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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.actinAnalysis
Operator for analyzing actin filament structures in 2D images.
ActinAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Default constructor.
ActinAnalyzer2D.CellMaskFormat - Enum in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Format of cell segmentation data.
ActinFeatureExtractorEigenStructures - Class in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Operator for extracting Eigen structures as features for the ActinAnalyzer2D.
ActinFeatureExtractorEigenStructures() - Constructor for class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Default constructor.
ActinFeatureExtractorHaralickMeasures - Class in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Operator for extracting Haralick texture measures from co-occurrence matrices as features for the ActinAnalyzer2D.
ActinFeatureExtractorHaralickMeasures() - Constructor for class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Default constructor.
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.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
 
activeSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Array with active snakes.
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(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.
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.
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
 
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
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.
addLast(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Appends the specified element to the end of this list.
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
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.
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(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.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.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
ALDMetaInfo - Annotation Type in de.unihalle.informatik.Alida.admin.annotations
Annotation for adding meta data to Alida classes.
ALDMetaInfo.ExportPolicy - Enum in de.unihalle.informatik.Alida.admin.annotations
Class export policy.
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
 
analyzeLobesAndNecks - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Flag to turn on/off analysis of lobes and necks.
analyzeLocalCurvatures() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Calculates and analyses pixel-wise local curvatures.
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.
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.
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.
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.
avgBranchLengths - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgConcavities - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgEndpointDistances - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
avgFactor - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
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.
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.
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
 

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
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
 
binaryMasks - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
(Optinal) stack with binary segmentation masks.
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
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
 
BorderConnectivity() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D.BorderConnectivity
 
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
 
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.actinAnalysis.ActinAnalyzer2D
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.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.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.
calcArea - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcArea() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcAverageSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Calculates the average size of the set.
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.
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.
calcDM() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransformPrecursorInfos
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(MTBImageHistogram) - Static method in class de.unihalle.informatik.MiToBo.enhance.HistogramEqualization
Calculates the Shannon entropy for the given histogram.
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.
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.
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.
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
 
calcPerimeter - Variable in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
calcPerimeter() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
 
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.
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
 
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.
calculateFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
 
calculateFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.FilamentFeatureExtractor
Performs the feature calculation.
calculateFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.FilamentFeatureExtractorTiles
 
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.actinAnalysis.ActinAnalyzer2D
Calculates pairwise Euclidean distances between all feature vectors.
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.analyzeLobesAndNecks or MorphologyAnalyzer2D.calcMarginRoughness.
callbackSolidity() - Method in class de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D
Callback function called in case of changes of parameter MorphologyAnalyzer2D.calcSolidity.
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.
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.
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
cellChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Channel for cell boundary detection.
cellContours - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Set of detected cell boundaries.
cellGroupNames - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
List of group names, filled in ActinAnalyzer2D.clusterFeatures().
cellGroups - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.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] > > ,
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.actinAnalysis.ActinAnalyzer2D.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
 
cellwiseDistros - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Map of cluster distributions per cell, filled in ActinAnalyzer2D.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
 
cgal_isClockwiseOriented(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.
 
cgal_isConvex(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.
 
cgal_isCounterclockwiseOriented(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.
 
cgal_isSimple(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.
Checks if a polygon is simple.
cgal_makePolySimple(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.
Simplifies the given polygon.
cgal_orientation(double[], double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.
 
cgal_signedArea(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.
Calculates the signed area of a polygon.
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
 
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.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
 
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.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(!)
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.
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.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.MTBNeuriteSkelGraph
 
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.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.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.
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.
closestObjectPixelMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransformPrecursorInfos
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.actinAnalysis.ActinAnalyzer2D
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.actinAnalysis.ActinAnalyzer2D
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
 
codec - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
codec - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
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.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 - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Color value used, e.g., for color and transparent images.
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.
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.
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.
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
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.
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.
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.
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.
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
 
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.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.
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.
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
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
 
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.

