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

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 AlgorithmRegVOILandmark
extends AlgorithmBase
implements de.jtem.numericalMethods.calculus.function.RealFunctionOfSeveralVariables
```
AlgorithmRegVOILandmark First slice is template (base image) to which subsequent slices are registered. Trace kidney in 1st slice using polygon VOI. Minimize cost = -sum of Gradient magnitude under propagated ROI in match image

Version:

1.0 June, 2000

Author:

Delia McGarry

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private class`	`AlgorithmRegVOILandmark.CostFunction`	CostFunction - class for specifying optimization function for AlgorithmSimplexOpt slice - current fluoroscopy slice being operated on.

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`	DOCUMENT ME!
`protected int`	`costFunc`	DOCUMENT ME!
`static int`	`EXHAUSTIVEOPT`	DOCUMENT ME!
`private AlgorithmRegVOILandmark.CostFunction`	`func`
`private AlgorithmGradientMagnitude`	`gradientMagAlgo`	DOCUMENT ME!
`protected float[]`	`gradMagBuf`	DOCUMENT ME!
`protected ModelImage`	`gradMagVol`	DOCUMENT ME!
`private boolean`	`maskFlag`
`private double`	`maxRz`	DOCUMENT ME!
`static int`	`MAXSUM`	DOCUMENT ME!
`private double`	`maxTx`	DOCUMENT ME!
`private double`	`maxTy`	DOCUMENT ME!
`static int`	`MINDIFF`	DOCUMENT ME!
`private double`	`minRz`	DOCUMENT ME!
`private double`	`minTx`	DOCUMENT ME!
`private double`	`minTy`	DOCUMENT ME!
`protected int`	`opt`	DOCUMENT ME!
`private float[]`	`sigmas`
`private int`	`simplexDim`	DOCUMENT ME!
`static int`	`SIMPLEXOPT`	DOCUMENT ME!
`protected int`	`sliceSize`	DOCUMENT ME!
`private double`	`step`	DOCUMENT ME!
`protected int`	`tdim`	DOCUMENT ME!
`protected int`	`VOIlength`	DOCUMENT ME!
`protected VOIBase`	`VOIposition`	positions (x,y) of VOI in first slice
`protected int`	`volLength`	DOCUMENT ME!
`protected ModelImage`	`volume`	DOCUMENT ME!
`protected int`	`xdim`	DOCUMENT ME!
`protected int`	`ydim`	DOCUMENT ME!

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
`AlgorithmRegVOILandmark(ModelImage volume, ModelImage gradMagVol, float[] sigmas, boolean maskFlag, VOIBase position, double minTx, double maxTx, double minTy, double maxTy, double minRz, double maxRz, double step, int opt, int costFunc)`	Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`eval(double[] x)`
`private void`	`exhaustiveSearch(double[] p, AlgorithmRegVOILandmark.CostFunction func)`	Exhaustive search for global minimum.
`void`	`finalize()`	finalize - prepares this class for destruction.
`int`	`getNumberOfVariables()`
`protected TransMatrix`	`getTransform(double[] x)`	Converts row of p into 3x3 matrix.
`void`	`runAlgorithm()`	Starts the program.
`private void`	`search()`	Search.
`private void`	`transformSlice(int slice, TransMatrix xfrm, float[] imgBuf, float[] tImgBuf, WildMagic.LibFoundation.Mathematics.Vector3f center)`	Transforms a slice.

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

SIMPLEXOPT
```
public static final int SIMPLEXOPT
```
DOCUMENT ME!

See Also:

Constant Field Values

EXHAUSTIVEOPT
```
public static final int EXHAUSTIVEOPT
```
DOCUMENT ME!

See Also:

Constant Field Values

MINDIFF
```
public static final int MINDIFF
```
DOCUMENT ME!

See Also:

Constant Field Values

MAXSUM
```
public static final int MAXSUM
```
DOCUMENT ME!

See Also:

Constant Field Values

baseVOIGradMagSum
```
protected float baseVOIGradMagSum
```
DOCUMENT ME!

gradientMagAlgo

private AlgorithmGradientMagnitude gradientMagAlgo

DOCUMENT ME!

gradMagBuf
```
protected float[] gradMagBuf
```
DOCUMENT ME!

minTx
```
private double minTx
```
DOCUMENT ME!

maxTx
```
private double maxTx
```
DOCUMENT ME!

minTy
```
private double minTy
```
DOCUMENT ME!

