java.lang.Object
- gov.nih.mipav.model.algorithms.AlgorithmCostFunctions

All Implemented Interfaces:

AlgorithmOptimizeFunctionBase
```
public class AlgorithmCostFunctions
extends java.lang.Object
implements AlgorithmOptimizeFunctionBase
```
CostFunction - class for specifying optimization function.

Field Summary

Fields
Modifier and Type	Field	Description
`static int`	`CORRELATION_RATIO`	DOCUMENT ME!
`static int`	`CORRELATION_RATIO_SMOOTHED`	DOCUMENT ME!
`static int`	`CORRELATION_RATIO_SMOOTHED_WGT`	DOCUMENT ME!
`private int`	`costCalled`	DOCUMENT ME!
`private int`	`costFunctID`	DOCUMENT ME!
`private ModelSimpleImage`	`inputImage`	DOCUMENT ME!
`private ModelSimpleImage`	`inputWgtImage`	DOCUMENT ME!
`static int`	`LEAST_SQUARES`	DOCUMENT ME!
`static int`	`LEAST_SQUARES_COLOR`	DOCUMENT ME!
`static int`	`LEAST_SQUARES_SMOOTHED`	DOCUMENT ME!
`static int`	`LEAST_SQUARES_SMOOTHED_COLOR`	DOCUMENT ME!
`static int`	`LEAST_SQUARES_SMOOTHED_WGT`	DOCUMENT ME!
`static int`	`LEAST_SQUARES_SMOOTHED_WGT_COLOR`	DOCUMENT ME!
`private float[]`	`m_afJointHisto`
`private boolean`	`m_bPrint`
`private ImageRegistrationGPU`	`m_kGPUCost`
`static int`	`MUTUAL_INFORMATION`	DOCUMENT ME!
`static int`	`MUTUAL_INFORMATION_SMOOTHED`	DOCUMENT ME!
`static int`	`MUTUAL_INFORMATION_SMOOTHED_WGT`	DOCUMENT ME!
`private int`	`nBins`	DOCUMENT ME!
`static int`	`NORMALIZED_MUTUAL_INFORMATION`	DOCUMENT ME!
`static int`	`NORMALIZED_MUTUAL_INFORMATION_GPU`
`static int`	`NORMALIZED_MUTUAL_INFORMATION_GPU_LM`
`static int`	`NORMALIZED_MUTUAL_INFORMATION_SMOOTHED`	DOCUMENT ME!
`static int`	`NORMALIZED_MUTUAL_INFORMATION_SMOOTHED_WGT`	DOCUMENT ME!
`static int`	`NORMALIZED_XCORRELATION`	DOCUMENT ME!
`static int`	`NORMALIZED_XCORRELATION_SINC`	DOCUMENT ME!
`static int`	`NORMALIZED_XCORRELATION_SMOOTHED`	DOCUMENT ME!
`static int`	`NORMALIZED_XCORRELATION_SMOOTHED_WGT`	DOCUMENT ME!
`private int`	`nVoxels`	DOCUMENT ME!
`private double[]`	`pLogP`	DOCUMENT ME!
`private ModelSimpleImage`	`refImage`	DOCUMENT ME!
`private int`	`refSliceSize`	DOCUMENT ME!
`private ModelSimpleImage`	`refWgtImage`	DOCUMENT ME!
`private double[]`	`sincKernel`	DOCUMENT ME!
`private int`	`sincWidth`	DOCUMENT ME!
`private double[]`	`sincx`	DOCUMENT ME!
`private double[]`	`sincy`	DOCUMENT ME!
`private double[]`	`sincz`	DOCUMENT ME!
`private int`	`sliceSize`	DOCUMENT ME!
`private float`	`smoothSize`	DOCUMENT ME!
`private int`	`xDim`	DOCUMENT ME!
`private int`	`xEnd`	DOCUMENT ME!
`private double`	`xEnd2`	DOCUMENT ME!
`private int`	`xStart`
`private int`	`yDim`	DOCUMENT ME!
`private int`	`yEnd`	DOCUMENT ME!
`private double`	`yEnd2`	DOCUMENT ME!
`private int`	`yStart`
`private int`	`zDim`	DOCUMENT ME!
`private int`	`zEnd`	DOCUMENT ME!
`private double`	`zEnd2`	DOCUMENT ME!
`private int`	`zStart`

