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C

C26 - inra.ijpb.plugins.Connectivity3D
The 26-connectivity, that considers all neighbors in three dimensions
C4 - inra.ijpb.plugins.Connectivity2D
The 4 connectivity (only orthogonal neighbors)
C6 - inra.ijpb.plugins.Connectivity3D
The 6-connectivity, that considers orthogonal neighbors in three dimensions
C8 - inra.ijpb.plugins.Connectivity2D
The 8 connectivity (orthogonal and diagonal neighbors)
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 - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing centroid.
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
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(ImageStack, int[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
use Centroid3D.centroids(ImageStack, int[]) instead
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.
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(ImageProcessor, int[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
replaced by Centroid.centroids
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(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.
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 - 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.binary.distmap.ChamferDistanceTransform2DFloat
Creates a new algorithm for computing distance maps based on a chamfer mask.
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.binary.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 - 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.binary.distmap.ChamferDistanceTransform2DShort
Creates a new algorithm for computing distance maps based on a chamfer mask.
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.binary.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 - 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.binary.distmap.ChamferDistanceTransform3DFloat
Creates a new algorithm for computing 3D distance maps on binary images based on a chamfer mask.
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.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.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 - 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.binary.distmap.ChamferDistanceTransform3DShort
Creates a new algorithm for computing 3D distance maps based on a chamfer mask.
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.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.label.distmap.ChamferDistanceTransform3DShort
Creates a new algorithm for computing 3D distance maps on label images based on a chamfer mask.
ChamferLabelDilation2DShort - Class in inra.ijpb.label.filter
Apply a dilation by a specified radius to each label of a label map by constraining the dilation.
ChamferLabelDilation2DShort(ChamferMask2D, double) - Constructor for class inra.ijpb.label.filter.ChamferLabelDilation2DShort
Creates a new image processor for dilating labels using the specified chamfer mask, using 16-bits integer computation.
ChamferLabelDilation3DShort - Class in inra.ijpb.label.filter
Apply a dilation by a specified radius to each label of a label map by constraining the dilation.
ChamferLabelDilation3DShort(ChamferMask3D, double) - Constructor for class inra.ijpb.label.filter.ChamferLabelDilation3DShort
Creates a new 3D image for dilating labels using the specified chamfer mask, using 16-bits integer computation.
ChamferLabelErosion2DShort - Class in inra.ijpb.label.filter
Implementation of morphological erosion for 2D label images / label maps.
ChamferLabelErosion2DShort(ChamferMask2D, double) - Constructor for class inra.ijpb.label.filter.ChamferLabelErosion2DShort
Creates a new operator for erosion of label images based on Chamfer masks.
ChamferLabelErosion3DShort - Class in inra.ijpb.label.filter
Implementation of morphological erosion for 3D label images / label maps.
ChamferLabelErosion3DShort(ChamferMask3D, double) - Constructor for class inra.ijpb.label.filter.ChamferLabelErosion3DShort
Creates a new operator for erosion of label images based on Chamfer masks.
ChamferMask2D - Class in inra.ijpb.binary.distmap
Chamfer masks defines a series of weights associated to neighbors of current pixels.
ChamferMask2D() - Constructor for class inra.ijpb.binary.distmap.ChamferMask2D
 
ChamferMask2D.FloatOffset - Class in inra.ijpb.binary.distmap
The shift to a neighbor of a reference pixel, as a pair (dx,dy), and the associated weights given as a float.
ChamferMask2D.ShortOffset - Class in inra.ijpb.binary.distmap
The shift to a neighbor of a reference pixel, as a pair (dx,dy), and the associated weights given as a short.
ChamferMask2DW2 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights that manages two types of offsets, corresponding to orthogonal and diagonal neighbors.
ChamferMask2DW2(int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW2
Creates a new ChamferWeights3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW2(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW2
Creates a new ChamferMask2D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW2Float - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights that manages two types of offsets, corresponding to orthogonal, and diagonal neighbors.
ChamferMask2DW2Float(short[], float[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW2Float
Creates a new chamfer mask
ChamferMask2DW3 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights that manages three types of offsets types: orthogonal, diagonal neighbors and "chess-knight move" neighbors.
ChamferMask2DW3(int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW3
Creates a new ChamferWeights2DW3 object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW3(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW3
Creates a new ChamferMask3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW4 - Class in inra.ijpb.binary.distmap
Implementation of 2D Chamfer mask that manages four types of offsets types.
ChamferMask2DW4(int, int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW4
Creates a new ChamferWeights2DW3 object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask2DW4(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask2DW4
Creates a new ChamferMask3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask3D - Class in inra.ijpb.binary.distmap
A collection of weighted offsets for computing distance maps from 3D binary images.
ChamferMask3D() - Constructor for class inra.ijpb.binary.distmap.ChamferMask3D
 
