java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmConstPowellOptBase

All Implemented Interfaces:

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

Direct Known Subclasses:

AlgorithmConstPowellOpt3D
```
public abstract class AlgorithmConstPowellOptBase
extends AlgorithmBase
implements de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables
```
Powell's Method

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 a 1-dimensional minimization method. It continues like this until the point has moved by less than the tolerance. It 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".

This is an abstract class which contains many of the basic functions needed to run Powell's method. 2D and 3D versions extend this version.

This optimization technique is based on FLIRT. FLIRT stands for FMRIB's Linear Image Registration Tool. For more information on FLIRT, visit their homepage at http://www.fmrib.ox.ac.uk/fsl/flirt/. Their main paper is:

Jenkinson, M. and Smith, S. (2001a).
A global optimisation method for robust affine registration of brain images.
Medical Image Analysis, 5(2):143-156.

Version:

0.1 Oct 1, 2001

Author:

Neva Cherniavsky

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
`protected int`	`bracketBound`	The initial bracket size for first iteration of Powell.
`protected AlgorithmOptimizeFunctionBase`	`costFunction`	Cost function called to measure cost - 1D.
`protected double[]`	`finalPoint`	Final point when optimization is complete.
`protected TransMatrixd`	`fromOrigin`	The transformation matrix from the origin of the input image.
`protected double`	`functionAtBest`	The cost of the function at the best minimum.
`protected int`	`maxIterations`	The maximum number of iterations the optimization allows.
`protected ViewJProgressBar`	`myProgressBar`	Progress bar that may be set for long optimization runs.
`protected int`	`nDims`	Degress of freedom.
`protected AlgorithmBase`	`parent`	Parent algorithm that called this optimization.
`protected double[]`	`point`	Point that is currently being optimized.
`protected int`	`progressBegin`	Where progress is when sent in.
`protected int`	`progressMax`	The max the progress can go to.
`protected double[]`	`start`	Point that was initially passed into function.
`protected boolean`	`success`	Indicates whether the Powell algorithm succeeded in finding a minimum.
`protected double[]`	`tolerance`	Array of tolerances for each dimension.
`protected TransMatrixd`	`toOrigin`	The transformation matrix to the origin of the input image.
`protected 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
`AlgorithmConstPowellOptBase(AlgorithmBase parentAlgo, int degreeOfFreedom, AlgorithmOptimizeFunctionBase costFunc, double[] initial, double[] tols, int maxIter, int coords, int bracket)`	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, and some tolerance within that point to look for the minimum.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`abstract TransMatrixd`	`convertToMatrix(double[] vector)`	Helper method that converts a vector with certain values set to a matrix.
`protected void`	`debugPoint(double[] point, java.lang.String message)`	Method to display current point values.
`boolean`	`didSucceed()`	Returns whether or not a minimum was found.
`void`	`disposeLocal()`	Sets everything to null and prepares this class for destruction.
`double`	`eval(double[] x)`
`double`	`getCost()`	Returns the cost of the best transformation.
`abstract double[]`	`getFinal()`	Returns the final point with translations, rotations, scales, and skews representing the best Transformation.
`abstract double[]`	`getFinal(double[] point)`	Returns the final point with translations, rotations, scales, and skews representing the best Transformation.
`abstract TransMatrixd`	`getMatrix()`	Returns the matrix representing the best transformation.
`abstract TransMatrixd`	`getMatrix(double sample)`	Returns the matrix representing the best transformation.
`int`	`getNumberOfVariables()`
`double[]`	`getPoint()`	Returns the optimized point, with length == degrees of freedom.
`abstract void`	`measureCost()`	Calls cost function with inputed point and saves result in functionAtBest.
`abstract void`	`setInitialPoint(double[] initial)`	Sets the initial point to the value passed in.
`abstract void`	`setLimits(float[][] limits)`	Sets the limits on rotation and translation.
`void`	`setMaxIterations(int max)`	Sets the maximum number of iterations.

