java.lang.Object
- gov.nih.mipav.model.algorithms.registration.vabra.VabraSubjectTargetPairs

All Implemented Interfaces:: de.jtem.numericalMethods.calculus.function.RealFunctionOfOneVariable

public class VabraSubjectTargetPairs
extends java.lang.Object
implements de.jtem.numericalMethods.calculus.function.RealFunctionOfOneVariable

Field Summary

Fields
Modifier and Type	Field	Description
`private int[]`	`boundingBox`
`private int`	`chInterpType`
`private int[]`	`coarseLocalRegionCenter`
`private int`	`commitCount`
`private int[]`	`currentDeformedSubject`
`private float[]`	`currentDeformField`
`private double`	`currentDownSampleFactor`
`private int[]`	`currentJointST`
`private int`	`curX`
`private int`	`curY`
`private int`	`curZ`
`private int`	`defFieldUpdateMode`
`private VabraVolumeCollection`	`deformedSubject`
`private VabraVolumeCollection`	`deformedSubjectBinned`
`private VabraVolumeCollection`	`deformedSubjectCopy`
`private int[]`	`defSTxMinus`
`private int[]`	`defSTxPlus`
`private int[]`	`defSTyMinus`
`private int[]`	`defSTyPlus`
`private int[]`	`defSTzMinus`
`private int[]`	`defSTzPlus`
`private int[]`	`defSxMinus`
`private int[]`	`defSxPlus`
`private int[]`	`defSyMinus`
`private int[]`	`defSyPlus`
`private int[]`	`defSzMinus`
`private int[]`	`defSzPlus`
`private double[]`	`directionsOptmizationWeight`
`private double`	`domainMax`
`private double`	`domainMin`
`private static double`	`lambda`
`private int`	`levelCount`
`private double[]`	`localCoarseGradient`
`private int[]`	`localROI`
`private int`	`maxDimensions`
`private int`	`numOfBins`
`private int[]`	`origDeformedSubject`
`private int[]`	`origJointST`
`private ModelImage`	`origSubjectList`
`private int[]`	`origTarget`
`private ModelImage`	`origTargetList`
`private VabraRBF`	`rbf`
`private int`	`resCount`
`private float`	`RobustMaxThresh`
`private float`	`RobustMinThresh`
`private VabraVolumeCollection`	`subject`
`private VabraVolumeCollection`	`target`
`private VabraVolumeCollection`	`targetBinned`
`private double`	`tolerance`
`private float[]`	`totalDeformField`
`private ModelImage[]`	`totalDeformFieldSplit`

Constructor Summary

Constructors
Constructor	Description
`VabraSubjectTargetPairs(ModelImage subjectVols, ModelImage targetVols, float robustMaxT, float robustMinT, int numBins, int interpType, boolean useMNMI, double[] directionsOptmizationWeight, int defFieldUpdateMode)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`adjustBins(int[] subjectHist, int[] jointHist, int subBin, int tarBin, int newBin)`
`private void`	`adjustGradientBins(VabraVolumeCollection subject, double x, double y, double z, int[] subjectHist, int[] jointHist, int targetBins, int subjectBins)`
`private void`	`adjustOrigBins(int subBin, int tarBin, int newBin)`
`(package private) void`	`calculateBoundingBox()`
`private double`	`coarseCostFunction(double coeff)`
`private double`	`coarseCostFunctionCommit(double coeff, boolean commitUpdate)`
`void`	`coarseGradient(int[] regionCenter, double[] results)`
`int`	`coarseGradientParameters()`
`double`	`coarseOptimize(int[] regionCenter, double[] gradient)`
`private int[]`	`copyHist(int[] in)`
`private int[][]`	`copyHist(int[][] in)`
`private int[][][]`	`copyHist(int[][][] vol)`
`void`	`dispose()`
`double`	`eval(double arg0)`
`private double`	`getCurrentNMI()`
`(package private) ModelImage`	`getDeformationField()`
`(package private) ModelImage`	`getDeformedSubject()`
`double`	`getDomainMax()`
`double`	`getDomainMin()`
`double`	`getDomainTolerance()`
`private void`	`getNMIGradients(double[] results, double[] deltaC)`
`VabraRBF`	`getRBF()`
`double`	`getValue(double c)`
`int[]`	`prepareForNextLevel()`
`private void`	`resetCurrentHistograms()`
`private static float`	`robustMaximum(float[] image, float ratio, int scales, int nx, int ny, int nz)`	Robust maximum estimation
`private static float`	`robustMinimum(float[] image, float ratio, int scales, int nx, int ny, int nz)`	Robust maximum estimation
`void`	`setResolution(float downSampleFactor)`
`private void`	`threshAtRobustMaxAndMin(VabraVolumeCollection imgVec)`
`private void`	`updateDefField(int[] regionToUpdate)`
`(package private) void`	`updateFromCoarseOptimization(double coeff)`
`private void`	`updateHistograms(VabraVolumeCollection normedTarget, VabraVolumeCollection normedDeformedSubject, int[] boundingBox)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

