java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmPowellOptBase
    - - gov.nih.mipav.model.algorithms.AlgorithmPowellOpt3D

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 AlgorithmPowellOpt3D
extends AlgorithmPowellOptBase
```
Runs Powell's method for a 3D image. Check the parent class comment for more detailed information.

Version:

0.1 Oct 1, 2001, 0.2 March 27, 2008

Author:

Neva Cherniavsky, 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 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
`AlgorithmPowellOpt3D(AlgorithmBase parent, WildMagic.LibFoundation.Mathematics.Vector3f com, int degreeOfFreedom, AlgorithmOptimizeFunctionBase costFunc, double[] tols, int maxIter)`	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 12-dimension transformation vector from the partial transformation vector.
`TransMatrixd`	`convertToMatrix(TransMatrixd toOrigin, TransMatrixd fromOrigin, double[] vector)`	Convert a 12-dimension transformation vector to a 4x4 transformation matrix.
`double[]`	`convertToMidsagittal(double[] point)`	Converts a full transformation vector into a midsagittal transformation vector.
`double[]`	`extractPoint(double[] startPoint)`	Extract the partial or full transformation vector from the start transformation vector, which will be optimized.
`TransMatrixd`	`getMatrix(double[] point, double sample)`
`TransMatrixd`	`getMatrix(int index, double sample)`	Obtain the transformation vector and convert to the matrix representation, then scale the translation by sample.
`TransMatrixd`	`getMatrixHalf(int index)`	Obtain the transformation vector, scale it by 0.5, then convert it to transformation matrix.
`TransMatrixd`	`getMatrixHalf(int index, double sample)`	Obtain the transformation vector, scale it by 0.5, then convert it to transformation matrix and scale the translations by sample parameter.
`TransMatrixd`	`getMatrixMidsagittal(int index)`	Accessor that returns the matrix representing the best tranformation.
`TransMatrixd`	`getMatrixMidsagittal(int index, double sample)`	Accessor that returns the matrix representing the best tranformation.
`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

- Constructor Detail
  - AlgorithmPowellOpt3D
```
public AlgorithmPowellOpt3D(AlgorithmBase parent,
                            WildMagic.LibFoundation.Mathematics.Vector3f com,
                            int degreeOfFreedom,
                            AlgorithmOptimizeFunctionBase costFunc,
                            double[] tols,
                            int maxIter)
```
    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.
    
    tols - Tolerance for each dimension (tols.length == degreeOfFreedom).
    
    maxIter - Maximum number of iterations.
- Method Detail
  - constructPoint
```
public double[] constructPoint(double[] defaultPoint,
                               double[] point)
```
    Construct a full 12-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: 3: only 3 translations 4: 3 translation and global scaling 6: 3 rotations and translations 7: 3 rotations and translations, and global scaling 9: 3 rotations, translations and scalings 12: 3 rotations, translations, scalings and skewings.
    
    Specified by:
    
    constructPoint in class AlgorithmPowellOptBase
    
    Parameters:
    
    defaultPoint - a default full 12-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 12-dimension transformation vector to a 4x4 transformation matrix.
    
    Specified by:
    
    convertToMatrix in class AlgorithmPowellOptBase
    
    Parameters:
    
    vector - a 12-dimension transformation vector including 3 rotations, translations, scalings and skews.
    
    toOrigin - the matrix translating the origin to some specified point
    
    fromOrigin - the matrix translating the origin back.
    
    Returns:
    
    a 4x4 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 12-dimension transformation vector.
    
    Returns:
    
    the partial or full transformation vector which will be optimized.
  - 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)
  - getMatrix
```
public TransMatrixd getMatrix(double[] point,
                              double sample)
```
    See Also:
    
    AlgorithmPowellOptBase.getMatrix(int, double)
  - 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(TransMatrix, double)
  - getMatrixHalf
```
public TransMatrixd getMatrixHalf(int index)
```
    Obtain the transformation vector, scale it by 0.5, then convert it to transformation matrix.
    
    Parameters:
    
    index - the index of transformation vector.
    
    Returns:
    
    the scaled transformation matrix.
  - getMatrixHalf
```
public TransMatrixd getMatrixHalf(int index,
                                  double sample)
```
    Obtain the transformation vector, scale it by 0.5, then convert it to transformation matrix and scale the translations by sample parameter.
    
    Parameters:
    
    index - the index of transformation vector.
    
    sample - the translation scaling parameter.
    
    Returns:
    
    the scaled transformation matrix.
  - convertToMidsagittal
```
public double[] convertToMidsagittal(double[] point)
```
    Converts a full transformation vector into a midsagittal transformation vector.
    
    Parameters:
    
    point - the full 12-dimension transformation vector.
    
    Returns:
    
    the transformation vector complying with midsagittal alignment algorithm.
  - getMatrixMidsagittal
```
public TransMatrixd getMatrixMidsagittal(int index)
```
    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(int index,
                                         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.
  - 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.
    
    See Also:
    
    AlgorithmPowellOptBase.updatePoint(double[], double, Vectornd)

Class AlgorithmPowellOpt3D

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

Constructor Detail

AlgorithmPowellOpt3D

Method Detail

constructPoint

convertToMatrix

extractPoint

getMatrix

getMatrix

adjustTranslation

getMatrixHalf

getMatrixHalf

convertToMidsagittal

getMatrixMidsagittal

getMatrixMidsagittal

updatePoint