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, runAlgorithm, 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
  - bracketBound
```
protected int bracketBound
```
    The initial bracket size for first iteration of Powell.
  - costFunction
```
protected AlgorithmOptimizeFunctionBase costFunction
```
    Cost function called to measure cost - 1D.
  - finalPoint
```
protected double[] finalPoint
```
    Final point when optimization is complete.
  - fromOrigin
```
protected TransMatrixd fromOrigin
```
    The transformation matrix from the origin of the input image.
  - functionAtBest
```
protected double functionAtBest
```
    The cost of the function at the best minimum.
  - maxIterations
```
protected int maxIterations
```
    The maximum number of iterations the optimization allows.
  - myProgressBar
```
protected ViewJProgressBar myProgressBar
```
    Progress bar that may be set for long optimization runs.
  - nDims
```
protected int nDims
```
    Degress of freedom.
  - parent
```
protected AlgorithmBase parent
```
    Parent algorithm that called this optimization.
  - point
```
protected double[] point
```
    Point that is currently being optimized.
  - progressBegin
```
protected int progressBegin
```
    Where progress is when sent in.
  - progressMax
```
protected int progressMax
```
    The max the progress can go to.
  - start
```
protected double[] start
```
    Point that was initially passed into function.
  - success
```
protected boolean success
```
    Indicates whether the Powell algorithm succeeded in finding a minimum.
  - tolerance
```
protected double[] tolerance
```
    Array of tolerances for each dimension.
  - toOrigin
```
protected TransMatrixd toOrigin
```
    The transformation matrix to the origin of the input image.
  - trLimits
```
protected float[][] trLimits
```
    Array of translation and rotation limits for each dimension.
- Constructor Detail
  - AlgorithmConstPowellOptBase
```
public AlgorithmConstPowellOptBase(AlgorithmBase parentAlgo,
                                   int degreeOfFreedom,
                                   AlgorithmOptimizeFunctionBase costFunc,
                                   double[] initial,
                                   double[] tols,
                                   int maxIter,
                                   int coords,
                                   int bracket)
```
    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, and some tolerance within that point to look for the minimum. The initial point contains rotations, translations, scales, and skews.
    
    Parameters:
    
    parentAlgo - DOCUMENT ME!
    
    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 - The maximum iterations.
    
    coords - 2 or 3 for 2D or 3D
    
    bracket - the bracket bound for the first iteration of powell
- Method Detail
  - convertToMatrix
```
public abstract TransMatrixd convertToMatrix(double[] vector)
```
    Helper method that converts a vector with certain values set to a matrix. For values not set, uses those in start variable.
    
    Parameters:
    
    vector - Point with possible rotations, translations, etc. set.
    
    Returns:
    
    Matrix representation of that point.
  - getFinal
```
public abstract double[] getFinal()
```
    Returns the final point with translations, rotations, scales, and skews representing the best Transformation.
    
    Returns:
    
    A vector representing the best transformation in terms of translations, rotations, scales, and skews.
  - getFinal
```
public abstract double[] getFinal(double[] point)
```
    Returns the final point with translations, rotations, scales, and skews representing the best Transformation.
    
    Returns:
    
    A vector representing the best transformation in terms of translations, rotations, scales, and skews.
  - getMatrix
```
public abstract TransMatrixd getMatrix()
```
    Returns the matrix representing the best transformation.
    
    Returns:
    
    A matrix representing the best transformation.
  - getMatrix
```
public abstract TransMatrixd getMatrix(double sample)
```
    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 - Sample size.
    
    Returns:
    
    A matrix representing the best transformation.
  - measureCost
```
public abstract void measureCost()
```
    Calls cost function with inputed point and saves result in functionAtBest.
  - setInitialPoint
```
public abstract void setInitialPoint(double[] initial)
```
    Sets the initial point to the value passed in.
    
    Parameters:
    
    initial - Initial point.
  - setLimits
```
public abstract void setLimits(float[][] limits)
```
    Sets the limits on rotation and translation.
    
    Parameters:
    
    limits - limits
  - didSucceed
```
public boolean didSucceed()
```
    Returns whether or not a minimum was found.
    
    Returns:
    
    whether or not a minimum was found.
  - disposeLocal
```
public void disposeLocal()
```
    Sets everything to null and prepares this class for destruction.
  - 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.
  - debugPoint
```
protected void debugPoint(double[] point,
                          java.lang.String message)
```
    Method to display current point values.
    
    Parameters:
    
    point - DOCUMENT ME!
    
    message - 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

Class AlgorithmConstPowellOptBase

Nested Class Summary

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

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

bracketBound

costFunction

finalPoint

fromOrigin

functionAtBest

maxIterations

myProgressBar

nDims

parent

point

progressBegin

progressMax

start

success

tolerance

toOrigin

trLimits

Constructor Detail

AlgorithmConstPowellOptBase

Method Detail

convertToMatrix

getFinal

getFinal

getMatrix

getMatrix

measureCost

setInitialPoint

setLimits

didSucceed

disposeLocal

getCost

getPoint

setMaxIterations

debugPoint

eval

getNumberOfVariables