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A

ABS_DIFF - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
Abs_diff operator, that computes the absolute value of the difference of values of the two images
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
 
addBorder(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractStrel
Adds a border around the image, to avoid edge effects when performing morphological closing or opening.
addBorder(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
Adds a border around the image, to avoid edge effects when performing morphological closing or opening.
addBorders(ImageProcessor, int, int, int, int) - Method in interface inra.ijpb.data.border.BorderManager
Adds the specified number of pixels around the input image, and returns the resulting image.
addBorders(ImageStack, int, int, int, int, int, int) - Method in interface inra.ijpb.data.border.BorderManager3D
Adds the specified number of voxels around the input image, and returns the resulting image.
addBorders(ImageProcessor, int, int, int, int) - Static method in class inra.ijpb.shape.ImageShape
Adds the specified number of pixels around the input image, and returns the resulting image.
addBorders(ImageStack, int, int, int, int, int, int) - Static method in class inra.ijpb.shape.ImageShape
Adds the specified number of voxels around the input image, and returns the resulting image.
addLabelsAsOverlay(ImagePlus, int[], double[][]) - Method in class inra.ijpb.plugins.DrawLabelsAsOverlayPlugin
Draw the values onto the target image.
addResult(ResultsTable) - Method in class inra.ijpb.measure.ResultsBuilder
Add a results table to the already existing table.
addVertex(Point2D) - Method in class inra.ijpb.geometry.Polygon2D
Adds a new vertex in this polygon
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
Creates a new AlgoEvent.
AlgoEvent(Object, String) - Constructor for class inra.ijpb.algo.AlgoEvent
Creates a new AlgoEvent.
AlgoEvent(Object, double, double) - Constructor for class inra.ijpb.algo.AlgoEvent
Creates a new 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
The method devoted to manage the change in the progression of the algorithm.
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.algo.DefaultAlgoListener
 
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.binary.geodesic.GeodesicDiameter3DFloat
Deprecated.
 
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
 
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.measure.region3d.GeodesicDiameter3D
 
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
 
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.measure.region3d.RegionAnalyzer3D
 
algoProgressChanged(AlgoEvent) - Method in class inra.ijpb.morphology.filter.MorphologicalFilter
 
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
The method devoted to manage the change in the status of the algorithm.
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.algo.DefaultAlgoListener
 
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.binary.geodesic.GeodesicDiameter3DFloat
Deprecated.
 
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
 
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.measure.region3d.GeodesicDiameter3D
 
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
 
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.measure.region3d.RegionAnalyzer3D
 
algoStatusChanged(AlgoEvent) - Method in class inra.ijpb.morphology.filter.MorphologicalFilter
 
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(Vector2D, double) - Method in class inra.ijpb.geometry.Vector2D
Checks if this vector is close to the given vector, by checking each coordinate using the given threshold.
almostEquals(Vector3D, double) - Method in class inra.ijpb.geometry.Vector3D
Checks if this vector is close to the given vector, by checking each coordinate using the given threshold.
almostEquals(Vector3d, double) - Method in class inra.ijpb.measure.Vector3d
Deprecated.
Checks if this vector is close to the given vector, by checking each coordinate using the given threshold.
analyzeBinary(ImageProcessor, double[]) - Method in class inra.ijpb.measure.region2d.MaxFeretDiameter
Computes Maximum Feret diameter from a single region in a binary image.
analyzeImage(ImageProcessor) - Method in interface inra.ijpb.binary.geodesic.GeodesicDiameter
Deprecated.
computes geodesic diameter for each region of the input image.
analyzeImage(ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDiameterFloat
Deprecated.
Computes the geodesic diameter of each particle within the given label image.
analyzeImage(ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDiameterShort
Deprecated.
Computes the geodesic diameter of each particle within the given label image.
AnalyzeMicrostructure3D - Class in inra.ijpb.plugins
Plugin for computing densities of 3D intrinsic volumes (volume, surface area, mean breadth and Euler number) from 3D binary images.
AnalyzeMicrostructure3D() - Constructor for class inra.ijpb.plugins.AnalyzeMicrostructure3D
 
analyzeRegions(ImageProcessor, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
analyzeRegions(ImageProcessor, double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.AverageThickness
 
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.BoundingBox
Computes bounding box of each region in input label image.
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.Centroid
Computes centroid of each region in input label image.
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.Convexity
 
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.EquivalentEllipse
Computes the equivalent ellipse of each region within the input label image.
analyzeRegions(ImageProcessor) - Method in class inra.ijpb.measure.region2d.GeodesicDiameter
Computes the geodesic diameter of each particle within the given label image.
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.GeodesicDiameter
Computes the geodesic diameter of each region within the given label image.
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.InertiaEllipse
Deprecated.
Computes inertia ellipse of each region in input label image.
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
 
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.LargestInscribedCircle
Computes largest inscribed disk of each region within a label image.
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.MaxFeretDiameter
Computes maximum Feret Diameter for each label of the input label image.
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.OrientedBoundingBox2D
 
analyzeRegions(ImageProcessor, int[], Calibration) - Method in class inra.ijpb.measure.region2d.RegionAnalyzer2D
Computes an instance of the generic type T for each region in input label image.
analyzeRegions(ImageProcessor, Calibration) - Method in class inra.ijpb.measure.region2d.RegionAnalyzer2D
Identifies labels within image and computes an instance of the generic type T for each region in input label image.
analyzeRegions(ImagePlus) - Method in class inra.ijpb.measure.region2d.RegionAnalyzer2D
Default implementation of the analyzeRegions method, that calls the more specialized RegionAnalyzer2D.analyzeRegions(ImageProcessor, int[], Calibration) method and transforms the result into a map.
analyzeRegions(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.BoundingBox3D
Computes the bounding box of each region within a 3D label image.
analyzeRegions(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.Centroid3D
Computes centroid of each region in input label image.
analyzeRegions(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.EquivalentEllipsoid
Computes equivalent ellipsoid of each region in the input 3D label image.
analyzeRegions(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.GeodesicDiameter3D
Computes the geodesic diameter of each particle within the given label image.
analyzeRegions(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.InertiaEllipsoid
Deprecated.
Computes inertia ellipsoid of each region in the input 3D label image.
analyzeRegions(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
 
analyzeRegions(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.LargestInscribedBall
Computes largest inscribed ball of each region with a 3D label image.
analyzeRegions(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.MaxFeretDiameter3D
Computes maximum Feret Diameter for each label of the input label image.
analyzeRegions(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.RegionAnalyzer3D
Computes an instance of the generic type T for each region in input label image.
analyzeRegions(ImageStack, Calibration) - Method in class inra.ijpb.measure.region3d.RegionAnalyzer3D
Identifies labels within image and computes an instance of the generic type T for each region in input label image.
analyzeRegions(ImagePlus) - Method in class inra.ijpb.measure.region3d.RegionAnalyzer3D
Default implementation of the analyzeRegions method, that calls the more specialized RegionAnalyzer3D.analyzeRegions(ImageStack, int[], ij.measure.Calibration) method and transforms the result into a map.
analyzeRegions(ImagePlus) - Method in interface inra.ijpb.measure.RegionAnalyzer
Generic method to compute the result of an analysis on each region of a label or binary image.
AnalyzeRegions - Class in inra.ijpb.plugins
Plugin for computing morphological feature of regions from label images.
AnalyzeRegions() - Constructor for class inra.ijpb.plugins.AnalyzeRegions
 
AnalyzeRegions.Features - Class in inra.ijpb.plugins
The list of features to compute.
AnalyzeRegions3D - Class in inra.ijpb.plugins
Plugin for measuring geometric quantities such as volume, surface area, and eventually sphericity index.
AnalyzeRegions3D() - Constructor for class inra.ijpb.plugins.AnalyzeRegions3D
 
AND - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
And operator.
angle - Variable in class inra.ijpb.geometry.AngleDiameterPair
Angle in radians
angle() - Method in class inra.ijpb.geometry.PointPair2D
 
angle(Vector2D, Vector2D) - Static method in class inra.ijpb.geometry.Vector2D
Computes the angle between two vectors.
angle(Vector3D, Vector3D) - Static method in class inra.ijpb.geometry.Vector3D
Computes the angle between two 3D vectors.
angle(Vector3d, Vector3d) - Static method in class inra.ijpb.measure.Vector3d
Deprecated.
Computes the angle between two 3D vectors.
AngleDiameterPair - Class in inra.ijpb.geometry
Data structure used to return result of Feret diameters computation.
AngleDiameterPair(double, double) - Constructor for class inra.ijpb.geometry.AngleDiameterPair
Default constructor, using angle in degrees and diameter.
apply(ImageProcessor, Strel) - Method in enum inra.ijpb.morphology.directional.DirectionalFilter.Operation
Applies this operation to the input image.
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
Applies this operation to the specified image.
apply(ImageStack, int, Connectivity3D) - Method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.Operation
Applies this operation to the specified image.
apply(ImageStack, int, int) - Method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.Operation
Applies this operation to the specified image.
apply(ImageProcessor, int) - Method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
Applies this operation to the specified image.
apply(ImageProcessor, int, Connectivity2D) - Method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
Applies this operation to the specified image.
apply(ImageProcessor, int, int) - Method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
Applies this operation to the specified image.
apply(ImageStack, int) - Method in enum inra.ijpb.plugins.RegionalMinAndMax3DPlugin.Operation
Process to image given as argument.
apply(ImageProcessor, int) - Method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation
Process to image given as argument.
apply(ImageProcessor, Connectivity2D) - Method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation
Process to image given as argument.
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(ImagePlus, double[]) - Static method in class inra.ijpb.label.LabelImages
Applies the given Look-up table to the input label image.
applyLut(ImageProcessor, double[]) - Static method in class inra.ijpb.label.LabelImages
Applies the given Look-up table to the input 2D label image.
applyLut(ImageStack, double[]) - Static method in class inra.ijpb.label.LabelImages
Applies the given Look-up table to the input 3D label image.
applyLut(int[], double[]) - Static method in class inra.ijpb.measure.region2d.BinaryConfigurationsHistogram2D
Applies look-up-table of values for each configuration, based on the array of count for each binary configuration.
applyLut(int[], int[]) - Static method in class inra.ijpb.measure.region2d.BinaryConfigurationsHistogram2D
Applies look-up-table of values for each configuration, based on the array of count for each binary configuration.
applyLut(int[][], double[]) - Static method in class inra.ijpb.measure.region2d.BinaryConfigurationsHistogram2D
Applies look-up-table of values for each configuration for each label, based on the 16-array of count for each binary configuration.
applyLut(int[][], int[]) - Static method in class inra.ijpb.measure.region2d.BinaryConfigurationsHistogram2D
Applies look-up-table of values for each configuration for each label, based on the 16-array of count for each binary configuration.
applyLut(int[], double[]) - Static method in class inra.ijpb.measure.region3d.BinaryConfigurationsHistogram3D
Applies look-up-table of values for each configuration, based on the array of count for each binary configuration.
applyLut(int[][], double[]) - Static method in class inra.ijpb.measure.region3d.BinaryConfigurationsHistogram3D
Applies look-up-table of values for each configuration of each region, based on the array of count for each binary configuration.
applyTo(int, int) - Method in interface inra.ijpb.math.ImageCalculator.Operation
The method to override to make it possible to use an operation.
applyTo(float, float) - 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) - Method in enum inra.ijpb.plugins.ImposeMinAndMax3DPlugin.Operation
Process to image given as argument.
applyTo(ImageStack, ImageStack, int) - Method in enum inra.ijpb.plugins.ImposeMinAndMax3DPlugin.Operation
Process to image given as argument.
applyTo(ImageProcessor, ImageProcessor) - Method in enum inra.ijpb.plugins.ImposeMinAndMaxPlugin.Operation
Process to image given as argument.
applyTo(ImageProcessor, ImageProcessor, int) - Method in enum inra.ijpb.plugins.ImposeMinAndMaxPlugin.Operation
Process to image given as argument.
applyTo(ImageProcessor, ImageProcessor, Connectivity2D) - Method in enum inra.ijpb.plugins.ImposeMinAndMaxPlugin.Operation
Process to image given as argument.
applyTo(ImagePlus, int) - Method in enum inra.ijpb.plugins.LabelSizeFilteringPlugin.Operation
Applies the operator wrapped by this enumeration item to the input image.
applyTo(ImageStack, ImageStack, int) - Method in enum inra.ijpb.plugins.MorphologicalReconstruction3DPlugin.Operation
Process to image given as argument.
applyTo(ImageProcessor, ImageProcessor, int) - Method in enum inra.ijpb.plugins.MorphologicalReconstructionPlugin.Operation
Process to image given as argument.
applyTo(ImageProcessor, ImageProcessor, Connectivity2D) - Method in enum inra.ijpb.plugins.MorphologicalReconstructionPlugin.Operation
Process to image given as argument.
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() - Method in class inra.ijpb.geometry.Box2D
Computes the area of this bounding box.
area() - Method in class inra.ijpb.geometry.Circle2D
 
area() - Method in class inra.ijpb.geometry.Ellipse
 
area() - Method in class inra.ijpb.geometry.OrientedBox2D
Computes the area of this box.
area() - Method in class inra.ijpb.geometry.Polygon2D
Computes the area of this polygon
area(ImageProcessor, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
area(ImageProcessor, Calibration) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D
Measures the area of the foreground region within a binary image.
area - Variable in class inra.ijpb.measure.region2d.Convexity.Result
The area of the region in the original image.
area - Variable in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.Result
the area of the region.
area - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing area.
areaDensity(ImageProcessor) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D
Computes the area density for the 2D binary microstructure.
areaLut(Calibration) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumes2DUtils
Computes the Look-up table that is used for computing area.
areaLut(Calibration) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
Deprecated.
use IntrinsicVolumes2DUtils instead
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
 
areas(ImageProcessor, int[], Calibration) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D
Measures the area of each region within a label image, taking into account image resolution.
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
 
AverageThickness - Class in inra.ijpb.measure.region2d
Compute average thickness of a binary region, or of each region in a label image.
AverageThickness() - Constructor for class inra.ijpb.measure.region2d.AverageThickness
 
averageThickness - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing average thickness.
AverageThickness.Result - Class in inra.ijpb.measure.region2d
Inner class used for representing results of average thickness computations.
AverageThicknessPlugin - Class in inra.ijpb.plugins
 
AverageThicknessPlugin() - Constructor for class inra.ijpb.plugins.AverageThicknessPlugin
 
avgThickness - Variable in class inra.ijpb.measure.region2d.AverageThickness.Result
Average thickness value computed from the average distance.

B

BACKGROUND - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat
The value associated to the background in the result image.
BACKGROUND - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloatHybrid
The value associated to the background in the result image.
BACKGROUND - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort
The value associated to the background in the result image.
BACKGROUND - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShortHybrid
The value associated to the background in the result image.
BACKGROUND - Static variable in interface inra.ijpb.morphology.Strel
Default value for background pixels.
BACKGROUND - Static variable in interface inra.ijpb.morphology.Strel3D
Default value for background pixels.
BallStrel - Class in inra.ijpb.morphology.strel
A 3D structuring element with a ball shape, with same size in each direction.
binarize(ImagePlus) - Static method in class inra.ijpb.binary.BinaryImages
Converts a grayscale 2D or 3D image into a binary image by setting non-zero elements to 255.
binarize(ImageProcessor) - Static method in class inra.ijpb.binary.BinaryImages
Converts a grayscale 2D image into a binary 2D image by setting non-zero pixels to 255.
binarize(ImageStack) - Static method in class inra.ijpb.binary.BinaryImages
Converts a grayscale 3D image into a binary 3D image by setting non-zero voxels to 255.
binarize(ImageProcessor, int) - Static method in class inra.ijpb.label.LabelImages
Returns the binary image with value equals to true only when the corresponding value in the input image equals label.
binarizeBackground(ImagePlus) - Static method in class inra.ijpb.binary.BinaryImages
Converts a grayscale 2D or 3D image into a binary image by setting zero elements to 255, and non zero ones to 0.
binarizeBackground(ImageProcessor) - Static method in class inra.ijpb.binary.BinaryImages
Converts a grayscale 2D image into a binary 2D image by setting zero elements to 255, and non zero ones to 0.
binarizeBackground(ImageStack) - Static method in class inra.ijpb.binary.BinaryImages
Converts a grayscale 3D image into a binary 3D image by setting zero elements to 255, and non zero ones to 0.
BinaryConfigurationsHistogram2D - Class in inra.ijpb.measure.region2d
Computes histogram of binary configurations composed of 2-by-2 pixels (planar images).
BinaryConfigurationsHistogram2D() - Constructor for class inra.ijpb.measure.region2d.BinaryConfigurationsHistogram2D
Default empty constructor.
BinaryConfigurationsHistogram3D - Class in inra.ijpb.measure.region3d
Computes histogram of binary 2-by-2-by-2 configurations within a 3D image.
BinaryConfigurationsHistogram3D() - Constructor for class inra.ijpb.measure.region3d.BinaryConfigurationsHistogram3D
Empty constructor.
BinaryImages - Class in inra.ijpb.binary
A collection of static methods for operating on binary images (2D/3D).
binaryMarkers - Static variable in class inra.ijpb.plugins.MarkerControlledWatershed3DPlugin
flag set to TRUE if markers are binary, to FALSE if markers are labels
BinaryOrLabelOverlayPlugin - Class in inra.ijpb.plugins
Display a label map or a binary image as overlay onto a grayscale image.
BinaryOrLabelOverlayPlugin() - Constructor for class inra.ijpb.plugins.BinaryOrLabelOverlayPlugin
 
BinaryOverlay - Class in inra.ijpb.color
Computes overlay of a binary image mask onto a grayscale or color image, using the specified color.
BinaryOverlay() - Constructor for class inra.ijpb.color.BinaryOverlay
Empty constructor.
binaryOverlay(ImagePlus, ImagePlus, Color) - Static method in class inra.ijpb.data.image.ColorImages
Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color.
binaryOverlay(ImageProcessor, ImageProcessor, Color) - Static method in class inra.ijpb.data.image.ColorImages
Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color.
binaryOverlay(ImageStack, ImageStack, Color) - Static method in class inra.ijpb.data.image.ColorImages
Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color.
binaryOverlay(ImagePlus, ImagePlus, Color, double) - Static method in class inra.ijpb.data.image.ColorImages
Applies an overlay of a binary image mask onto a 2D or 3D grayscale image, using the specified color and opacity.
binaryOverlay(ByteProcessor, ImageProcessor, Color, double) - Static method in class inra.ijpb.data.image.ColorImages
Applies an overlay of a binary image mask onto a grayscale image, using the specified color and opacity.
binaryOverlay(ImageStack, ImageStack, Color, double) - Static method in class inra.ijpb.data.image.ColorImages
Computes the overlay of a binary image over a grayscale image, using an opacity for the binary layer.
BinaryOverlayPlugin - Class in inra.ijpb.plugins
 
BinaryOverlayPlugin() - Constructor for class inra.ijpb.plugins.BinaryOverlayPlugin
 
BlackTopHat - Class in inra.ijpb.morphology.filter
Performs morphological black top-hat on 2D/3D images.
BlackTopHat(Strel3D) - Constructor for class inra.ijpb.morphology.filter.BlackTopHat
Creates a new Black Top-Hat operator with the specified structuring element.
blackTopHat(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes black top hat (or "bottom hat") of the original image.
blackTopHat(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Computes black top hat (or "bottom hat") of the original image.
blackTopHat(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes black top hat (or "bottom hat") of the original image.
BorderManager - Interface in inra.ijpb.data.border
Manages borders of an image, by providing methods for accessing values also for position out of image bounds.
BorderManager.Type - Enum in inra.ijpb.data.border
A set of pre-defined border managers stored in an enumeration.
BorderManager3D - Interface in inra.ijpb.data.border
Manages borders of an image, by providing methods for accessing values also for position out of image bounds.
BorderManager3D.Type - Enum in inra.ijpb.data.border
A set of pre-defined border managers stored in an enumeration.
BORGEFORS - Static variable in class inra.ijpb.binary.distmap.ChamferMask2D
Use weights 3 for orthogonal neighbors and 4 for diagonal neighbors (best approximation for 3-by-3 masks).
BORGEFORS - Static variable in class inra.ijpb.binary.distmap.ChamferMask3D
Use weights 3 for orthogonal neighbors, 4 for square-diagonal neighbors, and 5 for cube-diagonals (best approximation for 3-by-3-by-3 masks).
boundaries - Variable in class inra.ijpb.label.conncomp.LabelBoundariesLabeling2D.Result
The map between the label of a boundary and the Boundary instances that store indices of adjacent regions.
boundaries - Variable in class inra.ijpb.label.conncomp.LabelBoundariesLabeling3D.Result
The map between the label of a boundary and the Boundary instances that store indices of adjacent regions.
Boundary - Class in inra.ijpb.label.conncomp
A boundary between several regions.
boundaryLabelMap - Variable in class inra.ijpb.label.conncomp.LabelBoundariesLabeling2D.Result
The label map containing boundary labels or zero for non-label pixels.
boundaryLabelMap - Variable in class inra.ijpb.label.conncomp.LabelBoundariesLabeling3D.Result
The label map containing boundary labels or zero for non-label pixels.
boundaryPixelsMiddleEdges(ImageProcessor) - Static method in class inra.ijpb.measure.region2d.RegionBoundaries
Extracts boundary points from a binary region, keeping middle points of pixel edges.
boundaryPixelsMiddleEdges(ImageProcessor, int[]) - Static method in class inra.ijpb.measure.region2d.RegionBoundaries
Extracts boundary points from the different regions.
BoundarySet - Class in inra.ijpb.label.conncomp
A list of boundaries, indexed by an integer label.
BoundarySet() - Constructor for class inra.ijpb.label.conncomp.BoundarySet
Creates a new (empty) BoundarySet.
boundingBox() - Method in class inra.ijpb.geometry.Polygon2D
Returns the bounding box of this polygon.
boundingBox(ImageProcessor) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
use BoundingBox class instead
boundingBox(ImageProcessor, int[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
use BoundingBox class instead
boundingBox(ImageStack) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
use BoundingBox3D instead
boundingBox(ImageStack, int[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
Computes bounding box of each label in input stack and returns the result as an array of double for each label.
BoundingBox - Class in inra.ijpb.measure.region2d
Compute bounding box of each region within a label or binary image.
BoundingBox() - Constructor for class inra.ijpb.measure.region2d.BoundingBox
Default constructor
boundingBox - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing bounding box.
BoundingBox3D - Class in inra.ijpb.measure.region3d
Compute bounding box of each region within a label or binary image.
BoundingBox3D() - Constructor for class inra.ijpb.measure.region3d.BoundingBox3D
Default constructor
BoundingBox3DPlugin - Class in inra.ijpb.plugins
Plugin for measuring extend of 3D bounding box from label images.
BoundingBox3DPlugin() - Constructor for class inra.ijpb.plugins.BoundingBox3DPlugin
 
boundingBoxes(ImageProcessor, int[], Calibration) - Static method in class inra.ijpb.measure.region2d.BoundingBox
Compute bounding box of each region in input image and returns the result as an array of Box2D for each label.
boundingBoxes(ImageStack, int[], Calibration) - Static method in class inra.ijpb.measure.region3d.BoundingBox3D
Compute bounding box of each region in input 3D label image and returns the result as an array of Box3D for each region.
BoundingBoxPlugin - Class in inra.ijpb.plugins
Plugin for computing (2D) bounding box of regions from label images.
BoundingBoxPlugin() - Constructor for class inra.ijpb.plugins.BoundingBoxPlugin
 
Box2D - Class in inra.ijpb.geometry
A bounding Box in 2 dimensions.
Box2D(double, double, double, double) - Constructor for class inra.ijpb.geometry.Box2D
Default constructor of the bounding box, that specifies the bounds along each dimension.
Box3D - Class in inra.ijpb.geometry
A bounding Box in 3 dimensions.
Box3D(double, double, double, double, double, double) - Constructor for class inra.ijpb.geometry.Box3D
Default constructor, that specifies the bounds along each dimension.
BoxDiagonalOpeningQueue - Class in inra.ijpb.morphology.attrfilt
Area opening using priority queue for updating each regional maxima.
BoxDiagonalOpeningQueue() - Constructor for class inra.ijpb.morphology.attrfilt.BoxDiagonalOpeningQueue
 
ByteStackWrapper - Class in inra.ijpb.data.image
Access the data of a 3D image containing gray8 values stored as bytes.
ByteStackWrapper(ImageStack) - Constructor for class inra.ijpb.data.image.ByteStackWrapper
Creates a new wrapper to the ImageStack.

C

center() - Method in class inra.ijpb.geometry.Ellipse
 
center() - Method in class inra.ijpb.geometry.Ellipsoid
 
center() - Method in class inra.ijpb.geometry.OrientedBox2D
 
center() - Method in class inra.ijpb.geometry.Sphere
 
centers(Ellipse[]) - Static method in class inra.ijpb.geometry.Ellipse
Initializes center array from ellipse array.
centers(Ellipsoid[]) - Static method in class inra.ijpb.geometry.Ellipsoid
Initializes center array from ellipsoid array.
centroid() - Method in class inra.ijpb.geometry.Polygon2D
Computes the centroid of this polygon
Centroid - Class in inra.ijpb.measure.region2d
Computes centroid position of regions within binary or label images.
Centroid() - Constructor for class inra.ijpb.measure.region2d.Centroid
Default constructor
centroid - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing centroid.
Centroid3D - Class in inra.ijpb.measure.region3d
Computes centroid position of regions within 3D binary or label images.
Centroid3D() - Constructor for class inra.ijpb.measure.region3d.Centroid3D
Default constructor
centroids(ImageProcessor, int[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
replaced by Centroid.centroids
centroids(ImageStack, int[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
centroids(ImageProcessor, int[], Calibration) - Static method in class inra.ijpb.measure.region2d.Centroid
Computes centroid of each label in input image and returns the result as an array of double for each label.
centroids(ImageProcessor, int[]) - Static method in class inra.ijpb.measure.region2d.Centroid
Computes centroid of each label in input image and returns the result as an array of double for each label.
centroids(ImageStack, int[], Calibration) - Static method in class inra.ijpb.measure.region3d.Centroid3D
Compute centroid of each region in input 3D label image and returns the result as an array of Point3D.
centroids(ImageStack, int[]) - Static method in class inra.ijpb.measure.region3d.Centroid3D
Computes centroid of each label in input image and returns the result as an array of double for each label.
ChamferDistanceMap3DPlugin - Class in inra.ijpb.plugins
Compute 3D distance map, with possibility to choose the chamfer mask, the result type (integer or floating point), and to normalize result or not.
ChamferDistanceMap3DPlugin() - Constructor for class inra.ijpb.plugins.ChamferDistanceMap3DPlugin
 
ChamferDistanceMapPlugin - Class in inra.ijpb.plugins
Compute distance map, with possibility to choose the chamfer mask, the result type (integer or floating point), and to normalize result or not.
ChamferDistanceMapPlugin() - Constructor for class inra.ijpb.plugins.ChamferDistanceMapPlugin
 
ChamferDistanceTransform2D - Interface in inra.ijpb.binary.distmap
Specialization of DistanceTransform based on the use of a chamfer mask.
ChamferDistanceTransform2D - Interface in inra.ijpb.label.distmap
Specialization of DistanceTransform based on the use of a chamfer mask.
ChamferDistanceTransform2DFloat - Class in inra.ijpb.binary.distmap
Computes distance transform on binary images by propagating distances using a ChamferMask2D, and using 32-bits floating-point computation.
ChamferDistanceTransform2DFloat(ChamferMask2D) - Constructor for class inra.ijpb.binary.distmap.ChamferDistanceTransform2DFloat
Creates a new algorithm for computing distance maps based on a chamfer mask.
ChamferDistanceTransform2DFloat(ChamferMask2D, boolean) - Constructor for class inra.ijpb.binary.distmap.ChamferDistanceTransform2DFloat
Creates a new algorithm for computing distance maps based on a chamfer mask.
ChamferDistanceTransform2DFloat - Class in inra.ijpb.label.distmap
Computes distance transform by propagating distances using a ChamferMask2D, and using 32-bits floating-point computation.
ChamferDistanceTransform2DFloat(ChamferMask2D) - Constructor for class inra.ijpb.label.distmap.ChamferDistanceTransform2DFloat
Creates a new algorithm for computing distance maps based on a chamfer mask.
ChamferDistanceTransform2DFloat(ChamferMask2D, boolean) - Constructor for class inra.ijpb.label.distmap.ChamferDistanceTransform2DFloat
Creates a new algorithm for computing distance maps based on a chamfer mask.
ChamferDistanceTransform2DShort - Class in inra.ijpb.binary.distmap
Computes distance transform by propagating distances using a ChamferMask2D, and using 16-bits integer computation.
ChamferDistanceTransform2DShort(ChamferMask2D) - Constructor for class inra.ijpb.binary.distmap.ChamferDistanceTransform2DShort
Creates a new algorithm for computing distance maps based on a chamfer mask.
ChamferDistanceTransform2DShort(ChamferMask2D, boolean) - Constructor for class inra.ijpb.binary.distmap.ChamferDistanceTransform2DShort
Creates a new algorithm for computing distance maps based on a chamfer mask.
ChamferDistanceTransform2DShort - Class in inra.ijpb.label.distmap
Computes distance transform by propagating distances using a ChamferMask2D, and using 16-bits integer computation.
ChamferDistanceTransform2DShort(ChamferMask2D) - Constructor for class inra.ijpb.label.distmap.ChamferDistanceTransform2DShort
Creates a new algorithm for computing distance maps based on a chamfer mask.
ChamferDistanceTransform2DShort(ChamferMask2D, boolean) - Constructor for class inra.ijpb.label.distmap.ChamferDistanceTransform2DShort
Creates a new algorithm for computing distance maps based on a chamfer mask.
ChamferDistanceTransform3D - Interface in inra.ijpb.binary.distmap
Specialization of DistanceTransform based on the use of a chamfer mask.
ChamferDistanceTransform3D - Interface in inra.ijpb.label.distmap
Specialization of DistanceTransform based on the use of a chamfer mask.
ChamferDistanceTransform3DFloat - Class in inra.ijpb.binary.distmap
Computes 3D distance transform on binary images using the chamfer weights provided by a ChamferMask3D object, and using 32-bits floating-point computation.
ChamferDistanceTransform3DFloat(ChamferMask3D) - Constructor for class inra.ijpb.binary.distmap.ChamferDistanceTransform3DFloat
Creates a new algorithm for computing 3D distance maps on binary images based on a chamfer mask.
ChamferDistanceTransform3DFloat(ChamferMask3D, boolean) - Constructor for class inra.ijpb.binary.distmap.ChamferDistanceTransform3DFloat
Creates a new algorithm for computing 3D distance maps on binary images based on a chamfer mask.
ChamferDistanceTransform3DFloat - Class in inra.ijpb.label.distmap
Computes 3D distance transform using the chamfer weights provided by a ChamferWeights3D object, and using floating-point computation.
ChamferDistanceTransform3DFloat(ChamferMask3D) - Constructor for class inra.ijpb.label.distmap.ChamferDistanceTransform3DFloat
Creates a new algorithm for computing 3D distance maps on label images based on a chamfer mask.
ChamferDistanceTransform3DFloat(ChamferMask3D, boolean) - Constructor for class inra.ijpb.label.distmap.ChamferDistanceTransform3DFloat
Creates a new algorithm for computing 3D distance maps on label images based on a chamfer mask.
ChamferDistanceTransform3DShort - Class in inra.ijpb.binary.distmap
Computes 3D distance transform using the chamfer weights provided by a ChamferMask3D object, and using 16-bits integer computation.
ChamferDistanceTransform3DShort(ChamferMask3D) - Constructor for class inra.ijpb.binary.distmap.ChamferDistanceTransform3DShort
Creates a new algorithm for computing 3D distance maps based on a chamfer mask.
ChamferDistanceTransform3DShort(ChamferMask3D, boolean) - Constructor for class inra.ijpb.binary.distmap.ChamferDistanceTransform3DShort
Creates a new algorithm for computing 3D distance maps based on a chamfer mask.
ChamferDistanceTransform3DShort - Class in inra.ijpb.label.distmap
Computes 3D distance transform on binary images using the chamfer weights provided by a ChamferWeights3D object, and using 16-bits integer computation.
ChamferDistanceTransform3DShort(ChamferMask3D) - Constructor for class inra.ijpb.label.distmap.ChamferDistanceTransform3DShort
Creates a new algorithm for computing 3D distance maps on label images based on a chamfer mask.
ChamferDistanceTransform3DShort(ChamferMask3D, boolean) - Constructor for class inra.ijpb.label.distmap.ChamferDistanceTransform3DShort
Creates a new algorithm for computing 3D distance maps on label images based on a chamfer mask.
ChamferLabelDilation2DShort - Class in inra.ijpb.label.filter
Apply a dilation by a specified radius to each label of a label map by constraining the dilation.
ChamferLabelDilation2DShort(ChamferMask2D, double) - Constructor for class inra.ijpb.label.filter.ChamferLabelDilation2DShort
Creates a new image processor for dilating labels using the specified chamfer mask, using 16-bits integer computation.
ChamferLabelDilation3DShort - Class in inra.ijpb.label.filter
Apply a dilation by a specified radius to each label of a label map by constraining the dilation.
ChamferLabelDilation3DShort(ChamferMask3D, double) - Constructor for class inra.ijpb.label.filter.ChamferLabelDilation3DShort
Creates a new 3D image for dilating labels using the specified chamfer mask, using 16-bits integer computation.
ChamferLabelErosion2DShort - Class in inra.ijpb.label.filter
Implementation of morphological erosion for 2D label images / label maps.
ChamferLabelErosion2DShort(ChamferMask2D, double) - Constructor for class inra.ijpb.label.filter.ChamferLabelErosion2DShort
Creates a new operator for erosion of label images based on Chamfer masks.
ChamferLabelErosion3DShort - Class in inra.ijpb.label.filter
Implementation of morphological erosion for 3D label images / label maps.
ChamferLabelErosion3DShort(ChamferMask3D, double) - Constructor for class inra.ijpb.label.filter.ChamferLabelErosion3DShort
Creates a new operator for erosion of label images based on Chamfer masks.
ChamferMask2D - Class in inra.ijpb.binary.distmap
Chamfer masks defines a series of weights associated to neighbors of current pixels.
ChamferMask2D() - Constructor for class inra.ijpb.binary.distmap.ChamferMask2D
 
