Package gov.nih.mipav.model.algorithms.registration

Class AlgorithmRegVOILandmark

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.registration.AlgorithmRegVOILandmark

All Implemented Interfaces:

de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables, ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmRegVOILandmark
extends AlgorithmBase
implements de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables

AlgorithmRegVOILandmark First slice is template (base image) to which subsequent slices are registered. Trace kidney in 1st slice using polygon VOI. Minimize cost = -sum of Gradient magnitude under propagated ROI in match image

Version:

1.0 June, 2000

Author:

Delia McGarry

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	AlgorithmRegVOILandmark.CostFunction	CostFunction - class for specifying optimization function for AlgorithmSimplexOpt slice - current fluoroscopy slice being operated on.

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
protected float	baseVOIGradMagSum	DOCUMENT ME!
protected int	costFunc	DOCUMENT ME!
static final int	EXHAUSTIVEOPT	DOCUMENT ME!
private AlgorithmRegVOILandmark.CostFunction	func
private AlgorithmGradientMagnitude	gradientMagAlgo	DOCUMENT ME!
protected float[]	gradMagBuf	DOCUMENT ME!
protected ModelImage	gradMagVol	DOCUMENT ME!
private boolean	maskFlag
private double	maxRz	DOCUMENT ME!
static final int	MAXSUM	DOCUMENT ME!
private double	maxTx	DOCUMENT ME!
private double	maxTy	DOCUMENT ME!
static final int	MINDIFF	DOCUMENT ME!
private double	minRz	DOCUMENT ME!
private double	minTx	DOCUMENT ME!
private double	minTy	DOCUMENT ME!
protected int	opt	DOCUMENT ME!
private float[]	sigmas
private int	simplexDim	DOCUMENT ME!
static final int	SIMPLEXOPT	DOCUMENT ME!
protected int	sliceSize	DOCUMENT ME!
private double	step	DOCUMENT ME!
protected int	tdim	DOCUMENT ME!
protected int	VOIlength	DOCUMENT ME!
protected VOIBase	VOIposition	positions (x,y) of VOI in first slice
protected int	volLength	DOCUMENT ME!
protected ModelImage	volume	DOCUMENT ME!
protected int	xdim	DOCUMENT ME!
protected int	ydim	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, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmRegVOILandmark(ModelImage volume, ModelImage gradMagVol, float[] sigmas, boolean maskFlag, VOIBase position, double minTx, double maxTx, double minTy, double maxTy, double minRz, double maxRz, double step, int opt, int costFunc)	Constructor.

Method Summary

Modifier and Type	Method	Description
double	eval(double[] x)
private void	exhaustiveSearch(double[] p, AlgorithmRegVOILandmark.CostFunction func)	Exhaustive search for global minimum.
void	finalize()	finalize - prepares this class for destruction.
int	getNumberOfVariables()
protected TransMatrix	getTransform(double[] x)	Converts row of p into 3x3 matrix.
void	runAlgorithm()	Starts the program.
private void	search()	Search.
private void	transformSlice(int slice, TransMatrix xfrm, float[] imgBuf, float[] tImgBuf, WildMagic.LibFoundation.Mathematics.Vector3f center)	Transforms a slice.

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

SIMPLEXOPT

public static final int SIMPLEXOPT

DOCUMENT ME!

See Also:

• Constant Field Values

EXHAUSTIVEOPT

public static final int EXHAUSTIVEOPT

DOCUMENT ME!

See Also:

• Constant Field Values

MINDIFF

public static final int MINDIFF

DOCUMENT ME!

See Also:

• Constant Field Values

MAXSUM

public static final int MAXSUM

DOCUMENT ME!

See Also:

• Constant Field Values

baseVOIGradMagSum

protected float baseVOIGradMagSum

DOCUMENT ME!

gradientMagAlgo

private AlgorithmGradientMagnitude gradientMagAlgo

DOCUMENT ME!

gradMagBuf

protected float[] gradMagBuf

DOCUMENT ME!

minTx

private double minTx

DOCUMENT ME!

maxTx

private double maxTx

DOCUMENT ME!

minTy

private double minTy

DOCUMENT ME!

maxTy

private double maxTy

DOCUMENT ME!

minRz

private double minRz

DOCUMENT ME!

maxRz

private double maxRz

DOCUMENT ME!

step

private double step

DOCUMENT ME!

opt

protected int opt

DOCUMENT ME!

costFunc

protected int costFunc

DOCUMENT ME!

simplexDim

private int simplexDim

DOCUMENT ME!

VOIlength

protected int VOIlength

DOCUMENT ME!

VOIposition

protected VOIBase VOIposition

positions (x,y) of VOI in first slice

volLength

protected int volLength

DOCUMENT ME!

sliceSize

protected int sliceSize

DOCUMENT ME!

volume

protected ModelImage volume

DOCUMENT ME!

gradMagVol

protected ModelImage gradMagVol

DOCUMENT ME!

xdim

protected int xdim

DOCUMENT ME!

ydim

protected int ydim

DOCUMENT ME!

tdim

protected int tdim

DOCUMENT ME!

sigmas

private float[] sigmas

maskFlag

private boolean maskFlag

func

private AlgorithmRegVOILandmark.CostFunction func

Constructor Details

AlgorithmRegVOILandmark

public AlgorithmRegVOILandmark(ModelImage volume,
 ModelImage gradMagVol,
 float[] sigmas,
 boolean maskFlag,
 VOIBase position,
 double minTx,
 double maxTx,
 double minTy,
 double maxTy,
 double minRz,
 double maxRz,
 double step,
 int opt,
 int costFunc)

Constructor.

Parameters:

volume - DOCUMENT ME!

gradMagVol - DOCUMENT ME!

sigmas - DOCUMENT ME!

maskFlag - DOCUMENT ME!

position - DOCUMENT ME!

minTx - DOCUMENT ME!

maxTx - DOCUMENT ME!

minTy - DOCUMENT ME!

maxTy - DOCUMENT ME!

minRz - DOCUMENT ME!

maxRz - DOCUMENT ME!

step - DOCUMENT ME!

opt - DOCUMENT ME!

costFunc - DOCUMENT ME!

Method Details

finalize

public void finalize()

finalize - prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

runAlgorithm

public void runAlgorithm()

Starts the program.

Specified by:

runAlgorithm in class AlgorithmBase

exhaustiveSearch

private void exhaustiveSearch(double[] p,
 AlgorithmRegVOILandmark.CostFunction func)

Exhaustive search for global minimum.

Parameters:

p - DOCUMENT ME!

func - DOCUMENT ME!

getTransform

protected TransMatrix getTransform(double[] x)

Converts row of p into 3x3 matrix.

Parameters:

x - = row of p[][]

Returns:

DOCUMENT ME!

search

private void search()

Search.

transformSlice

private void transformSlice(int slice,
 TransMatrix xfrm,
 float[] imgBuf,
 float[] tImgBuf,
 WildMagic.LibFoundation.Mathematics.Vector3f center)

Transforms a slice.

Parameters:

slice - DOCUMENT ME!

xfrm - DOCUMENT ME!

imgBuf - DOCUMENT ME!

tImgBuf - DOCUMENT ME!

eval

public double eval(double[] x)

Specified by:

eval in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables

getNumberOfVariables

public int getNumberOfVariables()

Specified by:

getNumberOfVariables in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables