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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmMask
extends AlgorithmBase
```
Allow the user to fill a VOI or fill everything outside the VOI with a specific fill value.

Version:

0.1 Feb 11, 1998

Author:

Matthew J. McAuliffe, Ph.D.

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 float`	`imageFill`	Set the mask areas to this value.
`private float`	`imageFillB`	DOCUMENT ME!
`private float`	`imageFillG`	DOCUMENT ME!
`private float`	`imageFillI`
`private float`	`imageFillR`	DOCUMENT ME!
`private boolean`	`polarity`	if true then fill inside the VOI.

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
`AlgorithmMask(ModelImage srcImg, float fill, boolean polarity, boolean useVOI)`	Creates a new AlgorithmMask object.
`AlgorithmMask(ModelImage srcImg, float fill, float fillI, boolean polarity, boolean useVOI)`	Creates a new AlgorithmMask object.
`AlgorithmMask(ModelImage srcImg, float fillR, float fillG, float fillB, boolean polarity, boolean useVOI)`	Creates a new AlgorithmMask object.
`AlgorithmMask(ModelImage destImg, ModelImage srcImg, float fill, boolean polarity, boolean useVOI)`	Creates a new AlgorithmMask object.
`AlgorithmMask(ModelImage destImg, ModelImage srcImg, float fill, float fillI, boolean polarity, boolean useVOI)`	Creates a new AlgorithmMask object.
`AlgorithmMask(ModelImage destImg, ModelImage srcImg, float fillR, float fillG, float fillB, boolean polarity, boolean useVOI)`	Creates a new AlgorithmMask object.
`AlgorithmMask(ModelImage srcImg, java.awt.Color _fillColor, boolean polarity, boolean useVOI)`	Creates a new AlgorithmMask object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`calcInPlace25D(java.util.BitSet mask, float fillValue, int tSlice)`	Fills VOI of the source image with fill value.
`void`	`calcInPlace25D(java.util.BitSet mask, float fillValue, int tSlice, java.util.Vector<java.lang.Integer> intensityLockVector, boolean showProgressBar)`	Fills VOI of the source image with fill value.
`void`	`calcInPlace25DC(java.util.BitSet mask, java.awt.Color fillColor, int tSlice, java.lang.String rgbString, java.util.Vector<java.lang.Integer> intensityLockVector, boolean showProgressBar)`	Fills VOI of the color source image with fill color.
`void`	`calcInPlace25DCMask(java.util.BitSet mask, java.awt.Color fillColor, int tSlice)`	Fills VOI of the color source image with fill color.
`void`	`calcInPlace25DMask(java.util.BitSet mask, float fillValue, int tSlice)`	Fills VOI of the source image with fill value.
`void`	`calcInPlace25DMask(java.util.BitSet mask, float fillValue, int tSlice, java.util.Vector<java.lang.Integer> intensityLockVector)`	Fills VOI of the source image with fill value.
`private void`	`calcInPlace2D()`	Fills VOI of source image with fill value.
`private void`	`calcInPlace2DComplex()`	Fills VOI of source image with fill value.
`private void`	`calcInPlace2DRGB()`	Fills VOI of source image with fill value.
`private void`	`calcInPlace3D()`	Fills VOI of the source image with fill value.
`private void`	`calcInPlace3DComplex()`	Fills VOI of the source image with fill value.
`private void`	`calcInPlace3DRGB()`	Fills VOI of the source image with fill value.
`private void`	`calcInPlace4D()`	Fills VOI of the source image with fill value.
`private void`	`calcInPlace4DComplex()`	Fills VOI of the source image with fill value.
`private void`	`calcInPlace4DRGB()`	Fills VOI of the source image with fill value.
`private void`	`calcStoreInDest2D()`	Fills new image/VOI with new fill value;
`private void`	`calcStoreInDest2DComplex()`	Fills new image/VOI with new fill value;
`private void`	`calcStoreInDest2DRGB()`	Fills new image/VOI with new fill value;
`private void`	`calcStoreInDest3D()`	Fills new image/VOI with new fill value;
`private void`	`calcStoreInDest3DComplex()`	Fills new image/VOI with new fill value;
`private void`	`calcStoreInDest3DRGB()`	Fills new image/VOI with new fill value;
`private void`	`calcStoreInDest4D()`	Fills new image/VOI with new fill value;
`private void`	`calcStoreInDest4DComplex()`	Fills new image/VOI with new fill value;
`private void`	`calcStoreInDest4DRGB()`	Fills new image/VOI with new fill value;
`void`	`finalize()`	Prepares this class for destruction.
`void`	`runAlgorithm()`	Starts the program.

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
  - imageFill
```
private float imageFill
```
    Set the mask areas to this value.
  - imageFillB
```
private float imageFillB
```
    DOCUMENT ME!
  - imageFillG
```
private float imageFillG
```
    DOCUMENT ME!
  - imageFillR
```
private float imageFillR
```
    DOCUMENT ME!
