Index

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P

p1 - Variable in class inra.ijpb.geometry.PointPair2D

The first point of the pair.

p1 - Variable in class inra.ijpb.geometry.PointPair3D

The first point of the pair.

p2 - Variable in class inra.ijpb.geometry.PointPair2D

The second point of the pair.

p2 - Variable in class inra.ijpb.geometry.PointPair3D

The second point of the pair.

parseLabelList(String) - Static method in class inra.ijpb.util.IJUtils

Extracts a list of integer labels from a string representation.

ParticleAnalysis3DPlugin - Class in inra.ijpb.plugins

Deprecated.

replaced by AnalyzeRegions3D

ParticleAnalysis3DPlugin() - Constructor for class inra.ijpb.plugins.ParticleAnalysis3DPlugin

Deprecated.

particleArea(ImageProcessor, int) - Static method in class inra.ijpb.measure.GeometricMeasures2D

Deprecated.

path - Variable in class inra.ijpb.measure.region2d.GeodesicDiameter.Result

The largest geodesic path within the particle, joining the first and the second geodesic extremities.

perimeter - 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.

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.

perimeterDensity(ImageProcessor, double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures2D

Deprecated.

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

Computes perimeter density of binary image.

perimeterLut(Calibration, int) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumes2DUtils

Computes the Look-up table that is used for computing perimeter.

perimeterLut(Calibration, int) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D

Deprecated.

use IntrinsicVolumes2DUtils instead

perimeters(ImageProcessor, int[], Calibration, int) - Static method in class inra.ijpb.measure.IntrinsicVolumes2D

Measures the perimeter of each region within a label image.

PERIODIC - inra.ijpb.data.border.BorderManager.Type

uses periodic boundary to populate border

PERIODIC - inra.ijpb.data.border.BorderManager3D.Type

uses periodic boundary to populate border

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

The boolean flag for computing pixel count.

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.

PixelRecord - Class in inra.ijpb.data

Class to store integer pixel coordinates and its corresponding double value

PixelRecord(int, int, double) - Constructor for class inra.ijpb.data.PixelRecord

Create pixel record with cursor position and double value

PixelRecord(Cursor2D, 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(Vector3d) - Method in class inra.ijpb.measure.Vector3d

Deprecated.

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

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(double[], double[]) - Constructor for class inra.ijpb.geometry.Polygon2D

Creates a new polygon from the coordinates of its vertices.

Polygon2D(int) - Constructor for class inra.ijpb.geometry.Polygon2D

Creates a new empty polygon by allocating enough space for storing vertex coordinates.

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(ImageStack) - Static method in class inra.ijpb.data.image.Images3D

Deprecated.

replaced by ImageUtils.print(ImageStack)

print(ImageStack) - Static method in class inra.ijpb.data.image.ImageUtils

Prints the content of the given 3D image on the console.

print(ColorProcessor) - Static method in class inra.ijpb.data.image.ColorImages

Prints the content of the input color image on the console.

print(ImageProcessor) - Static method in class inra.ijpb.data.image.ImageUtils

Prints the content of the given ImageProcessor on the console.

printImage(ImageProcessor) - Static method in class inra.ijpb.util.IJUtils

Deprecated.

use ImageUtils.print(ImageProcessor) instead

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(ImagePlus) - Method in class inra.ijpb.label.select.LabelSizeFiltering

Applies size filtering on the input image.

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(ImagePlus) - Method in class inra.ijpb.plugins.AnalyzeMicrostructure3D

Computes features from an ImagePlus object.

process(ImagePlus) - Method in class inra.ijpb.plugins.AnalyzeRegions

Deprecated.

replaced by static process(ImagePlus, Features) method

process(ImagePlus) - Method in class inra.ijpb.plugins.AnalyzeRegions3D

Computes features from an ImagePlus object.

process(ImagePlus) - Method in class inra.ijpb.plugins.ParticleAnalysis3DPlugin

Deprecated.

Computes features from an ImagePlus object.

process(ImagePlus, float[], float) - Method in class inra.ijpb.label.edit.ReplaceLabelValues

Replace all values specified in label array by the value 0.

process(ImagePlus, int) - Method in class inra.ijpb.plugins.RegionMorphometryPlugin

Deprecated.

Process the input image.

process(ImagePlus, int, boolean) - Method in class inra.ijpb.plugins.MicrostructureAnalysisPlugin

Main body of the plugin.

process(ImagePlus, short[]) - Method in class inra.ijpb.plugins.MaxInscribedCirclePlugin

Deprecated.

use LargestInscribedCircle class instead

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).

