inra.ijpb.measure.region2d

Class AverageThickness

java.lang.Object

inra.ijpb.algo.AlgoStub

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

inra.ijpb.measure.region2d.AverageThickness

All Implemented Interfaces:

Algo, RegionAnalyzer<AverageThickness.Result>

public class AverageThickness
extends RegionAnalyzer2D<AverageThickness.Result>

Compute average thickness of a binary region, or of each region in a label image. The average thickness is computed by:

1. computing the skeleton of the binary region,
2. computing the distance map of each foreground pixel of the original binary region,
3. measuring the value in the distance map for each pixel of the skeleton,
4. computing the average.

The result largely depends on the algorithms for computing skeleton and distance map. For skeleton, the an adaptation of ImageJ's algorithm is used. For distance maps, chamfer distance maps are used.

Author:

dlegland

See Also:

ImageJSkeleton, DistanceTransform2D

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	AverageThickness.Result Inner class used for representing results of average thickness computations.

Constructor Summary

Constructors

Constructor and Description
AverageThickness()

Method Summary

Modifier and Type	Method and Description
AverageThickness.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.
ij.measure.ResultsTable	createTable(Map<Integer,AverageThickness.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.

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

AverageThickness

public AverageThickness()

Method Detail

createTable

public ij.measure.ResultsTable createTable(Map<Integer,AverageThickness.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.

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 AverageThickness.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<AverageThickness.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