inra.ijpb.measure.region3d

Class IntrinsicVolumes3DUtils

java.lang.Object

inra.ijpb.measure.region3d.IntrinsicVolumes3DUtils

public class IntrinsicVolumes3DUtils
extends Object

Utility functions for classes that compute 3D intrinsic volumes measures.

Author:

dlegland

See Also:

IntrinsicVolumes3D

Method Summary

Modifier and Type	Method and Description
static double[]	directionWeights3d13(ij.measure.Calibration calib) Returns an array with seven values corresponding the unique direction vectors obtained with 13 directions.
static double[]	directionWeights3d3(ij.measure.Calibration calib) Returns an array with seven values corresponding the unique direction vectors obtained with 3 directions.
static double[]	eulerNumberLut(int conn) Computes the look-up table for measuring Euler number in binary 3D image, depending on the connectivity.
static double[]	meanBreadthLut(ij.measure.Calibration calib, int nDirs, int conn2d) Computes the Look-up table used to measure mean breadth within 3D images.
static double	samplingVolume(ij.ImageStack image, ij.measure.Calibration calib) Returns the "inner volume" of the 3D image, i.e.
static double[]	surfaceAreaLut(ij.measure.Calibration calib, int nDirs) Computes the Look-up table that is used to compute surface area.
static double[]	volumeLut(ij.measure.Calibration calib) Computes the Look-up table that is used to compute volume.

Methods inherited from class java.lang.Object

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

Method Detail

volumeLut

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

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

Parameters:

calib - the spatial calibration of the image

Returns:

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

surfaceAreaLut

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

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

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

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

directionWeights3d3

public static final double[] directionWeights3d3(ij.measure.Calibration calib)

Returns an array with seven values corresponding the unique direction vectors obtained with 3 directions. The results simply consists in 1/3 for the three main directions, and 0 otherwise. The method is provided for the sake of homogeneity with directionWeights3d13.

Parameters:

calib - the spatial calibration of the 3D image

Returns:

an array of seven values, corresponding to the three isothetic, three plane diagonal, and one cube diagonal directions.

directionWeights3d13

public static final double[] directionWeights3d13(ij.measure.Calibration calib)

Returns an array with seven values corresponding the unique direction vectors obtained with 13 directions.

Parameters:

calib - the spatial calibration of the 3D image

Returns:

an array of seven values, corresponding to the three isothetic, three plane diagonal, and one cube diagonal directions.

eulerNumberLut

public static final double[] eulerNumberLut(int conn)

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

samplingVolume

public static final double samplingVolume(ij.ImageStack image,
                                          ij.measure.Calibration calib)

Returns the "inner volume" of the 3D image, i.e. the calibrated volume of the image without taking into account the voxels at the border of the image.

Parameters:

image - the input 3D image

calib - the spatial calibration of the image

Returns:

the calibrated volume of the portion of image witout border voxels