  - imageFillI
```
private float imageFillI
```
  - polarity
```
private boolean polarity
```
    if true then fill inside the VOI. If false then fill outside
- Constructor Detail
  - AlgorithmMask
```
public AlgorithmMask(ModelImage srcImg,
                     float fill,
                     boolean polarity,
                     boolean useVOI)
```
    Creates a new AlgorithmMask object.
    
    Parameters:
    
    srcImg - source image model
    
    fill - value used to fill a region
    
    polarity - flag indicating fill location, true = fill inside; false fill outside
    
    useVOI - use the VOI to define the mask area else it will use the painted area to define the mask.
  - AlgorithmMask
```
public AlgorithmMask(ModelImage srcImg,
                     java.awt.Color _fillColor,
                     boolean polarity,
                     boolean useVOI)
```
    Creates a new AlgorithmMask object.
    
    Parameters:
    
    srcImg - source image model
    
    _fillColor - color used to fill a region
    
    polarity - flag indicating fill location, true = fill inside; false fill outside
    
    useVOI - use the VOI to define the mask area else it will use the painted area to define the mask.
  - AlgorithmMask
```
public AlgorithmMask(ModelImage destImg,
                     ModelImage srcImg,
                     float fill,
                     boolean polarity,
                     boolean useVOI)
```
    Creates a new AlgorithmMask object.
    
    Parameters:
    
    destImg - image model where result image is to stored
    
    srcImg - source image model
    
    fill - value used to fill a region
    
    polarity - flag indicating fill location, true = fill inside; false fill outside
    
    useVOI - use the VOI to define the mask area else it will use the painted area to define the mask.
  - AlgorithmMask
```
public AlgorithmMask(ModelImage srcImg,
                     float fillR,
                     float fillG,
                     float fillB,
                     boolean polarity,
                     boolean useVOI)
```
    Creates a new AlgorithmMask object.
    
    Parameters:
    
    srcImg - source image model
    
    fillR - red value used to fill a region
    
    fillG - green value used to fill a region
    
    fillB - blue value used to fill a region
    
    polarity - flag indicating fill location, true = fill inside; false fill outside
    
    useVOI - use the VOI to define the mask area else it will use the painted area to define the mask.
  - AlgorithmMask
```
public AlgorithmMask(ModelImage destImg,
                     ModelImage srcImg,
                     float fillR,
                     float fillG,
                     float fillB,
                     boolean polarity,
                     boolean useVOI)
```
    Creates a new AlgorithmMask object.
    
    Parameters:
    
    destImg - image model where result image is to stored
    
    srcImg - source image model
    
    fillR - red value used to fill a region
    
    fillG - green value used to fill a region
    
    fillB - blue value used to fill a region
    
    polarity - flag indicating fill location, true = fill inside; false fill outside
    
    useVOI - use the VOI to define the mask area else it will use the painted area to define the mask.
  - AlgorithmMask
```
public AlgorithmMask(ModelImage srcImg,
                     float fill,
                     float fillI,
                     boolean polarity,
                     boolean useVOI)
```
    Creates a new AlgorithmMask object.
    
    Parameters:
    
    srcImg - source image model
    
    fill - real value used to fill a region
    
    fillI - imaginary value used to fill a region
    
    polarity - flag indicating fill location, true = fill inside; false fill outside
    
    useVOI - use the VOI to define the mask area else it will use the painted area to define the mask.
  - AlgorithmMask
```
public AlgorithmMask(ModelImage destImg,
                     ModelImage srcImg,
                     float fill,
                     float fillI,
                     boolean polarity,
                     boolean useVOI)
```
    Creates a new AlgorithmMask object.
    
    Parameters:
    
    destImg - image model where result image is to stored
    
    srcImg - source image model
    
    fill - real value used to fill a region
    
    fillI - imaginary value used to fill a region
    
    polarity - flag indicating fill location, true = fill inside; false fill outside
    
    useVOI - use the VOI to define the mask area else it will use the painted area to define the mask.
- Method Detail
  - calcInPlace25D
```
public void calcInPlace25D(java.util.BitSet mask,
                           float fillValue,
                           int tSlice)
```
    Fills VOI of the source image with fill value.
    
    Parameters:
    
    mask - DOCUMENT ME!
    
    fillValue - value to be placed in the image where the mask is true
    
    tSlice - indicates which volume should be painted (tSlice = 4th dimension)
  - calcInPlace25D
```
public void calcInPlace25D(java.util.BitSet mask,
                           float fillValue,
                           int tSlice,
                           java.util.Vector<java.lang.Integer> intensityLockVector,
                           boolean showProgressBar)
```
    Fills VOI of the source image with fill value.
    
    Parameters:
    
    mask - DOCUMENT ME!
    
    fillValue - value to be placed in the image where the mask is true
    
    tSlice - indicates which volume should be painted (tSlice = 4th dimension)
    
    intensityLockVector - Vector containing Integer objects that represent the intensity values that are not mutable
  - calcInPlace25DC
```
public void calcInPlace25DC(java.util.BitSet mask,
                            java.awt.Color fillColor,
                            int tSlice,
                            java.lang.String rgbString,
                            java.util.Vector<java.lang.Integer> intensityLockVector,
                            boolean showProgressBar)
```
    Fills VOI of the color source image with fill color.