ChamferMask2D.FloatOffset - Class in inra.ijpb.binary.distmap
The shift to a neighbor of a reference pixel, as a pair (dx,dy), and the associated weights given as a float.
ChamferMask2D.ShortOffset - Class in inra.ijpb.binary.distmap
The shift to a neighbor of a reference pixel, as a pair (dx,dy), and the associated weights given as a short.
ChamferMask2DW2 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights that manages two types of offsets, corresponding to orthogonal and diagonal neighbors.
ChamferMask2DW2(int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW2
Creates a new ChamferWeights3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW2(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW2
Creates a new ChamferMask2D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW2Float - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights that manages two types of offsets, corresponding to orthogonal, and diagonal neighbors.
ChamferMask2DW2Float(short[], float[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW2Float
Creates a new chamfer mask
ChamferMask2DW3 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights that manages three types of offsets types: orthogonal, diagonal neighbors and "chess-knight move" neighbors.
ChamferMask2DW3(int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW3
Creates a new ChamferWeights2DW3 object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW3(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW3
Creates a new ChamferMask3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW4 - Class in inra.ijpb.binary.distmap
Implementation of 2D Chamfer mask that manages four types of offsets types.
ChamferMask2DW4(int, int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW4
Creates a new ChamferWeights2DW3 object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW4(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW4
Creates a new ChamferMask3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask3D - Class in inra.ijpb.binary.distmap
A collection of weighted offsets for computing distance maps from 3D binary images.
ChamferMask3D() - Constructor for class inra.ijpb.binary.distmap.ChamferMask3D
 
ChamferMask3D.FloatOffset - Class in inra.ijpb.binary.distmap
The shift to a neighbor of a reference voxel, as a triplet (dx,dy,dz), and the associated weights given as a float.
ChamferMask3D.ShortOffset - Class in inra.ijpb.binary.distmap
The shift to a neighbor of a reference voxel, as a triplet (dx,dy,dz), and the associated weights given as a short.
ChamferMask3DW3 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages three type offset types, corresponding to orthogonal, square-diagonal and cube-diagonal neighbors.
ChamferMask3DW3(int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW3
Creates a new ChamferWeights3D object by specifying the weights associated to orthogonal, square-diagonal and cube-diagonal neighbors, respectively.
ChamferMask3DW3(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW3
Creates a new ChamferMask3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask3DW3Float - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages three types of offsets, corresponding to orthogonal, square-diagonal and cube-diagonal neighbors.
ChamferMask3DW3Float(short[], float[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW3Float
Creates a new chamfer mask
ChamferMask3DW4 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages four types of offsets.
ChamferMask3DW4(int, int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW4
Creates a new ChamferWeights3D object by specifying the four weights associated to the four different kind of offsets.
ChamferMask3DW4(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW4
Creates a new ChamferWeights3D object by specifying the four weights associated to the four different kind of offsets.
ChamferMask3DW5 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages five types of offsets.
ChamferMask3DW5(int, int, int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW5
Creates a new ChamferWeights3D object by specifying the four weights associated to the four different kind of offsets.
ChamferMask3DW5(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW5
Creates a new ChamferMask3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask3DW6 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages six types of offsets (all the possibilities in a 5-by-5-by-5 neighborhood).
ChamferMask3DW6(int, int, int, int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW6
Creates a new ChamferWeights3D object by specifying the weights associated to the six different kind of offsets.
ChamferMask3DW6(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW6
Creates a new ChamferWeights3D object by specifying the four weights associated to the four different kind of offsets.
ChamferMasks2D - Enum in inra.ijpb.binary.distmap
A pre-defined set of weights that can be used to compute distance transform using chamfer approximations of euclidean metric.
ChamferMasks3D - Enum in inra.ijpb.binary.distmap
A pre-defined set of weights that can be used to compute 3D distance transform using chamfer approximations of euclidean metric.
ChamferStrel - Class in inra.ijpb.morphology.strel
Disk-shaped structuring element based on a chamfer mask and a radius.
ChamferStrel(ChamferMask2D, double) - Constructor for class inra.ijpb.morphology.strel.ChamferStrel
Creates a new ChamferStrel from a chamfer mask (used for computing distances) and a radius (used to computing the extent of propagation).
ChamferStrel3D - Class in inra.ijpb.morphology.strel
 
ChamferStrel3D(ChamferMask3D, double) - Constructor for class inra.ijpb.morphology.strel.ChamferStrel3D
Creates a new ChamferStrel3D from a chamfer mask (used for computing distances) and a radius (used to computing the extent of propagation).
ChamferWeights - Enum in inra.ijpb.binary
Deprecated.
replaced by inra.ijpb.binary.distmap.ChamferMask2D (since 1.5.0)
ChamferWeights3D - Enum in inra.ijpb.binary
Deprecated.
replaced by inra.ijpb.binary.distmap.ChamferMask2D (since 1.5.0)
ChamferWeights3D.FloatOffset - Class in inra.ijpb.binary
Deprecated.
ChamferWeights3D.ShortOffset - Class in inra.ijpb.binary
Deprecated.
CHESSBOARD - Static variable in class inra.ijpb.binary.distmap.ChamferMask2D
Use weight equal to 1 for all neighbors.
CHESSBOARD - Static variable in class inra.ijpb.binary.distmap.ChamferMask3D
Use weights equal to 1 for all neighbors.
CHESSKNIGHT - Static variable in class inra.ijpb.binary.distmap.ChamferMask2D
Use weights 5 for orthogonal neighbors, 7 for diagonal neighbors, and 11 for chess-knight moves (recommended approximation for 5-by-5 masks).
Circle2D - Class in inra.ijpb.geometry
Contains data for representing circle in the 2D plane.
Circle2D(Point2D, double) - Constructor for class inra.ijpb.geometry.Circle2D
Creates a new Circle from a center and a radius.
circularity() - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.Result
Computes the circularity value associated with this result.
circularity - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing circularity.
circularLut(byte[][], int) - Static method in class inra.ijpb.color.ColorMaps
Creates a cyclic LUT from base LUT values such that the result array has the specified number of colors.
CITY_BLOCK - Static variable in class inra.ijpb.binary.distmap.ChamferMask2D
Use weights 1 for orthogonal neighbors and 2 for diagonal neighbors, and 3 for cube-diagonals.
CITY_BLOCK - Static variable in class inra.ijpb.binary.distmap.ChamferMask3D
Use weights 1 for orthogonal neighbors, 2 for square-diagonal neighbors, and 3 for cube-diagonals.
clamp(int, int, int) - Static method in class inra.ijpb.morphology.filter.MorphologicalFilter
Clamps an integer value within an interval, by forcing the resulting value to lie within the input interval while being as close as possible from the input value.
clear() - Method in class inra.ijpb.morphology.strel.LocalBufferedHistogram
Reset inner counts with zero values, and min and max values.
clear() - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferDouble
Resets inner counts with default maximum values (+INFINITY for MAX, -INFINITY for MIN)
clear() - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferGray8
Resets inner counts with default maximal integer values (Integer.MIN_VALUE for MAX, Integer.MAX_VALUE for MIN)
closing(ImageProcessor) - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
 
Closing - Class in inra.ijpb.morphology.filter
Performs morphological closing on 2D/3D images.
Closing(Strel3D) - Constructor for class inra.ijpb.morphology.filter.Closing
Creates a new Morphological Closing operator with the specified structuring element.
closing(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological closing on the input image.
closing(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Performs closing on the input image.
closing(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological closing on the input 3D image.
closing(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
closing(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
closing(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel3D
 
closing(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel
 
closing(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel3D
 
closing(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractStrel
Performs a morphological closing on the input image, by applying first a dilation, then an erosion with the reversed structuring element.
closing(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel
 
closing(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
Performs a morphological closing on the input stack, by applying first a dilation, then an erosion with the reversed structuring element.
closing(ImageProcessor) - Method in interface inra.ijpb.morphology.Strel
Performs a morphological closing of the input image with this structuring element, and returns the result in a new ImageProcessor.
closing(ImageStack) - Method in class inra.ijpb.morphology.strel.Cross3DStrel
 
closing(ImageStack) - Method in interface inra.ijpb.morphology.Strel3D
Performs a morphological closing of the input image with this structuring element, and returns the result in a new ImageStack.
ColorImages - Class in inra.ijpb.data.image
A set of static methods for working with color images.
ColorMaps - Class in inra.ijpb.color
Contains static methods for creating common color maps.
ColorMaps() - Constructor for class inra.ijpb.color.ColorMaps
Protected constructor to prevent class instantiation while allowing sub-classing for retro-compatibility.
ColorMaps - Class in inra.ijpb.util
Deprecated.
use inra.ijpb.color.ColorMaps instead (v1.4.3)
ColorMaps.CommonLabelMaps - Enum in inra.ijpb.color
A collection of color maps useful for displaying label images.
combineImages(ImagePlus, ImagePlus, ImageCalculator.Operation) - Static method in class inra.ijpb.math.ImageCalculator
Combines two images using the specified operation.
combineImages(ImageProcessor, ImageProcessor, ImageCalculator.Operation) - Static method in class inra.ijpb.math.ImageCalculator
Example that computes the maximum over two images:
combineImages(ImageStack, ImageStack, ImageCalculator.Operation) - Static method in class inra.ijpb.math.ImageCalculator
Combines two images using the specified operation.
CommonColors - Enum in inra.ijpb.color
A collection of common colors used for creating overlays, choosing background color...
CommonColors - Enum in inra.ijpb.util
Deprecated.
use inra.ijpb.color.CommonColors instead (v1.4.3)
compactness - Static variable in class inra.ijpb.plugins.MarkerControlledWatershed3DPlugin
compactness constraint, c parameter in compact watershed algorithm [2]
compareTo(PixelRecord) - Method in class inra.ijpb.data.PixelRecord
Compare with a pixel record based on its value and timestamp
compareTo(VoxelRecord) - Method in class inra.ijpb.data.VoxelRecord
Compare with a voxel record based on its value and timestamp
compareTo(RegionAdjacencyGraph.LabelPair) - Method in class inra.ijpb.label.RegionAdjacencyGraph.LabelPair
 
complement(ImageStack, double) - Static method in class inra.ijpb.data.image.Images3D
Computes the complements of the input image using the specified value as reference, and returns the complemented image.
componentsLabeling(ImagePlus, int, int) - Static method in class inra.ijpb.binary.BinaryImages
Computes the labels in the binary 2D or 3D image contained in the given ImagePlus, and computes the maximum label to set up the display range of the resulting ImagePlus.
componentsLabeling(ImageProcessor, int, int) - Static method in class inra.ijpb.binary.BinaryImages
Computes the labels of the connected components in the given planar binary image.
componentsLabeling(ImageStack, int, int) - Static method in class inra.ijpb.binary.BinaryImages
Computes the labels of the connected components in the given 3D binary image.
computeAdjacencies(ImagePlus) - Static method in class inra.ijpb.label.RegionAdjacencyGraph
Returns the set of region adjacencies in an ImagePlus, that can contains either an ImageProcessor or an ImageStack.
computeAdjacencies(ImageProcessor) - Static method in class inra.ijpb.label.RegionAdjacencyGraph
Returns the set of region adjacencies in an ImageProcessor of labels.
computeAdjacencies(ImageStack) - Static method in class inra.ijpb.label.RegionAdjacencyGraph
Returns the set of region adjacencies in an ImageProcessor of labels.
computeCircularities(IntrinsicVolumesAnalyzer2D.Result[]) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumes2DUtils
Utility method that computes circularities as a numeric array from the result array
computeCircularities(IntrinsicVolumesAnalyzer2D.Result[]) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
Deprecated.
computeEllipsoidElongations(double[][]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
computeLabels(ImageProcessor) - Method in interface inra.ijpb.binary.conncomp.ConnectedComponentsLabeling
Computes labels corresponding to connected components in input image.
computeLabels(ImageStack) - Method in interface inra.ijpb.binary.conncomp.ConnectedComponentsLabeling3D
Computes labels corresponding to connected components in input image.
computeLabels(ImageProcessor) - Method in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling
 
computeLabels(ImageStack) - Method in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling3D
 
computeLabels(ImagePlus, int, int) - Static method in class inra.ijpb.binary.ConnectedComponents
Deprecated.
replaced by BinaryImages.componentsLabeling(ImagePlus, int, int)
computeLabels(ImageProcessor, int, int) - Static method in class inra.ijpb.binary.ConnectedComponents
Deprecated.
replaced by BinaryImages.componentsLabeling(ImageProcessor, int, int)
computeLabels(ImageStack, int, int) - Static method in class inra.ijpb.binary.ConnectedComponents
Deprecated.
replaced by BinaryImages.componentsLabeling(ImageStack, int, int)
computeLabels(ImageProcessor, int) - Method in class inra.ijpb.label.conncomp.FloodFillRegionComponentsLabeling
Computes labels corresponding to connected components of a region within a label map.
computeLabels(ImageStack, int) - Method in class inra.ijpb.label.conncomp.FloodFillRegionComponentsLabeling3D
Computes labels corresponding to connected components of a region within a label map.
computeLut(int, boolean) - Method in enum inra.ijpb.color.ColorMaps.CommonLabelMaps
Compute look-up table for current color map
computeMoments(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.EquivalentEllipsoid
Computes the matrix of moments for each region within the 3D label map.
computeMoments(ImageStack, int[], Calibration) - Method in class inra.ijpb.measure.region3d.InertiaEllipsoid
Deprecated.
Computes the matrix of moments for each region within the 3D label map.
computeResult(ImageProcessor) - Method in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling
Computes connected components labeling on the input binary image, and returns the results encapsulated into a Result class together with the largest label index.
computeResult(ImageStack) - Method in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling3D
Computes connected components labeling on the input binary image, and returns the results encapsulated into a Result class together with the largest label index.
computeSphericity(double[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
use IntrinsicVolumes3D instead
computeTable(ImagePlus) - Method in class inra.ijpb.measure.region2d.RegionAnalyzer2D
Default implementation of computeTable method, using the two other methods RegionAnalyzer2D.analyzeRegions(ImagePlus) and RegionAnalyzer.createTable(Map):
computeTable(ImagePlus) - Method in class inra.ijpb.measure.region3d.RegionAnalyzer3D
Default implementation of computeTable method, using the two other methods RegionAnalyzer3D.analyzeRegions(ImagePlus) and RegionAnalyzer.createTable(Map):
computeTable(ImagePlus) - Method in interface inra.ijpb.measure.RegionAnalyzer
Returns the result of the analysis in the form of a ResultsTable, to facilitate concatenation of results obtained from several instances of RegionAnalyzer.
computeWatershed(ImagePlus, ImagePlus, int) - Static method in class inra.ijpb.watershed.Watershed
Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
computeWatershed(ImagePlus, ImagePlus, int, double, double) - Static method in class inra.ijpb.watershed.Watershed
Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
computeWatershed(ImagePlus, ImagePlus, int, double, double, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
computeWatershed(ImageStack, ImageStack, boolean, int) - Static method in class inra.ijpb.watershed.Watershed
Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
computeWatershed(ImageStack, ImageStack, int) - Static method in class inra.ijpb.watershed.Watershed
Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
computeWatershed(ImageProcessor, ImageProcessor, boolean, int) - Static method in class inra.ijpb.watershed.Watershed
Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
computeWatershed(ImageProcessor, ImageProcessor, int) - Static method in class inra.ijpb.watershed.Watershed
Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
computeWatershed(ImagePlus, ImagePlus, ImagePlus, int, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers with an optional binary mask to restrict the regions of application.
computeWatershed(ImagePlus, ImagePlus, ImagePlus, int, boolean, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers with an optional binary mask to restrict the regions of application.
computeWatershed(ImagePlus, ImagePlus, ImagePlus, int, boolean, double, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers with an optional binary mask to restrict the regions of application.
computeWatershed(ImageStack, ImageStack, ImageStack, int, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers with an optional binary mask to restrict the regions of application.
computeWatershed(ImageStack, ImageStack, ImageStack, int, boolean, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers with an optional binary mask to restrict the regions of application
computeWatershed(ImageProcessor, ImageProcessor, ImageProcessor, int, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers with an optional binary mask to restrict the regions of application.
computeWatershed(ImageProcessor, ImageProcessor, ImageProcessor, int, boolean, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers with an optional binary mask to restrict the regions of application.
computeWatershed(ImagePlus, ImagePlus, int, boolean, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers
computeWatershed(ImagePlus, ImagePlus, int, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers.
computeWatershed(ImageStack, ImageStack, int, boolean, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers.
computeWatershed(ImageStack, ImageStack, int, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers.
computeWatershed(ImageProcessor, ImageProcessor, int, boolean, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers.
computeWatershed(ImageProcessor, ImageProcessor, int, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers.
ConnectedComponents - Class in inra.ijpb.binary
Deprecated.
all methods have been moved to the BinaryImages class
ConnectedComponents() - Constructor for class inra.ijpb.binary.ConnectedComponents
Deprecated.
 
ConnectedComponentsLabeling - Interface in inra.ijpb.binary.conncomp
Computes labels corresponding to connected components in input image.
ConnectedComponentsLabeling3D - Interface in inra.ijpb.binary.conncomp
Computes labels corresponding to connected components in input 3D image.
connectivity - Variable in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
The connectivity of the algorithm, either 6 or 26.
connectivity - Variable in class inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgoStub
The connectivity of the algorithm, either 4 or 8.
Connectivity2D - Enum in inra.ijpb.plugins
An enumeration of connectivity options for 2D Mathematical Morphology operators.
Connectivity3D - Enum in inra.ijpb.plugins
An enumeration of connectivity options for 3D Mathematical Morphology operators.
ConstantBorder - Class in inra.ijpb.data.border
Returns either image pixel when position is inside image bounds, or a constant value when position is outside of image bounds.
ConstantBorder(ImageProcessor, float) - Constructor for class inra.ijpb.data.border.ConstantBorder
Creates a new Constant Border Manager
ConstantBorder3D - Class in inra.ijpb.data.border
Returns either image pixel when position is inside image bounds, or a constant value when position is outside of image bounds.
ConstantBorder3D(ImageStack, int) - Constructor for class inra.ijpb.data.border.ConstantBorder3D
Creates a new Constant Border Manager
contains(Point2D) - Method in class inra.ijpb.geometry.Polygon2D
Checks if this polygon contains the query point.
convertMaskToShifts(int[][]) - Static method in class inra.ijpb.morphology.strel.AbstractStrel
Converts the specified (binary) mask into a series of shifts, assuming the offset of the mask is located at its center.
convertMaskToShifts(int[][][]) - Static method in class inra.ijpb.morphology.strel.AbstractStrel3D
Converts the specified (binary) mask into a series of shifts, assuming the offset of the mask is located at its center.
convexArea - Variable in class inra.ijpb.measure.region2d.Convexity.Result
The area of the convex hull of the region.
convexHull(ArrayList<? extends Point2D>) - Static method in class inra.ijpb.geometry.Polygons2D
Uses the gift wrap algorithm with floating point values to find the convex hull and returns it as a list of points.
convexHull_int(ArrayList<Point>) - Static method in class inra.ijpb.geometry.Polygons2D
Uses the gift wrap algorithm with integer values to find the convex hull of a list of vertices, and returns it as an ordered list of points.
convexify(ImageProcessor) - Static method in class inra.ijpb.measure.region2d.Convexity
Computes the binary image representing the convex hull of the input binary image.
ConvexifyPlugin - Class in inra.ijpb.plugins
Computes the Convex equivalent of a binary image.
ConvexifyPlugin() - Constructor for class inra.ijpb.plugins.ConvexifyPlugin
 
Convexity - Class in inra.ijpb.measure.region2d
Computes convex area and convexity for regions within a binary or label image.
Convexity() - Constructor for class inra.ijpb.measure.region2d.Convexity
 
convexity - Variable in class inra.ijpb.measure.region2d.Convexity.Result
The convexity of the region, computed as the ratio of area over convex area.
convexity - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing convexity.
Convexity.Result - Class in inra.ijpb.measure.region2d
Simple class for storing the results of convexity computations.
countForegroundPixels(ImageProcessor) - Static method in class inra.ijpb.binary.BinaryImages
Counts the number of foreground pixels.
countForegroundVoxels(ImageStack) - Static method in class inra.ijpb.binary.BinaryImages
Counts the number of foreground voxels.
CREATE_IMAGE - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
name of the macro method to show current segmentation result in a new window
CREATE_IMAGE - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
name of the macro method to show current segmentation result in a new window
createBorderManager(ImageProcessor) - Method in enum inra.ijpb.data.border.BorderManager.Type
Creates a new Border Manager for the input image.
createBorderManager(ImageStack) - Method in enum inra.ijpb.data.border.BorderManager3D.Type
Creates a new Border Manager for the input image.
createBoundary(Collection<Integer>) - Method in class inra.ijpb.label.conncomp.BoundarySet
Creates a new Boundary from the list of adjacent regions, add it to the set, and returns the new instance of Boundary.
createByteProcessor(int[][]) - Static method in class inra.ijpb.data.image.ImageUtils
Creates a new ByteProcessor initialized with the content of the input array.
createColorModel(byte[][]) - Static method in class inra.ijpb.color.ColorMaps
Creates a Java.awt.image.ColorModel from a color map given as an triplet of byte arrays.
createColorModel(byte[][], Color) - Static method in class inra.ijpb.color.ColorMaps
Creates a Java.awt.image.ColorModel from a color map given as an triplet of byte arrays, and a color for the background that will be associated to label 0.
createFireLut(int) - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Fire LUT.
createFireLut() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Fire LUT.
createFloatProcessor(float[][]) - Static method in class inra.ijpb.data.image.ImageUtils
Creates a new FloatProcessor initialized with the content of the input array.
createGlasbeyBrightLut() - Static method in class inra.ijpb.color.ColorMaps
Create lookup table with a maximally distinct sets of colors, retaining only colors with high luminance, making it useful for displaying categorical data or label maps over a black background.
createGlasbeyDarkLut() - Static method in class inra.ijpb.color.ColorMaps
Create lookup table with a maximally distinct sets of colors, retaining only colors with low luminance, making it useful for displaying categorical data or label maps over a white background.
createGlasbeyLut() - Static method in class inra.ijpb.color.ColorMaps
Create lookup table with a maximally distinct sets of colors (copied from Fiji's Glasbey LUT).
createGoldenAngleLut(int) - Static method in class inra.ijpb.color.ColorMaps
Make lookup table with esthetically pleasing colors based on the golden angle
createGrayLut() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the gray LUT.
createIceLut(int) - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Ice LUT.
createIceLut() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Ice LUT.
createImageProcessor(int, int, int) - Static method in class inra.ijpb.data.image.ImageUtils
Creates a new ImageProcessor from image dimensions and bit depth.
createJetLut(int) - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Jet LUT.
createJetLut() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Jet LUT.
createLabelImage(int, int, int) - Static method in class inra.ijpb.label.LabelImages
Creates a label image with the appropriate class to store the required number of labels.
createLabelImage(ImageProcessor...) - Static method in class inra.ijpb.label.LabelImages
Creates a new label image from a set of binary images.
createLabelStack(int, int, int, int) - Static method in class inra.ijpb.label.LabelImages
Creates a new image stack with the appropriate class to store the required number of labels.
createMainColorsLut() - Static method in class inra.ijpb.color.ColorMaps
Returns a LUT with only the 6 main colors.
createMap(int[], T2[]) - Static method in class inra.ijpb.measure.region3d.RegionAnalyzer3D
Utility method that convert an array of result into a map using labels as keys.
createMixedColorsLut() - Static method in class inra.ijpb.color.ColorMaps
Returns a LUT with only the main colors and their mixture.
createPathRois(ImagePlus, Map<Integer, GeodesicDiameter.Result>) - Method in class inra.ijpb.plugins.GeodesicDiameterPlugin
Adds the specified paths to the list of ROI of the image plus.
createRedGreenLut() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing a color gradient from red to green.
createResultImage() - Static method in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
Show current result in a new image
createResultImage() - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
Show current result in a new image
createRGB332Lut() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the RGB332 LUT.
createRoi() - Method in class inra.ijpb.geometry.Polygon2D
Converts this polygon into an ImageJ Polygon ROI.
createShortProcessor(int[][]) - Static method in class inra.ijpb.data.image.ImageUtils
Creates a new ShortProcessor initialized with the content of the input array.
createSpectrumLut() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Spectrum LUT.
createStrel(double) - Method in class inra.ijpb.morphology.directional.OrientedLineStrelFactory
Creates a new instance of OrientedLineStrel with the length stored internally and the orientation given as argument.
createStrel(double) - Method in interface inra.ijpb.morphology.directional.OrientedStrelFactory
Creates an oriented structuring element with the given orientation (in degrees).
createTable(Map<Integer, AverageThickness.Result>) - Method in class inra.ijpb.measure.region2d.AverageThickness
 
createTable(Map<Integer, Box2D>) - Method in class inra.ijpb.measure.region2d.BoundingBox
Utility method that transforms the mapping between labels and bounding boxes instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, Point2D>) - Method in class inra.ijpb.measure.region2d.Centroid
Utility method that transforms the mapping between labels and Point2D instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, Convexity.Result>) - Method in class inra.ijpb.measure.region2d.Convexity
 
createTable(Map<Integer, Ellipse>) - Method in class inra.ijpb.measure.region2d.EquivalentEllipse
Utility method that transforms the mapping between labels and equivalent ellipses instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, GeodesicDiameter.Result>) - Method in class inra.ijpb.measure.region2d.GeodesicDiameter
Utility method that transforms the mapping between labels and result instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, Ellipse>) - Method in class inra.ijpb.measure.region2d.InertiaEllipse
Deprecated.
Utility method that transforms the mapping between labels and inertia ellipses instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, IntrinsicVolumesAnalyzer2D.Result>) - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
 
createTable(Map<Integer, Circle2D>) - Method in class inra.ijpb.measure.region2d.LargestInscribedCircle
Utility method that transforms the mapping between labels and inscribed circle instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, PointPair2D>) - Method in class inra.ijpb.measure.region2d.MaxFeretDiameter
Converts the result of maximum Feret diameters computation to a ResultsTable that can be displayed within ImageJ.
createTable(Map<Integer, OrientedBox2D>) - Method in class inra.ijpb.measure.region2d.OrientedBoundingBox2D
 
createTable(Map<Integer, Box3D>) - Method in class inra.ijpb.measure.region3d.BoundingBox3D
Utility method that transforms the mapping between labels and Box3D instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, Point3D>) - Method in class inra.ijpb.measure.region3d.Centroid3D
Utility method that transforms the mapping between labels and Point3D instances into a ResultsTable that can be displayed with ImageJ.
createTable(int[], Ellipsoid[]) - Method in class inra.ijpb.measure.region3d.EquivalentEllipsoid
Utility method that transforms a pair of arrays for labels and equivalent ellipsoids instances into a ResultsTable that can be displayed with ImageJ.
createTable(int[], EquivalentEllipsoid.Moments3D[]) - Method in class inra.ijpb.measure.region3d.EquivalentEllipsoid
Utility method that transforms a pair of arrays for labels and 3D moments instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, Ellipsoid>) - Method in class inra.ijpb.measure.region3d.EquivalentEllipsoid
Utility method that transforms the mapping between labels and equivalent ellipsoids instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, GeodesicDiameter3D.Result>) - Method in class inra.ijpb.measure.region3d.GeodesicDiameter3D
 
createTable(Map<Integer, Ellipsoid>) - Method in class inra.ijpb.measure.region3d.InertiaEllipsoid
Deprecated.
Utility method that transforms the mapping between labels and inertia ellipsoids instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, IntrinsicVolumesAnalyzer3D.Result>) - Method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
 
createTable(Map<Integer, Sphere>) - Method in class inra.ijpb.measure.region3d.LargestInscribedBall
Utility method that transforms the mapping between labels and inscribed ball instances into a ResultsTable that can be displayed with ImageJ.
createTable(Map<Integer, PointPair3D>) - Method in class inra.ijpb.measure.region3d.MaxFeretDiameter3D
Converts the result of maximum Feret diameters computation to a ResultsTable that can be displayed within ImageJ.
createTable(Map<Integer, T>) - Method in interface inra.ijpb.measure.RegionAnalyzer
Utility method that converts the detailed results of the RegionAnalyzer.analyzeRegions(ImagePlus) method into an instance of ResultsTable to facilitate display by ImageJ.
createWrapper(ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Converts the input ImageStack into an instance of Image3D, depending on the data type stored in the stack.
croftonPerimeter(ImageProcessor, double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
use analyzeRegions instead
croftonPerimeter(ImageProcessor, int[], double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
replaced by IntrinsicVolumes2D
croftonPerimeterD2(ImageProcessor, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
replaced by IntrinsicVolumes2D
croftonPerimeterD4(ImageProcessor, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
replaced by IntrinsicVolumes2D
cropBorder(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractStrel
Retrieve the portion of image that corresponds to the original image before adding border.
cropBorder(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
Retrieve the portion of image that corresponds to the original image before adding border.
cropLabel(ImagePlus, int, int) - Static method in class inra.ijpb.label.LabelImages
Returns a binary image that contains only the selected particle or region, by automatically cropping the image and eventually adding some borders.
cropLabel(ImageProcessor, int, int) - Static method in class inra.ijpb.label.LabelImages
Returns a binary image that contains only the selected particle or region, by automatically cropping the image and eventually adding some borders.
cropLabel(ImageStack, int, int) - Static method in class inra.ijpb.label.LabelImages
Returns a binary image that contains only the selected particle or region, by automatically cropping the image and eventually adding some borders.
CropLabelPlugin - Class in inra.ijpb.plugins
Crops a label image and binarize it to contain only the specified label.
CropLabelPlugin() - Constructor for class inra.ijpb.plugins.CropLabelPlugin
 
cropRect(ImageProcessor, int, int, int, int) - Static method in class inra.ijpb.shape.ImageShape
Crops a rectangular region from the input image.
cropRect(ImageStack, int, int, int, int, int, int) - Static method in class inra.ijpb.shape.ImageShape
Crops a rectangular region from the input 3D image.
Cross3DStrel - Class in inra.ijpb.morphology.strel
3D structuring element representing a 3x3x3 cross, that considers the center voxel together with the six orthogonal neighbors.
Cross3DStrel() - Constructor for class inra.ijpb.morphology.strel.Cross3DStrel
Create a new instance of this structuring element.
Cross3x3Strel - Class in inra.ijpb.morphology.strel
Structuring element representing a 3x3 cross, that considers the center pixels together with the four orthogonal neighbors.
Cross3x3Strel() - Constructor for class inra.ijpb.morphology.strel.Cross3x3Strel
 
crossProduct(Vector2D, Vector2D) - Static method in class inra.ijpb.geometry.Vector2D
Computes the cross product of the two vectors.
crossProduct(Vector3D, Vector3D) - Static method in class inra.ijpb.geometry.Vector3D
Computes the cross product of the two vectors.
crossProduct(Vector3d, Vector3d) - Static method in class inra.ijpb.measure.Vector3d
Deprecated.
Computes the cross product of the two vectors.
CubeStrel - Class in inra.ijpb.morphology.strel
A cubic structuring element, obtained by decomposition into linear structuring elements with the same size along each dimension.
CubeStrel(int) - Constructor for class inra.ijpb.morphology.strel.CubeStrel
Creates a new cubic structuring element of a given size.
CubeStrel(int, int) - Constructor for class inra.ijpb.morphology.strel.CubeStrel
Creates a new cubic structuring element of a given size and with a given offset.
CuboidStrel - Class in inra.ijpb.morphology.strel
A cuboid structuring element, obtained by decomposition into linear structuring elements (that can have different sizes) along each dimension.
Cursor2D - Class in inra.ijpb.data
A simple class to record the coordinates a pixel in a 2D image.
Cursor2D(int, int) - Constructor for class inra.ijpb.data.Cursor2D
Creates a new cursor from two coordinates.
Cursor3D - Class in inra.ijpb.data
Identifies the position of a voxel in a 3D image by using 3 integer coordinates.
Cursor3D(int, int, int) - Constructor for class inra.ijpb.data.Cursor3D
Creates a new cursor from two coordinates.

