Package gov.nih.mipav.model.algorithms

Class AlgorithmConstPowellOpt3D

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmConstPowellOptBase

gov.nih.mipav.model.algorithms.AlgorithmConstPowellOpt3D

All Implemented Interfaces:

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

public class AlgorithmConstPowellOpt3D
extends AlgorithmConstPowellOptBase

Runs Powell's method for a 3D image. Check the parent class comment for more detailed information.

Version:

0.1 Oct 1, 2001

Author:

Neva Cherniavsky

Nested Class Summary

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

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

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

bracketBound, costFunction, finalPoint, fromOrigin, functionAtBest, maxIterations, myProgressBar, nDims, parent, point, progressBegin, progressMax, start, success, tolerance, toOrigin, trLimits

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
AlgorithmConstPowellOpt3D(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.
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(double sample)	Accessor that returns the matrix representing the best transformation.
TransMatrixd	getMatrixHalf()	Accessor that returns the matrix representing the best tranformation.
TransMatrixd	getMatrixHalf(double sample)	Accessor that returns the matrix representing the best tranformation.
TransMatrixd	getMatrixMidsagittal()	Accessor that returns the matrix representing the best tranformation.
TransMatrixd	getMatrixMidsagittal(double sample)	Accessor that returns the matrix representing the best tranformation.
void	measureCost()	Calls cost function with point and saves result in functionAtBest.
void	runAlgorithm()	Runs Powell's method.
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	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.AlgorithmConstPowellOptBase

debugPoint, didSucceed, disposeLocal, eval, getCost, getNumberOfVariables, getPoint, setMaxIterations

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, 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

Constructor Details

AlgorithmConstPowellOpt3D

public AlgorithmConstPowellOpt3D(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 Details

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.

Specified by:

convertToMatrix in class AlgorithmConstPowellOptBase

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.

Specified by:

getFinal in class AlgorithmConstPowellOptBase

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.

Specified by:

getFinal in class AlgorithmConstPowellOptBase

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.

Specified by:

getMatrix in class AlgorithmConstPowellOptBase

Returns:

matrix representing the best transformation.

getMatrix

public TransMatrixd getMatrix(double 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.

Specified by:

getMatrix in class AlgorithmConstPowellOptBase

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(double 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(double 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.

Specified by:

measureCost in class AlgorithmConstPowellOptBase

runAlgorithm

public void runAlgorithm()

Runs Powell's method. Powell's method is a way to find minimums without finding derivatives. Basically, it starts at some point P in N-dimensional space, proceeds in a direction, and minimizes along that line using golden search. It then resets the point and minimizes again, until the point moves by less than the tolerance. This method starts with the initial point defined in the constructor and initial directions of (1 0 ... 0) (0 1 0 ... ) ..., the basis vectors. At the end, "point" is the best point found and functionAtBest is the value at "point".

Specified by:

runAlgorithm in class AlgorithmBase

setInitialPoint

public void setInitialPoint(double[] initial)

Sets the initial point to the value passed in.

Specified by:

setInitialPoint in class AlgorithmConstPowellOptBase

Parameters:

initial - Initial point.

setLimits

public void setLimits(float[][] limits)

Sets the limits on rotation and translation.

Specified by:

setLimits in class AlgorithmConstPowellOptBase

Parameters:

limits - limits

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.