Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y
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F

Features() - Constructor for class inra.ijpb.plugins.AnalyzeRegions.Features

FeretDiameters - Class in inra.ijpb.geometry

Utility methods for computing Feret diameters

FeretDiameters() - Constructor for class inra.ijpb.geometry.FeretDiameters

fill(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.LocalBufferedHistogram

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.

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

Fills the input 3D image 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(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.

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.

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(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).

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.

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

Computes maximum value in the input 3D image.

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

Computes maximum value within the input 2D image.

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.

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.

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(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.

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.

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(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.

findPositionOfMaxValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelImages

Deprecated.

use LavelValues.findPositionOfMaxValues instead

findPositionOfMaxValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelValues

For each label, finds the position of the point belonging to label region defined by labelImage and with maximal value in intensity image valueImage.

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.

findPositionOfMinValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelImages

Deprecated.

use LavelValues.findPositionOfMinValues instead

findPositionOfMinValues(ImageProcessor, ImageProcessor, int[]) - Static method in class inra.ijpb.label.LabelValues

For each label, finds the position of the point belonging to label region defined by labelImage and with minimal value in intensity image valueImage.

FIRE - inra.ijpb.color.ColorMaps.CommonLabelMaps

Colormap containing the Fire colors

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, 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.ChamferWeights3D.FloatOffset

Deprecated.

Creates a new offset for floating point computations.

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(ImageStack, int, int, int, double, int) - Static method in class inra.ijpb.morphology.FloodFill

Deprecated.

use FLoodFill3D.floodFill instead

floodFill(ImageStack, int, int, int, double, int) - Static method in class inra.ijpb.morphology.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, int, int) - Static method in class inra.ijpb.morphology.FloodFill

Deprecated.

use FloodFill3D.floodFill instead.

floodFill(ImageStack, int, int, int, int, int) - Static method in class inra.ijpb.morphology.FloodFill3D

Replaces all the pixels in the 6-neighborhood of (x0,y0,z0) that have the same values as the pixel in (x0,y0,z0) by the specified value.

floodFill(ImageStack, int, int, int, ImageStack, int, int) - Static method in class inra.ijpb.morphology.FloodFill

Deprecated.

use FloodFill3D.floodFill instead

floodFill(ImageStack, int, int, int, ImageStack, int, int) - Static method in class inra.ijpb.morphology.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.

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, 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, 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 - Class in inra.ijpb.morphology

Implements various flood-fill algorithms, for planar images.

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(ImageStack, int, int, int, ImageStack, float, int) - Static method in class inra.ijpb.morphology.FloodFill

Deprecated.

use FloodFill3D.floodFillFloat instead

floodFillFloat(ImageStack, int, int, int, ImageStack, float, int) - Static method in class inra.ijpb.morphology.FloodFill3D

Assigns to all the neighbor voxels of (x0,y0,z0) that have the same voxel value in inputImage, the specified new value (value) in outputImage, using the specified connectivity.

floodFillFloat(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(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(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.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(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(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) - 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(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(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.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(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(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) - 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(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(float[]) - 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.ChamferMask3D

Creates a new Chamfer mask from a list of weights.

fromWeights(int[]) - 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.ChamferMask2D

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.

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