maxTy
```
private double maxTy
```
DOCUMENT ME!

minRz
```
private double minRz
```
DOCUMENT ME!

maxRz
```
private double maxRz
```
DOCUMENT ME!

step
```
private double step
```
DOCUMENT ME!

opt
```
protected int opt
```
DOCUMENT ME!

costFunc
```
protected int costFunc
```
DOCUMENT ME!

simplexDim
```
private int simplexDim
```
DOCUMENT ME!

VOIlength
```
protected int VOIlength
```
DOCUMENT ME!

VOIposition
```
protected VOIBase VOIposition
```
positions (x,y) of VOI in first slice

volLength
```
protected int volLength
```
DOCUMENT ME!

sliceSize
```
protected int sliceSize
```
DOCUMENT ME!

volume
```
protected ModelImage volume
```
DOCUMENT ME!

gradMagVol
```
protected ModelImage gradMagVol
```
DOCUMENT ME!

xdim
```
protected int xdim
```
DOCUMENT ME!

ydim
```
protected int ydim
```
DOCUMENT ME!

tdim
```
protected int tdim
```
DOCUMENT ME!

sigmas
```
private float[] sigmas
```

maskFlag
```
private boolean maskFlag
```

func

private AlgorithmRegVOILandmark.CostFunction func

Constructor Detail

AlgorithmRegVOILandmark

public AlgorithmRegVOILandmark(ModelImage volume,
                               ModelImage gradMagVol,
                               float[] sigmas,
                               boolean maskFlag,
                               VOIBase position,
                               double minTx,
                               double maxTx,
                               double minTy,
                               double maxTy,
                               double minRz,
                               double maxRz,
                               double step,
                               int opt,
                               int costFunc)

Constructor.

Parameters:: volume - DOCUMENT ME!; gradMagVol - DOCUMENT ME!; sigmas - DOCUMENT ME!; maskFlag - DOCUMENT ME!; position - DOCUMENT ME!; minTx - DOCUMENT ME!; maxTx - DOCUMENT ME!; minTy - DOCUMENT ME!; maxTy - DOCUMENT ME!; minRz - DOCUMENT ME!; maxRz - DOCUMENT ME!; step - DOCUMENT ME!; opt - DOCUMENT ME!; costFunc - DOCUMENT ME!

Method Detail
- finalize
```
public void finalize()
```
  finalize - prepares this class for destruction.
  
  Overrides:
  
  finalize in class AlgorithmBase
- runAlgorithm
```
public void runAlgorithm()
```
  Starts the program.
  
  Specified by:
  
  runAlgorithm in class AlgorithmBase
- exhaustiveSearch
```
private void exhaustiveSearch(double[] p,
                              AlgorithmRegVOILandmark.CostFunction func)
```
  Exhaustive search for global minimum.
  
  Parameters:
  
  p - DOCUMENT ME!
  
  func - DOCUMENT ME!
- getTransform
```
protected TransMatrix getTransform(double[] x)
```
  Converts row of p into 3x3 matrix.
  
  Parameters:
  
  x - = row of p[][]
  
  Returns:
  
  DOCUMENT ME!
- search
```
private void search()
```
  Search.
- transformSlice
```
private void transformSlice(int slice,
                            TransMatrix xfrm,
                            float[] imgBuf,
                            float[] tImgBuf,
                            WildMagic.LibFoundation.Mathematics.Vector3f center)
```
  Transforms a slice.
  
  Parameters:
  
  slice - DOCUMENT ME!
  
  xfrm - DOCUMENT ME!
  
  imgBuf - DOCUMENT ME!
  
  tImgBuf - 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 AlgorithmRegVOILandmark

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

SIMPLEXOPT

EXHAUSTIVEOPT

MINDIFF

MAXSUM

baseVOIGradMagSum

gradientMagAlgo

gradMagBuf

minTx

maxTx

minTy

maxTy

minRz

maxRz

step

opt

costFunc

simplexDim

VOIlength

VOIposition

volLength

sliceSize

volume

gradMagVol

xdim

ydim

tdim

sigmas

maskFlag

func

Constructor Detail

AlgorithmRegVOILandmark

Method Detail

finalize

runAlgorithm

exhaustiveSearch

getTransform

search

transformSlice

eval

getNumberOfVariables