inra.ijpb.measure.region2d

Class IntrinsicVolumesAnalyzer2D

java.lang.Object

inra.ijpb.algo.AlgoStub

inra.ijpb.measure.region2d.RegionAnalyzer2D<IntrinsicVolumesAnalyzer2D.Result>

inra.ijpb.measure.region2d.IntrinsicVolumesAnalyzer2D

All Implemented Interfaces:

Algo, AlgoListener, RegionAnalyzer<IntrinsicVolumesAnalyzer2D.Result>

public class IntrinsicVolumesAnalyzer2D
extends RegionAnalyzer2D<IntrinsicVolumesAnalyzer2D.Result>
implements AlgoListener

Computation of intrinsic volumes (area, perimeter and Euler number) for binary or label 2D images.

Author:

dlegland

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	IntrinsicVolumesAnalyzer2D.Result Inner class for storing results.

Constructor Summary

Constructors

Constructor and Description
IntrinsicVolumesAnalyzer2D() 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.
IntrinsicVolumesAnalyzer2D.Result[]	analyzeRegions(ij.process.ImageProcessor image, int[] labels, ij.measure.Calibration calib) Computes an instance of the generic type T for each region in input label image.
static double[]	areaLut(ij.measure.Calibration calib) Deprecated. use IntrinsicVolumes2DUtils instead
static double[]	computeCircularities(IntrinsicVolumesAnalyzer2D.Result[] morphos) Deprecated.
ij.measure.ResultsTable	createTable(Map<Integer,IntrinsicVolumesAnalyzer2D.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 int[]	eulerNumberIntLut(int conn) Deprecated. use IntrinsicVolumes2DUtils instead
static double[]	eulerNumberLut(int conn) Deprecated. use IntrinsicVolumes2DUtils instead
int	getConnectivity()
int	getDirectionNumber()
static double[]	perimeterLut(ij.measure.Calibration calib, int nDirs) Deprecated. use IntrinsicVolumes2DUtils instead
void	setConnectivity(int connectivity)
void	setDirectionNumber(int directionNumber)

Methods inherited from class inra.ijpb.measure.region2d.RegionAnalyzer2D

analyzeRegions, analyzeRegions, computeTable

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

IntrinsicVolumesAnalyzer2D

public IntrinsicVolumesAnalyzer2D()

Default empty constructor.

Method Detail

areaLut

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

Deprecated. use IntrinsicVolumes2DUtils instead

Parameters:

calib - spatial calibration of image

Returns:

area lut

perimeterLut

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

Deprecated. use IntrinsicVolumes2DUtils instead

Computes the Look-up table that is used to compute perimeter. The result is an array with 16 entries, each entry corresponding to a binary 2-by-2 configuration of pixels.

Parameters:

calib - the calibration of the image

nDirs - the number of directions to use (2 or 4)

Returns:

an array containing for each 2-by-2 configuration index, the corresponding contribution to perimeter estimate

computeCircularities

@Deprecated
public static final double[] computeCircularities(IntrinsicVolumesAnalyzer2D.Result[] morphos)

Deprecated.

Utility method that computes circularities as a numeric array from the result array

Parameters:

morphos - the array of results

Returns:

the numeric array of circularities

eulerNumberLut

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

Deprecated. use IntrinsicVolumes2DUtils instead

Computes the Look-up table that is used to compute Euler number density. The result is an array with 16 entries, each entry corresponding to a binary 2-by-2 configuration of pixels.

Parameters:

conn - the connectivity to use (4 or 8)

Returns:

an array containing for each 2-by-2 configuration index, the corresponding contribution to euler number estimate

eulerNumberIntLut

@Deprecated
public static final int[] eulerNumberIntLut(int conn)

Deprecated. use IntrinsicVolumes2DUtils instead

Computes the Look-up table that is used to compute Euler number density. The result is an array with 16 entries, each entry corresponding to a binary 2-by-2 configuration of pixels.

Parameters:

conn - the connectivity to use (4 or 8)

Returns:

an array containing for each 2-by-2 configuration index, the corresponding contribution to euler number estimate

getDirectionNumber

public int getDirectionNumber()

Returns:

the number of directions used to compute perimeter

setDirectionNumber

public void setDirectionNumber(int directionNumber)

Parameters:

directionNumber - the number of directions used to compute perimeter (either 2 or 4, default is 4)

getConnectivity

public int getConnectivity()

Returns:

the connectivity used for computing Euler number

setConnectivity

public void setConnectivity(int connectivity)

Parameters:

connectivity - the connectivity for computing Euler number (either 4 or 8, default is 4)

createTable

public ij.measure.ResultsTable createTable(Map<Integer,IntrinsicVolumesAnalyzer2D.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<IntrinsicVolumesAnalyzer2D.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 IntrinsicVolumesAnalyzer2D.Result[] analyzeRegions(ij.process.ImageProcessor image,
                                                          int[] labels,
                                                          ij.measure.Calibration calib)

Description copied from class: RegionAnalyzer2D

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

Specified by:

analyzeRegions in class RegionAnalyzer2D<IntrinsicVolumesAnalyzer2D.Result>

Parameters:

image - the input 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

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

Parameters:

evt - the AlgoEvent instance containing info about the algorithm.