D

debug - Static variable in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
option for debugging
debug - Variable in class inra.ijpb.plugins.AnalyzeRegions3D
When this options is set to true, information messages are displayed on the console, and the number of counts for each direction is included in results table.
debug - Variable in class inra.ijpb.plugins.CropLabelPlugin
When this options is set to true, information messages are displayed on the console.
debug - Variable in class inra.ijpb.plugins.MaxFeretDiameterPlugin
When this options is set to true, information messages are displayed on the console.
debug - Variable in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
When this options is set to true, information messages are displayed on the console, and the number of counts for each direction is included in results table.
debug - Variable in class inra.ijpb.plugins.ParticleAnalysis3DPlugin
Deprecated.
When this options is set to true, information messages are displayed on the console, and the number of counts for each direction is included in results table.
debug - Variable in class inra.ijpb.plugins.RegionMorphometryPlugin
Deprecated.
When this options is set to true, information messages are displayed on the console, and the number of counts for each direction is included in results table.
debug - Variable in class inra.ijpb.plugins.SelectLabelsPlugin
When this options is set to true, information messages are displayed on the console, and the number of counts for each direction is included in results table.
decompose() - Method in class inra.ijpb.morphology.strel.CubeStrel
Returns a collection of three linear-shape structuring element, along each principal direction.
decompose() - Method in class inra.ijpb.morphology.strel.CuboidStrel
Returns a collection of three linear-shape structuring element, along each principal direction.
decompose() - Method in class inra.ijpb.morphology.strel.DiamondStrel
 
decompose() - Method in class inra.ijpb.morphology.strel.OctagonStrel
Returns a decomposition into four structuring elements, corresponding to horizontal, vertical, and diagonal linear structuring elements.
decompose() - Method in interface inra.ijpb.morphology.strel.SeparableStrel
Decompose this separable structuring element into a set of smaller structuring elements that can be used to accelerate processing.
decompose() - Method in interface inra.ijpb.morphology.strel.SeparableStrel3D
Decompose this separable structuring element into a set of smaller structuring elements that can be used to accelerate processing.
decompose() - Method in class inra.ijpb.morphology.strel.SquareStrel
 
DefaultAlgoListener - Class in inra.ijpb.algo
Utility class that catches algorithm events and displays them on ImageJ main Frame.
DefaultAlgoListener() - Constructor for class inra.ijpb.algo.DefaultAlgoListener
 
depth() - Method in class inra.ijpb.geometry.Box3D
Computes the depth of the bounding box, corresponding to the extent along the Z dimension.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.AreaOpeningPlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.ChamferDistanceMapPlugin
Called when a dialog widget has been modified: recomputes option values from dialog content.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.DirectionalFilteringPlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.DistanceTransformWatershed
Called when a dialog widget has been modified: recomputes option values from dialog content.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.DrawTableValuesPlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.ExtendedMinAndMaxPlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.GrayscaleAreaOpeningPlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.GrayscaleAttributeFilteringPlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.GrayscaleBoxDiameterOpeningPlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.InteractiveGeodesicDistanceMap
Called when a dialog widget has been modified: recomputes option values from dialog content.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.InteractiveMorphologicalReconstruction
Called when a dialog widget has been modified: recomputes option values from dialog content.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.LabelToValuePlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.MorphologicalFilterPlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.RegionalMinAndMaxPlugin
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class inra.ijpb.plugins.SetLabelMapPlugin
 
diameter - Variable in class inra.ijpb.geometry.AngleDiameterPair
Diameter computed in the direction of the angle
diameter() - Method in class inra.ijpb.geometry.PointPair2D
 
diameter() - Method in class inra.ijpb.geometry.PointPair3D
 
diameter - Variable in class inra.ijpb.measure.region2d.GeodesicDiameter.Result
The geodesic diameter of the region
diameter - Variable in class inra.ijpb.measure.region3d.GeodesicDiameter3D.Result
The geodesic diameter of the region
DiamondStrel - Class in inra.ijpb.morphology.strel
Structuring element representing a diamond of a given diameter.
DiamondStrel(int) - Constructor for class inra.ijpb.morphology.strel.DiamondStrel
Creates a new diamond structuring element of given diameter.
DiamondStrel(int, int) - Constructor for class inra.ijpb.morphology.strel.DiamondStrel
Creates a new diamond structuring element with a given diameter and offset.
dilateLabels(ImagePlus, double) - Static method in class inra.ijpb.label.LabelImages
Applies a constrained dilation to each region in the 3D label map: The dilation of each region is constrained by the other regions; The dilation extent is limited by the specified distance (in voxel unit)
dilateLabels(ImageProcessor, double) - Static method in class inra.ijpb.label.LabelImages
Applies a constrained dilation to each region in the label map: The dilation of each region is constrained by the other regions; The dilation extent is given by a radius value (in pixel unit).
dilateLabels(ImageStack, double) - Static method in class inra.ijpb.label.LabelImages
Applies a constrained dilation to each region in the 3D label map: The dilation of each region is constrained by the other regions; The dilation extent is limited by the the radius value (in voxel unit).
DilateLabelsPlugin - Class in inra.ijpb.plugins
Dilate all labels within a label image.
DilateLabelsPlugin() - Constructor for class inra.ijpb.plugins.DilateLabelsPlugin
 
dilation(ImageProcessor) - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
 
Dilation - Class in inra.ijpb.morphology.filter
Performs morphological dilation on 2D/3D images.
Dilation(Strel3D) - Constructor for class inra.ijpb.morphology.filter.Dilation
Creates a new Morphological Dilation operator with the specified structuring element.
dilation(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological dilation on the input image.
dilation(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological dilation on the input image.
dilation(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological dilation on the input 3D image.
dilation(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
dilation(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
dilation(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel3D
 
dilation(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel
 
dilation(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel3D
 
dilation(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractStrel
Implements a default algorithm for dilation, that consists in iterating over the neighbors of each pixel to compute the maximum value.
dilation(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel
 
dilation(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
Implements a default algorithm for dilation, that consists in iterating over the neighbors of each pixel to compute the maximum value.
dilation(ImageStack) - Method in class inra.ijpb.morphology.strel.BallStrel
Performs dilation with a ball structuring element by calling the ImageJ Filters3D.filter method, using Filters3D.MAX option.
dilation(ImageStack) - Method in class inra.ijpb.morphology.strel.Cross3DStrel
 
dilation(ImageProcessor) - Method in interface inra.ijpb.morphology.Strel
Performs a morphological dilation of the input image with this structuring element, and returns the result in a new ImageProcessor.
dilation(ImageStack) - Method in class inra.ijpb.morphology.strel.EllipsoidStrel
Performs dilation with a ball structuring element by calling the ImageJ Filters3D.filter method, using Filters3D.MAX option.
dilation(ImageStack) - Method in class inra.ijpb.morphology.strel.ExtrudedStrel
 
dilation(ImageStack) - Method in interface inra.ijpb.morphology.Strel3D
Performs a morphological dilation of the input image with this structuring element, and returns the result in a new ImageStack.
DirectionalFilter - Class in inra.ijpb.morphology.directional
Directional filtering of planar images.
DirectionalFilter(DirectionalFilter.Type, DirectionalFilter.Operation, int, int) - Constructor for class inra.ijpb.morphology.directional.DirectionalFilter
Creates new instance of directional filter using line structuring elements.
DirectionalFilter(DirectionalFilter.Type, DirectionalFilter.Operation, OrientedStrelFactory, int) - Constructor for class inra.ijpb.morphology.directional.DirectionalFilter
Creates new instance of directional filter for arbitrary structuring elements, by specifying the factory.
DirectionalFilter.Operation - Enum in inra.ijpb.morphology.directional
A pre-defined set of operations.
DirectionalFilter.Type - Enum in inra.ijpb.morphology.directional
Specifies how to combine the different orientations: min or max.
DirectionalFilteringPlugin - Class in inra.ijpb.plugins
Plugin for computing directional filtering.
DirectionalFilteringPlugin() - Constructor for class inra.ijpb.plugins.DirectionalFilteringPlugin
 
directionWeights3d13(Calibration) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumes3DUtils
Returns an array with seven values corresponding the unique direction vectors obtained with 13 directions.
directionWeights3d3(Calibration) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumes3DUtils
Returns an array with seven values corresponding the unique direction vectors obtained with 3 directions.
dirNumberLabels - Static variable in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
List of available numbers of directions
dirNumberLabels - Static variable in class inra.ijpb.plugins.RegionMorphometryPlugin
Deprecated.
List of available numbers of directions
dirNumbers - Static variable in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
Array of weights, in the same order than the array of names.
dirNumbers - Static variable in class inra.ijpb.plugins.RegionMorphometryPlugin
Deprecated.
Array of weights, in the same order than the array of names.
DiskStrel - Class in inra.ijpb.morphology.strel
Disk structuring element.
distance(Point3D) - Method in class inra.ijpb.geometry.Point3D
Computes the euclidean distance to another point.
distance(Point2D) - Method in class inra.ijpb.geometry.StraightLine2D
Computes the distance between this line and a query point.
distanceMap(ImagePlus) - Static method in class inra.ijpb.binary.BinaryImages
Computes the distance map (or distance transform) from a binary image processor.
distanceMap(ImageProcessor) - Static method in class inra.ijpb.binary.BinaryImages
Computes the distance map (or distance transform) from a binary image processor.
distanceMap(ImageProcessor, ChamferMask2D, boolean, boolean) - Static method in class inra.ijpb.binary.BinaryImages
Computes the distance map from a binary image processor, by specifying weights and normalization.
distanceMap(ImageProcessor, short[], boolean) - Static method in class inra.ijpb.binary.BinaryImages
Computes the distance map from a binary image processor, by specifying weights and normalization.
distanceMap(ImageProcessor, float[], boolean) - Static method in class inra.ijpb.binary.BinaryImages
Computes the distance map from a binary image processor, by specifying weights and normalization.
distanceMap(ImageStack) - Static method in class inra.ijpb.binary.BinaryImages
Computes the distance map from a binary 3D image.
distanceMap(ImageStack, ChamferMask3D, boolean, boolean) - Static method in class inra.ijpb.binary.BinaryImages
Computes the distance map from a binary 3D image.
distanceMap(ImageStack, short[], boolean) - Static method in class inra.ijpb.binary.BinaryImages
Computes the distance map from a binary 3D image.
distanceMap(ImageStack, float[], boolean) - Static method in class inra.ijpb.binary.BinaryImages
Computes the distance map from a binary 3D image.
distanceMap(ImageProcessor) - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform2DFloat
Computes the distance map of the distance to the nearest background pixel.
distanceMap(ImageProcessor) - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform2DShort
Computes the distance map of the distance to the nearest background pixel.
distanceMap(ImageStack) - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform3DFloat
Computes the distance map from a 3D binary image.
distanceMap(ImageStack) - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform3DShort
Computes the distance map from a 3D binary image.
distanceMap(ImageProcessor) - Method in interface inra.ijpb.binary.distmap.DistanceTransform
Computes the distance map from a binary image processor.
distanceMap(ImageStack) - Method in interface inra.ijpb.binary.distmap.DistanceTransform3D
Computes the distance map from a 3D binary image.
distanceMap(ImageStack) - Method in class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsFloat
Deprecated.
Computes the distance map from a 3D binary image.
distanceMap(ImageStack) - Method in class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsShort
Deprecated.
Computes the distance map from a 3D binary image.
distanceMap(ImageStack) - Method in class inra.ijpb.binary.distmap.DistanceTransform3DFloat
Deprecated.
Computes the distance map from a 3D binary image.
distanceMap(ImageStack) - Method in class inra.ijpb.binary.distmap.DistanceTransform3DShort
Deprecated.
Computes the distance map from a 3D binary image.
distanceMap(ImageProcessor) - Method in class inra.ijpb.binary.distmap.DistanceTransform3x3Float
Deprecated.
Computes the distance map of the distance to the nearest pixel with a different value.
distanceMap(ImageProcessor) - Method in class inra.ijpb.binary.distmap.DistanceTransform3x3Short
Deprecated.
Computes the distance map of the distance to the nearest pixel with a different value.
distanceMap(ImageProcessor) - Method in class inra.ijpb.binary.distmap.DistanceTransform5x5Float
Deprecated.
Computes the distance map of the distance to the nearest pixel with a different value.
distanceMap(ImageProcessor) - Method in class inra.ijpb.binary.distmap.DistanceTransform5x5Short
Deprecated.
Computes the distance map of the distance to the nearest pixel with a different value.
distanceMap(ImageProcessor) - Method in class inra.ijpb.label.distmap.ChamferDistanceTransform2DFloat
Computes the distance map of the distance to the nearest pixel with a different value.
distanceMap(ImageProcessor) - Method in class inra.ijpb.label.distmap.ChamferDistanceTransform2DShort
Computes the distance map of the distance to the nearest pixel with a different value.
distanceMap(ImageStack) - Method in class inra.ijpb.label.distmap.ChamferDistanceTransform3DFloat
Computes the distance map from a 3D label image.
distanceMap(ImageStack) - Method in class inra.ijpb.label.distmap.ChamferDistanceTransform3DShort
Computes the distance map from a 3D binary image.
distanceMap(ImageProcessor) - Method in interface inra.ijpb.label.distmap.DistanceTransform2D
Computes the distance map from a label image.
distanceMap(ImageStack) - Method in interface inra.ijpb.label.distmap.DistanceTransform3D
Computes the distance map from a 3D label image.
distanceMap(ImageStack) - Method in class inra.ijpb.label.distmap.DistanceTransform3DFloat
Deprecated.
Computes the distance map from a 3D binary image.
distanceMap(ImageStack) - Method in class inra.ijpb.label.distmap.DistanceTransform3DShort
Deprecated.
Computes the distance map from a 3D binary image.
distanceMap(ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Computes the distance map for each region within a label map.
distanceMap(ImageProcessor, ChamferMask2D, boolean, boolean) - Static method in class inra.ijpb.label.LabelImages
Computes the distance map for each region within a label map, by specifying the chamfer mask and the normalization.
distanceMap(ImageProcessor, short[], boolean) - Static method in class inra.ijpb.label.LabelImages
Computes the distance map for each region within a label map.
distanceMap(ImageProcessor, float[], boolean) - Static method in class inra.ijpb.label.LabelImages
Computes the distance map from a 3D image of labels Distance is computed for each label voxel, as the chamfer distance to the nearest voxel with a different value.
distanceMap(ImageStack) - Static method in class inra.ijpb.label.LabelImages
Computes the 3D distance map from an image of labels.
distanceMap(ImageStack, ChamferMask3D, boolean, boolean) - Static method in class inra.ijpb.label.LabelImages
Computes the 3D distance map from an image of labels, by specifying the chamfer mask and the normalization.
distanceMap(ImageStack, short[], boolean) - Static method in class inra.ijpb.label.LabelImages
Computes the distance map from a 3D image of labels Distance is computed for each label voxel, as the chamfer distance to the nearest voxel with a different value.
distanceMap(ImageStack, float[], boolean) - Static method in class inra.ijpb.label.LabelImages
Computes the distance map from a 3D image of labels Distance is computed for each label voxel, as the chamfer distance to the nearest voxel with a different value.
DistanceTransform - Interface in inra.ijpb.binary.distmap
Interface for computing distance maps from binary images.
DistanceTransform2D - Interface in inra.ijpb.label.distmap
Interface for computing distance maps for 2D label images.
DistanceTransform3D - Interface in inra.ijpb.binary.distmap
Interface for computing distance maps from binary 3D images.
DistanceTransform3D - Interface in inra.ijpb.label.distmap
Interface for computing distance maps for 3D label images.
DistanceTransform3D4WeightsFloat - Class in inra.ijpb.binary.distmap
Deprecated.
replaced by ChamferDistanceTransform3DFloat (since 1.5.0)
DistanceTransform3D4WeightsFloat(ChamferWeights3D) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsFloat
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3D4WeightsFloat(float[]) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsFloat
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3D4WeightsFloat(ChamferWeights3D, boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsFloat
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3D4WeightsFloat(float[], boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsFloat
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3D4WeightsShort - Class in inra.ijpb.binary.distmap
Deprecated.
replaced by ChamferDistanceTransform3DShort (since 1.5.0)
DistanceTransform3D4WeightsShort(ChamferWeights3D) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsShort
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3D4WeightsShort(short[]) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsShort
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3D4WeightsShort(ChamferWeights3D, boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsShort
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3D4WeightsShort(short[], boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3D4WeightsShort
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3DFloat - Class in inra.ijpb.binary.distmap
Deprecated.
replaced by ChamferDistanceTransform3DFloat (since 1.5.0)
DistanceTransform3DFloat(ChamferWeights3D) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3DFloat
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3DFloat(float[]) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3DFloat
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3DFloat(ChamferWeights3D, boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3DFloat
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3DFloat(float[], boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3DFloat
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3DFloat - Class in inra.ijpb.label.distmap
Deprecated.
replaced by ChamferDistanceTransform3DFloat (since 1.4.4)
DistanceTransform3DFloat(ChamferWeights3D) - Constructor for class inra.ijpb.label.distmap.DistanceTransform3DFloat
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3DFloat(float[]) - Constructor for class inra.ijpb.label.distmap.DistanceTransform3DFloat
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3DFloat(ChamferWeights3D, boolean) - Constructor for class inra.ijpb.label.distmap.DistanceTransform3DFloat
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3DFloat(float[], boolean) - Constructor for class inra.ijpb.label.distmap.DistanceTransform3DFloat
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3DShort - Class in inra.ijpb.binary.distmap
Deprecated.
replaced by ChamferDistanceTransform3DShort (since 1.5.0)
DistanceTransform3DShort(ChamferWeights3D) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3DShort
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3DShort(short[]) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3DShort
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3DShort(ChamferWeights3D, boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3DShort
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3DShort(short[], boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3DShort
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3DShort - Class in inra.ijpb.label.distmap
Deprecated.
replaced by ChamferDistanceTransform3DShort (since 1.4.4)
DistanceTransform3DShort(ChamferWeights3D) - Constructor for class inra.ijpb.label.distmap.DistanceTransform3DShort
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3DShort(short[]) - Constructor for class inra.ijpb.label.distmap.DistanceTransform3DShort
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3DShort(ChamferWeights3D, boolean) - Constructor for class inra.ijpb.label.distmap.DistanceTransform3DShort
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3DShort(short[], boolean) - Constructor for class inra.ijpb.label.distmap.DistanceTransform3DShort
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3x3Float - Class in inra.ijpb.binary.distmap
Deprecated.
replaced by ChamferDistanceTransform2DFloat (since 1.5.0)
DistanceTransform3x3Float(float[]) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3x3Float
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3x3Float(ChamferWeights, boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3x3Float
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3x3Float(float[], boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3x3Float
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3x3Short - Class in inra.ijpb.binary.distmap
Deprecated.
replaced by ChamferDistanceTransform2DShort (since 1.5.0)
DistanceTransform3x3Short(short[]) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3x3Short
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform3x3Short(ChamferWeights, boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3x3Short
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform3x3Short(short[], boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform3x3Short
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform5x5Float - Class in inra.ijpb.binary.distmap
Deprecated.
replaced by ChamferDistanceTransform2DFloat (since 1.5.0)
DistanceTransform5x5Float() - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Float
Deprecated.
Default constructor with predefined chamfer weights.
DistanceTransform5x5Float(ChamferWeights) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Float
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform5x5Float(float[]) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Float
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform5x5Float(ChamferWeights, boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Float
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform5x5Float(float[], boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Float
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform5x5Short - Class in inra.ijpb.binary.distmap
Deprecated.
replaced by ChamferDistanceTransform2DShort (since 1.5.0)
DistanceTransform5x5Short() - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Short
Deprecated.
Default constructor with predefined chamfer weights.
DistanceTransform5x5Short(ChamferWeights) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Short
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform5x5Short(short[]) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Short
Deprecated.
Default constructor that specifies the chamfer weights.
DistanceTransform5x5Short(ChamferWeights, boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Short
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransform5x5Short(short[], boolean) - Constructor for class inra.ijpb.binary.distmap.DistanceTransform5x5Short
Deprecated.
Constructor specifying the chamfer weights and the optional normalization.
DistanceTransformWatershed - Class in inra.ijpb.plugins
This plugin computes watershed on the inverse of the distance map of a binary image.
DistanceTransformWatershed() - Constructor for class inra.ijpb.plugins.DistanceTransformWatershed
 
DistanceTransformWatershed3D - Class in inra.ijpb.plugins
This plugin computes watershed on the inverse of the distance map of a 3D binary image.
DistanceTransformWatershed3D() - Constructor for class inra.ijpb.plugins.DistanceTransformWatershed3D
 
DIVIDES - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
Divides operator, that divides the values of the two images
dotProduct(Vector2D, Vector2D) - Static method in class inra.ijpb.geometry.Vector2D
Computes the dot product of two vectors, defined by:
dotProduct(Vector3D, Vector3D) - Static method in class inra.ijpb.geometry.Vector3D
Computes the dot product of two vectors, defined by:
dotProduct(Vector3d, Vector3d) - Static method in class inra.ijpb.measure.Vector3d
Deprecated.
Computes the dot product of two vectors, defined by:
drawDiameters(ImagePlus, Map<Integer, PointPair2D>) - Method in class inra.ijpb.plugins.MaxFeretDiameterPlugin
Draws the diameters on a target image.
DrawLabelsAsOverlayPlugin - Class in inra.ijpb.plugins
Draw the labels of the regions as overlay.
DrawLabelsAsOverlayPlugin() - Constructor for class inra.ijpb.plugins.DrawLabelsAsOverlayPlugin
 
drawPaths(ImagePlus, Map<Integer, GeodesicDiameter.Result>) - Method in class inra.ijpb.plugins.GeodesicDiameterPlugin
Displays the geodesic paths onto the given image.
DrawTableValuesPlugin - Class in inra.ijpb.plugins
Draw the values of a results table column into current image, using specified columns for x and y positions.
DrawTableValuesPlugin() - Constructor for class inra.ijpb.plugins.DrawTableValuesPlugin
 
drawValues(ImagePlus) - Method in class inra.ijpb.plugins.DrawTableValuesPlugin
Draw the values onto the target image.
dx - Variable in class inra.ijpb.binary.ChamferWeights3D.FloatOffset
Deprecated.
the offset along the X-axis
dx - Variable in class inra.ijpb.binary.ChamferWeights3D.ShortOffset
Deprecated.
the offset along the X-axis
dx - Variable in class inra.ijpb.binary.distmap.ChamferMask2D.FloatOffset
The offset along the X-axis
dx - Variable in class inra.ijpb.binary.distmap.ChamferMask2D.ShortOffset
The offset along the X-axis
dx - Variable in class inra.ijpb.binary.distmap.ChamferMask3D.FloatOffset
the offset along the X-axis
dx - Variable in class inra.ijpb.binary.distmap.ChamferMask3D.ShortOffset
the offset along the X-axis
dy - Variable in class inra.ijpb.binary.ChamferWeights3D.FloatOffset
Deprecated.
the offset along the Y-axis
dy - Variable in class inra.ijpb.binary.ChamferWeights3D.ShortOffset
Deprecated.
the offset along the Y-axis
dy - Variable in class inra.ijpb.binary.distmap.ChamferMask2D.FloatOffset
The offset along the Y-axis
dy - Variable in class inra.ijpb.binary.distmap.ChamferMask2D.ShortOffset
The offset along the Y-axis
dy - Variable in class inra.ijpb.binary.distmap.ChamferMask3D.FloatOffset
the offset along the Y-axis
dy - Variable in class inra.ijpb.binary.distmap.ChamferMask3D.ShortOffset
the offset along the Y-axis
dz - Variable in class inra.ijpb.binary.ChamferWeights3D.FloatOffset
Deprecated.
the offset along the Z-axis
dz - Variable in class inra.ijpb.binary.ChamferWeights3D.ShortOffset
Deprecated.
the offset along the Z-axis
dz - Variable in class inra.ijpb.binary.distmap.ChamferMask3D.FloatOffset
the offset along the Z-axis
dz - Variable in class inra.ijpb.binary.distmap.ChamferMask3D.ShortOffset
the offset along the Z-axis

E

eigenVectors() - Method in class inra.ijpb.measure.region3d.EquivalentEllipsoid.Moments3D
Return the eigen vector of the moments.
eigenVectors() - Method in class inra.ijpb.measure.region3d.InertiaEllipsoid.InertiaMoments3D
Deprecated.
 
Ellipse - Class in inra.ijpb.geometry
Represents a 2D ellipse.
Ellipse(Point2D, double, double, double) - Constructor for class inra.ijpb.geometry.Ellipse
Creates a new ellipse.
Ellipse(double, double, double, double, double) - Constructor for class inra.ijpb.geometry.Ellipse
Creates a new ellipse.
ellipseElongation - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing ellipse elongation.
Ellipsoid - Class in inra.ijpb.geometry
An ellipsoid in the 3D space, defined by a center, three radius, and three orientation angles.
Ellipsoid(Point3D, double, double, double) - Constructor for class inra.ijpb.geometry.Ellipsoid
Creates a new 3D Ellipsoid parallel to the three main axes.
Ellipsoid(Point3D, double, double, double, double, double, double) - Constructor for class inra.ijpb.geometry.Ellipsoid
Creates a new 3D Ellipsoid
Ellipsoid(double, double, double, double, double, double, double, double, double) - Constructor for class inra.ijpb.geometry.Ellipsoid
Creates a new 3D Ellipsoid
EllipsoidStrel - Class in inra.ijpb.morphology.strel
A 3D structuring element with an ellipsoidal shape, oriented along the three main axes of the image.
elongations(Ellipsoid[]) - Static method in class inra.ijpb.geometry.Ellipsoid
Computes the three elongation factors for an array of ellipsoids.
EQ - Static variable in interface inra.ijpb.label.select.RelationalOperator
Implementation of the "Equal" operator.
equals(Object) - Method in class inra.ijpb.data.Cursor2D
 
equals(Object) - Method in class inra.ijpb.data.Cursor3D
 
equals(Object) - Method in class inra.ijpb.label.RegionAdjacencyGraph.LabelPair
 
EquivalentEllipse - Class in inra.ijpb.measure.region2d
Compute parameters of equivalent ellipse from binar or label images.
EquivalentEllipse() - Constructor for class inra.ijpb.measure.region2d.EquivalentEllipse
Default constructor.
equivalentEllipse - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing equivalent ellipse.
EquivalentEllipsePlugin - Class in inra.ijpb.plugins
Computes equivalent ellipse of each region within a label image.
EquivalentEllipsePlugin() - Constructor for class inra.ijpb.plugins.EquivalentEllipsePlugin
 
equivalentEllipses(ImageProcessor, int[], Calibration) - Static method in class inra.ijpb.measure.region2d.EquivalentEllipse
Computes equivalent ellipse of each region in input label image.
EquivalentEllipsoid - Class in inra.ijpb.measure.region3d
Compute the parameters of 3D ellipsoids that has the same moments up to the second order than the region(s) within a 3D binary / label image.
EquivalentEllipsoid() - Constructor for class inra.ijpb.measure.region3d.EquivalentEllipsoid
Default constructor
equivalentEllipsoid() - Method in class inra.ijpb.measure.region3d.EquivalentEllipsoid.Moments3D
Converts the 3D moments stored in this instance into a 3D ellipsoid.
equivalentEllipsoid() - Method in class inra.ijpb.measure.region3d.InertiaEllipsoid.InertiaMoments3D
Deprecated.
Computes ellipsoid with same moments as those stored in this class.
EquivalentEllipsoid.Moments3D - Class in inra.ijpb.measure.region3d
Encapsulates the results of 3D Moments computations.
EquivalentEllipsoidPlugin - Class in inra.ijpb.plugins
Computes equivalent ellipsoid for each region with a binary or label 3D image.
EquivalentEllipsoidPlugin() - Constructor for class inra.ijpb.plugins.EquivalentEllipsoidPlugin
 
equivalentEllipsoids(ImageStack, int[], Calibration) - Static method in class inra.ijpb.measure.region3d.EquivalentEllipsoid
Computes equivalent ellipsoid of each region in the input 3D label image.
erosion(ImageProcessor) - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
 
Erosion - Class in inra.ijpb.morphology.filter
Performs morphological erosion on 2D/3D images.
Erosion(Strel3D) - Constructor for class inra.ijpb.morphology.filter.Erosion
Creates a new Morphological Erosion operator with the specified structuring element.
erosion(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological erosion on the input image.
erosion(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological erosion on the input image.
erosion(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological erosion on the input 3D image.
erosion(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
erosion(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
erosion(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel3D
 
erosion(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel
 
erosion(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel3D
 
erosion(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractStrel
Implements a default algorithm for erosion, that consists in iterating over the neighbors of each pixel to compute the minimum value.
erosion(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel
 
erosion(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
Implements a default algorithm for erosion, that consists in iterating over the neighbors of each pixel to compute the minimum value.
erosion(ImageStack) - Method in class inra.ijpb.morphology.strel.BallStrel
Performs erosion with a ball structuring element by calling the ImageJ Filters3D.filter method, using Filters3D.MIN option.
erosion(ImageStack) - Method in class inra.ijpb.morphology.strel.Cross3DStrel
 
erosion(ImageStack) - Method in class inra.ijpb.morphology.strel.EllipsoidStrel
Performs erosion with a ball structuring element by calling the ImageJ Filters3D.filter method, using Filters3D.MIN option.
erosion(ImageProcessor) - Method in interface inra.ijpb.morphology.Strel
Performs an morphological erosion of the input image with this structuring element, and returns the result in a new ImageProcessor.
erosion(ImageStack) - Method in class inra.ijpb.morphology.strel.ExtrudedStrel
 
erosion(ImageStack) - Method in interface inra.ijpb.morphology.Strel3D
Performs an morphological erosion of the input image with this structuring element, and returns the result in a new ImageStack.
euclideanDistance(Cursor2D) - Method in class inra.ijpb.data.Cursor2D
Calculate Euclidean distance to another cursor
euclideanDistance(Cursor3D) - Method in class inra.ijpb.data.Cursor3D
Calculate Euclidean distance to another cursor
euclideanDistance(PixelRecord) - Method in class inra.ijpb.data.PixelRecord
Calculate Euclidean distance to another pixel record
euclideanDistance(VoxelRecord) - Method in class inra.ijpb.data.VoxelRecord
Calculate Euclidean distance to another voxel record
eulerNumber(ImageStack, int[], int) - Static method in class inra.ijpb.measure.GeometricMeasures3D
eulerNumber(ImageProcessor, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D
Measures the Euler number of the region within the binary image, using the specified connectivity.
eulerNumber(ImageStack, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
Measures the Euler number of the region within the binary image, using the specified connectivity.
eulerNumber - Variable in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.Result
the Euler Number of the region.
eulerNumber - Variable in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.Result
The Euler Number of the region
eulerNumber - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing Euler number.
eulerNumberDensity(ImageProcessor, Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D
Measures the Euler number density of the foreground region within a binary image, using the specified connectivity.
eulerNumberDensity(ImageStack, Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
Measures the Euler number density of the foreground region within a binary image, using the specified connectivity.
eulerNumberIntLut(int) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumes2DUtils
Computes the Look-up table that is used to compute Euler number density.
eulerNumberIntLut(int) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
Deprecated.
use IntrinsicVolumes2DUtils instead
eulerNumberLut(int) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumes2DUtils
Computes the Look-up table that is used to compute Euler number density.
eulerNumberLut(int) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
Deprecated.
use IntrinsicVolumes2DUtils instead
eulerNumberLut(int) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumes3DUtils
Computes the look-up table for measuring Euler number in binary 3D image, depending on the connectivity.
eulerNumberLut(int) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
Deprecated.
eulerNumbers(ImageProcessor, int[], int) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D
Measures the Euler number of each region given in the "labels" argument, using the specified connectivity.
eulerNumbers(ImageStack, int[], int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
Measures the Euler number of each region given in the "labels" argument, using the specified connectivity.
evaluate(int, int) - Method in interface inra.ijpb.label.select.RelationalOperator
Evaluates this operator from two integer values.
evaluate(double, double) - Method in interface inra.ijpb.label.select.RelationalOperator
Evaluates this operator from two floating-point values.
exec(ImagePlus, int, int, int, int, BorderManager) - Method in class inra.ijpb.plugins.ExtendBordersPlugin
Deprecated.
exec(ImagePlus, ImagePlus, String, float[]) - Method in class inra.ijpb.plugins.GeodesicDistanceMapPlugin
Deprecated.
exec(ImagePlus, ImagePlus, String, float[], boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMapPlugin
Deprecated.
use process method instead
exec(ImagePlus, ImagePlus, String, short[], boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMapPlugin
Deprecated.
use process method instead
exec(ImagePlus, short[]) - Method in class inra.ijpb.plugins.MaxInscribedCirclePlugin
Deprecated.
replaced by process method
exec(ImagePlus, int) - Method in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
Deprecated.
specify porosity
exec(ImagePlus, int, boolean) - Method in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
Deprecated.
use process method instead
exec(ImagePlus, Morphology.Operation, Strel) - Method in class inra.ijpb.plugins.MorphologicalFilterPlugin
Deprecated.
use the process method instead
exec(ImagePlus, int) - Method in class inra.ijpb.plugins.RegionMorphometryPlugin
Deprecated.
expandLabels(ImageProcessor, float) - Static method in class inra.ijpb.plugins.ExpandLabelsPlugin
Expand labels by a given factor
expandLabels(ImageStack, float) - Static method in class inra.ijpb.plugins.ExpandLabelsPlugin
Expand labels by a given factor
ExpandLabelsPlugin - Class in inra.ijpb.plugins
Creates a new image larger than the original one, and copies each label identically but shifted by a given dilation coefficient.
ExpandLabelsPlugin() - Constructor for class inra.ijpb.plugins.ExpandLabelsPlugin
 
ExtendBordersPlugin - Class in inra.ijpb.plugins
Pads the current image with the specified value or color.
ExtendBordersPlugin() - Constructor for class inra.ijpb.plugins.ExtendBordersPlugin
 
extendedMaxima(ImageProcessor, double) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the extended maxima in grayscale image image, keeping maxima with the specified dynamic, and using the default connectivity.
extendedMaxima(ImageProcessor, double, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the extended maxima in grayscale image image, keeping maxima with the specified dynamic, and using the specified connectivity.
extendedMaxima(ImageStack, double) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the extended maxima in grayscale image image, keeping maxima with the specified dynamic, and using the default connectivity.
extendedMaxima(ImageStack, double, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the extended maxima in grayscale image image, keeping maxima with the specified dynamic, and using the specified connectivity.
extendedMaxima(ImageStack, double, ImageStack) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the extended maxima in the grayscale image image, keeping maxima with the specified dynamic, restricted to the non-zero voxels of the binary mask, and using the default connectivity.
extendedMaxima(ImageStack, double, int, ImageStack) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the extended maxima in the grayscale image image, keeping maxima with the specified dynamic, restricted to the non-zero voxels of the binary mask, and using the specified connectivity.
ExtendedMinAndMax3DPlugin - Class in inra.ijpb.plugins
Plugin for computing regional minima and maxima in grayscale images.
ExtendedMinAndMax3DPlugin() - Constructor for class inra.ijpb.plugins.ExtendedMinAndMax3DPlugin
 
ExtendedMinAndMax3DPlugin.Operation - Enum in inra.ijpb.plugins
A customized enumeration to choose between extended minima or maxima.
ExtendedMinAndMaxPlugin - Class in inra.ijpb.plugins
Plugin for computing extended minima and maxima in grayscale images.
ExtendedMinAndMaxPlugin() - Constructor for class inra.ijpb.plugins.ExtendedMinAndMaxPlugin
 
ExtendedMinAndMaxPlugin.Operation - Enum in inra.ijpb.plugins
A customized enumeration to choose between extended minima or maxima.
extendedMinima(ImageProcessor, double) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the extended minima in grayscale image image, keeping minima with the specified dynamic, and using the default connectivity.
extendedMinima(ImageProcessor, double, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the extended minima in grayscale image image, keeping minima with the specified dynamic, and using the specified connectivity.
extendedMinima(ImageStack, double) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the extended minima in grayscale image image, keeping minima with the specified dynamic, and using the default connectivity.
extendedMinima(ImageStack, double, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the extended minima in grayscale image image, keeping minima with the specified dynamic, and using the specified connectivity.
ExtendedMinimaWatershed - Class in inra.ijpb.watershed
Static methods for directly computing result of watershed after imposition of extended minima.
ExtendedMinimaWatershed() - Constructor for class inra.ijpb.watershed.ExtendedMinimaWatershed
 
extendedMinimaWatershed(ImagePlus, int, int) - Static method in class inra.ijpb.watershed.ExtendedMinimaWatershed
Computes watershed on a gray scale image after imposition of extended minima.
extendedMinimaWatershed(ImageProcessor, int, int, int) - Static method in class inra.ijpb.watershed.ExtendedMinimaWatershed
Computes watershed on a gray scale image after imposition of extended minima.
extendedMinimaWatershed(ImageProcessor, ImageProcessor, int, int, int, boolean) - Static method in class inra.ijpb.watershed.ExtendedMinimaWatershed
Computes watershed on a gray scale image after imposition of extended minima.
extendedMinimaWatershed(ImageStack, ImageStack, int, int, int, boolean) - Static method in class inra.ijpb.watershed.ExtendedMinimaWatershed
Computes watershed on a gray scale image after imposition of extended minima.
extendedMinimaWatershed(ImageStack, int, int, int) - Static method in class inra.ijpb.watershed.ExtendedMinimaWatershed
Computes watershed on a gray scale image after imposition of extended minima.
extendedMinimaWatershed(ImageProcessor, int, int) - Static method in class inra.ijpb.watershed.ExtendedMinimaWatershed
Computes watershed on a gray scale image after imposition of extended minima.
extendedMinimaWatershed(ImageProcessor, ImageProcessor, int, int, boolean) - Static method in class inra.ijpb.watershed.ExtendedMinimaWatershed
Computes watershed on a gray scale image after imposition of extended minima.
extendedMinimaWatershed(ImageStack, ImageStack, int, int, boolean) - Static method in class inra.ijpb.watershed.ExtendedMinimaWatershed
Computes watershed on a gray scale image after imposition of extended minima.
extendedMinimaWatershed(ImageStack, int, int) - Static method in class inra.ijpb.watershed.ExtendedMinimaWatershed
Computes watershed on a gray scale image after imposition of extended minima.
ExternalGradient - Class in inra.ijpb.morphology.filter
Performs morphological external gradient on 2D/3D images.
ExternalGradient(Strel3D) - Constructor for class inra.ijpb.morphology.filter.ExternalGradient
Creates a new External Gradient operator with the specified structuring element.
externalGradient(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological external gradient of the input image.
externalGradient(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological external gradient of the input image.
externalGradient(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological external gradient of the input 3D image.
extractPixelValues(ImageProcessor, ImageProcessor, int[][]) - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Extract pixel values from input and labeled marker images.
extractPixelValues(ImageProcessor, double, double) - Method in class inra.ijpb.watershed.WatershedTransform2D
Extract pixel values from input image such that they have value h, hMin <= h <= hMax.
extractPixelValuesPriorityQueue(ImageProcessor, ImageProcessor, int[][]) - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Extract pixel values from input and seed images
extractVoxelValues(ImageStack, ImageStack, int[][][]) - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
Extract voxel values from input and labeled marker images.
extractVoxelValues(ImageStack, double, double) - Method in class inra.ijpb.watershed.WatershedTransform3D
Extract voxel values from input image such that they have value h, hMin <= h <= hMax.
extractVoxelValuesPriorityQueue(ImageStack, ImageStack, int[][][]) - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
Extract voxel values from input and seed images
ExtremaType - Enum in inra.ijpb.morphology.extrema
One of the two types of extrema.
ExtrudedStrel - Class in inra.ijpb.morphology.strel
Creates a 3D strel by replicating a 2D strel on a given number of slices.
ExtrudedStrel(Strel, int) - Constructor for class inra.ijpb.morphology.strel.ExtrudedStrel
Creates a 3D structuring element by extruding ("repeating") a 2D structuring element along the given number of slices.
ExtrudedStrel(Strel, int, int) - Constructor for class inra.ijpb.morphology.strel.ExtrudedStrel
Creates a 3D structuring element by extruding ("repeating") a 2D structuring element along the given number of slices.

