Package gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork

Class EstimateTensorLLMSE

  • public class EstimateTensorLLMSE
extends java.lang.Object

    • Field Summary

      Fields 
      Modifier and Type Field Description
      private static boolean detailedDebugging  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static float[][][][] estimate​(float[][][][] DWdata, double[] bvalues, double[][] grads, byte[][][] mask, boolean usePartialEstimates)
      estimate Use LLMSE to estimate tensors from DW imaging data on a voxel-wise basis.
      static ModelImage estimate​(ModelImage image, ModelImage maskImage, boolean usePartialEstimates)
      Uses LLMSE to estimate tensors from DW imaging data on a voxel-wise basis.
      static ModelImage estimate​(ModelImage dwiImage, ModelImage mask, WildMagic.LibFoundation.Mathematics.GMatrixd matrix, boolean usePartialEstimates)  
      static void estimateBallAndStickCamino​(float[][][][] DWdata, byte[][][] mask, inverters.BallStickInversion dtiFit, float[][][][] ballDiff, float[][][][] ballFrac, float[][][][] stickVec, float[][][][] exitcode, float[][][][] intensity)  
      private static void estimateCamino​(float[][][][] DWdata, byte[][][] mask, int dtiType, imaging.DW_Scheme scheme, inverters.DT_Inversion dtiFit, float[][][][] tensors, float[][][][] exitcode, float[][][][] intensity)  
      static ModelImage estimateCamino​(ModelImage image, ModelImage maskImage, int dtiType, boolean bSaveExitCode, boolean bDisplayExitCode, boolean bSaveIntensity, boolean bDisplayIntensity, java.lang.String kOutpuDir)
      Uses Camino algorithms to estimate tensors from DW imaging data on a voxel-wise basis.
      static void estimateCaminoRESTORE​(float[][][][] DWdata, byte[][][] mask, float[][][] noiseField, float[][][][] tensors, float[][][][] exitcode, float[][][][] intensity, imaging.DW_Scheme DTIscheme)  
      static void estimateCaminoThreeTensor​(float[][][][] DWdata, byte[][][] mask, inverters.ThreeTensorInversion dtiFit, float[][][][] mix1, float[][][][] tensors1, float[][][][] mix2, float[][][][] tensors2, float[][][][] mix3, float[][][][] tensors3, float[][][][] exitcode, float[][][][] intensity)  
      static void estimateCaminoTwoTensor​(float[][][][] DWdata, byte[][][] mask, inverters.TwoTensorInversion dtiFit, float[][][][] mix1, float[][][][] tensors1, float[][][][] mix2, float[][][][] tensors2, float[][][][] exitcode, float[][][][] intensity)  
      private static WildMagic.LibFoundation.Mathematics.GMatrixd getMatrix​(DTIParameters dtiparams)  
      static void main​(java.lang.String[] args)  
      private static ModelImage makeImage​(float[][][][] values, java.lang.String name)
      Creates and returns a ModelImage with the tensor data.
      private static ModelImage makeTensorImage​(float[][][][] tensors, float[][][][] exitCode, java.lang.String name)
      Creates and returns a ModelImage with the tensor data.
      static boolean test()  
      static boolean test​(int count)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • detailedDebugging

        private static boolean detailedDebugging

    • Constructor Detail

      • EstimateTensorLLMSE

        public EstimateTensorLLMSE()

    • Method Detail

      • estimate

        public static float[][][][] estimate​(float[][][][] DWdata,
                                     double[] bvalues,
                                     double[][] grads,
                                     byte[][][] mask,
                                     boolean usePartialEstimates)
        estimate Use LLMSE to estimate tensors from DW imaging data on a voxel-wise basis. Inputs: DWdata - 4D matrix indexed by [x][y][z][dw] where x,y,z are spatial location and dw is diffusion sensitization. bvalues - a list [dw] of b-values indicating the diffusion sensitization for each volume in the 4th dimension of the input data >0 for DW=yes (in s/mm2) =0 for reference images <0 for volumes to ignore grads - a set of unit vectors [dw][3] indicating the diffusion weighting for each of the input volumes. Vectors corresponding to reference or ignored volumes are ignored. mask - a boolean mask [x][y][z] indicating which voxels in the volume show be used for tensor estimation. If mask is null, then all voxels are processed. usePartialEstimates - boolean true - if any DW data are infinity, NaN, negative or zero (i.e., impossible values) then these data points will be ignored and a tensor will be computed with the remaining data (provided that at least 6 valid DW values and a reference value are available) false - any voxels with any missing DW data are ignored. Output: return value - set of tensors [x][y][z][6], where the tensor coefficients are ordered by upper triangular convention, i.e., xx,xy,xz,yy,yz,zz Units are in mm2/s. Notes: Voxels for which no tensors are computer are reported as all NaN. Last updated: 8/13/2008 Bennett Landman.