Constructor Summary

Constructors
Constructor	Description
`AlgorithmCostFunctions(ModelSimpleImage rImage, ModelSimpleImage iImage, int functionID, int nBins, float smoothSize)`	Creates a new AlgorithmCostFunctions object.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calcEntropy(TransMatrixd tMatrix, double[] jointEntropy, double[] margEntropyR, double[] margEntropyI)`	DOCUMENT ME!
`private void`	`calcEntropy(TransMatrix tMatrix, double[] jointEntropy, double[] margEntropyR, double[] margEntropyI)`	DOCUMENT ME!
`private void`	`calcEntropySmoothed(TransMatrixd tMatrix, double[] jointEntropy, double[] margEntropyR, double[] margEntropyI)`	DOCUMENT ME!
`private void`	`calcEntropySmoothed(TransMatrix tMatrix, double[] jointEntropy, double[] margEntropyR, double[] margEntropyI)`	DOCUMENT ME!
`private void`	`calcEntropySmoothedWgt(TransMatrixd tMatrix, double[] jointEntropy, double[] margEntropyR, double[] margEntropyI)`	DOCUMENT ME!
`private void`	`calcEntropySmoothedWgt(TransMatrix tMatrix, double[] jointEntropy, double[] margEntropyR, double[] margEntropyI)`	DOCUMENT ME!
`private double`	`correlationRatio(TransMatrix tMatrix)`	Correlation ratio cost function.
`private double`	`correlationRatio(TransMatrixd tMatrix)`	Correlation ratio cost function.
`private double`	`correlationRatioSmoothed(TransMatrix tMatrix)`	Correlation ratio cost function.
`private double`	`correlationRatioSmoothed(TransMatrixd tMatrix)`	Correlation ratio cost function.
`private double`	`correlationRatioSmoothedWgt(TransMatrix tMatrix)`	Correlation ratio cost function using weighting functions to mask out areas that should not be included in the cost function calculations.
`private double`	`correlationRatioSmoothedWgt(TransMatrixd tMatrix)`	Correlation ratio cost function using weighting functions to mask out areas that should not be included in the cost function calculations.
`double`	`cost(double[] data)`	Not implemented in this class.
`double`	`cost(TransMatrix affMatrix)`	Calculates the cost (dependent on the selected cost function) based on the reference image and the input image.
`double`	`cost(TransMatrixd affMatrix)`	Calculates the cost (dependent on the selected cost function) based on the reference image and the input image.
`void`	`disposeLocal()`	Sets class global array variables to null and calls the garbage collector.
`void`	`finalize()`	Calls disposeLocal of this class to ensure this class nulls the references to global class variables so that memory will be recovered.
`private void`	`findRangeX(java.awt.Point minMaxPt, double newPtX, double newPtY, double newPtZ, double aT00, double aT10, double aT20, double iT00, double iT10, double iT20)`	DOCUMENT ME!
`int`	`getCostCalled()`	Accessor that returns how many times the cost function has been called.
`int`	`getCostFunction()`
`private double`	`getSinc(float[] data, double x, double y, double z)`	DOCUMENT ME!
`private static double`	`hanning(double x, int w)`	DOCUMENT ME!
`boolean`	`isGPULineMin()`
`private double`	`kernelVal(double x, int w)`	DOCUMENT ME!
`private double`	`leastSquares(TransMatrix tMatrix)`	Least squares cost function.
`private double`	`leastSquares(TransMatrixd tMatrix)`	Least squares cost function.
`private double`	`leastSquaresColor(TransMatrix tMatrix)`	Least squares cost function.
`private double`	`leastSquaresColor(TransMatrixd tMatrix)`	Least squares cost function.
