Package gov.nih.mipav.model.algorithms

Class AlgorithmELSUNCOpt2D

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmELSUNCOpt2D

All Implemented Interfaces:

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

public class AlgorithmELSUNCOpt2D
extends AlgorithmBase

Runs ELSUNC, LEVENBERG_MARQUARDT, or NL2SOL for a 2D 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 22, 2012

Author:

William Gandler

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	AlgorithmELSUNCOpt2D.FitOAR2DELSUNCModel
(package private) class	AlgorithmELSUNCOpt2D.FitOAR2DLMModel
(package private) class	AlgorithmELSUNCOpt2D.FitOAR2DNL2solModel

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 AlgorithmOptimizeFunctionBase	costFunction	Cost function called to measure cost - 1D.
private int	ELSUNC
(package private) AlgorithmELSUNCOpt2D.FitOAR2DELSUNCModel	eModel
private double	epsilon
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 double	huge
private int	LEVENBERG_MARQUARDT
(package private) AlgorithmELSUNCOpt2D.FitOAR2DLMModel	lmModel
private int	maxIterations	The maximum number of iterations the optimization allows.
private double	minFunctionAtBest
private int	nDims	Degress of freedom.
private int	NL2SOL
(package private) AlgorithmELSUNCOpt2D.FitOAR2DNL2solModel	nModel
private double[]	OARTolerance	Array of tolerances for each dimension.
private AlgorithmBase	parent	Parent algorithm that called this optimization.
private boolean	pathRecorded	The flag to indicate whether the searching path need to be recorded.
protected java.util.Hashtable<java.lang.Long,java.util.Vector<java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>>>	paths	Store the paths for every thread.
private Vectornd[]	points	Array used to hold the initial points, final points and costs
private boolean	rigid	Flag indicating this is a rigid transformation.
private int	searchAlgorithm
private double[]	start	Point that was initially passed into function.
private int	status
private TransMatrixd	toOrigin	The transformation matrix to the origin of the input image.

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
AlgorithmELSUNCOpt2D(AlgorithmBase parent, WildMagic.LibFoundation.Mathematics.Vector2f com, int degreeOfFreedom, AlgorithmOptimizeFunctionBase costFunc, double[] tols, int maxIter, boolean _rigid, int searchAlgorithm)	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
void	adjustTranslation(TransMatrixd mat, float sample)
double[]	constructPoint(double[] defaultPoint, double[] point)	Construct a full 7-dimension transformation vector from the partial transformation vector.
TransMatrixd	convertToMatrix(double[] vector)	Convert a transformation vector to a transformation matrix.
TransMatrixd	convertToMatrix(TransMatrixd toOrigin, TransMatrixd fromOrigin, double[] vector)	Convert a 7-dimension transformation vector to a 3x3 transformation matrix.
private void	createTerrain(float[] terrain, float transXFrom, float transXTo, float transXStep, int xstart, int xdim, float transYFrom, float transYTo, float transYStep, int ystart, int ydim, float rotFrom, float rotTo, float rotStep, int zstart, int zdim)
float[]	createTerrain(float transXFrom, float transXTo, float transXStep, float transYFrom, float transYTo, float transYStep, float rotFrom, float rotTo, float rotStep)
private void	dfault(int[] iv, double[] v)
void	disposeLocal()	Sets everything to null and prepares this class for destruction.
double[]	extractPoint(double[] startPoint)	Extract the partial or full transformation vector from the start transformation vector, which will be optimized.
double	getCost(int index)	Returns the cost for the transformation vector.
double[]	getFinal(double[] point)	Accessor that returns the final point with translations, rotations, scales, and skews representing the best tranformation.
TransMatrixd	getMatrix(int index)	Obtain the transformation vector and convert to the matrix representation.
TransMatrixd	getMatrix(int index, float sample)
double[]	getPoint(int index)	Return the full transformation vector.
Vectornd[]	getPoints()	Return an array of transformation vector.
boolean	isPathRecorded()
double	measureCost(double[] point)	Measure the cost value for the given transformation vector.
double	measureCost(TransMatrixd m)	Measure the cost value for the given transformation matrix.
void	runAlgorithm()	Actually runs the algorithm.
private void	runELSUNC()	Runs ELSUNC along one dimension at a time as long as the costFunction improves during one cycle of runs along every dimension.
private void	runLM()	Runs Levneberg-Marqaurdt along one dimension at a time as long as the costFunction improves during one cycle of runs along every dimension.
private void	runNL2sol()
void	setMaxIterations(int max)	Accessor that sets the maximum number of iterations.
void	setPathRecorded(boolean pathRecorded)
void	setPoints(Vectornd[] points)	Sets the transformation vectors.
void	updatePoint(double[] point, double cost, Vectornd v)

