Package gov.nih.mipav.model.algorithms

Class AlgorithmConstELSUNCOpt3D

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmConstELSUNCOpt3D

All Implemented Interfaces:

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

public class AlgorithmConstELSUNCOpt3D
extends AlgorithmBase

Runs ELSUNC for a 3D image.

Based on ELSUNC allowed by the author with acknowledgement:

Gauss-Newton Based Algorithms For Constrained Nonlinear Least Squares Problems by Per Lindstrom and Per-Ake Wedin, Institute of Information Processing, University of Umea, S-901 87 Umea, Sweden This can be downleaded from http://www.cs.umu.se/~perl/reports/alg.ps.gz

Version:

0.1 March 19, 2012

Author:

William Gandler

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	AlgorithmConstELSUNCOpt3D.FitOAR3DConstrainedModel

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 int	bracketBound	The initial bracket size for first iteration of ELSUNC.
private AlgorithmOptimizeFunctionBase	costFunction	Cost function called to measure cost - 1D.
(package private) AlgorithmConstELSUNCOpt3D.FitOAR3DConstrainedModel	dModel
private double[]	finalPoint	Final point when optimization is complete.
private TransMatrixd	fromOrigin	The transformation matrix from the origin of the input image.
private double	functionAtBest	The cost of the function at the best minimum.
private int	maxIterations	The maximum number of iterations the optimization allows.
private double	minFunctionAtBest
private ViewJProgressBar	myProgressBar	Progress bar that may be set for long optimization runs.
private int	nDims	Degress of freedom.
private double[]	OARTolerance	Array of tolerances for each dimension.
private AlgorithmBase	parent	Parent algorithm that called this optimization.
private double[]	point	Point that is currently being optimized.
private int	progressBegin	Where progress is when sent in.
private int	progressMax	The max the progress can go to.
private double[]	start	Point that was initially passed into function.
private int	status
private boolean	success	Indicates whether the ELSUNC algorithm succeeded in finding a minimum.
protected TransMatrixd	toOrigin	The transformation matrix to the origin of the input image.
private float[][]	trLimits	Array of translation and rotation limits for each dimension.

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
AlgorithmConstELSUNCOpt3D(AlgorithmBase parent, WildMagic.LibFoundation.Mathematics.Vector3f com, int degreeOfFreedom, AlgorithmOptimizeFunctionBase costFunc, double[] initial, double[] tols, int maxIter, int bracketBound)	Constructs a new algorithm with the given centers of mass (needed for setting the transformations), the given cost function (which was constructed with the proper images), the initial point we're looking at, some tolerance within that point to look for the minimum, and the maximum number of iterations.

Method Summary

Modifier and Type	Method	Description
TransMatrixd	convertToMatrix(double[] vector)	Helper method to take the "point" we've been working with as a vector, and convert it into a transformation matrix.
TransMatrixd	convertToMatrixHalf(double[] vector)	Helper method to take the "point" we've been working with as a vector, and convert it into a transformation matrix.
TransMatrixd	convertToMatrixMidsagittal(double[] vector)	Helper method to take the "point" we've been working with as a vector, and convert it into a transformation matrix.
boolean	didSucceed()	Returns whether or not a minimum was found.
void	disposeLocal()	Sets everything to null and prepares this class for destruction.
double	getCost()	Returns the cost of the best transformation.
double[]	getFinal()	Accessor that returns the final point with translations, rotations, scales, and skews representing the best tranformation.
double[]	getFinal(double[] point)	Accessor that returns the final point with translations, rotations, scales, and skews representing the best tranformation.
double[]	getFinal(float sample)	Accessor that returns the final point with translations, rotations, scales, and skews representing the best tranformation.
TransMatrixd	getMatrix()	Accessor that returns the matrix representing the best transformation.
TransMatrixd	getMatrix(float sample)	Accessor that returns the matrix representing the best transformation.
TransMatrixd	getMatrixHalf()	Accessor that returns the matrix representing the best tranformation.
TransMatrixd	getMatrixHalf(float sample)	Accessor that returns the matrix representing the best tranformation.
TransMatrixd	getMatrixMidsagittal()	Accessor that returns the matrix representing the best tranformation.
TransMatrixd	getMatrixMidsagittal(float sample)	Accessor that returns the matrix representing the best tranformation.
double[]	getPoint()	Returns the optimized point, with length == degrees of freedom.
void	measureCost()	Calls cost function with point and saves result in functionAtBest.
void	runAlgorithm()	Runs ELSUNC along one dimension at a time as long as the costFunction improves during one cycle of runs along every dimension.
void	setInitialPoint(double[] initial)	Sets the initial point to the value passed in.
void	setLimits(float[][] limits)	Sets the limits on rotation and translation.
void	setMaxIterations(int max)	Sets the maximum number of iterations.
void	setProgressBar(ViewJProgressBar progress, int begin, int max)	Accessor that sets the progress bar so it can be updated from here.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, 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

dModel

AlgorithmConstELSUNCOpt3D.FitOAR3DConstrainedModel dModel

bracketBound

private int bracketBound

The initial bracket size for first iteration of ELSUNC.

