Package gov.nih.mipav.model.algorithms

Class AlgorithmCenterOfMass

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmCenterOfMass

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmCenterOfMass
extends AlgorithmBase

This algorithm calculates the center of mass for 2D and 3D black and white images.

Version:

1.0 February 26, 2008

Author:

William Gandler

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 boolean	allowDataWindow	If true, allow data window output
private boolean	entireImage	Flag, if true, indicates that the whole image should be processed.
private float[]	threshold	Array of two thresholds. threshold[0] = Minimum threshold, threshold[1] = Maximum threshold.
double	xCOM	x coordinate for center of mass, normalized by image resolution
double	yCOM	y coordinate for center of mass, normalized by image resolution
double	zCOM	z coordinate for center of mass, normalized by image resolution, if srcImage is 2D = 0

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
AlgorithmCenterOfMass(ModelImage srcImg, float[] threshold, boolean maskFlag)	Creates a new AlgorithmCenterOfMass object.

Method Summary

Modifier and Type	Method	Description
private void	calcInPlace2D()	Calculate center of mass of 2D black and white image.
private void	calcInPlace3D()	Calculate center of mass of 3D black and white image.
void	finalize()	Prepares this class for destruction.
double[]	getCenterOfMass()	Returns the computed center of mass.
void	runAlgorithm()	Starts the program.
void	setAllowDataWindow(boolean allowDataWindow)

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

entireImage

private boolean entireImage

Flag, if true, indicates that the whole image should be processed. If false on process the image over the mask areas.

threshold

private float[] threshold

Array of two thresholds. threshold[0] = Minimum threshold, threshold[1] = Maximum threshold.

allowDataWindow

private boolean allowDataWindow

If true, allow data window output

xCOM

public double xCOM

x coordinate for center of mass, normalized by image resolution

yCOM

public double yCOM

y coordinate for center of mass, normalized by image resolution

zCOM

public double zCOM

z coordinate for center of mass, normalized by image resolution, if srcImage is 2D = 0

Constructor Detail

AlgorithmCenterOfMass

public AlgorithmCenterOfMass(ModelImage srcImg,
                             float[] threshold,
                             boolean maskFlag)

Creates a new AlgorithmCenterOfMass object.

Parameters:

srcImg - source image model

threshold - array of two thresholds

maskFlag - true indicates that the whole image should be processed

Method Detail

setAllowDataWindow

public void setAllowDataWindow(boolean allowDataWindow)

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()

Calculate center of mass of 2D black and white image.

calcInPlace3D

private void calcInPlace3D()

Calculate center of mass of 3D black and white image.

getCenterOfMass

public double[] getCenterOfMass()

Returns the computed center of mass. If algorithm is not completed: returns null. If 2D: returns {xCenter, yCenter, 0} If 3D: returns {xCenter, yCenter, zCenter}