- 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
-
- 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
-
- 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
-
- applyWithSortedList() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
-
- applyWithSortedListAndDams() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
-
- applyWithSortedListAndDams() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform3D
-
- 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
-
- 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.
- 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
-
- boundingBox(ImageProcessor, int[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
-
- boundingBox(ImageStack) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
- 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.
- 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
-
- 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
-
- ChamferWeights3D - Enum in inra.ijpb.binary
-
- 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
-
- 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
-
- 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
-
- 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
-
- computeLabels(ImageProcessor, int, int) - Static method in class inra.ijpb.binary.ConnectedComponents
-
- computeLabels(ImageStack, int, int) - Static method in class inra.ijpb.binary.ConnectedComponents
-
- 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
-
- computeTable(ImagePlus) - Method in class inra.ijpb.measure.region2d.RegionAnalyzer2D
-
- computeTable(ImagePlus) - Method in class inra.ijpb.measure.region3d.RegionAnalyzer3D
-
- 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
-
- 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
-
- 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
-
- croftonPerimeter(ImageProcessor, int[], double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures2D
-
- croftonPerimeterD2(ImageProcessor, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
-
- croftonPerimeterD4(ImageProcessor, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
-
- 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.
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
- 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
-
- 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
-
- 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
-
- 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
-
- exec(ImagePlus, ImagePlus, String, short[], boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMapPlugin
-
- exec(ImagePlus, short[]) - Method in class inra.ijpb.plugins.MaxInscribedCirclePlugin
-
- exec(ImagePlus, int) - Method in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
-
- exec(ImagePlus, int, boolean) - Method in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
-
- exec(ImagePlus, Morphology.Operation, Strel) - Method in class inra.ijpb.plugins.MorphologicalFilterPlugin
-
- 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.
- 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
-
- 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
-
- 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
-
- floodFill(ImageStack, int, int, int, double, int) - Static method in class inra.ijpb.morphology.FloodFill
-
- floodFill(ImageStack, int, int, int, ImageStack, int, int) - Static method in class inra.ijpb.morphology.FloodFill
-
- 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
-
- 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.
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- GeodesicDistanceTransformShort(short[], boolean) - Constructor for class inra.ijpb.binary.geodesic.GeodesicDistanceTransformShort
-
- GeodesicDistanceTransformShort5x5 - Class in inra.ijpb.binary.geodesic
-
- 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
-
- GeodesicReconstruction3D - Class in inra.ijpb.morphology
-
- 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
-
- GeometricMeasures3D - Class in inra.ijpb.measure
-
- 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
-
- getAnimationSortedListAndDams() - Method in class inra.ijpb.watershed.MarkerControlledWatershedTransform2D
-
- 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.
- 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
-
- InertiaEllipse - Class in inra.ijpb.measure.region2d
-
- InertiaEllipse() - Constructor for class inra.ijpb.measure.region2d.InertiaEllipse
-
Deprecated.
Default constructor
- InertiaEllipsePlugin - Class in inra.ijpb.plugins
-
- 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
-
- inertiaEllipsoid(ImageStack, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
- inertiaEllipsoid(ImageStack, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
- InertiaEllipsoid - Class in inra.ijpb.measure.region3d
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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.
- 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
-
- maximumInscribedCircle(ImageProcessor, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
-
- maximumInscribedSphere(ImageStack, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
- 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
-
- 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.
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- process(ImageStack, int, int, int, int, int, int, BorderManager3D) - Static method in class inra.ijpb.plugins.ExtendBordersPlugin
-
- 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
-
- 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
-
- 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
-
- 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 in class inra.ijpb.plugins.RegionAdjacencyGraphPlugin
-
- run(String) - Method in class inra.ijpb.plugins.RegionalMinAndMax3DPlugin
-
- run(ImageProcessor) - Method in class inra.ijpb.plugins.RegionalMinAndMaxPlugin
-
- run(String) - Method in class inra.ijpb.plugins.RegionBoundariesLabelingPlugin
-
- run(ImageProcessor) - Method in class inra.ijpb.plugins.RegionMorphometryPlugin
-
Deprecated.