      • estimate

        public static ModelImage estimate​(ModelImage dwiImage,
                                  ModelImage mask,
                                  WildMagic.LibFoundation.Mathematics.GMatrixd matrix,
                                  boolean usePartialEstimates)

      • estimate

        public static ModelImage estimate​(ModelImage image,
                                  ModelImage maskImage,
                                  boolean usePartialEstimates)
        Uses LLMSE to estimate tensors from DW imaging data on a voxel-wise basis.
        Parameters:
        image - input DWI images series 4D
        maskImage - input mask image (or null) 3D
        usePartialEstimates - when true if any DW data are infinity, NaN, negative or zero (i.e., impossible values) then these data points will be ignored and a tensor will be computed with the remaining data (provided that at least 6 valid DW values and a reference value are available). When false - any voxels with any missing DW data are ignored.
        Returns:
        ModelImage with tensor data.

      • estimateBallAndStickCamino

        public static void estimateBallAndStickCamino​(float[][][][] DWdata,
                                              byte[][][] mask,
                                              inverters.BallStickInversion dtiFit,
                                              float[][][][] ballDiff,
                                              float[][][][] ballFrac,
                                              float[][][][] stickVec,
                                              float[][][][] exitcode,
                                              float[][][][] intensity)

      • estimateCamino

        private static void estimateCamino​(float[][][][] DWdata,
                                   byte[][][] mask,
                                   int dtiType,
                                   imaging.DW_Scheme scheme,
                                   inverters.DT_Inversion dtiFit,
                                   float[][][][] tensors,
                                   float[][][][] exitcode,
                                   float[][][][] intensity)

      • estimateCamino

        public static ModelImage estimateCamino​(ModelImage image,
                                        ModelImage maskImage,
                                        int dtiType,
                                        boolean bSaveExitCode,
                                        boolean bDisplayExitCode,
                                        boolean bSaveIntensity,
                                        boolean bDisplayIntensity,
                                        java.lang.String kOutpuDir)
        Uses Camino algorithms to estimate tensors from DW imaging data on a voxel-wise basis.
        Parameters:
        image - input DWI images series 4D
        maskImage - input mask image (or null) 3D
        dtiType - the type of estimation (Linear, Non-Linear, Restore, Weighted-Linear).

      • estimateCaminoRESTORE

        public static void estimateCaminoRESTORE​(float[][][][] DWdata,
                                         byte[][][] mask,
                                         float[][][] noiseField,
                                         float[][][][] tensors,
                                         float[][][][] exitcode,
                                         float[][][][] intensity,
                                         imaging.DW_Scheme DTIscheme)

      • estimateCaminoThreeTensor

        public static void estimateCaminoThreeTensor​(float[][][][] DWdata,
                                             byte[][][] mask,
                                             inverters.ThreeTensorInversion dtiFit,
                                             float[][][][] mix1,
                                             float[][][][] tensors1,
                                             float[][][][] mix2,
                                             float[][][][] tensors2,
                                             float[][][][] mix3,
                                             float[][][][] tensors3,
                                             float[][][][] exitcode,
                                             float[][][][] intensity)

      • estimateCaminoTwoTensor

        public static void estimateCaminoTwoTensor​(float[][][][] DWdata,
                                           byte[][][] mask,
                                           inverters.TwoTensorInversion dtiFit,
                                           float[][][][] mix1,
                                           float[][][][] tensors1,
                                           float[][][][] mix2,
                                           float[][][][] tensors2,
                                           float[][][][] exitcode,
                                           float[][][][] intensity)

      • main

        public static void main​(java.lang.String[] args)

      • test

        public static boolean test()

      • test

        public static boolean test​(int count)

      • makeTensorImage

        private static ModelImage makeTensorImage​(float[][][][] tensors,
                                          float[][][][] exitCode,
                                          java.lang.String name)
        Creates and returns a ModelImage with the tensor data.
        Parameters:
        tensors - tensor data
        name - name of the ModelImage
        Returns:
        new ModelImage.

      • makeImage

        private static ModelImage makeImage​(float[][][][] values,
                                    java.lang.String name)
        Creates and returns a ModelImage with the tensor data.
        Parameters:
        tensors - tensor data
        name - name of the ModelImage
        Returns:
        new ModelImage.

      • getMatrix

        private static WildMagic.LibFoundation.Mathematics.GMatrixd getMatrix​(DTIParameters dtiparams)