java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmVOIExtraction

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmVOIExtraction
extends AlgorithmBase
```
DOCUMENT ME!

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 VOI`	`addedVOI`	DOCUMENT ME!
`private java.awt.Color[]`	`colorTable`	DOCUMENT ME!
`private int`	`connected`
`private short[]`	`expImgBuffer`	DOCUMENT ME!
`private short[]`	`grayScaleArray`	DOCUMENT ME!
`private short[]`	`imgBuffer`	DOCUMENT ME!
`private java.util.BitSet`	`mask`	DOCUMENT ME!
`private java.util.BitSet`	`mask2`	DOCUMENT ME!
`private java.util.BitSet`	`maskAll`	DOCUMENT ME!
`private java.util.BitSet`	`maskExpanded`
`private short[][]`	`maskList`	DOCUMENT ME!
`private java.lang.String[]`	`nameTable`	DOCUMENT ME!
`private short[][]`	`nextMaskList`	DOCUMENT ME!
`private int`	`numVOIAdded`
`private short[]`	`objBuffer`	DOCUMENT ME!
`private java.util.BitSet`	`outMask`	DOCUMENT ME!
`private int[]`	`VOIIndexArray`	DOCUMENT ME!
`private int`	`xDim`	DOCUMENT ME!
`private int`	`xDimE`	DOCUMENT ME!
`private int`	`yDim`	DOCUMENT ME!
`private int`	`yDimE`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, 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

AlgorithmVOIExtraction(ModelImage srcImg)
Creates a new AlgorithmVOIExtraction object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calcInPlace()`	Calculates the VOI extraction.
`private void`	`calcInPlace2()`	From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.6 Inner Boundary Tracing, pp. 191-192.
`void`	`disposeLocal()`	DOCUMENT ME!
`private void`	`extendedBoundaryTracing()`	From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.8 Extended Boundary Tracing, pp. 195-196.
`void`	`finalize()`	Prepares this class for destruction.
`VOI`	`getAddedVOI()`	Retrieve the VOI generated by the mask to voi extraction.
`int`	`getNumVOIAdded()`
`private void`	`outerBoundaryTracing()`	From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.7 Outer Boundary Tracing, p. 193.
`void`	`runAlgorithm()`	Starts the program.
`void`	`setColorTable(java.awt.Color[] colorTable)`	DOCUMENT ME!
`void`	`setNameTable(java.lang.String[] nameTable)`	DOCUMENT ME!
`private void`	`setRegionMaskAll()`	Sets the mask of all points in the 4 connected region with a gray scale value.
`private void`	`setRegionMaskI(int xStart, int yStart, short objectValue)`	Sets the mask of all points in the 4 connected region with a gray scale value of objectValue Uses iteration.
`private void`	`setRegionOutMaskI(int xStart, int yStart, short objectValue)`	Sets the mask of all points in the 4 connected region with a gray scale value of objectValue Uses iteration.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, 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
  - addedVOI
```
private VOI addedVOI
```
    DOCUMENT ME!
  - colorTable
```
private java.awt.Color[] colorTable
```
    DOCUMENT ME!
  - expImgBuffer
```
private short[] expImgBuffer
```
    DOCUMENT ME!
  - grayScaleArray
```
private short[] grayScaleArray
```
    DOCUMENT ME!
  - imgBuffer
```
private short[] imgBuffer
```
    DOCUMENT ME!
  - mask
```
private java.util.BitSet mask
```
    DOCUMENT ME!
  - mask2
```
private java.util.BitSet mask2
```
    DOCUMENT ME!
  - maskAll
```
private java.util.BitSet maskAll
```
    DOCUMENT ME!
  - maskList
```
private short[][] maskList
```
    DOCUMENT ME!
  - nameTable
```
private java.lang.String[] nameTable
```
    DOCUMENT ME!
  - nextMaskList
```
private short[][] nextMaskList
```
    DOCUMENT ME!
  - objBuffer
```
private short[] objBuffer
```
    DOCUMENT ME!
  - outMask
```
private java.util.BitSet outMask
```
    DOCUMENT ME!
  - VOIIndexArray
```
private int[] VOIIndexArray
```
    DOCUMENT ME!
