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

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 AlgorithmVOISimplexOpt
extends AlgorithmBase
implements de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables
```
Perform Simplex Optimization on a VOI that has been propagated to a slice to find a transformation which will make an affine "fit" a structure which the VOI fit on the previous slice (used in RFASegTool when propagating liver segmentation VOIs). Minimize cost = -sum of Gradient magnitude under propagated ROI in match image

Version:

1.0 July, 2003

Author:

Evan McCreedy

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class AlgorithmVOISimplexOpt.CostFunction
Class for specifying optimization function for the simplex opt algorithm.
- 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 float`	`baseVOIGradMagSum`	The sum of the gradient magnitude along the polygon.
`protected int`	`costFunc`	Which cost function to use (MINDIFF or MAXSUM).
`private int`	`currentSlice`	The slice number the VOI is in.
`private AlgorithmVOISimplexOpt.CostFunction`	`func`
`protected float[]`	`gradMagBuf`	The gradient magnitude of the slice.
`private ModelImage`	`image`	The source image.
`protected VOIContour`	`inputGon`	The polygon of the VOI we are fitting.
`static int`	`MAXSUM`	Indicates that the maximum summation cost function should be used (this is the perferred cost function).
`static int`	`MINDIFF`	Indicates that the minimum difference cost function should be used (MAXSUM is perferred).
`private float[]`	`sigmas`	the kernel size to use in calculating the gradient magnitude image.
`private int`	`simplexDim`	Size of the simplex vertex array (5 == tx, ty, rot, zoomx, zoomy).
`private float[]`	`sliceBuf`	The image slice that holds the VOI we are working on.
`protected int`	`xDim`	The slice size in the x dimension.
`protected int`	`yDim`	The slice size in the y 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
`AlgorithmVOISimplexOpt(ModelImage image, float[] sigmas, int costFunc)`	Set up the algorithm to perform optimizations on an image.
`AlgorithmVOISimplexOpt(ModelImage image, VOIContour inputGon, float[] sigmas, int costFunc)`	Set up the algorithm to perform optimizations on an image.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`eval(double[] x)`
`void`	`finalize()`	Prepares this class for destruction.
`int`	`getNumberOfVariables()`
`protected TransMatrix`	`getTransform(double[] x)`	Converts a row of p into 3x3 transformation matrix.
`VOIContour`	`goOptimize(float[] sliceBuf, VOIContour inputGon)`	Run the simplex opt algorithm on a polygon (VOI) in a slice of an image.
`void`	`runAlgorithm()`	Run the algorithm on a polygon already specified through the constructor.
`private VOIContour`	`search()`	Find the best fit for the VOI polygon we have loaded into this algorithm.
`void`	`setCurrentSlice(int currentSlice)`	Specify the slice containing the VOI to optimize.
`void`	`setPolygon(VOIContour poly)`	Spefify the VOI polygon to optimize.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, 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
  - MINDIFF
```
public static final int MINDIFF
```
    Indicates that the minimum difference cost function should be used (MAXSUM is perferred).
    
    See Also:
    
    Constant Field Values
  - MAXSUM
```
public static final int MAXSUM
```
    Indicates that the maximum summation cost function should be used (this is the perferred cost function).
    
    See Also:
    
    Constant Field Values
  - baseVOIGradMagSum
```
protected float baseVOIGradMagSum
```
    The sum of the gradient magnitude along the polygon.
  - costFunc
```
protected int costFunc
```
    Which cost function to use (MINDIFF or MAXSUM).
  - currentSlice
```
private int currentSlice
```
    The slice number the VOI is in.
  - gradMagBuf
```
protected float[] gradMagBuf
```
    The gradient magnitude of the slice.
  - image
```
private ModelImage image
```
    The source image.
  - inputGon
```
protected VOIContour inputGon
```
    The polygon of the VOI we are fitting.
  - sigmas
```
private float[] sigmas
```
    the kernel size to use in calculating the gradient magnitude image.
  - simplexDim
```
private int simplexDim
```
    Size of the simplex vertex array (5 == tx, ty, rot, zoomx, zoomy).
  - sliceBuf
```
private float[] sliceBuf
```
    The image slice that holds the VOI we are working on.
  - xDim
```
protected int xDim
```
    The slice size in the x dimension.
  - yDim
```
protected int yDim
```
    The slice size in the y dimension.
  - func
```
private AlgorithmVOISimplexOpt.CostFunction func
```
- Constructor Detail
  - AlgorithmVOISimplexOpt
```
public AlgorithmVOISimplexOpt(ModelImage image,
                              float[] sigmas,
                              int costFunc)
```
    Set up the algorithm to perform optimizations on an image. The individual Polygons to optimize will be provided later (use goOptimize())
    
    Parameters:
    
    image - the image containing the VOI(s) to run the SimplexOpt algorithm on
    
    sigmas - the kernel size to use in calculating the gradient magnitude image
    
    costFunc - which cost function to use (MINDIFF or MAXSUM)
  - AlgorithmVOISimplexOpt
```
public AlgorithmVOISimplexOpt(ModelImage image,
                              VOIContour inputGon,
                              float[] sigmas,
                              int costFunc)
```
    Set up the algorithm to perform optimizations on an image. To be used in conjunction with the run method.
    
    Parameters:
    
    image - the image containing the VOI(s) to run the SimplexOpt algorithm on
    
    inputGon - the Polygon to optimize the fit of
    
    sigmas - the kernel size to use in calculating the gradient magnitude image
    
    costFunc - which cost function to use (MINDIFF or MAXSUM)
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - goOptimize
```
public VOIContour goOptimize(float[] sliceBuf,
                             VOIContour inputGon)
```
    Run the simplex opt algorithm on a polygon (VOI) in a slice of an image.
    
    Parameters:
    
    sliceBuf - the slice the polygon resides in
    
    inputGon - the polygon to optimize the fit of
    
    Returns:
    
    the optimized polygon
  - runAlgorithm
```
public void runAlgorithm()
```
    Run the algorithm on a polygon already specified through the constructor.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setCurrentSlice
```
public void setCurrentSlice(int currentSlice)
```
    Specify the slice containing the VOI to optimize.
    
    Parameters:
    
    currentSlice - the slice with the VOI to optimize
  - setPolygon
```
public void setPolygon(VOIContour poly)
```
    Spefify the VOI polygon to optimize.
    
    Parameters:
    
    poly - the polygon
  - getTransform
```
protected TransMatrix getTransform(double[] x)
```
    Converts a row of p into 3x3 transformation matrix.
    
    Parameters:
    
    x - row of p[][] (one of the simplex vertices)
    
    Returns:
    
    the transformation matrix corresponding to x
  - search
```
private VOIContour search()
```
    Find the best fit for the VOI polygon we have loaded into this algorithm.
    
    Returns:
    
    the optimized polygon
  - 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 AlgorithmVOISimplexOpt

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

MINDIFF

MAXSUM

baseVOIGradMagSum

costFunc

currentSlice

gradMagBuf

image

inputGon

sigmas

simplexDim

sliceBuf

xDim

yDim

func

Constructor Detail

AlgorithmVOISimplexOpt

AlgorithmVOISimplexOpt

Method Detail

finalize

goOptimize

runAlgorithm

setCurrentSlice

setPolygon

getTransform

search

eval

getNumberOfVariables