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A

ABS_DIFF - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
 
AbstractInPlaceStrel - Class in inra.ijpb.morphology.strel
Implementation stub for in place Structuring elements.
AbstractInPlaceStrel() - Constructor for class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
AbstractInPlaceStrel3D - Class in inra.ijpb.morphology.strel
Implementation stub for in place 3D Structuring elements.
AbstractInPlaceStrel3D() - Constructor for class inra.ijpb.morphology.strel.AbstractInPlaceStrel3D
 
AbstractSeparableStrel - Class in inra.ijpb.morphology.strel
Implementation stub for separable Structuring elements.
AbstractSeparableStrel() - Constructor for class inra.ijpb.morphology.strel.AbstractSeparableStrel
 
AbstractSeparableStrel3D - Class in inra.ijpb.morphology.strel
Implementation stub for separable 3D Structuring elements.
AbstractSeparableStrel3D() - Constructor for class inra.ijpb.morphology.strel.AbstractSeparableStrel3D
 
AbstractStrel - Class in inra.ijpb.morphology.strel
Implementation basis for planar structuring elements.
AbstractStrel() - Constructor for class inra.ijpb.morphology.strel.AbstractStrel
 
AbstractStrel3D - Class in inra.ijpb.morphology.strel
Implementation basis for 3D structuring elements
AbstractStrel3D() - Constructor for class inra.ijpb.morphology.strel.AbstractStrel3D
 
add(int) - Method in class inra.ijpb.morphology.strel.LocalBufferedHistogram
Adds a value to the local histogram, and update bounds if needed.
add(double) - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferDouble
Adds a value to the local histogram, and update bounds if needed.
add(int) - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferGray8
Adds a value to the local histogram, and update bounds if needed.
addAlgoListener(AlgoListener) - Method in interface inra.ijpb.algo.Algo
 
addAlgoListener(AlgoListener) - Method in class inra.ijpb.algo.AlgoStub
 
adjustDynamic(ImageStack, double, double) - Static method in class inra.ijpb.data.image.Images3D
Returns a new instance of ImageStack containing ByteProcessors such that display range is specified by vmin and vmax.
Algo - Interface in inra.ijpb.algo
An interface for managing progression and status changes of algorithms.
AlgoEvent - Class in inra.ijpb.algo
An event class for storing information about the status and progression of an algorithm.
AlgoEvent(Object, String, double, double) - Constructor for class inra.ijpb.algo.AlgoEvent
 
AlgoEvent(Object, String) - Constructor for class inra.ijpb.algo.AlgoEvent
 
AlgoEvent(Object, double, double) - Constructor for class inra.ijpb.algo.AlgoEvent
 
AlgoListener - Interface in inra.ijpb.algo
Interface for managing progression and status changes of an algorithm.
algoProgressChanged(AlgoEvent) - Method in interface inra.ijpb.algo.AlgoListener
 
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.algo.DefaultAlgoListener
 
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel
Propagates the event by changing the source.
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel3D
Propagates the event by changing the source.
algoStatusChanged(AlgoEvent) - Method in interface inra.ijpb.algo.AlgoListener
 
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.algo.DefaultAlgoListener
 
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel
Propagates the event by changing the source.
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel3D
Propagates the event by changing the source.
AlgoStub - Class in inra.ijpb.algo
A minimal implementation of algorithm for managing progression listeners.
AlgoStub() - Constructor for class inra.ijpb.algo.AlgoStub
 
almostEquals(Vector3d, double) - Method in class inra.ijpb.measure.Vector3d
Checks if this vector is close to the given vector, by checking each coordinate using the given threshold.
analyzeImage(ImageProcessor) - Method in interface inra.ijpb.binary.geodesic.GeodesicDiameter
 
analyzeImage(ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDiameterFloat
Computes the geodesic diameter of each particle within the given label image.
analyzeImage(ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDiameterShort
Computes the geodesic diameter of each particle within the given label image.
analyzeRegions(ImageProcessor, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Computes several morphometric features for each region in the input label image.
analyzeRegions(ImageProcessor, double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Computes several morphometric features for each region in the input label image and specifying number of directions to use for measuring perimeter.
AND - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
 
angle(Vector3d, Vector3d) - Static method in class inra.ijpb.measure.Vector3d
Computes the angle between two 3D vectors.
apply(ImageProcessor, Strel) - Method in enum inra.ijpb.morphology.Morphology.Operation
Applies the current operator to the input image.
apply(ImageStack, Strel3D) - Method in enum inra.ijpb.morphology.Morphology.Operation
Applies the current operator to the input 3D image.
apply(ImageStack, int) - Method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.Operation
 
apply(ImageStack, int, int) - Method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.Operation
 
apply(ImageProcessor, int) - Method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
 
apply(ImageProcessor, int, int) - Method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
 
apply(ImageStack, int) - Method in enum inra.ijpb.plugins.RegionalMinAndMax3DPlugin.Operation
 
apply(ImageProcessor, int) - Method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation
 
apply() - Method in class inra.ijpb.watershed.WatershedTransform2D
Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.
apply(double, double) - Method in class inra.ijpb.watershed.WatershedTransform2D
Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.
apply() - Method in class inra.ijpb.watershed.WatershedTransform3D
Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.
apply(double, double) - Method in class inra.ijpb.watershed.WatershedTransform3D
Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.
applyLut(ImageProcessor, double[]) - Static method in class inra.ijpb.label.LabelImages
Applies the given Look-up table to the input label image.
applyLut(ImageStack, double[]) - Static method in class inra.ijpb.label.LabelImages
Applies the given Look-up table to the input label image.
applyTo(int, int) - Method in interface inra.ijpb.math.ImageCalculator.Operation
The method to override to make it possible to use an operation.
applyTo(ImageStack) - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
Applies this regional extrema algorithm on the 3D image given as argument, and returns the result as a binary image stack.
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
Applies this regional extrema algorithm on the 3D image given as argument and using the given mask, and returns the result as a binary image stack.
applyTo(ImageStack) - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DByFlooding
 