F

Features() - Constructor for class inra.ijpb.plugins.AnalyzeRegions.Features
 
FeretDiameters - Class in inra.ijpb.geometry
Utility methods for computing Feret diameters
FeretDiameters() - Constructor for class inra.ijpb.geometry.FeretDiameters
 
fill(ImageStack, double) - Static method in class inra.ijpb.data.image.Images3D
Fills the input 3D image with the given value.
fill(int) - Method in class inra.ijpb.morphology.strel.LocalBufferedHistogram
Resets histogram by considering it is filled with the given value.
fill(double) - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferDouble
Resets histogram by considering it is filled with the given value.
fill(int) - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferGray8
Resets histogram by considering it is filled with the given value.
fillHoles(ImageStack) - Static method in class inra.ijpb.morphology.GeodesicReconstruction3D
Deprecated.
Fills the holes in the input image, by (1) inverting the image, (2) performing a geodesic reconstruction initialized with inverted image boundary and (3) by inverting the result.
fillHoles(ImageProcessor) - Static method in class inra.ijpb.morphology.Reconstruction
Fills the holes in the input image, by (1) inverting the image, (2) performing a morphological reconstruction initialized with inverted image boundary and (3) by inverting the result.
fillHoles(ImageStack) - Static method in class inra.ijpb.morphology.Reconstruction3D
Fills the holes in the input image, by (1) inverting the image, (2) performing a morphological reconstruction initialized with inverted image boundary and (3) by inverting the result.
FillHolesPlugin - Class in inra.ijpb.plugins
Plugin for filling holes (dark holes within bright structures) in 8-bits grayscale or binary 2D/3D images.
FillHolesPlugin() - Constructor for class inra.ijpb.plugins.FillHolesPlugin
 
FillLabelHolesPlugin - Class in inra.ijpb.plugins
Fills the holes within the region of a label image.
FillLabelHolesPlugin() - Constructor for class inra.ijpb.plugins.FillLabelHolesPlugin
 
fillRect(ImageProcessor, int, int, int, int, double) - Static method in class inra.ijpb.data.image.ImageUtils
Fills a rectangle within the image with the specified value.
fillRect3d(ImageStack, int, int, int, int, int, int, double) - Static method in class inra.ijpb.data.image.ImageUtils
Fills a 3D rectangle within the image with the specified value.
FindAllLabels - Class in inra.ijpb.label.edit
Extract the set of unique labels existing in the given image, excluding the value zero (used for background).
FindAllLabels() - Constructor for class inra.ijpb.label.edit.FindAllLabels
Default empty constructor.
findAllLabels(ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Returns the set of unique labels existing in the given image, excluding the value zero (used for background).
findAllLabels(ImageStack) - Static method in class inra.ijpb.label.LabelImages
Returns the set of unique labels existing in the given stack, excluding the value zero (used for background).
findAllLabels(ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Returns the set of unique labels existing in the given image, excluding the value zero (used for background).
findBoundary(Collection<Integer>) - Method in class inra.ijpb.label.conncomp.BoundarySet
Try to find a Boundary that has same adjacent regions as the ones specified in the argument.
findLargestLabel(ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Find largest label (by number of pixels/voxels) in input image
findMaxValue(ImagePlus) - Static method in class inra.ijpb.data.image.ImageUtils
Computes maximum value within the input image.
findMaxValue(ImageProcessor) - Static method in class inra.ijpb.data.image.ImageUtils
Computes maximum value within the input 2D image.
findMaxValue(ImageStack) - Static method in class inra.ijpb.data.image.ImageUtils
Computes maximum value in the input 3D image.
findMaxValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelValues
For each label, finds the position of the point belonging to label region defined by labelImage and with maximal value in intensity image valueImage.
findMaxValues(ImageStack, ImageStack, int[]) - Static method in class inra.ijpb.label.LabelValues
For each label, finds the position of the 3D point belonging to label region defined by the 3D labelImage and with maximal value in intensity 3D image valueImage.
findMinAndMax(ImagePlus) - Static method in class inra.ijpb.data.image.Images3D
Find minimum and maximum value of input image
findMinAndMax(ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Find minimum and maximum value of input image
findMinValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelValues
For each label, finds the position of the point belonging to label region defined by labelImage and with minimal value in intensity image valueImage.
findMinValues(ImageStack, ImageStack, int[]) - Static method in class inra.ijpb.label.LabelValues
For each label, finds the position of the 3D point belonging to 3D label region defined by labelImage and with minimal value in 3D intensity image valueImage.
findOrCreateBoundary(Collection<Integer>) - Method in class inra.ijpb.label.conncomp.BoundarySet
Try to find a Boundary that has same adjacent regions as the ones specified in the argument.
findPositionOfMaxValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelImages
Deprecated.
use LavelValues.findPositionOfMaxValues instead
findPositionOfMaxValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelValues
For each label, finds the position of the point belonging to label region defined by labelImage and with maximal value in intensity image valueImage.
findPositionOfMaxValues(ImageStack, ImageStack, int[]) - Static method in class inra.ijpb.label.LabelValues
For each label, finds the position of the point belonging to label region defined by labelImage and with maximal value in intensity image valueImage.
findPositionOfMinValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelImages
Deprecated.
use LavelValues.findPositionOfMinValues instead
findPositionOfMinValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelValues
For each label, finds the position of the point belonging to label region defined by labelImage and with minimal value in intensity image valueImage.
findPositionOfMinValues(ImageStack, ImageStack, int[]) - Static method in class inra.ijpb.label.LabelValues
For each label, finds the position of the point belonging to label region defined by labelImage and with minimal value in intensity image valueImage.
fireProgressChanged(Object, double, double) - Method in class inra.ijpb.algo.AlgoStub
 
fireProgressChanged(AlgoEvent) - Method in class inra.ijpb.algo.AlgoStub
 
fireProgressChanged(Object, double, double) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
 
fireProgressChanged(AlgoEvent) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
 
fireStatusChanged(Object, String) - Method in class inra.ijpb.algo.AlgoStub
 
fireStatusChanged(AlgoEvent) - Method in class inra.ijpb.algo.AlgoStub
 
fireStatusChanged(Object, String) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
 
fireStatusChanged(AlgoEvent) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
 
firstExtremity - Variable in class inra.ijpb.measure.region2d.GeodesicDiameter.Result
The first geodesic extremity found by the algorithm.
firstExtremity - Variable in class inra.ijpb.measure.region3d.GeodesicDiameter3D.Result
The first geodesic extremity found by the algorithm.
FloatOffset(int, int, int, float) - Constructor for class inra.ijpb.binary.ChamferWeights3D.FloatOffset
Deprecated.
Creates a new offset for floating point computations.
FloatOffset(int, int, float) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2D.FloatOffset
Creates a new Offset using a floating point weight.
FloatOffset(int, int, int, float) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3D.FloatOffset
Creates a new Offset using a floating point weight.
FloatStackWrapper - Class in inra.ijpb.data.image
Access the data of a 3D image containing intensity values stored as float.
FloatStackWrapper(ImageStack) - Constructor for class inra.ijpb.data.image.FloatStackWrapper
Creates a new wrapper to the ImageStack.
FloodFill - Class in inra.ijpb.morphology
Implements various flood-fill algorithms, for planar images.
floodFill(ImageProcessor, int, int, int, int) - Static method in class inra.ijpb.morphology.FloodFill
Replaces all the neighbor pixels of (x0,y0) that have the same values by the specified integer value, using the specified connectivity.
floodFill(ImageProcessor, int, int, float, int) - Static method in class inra.ijpb.morphology.FloodFill
Replaces all the neighbor pixels of (x,y) that have the same values by the specified integer value, using the specified connectivity.
floodFill(ImageProcessor, int, int, ImageProcessor, int, int) - Static method in class inra.ijpb.morphology.FloodFill
Assigns in outputImage all the pixels connected to (x0,y0) that have the same pixel value in image, the specified new value (value), using the specified connectivity.
floodFill(ImageStack, int, int, int, int, int) - Static method in class inra.ijpb.morphology.FloodFill
Deprecated.
use FloodFill3D.floodFill instead.
floodFill(ImageStack, int, int, int, double, int) - Static method in class inra.ijpb.morphology.FloodFill
Deprecated.
use FLoodFill3D.floodFill instead
floodFill(ImageStack, int, int, int, ImageStack, int, int) - Static method in class inra.ijpb.morphology.FloodFill
Deprecated.
use FloodFill3D.floodFill instead
floodFill(ImageStack, int, int, int, int, int) - Static method in class inra.ijpb.morphology.FloodFill3D
Replaces all the pixels in the 6-neighborhood of (x0,y0,z0) that have the same values as the pixel in (x0,y0,z0) by the specified value.
floodFill(ImageStack, int, int, int, double, int) - Static method in class inra.ijpb.morphology.FloodFill3D
Replaces all the pixels in the 6-neighborhood of (x0,y0,z0) that have the same values as the pixel in (x0,y0,z0) by the specified floating point value.
floodFill(ImageStack, int, int, int, ImageStack, int, int) - Static method in class inra.ijpb.morphology.FloodFill3D
Assign to all the neighbor voxels of (x0,y0,z0) that have the same voxel value in inputImage, the specified new value ( value) in outputImage, using the specified connectivity.
FloodFill3D - Class in inra.ijpb.morphology
Implements various flood-fill algorithms for 3D stacks.
FloodFillComponentsLabeling - Class in inra.ijpb.binary.conncomp
Computes the labels of the connected components in a binary image.
FloodFillComponentsLabeling() - Constructor for class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling
Constructor with default connectivity 4 and default output bitdepth equal to 16.
FloodFillComponentsLabeling(int) - Constructor for class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling
Constructor specifying the connectivity and using default output bitdepth equal to 16.
FloodFillComponentsLabeling(int, int) - Constructor for class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling
Constructor specifying the connectivity and the bitdepth of result label image
FloodFillComponentsLabeling.Result - Class in inra.ijpb.binary.conncomp
Data class that stores result of connected component labeling.
FloodFillComponentsLabeling3D - Class in inra.ijpb.binary.conncomp
Computes the labels of the connected components in a 3D binary image.
FloodFillComponentsLabeling3D() - Constructor for class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling3D
Constructor with default connectivity 6 and default output bitdepth equal to 16.
FloodFillComponentsLabeling3D(int) - Constructor for class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling3D
Constructor specifying the connectivity and using default output bitdepth equal to 16.
FloodFillComponentsLabeling3D(int, int) - Constructor for class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling3D
Constructor specifying the connectivity and the bitdepth of result label image
FloodFillComponentsLabeling3D.Result - Class in inra.ijpb.binary.conncomp
Data class that stores result of connected component labeling.
floodFillFloat(ImageProcessor, int, int, ImageProcessor, float, int) - Static method in class inra.ijpb.morphology.FloodFill
Assigns in labelImage all the neighbor pixels of (x0,y0) that have the same pixel value in image, the specified new label value (value), using the specified connectivity.
floodFillFloat(ImageStack, int, int, int, ImageStack, float, int) - Static method in class inra.ijpb.morphology.FloodFill
Deprecated.
use FloodFill3D.floodFillFloat instead
floodFillFloat(ImageStack, int, int, int, ImageStack, float, int) - Static method in class inra.ijpb.morphology.FloodFill3D
Assigns to all the neighbor voxels of (x0,y0,z0) that have the same voxel value in inputImage, the specified new value (value) in outputImage, using the specified connectivity.
floodFillFloat(Image3D, int, int, int, Image3D, float, int) - Static method in class inra.ijpb.morphology.FloodFill3D
Assigns to all the neighbor voxels of (x0,y0,z0) that have the same voxel value in inputImage, the specified new value ( value) in outputImage, using the specified connectivity.
FloodFillRegionComponentsLabeling - Class in inra.ijpb.label.conncomp
Computes the labels of the different connected components of a region within a label image.
FloodFillRegionComponentsLabeling() - Constructor for class inra.ijpb.label.conncomp.FloodFillRegionComponentsLabeling
Constructor with default connectivity 4 and default output bitdepth equal to 16.
FloodFillRegionComponentsLabeling(int) - Constructor for class inra.ijpb.label.conncomp.FloodFillRegionComponentsLabeling
Constructor specifying the connectivity and using default output bitdepth equal to 16.
FloodFillRegionComponentsLabeling(int, int) - Constructor for class inra.ijpb.label.conncomp.FloodFillRegionComponentsLabeling
Constructor specifying the connectivity and the bitdepth of result label image
FloodFillRegionComponentsLabeling3D - Class in inra.ijpb.label.conncomp
Computes the labels of the different connected components of a region within a 3D label image.
FloodFillRegionComponentsLabeling3D() - Constructor for class inra.ijpb.label.conncomp.FloodFillRegionComponentsLabeling3D
Constructor with default connectivity 6 and default output bitdepth equal to 16.
FloodFillRegionComponentsLabeling3D(int) - Constructor for class inra.ijpb.label.conncomp.FloodFillRegionComponentsLabeling3D
Constructor specifying the connectivity and using default output bitdepth equal to 16.
FloodFillRegionComponentsLabeling3D(int, int) - Constructor for class inra.ijpb.label.conncomp.FloodFillRegionComponentsLabeling3D
Constructor specifying the connectivity and the bitdepth of result label image
FOREGROUND - Static variable in interface inra.ijpb.morphology.Strel
Default value for foreground pixels.
FOREGROUND - Static variable in interface inra.ijpb.morphology.Strel3D
Default value for foreground pixels.
fromDiameter(double) - Static method in class inra.ijpb.morphology.strel.BallStrel
Creates a structuring element with a spherical shape of the given diameter.
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.CubeStrel
Creates a new cube-shape structuring element with the specified diameter (equal to cube side length).
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.CuboidStrel
Creates a new cube-shape structuring element with the specified diameter (equal to cube side length).
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.DiamondStrel
Creates a new diamond-shape structuring element with the specified diameter.
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.DiskStrel
Creates a structuring element with a circular shape of the given diameter.
fromDiameter(double) - Static method in class inra.ijpb.morphology.strel.EllipsoidStrel
Creates a structuring element with an ellipsoidal shape of the given diameter.
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.LinearDepthStrel3D
Creates a new line-shape structuring element with the specified diameter (equal to the length of the line).
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.LinearDiagDownStrel
Creates a new line-shape structuring element with the specified diameter (equal to the orthogonal length of the line).
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.LinearDiagUpStrel
Creates a new line-shape structuring element with the specified diameter (equal to the orthogonal length of the line).
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.LinearHorizontalStrel
Creates a new line-shape structuring element with the specified diameter (equal to the length of the line).
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.LinearVerticalStrel
Creates a new line-shape structuring element with the specified diameter (equal to the length of the line).
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.OctagonStrel
Creates an octagon-shape structuring element with specified diameter.
fromDiameter(int) - Method in enum inra.ijpb.morphology.Strel.Shape
Creates a structuring element of the given type and with the specified diameter.
fromDiameter(int) - Static method in class inra.ijpb.morphology.strel.SquareStrel
Creates a new square-shape structuring element with the specified diameter (equal to square side length).
fromDiameter(int) - Method in enum inra.ijpb.morphology.Strel3D.Shape
Creates a structuring element of the given type and with the specified diameter.
fromDiameterList(int, int, int) - Static method in class inra.ijpb.morphology.strel.CuboidStrel
Creates a 3D structuring element with a cuboid shape and different sizes depending on direction.
fromDiameterList(double, double, double) - Static method in class inra.ijpb.morphology.strel.EllipsoidStrel
Creates a structuring element with an ellipsoidal shape from a list of three diameters.
fromDiameterList(int, int, int) - Method in enum inra.ijpb.morphology.Strel3D.Shape
Creates a structuring element of the given type and with the specified diameter.
fromLabel(String) - Static method in enum inra.ijpb.binary.ChamferWeights
Deprecated.
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.binary.ChamferWeights3D
Deprecated.
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.binary.distmap.ChamferMasks2D
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.binary.distmap.ChamferMasks3D
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.color.ColorMaps.CommonLabelMaps
Determines the color map from its label.
fromLabel(String) - Static method in enum inra.ijpb.color.CommonColors
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.data.border.BorderManager.Type
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.data.border.BorderManager3D.Type
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.morphology.directional.DirectionalFilter.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.morphology.directional.DirectionalFilter.Type
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.morphology.Morphology.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.morphology.Strel.Shape
Determines the strel shape from its label.
fromLabel(String) - Static method in enum inra.ijpb.morphology.Strel3D.Shape
Determines the strel shape from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.Connectivity2D
Determines the connectivity type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.Connectivity3D
Determines the connectivity type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.ImposeMinAndMax3DPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.ImposeMinAndMaxPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.LabelSizeFilteringPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.MorphologicalReconstruction3DPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.MorphologicalReconstructionPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.RegionalMinAndMax3DPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation
Determines the operation type from its label.
fromLabel(String) - Static method in enum inra.ijpb.util.CommonColors
Deprecated.
Determines the operation type from its label.
fromRadius(double) - Static method in class inra.ijpb.morphology.strel.BallStrel
Creates a structuring element with a spherical shape of the given radius.
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.CubeStrel
Creates a new cube-shape structuring element with the specified radius (such that cube side length equals 2 * radius + 1).
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.CuboidStrel
Creates a new cube-shape structuring element with the specified radius (such that cube side length equals 2 * radius + 1).
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.DiamondStrel
Creates a new diamond-shape structuring element with the specified radius (such that diameter equals 2 * radius + 1).
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.DiskStrel
Creates a structuring element with a circular shape of the given radius.
fromRadius(double) - Static method in class inra.ijpb.morphology.strel.EllipsoidStrel
Creates a structuring element with an ellipsoidal shape of the given radius.
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.LinearDepthStrel3D
Creates a new line-shape structuring element with the specified radius (such that orthogonal diameter equals 2*radius+1).
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.LinearDiagDownStrel
Creates a new line-shape structuring element with the specified radius (such that orthogonal diameter equals 2*radius+1).
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.LinearDiagUpStrel
Creates a new line-shape structuring element with the specified radius (such that orthogonal diameter equals 2*radius+1).
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.LinearHorizontalStrel
Creates a new line-shape structuring element with the specified radius (such that orthogonal diameter equals 2*radius+1).
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.LinearVerticalStrel
Creates a new line-shape structuring element with the specified radius (such that orthogonal diameter equals 2*radius+1).
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.OctagonStrel
Creates an octagon-shape structuring element with specified radius.
fromRadius(int) - Method in enum inra.ijpb.morphology.Strel.Shape
Creates a structuring element of the given type and with the specified radius.
fromRadius(int) - Static method in class inra.ijpb.morphology.strel.SquareStrel
Creates a new square-shape structuring element with the specified radius.
fromRadius(int) - Method in enum inra.ijpb.morphology.Strel3D.Shape
Creates a structuring element of the given type and with the specified radius.
fromRadiusList(int, int, int) - Static method in class inra.ijpb.morphology.strel.CuboidStrel
Creates a 3D structuring element with a cuboid shape and different sizes depending on direction.
fromRadiusList(double, double, double) - Static method in class inra.ijpb.morphology.strel.EllipsoidStrel
Creates a structuring element with an ellipsoidal shape from a list of three radius.
fromRadiusList(int, int, int) - Method in enum inra.ijpb.morphology.Strel3D.Shape
Creates a structuring element of the given type and with the specified radius for each dimension.
fromWeights(int[]) - Static method in class inra.ijpb.binary.distmap.ChamferMask2D
Creates a new Chamfer mask from a list of weights.
fromWeights(short[]) - Static method in class inra.ijpb.binary.distmap.ChamferMask2D
Creates a new Chamfer mask from a list of weights.
fromWeights(float[]) - Static method in class inra.ijpb.binary.distmap.ChamferMask2D
Creates a new Chamfer mask from a list of weights.
fromWeights(int[]) - Static method in class inra.ijpb.binary.distmap.ChamferMask3D
Creates a new Chamfer mask from a list of weights.
fromWeights(short[]) - Static method in class inra.ijpb.binary.distmap.ChamferMask3D
Creates a new Chamfer mask from a list of weights.
fromWeights(float[]) - Static method in class inra.ijpb.binary.distmap.ChamferMask3D
Creates a new Chamfer mask from a list of weights.

G

GE - Static variable in interface inra.ijpb.label.select.RelationalOperator
Implementation of the "Greater Than Or Equal" operator.
GeodesicDiameter - Interface in inra.ijpb.binary.geodesic
Deprecated.
since 1.3.5, use inra.ijpb.measure.region2d.GeodesicDiameter instead
GeodesicDiameter - Class in inra.ijpb.measure.region2d
Computes geodesic diameter of a set of labeled particles or regions, using an inner instance of GeodesicDistanceTransform for propagating chamfer distances.
GeodesicDiameter() - Constructor for class inra.ijpb.measure.region2d.GeodesicDiameter
Empty constructor with default settings.
GeodesicDiameter(ChamferMask2D) - Constructor for class inra.ijpb.measure.region2d.GeodesicDiameter
Creates a new geodesic diameter computation operator.
GeodesicDiameter(ChamferWeights) - Constructor for class inra.ijpb.measure.region2d.GeodesicDiameter
Deprecated.
ChamferWeights is replaced by ChamferMask2D (since 1.4.4)
GeodesicDiameter(float[]) - Constructor for class inra.ijpb.measure.region2d.GeodesicDiameter
Deprecated.
GeodesicDiameter(GeodesicDistanceTransform) - Constructor for class inra.ijpb.measure.region2d.GeodesicDiameter
Creates a new geodesic diameter computation operator.
geodesicDiameter - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing geodesic diameter.
GeodesicDiameter.Result - Class in inra.ijpb.measure.region2d
Inner class used for representing results of geodesic diameters computations.
GeodesicDiameter3D - Interface in inra.ijpb.binary.geodesic
Deprecated.
since 1.3.5, use inra.ijpb.measure.region3d.GeodesicDiameter3D instead
GeodesicDiameter3D - Class in inra.ijpb.measure.region3d
Computes the 3D geodesic diameters of regions within a 3D binary or label images using floating point computation for propagating distances.
GeodesicDiameter3D(ChamferMask3D) - Constructor for class inra.ijpb.measure.region3d.GeodesicDiameter3D
Creates a new 3D geodesic diameter computation operator.
GeodesicDiameter3D.Result - Class in inra.ijpb.measure.region3d
Inner class used for representing results of 3D geodesic diameters computations.
GeodesicDiameter3DFloat - Class in inra.ijpb.binary.geodesic
Deprecated.
replaced by inra.ijpb.measure.region3d.GeodesicDiameter3D
GeodesicDiameter3DFloat(ChamferMask3D) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDiameter3DFloat
Deprecated.
Creates a new 3D geodesic diameter computation operator.
GeodesicDiameter3DFloat(ChamferWeights3D) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDiameter3DFloat
Deprecated.
new uses ChamferMask3D (since 1.4.4)
GeodesicDiameter3DFloat(float[]) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDiameter3DFloat
Deprecated.
Creates a new 3D geodesic diameter computation operator.
GeodesicDiameter3DPlugin - Class in inra.ijpb.plugins
Plugin for computing geodesic distances of 3D particles from label images using chamfer weights.
GeodesicDiameter3DPlugin() - Constructor for class inra.ijpb.plugins.GeodesicDiameter3DPlugin
 
GeodesicDiameterFloat - Class in inra.ijpb.binary.geodesic
Deprecated.
since 1.3.5, use inra.ijpb.measure.region2d.GeodesicDiameter instead
GeodesicDiameterFloat(ChamferWeights) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDiameterFloat
Deprecated.
Creates a new geodesic diameter computation operator.
GeodesicDiameterFloat(float[]) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDiameterFloat
Deprecated.
Creates a new geodesic diameter computation operator.
GeodesicDiameterPlugin - Class in inra.ijpb.plugins
Plugin for computing geodesic distances of labeled particles using chamfer weights.
GeodesicDiameterPlugin() - Constructor for class inra.ijpb.plugins.GeodesicDiameterPlugin
 
geodesicDiameters(ImageProcessor, int[], Calibration) - Static method in class inra.ijpb.measure.region2d.GeodesicDiameter
Computes the geodesic diameter of each region within the given label image.
GeodesicDiameterShort - Class in inra.ijpb.binary.geodesic
Deprecated.
since 1.3.5, use inra.ijpb.measure.region2d.GeodesicDiameter instead
GeodesicDiameterShort(ChamferWeights) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDiameterShort
Deprecated.
Creates a new geodesic diameter computation operator.
GeodesicDiameterShort(short[]) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDiameterShort
Deprecated.
Creates a new geodesic diameter computation operator.
geodesicDistanceMap(ImagePlus, ImagePlus) - Static method in class inra.ijpb.binary.BinaryImages
Computes the geodesic distance transform (or geodesic distance map) of a binary image of marker, constrained to a binary mask.
geodesicDistanceMap(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.binary.BinaryImages
Computes the geodesic distance transform (or geodesic distance map) of a binary image of marker, constrained to a binary mask.
geodesicDistanceMap(ImageProcessor, ImageProcessor, short[], boolean) - Static method in class inra.ijpb.binary.BinaryImages
Computes the geodesic distance transform (or geodesic distance map) of a binary image of marker, constrained to a binary mask.
geodesicDistanceMap(ImageProcessor, ImageProcessor, float[], boolean) - Static method in class inra.ijpb.binary.BinaryImages
Computes the geodesic distance transform (or geodesic distance map) of a binary image of marker, constrained to a binary mask.
geodesicDistanceMap(ImageProcessor, ImageProcessor) - Method in interface inra.ijpb.binary.geodesic.GeodesicDistanceTransform
Computes the geodesic distance transform (or geodesic distance map) of a binary image of marker, constrained to a binary mask.
geodesicDistanceMap(ImageStack, ImageStack) - Method in interface inra.ijpb.binary.geodesic.GeodesicDistanceTransform3D
Computes 3D geodesic distance transform (or geodesic distance map) of a binary image of marker, constrained to a binary mask.
geodesicDistanceMap(ImageStack, ImageStack) - Method in class inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat
 
geodesicDistanceMap(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat
Computes the geodesic distance function for each pixel in mask label image, using the given binary marker image.
geodesicDistanceMap(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat5x5
Deprecated.
Computes the geodesic distance function for each pixel in mask label image, using the given binary marker image.
geodesicDistanceMap(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloatHybrid
Computes the geodesic distance function for each pixel in mask label image, using the given binary marker image.
geodesicDistanceMap(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort
Computes the geodesic distance function for each pixel in mask label image, using the given binary marker image.
geodesicDistanceMap(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort5x5
Deprecated.
Computes the geodesic distance function for each pixel in mask label image, using the given binary marker image.
geodesicDistanceMap(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShortHybrid
Computes the geodesic distance function for each pixel in mask label image, using the given binary marker image.
GeodesicDistanceMap3D - Class in inra.ijpb.plugins
Deprecated.
use GeodesicDistanceMap3DPlugin instead
GeodesicDistanceMap3D() - Constructor for class inra.ijpb.plugins.GeodesicDistanceMap3D
Deprecated.
 
GeodesicDistanceMap3DPlugin - Class in inra.ijpb.plugins
Plugin for computing geodesic distance map from binary 3D images using chamfer weights.
GeodesicDistanceMap3DPlugin() - Constructor for class inra.ijpb.plugins.GeodesicDistanceMap3DPlugin
 
GeodesicDistanceMapPlugin - Class in inra.ijpb.plugins
Plugin for computing geodesic distance map from binary marker and constrained to binary or label images using chamfer distances propagation.
GeodesicDistanceMapPlugin() - Constructor for class inra.ijpb.plugins.GeodesicDistanceMapPlugin
 
GeodesicDistanceTransform - Interface in inra.ijpb.binary.geodesic
Interface for computing Geodesic distance transforms (or geodesic distance maps) from binary images.
GeodesicDistanceTransform3D - Interface in inra.ijpb.binary.geodesic
Interface for computing Geodesic distance transforms (or geodesic distance maps) from binary images.
GeodesicDistanceTransform3DFloat - Class in inra.ijpb.binary.geodesic
Computation of geodesic distance transform for 3D images, using floating point computation.
GeodesicDistanceTransform3DFloat(ChamferMask3D, boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransform3DFloat(float[]) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat
Deprecated.
GeodesicDistanceTransform3DFloat(float[], boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat
Deprecated.
GeodesicDistanceTransform3DFloat(ChamferWeights3D, boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransform3DFloat
Deprecated.
GeodesicDistanceTransformFloat - Class in inra.ijpb.binary.geodesic
Computation of Chamfer geodesic distances using floating point array for storing result.
GeodesicDistanceTransformFloat(ChamferMask2D) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformFloat(ChamferMask2D, boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformFloat(float[]) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat
Deprecated.
GeodesicDistanceTransformFloat(float[], boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat
Deprecated.
GeodesicDistanceTransformFloat5x5 - Class in inra.ijpb.binary.geodesic
Deprecated.
replaced by GeodesicDistanceTransformFloat (since 1.4.4)
GeodesicDistanceTransformFloat5x5() - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat5x5
Deprecated.
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformFloat5x5(float[]) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat5x5
Deprecated.
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformFloat5x5(ChamferWeights, boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat5x5
Deprecated.
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformFloat5x5(float[], boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat5x5
Deprecated.
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformFloatHybrid - Class in inra.ijpb.binary.geodesic
Computation of geodesic distances based on a chamfer mask using floating point array for storing result.
GeodesicDistanceTransformFloatHybrid(ChamferMask2D) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloatHybrid
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformFloatHybrid(ChamferMask2D, boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloatHybrid
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformShort - Class in inra.ijpb.binary.geodesic
Computation of geodesic distances based on a chamfer mask using short integer array for storing result.
GeodesicDistanceTransformShort(ChamferMask2D) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformShort(ChamferMask2D, boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformShort(short[]) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort
Deprecated.
should use an instance of ChamferMask2D at construction
GeodesicDistanceTransformShort(short[], boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort
Deprecated.
should use an instance of ChamferMask2D at construction
GeodesicDistanceTransformShort5x5 - Class in inra.ijpb.binary.geodesic
Deprecated.
replaced by GeodesicDistanceTransformShort (since 1.5.0)
GeodesicDistanceTransformShort5x5(short[]) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort5x5
Deprecated.
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformShort5x5(ChamferWeights, boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort5x5
Deprecated.
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformShort5x5(short[], boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort5x5
Deprecated.
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformShortHybrid - Class in inra.ijpb.binary.geodesic
Computation of geodesic distances based on a chamfer mask using short integer array for storing result.
GeodesicDistanceTransformShortHybrid(ChamferMask2D) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShortHybrid
Creates a new algorithm for propagating geodesic distances.
GeodesicDistanceTransformShortHybrid(ChamferMask2D, boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShortHybrid
Creates a new algorithm for propagating geodesic distances.
geodesicElongation - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing geodesic elongation.
GeodesicReconstruction - Class in inra.ijpb.morphology
Deprecated.
replaced by the Reconstruction class (2017.07.25)
GeodesicReconstruction3D - Class in inra.ijpb.morphology
Deprecated.
replaced by the Reconstruction class (2017.07.25)
GeodesicReconstruction3DAlgo - Interface in inra.ijpb.morphology.geodrec
Defines the interface for geodesic reconstruction algorithms applied to 3D stack images.
GeodesicReconstruction3DAlgoStub - Class in inra.ijpb.morphology.geodrec
Implementation basis for geodesic reconstruction algorithms for 3D images.
GeodesicReconstruction3DAlgoStub() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
 
GeodesicReconstruction3DHybrid0Float - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction for 3D stacks of floats, using hybrid algorithm.
GeodesicReconstruction3DHybrid0Float() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Float
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstruction3DHybrid0Float(GeodesicReconstructionType) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Float
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and using the connectivity 6.
GeodesicReconstruction3DHybrid0Float(GeodesicReconstructionType, int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Float
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and the connectivity to use.
GeodesicReconstruction3DHybrid0Float(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Float
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstruction3DHybrid0Gray16 - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction for 3D stacks of shorts, using hybrid algorithm.
GeodesicReconstruction3DHybrid0Gray16() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray16
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstruction3DHybrid0Gray16(GeodesicReconstructionType) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray16
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and using the connectivity 6.
GeodesicReconstruction3DHybrid0Gray16(GeodesicReconstructionType, int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray16
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and the connectivity to use.
GeodesicReconstruction3DHybrid0Gray16(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray16
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstruction3DHybrid0Gray8 - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction for 3D stacks of bytes, using hybrid algorithm.
GeodesicReconstruction3DHybrid0Gray8() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray8
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstruction3DHybrid0Gray8(GeodesicReconstructionType) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray8
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and using the connectivity 6.
GeodesicReconstruction3DHybrid0Gray8(GeodesicReconstructionType, int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray8
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and the connectivity to use.
GeodesicReconstruction3DHybrid0Gray8(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray8
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstruction3DHybrid1Image3D - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction for 3D stacks of any type, using hybrid algorithm and Image3D access class.
GeodesicReconstruction3DHybrid1Image3D() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid1Image3D
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstruction3DHybrid1Image3D(GeodesicReconstructionType) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid1Image3D
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and using the connectivity 6.
GeodesicReconstruction3DHybrid1Image3D(GeodesicReconstructionType, int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid1Image3D
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and the connectivity to use.
GeodesicReconstruction3DHybrid1Image3D(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid1Image3D
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionAlgo - Interface in inra.ijpb.morphology.geodrec
Defines the interface for geodesic reconstructions algorithms applied to planar images.
GeodesicReconstructionAlgoStub - Class in inra.ijpb.morphology.geodrec
Implementation basis for geodesic reconstruction algorithms for planar images.
GeodesicReconstructionAlgoStub() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgoStub
 