`private double`	`leastSquaresSmoothed(TransMatrix tMatrix)`	Least squares cost function.
`private double`	`leastSquaresSmoothed(TransMatrixd tMatrix)`	Least squares cost function.
`private double`	`leastSquaresSmoothedColor(TransMatrix tMatrix)`	Least squares cost function.
`private double`	`leastSquaresSmoothedColor(TransMatrixd tMatrix)`	Least squares cost function.
`private double`	`leastSquaresSmoothedWgt(TransMatrix tMatrix)`	Least squares cost function with weighting.
`private double`	`leastSquaresSmoothedWgt(TransMatrixd tMatrix)`	Least squares cost function with weighting.
`private double`	`leastSquaresSmoothedWgtColor(TransMatrix tMatrix)`	Least squares cost function with weighting.
`private double`	`leastSquaresSmoothedWgtColor(TransMatrixd tMatrix)`	Least squares cost function with weighting.
`float[]`	`lineMin(WildMagic.LibFoundation.Mathematics.Matrix4f kToOrigin, WildMagic.LibFoundation.Mathematics.Matrix4f kFromOrigin, float rigid, float dim, double[] startPoint, double[] pt, int ptLength, double[] unitDirections, double unit_tolerance, double fMinDist, double bracketA, double functionA, double bracketB, double functionB, double bracketC, double functionC)`
`private double`	`mutualInformation(TransMatrix tMatrix)`	DOCUMENT ME!
`private double`	`mutualInformation(TransMatrixd tMatrix)`	DOCUMENT ME!
`private double`	`mutualInformationSmoothed(TransMatrix tMatrix)`	DOCUMENT ME!
`private double`	`mutualInformationSmoothed(TransMatrixd tMatrix)`	DOCUMENT ME!
`private double`	`normalizedMutualInformation(TransMatrix tMatrix)`	DOCUMENT ME!
`private double`	`normalizedMutualInformation(TransMatrixd tMatrix)`	DOCUMENT ME!
`private double`	`normalizedMutualInformationSmoothed(TransMatrix tMatrix)`	DOCUMENT ME!
`private double`	`normalizedMutualInformationSmoothed(TransMatrixd tMatrix)`	DOCUMENT ME!
`private double`	`normalizedMutualInformationSmoothedWgt(TransMatrix tMatrix)`	DOCUMENT ME!
`private double`	`normalizedMutualInformationSmoothedWgt(TransMatrixd tMatrix)`	DOCUMENT ME!
`private double`	`normalizedXCorrelation(TransMatrix tMatrix)`	Normalized cross-correlation cost function.
`private double`	`normalizedXCorrelation(TransMatrixd tMatrix)`	Normalized cross-correlation cost function.
`private double`	`normalizedXCorrelationSinc(TransMatrix tMatrix)`	Normalized cross-correlation cost function.
`private double`	`normalizedXCorrelationSinc(TransMatrixd tMatrix)`	Normalized cross-correlation cost function.
`private double`	`normalizedXCorrelationSmoothed(TransMatrix tMatrix)`	Normalized cross-correlation cost function.
`private double`	`normalizedXCorrelationSmoothed(TransMatrixd tMatrix)`	Normalized cross-correlation cost function.
`private double`	`normalizedXCorrelationSmoothedWgt(TransMatrix tMatrix)`	Normalized cross-correlation cost function with weighting.
`private double`	`normalizedXCorrelationSmoothedWgt(TransMatrixd tMatrix)`	Normalized cross-correlation cost function with weighting.
`void`	`setGPUCost(ImageRegistrationGPU kGPUCost)`
`void`	`setInputWgtImage(ModelSimpleImage inputWgtImg)`	Sets the input weight image.
`private void`	`setPLogP(int nBins)`	Precalculates information and allocates buffers used in the calculation of mutual information statistics.
`void`	`setRefWgtImage(ModelSimpleImage refWgtImg)`	Sets the reference weight image.
`private void`	`setupKernel()`	DOCUMENT ME!
`private static double`	`sinc(double x)`	DOCUMENT ME!

