Uses of Interface
inra.ijpb.algo.Algo

Packages that use Algo

Package	Description
inra.ijpb.algo	Several classes for managing progress of algorithms.
inra.ijpb.binary.conncomp	Connected components labeling algorithms for binary 2D or 3D images.
inra.ijpb.binary.distmap	Computations of distance maps on binary images, using chamfer distances (integer approximation of Euclidean distances).
inra.ijpb.binary.geodesic	Algorithms for computing geodesic distances, geodesic diameters, tortuosity...
inra.ijpb.binary.skeleton	Extraction of skeleton from binary images.
inra.ijpb.color	Utilities for color images.
inra.ijpb.label.conncomp	Connected component labeling of a specific region within a label image.
inra.ijpb.label.distmap	Computation of distance maps for label images.
inra.ijpb.label.edit	Processing classes for edition of label images.
inra.ijpb.label.filter	Implementation of morphological filters for label images.
inra.ijpb.label.select	Selection of regions from label images based on size criterion.
inra.ijpb.measure.region2d	Quantitative measurements on 2D label / binary images of regions.
inra.ijpb.measure.region3d	Quantitative measurements on 3D label / binary images of regions.
inra.ijpb.morphology	Mathematical Morphology filters and reconstructions.
inra.ijpb.morphology.attrfilt	Attribute opening and filtering for grayscale images.
inra.ijpb.morphology.directional	Morphological directional filters.
inra.ijpb.morphology.extrema	Algorithms for computing regional minima and maxima.
inra.ijpb.morphology.filter	Morphological filtering operators implemented as classes.
inra.ijpb.morphology.geodrec	Geodesic reconstruction by erosion and dilation.
inra.ijpb.morphology.strel	A collection of Structuring Element ("Strel") implementations for mathematical morphology.

Uses of Algo in inra.ijpb.algo

Classes in inra.ijpb.algo that implement Algo

Modifier and Type	Class	Description
class	AlgoStub	A minimal implementation of algorithm for managing progression listeners.

Methods in inra.ijpb.algo with parameters of type Algo

Modifier and Type	Method	Description
static void	DefaultAlgoListener.monitor(Algo algo)	Static method that creates a new instance of DefaultAlgoListener, and add it to the given algorithm.

Uses of Algo in inra.ijpb.binary.conncomp

Subinterfaces of Algo in inra.ijpb.binary.conncomp

Modifier and Type	Interface	Description
interface	ConnectedComponentsLabeling	Computes labels corresponding to connected components in input image.
interface	ConnectedComponentsLabeling3D	Computes labels corresponding to connected components in input 3D image.

Classes in inra.ijpb.binary.conncomp that implement Algo

Modifier and Type	Class	Description
class	FloodFillComponentsLabeling	Computes the labels of the connected components in a binary image.
class	FloodFillComponentsLabeling3D	Computes the labels of the connected components in a 3D binary image.

Uses of Algo in inra.ijpb.binary.distmap

Subinterfaces of Algo in inra.ijpb.binary.distmap

Modifier and Type	Interface	Description
interface	ChamferDistanceTransform2D	Specialization of DistanceTransform based on the use of a chamfer mask.
interface	ChamferDistanceTransform3D	Specialization of DistanceTransform based on the use of a chamfer mask.
interface	DistanceTransform	Interface for computing distance maps from binary images.
interface	DistanceTransform3D	Interface for computing distance maps from binary 3D images.

Classes in inra.ijpb.binary.distmap that implement Algo

Modifier and Type	Class	Description
class	ChamferDistanceTransform2DFloat	Computes distance transform on binary images by propagating distances using a ChamferMask2D, and using 32-bits floating-point computation.
class	ChamferDistanceTransform2DShort	Computes distance transform by propagating distances using a ChamferMask2D, and using 16-bits integer computation.
class	ChamferDistanceTransform3DFloat	Computes 3D distance transform on binary images using the chamfer weights provided by a ChamferMask3D object, and using 32-bits floating-point computation.
class	ChamferDistanceTransform3DShort	Computes 3D distance transform using the chamfer weights provided by a ChamferMask3D object, and using 16-bits integer computation.
class	DistanceTransform3D4WeightsFloat	Deprecated. replaced by ChamferDistanceTransform3DFloat (since 1.5.0)
class	DistanceTransform3D4WeightsShort	Deprecated. replaced by ChamferDistanceTransform3DShort (since 1.5.0)
class	DistanceTransform3DFloat	Deprecated. replaced by ChamferDistanceTransform3DFloat (since 1.5.0)
class	DistanceTransform3DShort	Deprecated. replaced by ChamferDistanceTransform3DShort (since 1.5.0)
class	DistanceTransform3x3Float	Deprecated. replaced by ChamferDistanceTransform2DFloat (since 1.5.0)
class	DistanceTransform3x3Short	Deprecated. replaced by ChamferDistanceTransform2DShort (since 1.5.0)
class	DistanceTransform5x5Float	Deprecated. replaced by ChamferDistanceTransform2DFloat (since 1.5.0)
class	DistanceTransform5x5Short	Deprecated. replaced by ChamferDistanceTransform2DShort (since 1.5.0)

