inra.ijpb.measure.region3d

Class IntrinsicVolumesAnalyzer3D

java.lang.Object

inra.ijpb.algo.AlgoStub

inra.ijpb.measure.region3d.RegionAnalyzer3D<IntrinsicVolumesAnalyzer3D.Result>

inra.ijpb.measure.region3d.IntrinsicVolumesAnalyzer3D

All Implemented Interfaces:

Algo, AlgoListener, RegionAnalyzer<IntrinsicVolumesAnalyzer3D.Result>

public class IntrinsicVolumesAnalyzer3D
extends RegionAnalyzer3D<IntrinsicVolumesAnalyzer3D.Result>
implements AlgoListener

Computation of intrinsic volumes (Volume, Surface Area, Mean Breadth and Euler Number) for 3D binary or label images, based on the RegionAnalyzer3D interface. The IntrinsicVolumes3D class provides static classes to facilitate usage when no algorithm monitoring is necessary.

Author:

dlegland

See Also:

IntrinsicVolumes3D, IntrinsicVolumesAnalyzer2D

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	IntrinsicVolumesAnalyzer3D.Result Inner class for storing results.

Constructor Summary

Constructors

Constructor and Description
IntrinsicVolumesAnalyzer3D() Default empty constructor.

Method Summary

Modifier and Type	Method and Description
void	algoProgressChanged(AlgoEvent evt) The method devoted to manage the change in the progression of the algorithm.
void	algoStatusChanged(AlgoEvent evt) The method devoted to manage the change in the status of the algorithm.
IntrinsicVolumesAnalyzer3D.Result[]	analyzeRegions(ij.ImageStack image, int[] labels, ij.measure.Calibration calib) Computes an instance of the generic type T for each region in input label image.
ij.measure.ResultsTable	createTable(Map<Integer,IntrinsicVolumesAnalyzer3D.Result> results) Utility method that converts the detailed results of the RegionAnalyzer.analyzeRegions(ImagePlus) method into an instance of ResultsTable to facilitate display by ImageJ.
static double[]	eulerNumberLut(int conn) Deprecated. use IntrinsicVolumes3DUtils instead
int	getConnectivity()
int	getDirectionNumber()
static double[]	meanBreadthLut(ij.measure.Calibration calib, int nDirs, int conn2d) Deprecated. use IntrinsicVolumes3DUtils instead
void	setConnectivity(int connectivity)
void	setDirectionNumber(int directionNumber)
static double[]	surfaceAreaLut(ij.measure.Calibration calib, int nDirs) Deprecated. use IntrinsicVolumes3DUtils instead
static double[]	volumeLut(ij.measure.Calibration calib) Deprecated. use IntrinsicVolumes3DUtils instead

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

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

IntrinsicVolumesAnalyzer3D

public IntrinsicVolumesAnalyzer3D()

Default empty constructor.

Method Detail

volumeLut

@Deprecated
public static final double[] volumeLut(ij.measure.Calibration calib)

Deprecated. use IntrinsicVolumes3DUtils instead

Parameters:

calib - spatial calibration

Returns:

volume LUT

surfaceAreaLut

@Deprecated
public static final double[] surfaceAreaLut(ij.measure.Calibration calib,
                                                        int nDirs)

Deprecated. use IntrinsicVolumes3DUtils instead

Computes the Look-up table that is used to compute surface area.

Parameters:

calib - the spatial calibration of the image

nDirs - the number of directions to consider, either 3 or 13

Returns:

the look-up-table between binary voxel configuration index and contribution to surface area measure

meanBreadthLut

@Deprecated
public static final double[] meanBreadthLut(ij.measure.Calibration calib,
                                                        int nDirs,
                                                        int conn2d)

Deprecated. use IntrinsicVolumes3DUtils instead

Computes the Look-up table used to measure mean breadth within 3D images.

Parameters:

calib - the spatial calibration of image

nDirs - the number of directions (3 or 13)

conn2d - the connectivity to use on square faces of plane sections (4 or 8)

Returns:

a look-up table with 256 entries

eulerNumberLut

@Deprecated
public static final double[] eulerNumberLut(int conn)

Deprecated. use IntrinsicVolumes3DUtils instead

Computes the look-up table for measuring Euler number in binary 3D image, depending on the connectivity. The input structure should not touch image border. See "3D Images of Material Structures", from J. Ohser and K. Schladitz, Wiley 2009, tables 3.2 p. 52 and 3.3 p. 53.

Parameters:

conn - the 3D connectivity, either 6 or 26

Returns:

a look-up-table with 256 entries

getDirectionNumber

public int getDirectionNumber()

Returns:

the directionNumber used to compute surface area and mean breadth

setDirectionNumber

public void setDirectionNumber(int directionNumber)

Parameters:

directionNumber - the number of directions used to compute surface area and mean breadth (either 3 or 13, default is 13)

getConnectivity

public int getConnectivity()

Returns:

the connectivity used to compute Euler number

setConnectivity

public void setConnectivity(int connectivity)

Parameters:

connectivity - the connectivity used to compute Euler number (either 6 or 26, default is 6)

createTable

public ij.measure.ResultsTable createTable(Map<Integer,IntrinsicVolumesAnalyzer3D.Result> results)

Description copied from interface: RegionAnalyzer

Utility method that converts the detailed results of the RegionAnalyzer.analyzeRegions(ImagePlus) method into an instance of ResultsTable to facilitate display by ImageJ.

Specified by:

createTable in interface RegionAnalyzer<IntrinsicVolumesAnalyzer3D.Result>

Parameters:

results - the mapping between each region label and the result of the analysis

Returns:

an instance of ResultsTable containing results presented in a tabular format.

analyzeRegions

public IntrinsicVolumesAnalyzer3D.Result[] analyzeRegions(ij.ImageStack image,
                                                          int[] labels,
                                                          ij.measure.Calibration calib)

Description copied from class: RegionAnalyzer3D

Computes an instance of the generic type T for each region in input label image.

Specified by:

analyzeRegions in class RegionAnalyzer3D<IntrinsicVolumesAnalyzer3D.Result>

Parameters:

image - the input 3D image containing label of particles

labels - the array of labels within the image

calib - the spatial calibration of the image

Returns:

an array of the type used to represent the analysis result of each region

algoProgressChanged

public void algoProgressChanged(AlgoEvent evt)

Description copied from interface: AlgoListener

The method devoted to manage the change in the progression of the algorithm.

Specified by:

algoProgressChanged in interface AlgoListener

Overrides:

algoProgressChanged in class RegionAnalyzer3D<IntrinsicVolumesAnalyzer3D.Result>

Parameters:

evt - the AlgoEvent instance containing info about the algorithm.

algoStatusChanged

public void algoStatusChanged(AlgoEvent evt)

Description copied from interface: AlgoListener

The method devoted to manage the change in the status of the algorithm.

Specified by:

algoStatusChanged in interface AlgoListener

Overrides:

algoStatusChanged in class RegionAnalyzer3D<IntrinsicVolumesAnalyzer3D.Result>

Parameters:

evt - the AlgoEvent instance containing info about the algorithm.