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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmRegionGrow
extends AlgorithmBase
```
Fills a region based on average intensity +or- standard deviation. A VOI is used to calc an intensity within the region. The region grows if the intensity is bounded by average +/- the standard deviation. The a new VOI should be generated but for now the image is filled with with a flood value.
If variableThresholds is true, upperDelta = initialValue of upperBound - value of seed point lowerDelta = Value of seed point - initialValue of lowerBound Each time a new pixel is added to the region recalculate the mean and standard deviation of the region mean = (sum of the pixel values)/(pixel number) standard deviation = ((Sum of the squared values - (sum of values)*(sum of values)/(pixel number))/(pixel number) Then recalculate upperBound and lowBound as: upperBound = initialValue + (1.0 - Math.min(0.8, stdDev/mean)) * upperDelta lowBound = initialValue - (1.0 - Math.min(0.8, stdDev/mean)) * lowerDelta upperBound cannot become higher than its initial value, but it can become lower than its initial value. lowBound cannot become lower than its initial value, but it can become higher than its initial value. That is, upperBound - lowBound cannot exceed its initial value, but it can become lower than its initial value. Adaptive thresholding is useful in preventing bleeding across smooth image gradients. Reference: Automatic Image-To-Map-Registration of Remote Sensing Data by Heiner Hild, Photogrammetric Week '01', D. Fritsch & R. Spiller, Eds., Wichmann Verlag, Heidelberg, 2001.

Version:

0.5 Jan, 2000

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[]`	`blueBuffer`	DOCUMENT ME!
`private double`	`c`	DOCUMENT ME!
`private float[]`	`greenBuffer`	DOCUMENT ME!
`private RegionGrowDialog`	`growDialog`	DOCUMENT ME!
`private ViewJFrameImage`	`imageFrame`
`private double`	`mBMean`	DOCUMENT ME!
`private double`	`mGMean`	DOCUMENT ME!
`private double`	`mMean`	DOCUMENT ME!
`private double`	`mRMean`	DOCUMENT ME!
`private java.util.BitSet`	`paintMask`	DOCUMENT ME!
`private float[]`	`redBuffer`	DOCUMENT ME!
`private ModelImage`	`srcImage`	DOCUMENT ME!
`private double[][]`	`varInverse`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmRegionGrow(ModelImage srcImg, float _multiplier, float _floodValue)`	Creates a new AlgorithmRegionGrow object.
`AlgorithmRegionGrow(ModelImage destImg, ModelImage srcImg, float _multiplier, float _floodValue)`	Creates a new AlgorithmRegionGrow object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for destruction.
`int`	`regionGrow2D(java.util.BitSet paintMask, java.awt.Point seedPt, float th, boolean useVOI, boolean dp, RegionGrowDialog growDialog, float lowBoundR, float upperBoundR, float lowBoundG, float upperBoundG, float lowBoundB, float upperBoundB, int sizeLimit, float maxDistance)`	2D flood fill for color images that forms a bitset(boolean) mask.
`int`	`regionGrow2D(java.util.BitSet paintMask, java.awt.Point seedPt, float th, boolean useVOI, boolean dp, RegionGrowDialog growDialog, float lowBound, float upperBound, int sizeLimit, float maxDistance, boolean variableThresholds)`	2D flood fill that forms a bitset(boolean) mask.
`int`	`regionGrow3D(java.util.BitSet paintMask, Point3D seedPt, float th, boolean useVOI, boolean dp, RegionGrowDialog growDialog, float lowBoundR, float upperBoundR, float lowBoundG, float upperBoundG, float lowBoundB, float upperBoundB, int sizeLimit, float maxDistance, int timeSlice, CubeBounds regionBounds)`	3D flood fill for color images that forms a bitset(boolean) mask.
`int`	`regionGrow3D(java.util.BitSet paintMask, Point3D seedPt, float th, boolean useVOI, boolean dp, RegionGrowDialog growDialog, float lowBound, float upperBound, int sizeLimit, float maxDistance, boolean variableThresholds, int timeSlice, CubeBounds regionBounds)`	3D flood fill that forms a bitset(boolean) mask.