Uses of Algo in inra.ijpb.binary.geodesic

Subinterfaces of Algo in inra.ijpb.binary.geodesic

Modifier and Type	Interface	Description
interface	GeodesicDiameter	Deprecated. since 1.3.5, use inra.ijpb.measure.region2d.GeodesicDiameter instead
interface	GeodesicDiameter3D	Deprecated. since 1.3.5, use inra.ijpb.measure.region3d.GeodesicDiameter3D instead
interface	GeodesicDistanceTransform	Interface for computing Geodesic distance transforms (or geodesic distance maps) from binary images.
interface	GeodesicDistanceTransform3D	Interface for computing Geodesic distance transforms (or geodesic distance maps) from binary images.

Classes in inra.ijpb.binary.geodesic that implement Algo

Modifier and Type	Class	Description
class	GeodesicDiameter3DFloat	Deprecated. replaced by inra.ijpb.measure.region3d.GeodesicDiameter3D
class	GeodesicDiameterFloat	Deprecated. since 1.3.5, use inra.ijpb.measure.region2d.GeodesicDiameter instead
class	GeodesicDiameterShort	Deprecated. since 1.3.5, use inra.ijpb.measure.region2d.GeodesicDiameter instead
class	GeodesicDistanceTransform3DFloat	Computation of geodesic distance transform for 3D images, using floating point computation.
class	GeodesicDistanceTransformFloat	Computation of Chamfer geodesic distances using floating point array for storing result.
class	GeodesicDistanceTransformFloat5x5	Deprecated. replaced by GeodesicDistanceTransformFloat (since 1.4.4)
class	GeodesicDistanceTransformFloatHybrid	Computation of geodesic distances based on a chamfer mask using floating point array for storing result.
class	GeodesicDistanceTransformShort	Computation of geodesic distances based on a chamfer mask using short integer array for storing result.
class	GeodesicDistanceTransformShort5x5	Deprecated. replaced by GeodesicDistanceTransformShort (since 1.5.0)
class	GeodesicDistanceTransformShortHybrid	Computation of geodesic distances based on a chamfer mask using short integer array for storing result.

Uses of Algo in inra.ijpb.binary.skeleton

Classes in inra.ijpb.binary.skeleton that implement Algo

Modifier and Type	Class	Description
class	ImageJSkeleton	Adaptation of the skeletonization code from ImageJ.

Uses of Algo in inra.ijpb.color

Classes in inra.ijpb.color that implement Algo

Modifier and Type	Class	Description
class	BinaryOverlay	Computes overlay of a binary image mask onto a grayscale or color image, using the specified color.

Uses of Algo in inra.ijpb.label.conncomp

Classes in inra.ijpb.label.conncomp that implement Algo

Modifier and Type	Class	Description
class	FloodFillRegionComponentsLabeling	Computes the labels of the different connected components of a region within a label image.
class	FloodFillRegionComponentsLabeling3D	Computes the labels of the different connected components of a region within a 3D label image.
class	LabelBoundariesLabeling2D	Computes a label map of the boundaries between regions from a label map.
class	LabelBoundariesLabeling3D	Computes a label map of the boundaries between regions from a label map.

Uses of Algo in inra.ijpb.label.distmap

Subinterfaces of Algo in inra.ijpb.label.distmap

Modifier and Type	Interface	Description
interface	ChamferDistanceTransform2D	Specialization of DistanceTransform based on the use of a chamfer mask.
interface	ChamferDistanceTransform3D	Specialization of DistanceTransform based on the use of a chamfer mask.
interface	DistanceTransform2D	Interface for computing distance maps for 2D label images.
interface	DistanceTransform3D	Interface for computing distance maps for 3D label images.