GeodesicReconstructionByDilation - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction by dilation for planar images.
GeodesicReconstructionByDilation() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 4.
GeodesicReconstructionByDilation(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionByDilation3D - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction by dilation for 3D images of any type, using scanning algorithm and implemented only for C26 connectivity.
GeodesicReconstructionByDilation3D() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3D
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstructionByDilation3D(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3D
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionByDilation3DGray8 - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction by dilation for 3D stacks of byte processors, using hybrid algorithm and implemented only for 26 connectivity.
GeodesicReconstructionByDilation3DGray8() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DGray8
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstructionByDilation3DGray8(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DGray8
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionByDilation3DScanning - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction by dilation for 3D stacks using scanning algorithm, and Image3D access class.
GeodesicReconstructionByDilation3DScanning() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DScanning
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstructionByDilation3DScanning(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DScanning
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionByDilation3DScanningGray8 - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction by dilation for 3D stacks of byte processors, using scanning algorithm.
GeodesicReconstructionByDilation3DScanningGray8() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DScanningGray8
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstructionByDilation3DScanningGray8(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DScanningGray8
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionByErosion - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction by erosion for integer images.
GeodesicReconstructionByErosion() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion
Creates a new instance of geodesic reconstruction by erosion algorithm, using default connectivity 4.
GeodesicReconstructionByErosion(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion
Creates a new instance of geodesic reconstruction by erosion algorithm, that specifies the connectivity to use.
GeodesicReconstructionByErosion3DGray8 - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction by erosion for 3D stacks of byte processors, using hybrid algorithm and implemented only for the 26 connectivity.
GeodesicReconstructionByErosion3DGray8() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DGray8
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstructionByErosion3DGray8(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DGray8
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionByErosion3DScanning - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction by erosion for 3D stacks using scanning algorithm, and Image3D access class.
GeodesicReconstructionByErosion3DScanning() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanning
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstructionByErosion3DScanning(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanning
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionByErosion3DScanningGray8 - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction by erosion for 3D stacks of byte processors, using scanning algorithm.
GeodesicReconstructionByErosion3DScanningGray8() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanningGray8
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 6.
GeodesicReconstructionByErosion3DScanningGray8(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanningGray8
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionHybrid - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction for planar images, using hybrid algorithm.
GeodesicReconstructionHybrid() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionHybrid
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 4.
GeodesicReconstructionHybrid(GeodesicReconstructionType) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionHybrid
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and using the connectivity 4.
GeodesicReconstructionHybrid(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionHybrid
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionHybrid(GeodesicReconstructionType, int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionHybrid
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and the connectivity to use.
GeodesicReconstructionScanning - Class in inra.ijpb.morphology.geodrec
Geodesic reconstruction for planar images, using scanning algorithm.
GeodesicReconstructionScanning() - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionScanning
Creates a new instance of geodesic reconstruction by dilation algorithm, using the default connectivity 4.
GeodesicReconstructionScanning(GeodesicReconstructionType) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionScanning
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and using the connectivity 4.
GeodesicReconstructionScanning(int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionScanning
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the connectivity to use.
GeodesicReconstructionScanning(GeodesicReconstructionType, int) - Constructor for class inra.ijpb.morphology.geodrec.GeodesicReconstructionScanning
Creates a new instance of geodesic reconstruction by dilation algorithm, that specifies the type of reconstruction, and the connectivity to use.
GeodesicReconstructionType - Enum in inra.ijpb.morphology.geodrec
Enumeration of the two different types of geodesic reconstruction.
GeometricMeasures2D - Class in inra.ijpb.measure
Deprecated.
use IntrinsicVolumes2D instead
GeometricMeasures3D - Class in inra.ijpb.measure
Deprecated.
use IntrinsicVolumes3D instead
GeometryUtils - Class in inra.ijpb.measure.region3d
Some utilities for geometric computations.
get(int, int) - Method in interface inra.ijpb.data.border.BorderManager
Returns the value corresponding to (x,y) position.
get(int, int, int) - Method in interface inra.ijpb.data.border.BorderManager3D
Returns the value corresponding to (x,y) position.
get(int, int) - Method in class inra.ijpb.data.border.ConstantBorder
Returns either image pixel when position is inside image bounds, or a constant value when position is outside of image bounds.
get(int, int, int) - Method in class inra.ijpb.data.border.ConstantBorder3D
Returns either image pixel when position is inside image bounds, or a constant value when position is outside of image bounds.
get(int, int) - Method in class inra.ijpb.data.border.MirroringBorder
 
get(int, int, int) - Method in class inra.ijpb.data.border.MirroringBorder3D
 
get(int, int) - Method in class inra.ijpb.data.border.PeriodicBorder
 
get(int, int, int) - Method in class inra.ijpb.data.border.PeriodicBorder3D
 
get(int, int) - Method in class inra.ijpb.data.border.ReplicatedBorder
Forces both of x and y to be between 0 and the corresponding image size, and returns the corresponding image value.
get(int, int, int) - Method in class inra.ijpb.data.border.ReplicatedBorder3D
Forces both of x and y to be between 0 and the corresponding image size, and returns the corresponding image value.
get(int, int, int) - Method in class inra.ijpb.data.image.ByteStackWrapper
 
get(int, int, int) - Method in class inra.ijpb.data.image.FloatStackWrapper
 
get(int, int, int) - Method in interface inra.ijpb.data.image.Image3D
Returns the value at the specified coordinates as an integer.
get(int, int, int) - Method in class inra.ijpb.data.image.ShortStackWrapper
 
getAllLabels() - Static method in enum inra.ijpb.binary.ChamferWeights
Deprecated.
 
getAllLabels() - Static method in enum inra.ijpb.binary.ChamferWeights3D
Deprecated.
 
getAllLabels() - Static method in enum inra.ijpb.binary.distmap.ChamferMasks2D
 
getAllLabels() - Static method in enum inra.ijpb.binary.distmap.ChamferMasks3D
 
getAllLabels() - Static method in enum inra.ijpb.color.ColorMaps.CommonLabelMaps
 
getAllLabels() - Static method in enum inra.ijpb.color.CommonColors
 
getAllLabels() - Static method in enum inra.ijpb.data.border.BorderManager.Type
 
getAllLabels() - Static method in enum inra.ijpb.data.border.BorderManager3D.Type
 
getAllLabels() - Static method in enum inra.ijpb.morphology.directional.DirectionalFilter.Operation
Returns the labels for all operations within this enumeration.
getAllLabels() - Static method in enum inra.ijpb.morphology.directional.DirectionalFilter.Type
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.morphology.Morphology.Operation
Returns the list of labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.morphology.Strel.Shape
Returns a set of labels for most of classical structuring elements.
getAllLabels() - Static method in enum inra.ijpb.morphology.Strel3D.Shape
Returns a set of labels for most of classical structuring elements.
getAllLabels() - Static method in enum inra.ijpb.plugins.Connectivity2D
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.plugins.Connectivity3D
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.Operation
Returns all the labels of this enum.
getAllLabels() - Static method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
Returns all the labels of this enum.
getAllLabels() - Static method in enum inra.ijpb.plugins.ImposeMinAndMax3DPlugin.Operation
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.plugins.ImposeMinAndMaxPlugin.Operation
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin.Operation
Returns the list of labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.plugins.LabelSizeFilteringPlugin.Operation
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.plugins.MorphologicalReconstruction3DPlugin.Operation
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.plugins.MorphologicalReconstructionPlugin.Operation
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.plugins.RegionalMinAndMax3DPlugin.Operation
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation
Returns all the labels for this enumeration.
getAllLabels() - Static method in enum inra.ijpb.util.CommonColors
Deprecated.
Returns all the labels for this enumeration.
getAnimation(double, double) - Method in class inra.ijpb.watershed.WatershedTransform2D
Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.
getAnimationPriorityQueue() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Get animation of each h-step of the watershed transform on the inputImage, using the labeled markers from markerImage and restricted to the white areas of maskImage.
getAnimationPriorityQueueAndDams() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Get an animation of the different steps of the watershed transform applied on inputImage, using the labeled markers from markerImage and restricted to the white areas of maskImage (optionally).
getAnimationSortedList() - 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.
getAnimationSortedListAndDams() - 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.
getBackwardFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2D
 
getBackwardFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW2Float
 
getBackwardFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3D
 
getBackwardFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW3Float
 
getBackwardOffsets(short[]) - Static method in enum inra.ijpb.binary.ChamferWeights3D
Deprecated.
Computes the collection of weighted offsets corresponding to a scan of the voxels in a 3D image in the backward direction.
getBackwardOffsets(float[]) - Static method in enum inra.ijpb.binary.ChamferWeights3D
Deprecated.
Computes the collection of weighted offsets corresponding to a scan of the voxels in a 3D image in the backward direction.
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2D
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW2
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW2Float
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW3
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW4
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3D
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW3
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW3Float
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW4
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW5
 
getBackwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW6
 
getBoundary(int) - Method in class inra.ijpb.label.conncomp.BoundarySet
Retrieve a Boundary from its label.
getByteArrays(ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Extracts the byte arrays corresponding to the slices of a stack containing instances of ByteProcessor.
getCenter() - Method in class inra.ijpb.geometry.Circle2D
 
getChannelName() - Method in class inra.ijpb.morphology.strel.AbstractStrel
Returns the name of the channel currently processed, or null by default.
getChannelName() - Method in interface inra.ijpb.morphology.Strel
Returns the name of the channel currently processed, or null by default.
getColor() - Method in enum inra.ijpb.color.CommonColors
 
getColor() - Method in enum inra.ijpb.util.CommonColors
Deprecated.
 
getComputePaths() - Method in class inra.ijpb.measure.region2d.GeodesicDiameter
Returns the value of the computePaths option.
getConnectivity() - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
 
getConnectivity() - Method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
 
getConnectivity() - Method in class inra.ijpb.morphology.attrfilt.AreaOpeningQueue
Returns the current connectivity value for this algorithm.
getConnectivity() - Method in class inra.ijpb.morphology.attrfilt.BoxDiagonalOpeningQueue
Returns the current connectivity value for this algorithm.
getConnectivity() - Method in class inra.ijpb.morphology.attrfilt.SizeOpening3DQueue
Returns the current connectivity value for this algorithm.
getConnectivity() - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
Returns the connectivity value.
getConnectivity() - Method in class inra.ijpb.morphology.extrema.RegionalExtremaAlgo
Returns the connectivity value.
getConnectivity() - Method in interface inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgo
Returns the chosen connectivity of the algorithm, either 6 or 26.
getConnectivity() - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
 
getConnectivity() - Method in interface inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgo
Returns the chosen connectivity of the algorithm, either 4 or 8.
getConnectivity() - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgoStub
 
getConnectivity() - Method in class inra.ijpb.watershed.WatershedTransform2D
Get the pixel connectivity (4 or 8)
getConnectivity() - Method in class inra.ijpb.watershed.WatershedTransform3D
Get the voxel connectivity (6 or 26)
getCurrentProgress() - Method in class inra.ijpb.algo.AlgoEvent
 
getCursor() - Method in class inra.ijpb.data.Neighborhood2D
 
getCursor() - Method in class inra.ijpb.data.Neighborhood3D
 
getCursor() - Method in class inra.ijpb.data.PixelRecord
 
getCursor() - Method in class inra.ijpb.data.VoxelRecord
 
getDams - Static variable in class inra.ijpb.plugins.MarkerControlledWatershed3DPlugin
flag to calculate watershed dams
getDiceCoefficient(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the Dice coefficient between two label images.
getDiceCoefficient(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the Dice coefficient between two label images.
getDiceCoefficient(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the Dice coefficient between two label images.
getDiceCoefficientPerLabel(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the Dice coefficient per label (intersection over union overlap) between two label images.
getDiceCoefficientPerLabel(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the Dice coefficient per label (intersection over union overlap) between two label images.
getDiceCoefficientPerLabel(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the Dice coefficient per label (intersection over union overlap) between two label images.
getDirection() - Method in class inra.ijpb.geometry.StraightLine2D
 
getDirectionNumber() - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
 
getDirectionNumber() - Method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
 
getExtremaType() - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
Returns the type of extrema.
getExtremaType() - Method in class inra.ijpb.morphology.extrema.RegionalExtremaAlgo
Returns the type of extrema.
getf(int, int) - Method in interface inra.ijpb.data.border.BorderManager
Returns the floating-point value corresponding to (x,y) position.
getf(int, int) - Method in class inra.ijpb.data.border.ConstantBorder
Returns either image pixel when position is inside image bounds, or a constant value when position is outside of image bounds.
getf(int, int) - Method in class inra.ijpb.data.border.MirroringBorder
 
getf(int, int) - Method in class inra.ijpb.data.border.PeriodicBorder
 
getf(int, int) - Method in class inra.ijpb.data.border.ReplicatedBorder
Forces both of x and y to be between 0 and the corresponding image size, and returns the corresponding image value.
getFalseNegativeError(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the total false negative error between two label images (source and target).
getFalseNegativeError(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the total false negative error between two label images (source and target).
getFalseNegativeError(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the total false negative error between two label images (source and target).
getFalseNegativeErrorPerLabel(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the false negative error between two label images (source and target) per each individual labeled region.
getFalseNegativeErrorPerLabel(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the false negative error between two label images (source and target) per each individual labeled region.
getFalseNegativeErrorPerLabel(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the false negative error between two label images (source and target) per each individual labeled region.
getFalsePositiveError(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the total false positive error between two label images (source and target).
getFalsePositiveError(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the total false positive error between two label images (source and target).
getFalsePositiveError(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the total false positive error between two label images (source and target).
getFalsePositiveErrorPerLabel(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the false positive error between two label images (source and target) per each individual labeled region.
getFalsePositiveErrorPerLabel(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the false positive error between two label images (source and target) per each individual labeled region.
getFalsePositiveErrorPerLabel(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the false positive error between two label images (source and target) per each individual labeled region.
getFloatArrays(ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Extracts the float arrays corresponding to the slices of a stack containing instances of FloatProcessor.
getFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2D
 
getFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3D
 
getFloatWeights() - Method in enum inra.ijpb.binary.ChamferWeights
Deprecated.
 
getFloatWeights() - Method in enum inra.ijpb.binary.ChamferWeights3D
Deprecated.
 
getForwardFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2D
 
getForwardFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW2Float
 
getForwardFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3D
 
getForwardFloatOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW3Float
 
getForwardOffsets(short[]) - Static method in enum inra.ijpb.binary.ChamferWeights3D
Deprecated.
Computes the collection of weighted offsets corresponding to a scan of the voxels in a 3D image in the forward direction.
getForwardOffsets(float[]) - Static method in enum inra.ijpb.binary.ChamferWeights3D
Deprecated.
Computes the collection of weighted offsets corresponding to a scan of the voxels in a 3D image in the forward direction.
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2D
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW2
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW2Float
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW3
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW4
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3D
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW3
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW3Float
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW4
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW5
 
getForwardOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW6
 
getJaccardIndex(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the Jaccard index (intersection over union overlap) between two label images.
getJaccardIndex(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the Jaccard index (intersection over union overlap) between two label images.
getJaccardIndex(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the Jaccard index (intersection over union overlap) between two label images.
getJaccardIndexPerLabel(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the Jaccard index per label (intersection over union overlap) between two label images.
getJaccardIndexPerLabel(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the Jaccard index per label (intersection over union overlap) between two label images.
getJaccardIndexPerLabel(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the Jaccard index per label (intersection over union overlap) between two label images.
getKurtosis() - Method in class inra.ijpb.measure.IntensityMeasures
Get kurtosis voxel values per label
getLabel() - Method in enum inra.ijpb.color.ColorMaps.CommonLabelMaps
Get label name associated to color map
getLabel() - Method in enum inra.ijpb.color.CommonColors
 
getLabel() - Method in enum inra.ijpb.data.border.BorderManager.Type
 
getLabel() - Method in enum inra.ijpb.data.border.BorderManager3D.Type
 
getLabel() - Method in enum inra.ijpb.util.CommonColors
Deprecated.
 
getLargestPossibleLabel(ImageProcessor) - Static method in class inra.ijpb.label.LabelUtils
Determine the largest possible label that can be used with the specified image.
getLargestPossibleLabel(ImageStack) - Static method in class inra.ijpb.label.LabelUtils
Determine the largest possible label that can be used with the specified image.
getMask() - Method in enum inra.ijpb.binary.distmap.ChamferMasks2D
 
getMask() - Method in enum inra.ijpb.binary.distmap.ChamferMasks3D
 
getMask() - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
Returns the structuring element as a mask.
getMask() - Method in class inra.ijpb.morphology.strel.ChamferStrel
 
getMask() - Method in class inra.ijpb.morphology.strel.Cross3x3Strel
 
getMask() - Method in class inra.ijpb.morphology.strel.DiamondStrel
 
getMask() - Method in class inra.ijpb.morphology.strel.DiskStrel
 
getMask() - Method in interface inra.ijpb.morphology.Strel
Returns the structuring element as a mask.
getMask() - Method in class inra.ijpb.morphology.strel.LinearDiagDownStrel
 
getMask() - Method in class inra.ijpb.morphology.strel.LinearDiagUpStrel
 
getMask() - Method in class inra.ijpb.morphology.strel.LinearHorizontalStrel
 
getMask() - Method in class inra.ijpb.morphology.strel.LinearVerticalStrel
 
getMask() - Method in class inra.ijpb.morphology.strel.OctagonStrel
 
getMask() - Method in class inra.ijpb.morphology.strel.SquareStrel
 
getMask3D() - Method in class inra.ijpb.morphology.strel.AbstractStrel
 
getMask3D() - Method in class inra.ijpb.morphology.strel.BallStrel
 
getMask3D() - Method in class inra.ijpb.morphology.strel.ChamferStrel3D
 
getMask3D() - Method in class inra.ijpb.morphology.strel.Cross3DStrel
 
getMask3D() - Method in class inra.ijpb.morphology.strel.CubeStrel
 
getMask3D() - Method in class inra.ijpb.morphology.strel.CuboidStrel
 
getMask3D() - Method in class inra.ijpb.morphology.strel.EllipsoidStrel
 
getMask3D() - Method in class inra.ijpb.morphology.strel.ExtrudedStrel
 
getMask3D() - Method in class inra.ijpb.morphology.strel.LinearDepthStrel3D
 
getMask3D() - Method in interface inra.ijpb.morphology.Strel3D
Returns the structuring element as a mask.
getMax() - Method in class inra.ijpb.measure.IntensityMeasures
Get maximum voxel values per label
getMax() - Method in class inra.ijpb.morphology.strel.LocalBufferedHistogram
Returns the maximum value stored in this local histogram
getMax() - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferDouble
Returns the maximum value stored in this local histogram
getMax() - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferGray8
Returns the maximum value stored in this local histogram
getMaxPossibleValue(ImageStack) - Static method in class inra.ijpb.morphology.filter.MorphologicalFilter
Determines max possible value from bit depth.
getMean() - Method in class inra.ijpb.measure.IntensityMeasures
Get mean voxel values per label
getMedian() - Method in class inra.ijpb.measure.IntensityMeasures
Get median voxel values per label
getMin() - Method in class inra.ijpb.measure.IntensityMeasures
Get minimum voxel values per label
getMin() - Method in class inra.ijpb.morphology.strel.LocalBufferedHistogram
Returns the minimum value stored in this local histogram
getMode() - Method in class inra.ijpb.measure.IntensityMeasures
Get mode voxel values per label
getNeighbors() - Method in class inra.ijpb.data.Neighborhood2D
 
getNeighbors() - Method in class inra.ijpb.data.Neighborhood2DC4
 
getNeighbors() - Method in class inra.ijpb.data.Neighborhood2DC8
 
getNeighbors() - Method in class inra.ijpb.data.Neighborhood3D
 
getNeighbors() - Method in class inra.ijpb.data.Neighborhood3DC26
 
getNeighbors() - Method in class inra.ijpb.data.Neighborhood3DC6
 
getNeighborsKurtosis() - Method in class inra.ijpb.measure.IntensityMeasures
Get the intensity kurtosis values of the neighbor labels
getNeighborsMax() - Method in class inra.ijpb.measure.IntensityMeasures
Get the maximum intensity values of the neighbor labels
getNeighborsMean() - Method in class inra.ijpb.measure.IntensityMeasures
Get the mean intensity values of the neighbor labels
getNeighborsMedian() - Method in class inra.ijpb.measure.IntensityMeasures
Get the median intensity values of the neighbor labels
getNeighborsMin() - Method in class inra.ijpb.measure.IntensityMeasures
Get the minimum intensity values of the neighbor labels
getNeighborsMode() - Method in class inra.ijpb.measure.IntensityMeasures
Get the intensity mode value of the neighbor labels
getNeighborsSkewness() - Method in class inra.ijpb.measure.IntensityMeasures
Get the intensity skewness values of the neighbor labels
getNeighborsStdDev() - Method in class inra.ijpb.measure.IntensityMeasures
Get the standard deviation of the intensity values of the neighbor labels
getNorm() - Method in class inra.ijpb.geometry.Vector2D
Computes the norm of the vector, given as the square root of the sum of squared coordinates.
getNorm() - Method in class inra.ijpb.geometry.Vector3D
Computes the norm of the vector, given as the square root of the sum of squared coordinates.
getNorm() - Method in class inra.ijpb.measure.Vector3d
Deprecated.
Computes the norm of the vector, given as the square root of the sum of squared coordinates.
getNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask2D
 
getNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW2Float
 
getNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask3D
 
getNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW3Float
 
getNumberOfVoxels() - Method in class inra.ijpb.measure.LabeledVoxelsMeasure
Get number of voxels per label
getOffset() - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
Returns the offset in the mask.
getOffset() - Method in class inra.ijpb.morphology.strel.BallStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.ChamferStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.ChamferStrel3D
 
getOffset() - Method in class inra.ijpb.morphology.strel.Cross3DStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.Cross3x3Strel
 
getOffset() - Method in class inra.ijpb.morphology.strel.CubeStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.CuboidStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.DiamondStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.DiskStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.EllipsoidStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.ExtrudedStrel
 
getOffset() - Method in interface inra.ijpb.morphology.Strel
Returns the offset in the mask.
getOffset() - Method in class inra.ijpb.morphology.strel.LinearDepthStrel3D
 
getOffset() - Method in class inra.ijpb.morphology.strel.LinearDiagDownStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.LinearDiagUpStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.LinearHorizontalStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.LinearVerticalStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.OctagonStrel
 
getOffset() - Method in class inra.ijpb.morphology.strel.SquareStrel
 
getOffset() - Method in interface inra.ijpb.morphology.Strel3D
Returns the offset in the mask for each direction.
getOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask2D
 
getOffsets() - Method in class inra.ijpb.binary.distmap.ChamferMask3D
 
getOpenImageNames() - Static method in class inra.ijpb.util.IJUtils
Return an array of String containing the name of all the currently open images.
getOrigin() - Method in class inra.ijpb.geometry.StraightLine2D
 
getPosition() - Method in class inra.ijpb.label.LabelValues.Position3DValuePair
Returns the position of the voxel.
getPosition() - Method in class inra.ijpb.label.LabelValues.PositionValuePair
Returns the position of the pixel.
getProgressRatio() - Method in class inra.ijpb.algo.AlgoEvent
 
getRadius() - Method in class inra.ijpb.geometry.Circle2D
 
getReconstructionType() - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Float
 
getReconstructionType() - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray16
 
getReconstructionType() - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray8
 
getReconstructionType() - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid1Image3D
 
getReconstructionType() - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionHybrid
 
getReconstructionType() - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionScanning
 
getResultsTable() - Method in class inra.ijpb.measure.ResultsBuilder
Get the current results table.
getSelectedLabels(ImagePlus, Roi) - Static method in class inra.ijpb.label.LabelImages
Get list of selected labels in label image.
getShifts() - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
Returns the structuring element as a set of shifts.
getShifts() - Method in class inra.ijpb.morphology.strel.ChamferStrel
 
getShifts() - Method in class inra.ijpb.morphology.strel.Cross3x3Strel
 
getShifts() - Method in class inra.ijpb.morphology.strel.DiamondStrel
 
getShifts() - Method in class inra.ijpb.morphology.strel.DiskStrel
 
getShifts() - Method in interface inra.ijpb.morphology.Strel
Returns the structuring element as a set of shifts.
getShifts() - Method in class inra.ijpb.morphology.strel.LinearDiagDownStrel
 
getShifts() - Method in class inra.ijpb.morphology.strel.LinearDiagUpStrel
 
getShifts() - Method in class inra.ijpb.morphology.strel.LinearHorizontalStrel
 
getShifts() - Method in class inra.ijpb.morphology.strel.LinearVerticalStrel
 
getShifts() - Method in class inra.ijpb.morphology.strel.OctagonStrel
 
getShifts() - Method in class inra.ijpb.morphology.strel.SquareStrel
 
getShifts3D() - Method in class inra.ijpb.morphology.strel.AbstractStrel
 
getShifts3D() - Method in class inra.ijpb.morphology.strel.BallStrel
 
getShifts3D() - Method in class inra.ijpb.morphology.strel.ChamferStrel3D
 
getShifts3D() - Method in class inra.ijpb.morphology.strel.Cross3DStrel
 
getShifts3D() - Method in class inra.ijpb.morphology.strel.CubeStrel
 
getShifts3D() - Method in class inra.ijpb.morphology.strel.CuboidStrel
 
getShifts3D() - Method in class inra.ijpb.morphology.strel.EllipsoidStrel
 
getShifts3D() - Method in class inra.ijpb.morphology.strel.ExtrudedStrel
 
getShifts3D() - Method in class inra.ijpb.morphology.strel.LinearDepthStrel3D
 
getShifts3D() - Method in interface inra.ijpb.morphology.Strel3D
Returns the structuring element as a set of shifts.
getShortArrays(ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Extracts the short arrays corresponding to the slices of a stack containing instances of ShortProcessor.
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask2D
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW2
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW2Float
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW3
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask2DW4
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask3D
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW3
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW3Float
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW4
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW5
 
getShortNormalizationWeight() - Method in class inra.ijpb.binary.distmap.ChamferMask3DW6
 
getShortWeights() - Method in enum inra.ijpb.binary.ChamferWeights
Deprecated.
 
getShortWeights() - Method in enum inra.ijpb.binary.ChamferWeights3D
Deprecated.
 
getSign() - Method in enum inra.ijpb.morphology.geodrec.GeodesicReconstructionType
Returns the sign that can be used in algorithms generic for dilation and erosion.
getSize(int) - Method in class inra.ijpb.data.image.ByteStackWrapper
 
getSize(int) - Method in class inra.ijpb.data.image.FloatStackWrapper
 
getSize(int) - Method in interface inra.ijpb.data.image.Image3D
Returns the number of voxels along the specified dimension.
getSize(int) - Method in class inra.ijpb.data.image.ShortStackWrapper
 
getSize() - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
Returns the size of the structuring element, as an array of size in each direction.
getSize() - Method in class inra.ijpb.morphology.strel.BallStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.ChamferStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.ChamferStrel3D
 
getSize() - Method in class inra.ijpb.morphology.strel.Cross3DStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.Cross3x3Strel
 
getSize() - Method in class inra.ijpb.morphology.strel.CubeStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.CuboidStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.DiamondStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.DiskStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.EllipsoidStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.ExtrudedStrel
 
getSize() - Method in interface inra.ijpb.morphology.Strel
Returns the size of the structuring element, as an array of size in each direction.
getSize() - Method in class inra.ijpb.morphology.strel.LinearDepthStrel3D
 
getSize() - Method in class inra.ijpb.morphology.strel.LinearDiagDownStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.LinearDiagUpStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.LinearHorizontalStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.LinearVerticalStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.OctagonStrel
 
getSize() - Method in class inra.ijpb.morphology.strel.SquareStrel
 
getSize() - Method in interface inra.ijpb.morphology.Strel3D
Returns the size of the structuring element, as an array of size in each direction.
getSkewness() - Method in class inra.ijpb.measure.IntensityMeasures
Get skewness voxel values per label
getSource() - Method in class inra.ijpb.algo.AlgoEvent
 
getStatus() - Method in class inra.ijpb.algo.AlgoEvent
 
getStdDev() - Method in class inra.ijpb.measure.IntensityMeasures
Get standard deviation of voxel values per label
getStrel() - Method in class inra.ijpb.morphology.filter.MorphologicalFilter
 
getSuffix() - Method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.Operation
Returns the suffix to add to new ImagePlus created with thin operation.
getSuffix() - Method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
Returns the suffix to add to new ImagePlus created with thin operation.
getSuffix() - Method in enum inra.ijpb.plugins.RegionalMinAndMax3DPlugin.Operation
Returns the suffix added to processed images.
getSuffix() - Method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation
Returns the suffix added to processed images.
getSumOfVoxels() - Method in class inra.ijpb.measure.LabeledVoxelsMeasure
Get sum of all voxel intensities per labeled object
getTableWindows() - Static method in class inra.ijpb.util.IJUtils
Iterates on the list of TextWindows, and keeps only the ones containing a non-null ResultsTable
getTargetOverlapPerLabel(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the target overlap between two label images (source and target) per each individual labeled region.
getTargetOverlapPerLabel(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the target overlap between two label images (source and target) per each individual labeled region.
getTargetOverlapPerLabel(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the target overlap between two label images (source and target) per each individual labeled region.
getTotalOverlap(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the total overlap between two label images (source and target).
getTotalOverlap(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the total overlap between two label images (source and target).
getTotalOverlap(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the total overlap between two label images (source and target).
getTotalProgress() - Method in class inra.ijpb.algo.AlgoEvent
 
getValue(int, int, int) - Method in class inra.ijpb.data.image.ByteStackWrapper
 
getValue(Cursor3D) - Method in class inra.ijpb.data.image.ByteStackWrapper
 
getValue(int, int, int) - Method in class inra.ijpb.data.image.FloatStackWrapper
 
getValue(Cursor3D) - Method in class inra.ijpb.data.image.FloatStackWrapper
 
getValue(int, int, int) - Method in interface inra.ijpb.data.image.Image3D
Returns the value at the specified coordinates as a double.
getValue(Cursor3D) - Method in interface inra.ijpb.data.image.Image3D
Returns the value at the specified coordinates as a double.
getValue(int, int, int) - Method in class inra.ijpb.data.image.ShortStackWrapper
 
getValue(Cursor3D) - Method in class inra.ijpb.data.image.ShortStackWrapper
 
getValue() - Method in class inra.ijpb.data.PixelRecord
 
getValue() - Method in class inra.ijpb.data.VoxelRecord
 
getValue() - Method in class inra.ijpb.label.LabelValues.Position3DValuePair
Returns the value of the voxel.
getValue() - Method in class inra.ijpb.label.LabelValues.PositionValuePair
Returns the value of the pixel.
getValue() - Method in enum inra.ijpb.plugins.Connectivity2D
Returns the integer value associated to this connectivity.
getValue() - Method in enum inra.ijpb.plugins.Connectivity3D
Returns the integer value associated to this connectivity.
getVertex(int) - Method in class inra.ijpb.geometry.Polygon2D
Returns index at the specific index
getVolume() - Method in class inra.ijpb.measure.LabeledVoxelsMeasure
Get volume per labeled object based on the input image calibration
getVolumeSimilarity(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the total volume similarity between two label images (source and target).
getVolumeSimilarity(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the total volume similarity between two label images (source and target).
getVolumeSimilarity(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the total volume similarity between two label images (source and target).
getVolumeSimilarityPerLabel(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Get the volume similarity between two label images (source and target) per each individual labeled region.
getVolumeSimilarityPerLabel(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelImages
Get the volume similarity between two label images (source and target) per each individual labeled region.
getVolumeSimilarityPerLabel(ImagePlus, ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Get the volume similarity between two label images (source and target) per each individual labeled region.
getX() - Method in class inra.ijpb.data.Cursor2D
 
getX() - Method in class inra.ijpb.data.Cursor3D
 
getX() - Method in class inra.ijpb.geometry.Point3D
 
getX() - Method in class inra.ijpb.geometry.Vector2D
Returns the x coordinate of the vector.
getX() - Method in class inra.ijpb.geometry.Vector3D
Returns the x coordinate of the vector.
getX() - Method in class inra.ijpb.measure.Vector3d
Deprecated.
Returns the x coordinate of the vector.
getXMax() - Method in class inra.ijpb.geometry.Box2D
 
getXMax() - Method in class inra.ijpb.geometry.Box3D
 
getXMin() - Method in class inra.ijpb.geometry.Box2D
 
getXMin() - Method in class inra.ijpb.geometry.Box3D
 
getY() - Method in class inra.ijpb.data.Cursor2D
 
getY() - Method in class inra.ijpb.data.Cursor3D
 
getY() - Method in class inra.ijpb.geometry.Point3D
 
getY() - Method in class inra.ijpb.geometry.Vector2D
Returns the y coordinate of the vector.
getY() - Method in class inra.ijpb.geometry.Vector3D
Returns the y coordinate of the vector.
getY() - Method in class inra.ijpb.measure.Vector3d
Deprecated.
Returns the y coordinate of the vector.
getYMax() - Method in class inra.ijpb.geometry.Box2D
 
getYMax() - Method in class inra.ijpb.geometry.Box3D
 
getYMin() - Method in class inra.ijpb.geometry.Box2D
 
getYMin() - Method in class inra.ijpb.geometry.Box3D
 
getZ() - Method in class inra.ijpb.data.Cursor3D
 
getZ() - Method in class inra.ijpb.geometry.Point3D
 
getZ() - Method in class inra.ijpb.geometry.Vector3D
Returns the z coordinate of the vector.
getZ() - Method in class inra.ijpb.measure.Vector3d
Deprecated.
Returns the z coordinate of the vector.
getZMax() - Method in class inra.ijpb.geometry.Box3D
 
getZMin() - Method in class inra.ijpb.geometry.Box3D
 
Gradient - Class in inra.ijpb.morphology.filter
Performs morphological gradient, also known as "Beucher Gradient", on 2D/3D images.
Gradient(Strel3D) - Constructor for class inra.ijpb.morphology.filter.Gradient
Creates a new Morphological Gradient operator with the specified structuring element.
gradient(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological gradient of the input image.
gradient(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological gradient of the input image.
gradient(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological gradient of the input 3D image.
GrayscaleAreaOpeningPlugin - Class in inra.ijpb.plugins
Select binary particles in a planar image based on number of pixels.
GrayscaleAreaOpeningPlugin() - Constructor for class inra.ijpb.plugins.GrayscaleAreaOpeningPlugin
 
GrayscaleAttributeFiltering3D - Class in inra.ijpb.plugins
Plugin to perform between attribute opening, closing, and black or white top-hat on a 3D grayscale image.
GrayscaleAttributeFiltering3D() - Constructor for class inra.ijpb.plugins.GrayscaleAttributeFiltering3D
 
GrayscaleAttributeFilteringPlugin - Class in inra.ijpb.plugins
Select binary particles in a planar image based on number of pixels.
GrayscaleAttributeFilteringPlugin() - Constructor for class inra.ijpb.plugins.GrayscaleAttributeFilteringPlugin
 
GrayscaleBoxDiameterOpeningPlugin - Class in inra.ijpb.plugins
Select binary particles in a planar image based on number of pixels.
GrayscaleBoxDiameterOpeningPlugin() - Constructor for class inra.ijpb.plugins.GrayscaleBoxDiameterOpeningPlugin
 
GT - Static variable in interface inra.ijpb.label.select.RelationalOperator
Implementation of the "Greater Than" operator.