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

ELSUNC

private final int ELSUNC

See Also:

Constant Field Values

LEVENBERG_MARQUARDT

private final int LEVENBERG_MARQUARDT

See Also:

Constant Field Values

NL2SOL

private final int NL2SOL

See Also:

Constant Field Values

searchAlgorithm

private int searchAlgorithm

rigid

private boolean rigid

Flag indicating this is a rigid transformation.

nDims

private int nDims

Degress of freedom.

costFunction

private AlgorithmOptimizeFunctionBase costFunction

Cost function called to measure cost - 1D.

OARTolerance

private double[] OARTolerance

Array of tolerances for each dimension.

maxIterations

private int maxIterations

The maximum number of iterations the optimization allows.

parent

private AlgorithmBase parent

Parent algorithm that called this optimization.

toOrigin

private TransMatrixd toOrigin

The transformation matrix to the origin of the input image.

fromOrigin

private TransMatrixd fromOrigin

The transformation matrix from the origin of the input image.

points

private Vectornd[] points

Array used to hold the initial points, final points and costs

functionAtBest

private double functionAtBest

The cost of the function at the best minimum.

minFunctionAtBest

private double minFunctionAtBest

eModel

AlgorithmELSUNCOpt2D.FitOAR2DELSUNCModel eModel

nModel

AlgorithmELSUNCOpt2D.FitOAR2DNL2solModel nModel

lmModel

AlgorithmELSUNCOpt2D.FitOAR2DLMModel lmModel

status

private int status

start

private double[] start

Point that was initially passed into function.

pathRecorded

private boolean pathRecorded

The flag to indicate whether the searching path need to be recorded.

paths

protected java.util.Hashtable<java.lang.Long,java.util.Vector<java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>>> paths

Store the paths for every thread.

epsilon

private double epsilon

huge

private double huge

Constructor Detail

AlgorithmELSUNCOpt2D

public AlgorithmELSUNCOpt2D(AlgorithmBase parent,
                            WildMagic.LibFoundation.Mathematics.Vector2f com,
                            int degreeOfFreedom,
                            AlgorithmOptimizeFunctionBase costFunc,
                            double[] tols,
                            int maxIter,
                            boolean _rigid,
                            int searchAlgorithm)

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 2, 3, 4, 5, 7).

costFunc - Cost function to use.

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

maxIter - Maximum number of iterations.

_rigid - true means this was a rigid transformation

searchAlgorithm - ELSUNC, LEVENBERG_MARQUARDT, or NL2SOL;

Method Detail

disposeLocal

public void disposeLocal()

Sets everything to null and prepares this class for destruction.

getPoints

public Vectornd[] getPoints()

Return an array of transformation vector. The meanings of those transformation vector are as following: the initial transformation vector: before algorithm is performed the final transformation vector: after algorithm was performed.

Returns:

setPoints

public void setPoints(Vectornd[] points)

Sets the transformation vectors.

Parameters:

points - the transformation vectors.