Classes in inra.ijpb.label.distmap that implement Algo

Modifier and Type	Class	Description
class	ChamferDistanceTransform2DFloat	Computes distance transform by propagating distances using a ChamferMask2D, and using 32-bits floating-point computation.
class	ChamferDistanceTransform2DShort	Computes distance transform by propagating distances using a ChamferMask2D, and using 16-bits integer computation.
class	ChamferDistanceTransform3DFloat	Computes 3D distance transform using the chamfer weights provided by a ChamferWeights3D object, and using floating-point computation.
class	ChamferDistanceTransform3DShort	Computes 3D distance transform on binary images using the chamfer weights provided by a ChamferWeights3D object, and using 16-bits integer computation.
class	DistanceTransform3DFloat	Deprecated. replaced by ChamferDistanceTransform3DFloat (since 1.4.4)
class	DistanceTransform3DShort	Deprecated. replaced by ChamferDistanceTransform3DShort (since 1.4.4)
class	LabelDilation2DShort	Deprecated. replaced by inra.ijpb.label.filter.ChamferLabelDilation2DShort
class	LabelDilation3D4WShort	Deprecated. replaced by LabelDilation3DShort (since 1.4.4)
class	LabelDilation3DShort	Deprecated. replaced by inra.ijpb.label.filter.ChamferLabelDilation3DShort
class	LabelDilationShort5x5	Deprecated. replaced by LabelDilation2DShort (since 1.5.0)

Uses of Algo in inra.ijpb.label.edit

Classes in inra.ijpb.label.edit that implement Algo

Modifier and Type	Class	Description
class	FindAllLabels	Extract the set of unique labels existing in the given image, excluding the value zero (used for background).
class	ReplaceLabelValues	Provides several methods for replacing label values within a label map (stored as 8-, 16- or 32-bits).

Uses of Algo in inra.ijpb.label.filter

Classes in inra.ijpb.label.filter that implement Algo

Modifier and Type	Class	Description
class	ChamferLabelDilation2DShort	Apply a dilation by a specified radius to each label of a label map by constraining the dilation.
class	ChamferLabelDilation3DShort	Apply a dilation by a specified radius to each label of a label map by constraining the dilation.
class	ChamferLabelErosion2DShort	Implementation of morphological erosion for 2D label images / label maps.
class	ChamferLabelErosion3DShort	Implementation of morphological erosion for 3D label images / label maps.

Uses of Algo in inra.ijpb.label.select

Classes in inra.ijpb.label.select that implement Algo

Modifier and Type	Class	Description
class	LabelSizeFiltering	Filter labels using a size criterion.

Uses of Algo in inra.ijpb.measure.region2d

Classes in inra.ijpb.measure.region2d that implement Algo

Modifier and Type	Class	Description
class	AverageThickness	Compute average thickness of a binary region, or of each region in a label image.
class	BinaryConfigurationsHistogram2D	Computes histogram of binary configurations composed of 2-by-2 pixels (planar images).
class	BoundingBox	Compute bounding box of each region within a label or binary image.
class	Centroid	Computes centroid position of regions within binary or label images.
class	Convexity	Computes convex area and convexity for regions within a binary or label image.
class	EquivalentEllipse	Compute parameters of equivalent ellipse from binar or label images.
class	GeodesicDiameter	Computes geodesic diameter of a set of labeled particles or regions, using an inner instance of GeodesicDistanceTransform for propagating chamfer distances.
class	InertiaEllipse	Deprecated. Replaced by EquivalentEllipse (since 1.4.2)
class	IntrinsicVolumesAnalyzer2D	Computation of intrinsic volumes (area, perimeter and Euler number) for binary or label 2D images.
class	LargestInscribedCircle	Computes the largest inscribed circle for each region of a label or binary image.
class	MaxFeretDiameter	Computes maximum Feret Diameter for each region of a binary or label image.
class	OrientedBoundingBox2D
class	RegionAnalyzer2D<T>	Base implementation of RegionAnalyzer interface for planar binary/label images.