maxDimensions
```
private int maxDimensions
```

subject
```
private VabraVolumeCollection subject
```

deformedSubject

private VabraVolumeCollection deformedSubject

target
```
private VabraVolumeCollection target
```

targetBinned

private VabraVolumeCollection targetBinned

deformedSubjectBinned

private VabraVolumeCollection deformedSubjectBinned

currentDownSampleFactor
```
private double currentDownSampleFactor
```

boundingBox
```
private int[] boundingBox
```

currentDeformField
```
private float[] currentDeformField
```

totalDeformField
```
private float[] totalDeformField
```

origSubjectList
```
private ModelImage origSubjectList
```

origTargetList
```
private ModelImage origTargetList
```

chInterpType
```
private int chInterpType
```

numOfBins
```
private int numOfBins
```

RobustMinThresh
```
private float RobustMinThresh
```

RobustMaxThresh
```
private float RobustMaxThresh
```

defFieldUpdateMode
```
private int defFieldUpdateMode
```

curX
```
private int curX
```

curY
```
private int curY
```

curZ
```
private int curZ
```

deformedSubjectCopy

private VabraVolumeCollection deformedSubjectCopy

totalDeformFieldSplit

private ModelImage[] totalDeformFieldSplit

levelCount
```
private int levelCount
```

resCount
```
private int resCount
```

rbf
```
private VabraRBF rbf
```

lambda
```
private static double lambda
```

localROI
```
private int[] localROI
```

localCoarseGradient
```
private double[] localCoarseGradient
```

coarseLocalRegionCenter
```
private int[] coarseLocalRegionCenter
```

directionsOptmizationWeight

private double[] directionsOptmizationWeight

domainMax
```
private double domainMax
```

domainMin
```
private double domainMin
```

tolerance
```
private double tolerance
```

commitCount
```
private int commitCount
```

origJointST
```
private int[] origJointST
```

currentJointST
```
private int[] currentJointST
```

defSTxPlus
```
private int[] defSTxPlus
```

defSTxMinus
```
private int[] defSTxMinus
```

defSTyPlus
```
private int[] defSTyPlus
```

defSTyMinus
```
private int[] defSTyMinus
```

defSTzPlus
```
private int[] defSTzPlus
```

defSTzMinus
```
private int[] defSTzMinus
```

defSxPlus
```
private int[] defSxPlus
```

defSxMinus
```
private int[] defSxMinus
```

defSyPlus
```
private int[] defSyPlus
```

defSyMinus
```
private int[] defSyMinus
```

defSzPlus
```
private int[] defSzPlus
```

defSzMinus
```
private int[] defSzMinus
```

origDeformedSubject
```
private int[] origDeformedSubject
```

origTarget
```
private int[] origTarget
```

currentDeformedSubject
```
private int[] currentDeformedSubject
```

Constructor Detail

VabraSubjectTargetPairs

public VabraSubjectTargetPairs(ModelImage subjectVols,
                               ModelImage targetVols,
                               float robustMaxT,
                               float robustMinT,
                               int numBins,
                               int interpType,
                               boolean useMNMI,
                               double[] directionsOptmizationWeight,
                               int defFieldUpdateMode)

Method Detail

robustMaximum

private static final float robustMaximum(float[] image,
                                         float ratio,
                                         int scales,
                                         int nx,
                                         int ny,
                                         int nz)

Robust maximum estimation

Parameters:: ratio - float fraction in [0,1]: the minimum number of points above or equal to the maximum over the total volume; scales - int: the number of times the scale is refined for finding the robust maximum; nx - ,ny,nz image dimensions
Returns:: the robust maximum value

robustMinimum

private static final float robustMinimum(float[] image,
                                         float ratio,
                                         int scales,
                                         int nx,
                                         int ny,
                                         int nz)