costFunction

private AlgorithmOptimizeFunctionBase costFunction

Cost function called to measure cost - 1D.

finalPoint

private double[] finalPoint

Final point when optimization is complete.

fromOrigin

private TransMatrixd fromOrigin

The transformation matrix from the origin of the input image.

functionAtBest

private double functionAtBest

The cost of the function at the best minimum.

minFunctionAtBest

private double minFunctionAtBest

maxIterations

private int maxIterations

The maximum number of iterations the optimization allows.

myProgressBar

private ViewJProgressBar myProgressBar

Progress bar that may be set for long optimization runs.

nDims

private int nDims

Degress of freedom.

parent

private AlgorithmBase parent

Parent algorithm that called this optimization.

point

private double[] point

Point that is currently being optimized.

progressBegin

private int progressBegin

Where progress is when sent in.

progressMax

private int progressMax

The max the progress can go to.

start

private double[] start

Point that was initially passed into function.

success

private boolean success

Indicates whether the ELSUNC algorithm succeeded in finding a minimum.

OARTolerance

private double[] OARTolerance

Array of tolerances for each dimension.

toOrigin

protected TransMatrixd toOrigin

The transformation matrix to the origin of the input image.

trLimits

private float[][] trLimits

Array of translation and rotation limits for each dimension.

status

private int status

Constructor Detail

AlgorithmConstELSUNCOpt3D

public AlgorithmConstELSUNCOpt3D(AlgorithmBase parent,
                                 WildMagic.LibFoundation.Mathematics.Vector3f com,
                                 int degreeOfFreedom,
                                 AlgorithmOptimizeFunctionBase costFunc,
                                 double[] initial,
                                 double[] tols,
                                 int maxIter,
                                 int bracketBound)

Constructs a new algorithm with the given centers of mass (needed for setting the transformations), the given cost function (which was constructed with the proper images), the initial point we're looking at, some tolerance within that point to look for the minimum, and the maximum number of iterations.

Parameters:

parent - Algorithm that called this optimization.

com - Center of Mass of the input image.

degreeOfFreedom - Degree of freedom for transformation (must be 3, 4, 6, 7, 9, or 12).

costFunc - Cost function to use.

initial - Initial point to start from, length of 12.

tols - Tolerance for each dimension (tols.length == degreeOfFreedom).

maxIter - Maximum number of iterations.

bracketBound - DOCUMENT ME!

Method Detail

disposeLocal

public void disposeLocal()

Sets everything to null and prepares this class for destruction.

convertToMatrix

public TransMatrixd convertToMatrix(double[] vector)

Helper method to take the "point" we've been working with as a vector, and convert it into a transformation matrix. The length of the vector should be equal to the global variable nDims, which in turn was initialized by the degrees of freedom originally sent to this algorithm. Therefore, if there are 3 degrees of freedom, we set only the translations; 4 means translation and global scaling; 6 means rotation and translation; 7 means rotation, translation, and global scaling; 9 means rotation, translation, and scaling; and 12 means rotation, translation, scaling, and skewing.

Parameters:

vector - Vector that represented a "point" in the algorithm which needs to be converted to a matrix.

Returns:

The transformation matrix created from the vector.

convertToMatrixHalf

public TransMatrixd convertToMatrixHalf(double[] vector)

Helper method to take the "point" we've been working with as a vector, and convert it into a transformation matrix. The length of the vector should be equal to the global variable nDims, which in turn was initialized by the degrees of freedom originally sent to this algorithm. Therefore, if there are 3 degrees of freedom, we set only the translations; 4 means translation and global scaling; 6 means rotation and translation; 7 means rotation, translation, and global scaling; 9 means rotation, translation, and scaling; and 12 means rotation, translation, scaling, and skewing.

Parameters:

vector - Vector that represented a "point" in the algorithm which needs to be converted to a matrix.