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

- Field Detail
  - CORRELATION_RATIO_SMOOTHED_WGT
```
public static final int CORRELATION_RATIO_SMOOTHED_WGT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - CORRELATION_RATIO_SMOOTHED
```
public static final int CORRELATION_RATIO_SMOOTHED
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - CORRELATION_RATIO
```
public static final int CORRELATION_RATIO
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - LEAST_SQUARES_SMOOTHED_WGT
```
public static final int LEAST_SQUARES_SMOOTHED_WGT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - LEAST_SQUARES_SMOOTHED
```
public static final int LEAST_SQUARES_SMOOTHED
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - LEAST_SQUARES
```
public static final int LEAST_SQUARES
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MUTUAL_INFORMATION_SMOOTHED_WGT
```
public static final int MUTUAL_INFORMATION_SMOOTHED_WGT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MUTUAL_INFORMATION_SMOOTHED
```
public static final int MUTUAL_INFORMATION_SMOOTHED
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MUTUAL_INFORMATION
```
public static final int MUTUAL_INFORMATION
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - NORMALIZED_MUTUAL_INFORMATION_SMOOTHED_WGT
```
public static final int NORMALIZED_MUTUAL_INFORMATION_SMOOTHED_WGT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - NORMALIZED_MUTUAL_INFORMATION_SMOOTHED
```
public static final int NORMALIZED_MUTUAL_INFORMATION_SMOOTHED
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - NORMALIZED_MUTUAL_INFORMATION
```
public static final int NORMALIZED_MUTUAL_INFORMATION
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - NORMALIZED_XCORRELATION_SMOOTHED_WGT
```
public static final int NORMALIZED_XCORRELATION_SMOOTHED_WGT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - NORMALIZED_XCORRELATION_SINC
```
public static final int NORMALIZED_XCORRELATION_SINC
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - NORMALIZED_XCORRELATION_SMOOTHED
```
public static final int NORMALIZED_XCORRELATION_SMOOTHED
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - NORMALIZED_XCORRELATION
```
public static final int NORMALIZED_XCORRELATION
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - LEAST_SQUARES_SMOOTHED_WGT_COLOR
```
public static final int LEAST_SQUARES_SMOOTHED_WGT_COLOR
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - LEAST_SQUARES_SMOOTHED_COLOR
```
public static final int LEAST_SQUARES_SMOOTHED_COLOR
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - LEAST_SQUARES_COLOR
```
public static final int LEAST_SQUARES_COLOR
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - NORMALIZED_MUTUAL_INFORMATION_GPU
```
public static final int NORMALIZED_MUTUAL_INFORMATION_GPU
```
    See Also:
    
    Constant Field Values
  - NORMALIZED_MUTUAL_INFORMATION_GPU_LM
```
public static final int NORMALIZED_MUTUAL_INFORMATION_GPU_LM
```
    See Also:
    
    Constant Field Values
  - costCalled
```
private int costCalled
```
    DOCUMENT ME!
  - costFunctID
```
private int costFunctID
```
    DOCUMENT ME!
  - inputImage
```
private ModelSimpleImage inputImage
```
    DOCUMENT ME!
  - inputWgtImage
```
private ModelSimpleImage inputWgtImage
```
    DOCUMENT ME!
  - nBins
```
private final int nBins
```
    DOCUMENT ME!
  - nVoxels
```
private int nVoxels
```
    DOCUMENT ME!
  - pLogP
```
private double[] pLogP
```
    DOCUMENT ME!
  - refImage
```
private ModelSimpleImage refImage
```
    DOCUMENT ME!
  - refSliceSize
```
private final int refSliceSize
```
    DOCUMENT ME!
  - refWgtImage
```
private ModelSimpleImage refWgtImage
```
    DOCUMENT ME!
  - sincKernel
```
private final double[] sincKernel
```
    DOCUMENT ME!
  - sincWidth
```
private final int sincWidth
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - sincx
```
private final double[] sincx
```
    DOCUMENT ME!
  - sincy
```
private final double[] sincy
```
    DOCUMENT ME!
  - sincz
```
private final double[] sincz
```
    DOCUMENT ME!
  - sliceSize
```
private final int sliceSize
```
    DOCUMENT ME!
  - smoothSize
```
private final float smoothSize
```
    DOCUMENT ME!
  - xDim
```
private final int xDim
```
    DOCUMENT ME!
  - xEnd
```
private int xEnd
```
    DOCUMENT ME!
  - xEnd2
```
private final double xEnd2
```
    DOCUMENT ME!
  - xStart
```
private int xStart
```
  - yDim
```
private final int yDim
```
    DOCUMENT ME!
  - yEnd
```
private int yEnd
```
    DOCUMENT ME!
  - yEnd2
```
private final double yEnd2
```
    DOCUMENT ME!
  - yStart
```
private int yStart
```
  - zDim
```
private final int zDim
```
    DOCUMENT ME!
  - zEnd
```
private int zEnd
```
    DOCUMENT ME!
  - zEnd2
```
private final double zEnd2
```
    DOCUMENT ME!
  - zStart
```
private int zStart
```
  - m_afJointHisto
```
private float[] m_afJointHisto
```
  - m_bPrint
```
private final boolean m_bPrint
```
    See Also:
    