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, 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(ImagePlus, ImagePlus, String, float[], boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMap3DPlugin

Deprecated.

process(ImagePlus, ImagePlus, String, 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(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, 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(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, 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, 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(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(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(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(ImageStack) - Method in class inra.ijpb.label.filter.ChamferLabelDilation3DShort

Computes dilation of labels within label image by a specified radius.

process(ImageStack) - Method in class inra.ijpb.label.filter.ChamferLabelErosion3DShort

Apply morphological erosion of the labels within the specified input image.

process(ImageStack) - Method in class inra.ijpb.label.select.LabelSizeFiltering

Applies size filtering on the input 3D 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) - Method in class inra.ijpb.morphology.filter.BlackTopHat

process(ImageStack) - Method in class inra.ijpb.morphology.filter.Closing

process(ImageStack) - Method in class inra.ijpb.morphology.filter.Dilation

process(ImageStack) - Method in class inra.ijpb.morphology.filter.Erosion

process(ImageStack) - Method in class inra.ijpb.morphology.filter.ExternalGradient

process(ImageStack) - Method in class inra.ijpb.morphology.filter.Gradient

process(ImageStack) - Method in class inra.ijpb.morphology.filter.InternalGradient

process(ImageStack) - Method in class inra.ijpb.morphology.filter.Laplacian

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(ImageStack) - Method in class inra.ijpb.morphology.filter.Opening

process(ImageStack) - Method in class inra.ijpb.morphology.filter.WhiteTopHat

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(ImageStack, float[], float) - Method in class inra.ijpb.label.edit.ReplaceLabelValues

Replace all values specified in label array by the specified value.

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(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) - Method in class inra.ijpb.label.edit.ReplaceLabelValues

Replace all values specified in label array by a new value.

process(ImageStack, int, int, int, int, int, int, BorderManager3D) - Static method in class inra.ijpb.plugins.ExtendBordersPlugin

Deprecated.

replaced by inra.ijpb.data.border.BorderManager3D.addBorders(...) method

process(ImageStack, int, int, Calibration) - Method in class inra.ijpb.measure.region3d.InterfaceSurfaceArea

Computes the interface surface area between two regions.

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(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(ImageStack, Calibration) - Method in class inra.ijpb.plugins.AnalyzeMicrostructure3D

Computes features from an ImageStack object, specifying the calibration.

process(ImageStack, Calibration) - Method in class inra.ijpb.plugins.AnalyzeRegions3D

Computes features from an ImageStack object, specifying the calibration.

process(ImageStack, Calibration) - Method in class inra.ijpb.plugins.ParticleAnalysis3DPlugin

Deprecated.

Computes features from an ImageStack object, specifying the calibration.

process(ImageStack, ChamferMask3D, double) - Method in enum inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin.Operation

Applies the current operator to the input 3D 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(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(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(ImageProcessor) - Method in class inra.ijpb.label.filter.ChamferLabelDilation2DShort

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(ImageProcessor) - Method in class inra.ijpb.label.select.LabelSizeFiltering

Applies size filtering on the input 2D 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) - 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(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Closing

process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Dilation

process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Erosion

process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.ExternalGradient

process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Gradient

process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.InternalGradient

process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Laplacian

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(ImageProcessor) - Method in class inra.ijpb.morphology.filter.Opening

process(ImageProcessor) - Method in class inra.ijpb.morphology.filter.WhiteTopHat

process(ImageProcessor, double) - Method in class inra.ijpb.label.distmap.LabelDilation2DShort

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(ImageProcessor, float[], float) - Method in class inra.ijpb.label.edit.ReplaceLabelValues

Replace all values specified in label array by the value 0.

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(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(ImageProcessor, int[], int) - Method in class inra.ijpb.label.edit.ReplaceLabelValues

Replace all values specified in label array by a new value.

process(ImageProcessor, int, int, int, int, BorderManager) - Static method in class inra.ijpb.plugins.ExtendBordersPlugin

Deprecated.

replaced by inra.ijpb.data.border.BorderManager.addBorders(...) method

process(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, 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, ImageProcessor, float[], boolean) - Method in class inra.ijpb.plugins.GeodesicDistanceMapPlugin

Deprecated.

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(ImageProcessor, ChamferMask2D, double) - Method in enum inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin.Operation

Applies the current operator to the input image.

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.

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.

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.

psi() - Method in class inra.ijpb.geometry.Ellipsoid

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