Returns:

The transformation matrix created from the vector.

convertToMatrixMidsagittal

public TransMatrixd convertToMatrixMidsagittal(double[] vector)

Helper method to take the "point" we've been working with as a vector, and convert it into a transformation matrix. The length of the vector should be equal to the global variable nDims, which in turn was initialized by the degrees of freedom originally sent to this algorithm. Therefore, if there are 3 degrees of freedom, we set only the translations; 4 means translation and global scaling; 6 means rotation and translation; 7 means rotation, translation, and global scaling; 9 means rotation, translation, and scaling; and 12 means rotation, translation, scaling, and skewing.

Parameters:

vector - Vector that represented a "point" in the algorithm which needs to be converted to a matrix.

Returns:

The transformation matrix created from the vector.

getFinal

public double[] getFinal()

Accessor that returns the final point with translations, rotations, scales, and skews representing the best tranformation.

Returns:

vector representing the best transformation in terms of translations, rotations, scales, and skews.

getFinal

public double[] getFinal(double[] point)

Accessor that returns the final point with translations, rotations, scales, and skews representing the best tranformation.

Returns:

vector representing the best transformation in terms of translations, rotations, scales, and skews.

getFinal

public double[] getFinal(float sample)

Accessor that returns the final point with translations, rotations, scales, and skews representing the best tranformation.

Parameters:

sample - the voxel resolution

Returns:

vector representing the best transformation in terms of translations, rotations, scales, and skews.

getMatrix

public TransMatrixd getMatrix()

Accessor that returns the matrix representing the best transformation.

Returns:

matrix representing the best transformation.

getMatrix

public TransMatrixd getMatrix(float sample)

Accessor that returns the matrix representing the best transformation. The passed in parameter represents the resolution (same in all directions and for both input and reference images, since resampled isotropically). Since the optimization was done in pixel space, not millimeter space, the translation parameters need to be scaled by the sample value.

Parameters:

sample - the voxel resolution

Returns:

matrix representing the best transformation.

getMatrixHalf

public TransMatrixd getMatrixHalf()

Accessor that returns the matrix representing the best tranformation. All of the components of the transformation are halved from the 'best transformation' matrix.

Returns:

matrix representing the best transformation with its components halved.

getMatrixHalf

public TransMatrixd getMatrixHalf(float sample)

Accessor that returns the matrix representing the best tranformation. The passed in parameter represents the resolution (same in all directions and for both input and reference images, since resampled isotropically). Since the optimization was done in pixel space, not millimeter space, the translation parameters need to be scaled by the sample value. All of the components of the transformation are halved from the 'best transformation' matrix.

Parameters:

sample - the voxel resolution

Returns:

matrix representing the best transformation with its components halved.

getMatrixMidsagittal

public TransMatrixd getMatrixMidsagittal()

Accessor that returns the matrix representing the best tranformation. This transformation contains only the z rotation and the x and y translation, to be used in the midsagittal alignment algorithm.

Returns:

matrix representing the best transformation's z rot and x and y trans.

getMatrixMidsagittal

public TransMatrixd getMatrixMidsagittal(float sample)

Accessor that returns the matrix representing the best tranformation. The passed in parameter represents the resolution (same in all directions and for both input and reference images, since resampled isotropically). Since the optimization was done in pixel space, not millimeter space, the translation parameters need to be scaled by the sample value. This transformation contains only the z rotation and the x and y translation, to be used in the midsagittal alignment algorithm.

Parameters:

sample - the voxel resolution

Returns:

matrix representing the best transformation's z rot and x and y trans.

measureCost

public void measureCost()

Calls cost function with point and saves result in functionAtBest.

runAlgorithm

public void runAlgorithm()

Runs ELSUNC along one dimension at a time as long as the costFunction improves during one cycle of runs along every dimension.

Specified by:

runAlgorithm in class AlgorithmBase

setInitialPoint

public void setInitialPoint(double[] initial)

Sets the initial point to the value passed in.

Parameters:

initial - Initial point.

setLimits

public void setLimits(float[][] limits)

Sets the limits on rotation and translation.

Parameters:

limits - limits

getCost

public double getCost()

Returns the cost of the best transformation.

Returns:

The cost of the best transformation.

getPoint

public double[] getPoint()

Returns the optimized point, with length == degrees of freedom.

Returns:

The optimized point.

setMaxIterations

public void setMaxIterations(int max)

Sets the maximum number of iterations.

Parameters:

max - The max number of iterations.

didSucceed

public boolean didSucceed()

Returns whether or not a minimum was found.

Returns:

whether or not a minimum was found.

setProgressBar

public void setProgressBar(ViewJProgressBar progress,
                           int begin,
                           int max)

Accessor that sets the progress bar so it can be updated from here.

Parameters:

progress - DOCUMENT ME!

begin - Value of progress bar when sent here.

max - Maximum value allowed.