    Constant Field Values
  - m_kGPUCost
```
private ImageRegistrationGPU m_kGPUCost
```
- Constructor Detail
  - AlgorithmCostFunctions
```
public AlgorithmCostFunctions(ModelSimpleImage rImage,
                              ModelSimpleImage iImage,
                              int functionID,
                              int nBins,
                              float smoothSize)
```
    Creates a new AlgorithmCostFunctions object.
    
    Parameters:
    
    rImage - DOCUMENT ME!
    
    iImage - DOCUMENT ME!
    
    functionID - DOCUMENT ME!
    
    nBins - DOCUMENT ME!
    
    smoothSize - DOCUMENT ME!
- Method Detail
  - getCostFunction
```
public int getCostFunction()
```
    Specified by:
    
    getCostFunction in interface AlgorithmOptimizeFunctionBase
  - cost
```
public double cost(double[] data)
```
    Not implemented in this class.
    
    Specified by:
    
    cost in interface AlgorithmOptimizeFunctionBase
    
    Parameters:
    
    data - Array of data.
    
    Returns:
    
    Double.MAX_VALUE
  - cost
```
public double cost(TransMatrix affMatrix)
```
    Calculates the cost (dependent on the selected cost function) based on the reference image and the input image.
    
    Specified by:
    
    cost in interface AlgorithmOptimizeFunctionBase
    
    Parameters:
    
    affMatrix - Transformation matrix to test cost of.
    
    Returns:
    
    Cost at a supplied transformation.
  - cost
```
public double cost(TransMatrixd affMatrix)
```
    Calculates the cost (dependent on the selected cost function) based on the reference image and the input image.
    
    Specified by:
    
    cost in interface AlgorithmOptimizeFunctionBase
    
    Parameters:
    
    affMatrix - Transformation matrix to test cost of.
    
    Returns:
    
    Cost at a supplied transformation.
  - disposeLocal
```
public void disposeLocal()
```
    Sets class global array variables to null and calls the garbage collector.
  - finalize
```
public void finalize()
              throws java.lang.Throwable
```
    Calls disposeLocal of this class to ensure this class nulls the references to global class variables so that memory will be recovered.
    
    Overrides:
    
    finalize in class java.lang.Object
    
    Throws:
    
    java.lang.Throwable - DOCUMENT ME!
  - setGPUCost
```
public void setGPUCost(ImageRegistrationGPU kGPUCost)
```
  - getCostCalled
```
public int getCostCalled()
```
    Accessor that returns how many times the cost function has been called.
    
