java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmConstELSUNCOpt3D

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmConstELSUNCOpt3D
extends AlgorithmBase
```
Runs ELSUNC for a 3D image.

Based on ELSUNC allowed by the author with acknowledgement:

Gauss-Newton Based Algorithms For Constrained Nonlinear Least Squares Problems by Per Lindstrom and Per-Ake Wedin, Institute of Information Processing, University of Umea, S-901 87 Umea, Sweden This can be downleaded from http://www.cs.umu.se/~perl/reports/alg.ps.gz

Version:

0.1 March 19, 2012

Author:

William Gandler

Nested Class Summary

Nested Classes
Modifier and Type Class Description

(package private) class AlgorithmConstELSUNCOpt3D.FitOAR3DConstrainedModel
- 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 int`	`bracketBound`	The initial bracket size for first iteration of ELSUNC.
`private AlgorithmOptimizeFunctionBase`	`costFunction`	Cost function called to measure cost - 1D.
`(package private) AlgorithmConstELSUNCOpt3D.FitOAR3DConstrainedModel`	`dModel`
`private double[]`	`finalPoint`	Final point when optimization is complete.
`private TransMatrixd`	`fromOrigin`	The transformation matrix from the origin of the input image.
`private double`	`functionAtBest`	The cost of the function at the best minimum.
`private int`	`maxIterations`	The maximum number of iterations the optimization allows.
`private double`	`minFunctionAtBest`
`private ViewJProgressBar`	`myProgressBar`	Progress bar that may be set for long optimization runs.
`private int`	`nDims`	Degress of freedom.
`private double[]`	`OARTolerance`	Array of tolerances for each dimension.
`private AlgorithmBase`	`parent`	Parent algorithm that called this optimization.
`private double[]`	`point`	Point that is currently being optimized.
`private int`	`progressBegin`	Where progress is when sent in.
`private int`	`progressMax`	The max the progress can go to.
`private double[]`	`start`	Point that was initially passed into function.
`private int`	`status`
`private boolean`	`success`	Indicates whether the ELSUNC algorithm succeeded in finding a minimum.
`protected TransMatrixd`	`toOrigin`	The transformation matrix to the origin of the input image.
`private 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
`AlgorithmConstELSUNCOpt3D(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

All Methods Instance Methods Concrete Methods
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.
`boolean`	`didSucceed()`	Returns whether or not a minimum was found.
`void`	`disposeLocal()`	Sets everything to null and prepares this class for destruction.
`double`	`getCost()`	Returns the cost of the best transformation.
`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(float sample)`	Accessor that returns the matrix representing the best transformation.
`TransMatrixd`	`getMatrixHalf()`	Accessor that returns the matrix representing the best tranformation.
`TransMatrixd`	`getMatrixHalf(float sample)`	Accessor that returns the matrix representing the best tranformation.
`TransMatrixd`	`getMatrixMidsagittal()`	Accessor that returns the matrix representing the best tranformation.
`TransMatrixd`	`getMatrixMidsagittal(float sample)`	Accessor that returns the matrix representing the best tranformation.
`double[]`	`getPoint()`	Returns the optimized point, with length == degrees of freedom.
`void`	`measureCost()`	Calls cost function with point and saves result in functionAtBest.
`void`	`runAlgorithm()`	Runs ELSUNC along one dimension at a time as long as the costFunction improves during one cycle of runs along every dimension.
`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`	`setMaxIterations(int max)`	Sets the maximum number of iterations.
`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.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
  - dModel
```
AlgorithmConstELSUNCOpt3D.FitOAR3DConstrainedModel dModel
```
  - bracketBound
```
private int bracketBound
```
    The initial bracket size for first iteration of ELSUNC.
  - costFunction
```
private AlgorithmOptimizeFunctionBase costFunction
```
    Cost function called to measure cost - 1D.
  - finalPoint
```
private double[] finalPoint
```
    Final point when optimization is complete.
  - fromOrigin
```
private TransMatrixd fromOrigin
```
    The transformation matrix from the origin of the input image.
  - functionAtBest
```
private double functionAtBest
```
    The cost of the function at the best minimum.
  - minFunctionAtBest
```
private double minFunctionAtBest
```
  - maxIterations
```
private int maxIterations
```
    The maximum number of iterations the optimization allows.
  - myProgressBar
```
private ViewJProgressBar myProgressBar
```
    Progress bar that may be set for long optimization runs.
  - nDims
```
private int nDims
```
    Degress of freedom.
  - parent
```
private AlgorithmBase parent
```
    Parent algorithm that called this optimization.
  - point
```
private double[] point
```
    Point that is currently being optimized.
  - progressBegin
```
private int progressBegin
```
    Where progress is when sent in.
  - progressMax
```
private int progressMax
```
    The max the progress can go to.
  - start
```
private double[] start
```
    Point that was initially passed into function.
  - success
```
private boolean success
```
    Indicates whether the ELSUNC algorithm succeeded in finding a minimum.
  - OARTolerance
```
private double[] OARTolerance
```
    Array of tolerances for each dimension.
  - toOrigin
```
protected TransMatrixd toOrigin
```
    The transformation matrix to the origin of the input image.
  - trLimits
```
private float[][] trLimits
```
    Array of translation and rotation limits for each dimension.
  - status
```
private int status
```
- Constructor Detail
  - AlgorithmConstELSUNCOpt3D
```
public AlgorithmConstELSUNCOpt3D(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 Detail
  - disposeLocal
```
public void disposeLocal()
```
    Sets everything to null and prepares this class for destruction.
  - 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.
    
    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.
    
    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.
    
    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.
    
    Returns:
    
    matrix representing the best transformation.
  - getMatrix
```
public TransMatrixd getMatrix(float 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.
    
    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(float 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(float 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.
  - runAlgorithm
```
public void runAlgorithm()
```
    Runs ELSUNC along one dimension at a time as long as the costFunction improves during one cycle of runs along every dimension.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setInitialPoint
```
public void setInitialPoint(double[] initial)
```
    Sets the initial point to the value passed in.
    
    Parameters:
    
    initial - Initial point.
  - setLimits
```
public void setLimits(float[][] limits)
```
    Sets the limits on rotation and translation.
    
    Parameters:
    
    limits - limits
  - 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.
  - didSucceed
```
public boolean didSucceed()
```
    Returns whether or not a minimum was found.
    
    Returns:
    
    whether or not a minimum was found.
  - 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.

Class AlgorithmConstELSUNCOpt3D

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

dModel

bracketBound

costFunction

finalPoint

fromOrigin

functionAtBest

minFunctionAtBest

maxIterations

myProgressBar

nDims

parent

point

progressBegin

progressMax

start

success

OARTolerance

toOrigin

trLimits

status

Constructor Detail

AlgorithmConstELSUNCOpt3D

Method Detail

disposeLocal

convertToMatrix

convertToMatrixHalf

convertToMatrixMidsagittal

getFinal

getFinal

getFinal

getMatrix

getMatrix

getMatrixHalf

getMatrixHalf

getMatrixMidsagittal

getMatrixMidsagittal

measureCost

runAlgorithm

setInitialPoint

setLimits

getCost

getPoint

setMaxIterations

didSucceed

setProgressBar