Field Detail

• derivativeScale

  float derivativeScale

  Gaussian scale for derivative operations.

• do25D

  boolean do25D

  flag indicating 2.5D processing.

• gaussianScale

  float gaussianScale

  Gaussian scale for structure tensor smoothing.

• k

  double k

  diffusitivity denominator.

• k2

  double k2

  diffusitivity denominator squared.

• numIterations

  int numIterations

  The number of iterations.

• timeStep

  float timeStep

  The time parameter step size, called tau in the algorithm description In 2D for stability the time step should be

  • dxKernelX

    private float[] dxKernelX

    Kernels for the X derivative.

  • dxKernelY

    private float[] dxKernelY

    DOCUMENT ME!

  • dxKernelZ

    private float[] dxKernelZ

    DOCUMENT ME!

  • dyKernelX

    private float[] dyKernelX

    Kernels for the Y derivative.

  • dyKernelY

    private float[] dyKernelY

    DOCUMENT ME!

  • dyKernelZ

    private float[] dyKernelZ

    DOCUMENT ME!

  • dzKernelX

    private float[] dzKernelX

    Kernels for the Z derivative.

  • dzKernelY

    private float[] dzKernelY

    DOCUMENT ME!

  • dzKernelZ

    private float[] dzKernelZ

    DOCUMENT ME!

  • eigenSystemAlgo

    private WildMagic.LibFoundation.NumericalAnalysis.Eigenf eigenSystemAlgo

    Eigensystem solver.

  • entireImage

    private boolean entireImage

    Whether to process the entire image, or just the portion within the currently selected VOI.

  • intermediateBuffer

    private float[] intermediateBuffer

    Reference to intermediate buffer.

  • kRadius

    private int kRadius

    Width of the derivative buffer.

  • skernelX

    private float[] skernelX

    Kernels for the Smoothing kernel.

  • skernelY

    private float[] skernelY

    DOCUMENT ME!

  • skernelZ

    private float[] skernelZ

    DOCUMENT ME!

  • skRadius

    private int skRadius

    Width of the smoothing buffer.

  • xDim

    private int xDim

    image dimensions.

  • yDim

    private int yDim

    image dimensions.

  • zDim

    private int zDim

    image dimensions.

  • Constructor Detail

    • AlgorithmCoherenceEnhancingDiffusion

      public AlgorithmCoherenceEnhancingDiffusion​(ModelImage srcImg,
                                                  int numI,
                                                  float k,
                                                  float derivativeScale,
                                                  float gaussianScale,
                                                  boolean do25D,
                                                  boolean entireImage)

      Creates a new AlgorithmCoherenceEnhancingDiffusion object.

      Parameters:

      srcImg - Source image model

      numI - Number of iterations

      k - Diffusitivity denominator

      derivativeScale - Scale of the gaussian when taking derivatives

      gaussianScale - Scale of the gaussian for smoothing the structure tensor

      do25D - Flag indicating 2.5D processing

      entireImage - whether to filter the entire image or just the VOI region

    • AlgorithmCoherenceEnhancingDiffusion

      public AlgorithmCoherenceEnhancingDiffusion​(ModelImage destImg,
                                                  ModelImage srcImg,
                                                  int numI,
                                                  float k,
                                                  float derivativeScale,
                                                  float gaussianScale,
                                                  boolean do25D,
                                                  boolean entireImage)

      Creates a new AlgorithmCoherenceEnhancingDiffusion object.

      Parameters:

      destImg - Image model where result image is to stored

      srcImg - Source image model

      numI - Number of iterations

      k - Diffusitivity denominator

      derivativeScale - Scale of the gaussian when taking derivatives

      gaussianScale - Scale of the gaussian for smoothing the structure tensor

      do25D - Flag indicating 2.5D processing

      entireImage - whether to filter the entire image or just the VOI region

  • Method Detail

    • finalize

      public void finalize()

      Prepares this class for destruction.

      Overrides:

      finalize in class AlgorithmBase

    • runAlgorithm

      public void runAlgorithm()

      Starts the program.

      Specified by:

      runAlgorithm in class AlgorithmBase

    • max

      private static float max​(float a,
                               float b)

      Computes the maximum of two floating point numbers passed in.

      Parameters:

      a - float The first value

      b - float The second value

      Returns:

      float The maximum of values a and b

    • computeDx

      private void computeDx​(float[] dx,
                             float[] src)

      DOCUMENT ME!

      Parameters:

      dx - float [] destination buffer

      src - float [] source buffer

      Member function computes the derivative of the source buffer in the X-direction using the kernel formulation as specified in the MATLAB paper. The function uses seperable convolution, which means it first does a 1D convolution with the derivative of a Gaussian kernel in the X-direction and stores the result in an intermediate buffer. Once the intermediate buffer is completely filled, a smoothing in the Y-direction is performed using a 1D Gaussian kernel computed as in the MATLAB paper.

    • computeDx3D

      private void computeDx3D​(float[] dx,
                               float[] src)

      DOCUMENT ME!

      Parameters:

      dx - float [] destination buffer

      src - float [] source buffer

      Member function computes the derivative of the source buffer in the X-direction using the kernel formulation as specified in the MATLAB paper. The function uses seperable convolution, which means it first does a 1D convolution with the derivative of a Gaussian kernel in the X-direction and stores the result in dx buffer. Once dx is completely filled, a smoothing in the Y-direction is performed using a 1D Gaussian kernel and the intermediate result is stored in intermediateBuffer. Once intermediateBuffer is completely filled, a smoothing in the Z-direction is performed and the final result is placed in dx.