    Returns:
    
    The number of times the cost function has been called.
  - isGPULineMin
```
public boolean isGPULineMin()
```
  - lineMin
```
public float[] lineMin(WildMagic.LibFoundation.Mathematics.Matrix4f kToOrigin,
                       WildMagic.LibFoundation.Mathematics.Matrix4f kFromOrigin,
                       float rigid,
                       float dim,
                       double[] startPoint,
                       double[] pt,
                       int ptLength,
                       double[] unitDirections,
                       double unit_tolerance,
                       double fMinDist,
                       double bracketA,
                       double functionA,
                       double bracketB,
                       double functionB,
                       double bracketC,
                       double functionC)
```
  - setInputWgtImage
```
public void setInputWgtImage(ModelSimpleImage inputWgtImg)
```
    Sets the input weight image. If the weight values are outside the range [0:1] then the weigthts will be remapped to be between 0:1.
    
    Parameters:
    
    inputWgtImg - the input weight image
  - setRefWgtImage
```
public void setRefWgtImage(ModelSimpleImage refWgtImg)
```
    Sets the reference weight image. If the weight values are outside the range [0:1] then the weigthts will be remapped to be between 0:1.
    
    Parameters:
    
    refWgtImg - the reference weight image
  - calcEntropy
```
private void calcEntropy(TransMatrix tMatrix,
                         double[] jointEntropy,
                         double[] margEntropyR,
                         double[] margEntropyI)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    jointEntropy - DOCUMENT ME!
    
    margEntropyR - DOCUMENT ME!
    
    margEntropyI - DOCUMENT ME!
  - calcEntropy
```
private void calcEntropy(TransMatrixd tMatrix,
                         double[] jointEntropy,
                         double[] margEntropyR,
                         double[] margEntropyI)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    jointEntropy - DOCUMENT ME!
    
    margEntropyR - DOCUMENT ME!
    
    margEntropyI - DOCUMENT ME!
  - calcEntropySmoothed
```
private void calcEntropySmoothed(TransMatrix tMatrix,
                                 double[] jointEntropy,
                                 double[] margEntropyR,
                                 double[] margEntropyI)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    jointEntropy - DOCUMENT ME!
    
    margEntropyR - DOCUMENT ME!
    
    margEntropyI - DOCUMENT ME!
  - calcEntropySmoothed
```
private void calcEntropySmoothed(TransMatrixd tMatrix,
                                 double[] jointEntropy,
                                 double[] margEntropyR,
                                 double[] margEntropyI)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    jointEntropy - DOCUMENT ME!
    
    margEntropyR - DOCUMENT ME!
    
    margEntropyI - DOCUMENT ME!
  - calcEntropySmoothedWgt
```
private void calcEntropySmoothedWgt(TransMatrix tMatrix,
                                    double[] jointEntropy,
                                    double[] margEntropyR,
                                    double[] margEntropyI)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    jointEntropy - DOCUMENT ME!
    
    margEntropyR - DOCUMENT ME!
    
    margEntropyI - DOCUMENT ME!
  - calcEntropySmoothedWgt
```
private void calcEntropySmoothedWgt(TransMatrixd tMatrix,
                                    double[] jointEntropy,
                                    double[] margEntropyR,
                                    double[] margEntropyI)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    jointEntropy - DOCUMENT ME!
    
    margEntropyR - DOCUMENT ME!
    