D

d - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D
Implicit curve parameter d.
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
 
DE - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation
Check if you want to compute the Detection Errors
de.unihalle.informatik.Alida.admin.annotations - package de.unihalle.informatik.Alida.admin.annotations
 
de.unihalle.informatik.MiToBo.apps.actinAnalysis - package de.unihalle.informatik.MiToBo.apps.actinAnalysis
Provides tools and applications for quantifying actin filament structures in microscopy images of cells.
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.datatypes.cellImages - package de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
 
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.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.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.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.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.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.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.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.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
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.actinAnalysis.ActinFeatureExtractorHaralickMeasures
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
 
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).
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
 
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
 
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.visualization.drawing.DrawTracks2D
 
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
 
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
 
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.
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.
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.
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.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Directions for calculating cooccurrence matrices.
directions - Variable in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Directions.
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.
dirProvider - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Provider to read input directory.
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.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.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.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.actinAnalysis.ActinFeatureExtractorHaralickMeasures
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.
distanceImg - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransformPrecursorInfos
The distance field as MTBImage.
distanceMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
The distance field as two-dimensional double array.
distanceMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransformPrecursorInfos
The distance field as two-dimensional double array.
distanceMetric - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
 
DistanceMetric() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric
 
distanceMetric - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransformPrecursorInfos
Distance metric to apply.
DistanceTargetFunction(Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBQuadraticCurve2D.DistanceTargetFunction
Default constructor.
DistanceTransform - Class in de.unihalle.informatik.MiToBo.morphology
Class to calculate a distance map / field from a binary image using the Champfer-algorithm from G.
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.
DistanceTransformPrecursorInfos - Class in de.unihalle.informatik.MiToBo.morphology
Calculate Champfer distance transform including precursor infos.
DistanceTransformPrecursorInfos() - Constructor for class de.unihalle.informatik.MiToBo.morphology.DistanceTransformPrecursorInfos
Standard constructor.
DistanceTransformPrecursorInfos(MTBImageByte, DistanceTransform.DistanceMetric, DistanceTransform.ForegroundColor) - Constructor for class de.unihalle.informatik.MiToBo.morphology.DistanceTransformPrecursorInfos
Constructor to create a new DistanceTransform object.
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.
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.actinAnalysis.ActinAnalyzer2D
Cluster distribution data, rows refer to clusters and columns to cells.
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)
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.actinAnalysis.ActinAnalyzer2D
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.actinAnalysis.ActinAnalyzer2D
Perform PCA in second stage?
doPCA() - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Performs a Karhunen-Loeve transformation on the cluster distribution data.
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(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.
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.
DrawLine - Class in de.unihalle.informatik.MiToBo.visualization.drawing
Implementation of the Bresenham line drawing algorithm according to http://en.wikipedia.org/wiki/Bresenham%27s_line_algorithm
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(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.
DrawPolygon2DSet(MTBPolygon2DSet, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Complete constructor.
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.
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
 
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
 
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(MTBImage, String, int, int) - Static method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Draws string at given position into image.
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 - 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.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.
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.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.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
 
endPointHash - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
 
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.
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
 
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
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
 
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.
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.
ExportPolicy() - Constructor for enum de.unihalle.informatik.Alida.admin.annotations.ALDMetaInfo.ExportPolicy
 
ext - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
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
 
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.
extractProfiles - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
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.
FeatureCalculatorResult - Interface in de.unihalle.informatik.MiToBo.features
Interface for result data returned from classes extending FeatureCalculator.
featureDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Feature directory.
featureExtractor - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
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.
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.
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.
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.
FilamentFeatureExtractor - Class in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Operator for extracting features for the ActinAnalyzer2D.
FilamentFeatureExtractor() - Constructor for class de.unihalle.informatik.MiToBo.apps.actinAnalysis.FilamentFeatureExtractor
Default constructor.
FilamentFeatureExtractorTiles - Class in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Operator for extracting features for the ActinAnalyzer2D.
FilamentFeatureExtractorTiles() - Constructor for class de.unihalle.informatik.MiToBo.apps.actinAnalysis.FilamentFeatureExtractorTiles
Default constructor.
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!)
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
 
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 image.
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
 
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
 
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.
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.
foreground - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransformPrecursorInfos
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.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.
gauss2poisson(MTBImage) - 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.
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
 
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.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.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.
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.
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.
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
 
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.
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.
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
 
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() - 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.
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.
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.
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.
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.DistanceTransformPrecursorInfos
Get the calculated map of closest object pixels.
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)
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.
getColumnCount() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
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.
getConnectivity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Query the connectivity of pixels within border.
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.
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.
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.
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(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.io.tools.ImageFilter
 
getDestinationImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get value of Input argument DestinationImage.
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.
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.
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