ChamferMask3D.FloatOffset - Class in inra.ijpb.binary.distmap
The shift to a neighbor of a reference voxel, as a triplet (dx,dy,dz), and the associated weights given as a float.
ChamferMask3D.ShortOffset - Class in inra.ijpb.binary.distmap
The shift to a neighbor of a reference voxel, as a triplet (dx,dy,dz), and the associated weights given as a short.
ChamferMask3DW3 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages three type offset types, corresponding to orthogonal, square-diagonal and cube-diagonal neighbors.
ChamferMask3DW3(int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW3
Creates a new ChamferWeights3D object by specifying the weights associated to orthogonal, square-diagonal and cube-diagonal neighbors, respectively.
ChamferMask3DW3(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW3
Creates a new ChamferMask3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask3DW3Float - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages three types of offsets, corresponding to orthogonal, square-diagonal and cube-diagonal neighbors.
ChamferMask3DW3Float(short[], float[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW3Float
Creates a new chamfer mask
ChamferMask3DW4 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages four types of offsets.
ChamferMask3DW4(int, int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW4
Creates a new ChamferWeights3D object by specifying the four weights associated to the four different kind of offsets.
ChamferMask3DW4(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW4
Creates a new ChamferWeights3D object by specifying the four weights associated to the four different kind of offsets.
ChamferMask3DW5 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages five types of offsets.
ChamferMask3DW5(int, int, int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW5
Creates a new ChamferWeights3D object by specifying the four weights associated to the four different kind of offsets.
ChamferMask3DW5(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW5
Creates a new ChamferMask3D object by specifying the weights associated to orthogonal and diagonal neighbors.
ChamferMask3DW6 - Class in inra.ijpb.binary.distmap
Implementation of Chamfer Weights for 3D images that manages six types of offsets (all the possibilities in a 5-by-5-by-5 neighborhood).
ChamferMask3DW6(int, int, int, int, int, int) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW6
Creates a new ChamferWeights3D object by specifying the weights associated to the six different kind of offsets.
ChamferMask3DW6(short[]) - Constructor for class inra.ijpb.binary.distmap.ChamferMask3DW6
Creates a new ChamferWeights3D object by specifying the four weights associated to the four different kind of offsets.
ChamferMasks2D - Enum in inra.ijpb.binary.distmap
A pre-defined set of weights that can be used to compute distance transform using chamfer approximations of euclidean metric.
ChamferMasks3D - Enum in inra.ijpb.binary.distmap
A pre-defined set of weights that can be used to compute 3D distance transform using chamfer approximations of euclidean metric.
ChamferStrel - Class in inra.ijpb.morphology.strel
Disk-shaped structuring element based on a chamfer mask and a radius.
ChamferStrel(ChamferMask2D, double) - Constructor for class inra.ijpb.morphology.strel.ChamferStrel
Creates a new ChamferStrel from a chamfer mask (used for computing distances) and a radius (used to computing the extent of propagation).
ChamferStrel3D - Class in inra.ijpb.morphology.strel
 
