inra.ijpb.measure.region3d

Class Centroid3D

java.lang.Object

inra.ijpb.algo.AlgoStub

inra.ijpb.measure.region3d.RegionAnalyzer3D<Point3D>

inra.ijpb.measure.region3d.Centroid3D

All Implemented Interfaces:

Algo, AlgoListener, RegionAnalyzer<Point3D>

public class Centroid3D
extends RegionAnalyzer3D<Point3D>

Computes centroid position of regions within 3D binary or label images.

Author:

dlegland

Constructor Summary

Constructors

Constructor and Description
Centroid3D() Default constructor

Method Summary

Modifier and Type	Method and Description
Point3D[]	analyzeRegions(ij.ImageStack image, int[] labels, ij.measure.Calibration calib) Computes centroid of each region in input label image.
static double[][]	centroids(ij.ImageStack labelImage, int[] labels) Computes centroid of each label in input image and returns the result as an array of double for each label.
static Point3D[]	centroids(ij.ImageStack labelImage, int[] labels, ij.measure.Calibration calib) Compute centroid of each region in input 3D label image and returns the result as an array of Point3D.
ij.measure.ResultsTable	createTable(Map<Integer,Point3D> map) Utility method that transforms the mapping between labels and Point3D instances into a ResultsTable that can be displayed with ImageJ.

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

Centroid3D

public Centroid3D()

Default constructor

Method Detail

centroids

public static final Point3D[] centroids(ij.ImageStack labelImage,
                                        int[] labels,
                                        ij.measure.Calibration calib)

Compute centroid of each region in input 3D label image and returns the result as an array of Point3D.

Parameters:

labelImage - the input image containing region labels

labels - the array of unique labels in image

calib - the calibration of the image

Returns:

an array of Point3D instances, corresponding to the centroid of each region

centroids

public static final double[][] centroids(ij.ImageStack labelImage,
                                         int[] labels)

Computes centroid of each label in input image and returns the result as an array of double for each label. This version does not take into account the spatial calibration, and returns the centroids in pixel coordinates.

Parameters:

labelImage - the input image containing label of particles

labels - the array of unique labels in image the number of directions to process, either 2 or 4

Returns:

an array containing for each label, the coordinates of the centroid, in pixel coordinates

createTable

public ij.measure.ResultsTable createTable(Map<Integer,Point3D> map)

Utility method that transforms the mapping between labels and Point3D instances into a ResultsTable that can be displayed with ImageJ.

Parameters:

map - the mapping between labels and Point3Ds

Returns:

a ResultsTable that can be displayed with ImageJ.

analyzeRegions

public Point3D[] analyzeRegions(ij.ImageStack image,
                                int[] labels,
                                ij.measure.Calibration calib)

Computes centroid of each region in input label image.

Specified by:

analyzeRegions in class RegionAnalyzer3D<Point3D>

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 Point3D representing the calibrated centroid coordinates