inra.ijpb.measure.region3d

Class EquivalentEllipsoid

java.lang.Object

inra.ijpb.algo.AlgoStub

inra.ijpb.measure.region3d.RegionAnalyzer3D<Ellipsoid>

inra.ijpb.measure.region3d.EquivalentEllipsoid

All Implemented Interfaces:

Algo, AlgoListener, RegionAnalyzer<Ellipsoid>

public class EquivalentEllipsoid
extends RegionAnalyzer3D<Ellipsoid>

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.

Author:

dlegland

See Also:

EquivalentEllipse

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	EquivalentEllipsoid.Moments3D Encapsulates the results of 3D Moments computations.

Constructor Summary

Constructors

Constructor and Description
EquivalentEllipsoid() Default constructor

Method Summary

Modifier and Type	Method and Description
Ellipsoid[]	analyzeRegions(ij.ImageStack image, int[] labels, ij.measure.Calibration calib) Computes equivalent ellipsoid of each region in the input 3D label image.
EquivalentEllipsoid.Moments3D[]	computeMoments(ij.ImageStack image, int[] labels, ij.measure.Calibration calib) Computes the matrix of moments for each region within the 3D label map.
ij.measure.ResultsTable	createTable(int[] labels, Ellipsoid[] ellipsoids) Utility method that transforms a pair of arrays for labels and equivalent ellipsoids instances into a ResultsTable that can be displayed with ImageJ.
ij.measure.ResultsTable	createTable(int[] labels, EquivalentEllipsoid.Moments3D[] moments) Utility method that transforms a pair of arrays for labels and 3D moments instances into a ResultsTable that can be displayed with ImageJ.
ij.measure.ResultsTable	createTable(Map<Integer,Ellipsoid> map) Utility method that transforms the mapping between labels and equivalent ellipsoids instances into a ResultsTable that can be displayed with ImageJ.
static Ellipsoid[]	equivalentEllipsoids(ij.ImageStack image, int[] labels, ij.measure.Calibration calib) Computes equivalent ellipsoid of each region in the input 3D label image.
Ellipsoid[]	momentsToEllipsoids(EquivalentEllipsoid.Moments3D[] moments) Converts an array of 3D moments into equivalent ellipsoid representation.

Methods inherited from class inra.ijpb.measure.region3d.RegionAnalyzer3D

algoProgressChanged, algoStatusChanged, analyzeRegions, analyzeRegions, computeTable, createMap

Methods inherited from class inra.ijpb.algo.AlgoStub

addAlgoListener, fireProgressChanged, fireProgressChanged, fireStatusChanged, fireStatusChanged, removeAlgoListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

EquivalentEllipsoid

public EquivalentEllipsoid()

Default constructor

Method Detail

equivalentEllipsoids

public static final Ellipsoid[] equivalentEllipsoids(ij.ImageStack image,
                                                     int[] labels,
                                                     ij.measure.Calibration calib)

Computes equivalent ellipsoid of each region in the input 3D label image.

Parameters:

image - the input image containing label of particles

labels - the array of labels within the image

calib - the calibration of the image

Returns:

an array of Ellipsoid instances representing the calibrated coordinates of the equivalent ellipsoid of each region

createTable

public ij.measure.ResultsTable createTable(int[] labels,
                                           Ellipsoid[] ellipsoids)

Utility method that transforms a pair of arrays for labels and equivalent ellipsoids instances into a ResultsTable that can be displayed with ImageJ.

Parameters:

labels - the array of region labels

ellipsoids - the array of region ellipsoids (the same size as the array of labels)

Returns:

a ResultsTable that can be displayed with ImageJ.

createTable

public ij.measure.ResultsTable createTable(int[] labels,
                                           EquivalentEllipsoid.Moments3D[] moments)

Utility method that transforms a pair of arrays for labels and 3D moments instances into a ResultsTable that can be displayed with ImageJ.

Parameters:

labels - the array of region labels

moments - the array of moments (the same size as the array of labels)

Returns:

a ResultsTable that can be displayed with ImageJ.

momentsToEllipsoids

public Ellipsoid[] momentsToEllipsoids(EquivalentEllipsoid.Moments3D[] moments)

Converts an array of 3D moments into equivalent ellipsoid representation.

Parameters:

moments - the moments to convert

Returns:

the array of ellipsoids corresponding to the moments

computeMoments

public EquivalentEllipsoid.Moments3D[] computeMoments(ij.ImageStack image,
                                                      int[] labels,
                                                      ij.measure.Calibration calib)

Computes the matrix of moments for each region within the 3D label map.

Parameters:

image - the 3D image of labels (label map)

labels - the array of region labels to process

calib - the spatial calibration of the image

Returns:

an array the same size as labels, containing for each processed region result of 3D Moments computations

analyzeRegions

public Ellipsoid[] analyzeRegions(ij.ImageStack image,
                                  int[] labels,
                                  ij.measure.Calibration calib)

Computes equivalent ellipsoid of each region in the input 3D label image.

Specified by:

analyzeRegions in class RegionAnalyzer3D<Ellipsoid>

Parameters:

image - the input image containing label of particles

labels - the array of labels within the image

calib - the calibration of the image

Returns:

an array of Ellipsoid instances representing the calibrated coordinates of the equivalent ellipsoid of each region

createTable

public ij.measure.ResultsTable createTable(Map<Integer,Ellipsoid> map)

Utility method that transforms the mapping between labels and equivalent ellipsoids instances into a ResultsTable that can be displayed with ImageJ.

Parameters:

map - the mapping between labels and Equivalent Ellipsoids

Returns:

a ResultsTable that can be displayed with ImageJ.