H

hashCode() - Method in class inra.ijpb.label.RegionAdjacencyGraph.LabelPair
 
hasSameRegions(Collection<Integer>) - Method in class inra.ijpb.label.conncomp.Boundary
 
height() - Method in class inra.ijpb.geometry.Box2D
Computes the height of the bounding box, corresponding to the extent along the Y dimension.
height() - Method in class inra.ijpb.geometry.Box3D
Computes the height of the bounding box, corresponding to the extent along the Y dimension.
hMax - Static variable in class inra.ijpb.plugins.Watershed3DPlugin
the maximum value for dynamic
hMin - Static variable in class inra.ijpb.plugins.Watershed3DPlugin
the minimum value for dynamic

I

IJUtils - Class in inra.ijpb.util
A collection of utility methods for interacting with ImageJ.
Image3D - Interface in inra.ijpb.data.image
Interface for accessing the values of a 3D stack.
ImageCalculator - Class in inra.ijpb.math
Provides some methods for combining two images, in a more comprehensive way than standard ImageJ, and providing the possibility of defining its own local operation.
ImageCalculator() - Constructor for class inra.ijpb.math.ImageCalculator
 
ImageCalculator.Operation - Interface in inra.ijpb.math
General interface for defining an operation that combines the values of two pixels to create a new one.
ImageJSkeleton - Class in inra.ijpb.binary.skeleton
Adaptation of the skeletonization code from ImageJ.
ImageJSkeleton() - Constructor for class inra.ijpb.binary.skeleton.ImageJSkeleton
Creates a new skeletonizer.
Images3D - Class in inra.ijpb.data.image
A collection of static methods for working on 3D images.
ImageShape - Class in inra.ijpb.shape
A collection of utility method for processing global shape of images: crop, add borders...
ImageUtils - Class in inra.ijpb.data.image
A collection of static utility methods for processing 2D or 3D images.
imposeMaxima(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Imposes the maxima given by marker image into the input image, using the default connectivity.
imposeMaxima(ImageProcessor, ImageProcessor, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Imposes the maxima given by marker image into the input image, using the specified connectivity.
imposeMaxima(ImageStack, ImageStack) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Imposes the maxima given by marker image into the input image, using the default connectivity.
imposeMaxima(ImageStack, ImageStack, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Imposes the maxima given by marker image into the input image, using the specified connectivity.
ImposeMinAndMax3DPlugin - Class in inra.ijpb.plugins
Plugin for imposing minima or maxima on a grayscale 3D image, using a specific connectivity.
ImposeMinAndMax3DPlugin() - Constructor for class inra.ijpb.plugins.ImposeMinAndMax3DPlugin
 
ImposeMinAndMax3DPlugin.Operation - Enum in inra.ijpb.plugins
A customized enumeration to choose between minima or maxima imposition.
ImposeMinAndMaxPlugin - Class in inra.ijpb.plugins
Plugin for imposing minima or maxima on a grayscale image, using a specific connectivity.
ImposeMinAndMaxPlugin() - Constructor for class inra.ijpb.plugins.ImposeMinAndMaxPlugin
 
ImposeMinAndMaxPlugin.Operation - Enum in inra.ijpb.plugins
A customized enumeration to choose between minima or maxima imposition.
imposeMinima(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Imposes the minima given by marker image into the input image, using the default connectivity.
imposeMinima(ImageProcessor, ImageProcessor, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Imposes the minima given by marker image into the input image, using the specified connectivity.
imposeMinima(ImageStack, ImageStack) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Imposes the minima given by marker image into the input image, using the default connectivity.
imposeMinima(ImageStack, ImageStack, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Imposes the minima given by marker image into the input image, using the specified connectivity.
inertiaEllipse(ImageProcessor) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
use inra.ijpb.measure.region2d.InertiaEllipse instead
InertiaEllipse - Class in inra.ijpb.measure.region2d
Deprecated.
Replaced by EquivalentEllipse (since 1.4.2)
InertiaEllipse() - Constructor for class inra.ijpb.measure.region2d.InertiaEllipse
Deprecated.
Default constructor
InertiaEllipsePlugin - Class in inra.ijpb.plugins
Deprecated.
replaced by EquivalentEllipsePlugin (since 1.4.2).
InertiaEllipsePlugin() - Constructor for class inra.ijpb.plugins.InertiaEllipsePlugin
Deprecated.
 
inertiaEllipses(ImageProcessor, int[], Calibration) - Static method in class inra.ijpb.measure.region2d.InertiaEllipse
Deprecated.
Computes inertia ellipse of each region in input label image.
inertiaEllipsoid(ImageStack) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
use InertiaEllipsoid instead
inertiaEllipsoid(ImageStack, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
use InertiaEllipsoid instead
inertiaEllipsoid(ImageStack, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
use InertiaEllipsoid instead
InertiaEllipsoid - Class in inra.ijpb.measure.region3d
Deprecated.
replaced by EquivalentEllipsoid (since 1.4.1)
InertiaEllipsoid() - Constructor for class inra.ijpb.measure.region3d.InertiaEllipsoid
Deprecated.
Default constructor
InertiaEllipsoid.InertiaMoments3D - Class in inra.ijpb.measure.region3d
Deprecated.
Inner class for storing result if moments computation.
InertiaEllipsoidPlugin - Class in inra.ijpb.plugins
Deprecated.
replaced by EquivalentEllipsoidPlugin (since 1.4.1)
InertiaEllipsoidPlugin() - Constructor for class inra.ijpb.plugins.InertiaEllipsoidPlugin
Deprecated.
 
inertiaEllipsoids(ImageStack, int[], Calibration) - Static method in class inra.ijpb.measure.region3d.InertiaEllipsoid
Deprecated.
Computes inertia ellipsoid of each region in the input 3D label image.
InertiaMoments3D() - Constructor for class inra.ijpb.measure.region3d.InertiaEllipsoid.InertiaMoments3D
Deprecated.
 
initialPoint - Variable in class inra.ijpb.measure.region2d.GeodesicDiameter.Result
The initial point used for propagating distances, corresponding the center of one of the minimum inscribed circles.
initialPoint - Variable in class inra.ijpb.measure.region3d.GeodesicDiameter3D.Result
The initial point used for propagating distances, corresponding the center of one of the minimum inscribed circles.
innerRadius - Variable in class inra.ijpb.measure.region2d.GeodesicDiameter.Result
The radius of the largest inner circle.
innerRadius - Variable in class inra.ijpb.measure.region3d.GeodesicDiameter3D.Result
The radius of the largest inner ball.
inPlaceDilation(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
inPlaceDilation(ImageProcessor) - Method in class inra.ijpb.morphology.strel.Cross3x3Strel
 
inPlaceDilation(ImageProcessor) - Method in class inra.ijpb.morphology.strel.DiskStrel
Performs in-place dilation with a disk structuring element by calling the ImageJ native RankFilters algorithm, using RankFilters.MAX option.
inPlaceDilation(ImageProcessor) - Method in interface inra.ijpb.morphology.strel.InPlaceStrel
Performs dilation of the image given as argument, and stores the result in the same image.
inPlaceDilation(ImageStack) - Method in interface inra.ijpb.morphology.strel.InPlaceStrel3D
Performs dilation of the stack given as argument, and stores the result in the same image.
inPlaceDilation(ImageStack) - Method in class inra.ijpb.morphology.strel.LinearDepthStrel3D
 
inPlaceDilation(ImageProcessor) - Method in class inra.ijpb.morphology.strel.LinearDiagDownStrel
 
inPlaceDilation(ImageProcessor) - Method in class inra.ijpb.morphology.strel.LinearDiagUpStrel
 
inPlaceDilation(ImageProcessor) - Method in class inra.ijpb.morphology.strel.LinearHorizontalStrel
 
inPlaceDilation(ImageProcessor) - Method in class inra.ijpb.morphology.strel.LinearVerticalStrel
 
inPlaceErosion(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
inPlaceErosion(ImageProcessor) - Method in class inra.ijpb.morphology.strel.Cross3x3Strel
 
inPlaceErosion(ImageProcessor) - Method in class inra.ijpb.morphology.strel.DiskStrel
Performs in-place erosion with a disk structuring element by calling the ImageJ native RankFilters algorithm, using RankFilters.MIN option.
inPlaceErosion(ImageProcessor) - Method in interface inra.ijpb.morphology.strel.InPlaceStrel
Performs erosion of the image given as argument, and stores the result in the same image.
inPlaceErosion(ImageStack) - Method in interface inra.ijpb.morphology.strel.InPlaceStrel3D
Performs erosion of the image given as argument, and stores the result in the same image.
inPlaceErosion(ImageStack) - Method in class inra.ijpb.morphology.strel.LinearDepthStrel3D
 
inPlaceErosion(ImageProcessor) - Method in class inra.ijpb.morphology.strel.LinearDiagDownStrel
 
inPlaceErosion(ImageProcessor) - Method in class inra.ijpb.morphology.strel.LinearDiagUpStrel
 
inPlaceErosion(ImageProcessor) - Method in class inra.ijpb.morphology.strel.LinearHorizontalStrel
 
inPlaceErosion(ImageProcessor) - Method in class inra.ijpb.morphology.strel.LinearVerticalStrel
 
InPlaceStrel - Interface in inra.ijpb.morphology.strel
A structuring element that can performs erosion or dilation directly in the original image buffer.
InPlaceStrel3D - Interface in inra.ijpb.morphology.strel
A structuring element that can performs erosion or dilation directly in the original image stack.
inra.ijpb.algo - package inra.ijpb.algo
Several classes for managing progress of algorithms.
inra.ijpb.binary - package inra.ijpb.binary
Operators taking binary images as input, such as connected component labeling or distance maps.
inra.ijpb.binary.conncomp - package inra.ijpb.binary.conncomp
Connected components labeling algorithms for binary 2D or 3D images.
inra.ijpb.binary.distmap - package inra.ijpb.binary.distmap
Computations of distance maps on binary images, using chamfer distances (integer approximation of Euclidean distances).
inra.ijpb.binary.geodesic - package inra.ijpb.binary.geodesic
Algorithms for computing geodesic distances, geodesic diameters, tortuosity...
inra.ijpb.binary.skeleton - package inra.ijpb.binary.skeleton
Extraction of skeleton from binary images.
inra.ijpb.color - package inra.ijpb.color
Utilities for color images.
inra.ijpb.data - package inra.ijpb.data
Some utility classes for accessing image data.
inra.ijpb.data.border - package inra.ijpb.data.border
Management of pixels outside image bounds.
inra.ijpb.data.image - package inra.ijpb.data.image
Some classes to access image data in a unified and hopefully efficient way.
inra.ijpb.geometry - package inra.ijpb.geometry
Utility functions for geometric computing applied to image analysis.
inra.ijpb.label - package inra.ijpb.label
Utility methods for label images (stored as 8-, 16- or 32-bits).
inra.ijpb.label.conncomp - package inra.ijpb.label.conncomp
Connected component labeling of a specific region within a label image.
inra.ijpb.label.distmap - package inra.ijpb.label.distmap
Computation of distance maps for label images.
inra.ijpb.label.edit - package inra.ijpb.label.edit
Processing classes for edition of label images.
inra.ijpb.label.filter - package inra.ijpb.label.filter
Implementation of morphological filters for label images.
inra.ijpb.label.select - package inra.ijpb.label.select
Selection of regions from label images based on size criterion.
inra.ijpb.math - package inra.ijpb.math
Some math operators for images that do not need calling ImageJ plugins.
inra.ijpb.measure - package inra.ijpb.measure
Quantitative measurements on 2D and 3D images.
inra.ijpb.measure.region2d - package inra.ijpb.measure.region2d
Quantitative measurements on 2D label / binary images of regions.
inra.ijpb.measure.region3d - package inra.ijpb.measure.region3d
Quantitative measurements on 3D label / binary images of regions.
inra.ijpb.morphology - package inra.ijpb.morphology
Mathematical Morphology filters and reconstructions.
inra.ijpb.morphology.attrfilt - package inra.ijpb.morphology.attrfilt
Attribute opening and filtering for grayscale images.
inra.ijpb.morphology.directional - package inra.ijpb.morphology.directional
Morphological directional filters.
inra.ijpb.morphology.extrema - package inra.ijpb.morphology.extrema
Algorithms for computing regional minima and maxima.
inra.ijpb.morphology.filter - package inra.ijpb.morphology.filter
Morphological filtering operators implemented as classes.
inra.ijpb.morphology.geodrec - package inra.ijpb.morphology.geodrec
Geodesic reconstruction by erosion and dilation.
inra.ijpb.morphology.strel - package inra.ijpb.morphology.strel
A collection of Structuring Element ("Strel") implementations for mathematical morphology.
inra.ijpb.plugins - package inra.ijpb.plugins
Contains plugins, for integration with ImageJ GUI.
inra.ijpb.segment - package inra.ijpb.segment
Aims at gathering various segmentation algorithms.
inra.ijpb.shape - package inra.ijpb.shape
Operators for changing the "shape" of images: crop, padd, rotate...
inra.ijpb.util - package inra.ijpb.util
Various utility classes (mainly gui utils...).
inra.ijpb.watershed - package inra.ijpb.watershed
Image segmentation using a marker-controlled watershed transform.
IntensityMeasures - Class in inra.ijpb.measure
Class to facilitate the calculation of intensity measures by grouping together voxels belonging to the same label.
IntensityMeasures(ImagePlus, ImagePlus) - Constructor for class inra.ijpb.measure.IntensityMeasures
Initialize the measurements by reading the input (grayscale) image and its corresponding labels.
IntensityMeasures3D - Class in inra.ijpb.plugins
This class implements a set of photometric (intensity) measurements over an input grayscale image (2D or 3D) and its set of corresponding labels.
IntensityMeasures3D() - Constructor for class inra.ijpb.plugins.IntensityMeasures3D
 
InteractiveGeodesicDistanceMap - Class in inra.ijpb.plugins
Plugin for computing geodesic distance map from binary images using chamfer weights.
InteractiveGeodesicDistanceMap() - Constructor for class inra.ijpb.plugins.InteractiveGeodesicDistanceMap
 
InteractiveMarkerControlledWatershed - Class in inra.ijpb.plugins
Plugin to perform automatic segmentation of 2D and 3D images using marker-controlled watershed with manually selected seeds.
InteractiveMarkerControlledWatershed() - Constructor for class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
 
InteractiveMarkerControlledWatershed.ResultMode - Enum in inra.ijpb.plugins
enumeration of result modes
InteractiveMorphologicalReconstruction - Class in inra.ijpb.plugins
Plugin for performing interactive morphological reconstruction by dilation or by erosion on grayscale images.
InteractiveMorphologicalReconstruction() - Constructor for class inra.ijpb.plugins.InteractiveMorphologicalReconstruction
 
InteractiveMorphologicalReconstruction3D - Class in inra.ijpb.plugins
Plugin for performing interactive geodesic reconstruction by dilation erosion on grayscale images.
InteractiveMorphologicalReconstruction3D() - Constructor for class inra.ijpb.plugins.InteractiveMorphologicalReconstruction3D
 
interfaceSurfaceArea(ImageStack, int, int, Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
Measures the surface area of the interface between two regions in a 3D label image.
InterfaceSurfaceArea - Class in inra.ijpb.measure.region3d
Computes the surface area of the interface between two labels.
InterfaceSurfaceArea() - Constructor for class inra.ijpb.measure.region3d.InterfaceSurfaceArea
Default empty constructor.
InterfaceSurfaceArea(int) - Constructor for class inra.ijpb.measure.region3d.InterfaceSurfaceArea
Constructor that specifies the number of directions to use.
InterfaceSurfaceArea3D - Class in inra.ijpb.plugins
Plugin for measuring the surface area of the interface between two labels within a 3D label image.
InterfaceSurfaceArea3D() - Constructor for class inra.ijpb.plugins.InterfaceSurfaceArea3D
 
InternalGradient - Class in inra.ijpb.morphology.filter
Computes the morphological internal gradient of the input image.
InternalGradient(Strel3D) - Constructor for class inra.ijpb.morphology.filter.InternalGradient
Creates a new Internal Gradient operator with the specified structuring element.
internalGradient(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological internal gradient of the input image.
internalGradient(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological internal gradient of the input image.
internalGradient(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological internal gradient of the 3D input image.
interpolateLut(byte[][], int) - Static method in class inra.ijpb.color.ColorMaps
Interpolates between LUT values such that the result array has the specified number of colors.
IntrinsicVolumes2D - Class in inra.ijpb.measure
Computation of intrinsic volumes(area, perimeter, Euler number) in planar binary or label images.
IntrinsicVolumes2DUtils - Class in inra.ijpb.measure.region2d
Utility functions for classes that compute 2D intrinsic volumes measures.
IntrinsicVolumes3D - Class in inra.ijpb.measure
Collection of static classes for the computation of intrinsic volumes (volume, surface area, mean breadth and Euler number) for binary or label 3D images.
IntrinsicVolumes3DUtils - Class in inra.ijpb.measure.region3d
Utility functions for classes that compute 3D intrinsic volumes measures.
IntrinsicVolumesAnalyzer2D - Class in inra.ijpb.measure.region2d
Computation of intrinsic volumes (area, perimeter and Euler number) for binary or label 2D images.
IntrinsicVolumesAnalyzer2D() - Constructor for class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
Default empty constructor.
IntrinsicVolumesAnalyzer2D.Result - Class in inra.ijpb.measure.region2d
Inner class for storing results.
IntrinsicVolumesAnalyzer3D - Class in inra.ijpb.measure.region3d
Computation of intrinsic volumes (Volume, Surface Area, Mean Breadth and Euler Number) for 3D binary or label images, based on the RegionAnalyzer3D interface.
IntrinsicVolumesAnalyzer3D() - Constructor for class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
Default empty constructor.
IntrinsicVolumesAnalyzer3D.Result - Class in inra.ijpb.measure.region3d
Inner class for storing results.
invert(ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Inverts the values of a 3D image
invert() - Method in class inra.ijpb.geometry.Polygon2D
Computes the complementary polygon, whose interior is the exterior of this polygon.
isBinaryImage(ImagePlus) - Static method in class inra.ijpb.binary.BinaryImages
Check if input image is binary (8-bit with only 0 or 255 values)
isBinaryImage(ImageProcessor) - Static method in class inra.ijpb.binary.BinaryImages
Check if input image is binary (8-bit with only 0 or 255 values)
isColorImage(ImagePlus) - Static method in class inra.ijpb.data.image.ImageUtils
Checks if the specified image is a color image.
isLabelImageType(ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Checks if the input image may be a label image, and returns false if the type is not valid for label images.
isProgressVisible() - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
Returns the value of progress visibility option.
isProgressVisible() - Method in class inra.ijpb.morphology.extrema.RegionalExtremaAlgo
Returns the value of progress visibility option.
isSameSize(ImageStack, ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Deprecated.
replaced by ImageUtils.isSameSize(...)
isSameSize(ImagePlus, ImagePlus) - Static method in class inra.ijpb.data.image.ImageUtils
Checks if the two input images have the same dimensionality and the same size in each direction.
isSameSize(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.data.image.ImageUtils
Checks if the two input images have the same size in each direction.
isSameSize(ImageStack, ImageStack) - Static method in class inra.ijpb.data.image.ImageUtils
Checks if the two input 3D images have the same size in each direction.
isSameType(ImageStack, ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Deprecated.
replaced by ImageUtils.isSameType(...)
isSameType(ImagePlus, ImagePlus) - Static method in class inra.ijpb.data.image.ImageUtils
Checks if the two input images have the same data type.
isSameType(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.data.image.ImageUtils
Checks if the two input images have the same data type.
isSameType(ImageStack, ImageStack) - Static method in class inra.ijpb.data.image.ImageUtils
Checks if the two input 3D images have the same data type.
iterator() - Method in class inra.ijpb.geometry.Polygon2D
 

K

keepLabels(ImagePlus, int[]) - Static method in class inra.ijpb.label.LabelImages
Creates a new image containing only the specified labels.
keepLabels(ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelImages
Creates a new image containing only the specified labels.
keepLabels(ImageStack, int[]) - Static method in class inra.ijpb.label.LabelImages
Creates a new image containing only the specified labels.
keepLargestLabel(ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Returns a binary image that contains only the largest label.
keepLargestLabel(ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Returns a binary image that contains only the largest label.
keepLargestLabel(ImageStack) - Static method in class inra.ijpb.label.LabelImages
Returns a binary image that contains only the largest label.
KeepLargestLabelPlugin - Class in inra.ijpb.plugins
Removes all the labels in a 2D/3D image but the largest one.
KeepLargestLabelPlugin() - Constructor for class inra.ijpb.plugins.KeepLargestLabelPlugin
 
keepLargestRegion(ImagePlus) - Static method in class inra.ijpb.binary.BinaryImages
Returns a binary image that contains only the largest region.
keepLargestRegion(ImageProcessor) - Static method in class inra.ijpb.binary.BinaryImages
Returns a binary image that contains only the largest region.
keepLargestRegion(ImageStack) - Static method in class inra.ijpb.binary.BinaryImages
Returns a binary image that contains only the largest label.
KeepLargestRegionPlugin - Class in inra.ijpb.plugins
Removes all the regions in a binary 2D or 3D image but the largest one.
KeepLargestRegionPlugin() - Constructor for class inra.ijpb.plugins.KeepLargestRegionPlugin
 
killBorders(ImageStack) - Static method in class inra.ijpb.morphology.GeodesicReconstruction3D
Deprecated.
Removes the border of the input image, by performing a geodesic reconstruction initialized with image boundary.
killBorders(ImageProcessor) - Static method in class inra.ijpb.morphology.Reconstruction
Removes the border of the input image, by performing a morphological reconstruction initialized with image boundary.
killBorders(ImageStack) - Static method in class inra.ijpb.morphology.Reconstruction3D
Removes the border of the input image, by performing a morphological reconstruction initialized with image boundary.
KillBordersPlugin - Class in inra.ijpb.plugins
Plugin for removing borders in 8-bits grayscale or binary 2D or 3D image.
KillBordersPlugin() - Constructor for class inra.ijpb.plugins.KillBordersPlugin
 

L

label1 - Variable in class inra.ijpb.label.RegionAdjacencyGraph.LabelPair
The first label.
label2 - Variable in class inra.ijpb.label.RegionAdjacencyGraph.LabelPair
The second label.
LabelAreaOpeningPlugin - Class in inra.ijpb.plugins
 
LabelAreaOpeningPlugin() - Constructor for class inra.ijpb.plugins.LabelAreaOpeningPlugin
 
labelBoundaries(ImageStack) - Static method in class inra.ijpb.label.LabelImages
Creates a binary 3D image that contains 255 for voxels that are boundaries between two labels.
labelBoundaries(ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Creates a binary 2D image that contains 255 for pixels that are boundaries between two labels.
LabelBoundariesLabeling2D - Class in inra.ijpb.label.conncomp
Computes a label map of the boundaries between regions from a label map.
LabelBoundariesLabeling2D() - Constructor for class inra.ijpb.label.conncomp.LabelBoundariesLabeling2D
 
LabelBoundariesLabeling2D.Result - Class in inra.ijpb.label.conncomp
Provides the result of a boundary labeling.
LabelBoundariesLabeling3D - Class in inra.ijpb.label.conncomp
Computes a label map of the boundaries between regions from a label map.
LabelBoundariesLabeling3D() - Constructor for class inra.ijpb.label.conncomp.LabelBoundariesLabeling3D
 
LabelBoundariesLabeling3D.Result - Class in inra.ijpb.label.conncomp
Provides the result of a boundary labeling.
LabelBoundariesPlugin - Class in inra.ijpb.plugins
 
LabelBoundariesPlugin() - Constructor for class inra.ijpb.plugins.LabelBoundariesPlugin
 
LabelDilation2DShort - Class in inra.ijpb.label.distmap
Deprecated.
replaced by inra.ijpb.label.filter.ChamferLabelDilation2DShort
LabelDilation2DShort(ChamferMask2D) - Constructor for class inra.ijpb.label.distmap.LabelDilation2DShort
Deprecated.
Creates a new image processor for dilating labels using the specified chamfer mask, using 16-bits integer computation.
LabelDilation3D4WShort - Class in inra.ijpb.label.distmap
Deprecated.
replaced by LabelDilation3DShort (since 1.4.4)
LabelDilation3D4WShort(ChamferWeights3D) - Constructor for class inra.ijpb.label.distmap.LabelDilation3D4WShort
Deprecated.
Creates a new image processor for dilating labels using chamfer weight stored using shorts.
LabelDilation3D4WShort(short[]) - Constructor for class inra.ijpb.label.distmap.LabelDilation3D4WShort
Deprecated.
Creates a new image processor for dilating labels using chamfer weight stored using shorts.
LabelDilation3DShort - Class in inra.ijpb.label.distmap
Deprecated.
replaced by inra.ijpb.label.filter.ChamferLabelDilation3DShort
LabelDilation3DShort(ChamferMask3D) - Constructor for class inra.ijpb.label.distmap.LabelDilation3DShort
Deprecated.
Creates a new 3D image for dilating labels using the specified chamfer mask, using 16-bits integer computation.
LabelDilationShort5x5 - Class in inra.ijpb.label.distmap
Deprecated.
replaced by LabelDilation2DShort (since 1.5.0)
LabelDilationShort5x5(ChamferWeights) - Constructor for class inra.ijpb.label.distmap.LabelDilationShort5x5
Deprecated.
Creates a new LabelDilation operator.
LabelDilationShort5x5(short[]) - Constructor for class inra.ijpb.label.distmap.LabelDilationShort5x5
Deprecated.
Creates a new LabelDilation operator.
LabelEdition - Class in inra.ijpb.plugins
Plugin for the manual edition of label images (2D and 3D).
LabelEdition() - Constructor for class inra.ijpb.plugins.LabelEdition
 
LabeledVoxelsMeasure - Class in inra.ijpb.measure
Mother class to extract measures from pairs of grayscale and labeled images.
LabeledVoxelsMeasure(ImagePlus, ImagePlus) - Constructor for class inra.ijpb.measure.LabeledVoxelsMeasure
Initialize the measurements by reading the input (grayscale) image and its corresponding labels.
LabelImages - Class in inra.ijpb.label
Utility methods for label images (stored as 8-, 16- or 32-bits).
LabelImages() - Constructor for class inra.ijpb.label.LabelImages
Private constructor to prevent class instantiation.
LabelImages - Class in inra.ijpb.morphology
Deprecated.
as from 2014.11.03, replaced by class inra.ijpb.label.LabelImages
LabelingPlugin - Class in inra.ijpb.plugins
Computes label image of connected components in a binary planar image or 3D stack.
LabelingPlugin() - Constructor for class inra.ijpb.plugins.LabelingPlugin
 
labelMap - Variable in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling.Result
The image processor containing labels of connected components, or 0 for background.
labelMap - Variable in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling3D.Result
The image stack containing labels of connected components, or 0 for background.
LabelMapMorphologicalFilteringPlugin - Class in inra.ijpb.plugins
Applies morphological filtering on a label image.
LabelMapMorphologicalFilteringPlugin() - Constructor for class inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin
 
LabelMapMorphologicalFilteringPlugin.Operation - Enum in inra.ijpb.plugins
A pre-defined set of basis morphological operations, that can be easily used with a GenericDialog.
labelMapOverlay(ImagePlus, ImagePlus, double) - Static method in class inra.ijpb.data.image.ColorImages
Applies an overlay of a label map onto a 2D/3D grayscale image, using the specified opacity.
labelMapOverlay(ImageProcessor, ImageProcessor, double) - Static method in class inra.ijpb.data.image.ColorImages
Applies an overlay of a label map onto a grayscale image, using the specified opacity.
labelMapOverlay(ImageStack, ImageStack, double) - Static method in class inra.ijpb.data.image.ColorImages
Applies an overlay of a label map onto a 3D grayscale image, using the specified opacity.
LabelOverlapMeasures - Class in inra.ijpb.plugins
This class implements a plugin to calculate overlap measurements over an source and a target label image (2D or 3D).
LabelOverlapMeasures() - Constructor for class inra.ijpb.plugins.LabelOverlapMeasures
 
LabelPair(int, int) - Constructor for class inra.ijpb.label.RegionAdjacencyGraph.LabelPair
Creates a new Label Pair.
LabelSizeFiltering - Class in inra.ijpb.label.select
Filter labels using a size criterion.
LabelSizeFiltering(RelationalOperator, int) - Constructor for class inra.ijpb.label.select.LabelSizeFiltering
Default constructor, specifying the operator and the size limit.
LabelSizeFilteringPlugin - Class in inra.ijpb.plugins
Filter labels within a label image using a size criterion.
LabelSizeFilteringPlugin() - Constructor for class inra.ijpb.plugins.LabelSizeFilteringPlugin
 
LabelSizeFilteringPlugin.Operation - Enum in inra.ijpb.plugins
A pre-defined set of Labels for populating plugin.
labelToRgb(ImagePlus, byte[][], Color) - Static method in class inra.ijpb.label.LabelImages
Creates a new Color image from a label image, a LUT, and a color for background.
labelToRgb(ImageProcessor, byte[][], Color) - Static method in class inra.ijpb.label.LabelImages
Creates a new Color image from a label planar image, a LUT, and a color for background.
labelToRgb(ImageStack, byte[][], Color) - Static method in class inra.ijpb.label.LabelImages
Creates a new Color image stack from a label image stack, a LUT, and a color for background.
LabelToRgbPlugin - Class in inra.ijpb.plugins
Creates a new Color Image that associate a given color to each label of the input image.
LabelToRgbPlugin() - Constructor for class inra.ijpb.plugins.LabelToRgbPlugin
 
LabelToValuePlugin - Class in inra.ijpb.plugins
Combines a label image and the values within a column of a results table to create a new image with intensity corresponding to the vales in the table column.
LabelToValuePlugin() - Constructor for class inra.ijpb.plugins.LabelToValuePlugin
 
LabelUtils - Class in inra.ijpb.label
A collection of utility methods for working with label images.
LabelValues - Class in inra.ijpb.label
Utility methods for combining label images and intensity images.
LabelValues.Position3DValuePair - Class in inra.ijpb.label
Inner class for storing a value associated to a 3D position.
LabelValues.PositionValuePair - Class in inra.ijpb.label
Inner class for storing a value associated to a 2D position.
Laplacian - Class in inra.ijpb.morphology.filter
Computes the morphological Laplacian of the input image.
Laplacian(Strel3D) - Constructor for class inra.ijpb.morphology.filter.Laplacian
Creates a new Morphological Laplacian operator with the specified structuring element.
laplacian(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological Laplacian of the 3D input image.
laplacian(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological Laplacian of the input image.
laplacian(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Computes the morphological Laplacian of the 3D input image.
LargestInscribedBall - Class in inra.ijpb.measure.region3d
Computes the largest inscribed ball for each region of a label or binary image.
LargestInscribedBall() - Constructor for class inra.ijpb.measure.region3d.LargestInscribedBall
Empty constructor.
largestInscribedBalls(ImageStack, int[], Calibration) - Static method in class inra.ijpb.measure.region3d.LargestInscribedBall
Computes largest inscribed ball of each region with a 3D label image.
LargestInscribedCircle - Class in inra.ijpb.measure.region2d
Computes the largest inscribed circle for each region of a label or binary image.
LargestInscribedCircle() - Constructor for class inra.ijpb.measure.region2d.LargestInscribedCircle
Default empty constructor.
largestInscribedCircles(ImageProcessor, int[], Calibration) - Static method in class inra.ijpb.measure.region2d.LargestInscribedCircle
Computes largest inscribed disk of each region within a label image.
largestPossibleLabel(int) - Static method in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling
Returns the largest possible label that can be obtained given the specified bit-depth.
LE - Static variable in interface inra.ijpb.label.select.RelationalOperator
Implementation of the "Lower Than Or Equal" operator.
LEFT - Static variable in class inra.ijpb.morphology.strel.ShiftedCross3x3Strel
A cross-shaped structuring element located on the left of the reference pixel.
length() - Method in class inra.ijpb.geometry.OrientedBox2D
 
LinearDepthStrel3D - Class in inra.ijpb.morphology.strel
An horizontal linear structuring element of a given length.
LinearDepthStrel3D(int) - Constructor for class inra.ijpb.morphology.strel.LinearDepthStrel3D
Creates a new horizontal linear structuring element of a given size.
LinearDepthStrel3D(int, int) - Constructor for class inra.ijpb.morphology.strel.LinearDepthStrel3D
Creates a new horizontal linear structuring element of a given size and with a given offset.
LinearDiagDownStrel - Class in inra.ijpb.morphology.strel
A diagonal linear structuring element of a given length, with direction vector (+1,+1) in image coordinate system.
LinearDiagDownStrel(int) - Constructor for class inra.ijpb.morphology.strel.LinearDiagDownStrel
Creates a new diagonal linear structuring element of a given size.
LinearDiagDownStrel(int, int) - Constructor for class inra.ijpb.morphology.strel.LinearDiagDownStrel
Creates a new diagonal linear structuring element of a given size and with a given offset.
LinearDiagUpStrel - Class in inra.ijpb.morphology.strel
A diagonal linear structuring element of a given length, with direction vector (+1,-1) in image coordinate system.
LinearDiagUpStrel(int) - Constructor for class inra.ijpb.morphology.strel.LinearDiagUpStrel
Creates a new diagonal linear structuring element of a given size.
LinearDiagUpStrel(int, int) - Constructor for class inra.ijpb.morphology.strel.LinearDiagUpStrel
Creates a new diagonal linear structuring element of a given size and with a given offset.
LinearHorizontalStrel - Class in inra.ijpb.morphology.strel
An horizontal linear structuring element of a given length.
LinearHorizontalStrel(int) - Constructor for class inra.ijpb.morphology.strel.LinearHorizontalStrel
Creates a new horizontal linear structuring element of a given size.
LinearHorizontalStrel(int, int) - Constructor for class inra.ijpb.morphology.strel.LinearHorizontalStrel
Creates a new horizontal linear structuring element of a given size and with a given offset.
LinearVerticalStrel - Class in inra.ijpb.morphology.strel
A vertical linear structuring element of a given length.
LinearVerticalStrel(int) - Constructor for class inra.ijpb.morphology.strel.LinearVerticalStrel
Creates a new vertical linear structuring element of a given size.
LinearVerticalStrel(int, int) - Constructor for class inra.ijpb.morphology.strel.LinearVerticalStrel
Creates a new vertical linear structuring element of a given size and with a given offset.
LocalBufferedHistogram - Class in inra.ijpb.morphology.strel
Local histogram in a linear neighborhood of a pixel.
LocalBufferedHistogram(int) - Constructor for class inra.ijpb.morphology.strel.LocalBufferedHistogram
Main constructor.
LocalBufferedHistogram(int, int) - Constructor for class inra.ijpb.morphology.strel.LocalBufferedHistogram
Initializes an histogram filled with the given value.
LocalExtremum - Interface in inra.ijpb.morphology.strel
Computes the extremum in a local sliding neighborhood of the current pixel.
LocalExtremum.Type - Enum in inra.ijpb.morphology.strel
An enumeration of the types of possible extremum.
LocalExtremumBufferDouble - Class in inra.ijpb.morphology.strel
Computes the maximum in a local buffer around current point.
LocalExtremumBufferDouble(int) - Constructor for class inra.ijpb.morphology.strel.LocalExtremumBufferDouble
Main constructor.
LocalExtremumBufferDouble(int, LocalExtremum.Type) - Constructor for class inra.ijpb.morphology.strel.LocalExtremumBufferDouble
Constructor from size and type of extremum (minimum or maximum).
LocalExtremumBufferDouble(int, double) - Constructor for class inra.ijpb.morphology.strel.LocalExtremumBufferDouble
Initializes an histogram filled with the given value.
LocalExtremumBufferGray8 - Class in inra.ijpb.morphology.strel
Computes the maximum in a local buffer around current point.
LocalExtremumBufferGray8(int) - Constructor for class inra.ijpb.morphology.strel.LocalExtremumBufferGray8
Main constructor.
LocalExtremumBufferGray8(int, LocalExtremum.Type) - Constructor for class inra.ijpb.morphology.strel.LocalExtremumBufferGray8
Constructor from size and type of extremum (minimum or maximum).
LocalExtremumBufferGray8(int, int) - Constructor for class inra.ijpb.morphology.strel.LocalExtremumBufferGray8
Initializes an histogram filled with the given value.
longestGeodesicPaths() - Method in class inra.ijpb.binary.geodesic.GeodesicDiameterFloat
Deprecated.
Computes the geodesic path of each particle within the given label image.
longestGeodesicPaths() - Method in class inra.ijpb.binary.geodesic.GeodesicDiameterShort
Deprecated.
Computes the geodesic path of each particle within the given label image.
LT - Static variable in interface inra.ijpb.label.select.RelationalOperator
Implementation of the "Lower Than" operator.

