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

All Methods Instance Methods Concrete Methods
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

Class AlgorithmTextureSegmentation

Nested Class Summary

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

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

filterOp

operationType

filter

windowSize

segmentNumber

pt

contourMask

nonNegativity

removeSmallRegions

omega

filterNumber

binNumber

xDim

yDim

Constructor Detail

AlgorithmTextureSegmentation

Method Detail

runAlgorithm

RmSmRg

expand

expand2

SHedge_ls

x2dist

l2dist

SHcomp

algorithmPerformed