Package gov.nih.mipav.model.algorithms

Class AlgorithmRegionGrow

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmRegionGrow

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, 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 invalid input: '&' 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

Thread.Builder, Thread.State, 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 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

Modifier and Type	Method	Description
void	finalize()	Prepares this class for destruction.
int	regionGrow2D(BitSet paintMask, 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(BitSet paintMask, 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(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(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, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

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

Field Details

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 BitSet paintMask

DOCUMENT ME!

redBuffer

private float[] redBuffer

DOCUMENT ME!

srcImage

private ModelImage srcImage

DOCUMENT ME!

varInverse

private double[][] varInverse

DOCUMENT ME!

Constructor Details

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 Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

regionGrow2D

public int regionGrow2D(BitSet paintMask,
 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(BitSet paintMask,
 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(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(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 -