`void`	`runAlgorithm()`	Starts the program.
`void`	`setNewThreshold(float threshold, PaintGrowListener compImage, boolean dp)`	DOCUMENT ME!

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
  - blueBuffer
```
private float[] blueBuffer
```
    DOCUMENT ME!
  - c
```
private double c
```
    DOCUMENT ME!
  - greenBuffer
```
private float[] greenBuffer
```
    DOCUMENT ME!
  - growDialog
```
private RegionGrowDialog growDialog
```
    DOCUMENT ME!
  - imageFrame
```
private ViewJFrameImage imageFrame
```
  - mMean
```
private double mMean
```
    DOCUMENT ME!
  - mRMean
```
private double mRMean
```
    DOCUMENT ME!
  - mGMean
```
private double mGMean
```
    DOCUMENT ME!
  - mBMean
```
private double mBMean
```
    DOCUMENT ME!
  - paintMask
```
private java.util.BitSet paintMask
```
    DOCUMENT ME!
  - redBuffer
```
private float[] redBuffer
```
    DOCUMENT ME!
  - srcImage
```
private ModelImage srcImage
```
    DOCUMENT ME!
  - varInverse
```
private double[][] varInverse
```
    DOCUMENT ME!
- Constructor Detail
  - AlgorithmRegionGrow
```
public AlgorithmRegionGrow(ModelImage srcImg,
                           float _multiplier,
                           float _floodValue)
```
    Creates a new AlgorithmRegionGrow object.
    
    Parameters:
    
    srcImg - source image model
    
    _multiplier - aaaaa
    
    _floodValue - aaaaa
  - AlgorithmRegionGrow
```
public AlgorithmRegionGrow(ModelImage destImg,
                           ModelImage srcImg,
                           float _multiplier,
                           float _floodValue)
```
    Creates a new AlgorithmRegionGrow object.
    
    Parameters:
    
    destImg - image model where result image is to stored
    
    srcImg - source image model
    
    _multiplier - placeholder
    
    _floodValue - placeholder
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - regionGrow2D
```
public int regionGrow2D(java.util.BitSet paintMask,
                        java.awt.Point seedPt,
                        float th,
                        boolean useVOI,
                        boolean dp,
                        RegionGrowDialog growDialog,
                        float lowBound,
                        float upperBound,
                        int sizeLimit,
                        float maxDistance,
                        boolean variableThresholds)
```
    2D flood fill that forms a bitset(boolean) mask.
    
    Parameters:
    
    paintMask - mask used to indicated where region has grown
    
    seedPt - seed point for flood fill
    
    th -
    
    useVOI - use selected VOI for initial variance
    
    dp -
    
    growDialog - the RegionGrowDialog
    
    lowBound - lower bound of values which are included in the region
    
    upperBound - upper bound of values which are included in the region
    
    sizeLimit - stop region grow when objects exceeds size limit in pixels
    
    maxDistance - max distance from the seed point (in pixels) that the region is allowed to grow.
    
    variableThresholds - If true vary thresholds as region grows
    
    Returns:
    
    returns the area region
  - regionGrow2D
```
public int regionGrow2D(java.util.BitSet paintMask,
                        java.awt.Point seedPt,
                        float th,
                        boolean useVOI,
                        boolean dp,
                        RegionGrowDialog growDialog,
                        float lowBoundR,
                        float upperBoundR,
                        float lowBoundG,
                        float upperBoundG,
                        float lowBoundB,
                        float upperBoundB,
                        int sizeLimit,
                        float maxDistance)
```
    2D flood fill for color images that forms a bitset(boolean) mask.
