified by the actual slice index
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the slice label of the slice specified by the actual slice index
setCurrentZStackCoordinates(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the current z-stack coordinates for functions that work on (spatial) 3D only.
setCytoskeletonChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Specify channel with stained cytoskeleton.
setDarkLine(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify if to detect dark lines on bright background.
setData(Vector<?>, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Set data for current MTBGraphEdge with the given cost.
setData(Vector<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Set data for current MTBGraphEdge.
setData(MTBTreeNodeData) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Set the data object of the node.
setData(MTBDataExportableToImageJROI) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
Specify the data to save.
setData(HashMap<String, HashMap<String, LinkedList<Double>>>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set the data to plot.
setData(HashMap<String, HashMap<String, Double>>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set the data to plot.
setDataIsPeriodic(boolean) - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D
Specify if data is periodic or not.
setDataset(double[][]) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Specify an input dataset.
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of debug.
setDebug(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of debug.
setDebug(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Set value of debug.
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Set debug bit mask
setDefaultFps(int) - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Set a default fps to show in the option panel, e.g. if the fps can be determined from some image metadata
setDelimiter(ALDTableWindow.TableModelDelimiter) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Configure the delimiter to be used when exporting the table.
setDelta(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set distance between threshold images to be compared.
setDeltaT(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setDeltaT(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set the time between two frames
setDeltaX(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setDeltaX(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set pixel length in x-direction
setDeltaX(Double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
setDeltaXY(Double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
setDeltaY(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setDeltaY(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set pixel length in y-direction
setDeltaY(Double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
setDeltaZ(Double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
setDenoise(boolean) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set the denoising flag. true to activate denoising.
setDestinationImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set value of Input argument DestinationImage.
setDetectionChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
setDetectionMode(CytoplasmAnalyzer2D.DetectMode) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Specify detection mode.
setDetector(ParticleDetectorUWT2D) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
Specify particle detector to apply.
setDiagonalNeighbors(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
If true 8-neighborhood, i.e. diagonal neighbors, will be used in mode 'VORONOI_EXPAND' for Voronoi dilation.
setDiagonalNeighborsFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set the neighborhood flag.
setDiameter(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
setDilateMaskSize(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Specify mask size for topology-preserving dilation.
setDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection>) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Directions to be analyzed.
setDistance(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
Specify distance for calculating cooccurrence matrices.
setDistance(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Specify distance to be used in calculations.
setDistmet(DistanceTransform.DistanceMetric) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Specify the metric for the distance transformation.
setDistMetric(DistanceTransform.DistanceMetric) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Set the distance metric.
setDoErosion(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of doErosion.
setDoGauss(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify if cell channel is to be smoothed prior to detection.
setDomainXMax(double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Set maximal x value of user-specified domain.
setDomainXMin(double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Set minimal x value of user-specified domain.
setDomainYMax(double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Set maximal y value of user-specified domain.
setDomainYMin(double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Set minimal y value of user-specified domain.
setDotGlobalAttributes(String[]) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set global attributes of the graph e.g. the style of the nodes etc.
setDrawCurvatureInfoImage(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Enable/disable display of curvature info image.
setDrawSkeletonInfoImage(boolean) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Enable/disable display of skeleton info image.
setDrawType(DrawRegion2DSet.DrawType) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the kind of region image to be drawn
setEightconnected(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Set which neighborhood to use for labeling components.
setElementAt(MTBBorder2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Set the i-th border of the set.
setElementAt(MTBContour2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Set the i-th contour from the set.
setElementAt(MTBLineSegment2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Replace the i-th line segment of the set.
setElementAt(int, MTBPolygon2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Set a polygon at i-th position of the set.
setElementAt(MTBRegion2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Set the i-th region from the set
setElementAt(MTBRegion3D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Set the i-th region from the set
setElementAt(MTBSurface3D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Set the i-th region from the set
setElementAt(int, MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Replaces the element at the specified position in this list with the specified element.
setElementAt(int, MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Replaces the element at the specified position in this list with the specified element.
setEllipse(MTBQuadraticCurve2D) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Specify ellipse to draw.
setEndPixel(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Specify end pixel of path.
setEnergy(MTBGenericEnergyNonPDE) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of energy.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Sets list of energies.
setEnergyList(Vector<T>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Specify a new set of energies, all weights are reset to 1.0.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Specify a new set of energies, all weights are reset to 1.0.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Specify a new set of energies, all weights are reset to 1.0.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Specify a new set of energies, all weights are reset to 1.0.
setEnergySet(MTBSet_ActiveContourEnergy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Specify set of energies.
setEnergySet(MTBSet_ActiveContourEnergy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
setEnergySet(MTBSet_ActiveContourEnergy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
setEqualWeightsFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Set the "equal weights"-flag
setErodeSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of erodeSize.
setErodSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set the size of the eroding element in pixel.
setESSPercentage(double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
Set percentage of number of samples used to determine if resampling is required, i.e. if it is below the current effective sample size (ESS).
setEstimateWidth(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify if to estimate width.
setExcluded(Vector<Integer>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
setExcludeList(int[]) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Specify attributes to be excluded.
setExcludeMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Specify exclude mask.
setExcludeMask(boolean[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Set exclude mask.
setExcludeMask(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
setExtendLine(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify if to extend lines.
setFactor(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setFactoryMethod(MTBImage.FactoryMethod) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setFeatureOperators(Vector<FeatureCalculator>) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Set feature operators.
setFeatureType(FeatureCalculatorLBPJFeatureLib.FeatureType) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Specify type of features to be calculated.
setFG_Value(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
set the intensity value of the remaining foreground regions
setFGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Tell the thresholder to use the original pixel value for foreground pixels
setFGValue(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set value of Parameter argument FGValue.
setFieldSizeX(int) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Set the field size in x-direction.
setFieldSizeY(int) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Set the field size in y-direction.
setFilename(String) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set the filename for output
setFileName(String) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set the filename of the image that has to be read.
setFileName(String) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set image filename
setFill(Color) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setFill(double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setFilterImage(Boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set flag to use gaussian filter.
setFilterMode(MedialnessMultiScaleFilter2D.FilterMode) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set filter mode to define relation of foreground to background.
setFlagIsotropicCalculations(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
Enable/disable isotropic calculations.
setFlagThrinkMatrix(boolean) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Flag for thrinking matrix if possible.
setForeground(DistanceTransform.ForegroundColor) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Set the foreground color.
setForwardTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Toggle computation of the (forward) transform (image to wavelet)
setFps(Integer) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the frames per second for movie writers (*.avi,*.mov).
setFractionalDigits(int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
specify the number of fractional digits for the results table
setFractionalDigits(int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
specify the number of fractional digits for the results table
setFrequency(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify frequency.
setGamma(Double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set gamma correction value.
setGamma(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
setGamma(Double) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Set the gamma value.
setGammaToAuto(boolean) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Set if gamma should be calculated automatically or not.
setGaussianSigmaCurvatureSmoothing(double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Set Gaussian standard deviation for smoothing curvature values.
setGaussSigma(double) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify sigma for Gaussian smoothing.
setGradientMode(GradientFieldCalculator2D.GradientMode) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Set the used gradient mode for field calculation.
setGraph(MTBGraph) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set the main graph using MTBGraph
setGrayValue(Double) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the gray value of the regions in a mask image.
setGroundtruthObservations(Vector<MultiState<MotionModelID>>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
setGrownRegions(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setH(double) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Set current h-parameter (max height of the h-domes).
setHaralickDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection>) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures
Set directions for which to calculate cooccurence matrices.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Set image height.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Set image height.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Specify height of filter mask.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Specify height of filter mask.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Specify height of filter mask.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set image height.
setHighContrast(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify high contrast.
setHigherThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Specify higher threshold.
setHighQualityData(boolean) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Enable or disable extraction of high quality data.
setHistBins(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPs
Specify number of histogram bins.
setHistBins(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorLBPsRIU
Specify number of histogram bins.
setHistBins(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Specify number of histogram bins.
setHistogram(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
setHistoRegionSize(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Specify region for histogram binning.
setHistoryLink(Object, ALDPort) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Sets the port to which the object is to be linked in history.
setHSIInput(double[]) - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Specify HSI value to be converted.
setHueMTBImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Set the hue channel image.
setHueThresh(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setID(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
setID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Set the ID of the region.
setID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Set the ID of the region.
setID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
Set the ID of the region.
setIgnoreBorderFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Set flag to include/ignore structures along image border.
setIgnoreInvalidStackSpecification(boolean) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the flag to ignore an invalid stack specification.
setIgnoreMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Specfiy additional mask of pixels to ignore.
setIgnoreMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Specfiy additional mask of pixels to ignore.
setImageDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Specify input image directory.
setImageJPref(String, String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This functions sets a given property to the specified value.
setImagePart(MTBImageManipulator, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set a part of this image to the values of the source
setImagePlus(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Stores given image to the container.
setImageProcessor(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.JFeatureLibLBPAdapter
 
setImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Set output image type.
setImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the resulting image's datatype.
setImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set the image domain image
setInactive() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Set marker inactive.
setInConst(double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setIndexOfImageToRead(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set the index of the image that has to be read from the file.
setIndividually(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Set how to treat the components, individually or as a whole.
setInfo(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Set info string of set.
setInfo(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
setInImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
Specify input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Specify gray-scale input image.
setInImg(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Specify binary input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Input argument inImg.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
Set input image for morphological operation.
setInImg(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Set the input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of inImg.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Set input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Set input image.
setInImg1(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setInImg2(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setInitalSegmentation(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setInitBinImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of initBinImg.
setInitialSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify set of initial snakes.
setInitialSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Specify initial snakes.
setInitialSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Specify initial snakes.
setInitLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of initLabelImg.
setInitMask(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
setInitSegImageByte(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setInner(Vector<MTBBorder2D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Set the inner borders of the border object.
setInner(Vector<MTBBorder2D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Set the inner contours of the contour object.
setInnerContourLengthMin(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set the minimum number of pixels in the inner contour (length of the contour).
setInputArray(double[]) - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.ArrayFilterDouble1D
Set array to process.
setInputData(String, int[]) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
Set input data.
setInputData(MTBTableModel) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Specify input data.
setInputGrayScaleImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Specify input gray-scale image.
setInputGrayScaleImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Specify input gray-scale image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
Set input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Specify input image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set input image
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidDetector2DParticlesUWT
Specify input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Set the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Set uneven illuminated input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Specify the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Set low contrast input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Sets the input image to work on.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Set the underlying input image of the gradient field.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Set input image to analyze.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Specify the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify input image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Set input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Set input image (if ConvexHullExtraction.inType is InputType.IMAGE).
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Set input image
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor
Set input image to process.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Set input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Set the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Set input image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set reference to the current input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set a new input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Specify an input image for the segmentation.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set input image
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Set input image.
setInputImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawContour2DSet
Set input image into which to draw the contours.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Specify input image.
setInputImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Set input image into which to draw the polygons.
setInputImagePlus(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set ImagePlus to store to disk
setInputImages(HashMap<Integer, ImagePlus>) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Setter for the input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set input image
setInputLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Specify label input image.
setInputLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Specify label input image.
setInputLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Set input label image to process.
setInputMode(SegmentationInitializer.InputMode) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set input mode.
setInputMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set MTBImage to store to disk
setInputMTBImgRGB(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Set the input image.
setInputObservations(Vector<MultiState<MotionModelID>>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Set input regions (if ConvexHullExtraction.inType is InputType.REGIONS).
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Set input regions.
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set reference to the the input regions.
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the input regions to be drawn.
setInputRegs(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Specify set of input regions.
setInputTreelines(HashMap<Integer, Vector<MTBRootTree>>) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator
Provide treelines to be enhanced.
setInputType(ConvexHullExtraction.InputType) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
Specify input image type.
setIntensityImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setIntermediateLS(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
setIntermediateResultDirectory(String) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Set intermediate result directory.
setIntermediateResultPath(String) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Set path for intermediate results.
setInvalidImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of invalidImg.
setInvalidTilesNum(int) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Set number of invalid tiles.
setInverseTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set computation of the inverse transform (wavelet to image)
setInvert() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Enable/disable inversion of mask.
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Enable/disable inversion of mask.
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Enable/disable inversion of mask.
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Enable/disable inversion of mask.
setInvertPixelValues(boolean) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Enable/disable pixel values invertion.
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setInvisible(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set position (x,y) invisible.
setInvisible(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set position (x,y,z) invisible.
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setJmax(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set Jmax
setJmax(int) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set Jmax (maximum scale 2^Jmax - 1)
setJmin(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set Jmin
setK(int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
setKernelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set convolution kernel (image).
setKernelNormalization(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set value of Parameter argument kernelNormalization.
setKernelOrigin(int[]) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set value of Parameter argument kernelOrigin.
setKernelPart(GaborFilter2D.KernelPart) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify which kernel part should be generated.
setKernels(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set smoothing kernels
setKernelSize(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify size of the kernel.
setKernelTruncation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set kernel truncation factor.
setKLower(int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
setKUpper(int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Set label image of detected nuclei.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Set input label image.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set the label image.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Set Label image.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set image of region labels
setLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of labelImg.
setLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Specify label input image.
setLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
setLambda(double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
setLambdaArray(double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
setLambdaArray(double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
setLayer(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Set the layer where the node is located.
setLength(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify length of vessels.
setLevel(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Set the tree level (level identifier).
setLineWidth(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify line width.
setLinkageMode(XylemGrower.GrowingMode) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setLocation(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Set coordinates of current 3D point object.
setLocation(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Overwrites Java Point2D method.
setLocation(Point2D) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Overwrites Java Point2D method.
setLocation(Point2D.Double, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Sets the location of this SnakePoint2D to the same coordinates as the specified Point2D.Double object.
setLocation(double, double, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Sets the location of this SnakePoint2D to the specified double coordinates.
setLowContrast(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify low contrast.
setLowerThresh(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify lower threshold.
setLowerThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Specify lower threshold.
setMad(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets maximal allowed discrepancy of direct connection to actual profile between two peaks.
setMad(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Sets maximal allowed discrepancy of direct connection to actual profile between two peaks.
setMappingFile(String) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Specify mapping file.
setMarkerVectors(HashMap<Integer, CellCntrMarkerVector>) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Set currently available marker vectors.
setMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify binary mask of nuclei.
setMask(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Set optional exclude mask.
setMask(BasicMorphology.maskShape, int) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
setMask(MTBStructuringElement) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
setMaskDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Specify input mask directory.
setMaskFormat(CytoskeletonFeatureExtractor.CellMaskFormat) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Specify input mask format.
setMaskRadiusC(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusC.
setMaskRadiusT(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusT.
setMaskRadiusX(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusX.
setMaskRadiusY(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusY.
setMaskRadiusZ(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusZ.
setMax_d2c(float) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets factor to adjust maximal allowed distance from lower to upper peak.
setMax_d2c(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Sets factor to adjust maximal allowed distance from lower to upper peak.
setMaxAngle(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Specify maximal angle to apply.
setMaxAreaChange(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
setMaxDistance(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
setMaximalComponentDistance(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set maximal component/pixel distance for linking.
setMaximalComponentSize(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set maximal component size for erasing large components.
setMaximalInstabilityScore(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set maximal instability score.
setMaximalSize(long) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set maximal size of valid regions.
setMaximalSpineLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
Set maximal length of spines.
setMaximalSpineLength(int) - Method in class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Set maximal length of spines.
setMaximalVoronoiExpansionDistance(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set radius of dilation mask in Voronoi expansion.
setMaximumObjectArea(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
set the maximum area (number of pixels) a region must have in order to be kept
setMaxIter(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of maxIter.
setMaxIteration(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
setMaxIterations(int) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
set maximum number of iterations for level set segmentation
setMaxIterations(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Set value of maxIterations.
setMaxLevels(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Specify maximum number of levels for iterative mode.
setMaxLineLength(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify maximal line length.
setMaxSpineLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set maximum length of a spine (filopodia-like protrusion) in pixel.
setMaxWeight(double) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Specify the maximum weight in the graph.
setMean(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
setMeanFreeData(boolean) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Set flag to indicate if data is already mean-free.
setMeasure(ImageStatistics.StatValue) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
Specify feature measure to extract.
setMeasurementUnit(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify unit for measurements.
setMeasureUnits(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify how to measure lengths and areas.
setMeasureUnits(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Specify units in which to measure areas.
setMeasureUnits(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Specify units in which to measure areas.
setMinAngle(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Specify minimal angle to apply.
setMinAreaAfterErosion(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setMinAreaAfterOpening(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setminAreaSeedRegions(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setMinCompactness(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setMinimalBorderLength(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Set the minimal border length.
setMinimalComponentSize(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set minimal component size for erasing small components.
setMinimalCurvatureThreshold(double) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Set minimal curvature threshold.
setMinimalDiversity(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set minimal diversity.
setMinimalLobeLength(int) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Set minimal pixel count a lobe requires.
setMinimalRegionSize(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Specify minimal size of regions considered.
setMinimalSize(long) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set minimal size of valid regions.
setMinimumObjectArea(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
set the minimum area (number of pixels) a region must have in order to be kept
setMinLineLength(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify minimal line length.
setMinRegionArea(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setMinRegionSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set the minimum size of detected regions.
setMinSeedSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
setMinSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of minSize.
setMinSizeFraction(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of minSizeFraction.
setMinTrackLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setMinTrackLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set minimum track length
setMode(BasicMorphology.opMode) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
setModification(ImageValueTools.ImageValueModification) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setMorphOp(BasicMorphology) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Set morphological operation for illumination correction, default is closing.
setMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Stores given image to the container.
setMultiphase(Boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of multiphase.
setNarrowBandWidth(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Set width of narrow band.
setNegativeColor(ArrayToColorMapImage.RangeColor) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Color for negative values.
setNeighbourhood(XylemGrower.Neighbourhood) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setNeurite(MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
setNeuriteMaskSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set neurite mask size in pixel.
setNeuriteSet(MTBNeurite2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Set the input set of neurites.
setNeuronColor(NeuriteExtractor2D.NeuronColor) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set binary neuron color.
setNeuronImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set input image of the binary neuron.
setNewObservations(AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
 
setNewObservations(AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
setNewObservations(AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
 
setNode(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
Sets the node the object is associated with.
setNodeThreshold(double) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Set threshold for filtering nodes.
setNodeType(MTBNeuriteSkelGraphNode.MTBSkeletonNodeType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
 
setNormalizationMode(SnakeOptimizerSingle.EnergyNormalizationMode) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Set energy normalization mode.
setNormFromTo(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setNormTo(double, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setNucDetector(NucleusDetector2D) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set detector for nuclei.
setNucleiAvgSize(double) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify average size of nuclei.
setNucleiChannel(Integer) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set nuclei channel number.
setNucleiCount(int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify number of segmented nuclei regions.
setNucleiMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Specify nuclei mask.
setNucleiRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify set of regions.
setNucleiResult(SegResult_Nuclei) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Set nuclei detection result.
setNucleusChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify image channel containing nuclei (just for reference).
setNumberNeighbors(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Specify number of neighbors to consider for LBP code calculation.
setNumberOfComponents(int) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Number of sub-space components if reduction mode is NUMBER_COMPONENTS.
setNumIterations(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Set number of iterations for the GVF field.
setNumIterations(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of numIterations Explanation: Number of iterations performed
setNx(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
 
setNx(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
setNy(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
 
setNy(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
setObjectsEightConnected(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
are regions to be considered 8-connected (4-connected otherwise)
setObjectsEightConnected(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
setOldId(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Set old index of current snake point within the snake.
setOpen() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Set polygon opened (not closed).
setOpeningSESize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setOperationType(FieldOperations2D.FieldOperation) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
 