    
    Parameters:
    
    mask - DOCUMENT ME!
    
    fillColor - color to be placed in the image where the mask is true
    
    tSlice - indicates which volume should be painted (tSlice = 4th dimension)
  - calcInPlace25DCMask
```
public void calcInPlace25DCMask(java.util.BitSet mask,
                                java.awt.Color fillColor,
                                int tSlice)
```
    Fills VOI of the color source image with fill color.
    
    Parameters:
    
    mask - DOCUMENT ME!
    
    fillColor - color to be placed in the image where the mask is true
    
    tSlice - indicates which volume should be painted (tSlice = 4th dimension)
  - calcInPlace25DMask
```
public void calcInPlace25DMask(java.util.BitSet mask,
                               float fillValue,
                               int tSlice)
```
    Fills VOI of the source image with fill value.
    
    Parameters:
    
    mask - DOCUMENT ME!
    
    fillValue - value to be placed in the image where the mask is true
    
    tSlice - indicates which volume should be painted (tSlice = 4th dimension)
  - calcInPlace25DMask
```
public void calcInPlace25DMask(java.util.BitSet mask,
                               float fillValue,
                               int tSlice,
                               java.util.Vector<java.lang.Integer> intensityLockVector)
```
    Fills VOI of the source image with fill value.
    
    Parameters:
    
    mask - DOCUMENT ME!
    
    fillValue - value to be placed in the image where the mask is true
    
    tSlice - indicates which volume should be painted (tSlice = 4th dimension)
    
    intensityLockVector - 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
  - calcInPlace2D
```
private void calcInPlace2D()
```
    Fills VOI of source image with fill value.
  - calcInPlace2DComplex
```
private void calcInPlace2DComplex()
```
    Fills VOI of source image with fill value.
  - calcInPlace2DRGB
```
private void calcInPlace2DRGB()
```
    Fills VOI of source image with fill value.
  - calcInPlace3D
```
private void calcInPlace3D()
```
    Fills VOI of the source image with fill value.
  - calcInPlace3DComplex
```
private void calcInPlace3DComplex()
```
    Fills VOI of the source image with fill value.
  - calcInPlace3DRGB
```
private void calcInPlace3DRGB()
```
    Fills VOI of the source image with fill value.
  - calcInPlace4D
```
private void calcInPlace4D()
```
    Fills VOI of the source image with fill value.
  - calcInPlace4DComplex
```
private void calcInPlace4DComplex()
```
    Fills VOI of the source image with fill value.
  - calcInPlace4DRGB
```
private void calcInPlace4DRGB()
```
    Fills VOI of the source image with fill value.
  - calcStoreInDest2D
```
private void calcStoreInDest2D()
```
    Fills new image/VOI with new fill value;
  - calcStoreInDest2DComplex
```
private void calcStoreInDest2DComplex()
```
    Fills new image/VOI with new fill value;
  - calcStoreInDest2DRGB
```
private void calcStoreInDest2DRGB()
```
    Fills new image/VOI with new fill value;
  - calcStoreInDest3D
```
private void calcStoreInDest3D()
```
    Fills new image/VOI with new fill value;
  - calcStoreInDest3DComplex
```
private void calcStoreInDest3DComplex()
```
    Fills new image/VOI with new fill value;
  - calcStoreInDest3DRGB
```
private void calcStoreInDest3DRGB()
```
    Fills new image/VOI with new fill value;
  - calcStoreInDest4D
```
private void calcStoreInDest4D()
```
    Fills new image/VOI with new fill value;
  - calcStoreInDest4DComplex
```
private void calcStoreInDest4DComplex()
```
    Fills new image/VOI with new fill value;
  - calcStoreInDest4DRGB
```
private void calcStoreInDest4DRGB()
```
    Fills new image/VOI with new fill value;

Class AlgorithmMask

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

imageFill

imageFillB

imageFillG

imageFillR

imageFillI

polarity

Constructor Detail

AlgorithmMask

AlgorithmMask

AlgorithmMask

AlgorithmMask

AlgorithmMask

AlgorithmMask

AlgorithmMask

Method Detail

calcInPlace25D

calcInPlace25D

calcInPlace25DC

calcInPlace25DCMask

calcInPlace25DMask

calcInPlace25DMask

finalize

runAlgorithm

calcInPlace2D

calcInPlace2DComplex

calcInPlace2DRGB

calcInPlace3D

calcInPlace3DComplex

calcInPlace3DRGB

calcInPlace4D

calcInPlace4DComplex

calcInPlace4DRGB

calcStoreInDest2D

calcStoreInDest2DComplex

calcStoreInDest2DRGB

calcStoreInDest3D

calcStoreInDest3DComplex

calcStoreInDest3DRGB

calcStoreInDest4D

calcStoreInDest4DComplex

calcStoreInDest4DRGB