Package gov.nih.mipav.model.algorithms

Class AlgorithmFloodFill

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmFloodFill

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmFloodFill
extends AlgorithmBase

Stack based flood-fill for 2D and 3D images. The input is a binary (BitSet) object and produces a BitSet or short mask. A short mask allows for different label values for disconnected objects in a BitSet image. For example, in a binarized image of cells, each cell could be labeled(filled) with a separate value. However, a short mask uses 16X more memory than does the BitSet mask.

Version:

0.1 Jan 5, 1998

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
static final short	BITSET	DOCUMENT ME!
private int[]	dims	Dimensionality of the data.
private short	floodValue	Flood value.
private BitSet	mask	DOCUMENT ME!
private int	mode	Indicates the type of result mask: BITSET or SHORT.
private int	nDims	The number of dimensions.
private BitSet	newMask	DOCUMENT ME!
private short[]	newShortMask	Reference to short mask.
private Point	seed2DPt	Seed point for 2D datasets.
private Point3D	seed3DPt	Seed point for 3D datasets.
static final short	SHORT	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
AlgorithmFloodFill(BitSet mask, int[] dims, int mode, Point3D pt)	Stack based flood-fill for 2D and 3D images.
AlgorithmFloodFill(BitSet mask, int[] dims, int mode, Point pt)	Stack based flood-fill for 2D and 3D images.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for destruction.
BitSet	floodFill2DBitSet()	2D flood fill that forms a binary(BitSet) mask.
short[]	floodFill2DShort()	2D flood fill that forms a short mask.
BitSet	floodFill3DBitSet()	3D flood fill that forms a binary(BitSet) mask.
short[]	floodFill3DShort()	3D flood fill that forms a short mask.
BitSet	getBitSetMask()	Gets the Mask image returned as a Java Bitset object.
short[]	getShortMask()	Gets the mask image (array of short values).
void	runAlgorithm()	Starts the program.
void	setBitSetMask(BitSet mask)	Sets this classes BitSet mask to new mask.
void	setFloodValue(short floodValue)	Sets the value to be placed in the flood region.
void	setSeed2DPt(Point seedPt)	Sets the seed point for the flood fill for a 2D image region grow.
void	setSeed3DPt(Point3D seedPt)	Sets the point at which a the flood filling begins.
void	setShortMask(short[] mask)	Sets this classes short mask to the new mask.

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

BITSET

public static final short BITSET

DOCUMENT ME!

See Also:

• Constant Field Values

SHORT

public static final short SHORT

DOCUMENT ME!

See Also:

• Constant Field Values

dims

private int[] dims

Dimensionality of the data.

floodValue

private short floodValue

Flood value. Default in 1.

mask

private BitSet mask

DOCUMENT ME!

mode

private int mode

Indicates the type of result mask: BITSET or SHORT.

nDims

private int nDims

The number of dimensions.

newMask

private BitSet newMask

DOCUMENT ME!

newShortMask

private short[] newShortMask

Reference to short mask.

seed2DPt

private Point seed2DPt

Seed point for 2D datasets.

seed3DPt

private Point3D seed3DPt

Seed point for 3D datasets.

Constructor Details

AlgorithmFloodFill

public AlgorithmFloodFill(BitSet mask,
 int[] dims,
 int mode,
 Point pt)

Stack based flood-fill for 2D and 3D images.

Parameters:

mask - BitSet object that has the binary object(s) that needs to be filled

dims - dimensionality of mask

mode - BITSET or SHORT mode for result mask

pt - seed point for the flood fill to begin for 2D image

AlgorithmFloodFill

public AlgorithmFloodFill(BitSet mask,
 int[] dims,
 int mode,
 Point3D pt)

Stack based flood-fill for 2D and 3D images.

Parameters:

mask - BitSet object that has the binary object(s) that needs to be filled

dims - dimensionality of mask

mode - BITSET or SHORT mode for result mask

pt - seed point for the flood fill to begin for 3D image

Method Details

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

floodFill2DBitSet

public BitSet floodFill2DBitSet()

2D flood fill that forms a binary(BitSet) mask.

Returns:

mask of flooded image

floodFill2DShort

public short[] floodFill2DShort()

2D flood fill that forms a short mask.

Returns:

mask of flooded image

floodFill3DBitSet

public BitSet floodFill3DBitSet()

3D flood fill that forms a binary(BitSet) mask.

Returns:

mask of flooded image

floodFill3DShort

public short[] floodFill3DShort()

3D flood fill that forms a short mask.

Returns:

mask of flooded image

getBitSetMask

public BitSet getBitSetMask()

Gets the Mask image returned as a Java Bitset object.

Returns:

BitSet mask of flooded image

getShortMask

public short[] getShortMask()

Gets the mask image (array of short values).

Returns:

short mask of flooded image

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

setBitSetMask

public void setBitSetMask(BitSet mask)

Sets this classes BitSet mask to new mask.

Parameters:

mask - sets BitSet mask

setFloodValue

public void setFloodValue(short floodValue)

Sets the value to be placed in the flood region.

Parameters:

floodValue - sets the flood-fill value used when generating a short type mask

setSeed2DPt

public void setSeed2DPt(Point seedPt)

Sets the seed point for the flood fill for a 2D image region grow.

Parameters:

seedPt - sets 2D seed point for beginning of flood fill

setSeed3DPt

public void setSeed3DPt(Point3D seedPt)

Sets the point at which a the flood filling begins.

Parameters:

seedPt - sets 3D seed point for beginning of flood fill

setShortMask

public void setShortMask(short[] mask)

Sets this classes short mask to the new mask.

Parameters:

mask - sets short mask