setOpMode(NucleusSeparator2DBeamCut.NuclSeparateMode) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of opMode.
setOrientedFilter(OrientedFilter2D) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Specify the oriented filter to apply.
setOutImageType(ImageReaderMTB.OutImageType) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set the type of image object that is created as result image.
setOutOfRangeValueHandlingMode(GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Specify how to handle values out of range.
setOutputDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Specify output directory.
setOutputFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter
Specify the file where to save the data.
setOutputType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set output image type
setOverlapOpt(OverlapOption) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify overlap handling mode.
setOverwrite(boolean) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the overwrite permission flag
setParent(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Set the parent of this node.
setParentID(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
setPartChannel(Integer) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set particle channel number.
setPartDetector(ParticleDetectorUWT2D) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set detector for particles.
setParticle(int, G) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Set idx-th particle
setParticleImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Set particle image for particle detector.
setParticleResult(SegResult_Particles, int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Set particle counts per channel.
setPath(String) - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Specify path associated with the node.
setPdf(int, ProbabilityDensityFunction) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
setPdf(int, ProbabilityDensityFunction) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
setPerCellAvgSize(HashMap<Integer, Double>) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Sets particle average sizes per cell.
setPerCellCount(HashMap<Integer, Integer>) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Sets particle counts per cell.
setPercentageOfVariance(double) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Fraction of variance to be represented in the sub-space if the reduction mode is PERCENTAGE_VARIANCE.
setPixelLength(double) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Set length of a pixel.
setPoints(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
setPoints(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Set all points of the polygon from the specified point vector object.
setPoints(Vector<MTBPoint3D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3D
set points of this surface
setPoints(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Overwrite Polygon2D method to set all points of the snake from the specified point vector object.
setPointSet(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet
Set input set of 2D points.
setPointSet(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet
Set input set of 2D points.
setPoisson2Gauss(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set flag if input image with poisson noise is to be transformed to image with gaussian noise following J.
setPositionC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 'c' in the c-dimension
setPositionT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 't' in the t-dimension
setPositionX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 'x' in the x-dimension
setPositionY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 'y' in the y-dimension
setPositionZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 'z' in the z-dimension
setPositiveColor(ArrayToColorMapImage.RangeColor) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Color for positive values.
setPrecursorInfosEnabled(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Enable or disable extraction of additional precursor infos.
setPredecessor(int) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
setPreserveTopology(Boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of preserveTopology.
setPreserveTopology(Boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Set value of preserveTopology.
setProcessMode(ComponentPostprocess.ProcessMode) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Specify process mode.
setProfile(double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Pass profile data to the profile.
setProfilePoints(Vector<Vector<Point2D.Double>>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Set the points of the neurite region where the profiles are calculated from.
setQuality(Integer) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the quality (quicktime only).
setRadius(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Set the radius of the node.
setRadius(int) - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DConcavityCalculator
Specify radius of local mask.
setRadius(double) - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib
Specify radius of neighborhood for LBP code calculation.
setRandom(Random) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
setRandom(Random) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set a random number generator to draw each region in a random color.
setRangeMaximum(double) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Specify maximum of heat map range.
setRangeMinimum(double) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Specify minimum of heat map range.
setRankOpMode(RankOperator.RankOpMode) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument rankOpMode.
setReduceC(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enable/disable projection along c-dimension.
setReduceT(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enable/disable projection along t-dimension.
setReduceX(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enable/disable projection along x-dimension.
setReduceY(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enable/disable projection along y-dimension.
setReduceZ(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Enable/disable projection along z-dimension.
setReductionMode(PCA.ReductionMode) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Specify the mode for selecting the sub-space dimensionality.
setReductionMode(ImageDimensionReducer.ReducerMethod) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Specify projection mode.
setRegionBinaryMode(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Specify region input mode.
setRegionID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Set the region id.
setRegionSet(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Set regions.
setRegionSet(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set the region set.
setREngine(Rengine) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set R engine.
setResultCellImg(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Specify (optional) result image with cell contours.
setResultContourImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of ResultContourImage.
setResultDirs() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Create all output directories for the single detection steps.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose
Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Set value of resultImg.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of ResultImage.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the resulting image.
setResultImageHeight(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set target image height, overwrites all other internal settings.
setResultImageOffsetX(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set desired offset for target image in x direction.
setResultImageOffsetY(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set desired offset for target image in y direction.
setResultImagePlus(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set resulting image
setResultImageStack(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Set stack with result segmentation images.
setResultImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
setResultImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
setResultImageWidth(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set target image width, overwrites all other internal settings.
setResultImg(MTBImageShort) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Set value of resultImg.
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Output argument resultImg.
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set result image
setResultingRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Attach the vector of resulting regions.
setResultMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set resulting image
setResults(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set detected regions
setResultsTable(MTBTableModel) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setResultType(GaborFilter2D.ResultType) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify result type.
setResultValueSelectionMode(ImageContrastReducer.ResultValueMode) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Set value selection mode.
setRevisionFile(String) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Set the name of the revision file.
setROIFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter
Specify the ROI file to process.
setRoundnessThreshold(double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set roundness threshold for eliminating round components.
setSampling(int) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify angular sampling.
setSatMTBImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Set the saturation channel image.
setSatTresh(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setSaveIntermediateResultPath(String) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set path where to save intermediate results.
setSavePath(String) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets the path to where intermediate snake results are to be written.
setSaveSnakes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
(De)activates saving of iteration step results.
setScaleDown(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setScaleFactor(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
set the scale factor if normalization is requested.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Set the scaling factor.
setScaleFactor(double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Set the scaling factor.
setScaleFactor(double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Set the scaling factor.
setScaleIntervalSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set the size of the scale interval for correlation images
setScaleMax(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set maximum of scales.
setScaleMin(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set minimum of scales.
setScaleNum(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set number of scales.
setScaleValues(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set flag if values are scaled to match the range of output type values if necessary
setSeedImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setSeedPointImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
setSeErosionSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setSegDim(SegmentationInitializer.SegmentationDimension) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set target dimension.
setSegmentation(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Specifiy image segmentation.
setSegmentationDomain(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Specify the domain of the underlying segmentation.
setSeOpeningSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setShape(CellCntrMarkerShape) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Set shape of marker.
setShape(SegmentationInitializer.ShapeType) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Specify shape for synthetic initialization.
setShapeDimX(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set extent of shape in x dimension.
setShapeDimY(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set extent of shape in y dimension.
setShapeDimZ(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set extent of shape in z dimension.
setShapeForErosion(BasicMorphology.maskShape) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setShapeForOpening(BasicMorphology.maskShape) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setShapeMaskSizeX(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set size of shape mask in x dimension.
setShapeMaskSizeY(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set size of shape mask in y dimension.
setShapeMaskSizeZ(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set size of shape mask in z dimension.
setShapePosX(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set position of shape in x dimension.
setShapePosY(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set position of shape in y dimension.
setShapePosZ(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set position of shape in z dimension.
setShowSnakes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
(De)activates displaying of intermediate results during snake-iterations.
setSigma(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
setSigma(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify sigma value.
setSigma(double) - Method in class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D
Set standard deviation of Gaussian kernel.
setSigmaC(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in c-dimension.
setSigmaInterpretation(GaussFilter.SigmaInterpretation) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set the mode of how sigmas are interpreted.
setSigmaT(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in t-dimension.
setSigmaX(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify Gaussian standard deviation in x.
setSigmaX(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in x-dimension.
setSigmaY(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify Gaussian standard deviation in y.
setSigmaY(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in y-dimension.
setSigmaZ(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in z-dimension.
setSizeC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeC(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in c-dimension.
setSizeDilation(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of sizeDilation.
setSizeOpening(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of sizeOpening.
setSizeT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeT(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in t-dimension.
setSizeTH(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of sizeTH.
setSizeX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeX(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in x-dimension.
setSizeY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeY(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in y-dimension.
setSizeZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeZ(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in z-dimension.
setSlice(MTBImageManipulator, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Copy the value of source to the specified slice
setSliceLabel(String, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the slice label of the slice specified by (z,t,c)
setSliceZid(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
Set index of slice in stack, starting with 0 for first slice.
setSnakeIterations(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets number of iterations for snake optimization.
setSnakePoints(Vector<MTBSnakePoint2D>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Set all points of the snake from the specified SnakePoint2D vector object.
setSource(MTBImageManipulator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set a new source for the window.
setSpacing(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of spacing.
setSpacingIntermediate(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Set value of spacingIntermediate.
setSrcNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Set source node of the MTBGraphEdge.
setStandardDeviation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Specify standard deviation of Gaussian.
setStandardDeviation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Specify standard deviation of Gaussian.
setStandardDeviation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Specify standard deviation of Gaussian.
setStartFrame(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
setStartNode(MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Set a new start node.
setStartPixel(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Specify start pixel of path.
setState(int, Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Set the idx-th state (indices start from 0)
setState(int, Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
setStatus(byte) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Set the status of the node (segment).
setStepsizeT(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the stepsize in t-dimension (timestep)
setStepsizeT(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the stepsize in t-dimension (timestep).
setStepsizeX(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the physical size of a voxel (stepsize) in x-dimension
setStepsizeX(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the physical size of a voxel (stepsize) in x-dimension.
setStepsizeY(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the physical size of a voxel (stepsize) in y-dimension
setStepsizeY(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the physical size of a voxel (stepsize) in y-dimension.
setStepsizeZ(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the physical size of a voxel (stepsize) in z-dimension
setStepsizeZ(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the physical size of a voxel (stepsize) in z-dimension.
setString(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData
Set the string data of the MTBStringData object.
setString(String) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
Specify string.
setSuppressor(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets threshold to suppress peak analysis close to scraggy contours.
setSuppressor(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Sets threshold to suppress peak analysis close to scraggy contours.
setSVMFile(String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
setSVMParameters(svm_parameter) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
setT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setTargetContrast(ImageContrastReducer.TargetContrast) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Set target contrast.
setTargetImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Set target image.
setTargetImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Specify a target image to which the regions are drawn.
setTargetImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setTargets(Vector<CalcSegmentationStatistics.CalcTargets>) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Specify targets to calculate.
setTgtNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Set target node of the MTBGraphEdge.
setTheta(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set coefficient to relate vessel radius and scale.
setThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set threshold for threshold mode.
setThreshold(Double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of threshold.
setThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set threshold
setThresholdImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set image for thresholding.
setThresholdingDirection(DetectMSERs.Thresholding_Direction) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set direction of threshold compuations.
setThresTH(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of thresTH.
setTickLabelSize(int) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set size of tick labels on both axes.
setTickLabelSize(int) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set size of tick labels on both axes.
setTileShiftX(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Specify shift of tiles in x-direction.
setTileShiftY(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Specify shift of tiles in y-direction.
setTileSizeX(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Specify size of tiles in x-direction.
setTileSizeY(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Specify size of tiles in y-direction.
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the image's title.
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the images title
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set title of chart plot.
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set title of chart plot.
setType(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Set type of markers.
setU(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Set vector U of the field.
setU(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Set value on (x,y) for vector U of the field.
setUnitAngle(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set unit of angles
setUnitSpace(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set unit of space
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the unit of the t-dimension
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the unit of the t-dimension.
setUnitTime(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set unit of time
setUnitX(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the unit of the x-dimension
setUnitX(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the unit of the x-dimension.
setUnitXY(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setUnitXY(String) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
setUnitXYZ(String) - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
setUnitY(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the unit of the y-dimension
setUnitY(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the unit of the y-dimension.
setUnitZ(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the unit of the z-dimension
setUnitZ(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the unit of the z-dimension.
setup() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
Initialize the class for the region
setupEnergyTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Inits the table for sampled energy values.
setupEnergyTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Inits the table for sampled energy values.
setupParamConfigPanel() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
 
setupParamConfigPanel() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
 
setUpperThresh(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Specify upper threshold.
setupWindow() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Construct the frame to configure an operator.
setUseThresh(Boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set adaptive thresholding tag.
setUWT(MTBImageSet) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set UWT coefficient images
setV(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Set value on (x,y) for vector V of the field.
setV(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Set value on (x,y) for vector V of the field.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperDataIOFileInPanel
Sets panel to given object value.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Returns the contents of the text field.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
setValue(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Displays specified coordinates.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
 
