Package gov.nih.mipav.model.algorithms

Class AlgorithmCostFunctions2D

    • Field Detail

      • CORRELATION_RATIO_SMOOTHED_WGT

        public static final int CORRELATION_RATIO_SMOOTHED_WGT
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      • CORRELATION_RATIO_SMOOTHED

        public static final int CORRELATION_RATIO_SMOOTHED
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      • CORRELATION_RATIO

        public static final int CORRELATION_RATIO
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      • LEAST_SQUARES_SMOOTHED_WGT

        public static final int LEAST_SQUARES_SMOOTHED_WGT
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      • LEAST_SQUARES_SMOOTHED

        public static final int LEAST_SQUARES_SMOOTHED
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      • MUTUAL_INFORMATION_SMOOTHED_WGT

        public static final int MUTUAL_INFORMATION_SMOOTHED_WGT
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      • MUTUAL_INFORMATION_SMOOTHED

        public static final int MUTUAL_INFORMATION_SMOOTHED
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      • MUTUAL_INFORMATION

        public static final int MUTUAL_INFORMATION
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      • NORMALIZED_MUTUAL_INFORMATION_SMOOTHED_WGT

        public static final int NORMALIZED_MUTUAL_INFORMATION_SMOOTHED_WGT
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      • NORMALIZED_MUTUAL_INFORMATION_SMOOTHED

        public static final int NORMALIZED_MUTUAL_INFORMATION_SMOOTHED
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      • NORMALIZED_MUTUAL_INFORMATION

        public static final int NORMALIZED_MUTUAL_INFORMATION
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      • NORMALIZED_XCORRELATION_SMOOTHED_WGT

        public static final int NORMALIZED_XCORRELATION_SMOOTHED_WGT
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      • NORMALIZED_XCORRELATION_SINC

        public static final int NORMALIZED_XCORRELATION_SINC
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      • NORMALIZED_XCORRELATION_SMOOTHED

        public static final int NORMALIZED_XCORRELATION_SMOOTHED
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      • NORMALIZED_XCORRELATION

        public static final int NORMALIZED_XCORRELATION
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      • LEAST_SQUARES_SMOOTHED_WGT_COLOR

        public static final int LEAST_SQUARES_SMOOTHED_WGT_COLOR
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      • LEAST_SQUARES_SMOOTHED_COLOR

        public static final int LEAST_SQUARES_SMOOTHED_COLOR
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      • LEAST_SQUARES_COLOR

        public static final int LEAST_SQUARES_COLOR
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      • NORMALIZED_MUTUAL_INFORMATION_GPU

        public static final int NORMALIZED_MUTUAL_INFORMATION_GPU
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      • NORMALIZED_MUTUAL_INFORMATION_GPU_LM

        public static final int NORMALIZED_MUTUAL_INFORMATION_GPU_LM
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      • costCalled

        private int costCalled
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      • costFunctID

        private int costFunctID
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      • nBins

        private int nBins
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      • pLogP

        private double[] pLogP
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      • smoothSize

        private float smoothSize
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      • xDim

        private int xDim
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      • xStart

        private int xStart

      • xEnd

        private int xEnd
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      • xEnd2

        private double xEnd2
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      • yDim

        private int yDim
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      • yStart

        private int yStart

      • yEnd

        private int yEnd
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      • yEnd2

        private double yEnd2
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    • 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

      • 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!

      • 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)
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        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)
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        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)
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        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)
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        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