- run(String) - Method in class inra.ijpb.plugins.RemapLabelsPlugin
-
- run(String) - Method in class inra.ijpb.plugins.RemoveBorderLabelsPlugin
-
- run(String) - Method in class inra.ijpb.plugins.RemoveLargestLabelPlugin
-
- run(String) - Method in class inra.ijpb.plugins.RemoveLargestRegionPlugin
-
- run(String) - Method in class inra.ijpb.plugins.ReplaceLabelValuesPlugin
-
- run(String) - Method in class inra.ijpb.plugins.ReplaceValuePlugin
-
- run(String) - Method in class inra.ijpb.plugins.SelectLabelsPlugin
-
- run(String) - Method in class inra.ijpb.plugins.SetLabelMapPlugin
-
- run(String) - Method in class inra.ijpb.plugins.SizeOpeningPlugin
-
- run(String) - Method in class inra.ijpb.plugins.Watershed3DPlugin
-
Plugin run method, to be called from ImageJ.
- RUN_SEGMENTATION - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
name of the macro method to segment the
current image based on the current parameters
- RUN_SEGMENTATION - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
-
name of the macro method to segment the
current image based on the current parameters
- runLengthsCorners(ImageProcessor) - Static method in class inra.ijpb.measure.region2d.RegionBoundaries
-
Returns a set of points located at the corners of a binary particle.
- runlengthsCorners(ImageProcessor, int[]) - Static method in class inra.ijpb.measure.region2d.RegionBoundaries
-
Returns a set of points located at the corners of a binary particle.
- runLengthsCornersMap(ImageProcessor, int[]) - Static method in class inra.ijpb.measure.region2d.RegionBoundaries
-
Returns a set of points located at the corners of each region.
- samplingVolume(ImageStack, Calibration) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
-
Returns the "inner volume" of the 3D image, i.e.
- samplingVolume(ImageStack, Calibration) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumes3DUtils
-
Returns the "inner volume" of the 3D image, i.e.
- secondExtremity - Variable in class inra.ijpb.measure.region2d.GeodesicDiameter.Result
-
The second geodesic extremity found by the algorithm.
- secondExtremity - Variable in class inra.ijpb.measure.region3d.GeodesicDiameter3D.Result
-
The second geodesic extremity found by the algorithm.
- segment(String, String, String) - Static method in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
Segment current image (GUI needs to be running)
- segment(String, String, String, String) - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
-
- segment(String, String, String) - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
-
Segment current image (GUI needs to be running)
- selectedLabelsToMask(ImagePlus, int[]) - Static method in class inra.ijpb.plugins.NeighborLabelsPlugin
-
Creates a new image containing only the specified labels.
- SelectLabelsPlugin - Class in inra.ijpb.plugins
-
Creates a new binary image containing only the selected label(s).
- SelectLabelsPlugin() - Constructor for class inra.ijpb.plugins.SelectLabelsPlugin
-
- SeparableStrel - Interface in inra.ijpb.morphology.strel
-
Interface for structuring elements that can be decomposed into several
"simpler" structuring elements.
- SeparableStrel3D - Interface in inra.ijpb.morphology.strel
-
Interface for structuring elements that can be decomposed into several
"simpler" structuring elements.
- set(int, int) - Method in class inra.ijpb.data.Cursor2D
-
Sets the position of this cursor.
- set(int, int, int) - Method in class inra.ijpb.data.Cursor3D
-
Sets the position of this cursor.
- set(int, int, int, int) - Method in class inra.ijpb.data.image.ByteStackWrapper
-
- set(int, int, int, int) - Method in class inra.ijpb.data.image.FloatStackWrapper
-
- set(int, int, int, int) - Method in interface inra.ijpb.data.image.Image3D
-
Changes the value at the specified coordinates, using an integer to
specify the new value.
- set(int, int, int, int) - Method in class inra.ijpb.data.image.ShortStackWrapper
-
- SET_DISPLAY - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
name of the macro method to set the output display format
- SET_DISPLAY - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
-
name of the macro method to set the output display format
- SET_GRADIENT_TYPE - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
-
name of the macro method to set the gradient method
- SET_INPUT_TYPE - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
name of the macro method to set the input image type
- SET_INPUT_TYPE - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
-
name of the macro method to set the input image type
- SET_RADIUS - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
name of the macro method to set the gradient radius
- SET_RADIUS - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
-
name of the macro method to set the gradient radius
- setAll(boolean) - Method in class inra.ijpb.plugins.AnalyzeRegions.Features
-
Set the state of all features.
- setChamferWeights(float[]) - Method in class inra.ijpb.measure.region2d.GeodesicDiameter
-
Deprecated.
- setChannelName(String) - Method in class inra.ijpb.morphology.strel.AbstractStrel
-
Sets the name of the currently processed channel.
- setChannelName(String) - Method in interface inra.ijpb.morphology.Strel
-
Sets the name of the currently processed channel, for process monitoring.
- setComputePaths(boolean) - Method in class inra.ijpb.measure.region2d.GeodesicDiameter
-
Updates the value of the computePahs option.
- setConnectivity(int) - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
-
- setConnectivity(int) - Method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
-
- setConnectivity(int) - Method in class inra.ijpb.morphology.attrfilt.AreaOpeningQueue
-
Changes the connectivity of this algorithm.
- setConnectivity(int) - Method in class inra.ijpb.morphology.attrfilt.BoxDiagonalOpeningQueue
-
Changes the connectivity of this algorithm.
- setConnectivity(int) - Method in class inra.ijpb.morphology.attrfilt.SizeOpening3DQueue
-
Changes the connectivity used by this algorithm.
- setConnectivity(int) - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
-
Sets the connectivity value.
- setConnectivity(int) - Method in class inra.ijpb.morphology.extrema.RegionalExtremaAlgo
-
Sets the connectivity value.
- setConnectivity(int) - Method in interface inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgo
-
Changes the connectivity of the algorithm to either 6 or 26.
- setConnectivity(int) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
-
- setConnectivity(int) - Method in interface inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgo
-
Changes the connectivity of the algorithm to either 4 or 8.
- setConnectivity(int) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgoStub
-
- setConnectivity(int) - Method in class inra.ijpb.watershed.WatershedTransform2D
-
Set the pixel connectivity (4 or 8)
- setConnectivity(int) - Method in class inra.ijpb.watershed.WatershedTransform3D
-
Set the voxel connectivity (6 or 26)
- setCursor(Cursor2D) - Method in class inra.ijpb.data.Neighborhood2D
-
Sets the position of the Neighborhood2D.
- setCursor(Cursor3D) - Method in class inra.ijpb.data.Neighborhood3D
-
Sets the position of the Neighborhood3D.
- setDirectionNumber(int) - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
-
- setDirectionNumber(int) - Method in class inra.ijpb.measure.region3d.InterfaceSurfaceArea
-
Specifies the number of directions to use.
- setDirectionNumber(int) - Method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
-
- setDisplayFormat(String) - Static method in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
Set the display format in the GUI
- setDisplayFormat(String) - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
-
Set the display format in the GUI
- setExtremaType(ExtremaType) - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
-
Sets the type of extrema.
- setExtremaType(ExtremaType) - Method in class inra.ijpb.morphology.extrema.RegionalExtremaAlgo
-
Sets the type of extrema.
- setGradientRadius(String) - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
-
Set the gradient radius
- setGradientType(String) - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
-
Set the gradient method to use
- setInputImageType(String) - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
-
Set input image type
- SetLabelMapPlugin - Class in inra.ijpb.plugins
-
Changes the current LUT such that each label is associated to a different
color, and specifies color of background.
- SetLabelMapPlugin() - Constructor for class inra.ijpb.plugins.SetLabelMapPlugin
-
- setMinMaxSign(int) - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferDouble
-
Changes the sign used for distinguishing minimum and maximum.
- setMinMaxSign(int) - Method in class inra.ijpb.morphology.strel.LocalExtremumBufferGray8
-
Changes the sign used for distinguishing minimum and maximum.