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.MTBDataIOFileInPanel
Sets panel to given object value.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Selects the given image object in combobox.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
 
setValue(Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
Set the value of the double datat object.
setValue(Integer) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
sets the value for this object
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Updates GUI component with given value.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Extracts current collection data.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayButton
Updates GUI component with given value.
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Set new value.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Set new values.
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Updates current initializer configuration.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
 
setValueAt(Object, int, int) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
setVectorField(MTBVectorField2D) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Set the operation based 2D vector field.
setVectorFieldImage(MTBImageDouble) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Set the operation based 2D vector field image.
setVerbose(boolean) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
setVesselMode(MFFDOGFilter2D.VesselMode) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify detection scenario.
setVisibilityMask(boolean[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Set the valid mask from external mask data.
setVisibilityMask(boolean[][][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Set the valid mask from external.
setVisibilityMask(boolean[][], int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Set the valid mask from external mask data.
setVisible(boolean) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Set visibility of configuration window.
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setVisible(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set position (x,y) visible.
setVisible(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set position (x,y,z) visible.
setVisible(boolean[][][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Set visibility of positions.
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setVisualizeAnalysisResults(boolean) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Enable/disable creation of image with analysis data.
setVoronoiImg(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Specify an image to be filled with voronoi data.
setVotesAdjacency(int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
setVotesClutter(int, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
setVotesTarget(int, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
setWeight(int, double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
setWeight(int, double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Set weight for particle specified by idx.
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setWeight(int, int, double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Sets the pixel weight of position (x,y) to c.
setWeight(int, int, int, double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Sets the pixel weight of position (x,y,z) to c.
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setWeight(PartitGraphNodeID, PartitGraphNodeID, double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
setWeight(T, T, double) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Set weight of edge from nodeSrc to nodeTgt.
setWeightAsEdgeThickness(boolean) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set flag how edge weights are visualized.
setWeightModel(DijkstraShortestPixelPathFinder.WeightModel) - Method in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Select model for choosing edge weights.
setWeights(double[]) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
setWeights(Vector<Double>) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Sets the weights for the energies.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Specify new weights.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Specify new weights.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Specify new weights.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Specify new weights.
setWidth(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Set the width associated with the segment.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Set image width.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Set image width.
setWidth(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify width of vessels.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set image width.
setWindowPosition(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position in the source image.
setWthMaskSize(Integer) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Set mask size of white top-hat.
setX(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
setX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setX(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Set coordinate of x-dimension.
setX(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Set x-coordinate of marker.
setXAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set label of x-axis.
setXAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set label of x-axis.
setXmax(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Set maximal x coordinate of region set domain.
setXmin(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Set minimal x coordinate of region set domain.
setXML(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the XML file description string if one was available
setXMTBImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Set the value channel image.
setXPos(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Set x-position of the node.
setXThresh(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set the Intensity/Brighntness/Value-Parameter (depending on the used input image type).
setXylemImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set the Hue/Saturation/{Intensity|Brightness|Value}-MTBImage.
setXylemImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Set the input xylem image - this must be an 8bit image.
setXylemResultRegions(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set the binary image after the morphological processing on the grown region image.
setY(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
setY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setY(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Set coordinate of y-dimension.
setY(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Set y-coordinate of marker.
setYAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set label of y-axis.
setYAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set label of y-axis.
setYmax(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Set maximal y coordinate of region set domain.
setYmin(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Set minimal y coordinate of region set domain.
setYPos(double) - Method in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Set y-position of the node.
setZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setZ(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Set coordinate of z-dimension.
setZ(int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
Set z-coordinate of marker.
setZTCCoordinates(int, int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Specify optional coordinates if input image is a stack.
sgIDs - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Match list of set entries to original segmentation labels.
sgIDs - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Match list of set entries to original segmentation labels.
sgn(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Signum function.
sgn(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Returns the sign of a value.
sgnSum(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Computes scaled sign in neighborhood.
shape - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
(Optional) shape of marker.
shape - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
shape - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
ShapeAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
ShapeAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
constructor
shapeDataAvailable() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Check if there is shape data available.
shapeDimX - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeDimY - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeDimZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeForErosion - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
The shape of structuring element for the Erosion.
shapeForOpening - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
The shape of structuring element for the opening.
shapeIOShape - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to select shape.
shapeIOxDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to set x dimension of shape mask.
shapeIOxPos - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to set x position of shape.
shapeIOxSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to set size of shape in x.
shapeIOyDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to set y dimension of shape mask.
shapeIOyPos - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to set y position of shape.
shapeIOySize - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to set size of shape in y.
shapeIOzDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to set z dimension of shape mask.
shapeIOzPos - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to set z position of shape.
shapeIOzSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to set size of shape in z.
shapeMaskSizeX - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeMaskSizeY - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeMaskSizeZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapePosX - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapePosY - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapePosZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
shapeReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
ShapeType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.ShapeType
 
shift(double, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Method to shift the whole polygon outward (positive value) ore inward (negative value) to its normal vector from every line segment.
shift(double, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Method to shift the whole snake outward (positive value) ore inward (negative value) to its normal vector from every line segment.
shiftX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Offset of the tiles in x dimension.
shiftY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Offset of the tiles in y dimension.
show() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Display the image as an ImagePlus.
showAboutBox() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
 
showAdditionalResultImages - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Flag to enable/disable showing additional and intermediate result images.
showAdditionalResultImages - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Flag to enable/disable showing additional and intermediate result images.
showAdditionalResults - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Enable/disable display of additional intermediate results.
showAdditionalResults - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Show additional result images.
showButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Button to show currently configured segmentation.
showCodeStack - Variable in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal
Show additional result image.
showContours(MTBImage, ArrayList<ArrayList<Point>>) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasureContours
This method shows the contour pixel on a given image.
showDegreeTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
showDocuFrame() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
Show the documentation for the chooser.
showHistogram(double[]) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.Histogram
 
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Flag for showing intermediate results.
showIntermediateResults(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set flag to display intermediate results.
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Flag for displaying intermediate results.
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag to enable/disable showing of intermediate results.
showKTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
showMaskChannelTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
showMaskChannelTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
showMasksOnly(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set flag indicating whether to show masks or overlays in result stack.
showMaxDistTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
showMaxDistTextbox() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
showOverlayImage - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
showOverlayImage - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
showOverlayImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
showParametersForChecking() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
showResultFeatureStack - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Flag to enable/disable showing feature visualization stack.
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Display current result contour by overlaying the current snake result onto the input image.
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Display input image with current snake overlayed.
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Display intermediate results by overlaying the input image with the current snake result.
showSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Flag to enable/disable display of snake results.
showTrajectoryMap - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
showTrajectoryMap - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
showTrajectoryMap(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
sigma - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Sigma value of derivatives depending on line width.
sigma - Variable in class de.unihalle.informatik.MiToBo.math.arrays.filter.GaussFilterDouble1D
Standard deviation of the Gaussian kernel to be applied.
sigmaC - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
sigmaInterpretation - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
SigmaInterpretation() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.GaussFilter.SigmaInterpretation
 
sigmaT - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
sigmaX - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
sigmaY - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
sigmaZ - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
signDistance(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Transform function into signed distance function.
signedExpandation(MTBLevelsetFunctionPDE.SortedList<MTBPoint3D>, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Expand signed distances around zero-level.
simplify() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Deprecated.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the number of borders of this set.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the number of contours of this contour set
size - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
number of bins
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2DSet
Get the number of line segments in the set.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Get the number of polygons of this polygon set.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Get the number of regions of this region set
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Number of region sets in this bag
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Get the number of regions of this region set
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Get the number of regions of this region set
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns the number of elements in this list.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Returns the number of elements in this list.
size - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
 
sizeC - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
sizeC - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeC - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeC - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
sizeC - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
sizeDilation - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
sizeEnergy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
sizeNeighborhood - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
The size of the neighborhood, i.e. numbers of pixels in the neighborhood
sizeOpening - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
sizePhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
sizesGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Array of sizes of groundtruth regions.
sizesGT - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Array of sizes of groundtruth regions.
sizesSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Array of sizes of segmented regions.
sizesSG - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Array of sizes of segmented regions.
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
sizeTH - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Image width.
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Image height.
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
skeleton_color - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
The color of the skeleton in the binary image.
SkeletonAnalysisHelper - Class in de.unihalle.informatik.MiToBo.morphology
Helper functions for analyzing region skeletons.
SkeletonAnalysisHelper() - Constructor for class de.unihalle.informatik.MiToBo.morphology.SkeletonAnalysisHelper
 
SkeletonExtractor - Class in de.unihalle.informatik.MiToBo.morphology
Extracts skeleton of foreground region.
SkeletonExtractor() - Constructor for class de.unihalle.informatik.MiToBo.morphology.SkeletonExtractor
Default constructor.
skeletonInfoImg - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Info image for skeleton analysis.
SkeletonPostprocessor() - Constructor for class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SkeletonPostprocessor
Default constructor.
SkeletonPostprocessor - Class in de.unihalle.informatik.MiToBo.morphology
Helper operator to post-process binary region skeletons.
SkeletonPostprocessor() - Constructor for class de.unihalle.informatik.MiToBo.morphology.SkeletonPostprocessor
Default constructor.
skelImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Binary skeleton image of the whole neuron.
skelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Intermediate result: final contour skeleton.
skipLines - Variable in class de.unihalle.informatik.MiToBo.io.importer.GetMTBContour2DSetFromXSVFiles
Skip header lines.
smallestNonEmptyBin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
smallest intensity value contained in the input image
smoothContour(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Smoothes the contour by convolving x and y coordinates with a Gaussian kernel.
smoothPointVector(Vector<Point2D.Double>, double) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Convolves a list of 2D points with a Gaussian kernel.
snake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
The snake on which the algorithm works.
Snake_status() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer.Snake_status
 
snakeArea - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
SnakeCloner(MTBSnake) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
Default constructor.
SnakeHelperOperators - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Helper class with internal operators for snakes.
SnakeHelperOperators() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators
 
SnakeHelperOperators.ContourConverter - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to convert a contour into a snake.
SnakeHelperOperators.ImageMaker - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to draw snake to an image.
SnakeHelperOperators.MaskMaker - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to generate 2D array mask for snake interior.
SnakeHelperOperators.RegionConverter - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to convert a region into a snake.
SnakeHelperOperators.RegionImageConverter - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to extract snakes from a region image.
snakeIterations - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Maximal number of snake iterations in iterative optimization.
snakeIterCount - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Number of snake iterations used in current optimization process.
snakeNum - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Number of snakes.
snakeNum - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Number of snakes to be optimized.
snakeNum - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Number of snakes currently managed.
snakeOpter - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Snake optimizer.
snakeOpters - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Array of individual snake optimizers.
SnakeOptimizer - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using parametric snakes.
SnakeOptimizer() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Default constructor
snakeOptimizer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Optimizer object for a single snake.
SnakeOptimizer.Snake_status - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Indicates the current (internal) state of the snake calculations.
SnakeOptimizerCoupled - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using multiple parametric snakes.
SnakeOptimizerCoupled() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Default constructor.
SnakeOptimizerCoupled(MTBImage, MTBPolygon2DSet, SnakeOptimizerSingle, boolean[]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Default constructor.
SnakeOptimizerSingle - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using parametric snakes.
SnakeOptimizerSingle() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Default constructor.
SnakeOptimizerSingle.EnergyNormalizationMode - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Snake normalization mode.
SnakeOptimizerSingle.IntensityNormalizationMode - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image intensity normalization mode.
SnakeOptimizerSingleGreedy - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using parametric snakes with greedy optimization.
SnakeOptimizerSingleGreedy() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
SnakeOptimizerSingleVarCalc - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using parametric snakes.
SnakeOptimizerSingleVarCalc() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Default constructor.
SnakeOptimizerSingleVarCalc(MTBImage, MTBPolygon2DSet, MTBSet_SnakeEnergyDerivable, MTBGammaUpdate, Double, MTBTermination, Boolean, Double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Default constructor with parameters.
snakePrimerEllipse - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Set of elliptical snake polygons.
snakePrimerVoronoi - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Set of snake polygons based on Voronoi tesselation.
snakes - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Set of resulting contours.
solidities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
solve() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
solve() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Solve this level set problem.
SortedList() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
create empty SortetList
SortedListElement(EType, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
SortMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.SortMode
 
sortRegionSetBy(MTBRegion2DSet, XylemGrower.SortMode) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
sortStringSet(Set<String>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Helper method to sort set of strings alphabetically in ascending order.
sortStringSet(Set<String>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Helper method to sort set of strings alphabetically in ascending order.
sourceObject - Variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
sp - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerShapeLine
Start point of segment.
spacing - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
spacingIntermediate - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
spbox - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
splitFilename(String) - Static method in class cmdTools.mtb_imagetools.ImageConvert
 