ChamferStrel3D(ChamferMask3D, double) - Constructor for class inra.ijpb.morphology.strel.ChamferStrel3D
Creates a new ChamferStrel3D from a chamfer mask (used for computing distances) and a radius (used to computing the extent of propagation).
ChamferWeights - Enum in inra.ijpb.binary
Deprecated.
replaced by inra.ijpb.binary.distmap.ChamferMask2D (since 1.5.0)
ChamferWeights3D - Enum in inra.ijpb.binary
Deprecated.
replaced by inra.ijpb.binary.distmap.ChamferMask2D (since 1.5.0)
ChamferWeights3D.FloatOffset - Class in inra.ijpb.binary
Deprecated.
ChamferWeights3D.ShortOffset - Class in inra.ijpb.binary
Deprecated.
CHESSBOARD - inra.ijpb.binary.ChamferWeights
Deprecated.
Use weight equal to 1 for all neighbors
CHESSBOARD - inra.ijpb.binary.ChamferWeights3D
Deprecated.
Use weight equal to 1 for all neighbors
CHESSBOARD - inra.ijpb.binary.distmap.ChamferMasks2D
Use weight equal to 1 for all neighbors
CHESSBOARD - inra.ijpb.binary.distmap.ChamferMasks3D
Use weight equal to 1 for all neighbors
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 - inra.ijpb.binary.ChamferWeights
Deprecated.
Use weights 5 for orthogonal neighbors and 7 for diagonal neighbors, and 11 for chess-knight moves (best approximation for 5-by-5 masks).
CHESSKNIGHT - inra.ijpb.binary.distmap.ChamferMasks2D
Use weights 5 for orthogonal neighbors and 7 for diagonal neighbors, and 11 for chess-knight moves (best approximation for 5-by-5 masks).
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 - Variable in class inra.ijpb.plugins.AnalyzeRegions.Features
The boolean flag for computing circularity.
circularity() - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D.Result
Computes the circularity value associated with this result.
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 - inra.ijpb.binary.ChamferWeights
Deprecated.
Use weights 1 for orthogonal neighbors and 2 for diagonal neighbors
CITY_BLOCK - inra.ijpb.binary.ChamferWeights3D
Deprecated.
Use weights 1 for orthogonal neighbors and 2 for diagonal neighbors, and 3 for cube-diagonals.
CITY_BLOCK - inra.ijpb.binary.distmap.ChamferMasks2D
Use weights 1 for orthogonal neighbors and 2 for diagonal neighbors, and 3 for cube-diagonals.
CITY_BLOCK - inra.ijpb.binary.distmap.ChamferMasks3D
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.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.
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(ImagePlus, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological closing on the input image.
closing(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
closing(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel3D
 
closing(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel3D
 
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(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.
closing(ImageStack, Strel3D) - Static method in class inra.ijpb.morphology.Morphology
Performs morphological closing on the input 3D image.
closing(ImageProcessor) - Method in class inra.ijpb.morphology.directional.OrientedLineStrel
 
closing(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractInPlaceStrel
 
closing(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractSeparableStrel
 
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(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(ImageProcessor, Strel) - Static method in class inra.ijpb.morphology.Morphology
Performs closing on the input image.
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 - inra.ijpb.morphology.directional.DirectionalFilter.Operation
The morphological closing operation
CLOSING - inra.ijpb.morphology.Morphology.Operation
Morphological closing (dilation followed by erosion)
CLOSING - inra.ijpb.plugins.LabelMapMorphologicalFilteringPlugin.Operation
Morphological closing (dilation followed by erosion)
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 - Class in inra.ijpb.util
Deprecated.
use inra.ijpb.color.ColorMaps instead (v1.4.3)
ColorMaps.CommonLabelMaps - Enum in inra.ijpb.color
A collection of color maps useful for displaying label images.
combineImages(ImagePlus, ImagePlus, ImageCalculator.Operation) - Static method in class inra.ijpb.math.ImageCalculator
Combines two images using the specified operation.
combineImages(ImageStack, ImageStack, 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:
CommonColors - Enum in inra.ijpb.color
A collection of common colors used for creating overlays, choosing background color...
CommonColors - Enum in inra.ijpb.util
Deprecated.
use inra.ijpb.color.CommonColors instead (v1.4.3)
compactness - Static variable in class inra.ijpb.plugins.MarkerControlledWatershed3DPlugin
compactness constraint, c parameter in compact watershed algorithm [2]
compareTo(PixelRecord) - Method in class inra.ijpb.data.PixelRecord
Compare with a pixel record based on its value and timestamp
compareTo(VoxelRecord) - Method in class inra.ijpb.data.VoxelRecord
Compare with a voxel record based on its value and timestamp
compareTo(RegionAdjacencyGraph.LabelPair) - Method in class inra.ijpb.label.RegionAdjacencyGraph.LabelPair
 