    
    Parameters:
    
    paintMask - mask used to indicated where region has grown
    
    seedPt - seed point for flood fill
    
    th -
    
    useVOI - use selected VOI for initial variance
    
    dp -
    
    growDialog - the RegionGrowDialog
    
    lowBoundR - lower bound of red values which are included in the region
    
    upperBoundR - upper bound of red values which are included in the region
    
    lowBoundG - lower bound of green values which are included in the region
    
    upperBoundG - upper bound of green values which are included in the region
    
    lowBoundB - lower bound of blue values which are included in the region
    
    upperBoundB - upper bound of blue values which are included in the region
    
    sizeLimit - stop region grow when objects exceeds size limit in pixels
    
    maxDistance - max distance from the seed point (in pixels) that the region is allowed to grow.
    
    Returns:
    
    returns the area region
  - regionGrow3D
```
public int regionGrow3D(java.util.BitSet paintMask,
                        Point3D seedPt,
                        float th,
                        boolean useVOI,
                        boolean dp,
                        RegionGrowDialog growDialog,
                        float lowBound,
                        float upperBound,
                        int sizeLimit,
                        float maxDistance,
                        boolean variableThresholds,
                        int timeSlice,
                        CubeBounds regionBounds)
```
    3D flood fill that forms a bitset(boolean) mask.
    
    Parameters:
    
    paintMask - mask used to indicated where region has grown
    
    seedPt - seed point for flood fill
    
    th -
    
    useVOI - use selected VOI for initial variance
    
    dp -
    
    growDialog - the RegionGrowDialog
    
    lowBound - lower bound of values which are included in the region
    
    upperBound - upper bound of values which are included in the region
    
    sizeLimit - stop region grow when objects exceeds size limit in pixels
    
    maxDistance - max distance from the seed point (in pixels) that the region is allowed to grow.
    
    variableThresholds - If true vary thresholds as region grows
    
    timeSlice - timeSlice that will be used in a 4D image
    
    regionBounds - DOCUMENT ME!
    
    Returns:
    
    returns the volume region
  - regionGrow3D
```
public int regionGrow3D(java.util.BitSet paintMask,
                        Point3D seedPt,
                        float th,
                        boolean useVOI,
                        boolean dp,
                        RegionGrowDialog growDialog,
                        float lowBoundR,
                        float upperBoundR,
                        float lowBoundG,
                        float upperBoundG,
                        float lowBoundB,
                        float upperBoundB,
                        int sizeLimit,
                        float maxDistance,
                        int timeSlice,
                        CubeBounds regionBounds)
```
    3D flood fill for color images that forms a bitset(boolean) mask.
    
    Parameters:
    
    paintMask - mask used to indicated where region has grown
    
    seedPt - seed point for flood fill
    
    th -
    
    useVOI - use selected VOI for initial variance
    
    dp -
    
    growDialog - the RegionGrowDialog
    
    lowBoundR - lower bound of red values which are included in the region
    
    upperBoundR - upper bound of red values which are included in the region
    
    lowBoundG - lower bound of green values which are included in the region
    
    upperBoundG - upper bound of green values which are included in the region
    
    lowBoundB - lower bound of blue values which are included in the region
    
    upperBoundB - upper bound of blue values which are included in the region
    
    sizeLimit - stop region grow when objects exceeds size limit in pixels
    
    maxDistance - max distance from the seed point (in pixels) that the region is allowed to grow.
    
    timeSlice - timeSlice that will be used in a 4D image
    
    regionBounds - DOCUMENT ME!
    
    Returns:
    
    returns the volume region
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setNewThreshold
```
public void setNewThreshold(float threshold,
                            PaintGrowListener compImage,
                            boolean dp)
```
    DOCUMENT ME!
    
    Parameters:
    
    threshold - DOCUMENT ME!
    
    compImage - DOCUMENT ME!
    
    dp -

Class AlgorithmRegionGrow

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

blueBuffer

c

greenBuffer

growDialog

imageFrame

mMean

mRMean

mGMean

mBMean

paintMask

redBuffer

srcImage

varInverse

Constructor Detail

AlgorithmRegionGrow

AlgorithmRegionGrow

Method Detail

finalize

regionGrow2D

regionGrow2D

regionGrow3D

regionGrow3D

runAlgorithm

setNewThreshold