Robust maximum estimation

Parameters:: ratio - float fraction in [0,1]: the minimum number of points below or equal to the minimum over the total volume; scales - int: the number of times the scale is refined for finding the robust minimum
Returns:: the robust minimum value

coarseGradientParameters
```
public int coarseGradientParameters()
```

dispose
```
public void dispose()
```

prepareForNextLevel
```
public int[] prepareForNextLevel()
```

setResolution

public void setResolution(float downSampleFactor)

threshAtRobustMaxAndMin

private void threshAtRobustMaxAndMin(VabraVolumeCollection imgVec)

updateDefField

private void updateDefField(int[] regionToUpdate)

calculateBoundingBox
```
void calculateBoundingBox()
```

getDeformationField
```
ModelImage getDeformationField()
```

getDeformedSubject
```
ModelImage getDeformedSubject()
```

getDomainMax
```
public double getDomainMax()
```

getDomainMin
```
public double getDomainMin()
```

getDomainTolerance
```
public double getDomainTolerance()
```

getValue
```
public double getValue(double c)
```

coarseGradient

public void coarseGradient(int[] regionCenter,
                           double[] results)

updateFromCoarseOptimization

void updateFromCoarseOptimization(double coeff)

coarseOptimize

public double coarseOptimize(int[] regionCenter,
                             double[] gradient)

coarseCostFunctionCommit

private double coarseCostFunctionCommit(double coeff,
                                        boolean commitUpdate)

coarseCostFunction

private double coarseCostFunction(double coeff)

getRBF
```
public VabraRBF getRBF()
```

copyHist
```
private int[] copyHist(int[] in)
```

copyHist

private int[][] copyHist(int[][] in)

copyHist

private int[][][] copyHist(int[][][] vol)

resetCurrentHistograms
```
private void resetCurrentHistograms()
```

updateHistograms

private void updateHistograms(VabraVolumeCollection normedTarget,
                              VabraVolumeCollection normedDeformedSubject,
                              int[] boundingBox)

getCurrentNMI
```
private double getCurrentNMI()
```

adjustOrigBins

private void adjustOrigBins(int subBin,
                            int tarBin,
                            int newBin)

getNMIGradients

private void getNMIGradients(double[] results,
                             double[] deltaC)

adjustGradientBins

private void adjustGradientBins(VabraVolumeCollection subject,
                                double x,
                                double y,
                                double z,
                                int[] subjectHist,
                                int[] jointHist,
                                int targetBins,
                                int subjectBins)

adjustBins

private void adjustBins(int[] subjectHist,
                        int[] jointHist,
                        int subBin,
                        int tarBin,
                        int newBin)

eval
```
public double eval(double arg0)
```
Specified by:

eval in interface de.jtem.numericalMethods.calculus.function.RealFunctionOfOneVariable

Class VabraSubjectTargetPairs

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

maxDimensions

subject

deformedSubject

target

targetBinned

deformedSubjectBinned

currentDownSampleFactor

boundingBox

currentDeformField

totalDeformField

origSubjectList

origTargetList

chInterpType

numOfBins

RobustMinThresh

RobustMaxThresh

defFieldUpdateMode

curX

curY

curZ

deformedSubjectCopy

totalDeformFieldSplit

levelCount

resCount

rbf

lambda

localROI

localCoarseGradient

coarseLocalRegionCenter

directionsOptmizationWeight

domainMax

domainMin

tolerance

commitCount

origJointST

currentJointST

defSTxPlus

defSTxMinus

defSTyPlus

defSTyMinus

defSTzPlus

defSTzMinus

defSxPlus

defSxMinus

defSyPlus

defSyMinus

defSzPlus

defSzMinus

origDeformedSubject

origTarget

currentDeformedSubject

Constructor Detail

VabraSubjectTargetPairs

Method Detail

robustMaximum

robustMinimum

coarseGradientParameters

dispose

prepareForNextLevel

setResolution

threshAtRobustMaxAndMin

updateDefField

calculateBoundingBox

getDeformationField

getDeformedSubject

getDomainMax

getDomainMin

getDomainTolerance

getValue

coarseGradient

updateFromCoarseOptimization

coarseOptimize

coarseCostFunctionCommit

coarseCostFunction