SQRT_2 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE
 
SQRT_2 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE
 
SQRT_2 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
 
SQRT_3 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
 
sqrtSizeMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
sqrtSizeMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
sqrtSizeMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
sqrtSizeMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
src - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Source node of the MTBGraphEdge.
stackedBarChart - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Resulting stacked bar chart.
StackedBarChartPlotter - Class in de.unihalle.informatik.MiToBo.visualization.plots
Operator that generates stacked bar plots using JFreeChart.
StackedBarChartPlotter() - Constructor for class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Default constructor.
stackedBarCharts - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Resulting stacked bar plot of cluster distributions.
stackedBarCharts - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Resulting stacked bar plot of cluster distributions.
stackSize - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Number of channels in image.
stageThreeMin - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Helper to make matrix minimum in stage three externally accessible.
standardization(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get unit vector.
standardization(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
 
start - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Variable to save start value.
start - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawLine
 
startC - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
startDetectionMode() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Method to start neurite detection mode with presegmentation, active contours and wavelet based neuron component detection.
startFrame - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
startPoint - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Start pixel of the path.
startPosOnContour - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Index of segment start pixel on contour.
startReal - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Variable to save real start value.
startT - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
startX - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
startY - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
startZ - Variable in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
stateConflict(Matrix, MultiState<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
statesCont - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
vector of the target states (continuous variables)
statesDiscr - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
vector of the target states (discrete variables)
StatisticsFilter - Class in de.unihalle.informatik.MiToBo.filters.nonlinear
class for calculating several statistical values for the neighborhood of the pixels
in an image
StatisticsFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
StatisticsFilter(MTBImage, StatisticsFilter.FilterMethod, int) - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
StatisticsFilter.FilterMethod - Enum in de.unihalle.informatik.MiToBo.filters.nonlinear
available filtermodes
statMeasure - Variable in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
Statistical measure to be calculated.
statMeasure - Variable in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
Statistical measure to be calculated.
status - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
Status associated with the node.
status - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Status of current snake.
statuslabel1 - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
statuslabel2 - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
statusListeners - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
vector of installed StatusListeners
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Vector of installed objects of type StatusListener.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
vector of installed StatusListeners
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
vector of installed StatusListeners
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
statusListeners - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
statusUpdated(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
 
statusUpdated(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
 
statusUpdated(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator
 
statValue - Variable in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
Result value, i.e. calculated statistical measure.
StatValue() - Constructor for enum de.unihalle.informatik.MiToBo.math.images.ImageStatistics.StatValue
 
stdDevConcavities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
stdDeviationFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
stdDevRatio - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Ratio of image standard deviation used as threshold for radius calculation.
StegerRidgeDetection2DWrapper - Class in de.unihalle.informatik.MiToBo.filters.vesselness
Wrapper for Ridge Detection plugin by Carsten Steger (and Thorsten Wagner).
StegerRidgeDetection2DWrapper() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Default constructor.
step() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Do one iteration, update all pixels of levelset function (in narrow band).
stepSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
stepSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Step size value for a snake step (gamma) during optimization.
stillActive - Variable in class de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor
Flag to indicate if process is still active.
str - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
stratifiedCrossValidation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
stratified k-fold cross validation, i.e. training and test tests contain approximately the same proportions of positive and negative samples in every iteration
StringAnalysis - Class in de.unihalle.informatik.MiToBo.tools.strings
Class providing helpers to analyze (sets of) strings.
StringAnalysis() - Constructor for class de.unihalle.informatik.MiToBo.tools.strings.StringAnalysis
 
stringToType(String) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
For a given String, return the corresponding MTBImageType.
StromulesDetector2D - Class in de.unihalle.informatik.MiToBo.apps.plantCells.stromules
Operator to detect stromules in microscope images of plastids.
StromulesDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Default constructor.
StromulesDetector2D.DetectMode - Enum in de.unihalle.informatik.MiToBo.apps.plantCells.stromules
Heuristic to use for detecting stromuli.
stromuliAngleThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Stromuli orientation angle criterion.
stromuliAngleThreshold - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Stromuli orientation angle criterion.
stromuliOp - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Operator for stromuli detection.
stromuliRegions - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Set of detected plastid regions with stromuli.
StructureCountMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics.StructureCountMode
 
structureMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Structure mask.
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Method to sub two images.
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Subtract the elements of two images (img1 - img2)
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Subtract the elements two images (img1 - img2)
subDim - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Dimensionality of the sub-space as either specified by the user or automatically determined based on the percentage of variance.
subgraphEdges - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
subgraphID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
The node's subgraphID
subgraphs - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
subgraphs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
subgraphs_adj - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
subgraphs_adj_color - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
subgraphs_color - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
subspaceData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Dimension-reduced cluster distribution data.
subspaceData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Dimension-reduced cluster distribution data.
sum - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
sum of all histogram entries
sumOfHueCartesian - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
sumSizeObject - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
supportConversion(Class<?>, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
suppressor - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
surfaceAreas - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
SurfaceExtraction - Class in de.unihalle.informatik.MiToBo.features
Operator for extracting the surface areas of 3D-objects.
SurfaceExtraction() - Constructor for class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
SurfaceExtraction(MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
surfaces - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
surfaces - Variable in class de.unihalle.informatik.MiToBo.features.SurfaceExtraction
 
surfaceSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
The set of surfaces represented as a Vector.
svmFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
svmFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
swap(Point2D.Double[], int, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction
exchange point with index i and point with index j
swapNuclei - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
switchGapCloseMode() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Callback routine called if gap closing mode parameter changes.
switchOpModeParameters() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Callback routine to change operator mode parameters.
switchOpModeParameters() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Callback routine to change operator mode parameters.
switchOpModeParameters() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
Callback routine to change operator mode parameters.
switchOpModeParameters() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
Callback routine to change operator mode parameters.
switchPhaseConfigParameters() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Callback routine to change phase parameters.
switchPixelCalibParameters() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Callback routine called if pixel calibration mode parameter changes.
switchSegmentationFormatParameter() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Callback routine called if format parameter changes.
synchronizeColorOptions() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Updates color parameter if a random generator is given.
SynchronizedImageWindows - Class in de.unihalle.informatik.MiToBo.gui
A class that synchronizes viewing of images for easier comparison.
SynchronizedImageWindows() - Constructor for class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
synchronizeRandomOptions() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Updates random parameter if a color is set.

T

t - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
t1 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
t2 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
table - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
table - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
 
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
 
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow.MTBSet_SnkEnergyPDEGUITableModel
 
TableModelShowButton(Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton
Constructor.
tableToString() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Converts the contents of the table to a string array in CSV format (suitable for import in Excel).
tabwin - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton
Associated window.
tail - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
 
targetClass - Variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
targetContrast - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Target contrast of result image.
TargetContrast() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.TargetContrast
 
targetDimensionIO - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to read the target dimension.
targetEnergyRange - Static variable in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Target interval boundaries of energy.
TargetFormat() - Constructor for enum de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader.TargetFormat
 
TargetID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A target-ID class.
TargetID(short) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
Constructor.
targetIDtoIdx - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
targetImage - Variable in class de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage
Optional target image for result.
targetImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Optional target image.
targetImageType - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
targetList - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
List of targets to calculate.
targetObject - Variable in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
tDirection - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Thresholding direction.
termCriterion - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Termination criterion.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Termination is done when the area difference of the former and the current snake is below a given fraction factor or if a maximum number of iterations is reached.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Termination is done when the area difference of the former and the current snake is below a given fraction factor or if a maximum number of iterations is reached.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Method to check termination status of the snake.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Termination is done when a maximum number of snake iterations is reached.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Termination is done when the snake control point motion of the former and the current snake is below a given fraction factor or if a maximum number of iterations is reached.
test(Vector<File>, int) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
testRegions(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Test whether the number of pixels from a neuron region contains more than 90% of the pixels from a nucleus region.
testRegions2(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Test whether a single pixel from a neuron region contains a pixel from a nucleus region.
text - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
String to draw into the image.
textField - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing.ColorMapperInputDirectoryIOPanel
Text field in the panel.
texturalEntropy - Variable in class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
TexturalParameterExtractor - Class in de.unihalle.informatik.MiToBo.apps.biofilms
operator for calculating textural parameters from biofilm images as described in Yang et al., Quantifying biofilm structure using image analysis.
TexturalParameterExtractor() - Constructor for class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
TexturalParameterExtractor(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.biofilms.TexturalParameterExtractor
 
tf - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
tgt - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Target node of the MTBGraphEdge.
theta - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
THREE_COMPONENTS_COLOR_SPACE - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
threshDWTCoeffs(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
threshDWTJeffreys(MTBImage[], double, double[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
threshHigh - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Upper threshold.
threshImage(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
threshImgNiblack(MTBImage, double, int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
threshLow - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Lower threshold.
threshold - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Higher threshold for binarization.
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Result threshold.
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
threshold(MTBImage, double, double, double, double, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Apply threshold to an MTBImage and create a new thresholded MTBImage.
threshold(MTBImage, MTBImage, double, double, double, double, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Apply threshold to an MTBImage and write results to a destination MTBImage.
thresholdImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
Thresholding_Direction() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs.Thresholding_Direction
 
thresholdIOImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to read an image for thresholding.
thresholdIOThresh - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
I/O component to read a threshold.
thresholdUnits - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Units for size thresholds.
threshScalingConstant - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Threshold scaling constant.
thresTH - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
thrinkMatrix - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Flag for thrinking matrix if possible.
tickLabelSize - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Size of axes' tick labels.
tickLabelSize - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Size of axes' tick labels.
ticks - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Variable to remember ticks.
tif - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
tiff - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
tileColumns - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Number of tile columns.
TileFeatureCalculator - Class in de.unihalle.informatik.MiToBo.features
Calculates features on images tile-wise, based on operators extending FeatureCalculator.
TileFeatureCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Default constructor.
TileFeatureCalculator(int, int) - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Constructor with non-default tile sizes.
TileFeatureCalculator(int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Constructor with non-default tile sizes.
TileFeatureCalculatorResult - Class in de.unihalle.informatik.MiToBo.features
Result data of the operator TileFeatureCalculator.
TileFeatureCalculatorResult() - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Default constructor.
TileIterator(MTBImageTileAdapter) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
Default constructor.
tileNumX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures
Number of tiles in x-dimension.
tileNumX - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Number of tiles in x dimension.
tileNumY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorEigenStructures
Number of tiles in y-dimension.
tileNumY - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Number of tiles in y dimension.
tileRows - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Number of tile rows.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Tile shift in x-direction.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Tile shift in x-direction.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Tile shift in x-direction.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Shift of tiles in x direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Tile size in y-direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Tile size in y-direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Tile size in y-direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Shift of tiles in y direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Tile size in x-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Tile size in x-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Tile size in x-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Size of a tile in x-dimension.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Size of tiles in x direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
Size of tiles in x dimension.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.ActinAnalyzer2D
Tile size in y-direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonAnalyzer2D
Tile size in y-direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor
Tile size in y-direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Size of a tile in y-dimension.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Size of tiles in y direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
Size of tiles in y dimension.
time - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
A variable to store time information
timeLib - Static variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Basename of the JNI library.
timeOffset - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
timer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Timer object for time measurements.
timing - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Consumed time in seconds where TimingMode states if this reflect user or real time.
timingMode - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Timing mode, may be user time or real time.
titleString - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Title string of window.
tmpImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
temp. binary image
tn - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
TNclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
toArray() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
toByteImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Draw the skeleton graph into a binary image.
toCartesianAsPoint2D(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Converts an angle in degree to its corresponding in cartesian coordinates.
toCartesianAsVector(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Converts an angle in degree to its correspondant in cartesian coordinates.
toImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Visualize the skeleton graph as RGB image.
toImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Draw the skeleton graph in the given RGB image.
toImage(Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Visualize the neurites skeleton graph as RGB image.
toImage(MTBImageRGB, Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Visualize the neurites skeleton graph in the given RGB image.
toInspectL - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
toMicrons(double, String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Convert a value of given space unit to microns.
toMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Draws border with all inner borders to a given image.
toMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to save a region with in a given MTBImage image.
toMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Method to draw and save the snake in a given MTBImage.
toMTBImageByte(String, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Draws a border with all inner borders to a binary image with given size.
toMTBImageByte(String, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to save the region on a binary image with specific width and height.
toMTBImageByte(String, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to save the region on a binary image with specific width, height and color.
toMTBImageByte() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Method to save all contours from the regions on a binary image with specific width and height.
toMTBImageByte(String, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Method to draw and save the snake in a binary image.
topHat1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
tophat_concave(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Apply a top hat operator to the image for concavity detection.
tophat_convex(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Apply a top hat operator to the image for convexity detection.
TopHatContrastEnhancement - Class in de.unihalle.informatik.MiToBo.enhance
This class enhances the contrast by top-hat operations, especially for gray value bright filed or DIC images.
TopHatContrastEnhancement() - Constructor for class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Standard constructor.
TopHatContrastEnhancement(MTBImageByte, Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Constructor to create a new IlluminationCorrection object.
tophatMode() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.ImgTophat.tophatMode
 
topologicalNumber2DN4 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Helper object used in topology preservation.
topologicalNumber2DN8 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Helper object used in topology preservation.
topologyPreservation - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
topoNumber2D - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
topoNumberIsOne(int[][][], int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Check if topological for the class c is one in the neighborhood nbClassess3D.
topoNumberIsOne(MTBSegmentationInterface, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Check if topological for the class c is one in the pixel with coordinate (x,y,z) in the segmentation object segmentation.
topoNumberIsOne(int[][][], int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2D
 
toPositiveAngle360(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Simple way to convert negative angles to 0-360 degree.
toPositiveAngle360(double) - Static method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Normalize angles (in the range -360 to 360 degree) to the range 0-360 degree.
toRGB() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
Method to convert colors from HSV color space to RGB color space.
toRGB(double, double, double) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Method to convert a single color from HSV color space into RGB color space.
toSeconds(double, String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Convert a value of given time unit to seconds.
toString() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputData
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Returns the String "IMG("title of the image")"
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint2DSet
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
 
toString() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Return an ascii representation identifying the energy and internal parameters, but not the state.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return a string representation.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
 
toString() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Get an identifier string for the energy object.
toString() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Get an identifier string for the energy object.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Method for short adaptation description name.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Method for short termination description name.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
 
toString() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
toSWC(String, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Method to save neurite skeleton graph as SWC file.
totalAreas - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
totalLength - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
totalNumberOfObjects - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
totalObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
total number of observations over all frames
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Convert contour object to MTB XML datatype.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Generate xml-representation of this 3D-point.
toXMLType(MTBXMLPolygon2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Convert object to XML representation.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Create a xml representation of this polygon set using MiToBo's xml-scheme MTBXMLPolygon2DSet.xsd
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Construct an object that represents this region by xml.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct an object that represents this region by xml.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Create a xml representation of this bag of region sets using MiToBo's xml-scheme MTBRegion2DSetBag.xsd
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
 
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct an xml-representation of this set of 3D-regions.
toXMLType(MTBXMLSnakeType) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Convert object to XML representation.
toXMLType(Matrix) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Convert a JAMA matrix to its xml-beans type
toXMLType(MultiState<MotionModelID>) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Convert a MultiState object to its xml-beans representation
toXMLType(Vector<MultiState<MotionModelID>>) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Convert a Vector> object to its xml-beans representation
toXMLType() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
Convert this object to its XML-representation.
tp - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
tp - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.PrecisionCalc
True positives.
tp - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcQualityMeasures.RecallCalc
True positives.
TPclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
TPtrackend - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
TPtracksegment - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
TPtrackstart - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
traceBranch(MTBImage, int, int, MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Traces a skeleton branch and extracts its length.
traceBranch(MTBImageByte, Vector<Point2D.Double>, Point2D.Double) - Static method in class de.unihalle.informatik.MiToBo.morphology.BinaryImageEndpointTools
Continues a given branch at the given pixel recursively.
traceBranch(MTBImage, int, int) - Static method in class de.unihalle.informatik.MiToBo.morphology.SkeletonAnalysisHelper
Traces a skeleton branch and returns the list of its pixels.
traceContour(int, int, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Trace contour, starting at (xS, yS) in direction dS.
track() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
the actual tracking method
TrackAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
class for analyzing movement and shape of already tracked objects in a given label image
TrackAnalyzer(Vector<Trajectory2D>) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
trackcolors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
trackcolors - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
trackerOutputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
trackEvalResult - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
TrackEvaluator - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
TrackEvaluator(Vector<MultiState<MotionModelID>>, Vector<Vector<MultiState<MotionModelID>>>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
TrackEvaluator.TrackEvaluatorResult - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
TrackEvaluator.TrackObservation - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
TrackEvaluator.TrackSegment - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
TrackEvaluatorResult() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
trackgraphs - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
trackImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
trackingtime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
time that elapsed for tracking
TrackObservation(int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
trackReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
trackReport - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
tracks - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
HashMap of the tracks represented by the sample.
TrackSegment(int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
TrackVisualizer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
TrackVisualizer(MTBImage, Vector<Trajectory2D>) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
trafo - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
train() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
the actual svm training
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingTrajectoryExtraction
 
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
Trajectory2D - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
Trajectory2D(int, int, Vector<Point2D.Double>) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
Trajectory2D(int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
Trajectory2D(int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
TrajectoryExtraction2D - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
TrajectoryExtraction2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
transform(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
Transform the (column) vector x and add noise sampled from the Gaussian noise distribution.
transform(GaussianDistribution) - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
Transform the Gaussian distribution gaussian with this transform.
transform(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Compute the h-dome transform
transform - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
TransformationMode() - Constructor for enum de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform.TransformationMode
 
translate(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Translate current coordinates of the 3D point object.
traversePolygonPointList(Vector<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Helper function for simplify().
traverseSubdir(String, String) - Static method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Recursive traversal of subdirectories.
trim(Hashtable<Integer, Vector<Double>>, int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
truncate(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
truncate the histogram to the specified interval
tSize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Size of input image in t dimension.
TwoColumnPanel - Class in de.unihalle.informatik.MiToBo.gui
A panel with a titled border and two columns for a variable number of generic components that are placed vertically with an additional label.
TwoColumnPanel(String) - Constructor for class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
Constructor
type - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
type - Variable in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException
Type of exception.
type - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InflectionPoint
Type of segment starting with this point.
type - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.InProContourSegment
Type of segment.
type - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Type of the input image and later the type of the calculated 2D vector field.
type - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarkerVector
Type ID of markers.
type - Variable in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException
Type of exception.
typeoftime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 

U

U - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Vector U including the x-values of the vector field.
U - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
U-component-vector of the vector field.
UDE(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.Measure_DetectionErrors
This method computes the underdetection error.
ulimits - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
UndecimatedWaveletTransform - Class in de.unihalle.informatik.MiToBo.transforms
Undecimated wavelet transform (UWT) operator.
UndecimatedWaveletTransform() - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for dimension x, y and z, no image and denoise set to false.
UndecimatedWaveletTransform(MTBImage, int, boolean, MTBImage[]) - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Constructor.
UndecimatedWaveletTransform(MTBImage, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for at most dimension x, y (and z if present).
UndecimatedWaveletTransform(MTBImage, int, boolean, boolean) - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Constructor with default Gaussian kernel for sd = 1 [1/16, 1/4, 3/8, 1/4, 1/16] for at most dimension x, y (and z if present) or sd=0.5 [0.0002638651, 0.1064507720, 0.7865707259, 0.1064507720, 0.0002638651] if sigmaEqualsOne is false
UndecimatedWaveletTransform.TransformationMode - Enum in de.unihalle.informatik.MiToBo.transforms
 
UniformDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A multivariate uniform distribution.
UniformDistribution(int, double[], double[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
Constructor for uniform distribution with hypercube shape in dimension DOF, given lower and upper limits in the corresponding dimension and a random generator for sampling.
unitAngle - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
units - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Units used in measurements, default is pixels.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Unit in which measurements are provided.
unitSpace - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
unitT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
unitT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
unitT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
unitTime - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
unitVector(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Return the unit vector of vector.
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Physical pixel size units.
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ManualTrackingMigrationAnalyzer
 
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
unitXY - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
unitXYZ - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
unsetActualSliceOnly() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
The whole image is thresholded (default)
unsetAssociation(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
Unsets the association of the specified observation and state.
unsetAssociation(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Unset the association between target and observation.
UNTITLED - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Title string for new and untitled images
update(AbstractMultiState<MotionModelID>, DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
update(T, DataAssociation) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilter
Update step method given a multi-target observation
update(AbstractMultiState<T>, DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
The DataAssociation object may be null and is interpreted as groundtruth if given.
update(LinearTransformGaussNoise, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
updateAndRepaintWindow() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Update and repaint the image window if the image is displayed by ImageJ
updateButtonColor(Color) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserPanel
Update the button icon with the given color.
updateGUI() - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
 
updateIDs(Vector<MTBSnakePoint2D>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Update method for snake point ID's after make snake simple.
updateImageAndColorSettings() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Updates output image type and gray values according to chosen draw type.
updateImageList(String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Updates image list and GUI.
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Should be used to create or update ImagePlus data if the MTBImage is not using an ImagePlus to store the data (MTB_INT, MTB_DOUBLE, MTB_RGB).
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Does nothing, because the underlying ImagePlus is updated immediately when values are changed in the MTBImage
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Creates or updates an ImagePlus of Float type from the MTBImage Double data, can be returned by getImagePlus() or displayed by show()
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Does nothing, because the underlying ImagePlus is updated immediately when values are changed in the MTBImage
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Creates or updates an ImagePlus of Float type from the MTBImage Int data, which can be returned by getImagePlus() or displayed by show()
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Creates or updates an ImagePlus of RGB type from the MTBImage RGB(3 byte-channels) data, can be returned by getImagePlus() or displayed by show()
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Does nothing, because the underlying ImagePlus is updated immediately when values are changed in the MTBImage
updateImageSize_ImgToProp() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Update the image size in the properties hashtable from the image's size
updateIndep(int, LinearTransformGaussNoise, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
updateIndep(int, int, LinearTransformGaussNoise, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Update i-th Gaussian component with j-th observation
updateOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Update current overlap mask for all snakes.
updateParameters(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Updates parameters according to given membership.
updateParameters(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Updates internal parameters according to given segmentation.
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBChanVeseEnergyNonPDE
 