- setNPasses(int) - Method in class inra.ijpb.plugins.AreaOpeningPlugin
-
- setNPasses(int) - Method in class inra.ijpb.plugins.ChamferDistanceMapPlugin
-
- setNPasses(int) - Method in class inra.ijpb.plugins.DirectionalFilteringPlugin
-
- setNPasses(int) - Method in class inra.ijpb.plugins.DistanceTransformWatershed
-
- setNPasses(int) - Method in class inra.ijpb.plugins.ExtendedMinAndMaxPlugin
-
- setNPasses(int) - Method in class inra.ijpb.plugins.GrayscaleAreaOpeningPlugin
-
- setNPasses(int) - Method in class inra.ijpb.plugins.GrayscaleAttributeFilteringPlugin
-
- setNPasses(int) - Method in class inra.ijpb.plugins.GrayscaleBoxDiameterOpeningPlugin
-
- setNPasses(int) - Method in class inra.ijpb.plugins.InteractiveGeodesicDistanceMap
-
- setNPasses(int) - Method in class inra.ijpb.plugins.InteractiveMorphologicalReconstruction
-
- setNPasses(int) - Method in class inra.ijpb.plugins.MorphologicalFilterPlugin
-
- setNPasses(int) - Method in class inra.ijpb.plugins.RegionalMinAndMaxPlugin
-
- setProgressVisible(boolean) - Method in class inra.ijpb.morphology.extrema.RegionalExtrema3DAlgo
-
Sets the value of progress visibility option.
- setProgressVisible(boolean) - Method in class inra.ijpb.morphology.extrema.RegionalExtremaAlgo
-
Sets the value of progress visibility option.
- setReconstructionType(GeodesicReconstructionType) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Float
-
- setReconstructionType(GeodesicReconstructionType) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray16
-
- setReconstructionType(GeodesicReconstructionType) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid0Gray8
-
- setReconstructionType(GeodesicReconstructionType) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DHybrid1Image3D
-
- setReconstructionType(GeodesicReconstructionType) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionHybrid
-
- setReconstructionType(GeodesicReconstructionType) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstructionScanning
-
- setShowGradient(String) - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
-
Set GUI to show gradient image in the main canvas
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.AnalyzeRegions
-
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.AreaOpeningPlugin
-
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.ChamferDistanceMapPlugin
-
Called at the beginning of the process to know if the plugin can be run
with current image, and at the end to finalize.
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.DirectionalFilteringPlugin
-
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.DistanceTransformWatershed
-
Called at the beginning of the process to know if the plugin can be run
with current image, and at the end to finalize.
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.ExtendedMinAndMaxPlugin
-
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.GrayscaleAreaOpeningPlugin
-
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.GrayscaleAttributeFilteringPlugin
-
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.GrayscaleBoxDiameterOpeningPlugin
-
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.InteractiveGeodesicDistanceMap
-
Called at the beginning of the process to know if the plugin can be run
with current image, and at the end to finalize.
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.InteractiveMorphologicalReconstruction
-
Called at the beginning of the process to know if the plugin can be run
with current image, and at the end to finalize.
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.MicrostructureAnalysisPlugin
-
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.MorphologicalFilterPlugin
-
Setup function is called in the beginning of the process, but also at the
end.
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.RegionalMinAndMaxPlugin
-
- setup(String, ImagePlus) - Method in class inra.ijpb.plugins.RegionMorphometryPlugin
-
Deprecated.
- setValue(int, int, int, double) - Method in class inra.ijpb.data.image.ByteStackWrapper
-
- setValue(Cursor3D, double) - Method in class inra.ijpb.data.image.ByteStackWrapper
-
- setValue(int, int, int, double) - Method in class inra.ijpb.data.image.FloatStackWrapper
-
- setValue(Cursor3D, double) - Method in class inra.ijpb.data.image.FloatStackWrapper
-
- setValue(int, int, int, double) - Method in interface inra.ijpb.data.image.Image3D
-
Changes the value at the specified coordinates, using a double to
specify the new value.
- setValue(Cursor3D, double) - Method in interface inra.ijpb.data.image.Image3D
-
Changes the value at the specified coordinates, using a double to
specify the new value.
- setValue(int, int, int, double) - Method in class inra.ijpb.data.image.ShortStackWrapper
-
- setValue(Cursor3D, double) - Method in class inra.ijpb.data.image.ShortStackWrapper
-
- setVerbose(boolean) - Method in class inra.ijpb.watershed.WatershedTransform2D
-
Set verbose flag
- setVerbose(boolean) - Method in class inra.ijpb.watershed.WatershedTransform3D
-
Set verbose flag
- setVertex(int, Point2D) - Method in class inra.ijpb.geometry.Polygon2D
-
Changes vertex coordinate at the specified index
- ShiftedCross3x3Strel - Class in inra.ijpb.morphology.strel
-
Structuring element representing a 3x3 cross, that considers the reference
pixel together with four neighbors located either on the left or on the
right of the reference pixel.