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

runELSUNC

private void runELSUNC()

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

runNL2sol

private void runNL2sol()

dfault

private void dfault(int[] iv,
                    double[] v)

runLM

private void runLM()

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

isPathRecorded

public boolean isPathRecorded()

setPathRecorded

public void setPathRecorded(boolean pathRecorded)

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.

constructPoint

public double[] constructPoint(double[] defaultPoint,
                               double[] point)

Construct a full 7-dimension transformation vector from the partial transformation vector. For missing values in point, the values in defaultPoint will be used. Different degree of freedom has different meanings: 2: only 2 translations 3: rigid: 1 rotation and 2 translations non-rigid: global scaling and 2 translations 4: 1 rotation, 2 translations and global scaling 5: 1 rotation, 2 translations and scalings 7: 1 rotation, 2 translations, scalings and skews

Parameters:

defaultPoint - a default full 7-dimension transformation vector.

point - a partial or full transformation vector.

Returns:

a full transformation vector.

convertToMatrix

public TransMatrixd convertToMatrix(TransMatrixd toOrigin,
                                    TransMatrixd fromOrigin,
                                    double[] vector)

Convert a 7-dimension transformation vector to a 3x3 transformation matrix.

Parameters:

vector - a 7-dimension transformation vector including 1 rotation, 2 translations, 2 scalings and 2 skews.

Returns:

a 3x3 transformation matrix

extractPoint

public double[] extractPoint(double[] startPoint)

Extract the partial or full transformation vector from the start transformation vector, which will be optimized.

Parameters:

startPoint - the start full 7-dimension transformation vector.

Returns:

the partial or full transformation vector which will be optimized.

getCost

public final double getCost(int index)

Returns the cost for the transformation vector.

Parameters:

index - the index of transformation vector.

Returns:

the cost for the transformation vector.

setMaxIterations

public void setMaxIterations(int max)

Accessor that sets the maximum number of iterations.

Parameters:

max - The max number of iterations.

adjustTranslation

public void adjustTranslation(TransMatrixd mat,
                              float sample)

See Also:

AlgorithmELSUNCOptBase#adjustTranslation(TransMatrix, float)

getMatrix

public TransMatrixd getMatrix(int index,
                              float sample)

See Also:

AlgorithmELSUNCOptBase#getMatrix(int, float)

getMatrix

public final TransMatrixd getMatrix(int index)

Obtain the transformation vector and convert to the matrix representation.

Parameters:

index - the index of transformation vector.

Returns:

the transformation matrix

getPoint

public double[] getPoint(int index)

Return the full transformation vector.

Parameters:

index - the index of the transformation vector.

Returns:

the full transformation vector.

convertToMatrix

public TransMatrixd convertToMatrix(double[] vector)

Convert a transformation vector to a transformation matrix.

Parameters:

vector - a transformation vector.

Returns:

a transformation matrix

updatePoint

public void updatePoint(double[] point,
                        double cost,
                        Vectornd v)

createTerrain

public float[] createTerrain(float transXFrom,
                             float transXTo,
                             float transXStep,
                             float transYFrom,
                             float transYTo,
                             float transYStep,
                             float rotFrom,
                             float rotTo,
                             float rotStep)

createTerrain

private void createTerrain(float[] terrain,
                           float transXFrom,
                           float transXTo,
                           float transXStep,
                           int xstart,
                           int xdim,
                           float transYFrom,
                           float transYTo,
                           float transYStep,
                           int ystart,
                           int ydim,
                           float rotFrom,
                           float rotTo,
                           float rotStep,
                           int zstart,
                           int zdim)

measureCost

public final double measureCost(double[] point)

Measure the cost value for the given transformation vector.

Parameters:

point - a transformation vector.

Returns:

the cost value.

measureCost

public final double measureCost(TransMatrixd m)

Measure the cost value for the given transformation matrix.

Parameters:

m - a transformation matrix.

Returns:

the cost value.