M

mapChannels(ImageProcessor) - Static method in class inra.ijpb.data.image.ColorImages
Splits the channels of the color image and returns the new ByteImages into a Map, using channel names as key.
mapChannels(ImageStack) - Static method in class inra.ijpb.data.image.ColorImages
Splits the channels of the 3D color image into three new instances of ImageStack containing ByteProcessors.
mapLabelIndices(int[]) - Static method in class inra.ijpb.label.LabelImages
Creates an associative array to retrieve the index corresponding to each label.
MarkerControlledWatershed3DPlugin - Class in inra.ijpb.plugins
A plugin to perform marker-controlled watershed on a 2D or 3D image.
MarkerControlledWatershed3DPlugin() - Constructor for class inra.ijpb.plugins.MarkerControlledWatershed3DPlugin
 
MarkerControlledWatershedTransform2D - Class in inra.ijpb.watershed
Marker-controlled version of the watershed transform in 2D.
MarkerControlledWatershedTransform2D(ImageProcessor, ImageProcessor, ImageProcessor) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Initialize a marker-controlled watershed transform
MarkerControlledWatershedTransform2D(ImageProcessor, ImageProcessor, ImageProcessor, int) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Initialize a marker-controlled watershed transform
MarkerControlledWatershedTransform2D(ImageProcessor, ImageProcessor, ImageProcessor, double) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Initialize a marker-controlled watershed transform.
MarkerControlledWatershedTransform2D(ImageProcessor, ImageProcessor, ImageProcessor, int, double) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
Initialize a marker-controlled watershed transform.
MarkerControlledWatershedTransform3D - Class in inra.ijpb.watershed
Marker-controlled version of the watershed transform (works for 2D and 3D images).
MarkerControlledWatershedTransform3D(ImagePlus, ImagePlus, ImagePlus) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
Initialize a marker-controlled watershed transform
MarkerControlledWatershedTransform3D(ImagePlus, ImagePlus, ImagePlus, int) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
Initialize a marker-controlled watershed transform
MarkerControlledWatershedTransform3D(ImagePlus, ImagePlus, ImagePlus, int, double) - Constructor for class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
Initialize a marker-controlled watershed transform
mask() - Method in interface inra.ijpb.binary.distmap.ChamferDistanceTransform2D
Return the chamfer mask used by this distance transform algorithm.
mask() - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform2DFloat
 
mask() - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform2DShort
 
mask() - Method in interface inra.ijpb.binary.distmap.ChamferDistanceTransform3D
 
mask() - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform3DFloat
 
mask() - Method in class inra.ijpb.binary.distmap.ChamferDistanceTransform3DShort
 
mask() - Method in interface inra.ijpb.label.distmap.ChamferDistanceTransform2D
Return the chamfer mask used by this distance transform algorithm.
mask() - Method in class inra.ijpb.label.distmap.ChamferDistanceTransform2DFloat
 
mask() - Method in class inra.ijpb.label.distmap.ChamferDistanceTransform2DShort
 
mask() - Method in interface inra.ijpb.label.distmap.ChamferDistanceTransform3D
 
MAX - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
Max operator, that computes the maximum of the values from the two images
MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat
The value used to initialize the distance map, corresponding to positive infinity.
MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloat5x5
Deprecated.
The value used to initialize the distance map, corresponding to positive infinity.
MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformFloatHybrid
The value used to initialize the distance map, corresponding to positive infinity.
MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort
The value used to initialize the distance map.
MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort5x5
Deprecated.
The value used to initialize the distance map.
MAX_DIST - Static variable in class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShortHybrid
The value used to initialize the distance map.
maxFeretDiameter(ArrayList<? extends Point2D>) - Static method in class inra.ijpb.geometry.FeretDiameters
Computes Maximum Feret diameter of a set of points.
MaxFeretDiameter - Class in inra.ijpb.measure.region2d
Computes maximum Feret Diameter for each region of a binary or label image.
MaxFeretDiameter() - Constructor for class inra.ijpb.measure.region2d.MaxFeretDiameter
Default constructor
maxFeretDiameter(ArrayList<? extends Point3D>) - Static method in class inra.ijpb.measure.region3d.MaxFeretDiameter3D
Computes Maximum Feret diameter of a set of points.
maxFeretDiameter - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing maximum Feret diameter.
MaxFeretDiameter3D - Class in inra.ijpb.measure.region3d
Computes maximum Feret Diameter for each region of a 3D binary or label image.
MaxFeretDiameter3D() - Constructor for class inra.ijpb.measure.region3d.MaxFeretDiameter3D
Default constructor
MaxFeretDiameterPlugin - Class in inra.ijpb.plugins
Computes Maximum Feret Diameters of a binary or label image.
MaxFeretDiameterPlugin() - Constructor for class inra.ijpb.plugins.MaxFeretDiameterPlugin
 
maxFeretDiameters(ImageProcessor, int[], Calibration) - Static method in class inra.ijpb.measure.region2d.MaxFeretDiameter
Computes Feret diameters as a PointPair2D for each of the specified regions within a label map.
maxFeretDiameters(ImageStack, int[], Calibration) - Static method in class inra.ijpb.measure.region3d.MaxFeretDiameter3D
Computes Feret diameters as a PointPair3D for each of the specified regions within a label map.
maximumInscribedCircle(ImageProcessor) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
use class inra.ijpb.measure.region2d.largestInscribedCircle instead
maximumInscribedCircle(ImageProcessor, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
use class inra.ijpb.measure.region2d.largestInscribedCircle instead
maximumInscribedSphere(ImageStack, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
use LargestInscribedBall instead
maximumInscribedSphere(ImageStack, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
Radius of maximum inscribed sphere of each particle within a label image.
MaxInscribedCirclePlugin - Class in inra.ijpb.plugins
Plugin for max inscribed circle of regions from label images.
MaxInscribedCirclePlugin() - Constructor for class inra.ijpb.plugins.MaxInscribedCirclePlugin
 
maxInscribedDisc - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing largest inscribed disc.
MaxInscribedSpherePlugin - Class in inra.ijpb.plugins
Plugin for computing largest inscribed balls within 3D regions.
MaxInscribedSpherePlugin() - Constructor for class inra.ijpb.plugins.MaxInscribedSpherePlugin
 
maxValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelValues
Find maximum value in intensity image for each label.
maxValues(ImageStack, ImageStack, int[]) - Static method in class inra.ijpb.label.LabelValues
Find maximum value in intensity image for each label.
maxValueWithinLabels(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.label.LabelValues
Computes the largest value within the valueImage, using the strictly positive values in labelImage as mask.
maxValueWithinLabels(ImageStack, ImageStack) - Static method in class inra.ijpb.label.LabelValues
Computes the largest value within the valueImage, using the strictly positive values in labelImage as mask.
MEAN - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
Mean operator, that computes the average of the values from the two images
mean(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.directional.DirectionalFilter
Computes the average value among the neighbors.
meanBreadth(ImageStack, Calibration, int, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
Measures the mean breadth of a single region within a 3D binary image.
meanBreadth - Variable in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.Result
The mean breadth of the region (proportional to the integral of average curvature)
meanBreadthDensity(ImageStack, Calibration, int, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
Measures the mean breadth density of a single region within a 3D binary image.
meanBreadthLut(Calibration, int, int) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumes3DUtils
Computes the Look-up table used to measure mean breadth within 3D images.
meanBreadthLut(Calibration, int, int) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
Deprecated.
meanBreadths(ImageStack, int[], Calibration, int, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
Measures the mean breadth of each region within a label image.
meanDist - Variable in class inra.ijpb.measure.region2d.AverageThickness.Result
Average distance computed along the skeleton
median(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.directional.DirectionalFilter
Computes the median value among the neighbors.
MERGE_LABELS - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
name of the macro method to merge selected labels
MERGE_LABELS - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
name of the macro method to merge selected labels
mergeChannels(Collection<ImageProcessor>) - Static method in class inra.ijpb.data.image.ColorImages
Creates a new ColorProcessor from a collection of three channels.
mergeChannels(ImageProcessor, ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.data.image.ColorImages
Creates a new ColorProcessor from the red, green and blue channels.
mergeChannels(ImageStack, ImageStack, ImageStack) - Static method in class inra.ijpb.data.image.ColorImages
Creates a new color ImageStack from the red, green and blue ImageStack instances.
mergeLabels(ImagePlus, Roi, boolean) - Static method in class inra.ijpb.label.LabelImages
Merge labels selected by freehand or point tool.
mergeLabels() - Static method in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
Merge labels that are selected either by a freehand or a point ROI.
mergeLabels() - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
Merge labels that are selected either by a freehand or a point ROI.
MergeLabelsPlugin - Class in inra.ijpb.plugins
 
MergeLabelsPlugin() - Constructor for class inra.ijpb.plugins.MergeLabelsPlugin
 
mergeLabelsWithGap(ImagePlus, Roi, int, boolean) - Static method in class inra.ijpb.label.LabelImages
Merge labels selected by freehand or point tool.
mergeLabelsWithGap(ImagePlus, float[], float, int) - Static method in class inra.ijpb.label.LabelImages
Merge several regions identified by their label, filling the gap between former regions.
mergeLabelsWithGap(ImageProcessor, float[], float, int) - Static method in class inra.ijpb.label.LabelImages
Merge several regions identified by their label, filling the gap between former regions.
mergeLabelsWithGap(ImageStack, float[], float, int) - Static method in class inra.ijpb.label.LabelImages
Merge several regions identified by their label, filling the gap between former regions.
MicrostructureAnalysisPlugin - Class in inra.ijpb.plugins
Plugin for quantifying microstructures from binary or label images.
MicrostructureAnalysisPlugin() - Constructor for class inra.ijpb.plugins.MicrostructureAnalysisPlugin
 
MIN - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
Min operator, that computes the minimum of the values from the two images
minFeretDiameter(ArrayList<? extends Point2D>) - Static method in class inra.ijpb.geometry.FeretDiameters
Computes Minimum Feret diameter of a set of points and returns both the diameter and the corresponding angle.
MinimaAndMaxima - Class in inra.ijpb.morphology
A collection of static methods for computing regional and extended minima and maxima.
MinimaAndMaxima3D - Class in inra.ijpb.morphology
A collection of static methods for computing regional and extended minima and maxima on 3D stacks.
minus(Vector2D) - Method in class inra.ijpb.geometry.Vector2D
Returns the result of the subtraction of this vector with another vector.
minus(Vector3D) - Method in class inra.ijpb.geometry.Vector3D
Returns the result of the subtraction of this vector with another vector.
MINUS - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
Minus operator, that subtracts values of the two images
minus(Vector3d) - Method in class inra.ijpb.measure.Vector3d
Deprecated.
Returns the result of the subtraction of this vector with another vector.
MirroringBorder - Class in inra.ijpb.data.border
Periodic border that considers image is mirrored indefinitely in all directions.
MirroringBorder(ImageProcessor) - Constructor for class inra.ijpb.data.border.MirroringBorder
Creates a new Mirroring Border Manager
MirroringBorder3D - Class in inra.ijpb.data.border
Periodic border that considers image is mirrored indefinitely in all directions.
MirroringBorder3D(ImageStack) - Constructor for class inra.ijpb.data.border.MirroringBorder3D
Creates a new Mirroring Border Manager
Moments3D() - Constructor for class inra.ijpb.measure.region3d.EquivalentEllipsoid.Moments3D
 
momentsToEllipsoids(EquivalentEllipsoid.Moments3D[]) - Method in class inra.ijpb.measure.region3d.EquivalentEllipsoid
Converts an array of 3D moments into equivalent ellipsoid representation.
monitor(Algo) - Static method in class inra.ijpb.algo.DefaultAlgoListener
Static method that creates a new instance of DefaultAlgoListener, and add it to the given algorithm.
MorphologicalFilter - Class in inra.ijpb.morphology.filter
Base class for morphological filters, based on a structuring element.
MorphologicalFilter(Strel3D, String) - Constructor for class inra.ijpb.morphology.filter.MorphologicalFilter
Creates a new MorphologicalFilter instance.
MorphologicalFilter3DPlugin - Class in inra.ijpb.plugins
Various morphological filters for 3D images.
MorphologicalFilter3DPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalFilter3DPlugin
 
MorphologicalFilterCross3DPlugin - Class in inra.ijpb.plugins
A simple plugin to test the Cross 3D strel.
MorphologicalFilterCross3DPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalFilterCross3DPlugin
 
MorphologicalFilterPlugin - Class in inra.ijpb.plugins
Plugin for computing various morphological filters on gray scale or color images.
MorphologicalFilterPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalFilterPlugin
 
MorphologicalReconstruction3DPlugin - Class in inra.ijpb.plugins
Plugin for performing geodesic reconstruction by dimation or by erosion on grayscale images.
MorphologicalReconstruction3DPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalReconstruction3DPlugin
 
MorphologicalReconstruction3DPlugin.Operation - Enum in inra.ijpb.plugins
A pre-defined set of operations for geodesic reconstruction.
MorphologicalReconstructionPlugin - Class in inra.ijpb.plugins
Plugin for performing morphological reconstruction by dilation or by erosion on grayscale images.
MorphologicalReconstructionPlugin() - Constructor for class inra.ijpb.plugins.MorphologicalReconstructionPlugin
 
MorphologicalReconstructionPlugin.Operation - Enum in inra.ijpb.plugins
A pre-defined set of operations for geodesic reconstruction.
MorphologicalSegmentation - Class in inra.ijpb.plugins
Plugin to perform automatic segmentation of 2D and 3D images based on morphological operations, mainly extended minima and watershed transforms.
MorphologicalSegmentation() - Constructor for class inra.ijpb.plugins.MorphologicalSegmentation
 
MorphologicalSegmentation.ResultMode - Enum in inra.ijpb.plugins
enumeration of result modes
Morphology - Class in inra.ijpb.morphology
Collection of static methods for morphological filters, as well as an enumeration of available methods.
Morphology.Operation - Enum in inra.ijpb.morphology
A pre-defined set of basis morphological operations, that can be easily used with a GenericDialog.

N

NE - Static variable in interface inra.ijpb.label.select.RelationalOperator
Implementation of the "Not Equal" operator.
Neighborhood2D - Class in inra.ijpb.data
Defines a neighborhood around a pixel in a 2D image.
Neighborhood2D() - Constructor for class inra.ijpb.data.Neighborhood2D
 
Neighborhood2DC4 - Class in inra.ijpb.data
Defines the four-neighborhood for pixels in a 2D image.
Neighborhood2DC4() - Constructor for class inra.ijpb.data.Neighborhood2DC4
 
Neighborhood2DC8 - Class in inra.ijpb.data
Defines the eight-neighborhood for pixels in a 2D image.
Neighborhood2DC8() - Constructor for class inra.ijpb.data.Neighborhood2DC8
 
Neighborhood3D - Class in inra.ijpb.data
Defines a neighborhood around a voxel in a 3D image.
Neighborhood3D() - Constructor for class inra.ijpb.data.Neighborhood3D
 
Neighborhood3DC26 - Class in inra.ijpb.data
Defines the 26-neighborhood around a voxel in a 3D image.
Neighborhood3DC26() - Constructor for class inra.ijpb.data.Neighborhood3DC26
 
Neighborhood3DC6 - Class in inra.ijpb.data
Defines the 6-neighborhood around a voxel in a 3D image.
Neighborhood3DC6() - Constructor for class inra.ijpb.data.Neighborhood3DC6
 
NeighborLabelsPlugin - Class in inra.ijpb.plugins
Extract the neighbor regions within a label image from a region label, or a list of region labels.
NeighborLabelsPlugin() - Constructor for class inra.ijpb.plugins.NeighborLabelsPlugin
 
nLabels - Variable in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling.Result
The number of labels within the label map.
nLabels - Variable in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling3D.Result
The number of labels within the label map.
normalize() - Method in class inra.ijpb.geometry.Vector2D
Returns a normalized vector with same direction as this vector
normalize() - Method in class inra.ijpb.geometry.Vector3D
Returns a normalized vector with same direction as this vector
normalize() - Method in class inra.ijpb.measure.Vector3d
Deprecated.
Returns a normalized vector with same direction as this vector
not(ImagePlus) - Static method in class inra.ijpb.math.ImageCalculator
Computes the binary "not" operation on the input image.
not(ImageProcessor) - Static method in class inra.ijpb.math.ImageCalculator
Computes the binary "not" operation on the input 2D image.
not(ImageStack) - Static method in class inra.ijpb.math.ImageCalculator
Computes the binary "not" operation on the input 3D image.

O

OctagonStrel - Class in inra.ijpb.morphology.strel
An Octagonal structuring element, obtained by decomposition into horizontal, vertical, and diagonal linear structuring elements.
OctagonStrel(int) - Constructor for class inra.ijpb.morphology.strel.OctagonStrel
Creates a new octagonal structuring element of a given orthogonal diameter.
OctagonStrel(int, int) - Constructor for class inra.ijpb.morphology.strel.OctagonStrel
Creates a new octagonal structuring element of a given orthogonal diameter and with a given offset.
OctagonStrel(int, int, int, int) - Constructor for class inra.ijpb.morphology.strel.OctagonStrel
Creates the octagonal structuring element by specifying both square and diagonal sizes and offsets.
opening(ImageProcessor) - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
 
Opening - Class in inra.ijpb.morphology.filter
Performs morphological opening on 2D/3D images.
Opening(Strel3D) - Constructor for class inra.ijpb.morphology.filter.Opening
Creates a new Morphological Opening operator with the specified structuring element.
opening(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological opening on the input image.
opening(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological opening on the input image.
opening(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological opening on the input 3D image.
opening(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
opening(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
opening(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel3D
 
opening(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel
 
opening(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel3D
 
opening(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractStrel
Performs a morphological opening on the input image, by applying first an erosion, then a dilation with the reversed structuring element.
opening(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel
 
opening(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
Performs a morphological opening on the input stack, by applying first an erosion, then a dilation with the reversed structuring element.
opening(ImageStack) - Method in class inra.ijpb.morphology.strel.Cross3DStrel
 
opening(ImageProcessor) - Method in interface inra.ijpb.morphology.Strel
Performs a morphological opening of the input image with this structuring element, and returns the result in a new ImageProcessor.
opening(ImageStack) - Method in interface inra.ijpb.morphology.Strel3D
Performs a morphological opening of the input image with this structuring element, and returns the result in a new ImageStack.
optimizeDisplayRange(ImagePlus) - Static method in class inra.ijpb.data.image.Images3D
Optimize display range of 2d/3d image based on its minimum and maximum values
OR - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
Or operator.
orientation() - Method in class inra.ijpb.geometry.Ellipse
 
orientation() - Method in class inra.ijpb.geometry.OrientedBox2D
 
orientedBoundingBox(ArrayList<? extends Point2D>) - Static method in class inra.ijpb.measure.region2d.OrientedBoundingBox2D
Computes the object-oriented bounding box of a set of points.
orientedBoundingBox(ArrayList<? extends Point2D>, Calibration) - Static method in class inra.ijpb.measure.region2d.OrientedBoundingBox2D
Computes the object-oriented bounding box of a set of points, computing convex hull in pixel coordinates.
OrientedBoundingBox2D - Class in inra.ijpb.measure.region2d
 
OrientedBoundingBox2D() - Constructor for class inra.ijpb.measure.region2d.OrientedBoundingBox2D
Default constructor.
OrientedBoundingBoxPlugin - Class in inra.ijpb.plugins
Plugin for computing oriented bounding box.
OrientedBoundingBoxPlugin() - Constructor for class inra.ijpb.plugins.OrientedBoundingBoxPlugin
 
orientedBox - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing oriented box.
OrientedBox2D - Class in inra.ijpb.geometry
An oriented Box in 2 dimensions, used to store results of oriented bounding box.
OrientedBox2D(Point2D, double, double, double) - Constructor for class inra.ijpb.geometry.OrientedBox2D
Default constructor for OrientedBox2D.
OrientedBox2D(double, double, double, double, double) - Constructor for class inra.ijpb.geometry.OrientedBox2D
Default constructor for OrientedBox2D, that specifies center as two coordinates.
orientedBoxElongation - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing elongation of oriented box.
OrientedLineStrel - Class in inra.ijpb.morphology.directional
A linear structuring element, defined by a length and an orientation.
OrientedLineStrel(double, double) - Constructor for class inra.ijpb.morphology.directional.OrientedLineStrel
Creates an new instance of linear structuring element.
OrientedLineStrelFactory - Class in inra.ijpb.morphology.directional
Factory for oriented linear structuring elements.
OrientedLineStrelFactory(double) - Constructor for class inra.ijpb.morphology.directional.OrientedLineStrelFactory
Constructs a new oriented line factory, that will generate lines with approximately the given length.
OrientedStrelFactory - Interface in inra.ijpb.morphology.directional
Factory for generating oriented structuring elements.

P

p1 - Variable in class inra.ijpb.geometry.PointPair2D
The first point of the pair.
p1 - Variable in class inra.ijpb.geometry.PointPair3D
The first point of the pair.
p2 - Variable in class inra.ijpb.geometry.PointPair2D
The second point of the pair.
p2 - Variable in class inra.ijpb.geometry.PointPair3D
The second point of the pair.
parseLabelList(String) - Static method in class inra.ijpb.util.IJUtils
Extracts a list of integer labels from a string representation.
ParticleAnalysis3DPlugin - Class in inra.ijpb.plugins
Deprecated.
replaced by AnalyzeRegions3D
ParticleAnalysis3DPlugin() - Constructor for class inra.ijpb.plugins.ParticleAnalysis3DPlugin
Deprecated.
 
particleArea(ImageProcessor, int) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
path - Variable in class inra.ijpb.measure.region2d.GeodesicDiameter.Result
The largest geodesic path within the particle, joining the first and the second geodesic extremities.
perimeter() - Method in class inra.ijpb.geometry.Circle2D
 
perimeter(ImageProcessor, Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D
Measures the perimeter of the foreground region within a binary image.
perimeter - Variable in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.Result
the perimeter of the region.
perimeter - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing perimeter.
perimeterDensity(ImageProcessor, double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
perimeterDensity(ImageProcessor, Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D
Computes perimeter density of binary image.
perimeterLut(Calibration, int) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumes2DUtils
Computes the Look-up table that is used for computing perimeter.
perimeterLut(Calibration, int) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
Deprecated.
use IntrinsicVolumes2DUtils instead
perimeters(ImageProcessor, int[], Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D
Measures the perimeter of each region within a label image.
PeriodicBorder - Class in inra.ijpb.data.border
Periodic border that considers image is repeated indefinitely in all directions.
PeriodicBorder(ImageProcessor) - Constructor for class inra.ijpb.data.border.PeriodicBorder
Creates a new Periodic Border Manager
PeriodicBorder3D - Class in inra.ijpb.data.border
Periodic border that considers image is repeated indefinitely in all directions.
PeriodicBorder3D(ImageStack) - Constructor for class inra.ijpb.data.border.PeriodicBorder3D
Creates a new Periodic Border Manager
phi() - Method in class inra.ijpb.geometry.Ellipsoid
 
pixelCount(ImagePlus, int[]) - Static method in class inra.ijpb.label.LabelImages
Computes the number of pixels (or voxels) composing each regions in the 2D or 3D label image.
pixelCount(ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelImages
Computes the number of pixels composing each particle in the label image.
pixelCount - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing pixel count.
PixelRecord - Class in inra.ijpb.data
Class to store integer pixel coordinates and its corresponding double value
PixelRecord(Cursor2D, double) - Constructor for class inra.ijpb.data.PixelRecord
Create pixel record with cursor position and double value
PixelRecord(int, int, double) - Constructor for class inra.ijpb.data.PixelRecord
Create pixel record with cursor position and double value
plus(Vector2D) - Method in class inra.ijpb.geometry.Vector2D
Returns the result of the addition of this vector with another vector.
plus(Vector3D) - Method in class inra.ijpb.geometry.Vector3D
Returns the result of the addition of this vector with another vector.
PLUS - Static variable in interface inra.ijpb.math.ImageCalculator.Operation
Plus operator, that adds values of the two images
plus(Vector3d) - Method in class inra.ijpb.measure.Vector3d
Deprecated.
Returns the result of the addition of this vector with another vector.
Point3D - Class in inra.ijpb.geometry
A point in the 3-dimensional Euclidean space, defined by x, y, and z coordinates.
Point3D() - Constructor for class inra.ijpb.geometry.Point3D
Creates a new point located at the origin.
Point3D(double, double, double) - Constructor for class inra.ijpb.geometry.Point3D
Creates a new point at the specified coordinates.
PointPair2D - Class in inra.ijpb.geometry
A pair of points in the plane, useful for representing result of Max Feret Diameter computation or similar problems.
PointPair2D(Point2D, Point2D) - Constructor for class inra.ijpb.geometry.PointPair2D
Creates a new point pair.
PointPair3D - Class in inra.ijpb.geometry
A pair of points in the 3D space, useful for representing result of Max Feret Diameter computation or similar problems.
PointPair3D(Point3D, Point3D) - Constructor for class inra.ijpb.geometry.PointPair3D
Creates a new 3D point pair.
Polygon2D - Class in inra.ijpb.geometry
A polygon shape in the plane.
Polygon2D() - Constructor for class inra.ijpb.geometry.Polygon2D
Creates a new empty polygon.
Polygon2D(int) - Constructor for class inra.ijpb.geometry.Polygon2D
Creates a new empty polygon by allocating enough space for storing vertex coordinates.
Polygon2D(double[], double[]) - Constructor for class inra.ijpb.geometry.Polygon2D
Creates a new polygon from the coordinates of its vertices.
Polygon2D(Collection<Point2D>) - Constructor for class inra.ijpb.geometry.Polygon2D
Creates a new polygon from a collection of vertices.
Polygons2D - Class in inra.ijpb.geometry
A set of static methods operating on polygons.
Position3DValuePair(Cursor3D, double) - Constructor for class inra.ijpb.label.LabelValues.Position3DValuePair
Creates a new Position3DValuePair instance based on a position and a value.
PositionValuePair(Point, double) - Constructor for class inra.ijpb.label.LabelValues.PositionValuePair
Creates a new PositionValuePair instance based on a position and a value.
print(ColorProcessor) - Static method in class inra.ijpb.data.image.ColorImages
Prints the content of the input color image on the console.
print(ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Deprecated.
print(ImageProcessor) - Static method in class inra.ijpb.data.image.ImageUtils
Prints the content of the given ImageProcessor on the console.
print(ImageStack) - Static method in class inra.ijpb.data.image.ImageUtils
Prints the content of the given 3D image on the console.
printImage(ImageProcessor) - Static method in class inra.ijpb.util.IJUtils
Deprecated.
process(ImageStack) - Method in interface inra.ijpb.binary.geodesic.GeodesicDiameter3D
Deprecated.
computes geodesic diameter for each region of the input image.
process(ImageStack) - Method in class inra.ijpb.binary.geodesic.GeodesicDiameter3DFloat
Deprecated.
Computes the geodesic diameter of each particle within the given label image.
process(ImageProcessor) - Method in class inra.ijpb.binary.skeleton.ImageJSkeleton
Computes the skeleton of the region within the binary image and returns the result in a new ImageProcessor.
process(ImagePlus, ImagePlus, Color) - Method in class inra.ijpb.color.BinaryOverlay
Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color.
process(ImageProcessor, ImageProcessor, Color) - Method in class inra.ijpb.color.BinaryOverlay
Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color.
process(ImageStack, ImageStack, Color) - Method in class inra.ijpb.color.BinaryOverlay
Applies an overlay of a binary image mask onto a grayscale or color image, using the specified color.
process(ImageProcessor) - Method in class inra.ijpb.label.conncomp.LabelBoundariesLabeling2D
Computes boundary labeling on the specified label map of regions, and returns the result in a Result instance.
process(ImageStack) - Method in class inra.ijpb.label.conncomp.LabelBoundariesLabeling3D
Computes boundary labeling on the specified label map of regions, and returns the result in a Result instance.
process(ImageProcessor, double) - Method in class inra.ijpb.label.distmap.LabelDilation2DShort
Deprecated.
Computes dilation of labels within label image by a specified radius.
process(ImageStack, double) - Method in class inra.ijpb.label.distmap.LabelDilation3D4WShort
Deprecated.
Computes dilation of labels within label image by a specified radius.
process(ImageStack, double) - Method in class inra.ijpb.label.distmap.LabelDilation3DShort
Deprecated.
Computes dilation of labels within label image by a specified radius.
process(ImageProcessor, double) - Method in class inra.ijpb.label.distmap.LabelDilationShort5x5
Deprecated.
Computes dilation of labels within label image by a specified radius.
process(ImagePlus) - Method in class inra.ijpb.label.edit.FindAllLabels
Returns the set of unique labels existing in the given image, excluding the value zero (used for background).
process(ImageProcessor) - Method in class inra.ijpb.label.edit.FindAllLabels
Returns the set of unique labels existing in the given image, excluding the value zero (used for background).
process(ImageStack) - Method in class inra.ijpb.label.edit.FindAllLabels
Returns the set of unique labels existing in the given stack, excluding the value zero (used for background).
process(ImagePlus, float[], float) - Method in class inra.ijpb.label.edit.ReplaceLabelValues
Replace all values specified in label array by the value 0.
process(ImageProcessor, int[], int) - Method in class inra.ijpb.label.edit.ReplaceLabelValues
Replace all values specified in label array by a new value.
process(ImageProcessor, float[], float) - Method in class inra.ijpb.label.edit.ReplaceLabelValues
Replace all values specified in label array by the value 0.
process(ImageStack, int[], int) - Method in class inra.ijpb.label.edit.ReplaceLabelValues
Replace all values specified in label array by a new value.
process(ImageStack, float[], float) - Method in class inra.ijpb.label.edit.ReplaceLabelValues
Replace all values specified in label array by the specified value.
process(ImageProcessor) - Method in class inra.ijpb.label.filter.ChamferLabelDilation2DShort
Computes dilation of labels within label image by a specified radius.
process(ImageStack) - Method in class inra.ijpb.label.filter.ChamferLabelDilation3DShort
Computes dilation of labels within label image by a specified radius.
process(ImageProcessor) - Method in class inra.ijpb.label.filter.ChamferLabelErosion2DShort
Apply morphological erosion of the labels within the specified input image.
process(ImageStack) - Method in class inra.ijpb.label.filter.ChamferLabelErosion3DShort
Apply morphological erosion of the labels within the specified input image.
process(ImagePlus) - Method in class inra.ijpb.label.select.LabelSizeFiltering
Applies size filtering on the input image.
process(ImageProcessor) - Method in class inra.ijpb.label.select.LabelSizeFiltering
Applies size filtering on the input 2D label image.
process(ImageStack) - Method in class inra.ijpb.label.select.LabelSizeFiltering
Applies size filtering on the input 3D label image.
process(ImageProcessor) - Method in class inra.ijpb.measure.region2d.BinaryConfigurationsHistogram2D
Computes the histogram of binary configurations for the region within the input binary image.
process(ImageProcessor, int[]) - Method in class inra.ijpb.measure.region2d.BinaryConfigurationsHistogram2D
Computes the histogram of binary configurations for each region of the input label image.
process(ImageStack) - Method in class inra.ijpb.measure.region3d.BinaryConfigurationsHistogram3D
Applies a look-up-table for each of the 2x2x2 voxel configurations containing at least one voxel of the input binary image, and returns the sum of contributions for each label.
process(ImageStack, int[]) - Method in class inra.ijpb.measure.region3d.BinaryConfigurationsHistogram3D
Applies a look-up-table for each of the 2x2x2 voxel configurations containing at least one voxel of the input image, and returns the sum of contributions for each label.
process(ImageStack, int, int, Calibration) - Method in class inra.ijpb.measure.region3d.InterfaceSurfaceArea
Computes the interface surface area between two regions.
process(ImageProcessor, int) - Method in interface inra.ijpb.morphology.attrfilt.AreaOpening
Applies area opening on the input grayscale image and returns the result.
process(ImageProcessor, int) - Method in class inra.ijpb.morphology.attrfilt.AreaOpeningNaive
 
process(ImageProcessor, int) - Method in class inra.ijpb.morphology.attrfilt.AreaOpeningQueue
 
process(ImageProcessor, int) - Method in class inra.ijpb.morphology.attrfilt.BoxDiagonalOpeningQueue
 
process(ImageStack, int) - Method in interface inra.ijpb.morphology.attrfilt.SizeOpening3D
Applies size opening on the input 3D grayscale image and returns the result.
process(ImageStack, int) - Method in class inra.ijpb.morphology.attrfilt.SizeOpening3DQueue
 
process(ImageProcessor) - Method in class inra.ijpb.morphology.directional.DirectionalFilter
Apply directional filter with current settings to the specified image.
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.BlackTopHat
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.BlackTopHat
 
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Closing
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.Closing
 
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Dilation
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.Dilation
 
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Erosion
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.Erosion
 
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.ExternalGradient
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.ExternalGradient
 
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Gradient
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.Gradient
 
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.InternalGradient
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.InternalGradient
 