- ShortOffset(int, int, int, short) - Constructor for class inra.ijpb.binary.ChamferWeights3D.ShortOffset
-
Deprecated.
Creates a new offset for integer computations.
- ShortOffset(int, int, short) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2D.ShortOffset
-
Creates a new Offset using a 16-bits integer weight.
- ShortOffset(int, int, int, short) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3D.ShortOffset
-
Creates a new Offset using a 16-bits integer weight.
- ShortStackWrapper - Class in inra.ijpb.data.image
-
Access the data of a 3D image containing gray16 values stored as short.
- ShortStackWrapper(ImageStack) - Constructor for class inra.ijpb.data.image.ShortStackWrapper
-
Creates a new wrapper to the ImageStack.
- SHOW_GRADIENT - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
name of the macro method to set the flag to show the gradient image
- SHOW_GRADIENT - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
-
name of the macro method to set the flag to show the gradient image
- SHOW_RESULT_OVERLAY - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
name of the macro method to toggle the current overlay
- SHOW_RESULT_OVERLAY - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
-
name of the macro method to toggle the current overlay
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.AreaOpeningPlugin
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.ChamferDistanceMapPlugin
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.DirectionalFilteringPlugin
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.DistanceTransformWatershed
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.ExtendedMinAndMaxPlugin
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.GrayscaleAreaOpeningPlugin
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.GrayscaleAttributeFilteringPlugin
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.GrayscaleBoxDiameterOpeningPlugin
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.InteractiveGeodesicDistanceMap
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.InteractiveMorphologicalReconstruction
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.MorphologicalFilterPlugin
-
- showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class inra.ijpb.plugins.RegionalMinAndMaxPlugin
-
- showDialog() - Method in class inra.ijpb.plugins.SetLabelMapPlugin
-
Displays the dialog.
- showElapsedTime(String, double, ImagePlus) - Static method in class inra.ijpb.util.IJUtils
-
Display elapsed time, converted into seconds, and computes number of
processed elements per second.
- showProgress - Variable in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
-
Boolean flag for the display of algorithm progress in ImageJ status bar
- showProgress(double, double) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
-
Displays the current progression of the algorithm in the status bar of
the ImageJ frame, if the showProgress flag is true.
- showProgress(double, double, String) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
-
Displays the current progression of the algorithm in the status bar of
the ImageJ frame, if the showProgress flag is true.
- showProgress - Variable in class inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgoStub
-
Boolean flag for the display of algorithm progress in ImageJ status bar
- showProgress() - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
-
- showProgress(boolean) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
-
- showProgress() - Method in interface inra.ijpb.morphology.Strel3D
-
Returns a boolean flag indicating whether or not this structuring
element should display its progress or not
- showProgress(boolean) - Method in interface inra.ijpb.morphology.Strel3D
-
Specifies if this structuring element should display its progress.
- showStatus - Variable in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
-
Boolean flag for the display of algorithm state in ImageJ status bar
- showStatus(String) - Method in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
-
Displays the specified message in the status bar of the ImageJ frame, if
the showStatus flag is true.
- showStatus - Variable in class inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgoStub
-
Boolean flag for the display of algorithm state in ImageJ status bar
- SHUFFLE_COLORS - Static variable in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
name of the macro method to shuffle color labels
- SHUFFLE_COLORS - Static variable in class inra.ijpb.plugins.MorphologicalSegmentation
-
name of the macro method to shuffle color labels
- shuffleColors() - Static method in class inra.ijpb.plugins.InteractiveMarkerControlledWatershed
-
Shuffle LUT of current display image.
- shuffleColors() - Static method in class inra.ijpb.plugins.MorphologicalSegmentation
-
Shuffle LUT of current display image.
- shuffleLut(byte[][]) - Static method in class inra.ijpb.color.ColorMaps
-
Creates a new LUT by applying a random permutation to the colors within the original LUT.
- shuffleLut(byte[][], long) - Static method in class inra.ijpb.color.ColorMaps
-
Shuffles the LUT, using the specified seed for initializing the random
generator.