    margEntropyI - DOCUMENT ME!
  - correlationRatio
```
private double correlationRatio(TransMatrix tMatrix)
```
    Correlation ratio cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - correlationRatio
```
private double correlationRatio(TransMatrixd tMatrix)
```
    Correlation ratio cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - correlationRatioSmoothed
```
private double correlationRatioSmoothed(TransMatrix tMatrix)
```
    Correlation ratio cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - correlationRatioSmoothed
```
private double correlationRatioSmoothed(TransMatrixd tMatrix)
```
    Correlation ratio cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - correlationRatioSmoothedWgt
```
private double correlationRatioSmoothedWgt(TransMatrix tMatrix)
```
    Correlation ratio cost function using weighting functions to mask out areas that should not be included in the cost function calculations.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - correlationRatioSmoothedWgt
```
private double correlationRatioSmoothedWgt(TransMatrixd tMatrix)
```
    Correlation ratio cost function using weighting functions to mask out areas that should not be included in the cost function calculations.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - findRangeX
```
private void findRangeX(java.awt.Point minMaxPt,
                        double newPtX,
                        double newPtY,
                        double newPtZ,
                        double aT00,
                        double aT10,
                        double aT20,
                        double iT00,
                        double iT10,
                        double iT20)
```
    DOCUMENT ME!
    
    Parameters:
    
    minMaxPt - DOCUMENT ME!
  - getSinc
```
private double getSinc(float[] data,
                       double x,
                       double y,
                       double z)
```
    DOCUMENT ME!
    
    Parameters:
    
    data - DOCUMENT ME!
    
    x - DOCUMENT ME!
    
    y - DOCUMENT ME!
    
    z - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - hanning
```
private static final double hanning(double x,
                                    int w)
```
    DOCUMENT ME!
    
    Parameters:
    
    x - DOCUMENT ME!
    
    w - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - kernelVal
```
private double kernelVal(double x,
                         int w)
```
    DOCUMENT ME!
    
    Parameters:
    
    x - DOCUMENT ME!
    
