at.mug.iqm.img.bundle.imagej

Class IqmSRM_8bitGray_ONLY

java.lang.Object

at.mug.iqm.img.bundle.imagej.IqmSRM_8bitGray_ONLY

All Implemented Interfaces:

ij.plugin.filter.PlugInFilter

public class IqmSRM_8bitGray_ONLY
extends Object
implements ij.plugin.filter.PlugInFilter

This is an expanded version of the ImageJ algorithm by Johannes Schindelin http://fiji.sc/wiki/index.php/Statistical_Region_Merging#cite_note-0 based on following algorithm: R. Nock, F. Nielsen (2004), "Statistical Region Merging", IEEE Trans. Pattern Anal. Mach. Intell. 26 (11): 1452-1458mages.

Since:

2012 01

Author:

Helmut Ahammer

Field Summary

Fields

Modifier and Type	Field and Description
(package private) float[]	average
(package private) int[]	count
protected float	delta
protected float	factor
(package private) float	g
(package private) ij.ImagePlus	image
protected float	logDelta
(package private) int[]	neighborBucket
(package private) int[]	nextNeighbor
protected float	Q
(package private) int[]	regionIndex

Fields inherited from interface ij.plugin.filter.PlugInFilter

CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors

Constructor and Description
IqmSRM_8bitGray_ONLY()

Method Summary

Modifier and Type	Method and Description
protected void	addNeighborPair(int neighborIndex, byte[] pixel, byte[] nextPixel, int i)
protected void	addNeighborPair(int neighborIndex, byte[] pixel, int i1, int i2)
(package private) int	consolidateRegions()
(package private) int	getRegionIndex(int i)
(package private) void	initializeNeighbors2D(byte[] pixel, int w, int h)
(package private) void	initializeNeighbors3D(int w, int h, int d)
(package private) void	initializeRegions2D(byte[] pixel, int w, int h)
(package private) void	initializeRegions3D(int w, int h, int d)
(package private) void	mergeAllNeighbors2D(int w)
(package private) void	mergeAllNeighbors3D(int w, int h)
(package private) void	mergeRegions(int i1, int i2)
(package private) boolean	predicate(int i1, int i2)
void	run(ij.process.ImageProcessor ip)
ij.ImagePlus	run(ij.process.ImageProcessor ip, int q, int out)
int	setup(String arg, ij.ImagePlus image)
protected ij.ImagePlus	srm2D(ij.process.ImageProcessor ip, boolean showAverages)
protected ij.ImagePlus	srm3D(boolean showAverages)

Methods inherited from class java.lang.Object

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

Field Detail

image

ij.ImagePlus image

g

final float g

See Also:

Constant Field Values

Q

protected float Q

delta

protected float delta

factor

protected float factor

logDelta

protected float logDelta

average

float[] average

count

int[] count

regionIndex

int[] regionIndex

nextNeighbor

int[] nextNeighbor

neighborBucket

int[] neighborBucket

Constructor Detail

IqmSRM_8bitGray_ONLY

public IqmSRM_8bitGray_ONLY()

Method Detail

setup

public int setup(String arg,
                 ij.ImagePlus image)

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

run

public void run(ij.process.ImageProcessor ip)

Specified by:

run in interface ij.plugin.filter.PlugInFilter

run

public ij.ImagePlus run(ij.process.ImageProcessor ip,
                        int q,
                        int out)

srm3D

protected ij.ImagePlus srm3D(boolean showAverages)

srm2D

protected ij.ImagePlus srm2D(ij.process.ImageProcessor ip,
                             boolean showAverages)

initializeRegions2D

void initializeRegions2D(byte[] pixel,
                         int w,
                         int h)

initializeRegions3D

void initializeRegions3D(int w,
                         int h,
                         int d)

addNeighborPair

protected void addNeighborPair(int neighborIndex,
                               byte[] pixel,
                               int i1,
                               int i2)

initializeNeighbors2D

void initializeNeighbors2D(byte[] pixel,
                           int w,
                           int h)

addNeighborPair

protected void addNeighborPair(int neighborIndex,
                               byte[] pixel,
                               byte[] nextPixel,
                               int i)

initializeNeighbors3D

void initializeNeighbors3D(int w,
                           int h,
                           int d)

getRegionIndex

int getRegionIndex(int i)

predicate

boolean predicate(int i1,
                  int i2)

mergeAllNeighbors2D

void mergeAllNeighbors2D(int w)

mergeAllNeighbors3D

void mergeAllNeighbors3D(int w,
                         int h)

mergeRegions

void mergeRegions(int i1,
                  int i2)

consolidateRegions

int consolidateRegions()