- signedArea() - Method in class inra.ijpb.geometry.Polygon2D
-
Computes the signed area of this polygon
- size() - Method in class inra.ijpb.label.conncomp.BoundarySet
-
- sizeOpening(ImagePlus, int) - Static method in class inra.ijpb.binary.BinaryImages
-
Applies size opening on a binary 2D or 3D image.
- sizeOpening(ImagePlus, int) - Static method in class inra.ijpb.label.LabelImages
-
Applies size opening on a label image: creates a new label image that
contains only particles with at least the specified number of pixels or
voxels.
- sizeOpening(ImagePlus, int) - Static method in class inra.ijpb.morphology.AttributeFiltering
-
Applies grayscale size opening on input image, by retaining only the
connected components that contain at least the specified number of elements
(pixels or voxels).
- SizeOpening3D - Interface in inra.ijpb.morphology.attrfilt
-
Size opening for 3D gray level images.
- SizeOpening3DQueue - Class in inra.ijpb.morphology.attrfilt
-
Volume opening on 3D grayscale image using priority queue for updating each
3D regional maxima.
- SizeOpening3DQueue() - Constructor for class inra.ijpb.morphology.attrfilt.SizeOpening3DQueue
-
- SizeOpeningPlugin - Class in inra.ijpb.plugins
-
Select binary particles in a 2D or 3D image based on number of pixels.
- SizeOpeningPlugin() - Constructor for class inra.ijpb.plugins.SizeOpeningPlugin
-
- skeleton(ImageProcessor) - Static method in class inra.ijpb.binary.BinaryImages
-
Computes the skeleton of a binary image, and returns another binary image.
- source - Variable in class inra.ijpb.algo.AlgoEvent
-
The algorithm object that threw this event
- Sphere - Class in inra.ijpb.geometry
-
Contains data for representing sphere in the 3D space.
- Sphere(Point3D, double) - Constructor for class inra.ijpb.geometry.Sphere
-
Creates a new sphere from a center and a radius.
- sphericalAngle(Vector3D, Vector3D, Vector3D) - Static method in class inra.ijpb.measure.region3d.GeometryUtils
-
Computes the spherical angle of three points on the unit sphere, based on
the vectors.
- sphericalVoronoiDomainArea(Vector3D, Vector3D[]) - Static method in class inra.ijpb.measure.region3d.GeometryUtils
-
Computes area of a spherical Voronoi domain, based on a germ and several
neighbors.
- sphericity(double, double) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
-
Helper function that computes the sphericity index of 3D particles, based
on the value of volume and surface area.
- sphericity(double[], double[]) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
-
Helper function that computes the sphericity index of 3D particles, based
on the value of volume and surface area.
- splitChannels(ImageProcessor) - Static method in class inra.ijpb.data.image.ColorImages
-
Splits the channels of the color image into three new instances of
ByteProcessor.
- splitChannels(ImageStack) - Static method in class inra.ijpb.data.image.ColorImages
-
Splits the channels of the color image into three new instances of
ByteProcessor.
- SquareStrel - Class in inra.ijpb.morphology.strel
-
A square structuring element, obtained by decomposition into horizontal
and vertical linear structuring elements with the same size.
- SquareStrel(int) - Constructor for class inra.ijpb.morphology.strel.SquareStrel
-
Creates a new square structuring element of a given size.
- SquareStrel(int, int) - Constructor for class inra.ijpb.morphology.strel.SquareStrel
-
Creates a new square structuring element of a given size and
with a given offset.
- status - Variable in class inra.ijpb.algo.AlgoEvent
-
- step - Variable in class inra.ijpb.algo.AlgoEvent
-
- StraightLine2D - Class in inra.ijpb.geometry
-
A straight line in the plane.
- StraightLine2D(Point2D, Vector2D) - Constructor for class inra.ijpb.geometry.StraightLine2D
-
Creates a new straight line from an origin and a direction vector.
- StraightLine2D(Point2D, Point2D) - Constructor for class inra.ijpb.geometry.StraightLine2D
-
Creates a new straight line from two points belonging to the line
- Strel - Interface in inra.ijpb.morphology
-
Interface for planar structuring elements.
- Strel.Shape - Enum in inra.ijpb.morphology
-
An enumeration of the different possible structuring element shapes.
