Index

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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(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.LocalBufferedHistogram

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(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.

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.

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(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.

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(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.

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, 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, String, 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(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(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(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(ImageProcessor) - Method in class inra.ijpb.measure.region2d.GeodesicDiameter

Computes the geodesic diameter of each particle within the given label image.

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, 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 - 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() - 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.WatershedTransform2D

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.

apply(ImageStack, int) - Method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.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(ImageStack, int, 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, Strel3D) - Method in enum inra.ijpb.morphology.Morphology.Operation

Applies the current operator to the input 3D image.

apply(ImageProcessor, int) - Method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation

Applies this operation to the specified image.

apply(ImageProcessor, int) - Method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation

Process to image given as argument.

apply(ImageProcessor, int, 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, 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(ImageProcessor, Connectivity2D) - Method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation

Process to image given as argument.

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[][], 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.

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.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.region3d.BinaryConfigurationsHistogram3D

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(ImagePlus, double[]) - Static method in class inra.ijpb.label.LabelImages

Applies the given Look-up table to the input label image.

applyLut(ImageStack, double[]) - Static method in class inra.ijpb.label.LabelImages

Applies the given Look-up table to the input 3D 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.

applyTo(float, float) - Method in interface inra.ijpb.math.ImageCalculator.Operation

The method to override to make it possible to use an operation.

applyTo(int, int) - Method in interface inra.ijpb.math.ImageCalculator.Operation

The method to override to make it possible to use an operation.

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) - 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) - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DByFlooding

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, ImageStack) - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DByFlooding

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) - 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) - 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) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3D

Run the reconstruction by dilation algorithm using the images specified as argument.

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) - 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) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DGray8

Run the reconstruction by dilation algorithm using the images specified as argument.

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) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanningGray8

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(ImageStack, ImageStack, int) - Method in enum inra.ijpb.plugins.MorphologicalReconstruction3DPlugin.Operation

Process to image given as argument.

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, 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.GeodesicReconstruction3DHybrid0Gray16

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, 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.GeodesicReconstructionByDilation3D

applyTo(ImageStack, ImageStack, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByDilation3DGray8

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, 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.GeodesicReconstructionByErosion3DGray8

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, ImageStack) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion3DScanningGray8

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(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(ImageProcessor, ImageProcessor) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionByErosion

Run the reconstruction by erosion algorithm using the images specified as argument.

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(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, 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.ImposeMinAndMaxPlugin.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 - 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.

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

Deprecated.

use IntrinsicVolumes2D.areas(ImageProcessor, int[], Calibration) instead

area(ImageProcessor, Calibration) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D

Measures the area of the foreground region within a binary image.

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(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.

AreaOpening - Interface in inra.ijpb.morphology.attrfilt

Area opening for gray level images.

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 - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features

The boolean flag for computing average thickness.

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.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.

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