    w - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquares
```
private double leastSquares(TransMatrix tMatrix)
```
    Least squares cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquares
```
private double leastSquares(TransMatrixd tMatrix)
```
    Least squares cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresColor
```
private double leastSquaresColor(TransMatrix tMatrix)
```
    Least squares cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresColor
```
private double leastSquaresColor(TransMatrixd tMatrix)
```
    Least squares cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresSmoothed
```
private double leastSquaresSmoothed(TransMatrix tMatrix)
```
    Least squares cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresSmoothed
```
private double leastSquaresSmoothed(TransMatrixd tMatrix)
```
    Least squares cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresSmoothedColor
```
private double leastSquaresSmoothedColor(TransMatrix tMatrix)
```
    Least squares cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresSmoothedColor
```
private double leastSquaresSmoothedColor(TransMatrixd tMatrix)
```
    Least squares cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresSmoothedWgt
```
private double leastSquaresSmoothedWgt(TransMatrix tMatrix)
```
    Least squares cost function with weighting.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresSmoothedWgt
```
private double leastSquaresSmoothedWgt(TransMatrixd tMatrix)
```
    Least squares cost function with weighting.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresSmoothedWgtColor
```
private double leastSquaresSmoothedWgtColor(TransMatrix tMatrix)
```
    Least squares cost function with weighting.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - leastSquaresSmoothedWgtColor
```
private double leastSquaresSmoothedWgtColor(TransMatrixd tMatrix)
```
    Least squares cost function with weighting.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - mutualInformation
```
private double mutualInformation(TransMatrix tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - mutualInformation
```
private double mutualInformation(TransMatrixd tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - mutualInformationSmoothed
```
private double mutualInformationSmoothed(TransMatrix tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - mutualInformationSmoothed
```
private double mutualInformationSmoothed(TransMatrixd tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedMutualInformation
```
private double normalizedMutualInformation(TransMatrix tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedMutualInformation
```
private double normalizedMutualInformation(TransMatrixd tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedMutualInformationSmoothed
```
private double normalizedMutualInformationSmoothed(TransMatrix tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedMutualInformationSmoothed
```
private double normalizedMutualInformationSmoothed(TransMatrixd tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedMutualInformationSmoothedWgt
```
private double normalizedMutualInformationSmoothedWgt(TransMatrix tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedMutualInformationSmoothedWgt
```
private double normalizedMutualInformationSmoothedWgt(TransMatrixd tMatrix)
```
    DOCUMENT ME!
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedXCorrelation
```
private double normalizedXCorrelation(TransMatrix tMatrix)
```
    Normalized cross-correlation cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedXCorrelation
```
private double normalizedXCorrelation(TransMatrixd tMatrix)
```
    Normalized cross-correlation cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedXCorrelationSinc
```
private double normalizedXCorrelationSinc(TransMatrix tMatrix)
```
    Normalized cross-correlation cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedXCorrelationSinc
```
private double normalizedXCorrelationSinc(TransMatrixd tMatrix)
```
    Normalized cross-correlation cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedXCorrelationSmoothed
```
private double normalizedXCorrelationSmoothed(TransMatrix tMatrix)
```
    Normalized cross-correlation cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedXCorrelationSmoothed
```
private double normalizedXCorrelationSmoothed(TransMatrixd tMatrix)
```
    Normalized cross-correlation cost function.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedXCorrelationSmoothedWgt
```
private double normalizedXCorrelationSmoothedWgt(TransMatrix tMatrix)
```
    Normalized cross-correlation cost function with weighting.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - normalizedXCorrelationSmoothedWgt
```
private double normalizedXCorrelationSmoothedWgt(TransMatrixd tMatrix)
```
    Normalized cross-correlation cost function with weighting.
    
    Parameters:
    
    tMatrix - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - setPLogP
```
private void setPLogP(int nBins)
```
    Precalculates information and allocates buffers used in the calculation of mutual information statistics.
    
    Parameters:
    
    nBins - the number of bins
  - setupKernel
```
private void setupKernel()
```
    DOCUMENT ME!
  - sinc
```
private static final double sinc(double x)
```
    DOCUMENT ME!
    
    Parameters:
    
    x - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!

Class AlgorithmCostFunctions

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

CORRELATION_RATIO_SMOOTHED_WGT

CORRELATION_RATIO_SMOOTHED

CORRELATION_RATIO

LEAST_SQUARES_SMOOTHED_WGT

LEAST_SQUARES_SMOOTHED

LEAST_SQUARES

MUTUAL_INFORMATION_SMOOTHED_WGT

MUTUAL_INFORMATION_SMOOTHED

MUTUAL_INFORMATION

NORMALIZED_MUTUAL_INFORMATION_SMOOTHED_WGT

NORMALIZED_MUTUAL_INFORMATION_SMOOTHED

NORMALIZED_MUTUAL_INFORMATION

NORMALIZED_XCORRELATION_SMOOTHED_WGT

NORMALIZED_XCORRELATION_SINC

NORMALIZED_XCORRELATION_SMOOTHED

NORMALIZED_XCORRELATION

LEAST_SQUARES_SMOOTHED_WGT_COLOR

LEAST_SQUARES_SMOOTHED_COLOR

LEAST_SQUARES_COLOR

NORMALIZED_MUTUAL_INFORMATION_GPU

NORMALIZED_MUTUAL_INFORMATION_GPU_LM

costCalled

costFunctID

inputImage

inputWgtImage

nBins

nVoxels

pLogP

refImage

refSliceSize

refWgtImage

sincKernel

sincWidth

sincx

sincy

sincz

sliceSize

smoothSize

xDim

xEnd

xEnd2

xStart

yDim

yEnd

yEnd2

yStart

zDim

zEnd

zEnd2

zStart

m_afJointHisto

m_bPrint

m_kGPUCost

Constructor Detail

AlgorithmCostFunctions

Method Detail

getCostFunction

cost

cost

cost

disposeLocal

finalize

setGPUCost

getCostCalled

isGPULineMin

lineMin

setInputWgtImage

setRefWgtImage

calcEntropy

calcEntropy

calcEntropySmoothed

calcEntropySmoothed

calcEntropySmoothedWgt

calcEntropySmoothedWgt