- Strel3D - Interface in inra.ijpb.morphology
-
Structuring element that process 3D stack.
- Strel3D.Shape - Enum in inra.ijpb.morphology
-
An enumeration of the different possible structuring element shapes.
- surfaceArea() - Method in class inra.ijpb.geometry.Sphere
-
- surfaceArea(ImageStack, double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
Deprecated.
Computes the surface area of each label in the 3D image, using the
specified resolution, and the given number of directions.
- surfaceArea(ImageStack, Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
-
Measures the surface area of a single region within a 3D binary image.
- surfaceArea - Variable in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.Result
-
The surface area of the region
- surfaceAreaCrofton(ImageStack, int[], double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
- surfaceAreaCrofton(ImageStack, int, double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
- surfaceAreaCroftonD3(ImageStack, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
- surfaceAreaDensity(ImageStack, Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
-
Measures the surface area density of a single region within a 3D binary image.
- surfaceAreaLut(Calibration, int) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumes3DUtils
-
Computes the Look-up table that is used to compute surface area.
- surfaceAreaLut(Calibration, int) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
-
- surfaceAreas(ImageStack, int[], Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
-
Measures the surface area of each region within a label image.
- SVENSSON_3_4_5_7 - Static variable in class inra.ijpb.binary.distmap.ChamferMask3D
-
Use weights 3 for orthogonal neighbors, 4 for square-diagonal neighbors,
5 for cube-diagonals, and 7 for (2,1,1) shifts.
- valueOf(String) - Static method in enum inra.ijpb.binary.ChamferWeights
-
Deprecated.
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.binary.ChamferWeights3D
-
Deprecated.
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.binary.distmap.ChamferMasks2D
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.binary.distmap.ChamferMasks3D
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.color.ColorMaps.CommonLabelMaps
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.color.CommonColors
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.data.border.BorderManager.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.data.border.BorderManager3D.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.morphology.directional.DirectionalFilter.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.morphology.directional.DirectionalFilter.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.morphology.extrema.ExtremaType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.morphology.geodrec.GeodesicReconstructionType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.morphology.Morphology.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.morphology.strel.LocalExtremum.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.morphology.Strel.Shape
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.morphology.Strel3D.Shape
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.Connectivity2D
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.Connectivity3D
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.ImposeMinAndMax3DPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.ImposeMinAndMaxPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.InteractiveMarkerControlledWatershed.ResultMode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.LabelSizeFilteringPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.MorphologicalReconstruction3DPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.MorphologicalReconstructionPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.MorphologicalSegmentation.ResultMode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.RegionalMinAndMax3DPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum inra.ijpb.util.CommonColors
-
Deprecated.
Returns the enum constant of this type with the specified name.
- values() - Static method in enum inra.ijpb.binary.ChamferWeights
-
Deprecated.
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.binary.ChamferWeights3D
-
Deprecated.
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.binary.distmap.ChamferMasks2D
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.binary.distmap.ChamferMasks3D
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.color.ColorMaps.CommonLabelMaps
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.color.CommonColors
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.data.border.BorderManager.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.data.border.BorderManager3D.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.morphology.directional.DirectionalFilter.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.morphology.directional.DirectionalFilter.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.morphology.extrema.ExtremaType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.morphology.geodrec.GeodesicReconstructionType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.morphology.Morphology.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.morphology.strel.LocalExtremum.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.morphology.Strel.Shape
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.morphology.Strel3D.Shape
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.Connectivity2D
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.Connectivity3D
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.ExtendedMinAndMax3DPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.ExtendedMinAndMaxPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.ImposeMinAndMax3DPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.ImposeMinAndMaxPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.InteractiveMarkerControlledWatershed.ResultMode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.LabelSizeFilteringPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.MorphologicalReconstruction3DPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.MorphologicalReconstructionPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.MorphologicalSegmentation.ResultMode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.RegionalMinAndMax3DPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.plugins.RegionalMinAndMaxPlugin.Operation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum inra.ijpb.util.CommonColors
-
Deprecated.
Returns an array containing the constants of this enum type, in
the order they are declared.
- Vector2D - Class in inra.ijpb.geometry
-
Represents a couple of coordinates in linear space, and provides some
computing methods.