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DByFlooding
 
applyTo(ImageProcessor) - Method in class inra.ijpb.morphology.extrema.RegionalExtremaAlgo
Applies this regional extrema algorithm on the image given as argument, and returns the result as a binary image.
applyTo(ImageProcessor) - Method in class inra.ijpb.morphology.extrema.RegionalExtremaByFlooding
 
applyTo(ImageStack, ImageStack) - Method in interface inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgo
Applies the geodesic reconstruction algorithm to the input marker and mask images.
applyTo(ImageStack, ImageStack, ImageStack) - Method in interface inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgo
Applies the geodesic reconstruction algorithm to the input marker and mask images, restricted by a binary mask.
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Float
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Float
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray16
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray16
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray8
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray8
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid1Image3D
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid1Image3D
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageProcessor, ImageProcessor) - Method in interface inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgo
Applies the geodesic reconstruction algorithm to the input marker and mask images.
applyTo(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3D
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3D
 
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DGray8
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DGray8
 
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DScanning
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DScanning
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DScanningGray8
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DScanningGray8
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion
Run the reconstruction by erosion algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DGray8
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DGray8
 
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanning
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanning
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanningGray8
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanningGray8
 
applyTo(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionHybrid
Run the geodesic reconstruction algorithm using the specified images as argument.
applyTo(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionScanning
Run the reconstruction by dilation algorithm using the images specified as argument.
applyTo(ImageStack, ImageStack, int) - Method in enum inra.ijpb.plugins.GeodesicReconstruction3DPlugin.Operation
 
applyTo(ImageProcessor, ImageProcessor, int) - Method in enum inra.ijpb.plugins.GeodesicReconstructionPlugin.Operation
 
applyTo(ImageStack, ImageStack) - Method in enum inra.ijpb.plugins.ImposeMinAndMax3DPlugin.Operation
 
applyTo(ImageStack, ImageStack, int) - Method in enum inra.ijpb.plugins.ImposeMinAndMax3DPlugin.Operation
 
applyTo(ImageProcessor, ImageProcessor) - Method in enum inra.ijpb.plugins.ImposeMinAndMaxPlugin.Operation
 
applyTo(ImageProcessor, ImageProcessor, int) - Method in enum inra.ijpb.plugins.ImposeMinAndMaxPlugin.Operation
 
applyToOld(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DGray8
Run the reconstruction by dilation algorithm using the images specified as argument.
applyToTmp(ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DGray8
Run the reconstruction by dilation algorithm using the images specified as argument.
applyWithPriorityQueue() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Apply watershed transform on inputImage, using the labeled markers from markerImage and restricted to the white areas of maskImage.
applyWithPriorityQueue() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
Apply watershed transform on inputImage, using the labeled markers from markerImage and restricted to the white areas of maskImage.
applyWithPriorityQueueAndDams() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Apply watershed transform on inputImage, using the labeled markers from markerImage and restricted to the white areas of maskImage (optionally).
applyWithPriorityQueueAndDams() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
Apply watershed transform on inputImage, using the labeled markers from markerImage and restricted to the white areas of maskImage (optionally).
applyWithSortedList() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Deprecated.
The algorithm with a sorted list does not visit the pixels based on their h value and proximity to markers so it is not a true watershed method.
applyWithSortedList() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
Deprecated.
The algorithm with a sorted list does not visit the voxels based on their h value and proximity to markers so it is not a true watershed method.
applyWithSortedListAndDams() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Deprecated.
The algorithm with a sorted list does not visit the pixels based on their h value and proximity to markers so it is not a true watershed method.
applyWithSortedListAndDams() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
Deprecated.
The algorithm with a sorted list does not visit the voxels based on their h value and proximity to markers so it is not a true watershed method.
area(ImageProcessor, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Computes the area for each particle in the label image, taking into account image resolution.
areaOpening(ImageProcessor, int) - Static method in class inra.ijpb.binary.BinaryImages
Applies area opening on a binary image: creates a new binary image that contains only particles with at least the specified number of pixels.
areaOpening(ImageProcessor, int) - Static method in class inra.ijpb.label.LabelImages
Applies area opening on a label image: creates a new label image that contains only particles with at least the specified number of pixels.
AreaOpening - Interface in inra.ijpb.morphology.attrfilt
Area opening for gray level images.
areaOpening(ImageProcessor, int) - Static method in class inra.ijpb.morphology.AttributeFiltering
Applies grayscale area opening on input image, by retaining only the connected components that contain at least the specified number of pixels.
AreaOpeningNaive - Class in inra.ijpb.morphology.attrfilt
Computes area opening using naive algorithm.
AreaOpeningNaive() - Constructor for class inra.ijpb.morphology.attrfilt.AreaOpeningNaive
 
AreaOpeningPlugin - Class in inra.ijpb.plugins
Select binary particles in a planar image based on number of pixels.
AreaOpeningPlugin() - Constructor for class inra.ijpb.plugins.AreaOpeningPlugin
 
AreaOpeningQueue - Class in inra.ijpb.morphology.attrfilt
Area opening using priority queue for updating each regional maxima.
AreaOpeningQueue() - Constructor for class inra.ijpb.morphology.attrfilt.AreaOpeningQueue
 
AttributeFiltering - Class in inra.ijpb.morphology
Several static methods for computation of attribute filtering (opening, thinning...) on gray level images.
AttributeFiltering() - Constructor for class inra.ijpb.morphology.AttributeFiltering
 
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