Package gov.nih.mipav.model.algorithms

Class AlgorithmTextureSegmentation

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmTextureSegmentation

All Implemented Interfaces:

AlgorithmInterface, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmTextureSegmentation
extends AlgorithmBase
implements AlgorithmInterface

This software implements the factorization-based segmentation algorithm. The original code was written in MATLAB and C by: Jiangye Yuan Computational Sciences and and Engineering Division Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 yuanj@ornl.gov Reference: [1] J. Yuan and D. L. Wang. Factorization-based texture segmentation. Technical Report OSU-CISRC-1/13 -TR01, 2013. The website for this code is: https://sites.google.com/site/factorizationsegmentation/ This code was ported to Java by William Gandler

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private int	binNumber
private java.util.BitSet	contourMask
private double[]	filter
private int	filterNumber
private static int	filterOp
private boolean	nonNegativity
private double	omega
private int	operationType
private WildMagic.LibFoundation.Mathematics.Vector3f[]	pt
private boolean	removeSmallRegions
private int	segmentNumber
private int	windowSize
private int	xDim
private int	yDim

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmTextureSegmentation(ModelImage destImage, ModelImage srcImage, int windowSize, int segmentNumber, WildMagic.LibFoundation.Mathematics.Vector3f[] pt, java.util.BitSet contourMask, boolean nonNegativity, boolean removeSmallRegions)

Method Summary

Modifier and Type	Method	Description
void	algorithmPerformed(AlgorithmBase algorithm)	Called after an algorithm this listener is registered to exits (maybe successfully, maybe not).
private void	expand(int y, int x, int[] stk, int[][] segLabelLarge, int[][] segLabel, int labelN, int[] cnt, int[] tb, int[] bb, int[] lb, int[] rb, int tgt)
private void	expand2(int y, int x, int[] stk, int[] mark, int[][] segLabel, int labelN, int[] cnt, int[] tb, int[] bb, int[] lb, int[] rb, int tgt)
private double	l2dist(double[] a, double[] b, int k)
private void	RmSmRg(int[][] segLabelLarge, int[][] segLabel, int minSize)
void	runAlgorithm()	Actually runs the algorithm.
private void	SHcomp(double[][][] sh_mx, int ws, double[][][] Ig)
private void	SHedge_ls(double[][] EdgeMap, int ws, int dism, double[][][] sh_mx)
private double	x2dist(double[] a, double[] b, int k)

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

filterOp

private static final int filterOp

See Also:

Constant Field Values

operationType

private int operationType

filter

private double[] filter

windowSize

private int windowSize

segmentNumber

private int segmentNumber

pt

private WildMagic.LibFoundation.Mathematics.Vector3f[] pt

contourMask

private java.util.BitSet contourMask

nonNegativity

private boolean nonNegativity

removeSmallRegions

private boolean removeSmallRegions

omega

private double omega

filterNumber

private int filterNumber

binNumber

private int binNumber

xDim

private int xDim

yDim

private int yDim

Constructor Detail

AlgorithmTextureSegmentation

public AlgorithmTextureSegmentation(ModelImage destImage,
                                    ModelImage srcImage,
                                    int windowSize,
                                    int segmentNumber,
                                    WildMagic.LibFoundation.Mathematics.Vector3f[] pt,
                                    java.util.BitSet contourMask,
                                    boolean nonNegativity,
                                    boolean removeSmallRegions)

Method Detail

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

RmSmRg

private void RmSmRg(int[][] segLabelLarge,
                    int[][] segLabel,
                    int minSize)

expand

private void expand(int y,
                    int x,
                    int[] stk,
                    int[][] segLabelLarge,
                    int[][] segLabel,
                    int labelN,
                    int[] cnt,
                    int[] tb,
                    int[] bb,
                    int[] lb,
                    int[] rb,
                    int tgt)

expand2

private void expand2(int y,
                     int x,
                     int[] stk,
                     int[] mark,
                     int[][] segLabel,
                     int labelN,
                     int[] cnt,
                     int[] tb,
                     int[] bb,
                     int[] lb,
                     int[] rb,
                     int tgt)

SHedge_ls

private void SHedge_ls(double[][] EdgeMap,
                       int ws,
                       int dism,
                       double[][][] sh_mx)

x2dist

private double x2dist(double[] a,
                      double[] b,
                      int k)

l2dist

private double l2dist(double[] a,
                      double[] b,
                      int k)

SHcomp

private void SHcomp(double[][][] sh_mx,
                    int ws,
                    double[][][] Ig)

algorithmPerformed

public void algorithmPerformed(AlgorithmBase algorithm)

Description copied from interface: AlgorithmInterface

Called after an algorithm this listener is registered to exits (maybe successfully, maybe not). If the algorithm is run in a separate thread, this call will be made within that thread. If not, this call will be made from that same, shared thread.

Specified by:

algorithmPerformed in interface AlgorithmInterface

Parameters:

algorithm - the algorithm which has just completed