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Update parameters (if any) of the energy object which depend on the associated level set function.
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Update parameters (if any) of the energy object which depend on the associated level set function.
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
updateParams(int, int, int, short, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBSizeEnergyNonPDE
 
updatePhysProperties_ImgToProp() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Update physical properties (stepsizes, units) in the properties hashtable from its member variables
updatePhysProperties_PropToImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Update physical properties (stepsizes, units) of the image (member variables) from its properties hashtable
updateRegions() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Update neurite shaft and growth cone regions, due to changes of this regions by adding features or something else.
updateSnakeSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Convenience function for updating the segmentation.
updateStatus(MTBLevelsetFunctionDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
updateStatus(MTBLevelsetFunctionDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
updateStatus(MTBLevelsetFunctionDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
updateStatus(MTBLevelsetFunctionDerivable) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Function which updates the internal status of the energy.
updateStatus(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
updateStatus(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
updateStatus(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Update internal state of energy object prior to querying derivatives and so on.
updateStatus(SnakeOptimizerCoupled) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled
Update internal state of energy object prior to querying derivatives and so on.
updateStatus(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Update internal state of energy object prior to usaging it.
updateTable() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Updates the result table as new data is added.
updateTargetImageDependencies() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Updates parameters depending on the target image.
upperBound - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
upperThresh - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
Pixels with a response above this threshold are immidiately accepted.
upperThreshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
useAngleCriterion - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Enable/disable angle criterion.
useAngleCriterion - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Enable/disable angle criterion.
useAutoDistance - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
useAutoDistance - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
useAutoDistanceDetermination(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
useAutoGamma() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Callback routine to change parameters.
useEllipseDistThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Enable/disable ellipse distance threshold.
useEllipseDistThreshold - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Enable/disable ellipse distance threshold.
useExternalSVM - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
useExternalSVM(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
useGammaCorrection() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Callback routine to change parameters.
useHeavideApproximation(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
useHeavideApproximation(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
useHeavideApproximation(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
useHeavideApproximation(boolean) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Enable or disable approximation of Heaviside function.
useHeavisideApprox - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
Flag to indicate if the Heaviside function should be approximated.
useHeavisideApprox - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
Flag to indicate if the Heaviside function should be approximated.
useHeavisideApprox - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
Flag to indicate if the Heaviside function should be approximated.
useJNI - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Does this instance use JNI and thus user time?
useMask - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
useMultiIntersectionCheck - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Enable/disable line multi-intersection check.
useMultiIntersectionCheck - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorStromules
Enable/disable line multi-intersection check.
UserTime - Class in de.unihalle.informatik.MiToBo.tools.system
This is a stopwatch to measure elapsed user or real time used.
UserTime() - Constructor for class de.unihalle.informatik.MiToBo.tools.system.UserTime
Creates a new time object and starts the clock.
UserTime(boolean) - Constructor for class de.unihalle.informatik.MiToBo.tools.system.UserTime
Creates a new time object and starts the clock elapsing real time.
useSpecifiedDomain - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Flag for using user-specified domain information.
useThresh - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
uwt - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D.UWTRunner
Reference to (external) UWT operator.
uwtImages - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
UWTRunner(UndecimatedWaveletTransform) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D.UWTRunner
Default constructor.

V

v - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBArrayConverter
Array of intensity values.
v - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Intensity of HSV space.
V - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Vector V including the y-values of the vector field.
V - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
V-component-vector of the vector field.
valid(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Validity of point (x,y,z).
valid(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
is this pixel valid?
validate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
validate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
validate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
validate() - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Function to validate configuration of energy object.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBP
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPRIU
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
The validation of parameters and inputs.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
The validation of parameters and inputs.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitEllipseToPointSet
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.fitting.FitQuadraticCurveToPointSet
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawStringToImage
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
validateSeedTextField() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
ValidationMethod() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ValidationMethod
 
validColor - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
validMultiState(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Test if the specified multistate is valid for this factory.
value - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
Double value for these object.
value - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
 
value(double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.ResponseDifference
 
value - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.BorderBackgroundContrast
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.GapCloseMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.ImageType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.LobeTypes
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.MeasurementUnits
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperatorPhasesToRun
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.PixelCalibration
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationInputFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.BorderBackgroundContrast
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.OperationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D.DetectMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor.CellMaskFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete.SegmentationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums.MeasureUnit
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.LayerSubset
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.OpWorkingMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.DrawType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.ROOTSEGMENT_STATUS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D.NeuriteDetector2DMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos.DetectorExternalEnergy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D.NeuronColor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D.NuclDetectMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D.ResultImageMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut.NuclSeparateMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D.ResultImageMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D.DetectMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.AbsenceDetectionMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.ScratchOrientation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.KERNEL_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ScratchOrientation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ValidationMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.Neighbourhood
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.SortMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.InputMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.OutputMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.FactoryMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow.BoundaryPadding
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D.BorderConnectivity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.CurveType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException.DatatypeExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader.TargetFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator.Algorithm
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D.FeatureNames
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.SegmentType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer.FeatureNames
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures.HaralickDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib.FeatureType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal.NeighborhoodSelection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.fields.FieldOperations2D.FieldOperation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D.GradientMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.KernelPart
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.ResultType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D.ApplicationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer.JoinMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.GaussFilter.SigmaInterpretation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator.RankOpMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter.FilterMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D.FilterMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D.VesselMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.VesselMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB.OutImageType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.WeightModel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageArithmetics.ArithOp
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageStatistics.StatValue
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm.ScoreInterpretation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.statistics.PCA.ReductionMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.maskShape
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.opMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess.ProcessMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction.InputType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.ForegroundColor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.ImgTophat.tophatMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException.ExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics.CalcTargets
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface.SegmentationDimension
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.InputMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.SegmentationDimension
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.ShapeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents.BorderType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents.ContourType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics.StructureCountMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper.ApproxVersion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE.VelocityExpansionMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs.Thresholding_Direction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer.Snake_status
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.EnergyNormalizationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.IntensityNormalizationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu.InputType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.ResultValueMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.TargetContrast
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.ReducerMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageValueTools.ImageValueModification
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.AType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform.TransformationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage.RangeColor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OperationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.OperationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet.DrawType
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.BorderBackgroundContrast
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.GapCloseMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.ImageType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.LobeTypes
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.MeasurementUnits
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.OperatorPhasesToRun
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.PixelCalibration
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant.SegmentationInputFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.BorderBackgroundContrast
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D.OperationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D.DetectMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor.CellMaskFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete.SegmentationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums.MeasureUnit
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.LayerSubset
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator.OpWorkingMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.DrawType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.minirhizotron.utils.Drawing.ROOTSEGMENT_STATUS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D.NeuriteDetector2DMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos.DetectorExternalEnergy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D.NeuronColor
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D.NuclDetectMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D.ResultImageMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut.NuclSeparateMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D.ResultImageMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D.DetectMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.AbsenceDetectionMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.ScratchOrientation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.KERNEL_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ScratchOrientation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ValidationMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.Neighbourhood
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.SortMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.InputMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.OutputMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.FactoryMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow.BoundaryPadding
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D.BorderConnectivity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.CurveType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException.DatatypeExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader.TargetFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator.Algorithm
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D.FeatureNames
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProData.SegmentType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer.FeatureNames
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures.HaralickDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPJFeatureLib.FeatureType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.texture.lbp.FeatureCalculatorLBPOriginal.NeighborhoodSelection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.fields.FieldOperations2D.FieldOperation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D.GradientMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.KernelPart
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.ResultType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D.ApplicationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer.JoinMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.GaussFilter.SigmaInterpretation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator.RankOpMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter.FilterMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D.FilterMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D.VesselMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.VesselMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB.OutImageType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.WeightModel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageArithmetics.ArithOp
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageStatistics.StatValue
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm.ScoreInterpretation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.statistics.PCA.ReductionMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.maskShape
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.opMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess.ProcessMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.ConvexHullExtraction.InputType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.ForegroundColor
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.ImgTophat.tophatMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException.ExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics.CalcTargets
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface.SegmentationDimension
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.InputMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.SegmentationDimension
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.ShapeType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents.BorderType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents.ContourType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics.StructureCountMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper.ApproxVersion
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE.VelocityExpansionMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs.Thresholding_Direction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer.Snake_status
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.EnergyNormalizationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.IntensityNormalizationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu.InputType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.ResultValueMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.TargetContrast
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.ReducerMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageValueTools.ImageValueModification
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.AType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform.TransformationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.ArrayToColorMapImage.RangeColor
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OperationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleImageToHeatmap.OutOfRangeValuesHandlingMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.IgnoredValuesHandlingMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.colormappings.GrayscaleToGrayscaleMapping.OperationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet.DrawType
Returns an array containing the constants of this enum type, in the order they are declared.
var - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
varCheckNB - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Size of neighborhood for local variance checks.
varCheckThresh - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Threshold for variance check.
variance(Vector<Double>, double) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
varianceFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
vectorDiff(double[], double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Subtract two vectors.
vectorField - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
The 2D vector field for several operations.
vectorField - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
The resulting 2D vector field.
vectorField - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The calculated GVF vector field.
VectorField2DPotentialFinder - Class in de.unihalle.informatik.MiToBo.fields
Routines for reconstructing potential from vector field.
VectorField2DPotentialFinder() - Constructor for class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Standard constructor.
VectorField2DPotentialFinder(MTBVectorField2D) - Constructor for class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Default constructor.
VectorField2DPotentialFinder.PotentialFinderOptFunction - Class in de.unihalle.informatik.MiToBo.fields
Optimization function for gradient-based potential reconstruction.
vectorFieldImage - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
The 2D vector field stored to an image.
vectorFieldImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
The resulting 2D vector field stored to an image.
vectorFieldImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldNonMaxSuppression
Image with input 2D gradient field.
vectorNorm(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Returns the norm of a vector.
vectorOfCurvatures - Variable in class de.unihalle.informatik.MiToBo.features.contours.Contour2DCurvatureCalculator
Resulting Curvatures for each Pixel on the given MTBContour2D.
vectorSum(double[], double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Sums up two vectors.
vectorToString(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
vectorToString(int, Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
VelocityExpansionMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE.VelocityExpansionMode
 
verbose - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Verbose flag for standard console outputs.
verbose - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
If true, verbose outputs are written to standard output.
verbose - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.ReadXML
 
verbose - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
verbose - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Flag to turn display of additional information on/off.
verbose - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Flag to turn display of additional information on/off.
verbosePrintln(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
prints the given text if the verbose flag is set
verbosePrintln(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
prints the given text if the verbose flag is set
version - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper
Type of approximating function to use.
vesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Result of vesselness detection (for internal use only).
vesselImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Intermediate result: vesselness image.
VesselMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D.VesselMode
 
VesselMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.VesselMode
 
vExpandMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
vidpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
visibilityMapHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Height of visibility map.
visibilityMapWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Width of visibility map.
visible - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Visibility array.
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Visibility map for hiding individual pixels.
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Visibility map for hiding individual pixels.
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Visibility map for hiding individual pixels.
visibleMapMaxX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Maximal x coordinate of visibility map.
visibleMapMaxY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Maximal y coordinate of visibility map.
visibleMapMinX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal x coordinate of visibility map.
visibleMapMinY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal y coordinate of visibility map.
visitCC(int, int, int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Visit (x,y,z): reset the corresponding entry in X to false and recursively visit all neighbors of (x,y,z) in X.
visitNeighboursOf(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
Inspect the eight/four neighbours of the pixel with the given coordinate.
visualizeAnalysisResults - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Enable/disable the creation of an image to visualize results.
vol - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
volume - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
The volume of the region (number of points included).
volumes - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D
 
voronoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Function to extract Voronoi primers.
VoronoiExpandComponents(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Deprecated.
voronoiImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Image filled with voronoi tesselation data during profile calculation if non-null.
votesClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
votesTarget - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
vx - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
vy - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 

W

w - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
weight for neighbors
wantStackWithIntermediateResults(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag for turning on/off generation of stack with intermediate results.
WatershedBinary - Class in de.unihalle.informatik.MiToBo.morphology
Watershed transformation on binary images.
WatershedBinary() - Constructor for class de.unihalle.informatik.MiToBo.morphology.WatershedBinary
Default constructor.
WatershedBinary(MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.morphology.WatershedBinary
Constructor.
weightAsEdgeThickness - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
weightmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Map of weights for the segmentation.
weightmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Map of weights for the segmentation.
weightModel - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Model for the edge weights.
WeightModel() - Constructor for enum de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.WeightModel
 
weights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
weights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
weights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
Used as a substitute for the same field in MTBSet_???
weights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
List of energy weights.
whiteTophat(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
calculates the white tophat transform, i.e. difference of image and the opening of the image
(also called opening tophat)
width - Variable in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant
Width of the input image.
width - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.CellBoundaryExtractor2D
Width of the input image.
width - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
width - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Image size in x-direction, given in pixel.
width - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Width of the binary neuron image.
width - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
width - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Width of the processed image.
width - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Width of the segment (for compatibility with ImageJ).
width - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Skeleton image size in x-direction.
width - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Width of the image where the vector field comes from.
width - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Width of currently processed image.
width - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2DInProHelper
Width of reference image domain.
width - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Width of input label image.
width - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Width of the image.
width - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Size of the image and the calculated gvf field in x-direction.
width - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
 
width - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Width of the given image.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Width of segmentation domain.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Width of segmentation domain.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Image width.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Image width.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Width of label images.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.EvaluationMeasure
Width of label images.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.helpers.LabelImageConverter
Input image width.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Width of the input image and levelset function.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Width of the input image.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Width of the given image for the energy.
widthLengthTab - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Table with vessel widths and lengths to apply.
widths - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
widths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Main frame.
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyDisplayWindow
Main frame.
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Main frame.
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
windowHeight - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Height of the frame.
windowWidth - Static variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Width of the frame.
winSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Size of local sliding window.
workImage - Variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Internal image to work on.
workImgMaxVal - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder
Maximum intensity value in working image, i.e. after potential inversion of image intensity values.
workingImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Image on which to actually do the segmentation.
workingMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Local copy of matrix modified during calculations.
workVectorField - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Local vector field variable actually used during operator run.
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Write this contour set into XML file filename.xml Additionally, its processing history is written.
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Write this polygon set as xml into file filename.xml Additionally the processing history is written.
write(String, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Write this polygon set as xml into file filename If flag is set to true, the processing history is written, too.
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Write this region set to disk in XML format using MiToBo's xml-scheme MTBRegion2DSet.xsd
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Write this bag of region sets to disk in XML format using MiToBo's xml-scheme MTBRegion2DSetBag.xsd
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Write this set of 3D-regions to disk in XML format using MiToBo's xml-scheme MTBRegion3DSet.xsd
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant_FeatureColorMapperInputDataIOSwing
 
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerImageData
 
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerRegion2DSet
 
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerSegResultParticlesMultiChannel
 
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerTableModel
 
writeData(Object, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
 
writeData(Object, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBWrapperDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.RandomGeneratorDataIOSwing
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtPoint2dDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
 
writeGlobalAttributes(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
writeGraph(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
writeImagePlus(String, ImagePlus) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Write ImagePlus to disk
writeMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Write an MTBImage to disk
writeMultiStates(Vector<MultiState<MotionModelID>>, String) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.MultiStateIO
Write a vector of MultiState objects to file in its xml-beans representation.
writeNodeLabels(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
writePartitions(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
WRITER_OPTIONS_APPROVED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Property change when writer options are approved (i.e. when filechooser selection is approved)
writeRoiToFile(MTBRegion2D, String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter
Writes the given region to the specified file in csv format.
writeSubgraphs(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
WriteXML - Class in de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml
Writes markers of an image to file in XML format.
WriteXML(String) - Constructor for class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML
Creates a new instance of ODWriteXMLODD
writeXML(String, Vector<?>, int) - Method in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML
 
wthImage - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
White top-hat image.
wthMaskSize - Variable in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
 

X

x - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Point coordinate at x-dimension.
x - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
x-coordinate of marker.
x - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
 
x - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
x - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
X - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
8- or 26 neighbors of the current pixel used to determine topological numbers represented as an 3x3x3 array center around the current pixel.
X_COMPONENT_INDEX - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
xc - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.GraphNode
x-coordinate associated with the node.
xField - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Field for x-coordinate.
xFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Vector field flow in x-direction.
xFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The flows of the field in x- and y-direction.
xLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Label of the x-axis.
xLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Label of the x-axis.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Maximal x-coordinate of the domain of this border set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Maximal x coordinate of the domain of this contour set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Maximal x coordinate of the domain of this polygon set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Maximal x coordinate of the domain of this region set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Maximal x coordinate of the domain of this region set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Maximal x coordinate of the domain of this region set.
xMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
xMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
xMean - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
xMeanSum - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingRegion2D
 
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Minimal x-coordinate of the domain of this border set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Minimal x coordinate of the domain of this contour set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Minimal x coordinate of the domain of this polygon set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Minimal x coordinate of the domain of this region set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Minimal x coordinate of the domain of this region set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Minimal x coordinate of the domain of this region set.
xMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
xMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
xml - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
File description XML string if available
XMLBuffOut - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML
 
XMLFileOut - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.xml.WriteXML
 
XMLTypeConverter - Class in de.unihalle.informatik.MiToBo.tools
A class providing static methods to convert specific object to and from their corresponding xml-types provided by xml-beans.
XMLTypeConverter() - Constructor for class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
 
xMTBImg - Variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Result Image.
xOffset - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
x-offset of the mask coordinate system.
xPos - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
y-position of the node in 2D image space.
xSize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Size of input image in x dimension.
xThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
The Intensity/Brightness/Value threshold.
xThresh - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The Intensity/Brightness/Value threshold.
XylemDetector - Class in de.unihalle.informatik.MiToBo.apps.xylem
This operator implements xylem detection in RGB or HSX images.
XylemDetector() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Default Constructor.
xylemGrayedImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
The Xylem Cell microscope MTBImageByte grey level image.
XylemGrower - Class in de.unihalle.informatik.MiToBo.apps.xylem
This operators implements region growing for xylem segmentation.
XylemGrower() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default Constructor.
XylemGrower(MTBImageByte, MTBImageByte, XylemGrower.GrowingMode) - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
XylemGrower.GrowingMode - Enum in de.unihalle.informatik.MiToBo.apps.xylem
The region growing modus.
XylemGrower.GrowingRegion2D - Class in de.unihalle.informatik.MiToBo.apps.xylem
This class is responsible for the growing of a single MTBRegion2D which is the result of the preprocessing steps.
XylemGrower.Neighbourhood - Enum in de.unihalle.informatik.MiToBo.apps.xylem
The kind of neighbourhood to inspect a pixel.
XylemGrower.SortMode - Enum in de.unihalle.informatik.MiToBo.apps.xylem
Sort Mode for different MTBRegion2D's.
xylemHsxImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
HS(X)-Color Channel Image.
xylemHsxImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
HS(X)-Color Channel Image.
XylemInitialSegmentation - Class in de.unihalle.informatik.MiToBo.apps.xylem
Purpose of this operator is to make an initial segmentation of Xylem Cell Images.
XylemInitialSegmentation() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Default constructor.
XylemInitialSegmentation(MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
xylemRegionsOverlay - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Resulting regions from growing.
xylemRGBImage - Variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
RGB-Color Channel Image.

Y

y - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.Node
 
y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Point coordinate at y-dimension.
y - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
y-coordinate of marker.
y - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
 
y - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
y - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
yc - Variable in class de.unihalle.informatik.MiToBo.math.graphs.DijkstraShortestPixelPathFinder.GraphNode
y-coordinate associated with the node.
yellow - Static variable in class de.unihalle.informatik.MiToBo.features.regions.Region2DSkeletonAnalyzer
Definition of yellow color.
yesnoOption - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperatorConfigWin
Deprecated.
Labels to be used on buttons of Yes/No message boxes.
yField - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Field for y-coordinate.
yFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Vector field flow in y-direction.
yFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The flows of the field in x- and y-direction.
yLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Label of the y-axis.
yLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Label of the y-axis.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Maximal y-coordinate of the domain of this border set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Maximal y coordinate of the domain of this contour set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Maximal y coordinate of the domain of this polygon set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Maximal y coordinate of the domain of this region set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Maximal y coordinate of the domain of this region set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Maximal y coordinate of the domain of this region set.
yMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
yMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Minimal y-coordinate of the domain of this border set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Minimal y coordinate of the domain of this contour set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Minimal y coordinate of the domain of this polygon set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Minimal y coordinate of the domain of this region set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Minimal y coordinate of the domain of this region set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Minimal y coordinate of the domain of this region set.
yMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
yMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
yOffset - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
y-offset of the mask coordinate system.
yPos - Variable in class de.unihalle.informatik.MiToBo.apps.minirhizotron.datatypes.MTBRootTreeNodeData
y-position of the node in 2D image space.
ySize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Size of input image in y dimension.

Z

z - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
z - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Point coordinate at z-dimension.
z - Variable in class de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.datatypes.CellCntrMarker
z-coordinate of marker.
z - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
 
z - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
z - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
Z - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
observations
Zadj - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
adjacency votes matrix: which observations are associated (same track) and how many particles vote for these associations
zMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Maximal z coordinate of the domain of this region set.
zMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Maximal z coordinate of the domain of this region set.
zMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Minimal z coordinate of the domain of this region set.
zMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBSurface3DSet
Minimal z coordinate of the domain of this region set.
zSize - Variable in class de.unihalle.informatik.MiToBo.apps.plantCells.stromules.StromulesDetector2D
Size of input image in z dimension.
ztcCoords - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawEllipse
Optional coordinates for slices in ztc stack.
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