Uses of Algo in inra.ijpb.measure.region3d

Classes in inra.ijpb.measure.region3d that implement Algo

Modifier and Type	Class	Description
class	BinaryConfigurationsHistogram3D	Computes histogram of binary 2-by-2-by-2 configurations within a 3D image.
class	BoundingBox3D	Compute bounding box of each region within a label or binary image.
class	Centroid3D	Computes centroid position of regions within 3D binary or label images.
class	EquivalentEllipsoid	Compute the parameters of 3D ellipsoids that has the same moments up to the second order than the region(s) within a 3D binary / label image.
class	GeodesicDiameter3D	Computes the 3D geodesic diameters of regions within a 3D binary or label images using floating point computation for propagating distances.
class	InertiaEllipsoid	Deprecated. replaced by EquivalentEllipsoid (since 1.4.1)
class	IntrinsicVolumesAnalyzer3D	Computation of intrinsic volumes (Volume, Surface Area, Mean Breadth and Euler Number) for 3D binary or label images, based on the RegionAnalyzer3D interface.
class	LargestInscribedBall	Computes the largest inscribed ball for each region of a label or binary image.
class	MaxFeretDiameter3D	Computes maximum Feret Diameter for each region of a 3D binary or label image.
class	RegionAnalyzer3D<T>	Base implementation of RegionAnalyzer interface for 3D binary/label images.

Uses of Algo in inra.ijpb.morphology

Subinterfaces of Algo in inra.ijpb.morphology

Modifier and Type	Interface	Description
interface	Strel	Interface for planar structuring elements.
interface	Strel3D	Structuring element that process 3D stack.

Uses of Algo in inra.ijpb.morphology.attrfilt

Subinterfaces of Algo in inra.ijpb.morphology.attrfilt

Modifier and Type	Interface	Description
interface	AreaOpening	Area opening for gray level images.
interface	SizeOpening3D	Size opening for 3D gray level images.

Classes in inra.ijpb.morphology.attrfilt that implement Algo

Modifier and Type	Class	Description
class	AreaOpeningNaive	Computes area opening using naive algorithm.
class	AreaOpeningQueue	Area opening using priority queue for updating each regional maxima.
class	BoxDiagonalOpeningQueue	Area opening using priority queue for updating each regional maxima.
class	SizeOpening3DQueue	Volume opening on 3D grayscale image using priority queue for updating each 3D regional maxima.

Uses of Algo in inra.ijpb.morphology.directional

Classes in inra.ijpb.morphology.directional that implement Algo

Modifier and Type	Class	Description
class	DirectionalFilter	Directional filtering of planar images.
class	OrientedLineStrel	A linear structuring element, defined by a length and an orientation.

Uses of Algo in inra.ijpb.morphology.extrema

Classes in inra.ijpb.morphology.extrema that implement Algo

Modifier and Type	Class	Description
class	RegionalExtrema3DAlgo	Interface for computing regional extrema (regional minima and regional maxima).
class	RegionalExtrema3DByFlooding	Computes regional extrema in 3D images using flooding algorithm.

Uses of Algo in inra.ijpb.morphology.filter

Classes in inra.ijpb.morphology.filter that implement Algo

Modifier and Type	Class	Description
class	BlackTopHat	Performs morphological black top-hat on 2D/3D images.
class	Closing	Performs morphological closing on 2D/3D images.
class	Dilation	Performs morphological dilation on 2D/3D images.
class	Erosion	Performs morphological erosion on 2D/3D images.
class	ExternalGradient	Performs morphological external gradient on 2D/3D images.
class	Gradient	Performs morphological gradient, also known as "Beucher Gradient", on 2D/3D images.
class	InternalGradient	Computes the morphological internal gradient of the input image.
class	Laplacian	Computes the morphological Laplacian of the input image.
class	MorphologicalFilter	Base class for morphological filters, based on a structuring element.
class	Opening	Performs morphological opening on 2D/3D images.
class	WhiteTopHat	Performs morphological White Top-Hat on 2D/3D images.

Uses of Algo in inra.ijpb.morphology.geodrec

Subinterfaces of Algo in inra.ijpb.morphology.geodrec

Modifier and Type	Interface	Description
interface	GeodesicReconstruction3DAlgo	Defines the interface for geodesic reconstruction algorithms applied to 3D stack images.