  - xDim
```
private int xDim
```
    DOCUMENT ME!
  - xDimE
```
private int xDimE
```
    DOCUMENT ME!
  - yDim
```
private int yDim
```
    DOCUMENT ME!
  - yDimE
```
private int yDimE
```
    DOCUMENT ME!
  - maskExpanded
```
private java.util.BitSet maskExpanded
```
  - connected
```
private int connected
```
  - numVOIAdded
```
private int numVOIAdded
```
- Constructor Detail
  - AlgorithmVOIExtraction
```
public AlgorithmVOIExtraction(ModelImage srcImg)
```
    Creates a new AlgorithmVOIExtraction object.
    
    Parameters:
    
    srcImg - source image model
- Method Detail
  - disposeLocal
```
public void disposeLocal()
```
    DOCUMENT ME!
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setColorTable
```
public void setColorTable(java.awt.Color[] colorTable)
```
    DOCUMENT ME!
    
    Parameters:
    
    colorTable - DOCUMENT ME!
  - setNameTable
```
public void setNameTable(java.lang.String[] nameTable)
```
    DOCUMENT ME!
    
    Parameters:
    
    nameTable - DOCUMENT ME!
  - extendedBoundaryTracing
```
private void extendedBoundaryTracing()
```
    From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.8 Extended Boundary Tracing, pp. 195-196.
  - outerBoundaryTracing
```
private void outerBoundaryTracing()
```
    From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.7 Outer Boundary Tracing, p. 193.
  - calcInPlace2
```
private void calcInPlace2()
```
    From text description in 4th edition Image Processing, Analysis, and Machine Vision International Edition by Milan Sonka, Vaclav Hlavac, and Roger Boyle, Algorithm 6.6 Inner Boundary Tracing, pp. 191-192. "Algorithm 6.6 works for all regions larger than one pixel. It is able to find region borders but does not find borders of region holes, which may be located by identifying border elements unallocated thus far to borders. The search for border elements always starts after a traced border is closed, and the search for "unused" border elements can continue in the same way as the search for the first border element. Note that if objects are of unit width, more conditions must be added." Can be used with either connected = 4 or connected = 8. Much less memory than calcInPlace.
  - calcInPlace
```
private void calcInPlace()
```
    Calculates the VOI extraction.
  - setRegionMaskAll
```
private void setRegionMaskAll()
```
    Sets the mask of all points in the 4 connected region with a gray scale value.
  - setRegionMaskI
```
private void setRegionMaskI(int xStart,
                            int yStart,
                            short objectValue)
```
    Sets the mask of all points in the 4 connected region with a gray scale value of objectValue Uses iteration.
    
    Parameters:
    
    xStart - the x coordinate of the starting point
    
    yStart - the y coordinate of the starting point
    
    objectValue - the gray scale value of the object
  - setRegionOutMaskI
```
private void setRegionOutMaskI(int xStart,
                               int yStart,
                               short objectValue)
```
    Sets the mask of all points in the 4 connected region with a gray scale value of objectValue Uses iteration.
    
    Parameters:
    
    xStart - the x coordinate of the starting point
    
    yStart - the y coordinate of the starting point
    
    objectValue - the gray scale value of the object
  - getAddedVOI
```
public VOI getAddedVOI()
```
    Retrieve the VOI generated by the mask to voi extraction.
    
    Returns:
    
    The generated VOI object.
  - getNumVOIAdded
```
public int getNumVOIAdded()
```

Class AlgorithmVOIExtraction

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

addedVOI

colorTable

expImgBuffer

grayScaleArray

imgBuffer

mask

mask2

maskAll

maskList

nameTable

nextMaskList

objBuffer

outMask

VOIIndexArray

xDim

xDimE

yDim

yDimE

maskExpanded

connected

numVOIAdded

Constructor Detail

AlgorithmVOIExtraction

Method Detail

disposeLocal

finalize

runAlgorithm

setColorTable

setNameTable

extendedBoundaryTracing

outerBoundaryTracing

calcInPlace2

calcInPlace

setRegionMaskAll

setRegionMaskI

setRegionOutMaskI

getAddedVOI

getNumVOIAdded