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

All Methods Instance Methods Concrete Methods
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.

Class AlgorithmPowellOpt2D

Nested Class Summary

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

Field Summary

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

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.AlgorithmPowellOptBase

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

rigid

Constructor Detail

AlgorithmPowellOpt2D

Method Detail

constructPoint

convertToMatrix

extractPoint

adjustTranslation

getMatrix

updatePoint