Package gov.nih.mipav.model.algorithms

Class AlgorithmPowellOpt2D

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmPowellOptBase

gov.nih.mipav.model.algorithms.AlgorithmPowellOpt2D

All Implemented Interfaces:

de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmPowellOpt2D
extends AlgorithmPowellOptBase

Runs Powell's method for a 2D image. Check the parent class comment for more detailed information.

Version:

0.1 Oct 1, 2001, 0.2 March 27, 2008

Author:

Neva Cherniavsky, Matthew McAuliffe, Hailong Wang, Ph.D

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	rigid	Flag indicating this is a rigid transformation.

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmPowellOptBase

costFunction, dof, fromOrigin, maxIterations, parallelPowell, parent, pathRecorded, paths, points, savedStartPoint, tolerance, toOrigin, useJTEM

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
AlgorithmPowellOpt2D(AlgorithmBase parent, WildMagic.LibFoundation.Mathematics.Vector2f com, int degreeOfFreedom, AlgorithmOptimizeFunctionBase costFunc, double[] tols, int maxIter, boolean _rigid)	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, double sample)	Adjust the translation of the transformation matrix by the sample pararmeter.
double[]	constructPoint(double[] defaultPoint, double[] point)	Construct a full 7-dimension transformation vector from the partial transformation vector.
TransMatrixd	convertToMatrix(TransMatrixd toOrigin, TransMatrixd fromOrigin, double[] vector)	Convert a 7-dimension transformation vector to a 3x3 transformation matrix.
double[]	extractPoint(double[] startPoint)	Extract the partial or full transformation vector from the start transformation vector, which will be optimized.
TransMatrixd	getMatrix(int index, double sample)	Obtain the transformation vector and convert to the matrix representation, then scale the translation by sample.
void	updatePoint(double[] point, double cost, Vectornd v)	Store the optimal point and cost to v

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

convertToMatrix, convertToMatrix, copyPoint, createTerrain, disposeLocal, eval, getCost, getFromOrigin, getMatrix, getMaxIterations, getNumberOfVariables, getPoint, getPoint, getPoints, getToOrigin, isParallelPowell, isPathRecorded, lineMinimization, measureCost, measureCost, optimize, optimizeBlock, print, runAlgorithm, scalePoint, scalePoint, setMaxIterations, setParallelPowell, setPathRecorded, setPoints, setUseJTEM

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

rigid

private boolean rigid

Flag indicating this is a rigid transformation.

Constructor Detail

AlgorithmPowellOpt2D

public AlgorithmPowellOpt2D(AlgorithmBase parent,
                            WildMagic.LibFoundation.Mathematics.Vector2f com,
                            int degreeOfFreedom,
                            AlgorithmOptimizeFunctionBase costFunc,
                            double[] tols,
                            int maxIter,
                            boolean _rigid)

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

Method Detail

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

Specified by:

constructPoint in class AlgorithmPowellOptBase

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.

Specified by:

convertToMatrix in class AlgorithmPowellOptBase

Parameters:

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

toOrigin - the matrix translating the origin to some specified point

fromOrigin - the matrix translating the origin back.

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.

Specified by:

extractPoint in class AlgorithmPowellOptBase

Parameters:

startPoint - the start full 7-dimension transformation vector.

Returns:

the partial or full transformation vector which will be optimized.

adjustTranslation

public void adjustTranslation(TransMatrixd mat,
                              double sample)

Description copied from class: AlgorithmPowellOptBase

Adjust the translation of the transformation matrix by the sample pararmeter.

Specified by:

adjustTranslation in class AlgorithmPowellOptBase

Parameters:

mat - the transformation matrix

sample - the resolution adjusting parameter.

See Also:

AlgorithmPowellOptBase.adjustTranslation(TransMatrixd, double)

getMatrix

public TransMatrixd getMatrix(int index,
                              double sample)

Description copied from class: AlgorithmPowellOptBase

Obtain the transformation vector and convert to the matrix representation, then scale the translation by sample.

Specified by:

getMatrix in class AlgorithmPowellOptBase

Parameters:

index - the index of transformation vector.

sample - the translation scaling parameter.

Returns:

the scaled transformation matrix.

See Also:

AlgorithmPowellOptBase.getMatrix(int, double)

updatePoint

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

Description copied from class: AlgorithmPowellOptBase

Store the optimal point and cost to v

Specified by:

updatePoint in class AlgorithmPowellOptBase

Parameters:

point - the optimal point.

cost - the optimal cost.

v - the Vectornd variable used by upper level algorithm.