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Laplacian
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.Laplacian
 
process(ImagePlus) - Method in class inra.ijpb.morphology.filter.MorphologicalFilter
Applies the morphological filter to the input ImagePlus, and returns a new instance of ImagePlus.
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.MorphologicalFilter
Apply filtering operation on the specified image, and returns the result as a new instance of ImageProcessor.
process(ImageStack) - Method in class inra.ijpb.morphology.filter.MorphologicalFilter
Apply filtering operation on the specified 3D image, and returns the result as a new instance of ImageStack.
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Opening
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.Opening
 
process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.WhiteTopHat
 
process(ImageStack) - Method in class inra.ijpb.morphology.filter.WhiteTopHat
 
process(ImagePlus) - Method in class inra.ijpb.plugins.AnalyzeMicrostructure3D
Computes features from an ImagePlus object.
process(ImageStack, Calibration) - Method in class inra.ijpb.plugins.AnalyzeMicrostructure3D
Computes features from an ImageStack object, specifying the calibration.
process(ImagePlus, AnalyzeRegions.Features) - Static method in class inra.ijpb.plugins.AnalyzeRegions
Computes a set of descriptive features from a label image and concatenates the results into a ResultsTable.
process(ImagePlus) - Method in class inra.ijpb.plugins.AnalyzeRegions
Deprecated.
replaced by static process(ImagePlus, Features) method
process(ImagePlus) - Method in class inra.ijpb.plugins.AnalyzeRegions3D
Computes features from an ImagePlus object.
process(ImageStack, Calibration) - Method in class inra.ijpb.plugins.AnalyzeRegions3D
Computes features from an ImageStack object, specifying the calibration.
process(ImageProcessor, int, int, int, int, BorderManager) - Static method in class inra.ijpb.plugins.ExtendBordersPlugin
Deprecated.
replaced by inra.ijpb.data.border.BorderManager.addBorders(...) method
process(ImageStack, int, int, int, int, int, int, BorderManager3D) - Static method in class inra.ijpb.plugins.ExtendBordersPlugin
Deprecated.
replaced by inra.ijpb.data.border.BorderManager3D.addBorders(...) method
process(ImagePlus, ImagePlus, String, ChamferMask3D, boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMap3D
Deprecated.
Computes the distance propagated from the boundary of the white particles, within the black phase.
process(ImagePlus, ImagePlus, String, ChamferMask3D, boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMap3DPlugin
Computes the distance propagated from the boundary of the white particles, within the white phase.
process(ImagePlus, ImagePlus, String, float[], boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMap3DPlugin
Deprecated.
process(ImageStack, ImageStack, float[], boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMap3DPlugin
Deprecated.
process(ImageStack, ImageStack, ChamferMask3D, boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMap3DPlugin
Computes the distance within the mask, starting from the marker image.
process(ImagePlus, ImagePlus, String, float[], boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMapPlugin
Deprecated.
process(ImageProcessor, ImageProcessor, float[], boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMapPlugin
Deprecated.
process(ImagePlus, ImagePlus, String, ChamferMask2D, boolean, boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMapPlugin
Computes the distance propagated from the boundary of the white particles, within the black phase.
process(ImageProcessor, Roi, ChamferMask2D, boolean, boolean) - Method in class inra.ijpb.plugins.InteractiveGeodesicDistanceMap
Computes the distance propagated from the boundary of the white particles, within the white phase.
process(ImageProcessor, Roi, float[], boolean) - Method in class inra.ijpb.plugins.InteractiveGeodesicDistanceMap
Deprecated.
process(ImageProcessor, Roi, short[], boolean) - Method in class inra.ijpb.plugins.InteractiveGeodesicDistanceMap
Deprecated.
process(ImageProcessor, ChamferMask2D, double) - Method in enum inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin.Operation
Applies the current operator to the input image.
process(ImageStack, ChamferMask3D, double) - Method in enum inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin.Operation
Applies the current operator to the input 3D image.
process(ImagePlus, ResultsTable, String) - Static method in class inra.ijpb.plugins.LabelToValuePlugin
Combines a label image and the values within a column of a ResultsTable to generate a parametric map of values that associates to each pixel / voxel the value of the row associated to the label it belongs to.
process(ImagePlus, ResultsTable, String, double, double) - Static method in class inra.ijpb.plugins.LabelToValuePlugin
Combines a label image and the values within a column of a ResultsTable to generate a parametric map of values that associates to each pixel / voxel the value of the row associated to the label it belongs to.
process(String, String, String, String) - Static method in class inra.ijpb.plugins.LabelToValuePlugin
Process the current image as a label image using the provided string arguments.
process(ImagePlus, ImagePlus, ImagePlus, int) - Method in class inra.ijpb.plugins.MarkerControlledWatershed3DPlugin
Apply marker-controlled watershed to a grayscale 2D or 3D image.
process(ImagePlus, ImagePlus, ImagePlus, int, double) - Method in class inra.ijpb.plugins.MarkerControlledWatershed3DPlugin
Apply marker-controlled watershed to a grayscale 2D or 3D image.
process(ImagePlus, short[]) - Method in class inra.ijpb.plugins.MaxInscribedCirclePlugin
Deprecated.
use LargestInscribedCircle class instead
process(ImagePlus, int, boolean) - Method in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
Main body of the plugin.
process(ImagePlus, Morphology.Operation, Strel3D) - Method in class inra.ijpb.plugins.MorphologicalFilter3DPlugin
Applies the given operation to the given image.
process(ImagePlus, Morphology.Operation, Strel3D) - Method in class inra.ijpb.plugins.MorphologicalFilterCross3DPlugin
Applies the given operation to the given image.
process(ImagePlus, Morphology.Operation, Strel) - Method in class inra.ijpb.plugins.MorphologicalFilterPlugin
Applies the specified morphological operation with specified structuring element to the input image.
process(ImagePlus) - Method in class inra.ijpb.plugins.ParticleAnalysis3DPlugin
Deprecated.
Computes features from an ImagePlus object.
process(ImageStack, Calibration) - Method in class inra.ijpb.plugins.ParticleAnalysis3DPlugin
Deprecated.
Computes features from an ImageStack object, specifying the calibration.
process(ImagePlus, int) - Method in class inra.ijpb.plugins.RegionMorphometryPlugin
Deprecated.
Process the input image.
process(ImagePlus, ImagePlus, int, double, double) - Method in class inra.ijpb.plugins.Watershed3DPlugin
Apply 3D watershed to a 2D or 3D image (it does work for 2D images too).
processColor(ColorProcessor) - Method in class inra.ijpb.morphology.filter.MorphologicalFilter
Performs morphological dilation on each channel, and reconstitutes the resulting color image.
processInnerFrame(ImageProcessor) - Method in class inra.ijpb.measure.region2d.BinaryConfigurationsHistogram2D
Applies a look-up-table for each of the 2x2 pixel configurations with all pixels within the input binary image, and returns the sum of contributions for each label.
processInnerFrame(ImageStack) - Method in class inra.ijpb.measure.region3d.BinaryConfigurationsHistogram3D
Applies a look-up-table for each of the 2x2x2 voxel configurations with all voxels within the input binary image, and returns the sum of contributions for each label.
psi() - Method in class inra.ijpb.geometry.Ellipsoid
 

Q

QUASI_EUCLIDEAN - Static variable in class inra.ijpb.binary.distmap.ChamferMask2D
Use weights 1 for orthogonal neighbors and sqrt(2) for diagonal neighbors.
QUASI_EUCLIDEAN - Static variable in class inra.ijpb.binary.distmap.ChamferMask3D
Use weights 1 for orthogonal neighbors, sqrt(2) for square-diagonal neighbors, and sqrt(3) for cube-diagonals.

R

radius() - Method in class inra.ijpb.geometry.Sphere
 
radius1() - Method in class inra.ijpb.geometry.Ellipse
 
radius1() - Method in class inra.ijpb.geometry.Ellipsoid
 
radius2() - Method in class inra.ijpb.geometry.Ellipse
 
radius2() - Method in class inra.ijpb.geometry.Ellipsoid
 
radius3() - Method in class inra.ijpb.geometry.Ellipsoid
 
recalibrate(Calibration) - Method in class inra.ijpb.measure.region2d.GeodesicDiameter.Result
Computes the result corresponding to the spatial calibration.
reconstructByDilation(ImageStack, ImageStack) - Static method in class inra.ijpb.morphology.GeodesicReconstruction3D
Deprecated.
Static method to computes the geodesic reconstruction by dilation of the marker image under the mask image.
reconstructByDilation(ImageStack, ImageStack, int) - Static method in class inra.ijpb.morphology.GeodesicReconstruction3D
Deprecated.
Static method to computes the geodesic reconstruction by dilation of the marker image under the mask image.
reconstructByDilation(ImageStack, ImageStack, int, ImageStack) - Static method in class inra.ijpb.morphology.GeodesicReconstruction3D
Deprecated.
Static method to computes the geodesic reconstruction by dilation of the marker image under the mask image, but restricted to a binary mask.
reconstructByDilation(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.morphology.Reconstruction
Static method to computes the morphological reconstruction by dilation of the marker image under the mask image.
reconstructByDilation(ImageProcessor, ImageProcessor, int) - Static method in class inra.ijpb.morphology.Reconstruction
Static method to computes the morphological reconstruction by dilation of the marker image under the mask image.
reconstructByDilation(ImageStack, ImageStack) - Static method in class inra.ijpb.morphology.Reconstruction3D
Static method to computes the morphological reconstruction by dilation of the marker image under the mask image.
reconstructByDilation(ImageStack, ImageStack, int) - Static method in class inra.ijpb.morphology.Reconstruction3D
Static method to computes the morphological reconstruction by dilation of the marker image under the mask image.
reconstructByDilation(ImageStack, ImageStack, int, ImageStack) - Static method in class inra.ijpb.morphology.Reconstruction3D
Static method to computes the morphological reconstruction by dilation of the marker image under the mask image, but restricted to a binary mask.
reconstructByErosion(ImageStack, ImageStack) - Static method in class inra.ijpb.morphology.GeodesicReconstruction3D
Deprecated.
Static method to computes the geodesic reconstruction by erosion of the marker image over the mask image.
reconstructByErosion(ImageStack, ImageStack, int) - Static method in class inra.ijpb.morphology.GeodesicReconstruction3D
Deprecated.
Static method to computes the geodesic reconstruction by erosion of the marker image over the mask image.
reconstructByErosion(ImageProcessor, ImageProcessor) - Static method in class inra.ijpb.morphology.Reconstruction
Static method to computes the morphological reconstruction by erosion of the marker image over the mask image.
reconstructByErosion(ImageProcessor, ImageProcessor, int) - Static method in class inra.ijpb.morphology.Reconstruction
Static method to computes the morphological reconstruction by erosion of the marker image over the mask image.
reconstructByErosion(ImageStack, ImageStack) - Static method in class inra.ijpb.morphology.Reconstruction3D
Static method to computes the morphological reconstruction by erosion of the marker image over the mask image.
reconstructByErosion(ImageStack, ImageStack, int) - Static method in class inra.ijpb.morphology.Reconstruction3D
Static method to computes the morphological reconstruction by erosion of the marker image over the mask image.
Reconstruction - Class in inra.ijpb.morphology
Morphological reconstruction for grayscale or binary images.
Reconstruction() - Constructor for class inra.ijpb.morphology.Reconstruction
Private constructor to prevent class instantiation.
Reconstruction3D - Class in inra.ijpb.morphology
Morphological reconstruction for 8-bits grayscale or binary stacks.
Reconstruction3D() - Constructor for class inra.ijpb.morphology.Reconstruction3D
Private constructor to prevent class instantiation.
record(String, String...) - Static method in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
Macro-record a specific command.
record(String, String...) - Static method in class inra.ijpb.plugins.LabelToValuePlugin
Macro-record a specific command.
record(String, String...) - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
Macro-record a specific command.
RegionAdjacencyGraph - Class in inra.ijpb.label
Contains several methods for extracting the set of adjacencies between regions in a label image.
RegionAdjacencyGraph.LabelPair - Class in inra.ijpb.label
Used to stores the adjacency information between two regions.
RegionAdjacencyGraphPlugin - Class in inra.ijpb.plugins
 
RegionAdjacencyGraphPlugin() - Constructor for class inra.ijpb.plugins.RegionAdjacencyGraphPlugin
 
RegionalExtrema3DAlgo - Class in inra.ijpb.morphology.extrema
Interface for computing regional extrema (regional minima and regional maxima).
RegionalExtrema3DAlgo() - Constructor for class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
Creates a new algorithm for computing regional extrema, that computes regional minima with connectivity 6.
RegionalExtrema3DAlgo(ExtremaType, int) - Constructor for class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
Creates a new algorithm for computing regional extrema, by choosing type of minima and connectivity.
RegionalExtrema3DByFlooding - Class in inra.ijpb.morphology.extrema
Computes regional extrema in 3D images using flooding algorithm.
RegionalExtrema3DByFlooding() - Constructor for class inra.ijpb.morphology.extrema.RegionalExtrema3DByFlooding
 
RegionalExtremaAlgo - Class in inra.ijpb.morphology.extrema
Interface for appying regional extrema (regional minima and maxima).
RegionalExtremaAlgo() - Constructor for class inra.ijpb.morphology.extrema.RegionalExtremaAlgo
Creates a new algorithm for computing regional extrema, that computes regional minima with connectivity 4.
RegionalExtremaAlgo(ExtremaType, int) - Constructor for class inra.ijpb.morphology.extrema.RegionalExtremaAlgo
Creates a new algorithm for computing regional extrema, by choosing type of minima and connectivity.
RegionalExtremaByFlooding - Class in inra.ijpb.morphology.extrema
Computes regional extrema in planar images using flooding algorithm.
RegionalExtremaByFlooding() - Constructor for class inra.ijpb.morphology.extrema.RegionalExtremaByFlooding
 
regionalMaxima(ImageProcessor) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the regional maxima in grayscale image image, using the default connectivity.
regionalMaxima(ImageProcessor, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the regional maxima in grayscale image image, using the specified connectivity.
regionalMaxima(ImageStack) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the regional maxima in 3D stack image, using the default connectivity.
regionalMaxima(ImageStack, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the regional maxima in grayscale image stack, using the specified connectivity.
regionalMaxima(ImageStack, int, ImageStack) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the regional maxima in grayscale image stack, using the specified connectivity and binary mask.
regionalMaximaByReconstruction(ImageProcessor, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the regional maxima in grayscale image image, using the specified connectivity, and a slower algorithm (used for testing).
regionalMaximaByReconstruction(ImageStack, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the regional maxima in 3D image stack, using the specified connectivity, and a slower algorithm (used for testing).
RegionalMinAndMax3DPlugin - Class in inra.ijpb.plugins
Plugin for computing regional minima and maxima in grayscale images.
RegionalMinAndMax3DPlugin() - Constructor for class inra.ijpb.plugins.RegionalMinAndMax3DPlugin
 
RegionalMinAndMax3DPlugin.Operation - Enum in inra.ijpb.plugins
A customized enumeration to choose between regional minima or maxima.
RegionalMinAndMaxPlugin - Class in inra.ijpb.plugins
Plugin for computing regional minima and maxima in grayscale images.
RegionalMinAndMaxPlugin() - Constructor for class inra.ijpb.plugins.RegionalMinAndMaxPlugin
 
RegionalMinAndMaxPlugin.Operation - Enum in inra.ijpb.plugins
A customized enumeration to choose between regional minima or maxima.
regionalMinima(ImageProcessor) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the regional minima in grayscale image image, using the default connectivity.
regionalMinima(ImageProcessor, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the regional minima in grayscale image image, using the specified connectivity.
regionalMinima(ImageStack) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the regional minima in 3D image stack, using the default connectivity.
regionalMinima(ImageStack, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the regional minima in 3D stack image, using the specified connectivity.
regionalMinima(ImageStack, int, ImageStack) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the regional minima in 3D image stack, using the specified connectivity.
regionalMinimaByReconstruction(ImageProcessor, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima
Computes the regional minima in grayscale image image, using the specified connectivity, and a slower algorithm (used for testing).
regionalMinimaByReconstruction(ImageStack, int) - Static method in class inra.ijpb.morphology.MinimaAndMaxima3D
Computes the regional minima in grayscale image image, using the specified connectivity, and a slower algorithm (used for testing).
RegionAnalyzer<T> - Interface in inra.ijpb.measure
Common interface for classes devoted to the extraction of information from each region of label or binary image.
RegionAnalyzer2D<T> - Class in inra.ijpb.measure.region2d
Base implementation of RegionAnalyzer interface for planar binary/label images.
RegionAnalyzer2D() - Constructor for class inra.ijpb.measure.region2d.RegionAnalyzer2D
 
RegionAnalyzer3D<T> - Class in inra.ijpb.measure.region3d
Base implementation of RegionAnalyzer interface for 3D binary/label images.
RegionAnalyzer3D() - Constructor for class inra.ijpb.measure.region3d.RegionAnalyzer3D
 
RegionBoundaries - Class in inra.ijpb.measure.region2d
Utility functions for computing position of boundary points/corners of regions within binary or label images.
RegionBoundaries3D - Class in inra.ijpb.measure.region3d
Utility functions for computing position of boundary points/corners of regions within 3D binary or label images.
RegionBoundariesLabelingPlugin - Class in inra.ijpb.plugins
 
RegionBoundariesLabelingPlugin() - Constructor for class inra.ijpb.plugins.RegionBoundariesLabelingPlugin
 
regionComponentsLabeling(ImagePlus, int, int, int) - Static method in class inra.ijpb.label.LabelImages
Computes the labels in the binary 2D or 3D image contained in the given ImagePlus, and computes the maximum label to set up the display range of the resulting ImagePlus.
regionComponentsLabeling(ImageProcessor, int, int, int) - Static method in class inra.ijpb.label.LabelImages
Computes the labels of the connected components in the given planar binary image.
regionComponentsLabeling(ImageStack, int, int, int) - Static method in class inra.ijpb.label.LabelImages
Computes the labels of the connected components in the given 3D binary image.
RegionMorphometryPlugin - Class in inra.ijpb.plugins
Deprecated.
replaced by AnalyzeRegions
RegionMorphometryPlugin() - Constructor for class inra.ijpb.plugins.RegionMorphometryPlugin
Deprecated.
 
regionsCorners(ImageStack, int[]) - Static method in class inra.ijpb.measure.region3d.RegionBoundaries3D
Returns a set of points located at the corners of a binary particle.
regionsCornersArray(ImageStack, int[]) - Static method in class inra.ijpb.measure.region3d.RegionBoundaries3D
Returns a set of points located at the corners of a binary particle.
RelationalOperator - Interface in inra.ijpb.label.select
Implementation of a relational operator that computes a boolean value from two scalar input values.
remapLabels(ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Ensures that the labels in the given label image range from 1 to Lmax.
remapLabels(ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Ensures that the labels in the given label image range from 1 to Lmax.
remapLabels(ImageStack) - Static method in class inra.ijpb.label.LabelImages
Ensures that the labels in the given label image range from 1 to Lmax.
RemapLabelsPlugin - Class in inra.ijpb.plugins
Ensures the labels in the current label image are numbered between 1 and LMax, where LMax is the number of labels.
RemapLabelsPlugin() - Constructor for class inra.ijpb.plugins.RemapLabelsPlugin
 
remove(ImagePlus, boolean, boolean, boolean, boolean, boolean, boolean) - Static method in class inra.ijpb.plugins.RemoveBorderLabelsPlugin
Remove labels in the border of the image
removeAlgoListener(AlgoListener) - Method in interface inra.ijpb.algo.Algo
 
removeAlgoListener(AlgoListener) - Method in class inra.ijpb.algo.AlgoStub
 
removeBorderLabels(ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Removes all regions that touch the borders of the image.
removeBorderLabels(ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Removes all regions that touch the borders of the image.
removeBorderLabels(ImageStack) - Static method in class inra.ijpb.label.LabelImages
Removes all regions that touch the borders of the image.
RemoveBorderLabelsPlugin - Class in inra.ijpb.plugins
Removes all labels that touch the selected border, and replace them with value 0.
RemoveBorderLabelsPlugin() - Constructor for class inra.ijpb.plugins.RemoveBorderLabelsPlugin
 
removeLabels(ImagePlus, Roi, boolean) - Static method in class inra.ijpb.label.LabelImages
Remove labels selected by freehand or point ROIs (in place).
removeLargestLabel(ImagePlus) - Static method in class inra.ijpb.label.LabelImages
Removes the regions corresponding to the largest label from a label image.
removeLargestLabel(ImageProcessor) - Static method in class inra.ijpb.label.LabelImages
Removes the regions corresponding to the largest label from a label image.
removeLargestLabel(ImageStack) - Static method in class inra.ijpb.label.LabelImages
Removes the regions corresponding to the largest label from a label image.
RemoveLargestLabelPlugin - Class in inra.ijpb.plugins
Removes all the labels in a 2D/3D image but the largest one.
RemoveLargestLabelPlugin() - Constructor for class inra.ijpb.plugins.RemoveLargestLabelPlugin
 
removeLargestRegion(ImagePlus) - Static method in class inra.ijpb.binary.BinaryImages
Returns a binary image in which the largest region has been replaced by background.
removeLargestRegion(ImageProcessor) - Static method in class inra.ijpb.binary.BinaryImages
Returns a binary image in which the largest region has been replaced by the background value.
removeLargestRegion(ImageStack) - Static method in class inra.ijpb.binary.BinaryImages
Returns a binary image in which the largest region has been replaced by the background value.
RemoveLargestRegionPlugin - Class in inra.ijpb.plugins
Removes the largest region of a binary 2D or 3D image.
RemoveLargestRegionPlugin() - Constructor for class inra.ijpb.plugins.RemoveLargestRegionPlugin
 
replaceLabels(ImagePlus, int[], int) - Static method in class inra.ijpb.label.LabelImages
Replace all values specified in label array by a new value.
replaceLabels(ImagePlus, float[], float) - Static method in class inra.ijpb.label.LabelImages
Replace all values specified in label array by the value 0.
replaceLabels(ImageProcessor, int[], int) - Static method in class inra.ijpb.label.LabelImages
Replace all values specified in label array by a new value.
replaceLabels(ImageProcessor, float[], float) - Static method in class inra.ijpb.label.LabelImages
Replace all values specified in label array by the value 0.
replaceLabels(ImageStack, int[], int) - Static method in class inra.ijpb.label.LabelImages
Replace all values specified in label array by a new value.
replaceLabels(ImageStack, float[], float) - Static method in class inra.ijpb.label.LabelImages
Replace all values specified in label array by the specified value.
ReplaceLabelValues - Class in inra.ijpb.label.edit
Provides several methods for replacing label values within a label map (stored as 8-, 16- or 32-bits).
ReplaceLabelValues() - Constructor for class inra.ijpb.label.edit.ReplaceLabelValues
 
ReplaceLabelValuesPlugin - Class in inra.ijpb.plugins
Replaces the value of selected label(s) by a given value, for 2D/3D images, for gray8, gray16 and float images.
ReplaceLabelValuesPlugin() - Constructor for class inra.ijpb.plugins.ReplaceLabelValuesPlugin
 
replaceValue(ImagePlus, double, double) - Static method in class inra.ijpb.data.image.Images3D
replaceValue(ImagePlus, double, double) - Static method in class inra.ijpb.data.image.ImageUtils
Replaces the elements of an image with a given value by a new value.
replaceValue(ImageProcessor, double, double) - Static method in class inra.ijpb.data.image.ImageUtils
Replaces the elements of a 2D image with a given value by a new value.
replaceValue(ImageStack, double, double) - Static method in class inra.ijpb.data.image.ImageUtils
Replaces the elements of a 3D image with a given value by a new value.
ReplaceValuePlugin - Class in inra.ijpb.plugins
Simple plugin to replace a value by another one, for 2D/3D images, for gray8, gray16 and float images.
ReplaceValuePlugin() - Constructor for class inra.ijpb.plugins.ReplaceValuePlugin
 
ReplicatedBorder - Class in inra.ijpb.data.border
Assess pixel outside image bounds have same value as the closest pixel on image border.
ReplicatedBorder(ImageProcessor) - Constructor for class inra.ijpb.data.border.ReplicatedBorder
Creates a new Replicating Border Manager
ReplicatedBorder3D - Class in inra.ijpb.data.border
Assess pixel outside image bounds have same value as the closest pixel on image border.
ReplicatedBorder3D(ImageStack) - Constructor for class inra.ijpb.data.border.ReplicatedBorder3D
Creates a new Replicating Border Manager
Result(ImageStack) - Constructor for class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling3D.Result
Creates a new Result class from an (empty) labelMap.
Result(ImageProcessor) - Constructor for class inra.ijpb.label.conncomp.LabelBoundariesLabeling2D.Result
Initializes a new Result instance from a boundary label map.
Result(ImageStack) - Constructor for class inra.ijpb.label.conncomp.LabelBoundariesLabeling3D.Result
Initializes a new Result instance from a boundary label map.
Result() - Constructor for class inra.ijpb.measure.region2d.AverageThickness.Result
 
Result(double, double) - Constructor for class inra.ijpb.measure.region2d.Convexity.Result
Creates a new result for storing convexity, based on the area and the convex area measures for the region.
Result() - Constructor for class inra.ijpb.measure.region2d.GeodesicDiameter.Result
 
Result() - Constructor for class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.Result
Default empty constructor.
Result(double, double, double) - Constructor for class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.Result
Creates a new data class for storing intrinsic volume measurements.
Result() - Constructor for class inra.ijpb.measure.region3d.GeodesicDiameter3D.Result
 
Result() - Constructor for class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.Result
Empty constructor.
Result(double, double, double, double) - Constructor for class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.Result
Creates a new data class for storing intrinsic volume measurements.
ResultsBuilder - Class in inra.ijpb.measure
Builder-type class to hold results Basically it will keep appending results to a larger results table Built in a way where we can chain them together
ResultsBuilder() - Constructor for class inra.ijpb.measure.ResultsBuilder
Basic constructor.
ResultsBuilder(ResultsTable) - Constructor for class inra.ijpb.measure.ResultsBuilder
Constructs a ResultsBuilder initializing the default table to the input one.
reverse() - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
Returns this structuring element, as oriented line structuring elements are symmetric by definition.
reverse() - Method in class inra.ijpb.morphology.strel.BallStrel
 
reverse() - Method in class inra.ijpb.morphology.strel.ChamferStrel
 
reverse() - Method in class inra.ijpb.morphology.strel.ChamferStrel3D
 
reverse() - Method in class inra.ijpb.morphology.strel.Cross3DStrel
 
reverse() - Method in class inra.ijpb.morphology.strel.Cross3x3Strel
Returns this structuring element, as is is self-reverse.
reverse() - Method in class inra.ijpb.morphology.strel.CubeStrel
 
reverse() - Method in class inra.ijpb.morphology.strel.CuboidStrel
Returns a cuboidal structuring element with same size, but offset located symmetrically with respect to structuring element center.
reverse() - Method in class inra.ijpb.morphology.strel.DiamondStrel
 
reverse() - Method in class inra.ijpb.morphology.strel.DiskStrel
 
reverse() - Method in class inra.ijpb.morphology.strel.EllipsoidStrel
Returns this instance, as an ellipsoid is symmetric.
reverse() - Method in class inra.ijpb.morphology.strel.ExtrudedStrel
 
reverse() - Method in interface inra.ijpb.morphology.strel.InPlaceStrel
The reverse structuring element of an InPlaceStrel is also an InPlaceStrel.
reverse() - Method in interface inra.ijpb.morphology.strel.InPlaceStrel3D
The reverse structuring element of an InPlaceStrel is also an InPlaceStrel.
reverse() - Method in class inra.ijpb.morphology.strel.LinearDepthStrel3D
Returns a linear horizontal line with same size and offset equal to size-offset-1.
reverse() - Method in class inra.ijpb.morphology.strel.LinearDiagDownStrel
Returns a linear diagonal line with same size and offset equal to size-offset.
reverse() - Method in class inra.ijpb.morphology.strel.LinearDiagUpStrel
Returns a linear diagonal line with same size and offset equal to size-offset.
reverse() - Method in class inra.ijpb.morphology.strel.LinearHorizontalStrel
Returns a linear horizontal line with same size and offset equal to size-offset-1.
reverse() - Method in class inra.ijpb.morphology.strel.LinearVerticalStrel
Returns a linear vertical line with same size and offset equal to size-offset-1.
reverse() - Method in class inra.ijpb.morphology.strel.OctagonStrel
 
reverse() - Method in interface inra.ijpb.morphology.Strel
Returns a reversed (i.e.
reverse() - Method in interface inra.ijpb.morphology.strel.SeparableStrel
The reversed structuring element of a separable strel is also separable.
reverse() - Method in interface inra.ijpb.morphology.strel.SeparableStrel3D
The reversed structuring element of a separable strel is also separable.
reverse() - Method in class inra.ijpb.morphology.strel.SquareStrel
 
reverse() - Method in interface inra.ijpb.morphology.Strel3D
Returns a reversed (i.e.
RIGHT - Static variable in class inra.ijpb.morphology.strel.ShiftedCross3x3Strel
A cross-shaped structuring element located on the right of the reference pixel.
run(String) - Method in class inra.ijpb.plugins.AnalyzeMicrostructure3D
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.AnalyzeRegions
 
run(String) - Method in class inra.ijpb.plugins.AnalyzeRegions3D
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.AreaOpeningPlugin
 
run(String) - Method in class inra.ijpb.plugins.AverageThicknessPlugin
 
run(String) - Method in class inra.ijpb.plugins.BinaryOrLabelOverlayPlugin
The run method used to start the plugin from the GUI.
run(String) - Method in class inra.ijpb.plugins.BinaryOverlayPlugin
 
run(String) - Method in class inra.ijpb.plugins.BoundingBox3DPlugin
 
run(String) - Method in class inra.ijpb.plugins.BoundingBoxPlugin
 
run(String) - Method in class inra.ijpb.plugins.ChamferDistanceMap3DPlugin
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.ChamferDistanceMapPlugin
Apply the current filter settings to process the given image.
run(String) - Method in class inra.ijpb.plugins.ConvexifyPlugin
 
run(String) - Method in class inra.ijpb.plugins.CropLabelPlugin
 
run(String) - Method in class inra.ijpb.plugins.DilateLabelsPlugin
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.DirectionalFilteringPlugin
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.DistanceTransformWatershed
Apply the current filter settings to process the given image.
run(String) - Method in class inra.ijpb.plugins.DistanceTransformWatershed3D
Plugin run method
run(String) - Method in class inra.ijpb.plugins.DrawLabelsAsOverlayPlugin
 
run(String) - Method in class inra.ijpb.plugins.DrawTableValuesPlugin
 
run(String) - Method in class inra.ijpb.plugins.EquivalentEllipsePlugin
 
run(String) - Method in class inra.ijpb.plugins.EquivalentEllipsoidPlugin
 
run(String) - Method in class inra.ijpb.plugins.ExpandLabelsPlugin
 
run(String) - Method in class inra.ijpb.plugins.ExtendBordersPlugin
 
run(String) - Method in class inra.ijpb.plugins.ExtendedMinAndMax3DPlugin
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.ExtendedMinAndMaxPlugin
 
run(String) - Method in class inra.ijpb.plugins.FillHolesPlugin
 
run(String) - Method in class inra.ijpb.plugins.FillLabelHolesPlugin
 
run(String) - Method in class inra.ijpb.plugins.GeodesicDiameter3DPlugin
 
run(String) - Method in class inra.ijpb.plugins.GeodesicDiameterPlugin
 
run(String) - Method in class inra.ijpb.plugins.GeodesicDistanceMap3D
Deprecated.
 
run(String) - Method in class inra.ijpb.plugins.GeodesicDistanceMap3DPlugin
 
run(String) - Method in class inra.ijpb.plugins.GeodesicDistanceMapPlugin
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.GrayscaleAreaOpeningPlugin
 
run(String) - Method in class inra.ijpb.plugins.GrayscaleAttributeFiltering3D
Plugin run method
run(ImageProcessor) - Method in class inra.ijpb.plugins.GrayscaleAttributeFilteringPlugin
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.GrayscaleBoxDiameterOpeningPlugin
 
run(String) - Method in class inra.ijpb.plugins.ImposeMinAndMax3DPlugin
 
run(String) - Method in class inra.ijpb.plugins.ImposeMinAndMaxPlugin
 
run(String) - Method in class inra.ijpb.plugins.InertiaEllipsePlugin
Deprecated.
 
run(String) - Method in class inra.ijpb.plugins.InertiaEllipsoidPlugin
Deprecated.
 
run(String) - Method in class inra.ijpb.plugins.IntensityMeasures3D
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.InteractiveGeodesicDistanceMap
Apply the current filter settings to process the given image.
run(String) - Method in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.InteractiveMorphologicalReconstruction
Apply the current filter settings to process the given image.
run(String) - Method in class inra.ijpb.plugins.InteractiveMorphologicalReconstruction3D
Apply the current filter settings to process the given image.
run(String) - Method in class inra.ijpb.plugins.InterfaceSurfaceArea3D
 
run(String) - Method in class inra.ijpb.plugins.KeepLargestLabelPlugin
 
run(String) - Method in class inra.ijpb.plugins.KeepLargestRegionPlugin
 
run(String) - Method in class inra.ijpb.plugins.KillBordersPlugin
 
run(String) - Method in class inra.ijpb.plugins.LabelAreaOpeningPlugin
 
run(String) - Method in class inra.ijpb.plugins.LabelBoundariesPlugin
 
run(String) - Method in class inra.ijpb.plugins.LabelEdition
Plug-in run method
run(String) - Method in class inra.ijpb.plugins.LabelingPlugin
 
run(String) - Method in class inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin
 
run(String) - Method in class inra.ijpb.plugins.LabelOverlapMeasures
 
run(String) - Method in class inra.ijpb.plugins.LabelSizeFilteringPlugin
 
run(String) - Method in class inra.ijpb.plugins.LabelToRgbPlugin
 
run(String) - Method in class inra.ijpb.plugins.LabelToValuePlugin
 
run(String) - Method in class inra.ijpb.plugins.MarkerControlledWatershed3DPlugin
Plugin run method to be called from ImageJ
run(String) - Method in class inra.ijpb.plugins.MaxFeretDiameterPlugin
 
run(String) - Method in class inra.ijpb.plugins.MaxInscribedCirclePlugin
 
run(String) - Method in class inra.ijpb.plugins.MaxInscribedSpherePlugin
 
run(String) - Method in class inra.ijpb.plugins.MergeLabelsPlugin
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
 
run(String) - Method in class inra.ijpb.plugins.MorphologicalFilter3DPlugin
 
run(String) - Method in class inra.ijpb.plugins.MorphologicalFilterCross3DPlugin
 
run(ImageProcessor) - Method in class inra.ijpb.plugins.MorphologicalFilterPlugin
 
run(String) - Method in class inra.ijpb.plugins.MorphologicalReconstruction3DPlugin
 
run(String) - Method in class inra.ijpb.plugins.MorphologicalReconstructionPlugin
 
run(String) - Method in class inra.ijpb.plugins.MorphologicalSegmentation
 
run(String) - Method in class inra.ijpb.plugins.NeighborLabelsPlugin
 
run(String) - Method in class inra.ijpb.plugins.OrientedBoundingBoxPlugin
 
run(String) - Method in class inra.ijpb.plugins.ParticleAnalysis3DPlugin
Deprecated.
 
run(String) - Method