Classes in inra.ijpb.morphology.geodrec that implement Algo

Modifier and Type	Class	Description
class	GeodesicReconstruction3DAlgoStub	Implementation basis for geodesic reconstruction algorithms for 3D images.
class	GeodesicReconstruction3DHybrid0Float	Geodesic reconstruction for 3D stacks of floats, using hybrid algorithm.
class	GeodesicReconstruction3DHybrid0Gray16	Geodesic reconstruction for 3D stacks of shorts, using hybrid algorithm.
class	GeodesicReconstruction3DHybrid0Gray8	Geodesic reconstruction for 3D stacks of bytes, using hybrid algorithm.
class	GeodesicReconstruction3DHybrid1Image3D	Geodesic reconstruction for 3D stacks of any type, using hybrid algorithm and Image3D access class.
class	GeodesicReconstructionAlgoStub	Implementation basis for geodesic reconstruction algorithms for planar images.
class	GeodesicReconstructionByDilation	Geodesic reconstruction by dilation for planar images.
class	GeodesicReconstructionByDilation3D	Geodesic reconstruction by dilation for 3D images of any type, using scanning algorithm and implemented only for C26 connectivity.
class	GeodesicReconstructionByDilation3DGray8	Geodesic reconstruction by dilation for 3D stacks of byte processors, using hybrid algorithm and implemented only for 26 connectivity.
class	GeodesicReconstructionByDilation3DScanning	Geodesic reconstruction by dilation for 3D stacks using scanning algorithm, and Image3D access class.
class	GeodesicReconstructionByDilation3DScanningGray8	Geodesic reconstruction by dilation for 3D stacks of byte processors, using scanning algorithm.
class	GeodesicReconstructionByErosion	Geodesic reconstruction by erosion for integer images.
class	GeodesicReconstructionByErosion3DGray8	Geodesic reconstruction by erosion for 3D stacks of byte processors, using hybrid algorithm and implemented only for the 26 connectivity.
class	GeodesicReconstructionByErosion3DScanning	Geodesic reconstruction by erosion for 3D stacks using scanning algorithm, and Image3D access class.
class	GeodesicReconstructionByErosion3DScanningGray8	Geodesic reconstruction by erosion for 3D stacks of byte processors, using scanning algorithm.
class	GeodesicReconstructionHybrid	Geodesic reconstruction for planar images, using hybrid algorithm.
class	GeodesicReconstructionScanning	Geodesic reconstruction for planar images, using scanning algorithm.

Uses of Algo in inra.ijpb.morphology.strel

Subinterfaces of Algo in inra.ijpb.morphology.strel

Modifier and Type	Interface	Description
interface	InPlaceStrel	A structuring element that can performs erosion or dilation directly in the original image buffer.
interface	InPlaceStrel3D	A structuring element that can performs erosion or dilation directly in the original image stack.
interface	SeparableStrel	Interface for structuring elements that can be decomposed into several "simpler" structuring elements.
interface	SeparableStrel3D	Interface for structuring elements that can be decomposed into several "simpler" structuring elements.

Classes in inra.ijpb.morphology.strel that implement Algo

Modifier and Type	Class	Description
class	AbstractInPlaceStrel	Implementation stub for in place Structuring elements.
class	AbstractInPlaceStrel3D	Implementation stub for in place 3D Structuring elements.
class	AbstractSeparableStrel	Implementation stub for separable Structuring elements.
class	AbstractSeparableStrel3D	Implementation stub for separable 3D Structuring elements.
class	AbstractStrel	Implementation basis for planar structuring elements.
class	AbstractStrel3D	Implementation basis for 3D structuring elements
class	BallStrel	A 3D structuring element with a ball shape, with same size in each direction.
class	ChamferStrel	Disk-shaped structuring element based on a chamfer mask and a radius.
class	ChamferStrel3D
class	Cross3DStrel	3D structuring element representing a 3x3x3 cross, that considers the center voxel together with the six orthogonal neighbors.
class	Cross3x3Strel	Structuring element representing a 3x3 cross, that considers the center pixels together with the four orthogonal neighbors.
class	CubeStrel	A cubic structuring element, obtained by decomposition into linear structuring elements with the same size along each dimension.
class	CuboidStrel	A cuboid structuring element, obtained by decomposition into linear structuring elements (that can have different sizes) along each dimension.
class	DiamondStrel	Structuring element representing a diamond of a given diameter.
class	DiskStrel	Disk structuring element.
class	EllipsoidStrel	A 3D structuring element with an ellipsoidal shape, oriented along the three main axes of the image.
class	ExtrudedStrel	Creates a 3D strel by replicating a 2D strel on a given number of slices.
class	LinearDepthStrel3D	An horizontal linear structuring element of a given length.
class	LinearDiagDownStrel	A diagonal linear structuring element of a given length, with direction vector (+1,+1) in image coordinate system.
class	LinearDiagUpStrel	A diagonal linear structuring element of a given length, with direction vector (+1,-1) in image coordinate system.
class	LinearHorizontalStrel	An horizontal linear structuring element of a given length.
class	LinearVerticalStrel	A vertical linear structuring element of a given length.
class	OctagonStrel	An Octagonal structuring element, obtained by decomposition into horizontal, vertical, and diagonal linear structuring elements.
class	SquareStrel	A square structuring element, obtained by decomposition into horizontal and vertical linear structuring elements with the same size.