java.lang.Object
- gov.nih.mipav.model.algorithms.AlgorithmCostFunctions2D

All Implemented Interfaces:

AlgorithmOptimizeFunctionBase
```
public class AlgorithmCostFunctions2D
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 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 double[]`	`pLogP`	DOCUMENT ME!
`private ModelSimpleImage`	`refImage`	DOCUMENT ME!
`private ModelSimpleImage`	`refWgtImage`	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`

Constructor Summary

Constructors
Constructor	Description
`AlgorithmCostFunctions2D(ModelSimpleImage rImage, ModelSimpleImage iImage, int functionID, int nBins, float smoothSize)`
`AlgorithmCostFunctions2D(ModelSimpleImage rImage, ModelSimpleImage iImage, int functionID, int nBins, float smoothSize, boolean calcMinMax)`	Creates a new AlgorithmCostFunctions2D object.

Method Summary

All 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 aT00, double aT10, double iT00, double iT10)`	DOCUMENT ME!
`int`	`getCostCalled()`	Accessor that returns how many times the cost function has been called.
`int`	`getCostFunction()`
`boolean`	`isGPULineMin()`
`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`	`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.

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 int nBins
```
    DOCUMENT ME!
  - pLogP
```
private double[] pLogP
```
    DOCUMENT ME!
  - refImage
```
private ModelSimpleImage refImage
```
    DOCUMENT ME!
  - refWgtImage
```
private ModelSimpleImage refWgtImage
```
    DOCUMENT ME!
  - smoothSize
```
private float smoothSize
```
    DOCUMENT ME!
  - xDim
```
private int xDim
```
    DOCUMENT ME!
  - xStart
```
private int xStart
```
  - xEnd
```
private int xEnd
```
    DOCUMENT ME!
  - xEnd2
```
private double xEnd2
```
    DOCUMENT ME!
  - yDim
```
private int yDim
```
    DOCUMENT ME!
  - yStart
```
private int yStart
```
  - yEnd
```
private int yEnd
```
    DOCUMENT ME!
  - yEnd2
```
private double yEnd2
```
    DOCUMENT ME!
  - m_kGPUCost
```
private ImageRegistrationGPU m_kGPUCost
```
- Constructor Detail
  - AlgorithmCostFunctions2D
```
public AlgorithmCostFunctions2D(ModelSimpleImage rImage,
                                ModelSimpleImage iImage,
                                int functionID,
                                int nBins,
                                float smoothSize)
```
  - AlgorithmCostFunctions2D
```
public AlgorithmCostFunctions2D(ModelSimpleImage rImage,
                                ModelSimpleImage iImage,
                                int functionID,
                                int nBins,
                                float smoothSize,
                                boolean calcMinMax)
```
    Creates a new AlgorithmCostFunctions2D 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)
```
  - 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)
```
  - 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.
  - 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 aT00,
                        double aT10,
                        double iT00,
                        double iT10)
```
    DOCUMENT ME!
    
    Parameters:
    
    minMaxPt - 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!
  - 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

Class AlgorithmCostFunctions2D

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

pLogP

refImage

refWgtImage

smoothSize

xDim

xStart

xEnd

xEnd2

yDim

yStart

yEnd

yEnd2

m_kGPUCost

Constructor Detail

AlgorithmCostFunctions2D

AlgorithmCostFunctions2D

Method Detail

getCostFunction

cost

cost

cost

disposeLocal

finalize

setGPUCost

isGPULineMin

lineMin

getCostCalled

setInputWgtImage

setRefWgtImage

calcEntropy

calcEntropy

calcEntropySmoothed

calcEntropySmoothed

calcEntropySmoothedWgt

calcEntropySmoothedWgt

correlationRatio

correlationRatio

correlationRatioSmoothed

correlationRatioSmoothed

correlationRatioSmoothedWgt

correlationRatioSmoothedWgt

findRangeX

leastSquares

leastSquares

leastSquaresColor

leastSquaresColor

leastSquaresSmoothed

leastSquaresSmoothed