complement(ImageStack, double) - Static method in class inra.ijpb.data.image.Images3D
Computes the complements of the input image using the specified value as reference, and returns the complemented image.
componentsLabeling(ImagePlus, int, int) - Static method in class inra.ijpb.binary.BinaryImages
Computes the labels in the binary 2D or 3D image contained in the given ImagePlus, and computes the maximum label to set up the display range of the resulting ImagePlus.
componentsLabeling(ImageStack, int, int) - Static method in class inra.ijpb.binary.BinaryImages
Computes the labels of the connected components in the given 3D binary image.
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.
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(ImageStack) - Static method in class inra.ijpb.label.RegionAdjacencyGraph
Returns the set of region adjacencies in an ImageProcessor of labels.
computeAdjacencies(ImageProcessor) - Static method in class inra.ijpb.label.RegionAdjacencyGraph
Returns the set of region adjacencies in an ImageProcessor of labels.
computeCircularities(IntrinsicVolumesAnalyzer2D.Result[]) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumes2DUtils
Utility method that computes circularities as a numeric array from the result array
computeCircularities(IntrinsicVolumesAnalyzer2D.Result[]) - Static method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
Deprecated.
computeEllipsoidElongations(double[][]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
use Ellipsoid.elongations(Ellipsoid[]) instead
computeLabels(ImagePlus, int, int) - Static method in class inra.ijpb.binary.ConnectedComponents
Deprecated.
replaced by BinaryImages.componentsLabeling(ImagePlus, int, int)
computeLabels(ImageStack) - Method in interface inra.ijpb.binary.conncomp.ConnectedComponentsLabeling3D
Computes labels corresponding to connected components in input image.
computeLabels(ImageStack) - Method in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling3D
 
computeLabels(ImageStack, int) - Method in class inra.ijpb.label.conncomp.FloodFillRegionComponentsLabeling3D
Computes labels corresponding to connected components of a region within a label map.
computeLabels(ImageStack, int, int) - Static method in class inra.ijpb.binary.ConnectedComponents
Deprecated.
replaced by BinaryImages.componentsLabeling(ImageStack, int, int)
computeLabels(ImageProcessor) - Method in interface inra.ijpb.binary.conncomp.ConnectedComponentsLabeling
Computes labels corresponding to connected components in input image.
computeLabels(ImageProcessor) - Method in class inra.ijpb.binary.conncomp.FloodFillComponentsLabeling
 
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(ImageProcessor, int, int) - Static method in class inra.ijpb.binary.ConnectedComponents
Deprecated.
replaced by BinaryImages.componentsLabeling(ImageProcessor, int, int)
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(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.
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.
computeSphericity(double[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures3D
Deprecated.
use IntrinsicVolumes3D instead
computeTable(ImagePlus) - Method in class inra.ijpb.measure.region2d.RegionAnalyzer2D
Default implementation of computeTable method, using the two other methods RegionAnalyzer2D.analyzeRegions(ImagePlus) and RegionAnalyzer.createTable(Map):
computeTable(ImagePlus) - Method in class inra.ijpb.measure.region3d.RegionAnalyzer3D
Default implementation of computeTable method, using the two other methods RegionAnalyzer3D.analyzeRegions(ImagePlus) and RegionAnalyzer.createTable(Map):
computeTable(ImagePlus) - Method in interface inra.ijpb.measure.RegionAnalyzer
Returns the result of the analysis in the form of a ResultsTable, to facilitate concatenation of results obtained from several instances of RegionAnalyzer.
computeWatershed(ImagePlus, ImagePlus, int) - Static method in class inra.ijpb.watershed.Watershed
Compute fast watershed using flooding simulations, as described by Soille, Pierre, and Luc M.
computeWatershed(ImagePlus, ImagePlus, int, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers.
computeWatershed(ImagePlus, ImagePlus, int, boolean, boolean) - Static method in class inra.ijpb.watershed.Watershed
Compute watershed with markers
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(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, 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(ImageStack, ImageStack, 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, 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, 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(ImageProcessor, ImageProcessor, 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, 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.
ConnectedComponents - Class in inra.ijpb.binary
Deprecated.
all methods have been moved to the BinaryImages class
ConnectedComponents() - Constructor for class inra.ijpb.binary.ConnectedComponents
Deprecated.
 