- Vector2D() - Constructor for class inra.ijpb.geometry.Vector2D
-
Empty constructor, with all coordinates initialized to zero.
- Vector2D(double, double) - Constructor for class inra.ijpb.geometry.Vector2D
-
Initialization constructor.
- Vector3D - Class in inra.ijpb.geometry
-
Represents a triplet of coordinates in linear space, and provides some
computing methods.
- Vector3D() - Constructor for class inra.ijpb.geometry.Vector3D
-
Empty constructor, with all coordinates initialized to zero.
- Vector3D(double, double, double) - Constructor for class inra.ijpb.geometry.Vector3D
-
Initialization constructor.
- Vector3d - Class in inra.ijpb.measure
-
- Vector3d() - Constructor for class inra.ijpb.measure.Vector3d
-
Deprecated.
Empty constructor, with all coordinates initialized to zero.
- Vector3d(double, double, double) - Constructor for class inra.ijpb.measure.Vector3d
-
Deprecated.
Initialization constructor.
- verbose - Variable in class inra.ijpb.morphology.geodrec.GeodesicReconstruction3DAlgoStub
-
Boolean flag for the display of debugging infos.
- verbose - Variable in class inra.ijpb.morphology.geodrec.GeodesicReconstructionAlgoStub
-
Boolean flag for the display of debugging infos.
- verbose - Variable in class inra.ijpb.watershed.WatershedTransform2D
-
flag to output the transform steps and their
execution times in the log window
- verbose - Variable in class inra.ijpb.watershed.WatershedTransform3D
-
flag to output the transform steps and their
execution times in the log window
- vertexNumber() - Method in class inra.ijpb.geometry.Polygon2D
-
Returns the number of vertices within this polygon
- vertices() - Method in class inra.ijpb.geometry.Polygon2D
-
- VERWER - Static variable in class inra.ijpb.binary.distmap.ChamferMask2D
-
Chamfer mask in the 7-by-7 neighborhood defined using four weights.
- volume() - Method in class inra.ijpb.geometry.Box3D
-
Computes the volume of this bounding box.
- volume() - Method in class inra.ijpb.geometry.Sphere
-
- volume(ImageStack, double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
- volume(ImageStack, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
-
- volume(ImageStack, Calibration) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
-
Measures the volume of a single region within a 3D binary image.
- volume - Variable in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D.Result
-
The volume of the region
- volumeDensity(ImageStack) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
-
Measures the volume density of a single region within a 3D binary image.
- volumeLut(Calibration) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumes3DUtils
-
Computes the Look-up table that is used to compute volume.
- volumeLut(Calibration) - Static method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
-
- volumeOpening(ImageStack, int) - Static method in class inra.ijpb.binary.BinaryImages
-
Applies area opening on a binary image: creates a new binary image that
contains only particle with at least the specified number of voxels.
- volumeOpening(ImageStack, int) - Static method in class inra.ijpb.label.LabelImages
-
Applies area opening on a 3D label image: creates a new label image that
contains only particle with at least the specified number of voxels.
- volumeOpening(ImageStack, int) - Static method in class inra.ijpb.morphology.AttributeFiltering
-
Applies grayscale volume opening on input 3D image, by retaining only the
connected components that contain at least the specified number of voxels.
- volumeOpening(ImageStack, int, int) - Static method in class inra.ijpb.morphology.AttributeFiltering
-
Applies grayscale volume opening on input 3D image, by retaining only the
connected components that contain at least the specified number of voxels.
- volumes(ImageStack, int[], Calibration) - Static method in class inra.ijpb.measure.IntrinsicVolumes3D
-
Measures the volume of each region within a 3D label image.
- voxelCount(ImageStack, int[]) - Static method in class inra.ijpb.label.LabelImages
-
Counts the number of voxels that compose each labeled particle in 3D
image.
- VoxelRecord - Class in inra.ijpb.data
-
Class to store integer voxel coordinates and its
corresponding double value
- VoxelRecord(Cursor3D, double) - Constructor for class inra.ijpb.data.VoxelRecord
-
Creates a voxel record from a cursor and a double value.
- VoxelRecord(int, int, int, double) - Constructor for class inra.ijpb.data.VoxelRecord
-
Creates a voxel record from a position and a double value.