    • computeDy

      private void computeDy​(float[] dy,
                             float[] src)

      DOCUMENT ME!

      Parameters:

      dy - float [] destination buffer

      src - float [] source buffer

      Member function computes the derivative of the source buffer in the Y-direction using the kernel formulation as specified in the MATLAB paper. The function uses seperable convolution, which means it first does a 1D convolution with a Gaussian kernel in the X-direction and stores the result in an intermediate buffer. Once the intermediate buffer is completely filled, a 1D convolution in the Y-direction is performed using a 1D Gaussian derivative kernel computed as in the MATLAB paper.

    • computeDy3D

      private void computeDy3D​(float[] dy,
                               float[] src)

      DOCUMENT ME!

      Parameters:

      dy - float [] destination buffer

      src - float [] source buffer

      Member function computes the derivative of the source buffer in the Y-direction using the kernel formulation as specified in the MATLAB paper. The function uses seperable convolution, which means it first does a 1D smoothing convolution with a Gaussian kernel in the X-direction and stores the result in dy buffer. Once dy is completely filled, a convolution in the Y-direction is performed using the derivative of a 1D Gaussian kernel and the intermediate result is stored in intermediateBuffer. Once intermediateBuffer is completely filled, a smoothing in the Z-direction is performed and the final result is placed in dy.

    • computeDz

      private void computeDz​(float[] dz,
                             float[] src)

      DOCUMENT ME!

      Parameters:

      dz - float [] destination buffer

      src - float [] source buffer

      Member function computes the derivative of the source buffer in the Z-direction using the kernel formulation as specified in the MATLAB paper. The function uses seperable convolution, which means it first does a 1D convolution with a Gaussian kernel in the X-direction and stores the result in dz buffer. Once dz is completely filled, a smoothing in the Y-direction is performed using a 1D Gaussian kernel and the intermediate result is stored in intermediateBuffer. Once intermediateBuffer is completely filled, a convolution with the derivative of a Gaussian kernel in the Z-direction is performed and the final result is placed in dz.

    • gaussianSmooth

      private void gaussianSmooth​(float[] gs,
                                  float[] src)

      DOCUMENT ME!

      Parameters:

      gs - float [] destination buffer

      src - float [] source buffer

      Member function gaussian smoothes the source buffer in the x and y directions using the kernel formulation as specified in the MATLAB paper. The function uses seperable convolution, which means it first does a 1D convolution with a Gaussian kernel in the X-direction and stores the result in an intermediate buffer. Once the intermediate buffer is completely filled, a 1D convolution in the Y-direction is performed using a 1D Gaussian kernel.

    • gaussianSmooth3D

      private void gaussianSmooth3D​(float[] gs,
                                    float[] src)

      DOCUMENT ME!

      Parameters:

      gs - float [] destination buffer

      src - float [] source buffer

      Member function gaussian smoothes the source buffer in the x,y, and z directions using the kernel formulation as specified in the MATLAB paper. The function uses seperable convolution, which means it first does a 1D convolution with a Gaussian kernel in the X-direction and stores the result in gs. Once the gs buffer is completely filled, a 1D convolution in the Y-direction is performed using a 1D Gaussian kernel and the result is stored in intermediateBuffer. Once intermediateBuffer is completely filled, a 1D convolution in the Z-direction is performed using a 1D Gaussian kernel and the result is placed in gs.

    • getVal

      private float getVal​(float[] buffer,
                           int col,
                           int row)

      Returns the value in a 2D image buffer of the pixel at location row, col.

      Parameters:

      buffer - float[] The image buffer

      col - int Column index

      row - int Row index

      Returns:

      float The pixel value

    • getVal

      private float getVal​(float[] buffer,
                           int col,
                           int row,
                           int slice)

      Returns the value in a 3D image buffer of the pixel at location slice, row, col.

      Parameters:

      buffer - float[] The image buffer

      col - int Column index

      row - int Row index

      slice - int Slice index

      Returns:

      float The pixel value

    • init

      private void init()

      Initialize buffers and kernels.

    • run2D

      private void run2D​(int numImages)

      Starts the algorithm for 2D images.

      Parameters:

      numImages - int The number of 2D images

    • run2DC

      private void run2DC​(int numImages)

      Starts the algorithm for 2D images.

      Parameters:

      numImages - int The number of 2D images

    • run3D

      private void run3D()

      Starts the algorithm for 3D images.

    • run3DC

      private void run3DC()

      Starts the algorithm for 3D color images.

    • setVal

      private void setVal​(float val,
                          float[] buffer,
                          int col,
                          int row)

      Sets the value in a 2D image buffer at location row, col.

      Parameters:

      val - float The value to set the pixel to

      buffer - float[] 2D image buffer

      col - int Column index

      row - int Row index

    • setVal

      private void setVal​(float val,
                          float[] buffer,
                          int col,
                          int row,
                          int slice)

      Sets the value in a 3D image buffer at location row, col.

      Parameters:

      val - float The value to set the pixel to

      buffer - float[] 3D image buffer

      col - int Column index

      row - int Row index

      slice - int Slice index