ConnectedComponentsLabeling - Interface in inra.ijpb.binary.conncomp
Computes labels corresponding to connected components in input image.
ConnectedComponentsLabeling3D - Interface in inra.ijpb.binary.conncomp
Computes labels corresponding to connected components in input 3D image.
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.
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 - 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 - 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.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(ImageStack) - Method in enum inra.ijpb.data.border.BorderManager3D.Type
Creates a new Border Manager for the input image.
createBorderManager(ImageProcessor) - Method in enum inra.ijpb.data.border.BorderManager.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() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Fire LUT.
createFireLut(int) - 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() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Ice LUT.
createIceLut(int) - 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() - Static method in class inra.ijpb.color.ColorMaps
Creates a byte array representing the Jet LUT.
createJetLut(int) - 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(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, 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, 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, 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, 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, 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, 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, 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, OrientedBox2D>) - Method in class inra.ijpb.measure.region2d.OrientedBoundingBox2D
 
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(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, 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, 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, AverageThickness.Result>) - Method in class inra.ijpb.measure.region2d.AverageThickness
 
createTable(Map<Integer, Convexity.Result>) - Method in class inra.ijpb.measure.region2d.Convexity
 
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, IntrinsicVolumesAnalyzer2D.Result>) - Method in class inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D
 
createTable(Map<Integer, GeodesicDiameter3D.Result>) - Method in class inra.ijpb.measure.region3d.GeodesicDiameter3D
 
createTable(Map<Integer, IntrinsicVolumesAnalyzer3D.Result>) - Method in class inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D
 
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, T>) - Method in interface inra.ijpb.measure.RegionAnalyzer
Utility method that converts the detailed results of the RegionAnalyzer.analyzeRegions(ImagePlus) method into an instance of ResultsTable to facilitate display by ImageJ.
createWrapper(ImageStack) - Static method in class inra.ijpb.data.image.Images3D
Converts the input ImageStack into an instance of Image3D, depending on the data type stored in the stack.
croftonPerimeter(ImageProcessor, double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
use analyzeRegions instead
croftonPerimeter(ImageProcessor, int[], double[], int) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
replaced by IntrinsicVolumes2D
croftonPerimeterD2(ImageProcessor, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
replaced by IntrinsicVolumes2D
croftonPerimeterD4(ImageProcessor, int[], double[]) - Static method in class inra.ijpb.measure.GeometricMeasures2D
Deprecated.
replaced by IntrinsicVolumes2D
cropBorder(ImageStack) - Method in class inra.ijpb.morphology.strel.AbstractStrel3D
Retrieve the portion of image that corresponds to the original image before adding border.
cropBorder(ImageProcessor) - Method in class inra.ijpb.morphology.strel.AbstractStrel
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(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.
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.
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(ImageStack, int, int, int, int, int, int) - Static method in class inra.ijpb.shape.ImageShape
Crops a rectangular region from the input 3D image.
cropRect(ImageProcessor, int, int, int, int) - Static method in class inra.ijpb.shape.ImageShape
Crops a rectangular region from the input 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.
CUBE - inra.ijpb.morphology.Strel3D.Shape
Cube of a given side
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.
CYAN - inra.ijpb.color.CommonColors
The cyan (light blue) color
CYAN - inra.ijpb.util.CommonColors
Deprecated.
The cyan (light blue) color
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