Package gov.nih.mipav.model.algorithms

Class DSC_MRI_toolbox

java.lang.Object
gov.nih.mipav.model.algorithms.CeresSolver
gov.nih.mipav.model.algorithms.DSC_MRI_toolbox
public class DSC_MRI_toolbox extends CeresSolver

  • Field Details

    • UI

      private ViewUserInterface UI

    • volumes

      private double[][][][] volumes

    • conc

      private double[][][][] conc

    • AIFslice

      private double[][][] AIFslice

    • srcImage

      private ModelImage srcImage

    • nC

      private int nC

    • nR

      private int nR

    • nS

      private int nS

    • nT

      private int nT

    • extents2D

      private int[] extents2D

    • extents3D

      private int[] extents3D

    • extents4D

      private int[] extents4D

    • resolutions3D

      float[] resolutions3D

    • units3D

      int[] units3D

    • resolutions4D

      float[] resolutions4D

    • units4D

      int[] units4D

    • length

      private int length

    • volume

      private int volume

    • time

      private double[] time

    • te

      private double te

    • tr

      private double tr

    • display

      private int display

    • waitbar

      private int waitbar

    • mask_npixel

      private int mask_npixel

    • options_conc

      private int options_conc

    • S0_nSamplesMin

      private int S0_nSamplesMin

    • S0_nSamplesMax

      private int S0_nSamplesMax

    • S0_thresh

      private double S0_thresh

    • aif_enable

      private int aif_enable

    • aif_recirculation

      private int aif_recirculation

    • aif_nSlice

      private int aif_nSlice

    • aif_semiMajorAxis

      private double aif_semiMajorAxis

    • aif_semiMinorAxis

      private double aif_semiMinorAxis

    • aif_pArea

      private double aif_pArea

    • aif_pTTP

      private double aif_pTTP

    • aif_pReg

      private double aif_pReg

    • aif_diffPeak

      private double aif_diffPeak

    • aif_nVoxelMax

      private int aif_nVoxelMax

    • aif_nVoxelMin

      private int aif_nVoxelMin

    • qr_enable

      private int qr_enable

    • qr_b

      private double qr_b

    • qr_a

      private double qr_a

    • qr_r

      private double qr_r

    • deconv_SVD_threshold

      private double deconv_SVD_threshold

    • deconv_SVD_residual

      private int deconv_SVD_residual

    • deconv_cSVD_threshold

      private double deconv_cSVD_threshold

    • deconv_cSVD_residual

      private int deconv_cSVD_residual

    • deconv_oSVD_OIthres

      private double deconv_oSVD_OIthres

    • deconv_oSVD_residual

      private int deconv_oSVD_residual

    • deconv_SS_residual

      private int deconv_SS_residual

    • deconv_method

      private String[] deconv_method

    • par_kh

      private double par_kh

    • par_rho

      private double par_rho

    • par_kvoi

      private double par_kvoi

    • mask_data

      private byte[][][] mask_data

    • mask_aif

      private byte[][][] mask_aif

    • mask_aif_slice

      private byte[][] mask_aif_slice

    • gauss2FittingObservations

      private int gauss2FittingObservations

    • gauss2FittingData

      private double[] gauss2FittingData

    • doCurveIntersect

      boolean doCurveIntersect

    • x_out

      double[] x_out

    • y_out

      double[] y_out

    • x_loc

      double[] x_loc

    • y_loc

      double[] y_loc

    • readTestImage

      boolean readTestImage

    • test2PerfectGaussians

      boolean test2PerfectGaussians

    • GxData

      private double[] GxData

    • GxxData

      private double[] GxxData

    • sigmas

      private double[] sigmas

    • firstGaussianMean

      double firstGaussianMean

    • firstGaussianMeanBin

      int firstGaussianMeanBin

    • firstGaussianAmplitude

      double firstGaussianAmplitude

    • firstGaussianStandardDeviation

      double firstGaussianStandardDeviation

    • c1

      double c1

    • secondGaussianMeanBin

      int secondGaussianMeanBin

    • secondGaussianAmplitude

      double secondGaussianAmplitude

    • secondGaussianStandardDeviation

      double secondGaussianStandardDeviation

    • secondGaussianMean

      double secondGaussianMean

    • c2

      double c2

    • minSum

      double minSum

    • maxSum

      double maxSum

    • outputFilePath

      private String outputFilePath

    • inputFileName

      private String inputFileName

    • outputPrefix

      private String outputPrefix

    • fileIO

      private FileIO fileIO

    • saveFileFormat

      private int saveFileFormat

    • doSaveAllOutputs

      private boolean doSaveAllOutputs

    • S0map

      double[][][] S0map

    • bolus

      int[] bolus

    • equalTimeSpacing

      boolean equalTimeSpacing

    • AIF_ROI

      byte[][] AIF_ROI

    • AIF_ROI_x

      double[] AIF_ROI_x

    • AIF_ROI_y

      double[] AIF_ROI_y

    • AIF_conc

      double[] AIF_conc

    • AIF_voxels

      int[][] AIF_voxels

    • data_peak1

      double[] data_peak1

    • weights_peak1

      double[] weights_peak1

    • fitParameters_peak1

      double[] fitParameters_peak1

    • cv_est_parGV_peak1

      double[] cv_est_parGV_peak1

    • TR

      double TR

    • Tmax

      double Tmax

    • Tmin

      double Tmin

    • TRfine

      double TRfine

    • nTfine

      int nTfine

    • tGrid

      double[] tGrid

    • dati_peak2

      double[] dati_peak2

    • weights_peak2

      double[] weights_peak2

    • fitParameters_peak2

      double[] fitParameters_peak2

    • cv_est_parGV_peak2

      double[] cv_est_parGV_peak2

    • AIF_fit_weights

      double[] AIF_fit_weights

    • AIF_fit_parameters

      double[] AIF_fit_parameters

    • AIF_fit_cv_est_parGV

      double[] AIF_fit_cv_est_parGV

    • AIF_fit_gv

      double[] AIF_fit_gv

    • t0_init

      double t0_init

    • alpha_init

      double alpha_init

    • beta_init

      double beta_init

    • A_init

      double A_init

    • td_init

      double td_init

    • K_init

      double K_init

    • tao_init

      double tao_init

    • gaussStandardDeviationCheck

      boolean gaussStandardDeviationCheck

    • gauss1FittingCheck

      boolean gauss1FittingCheck

    • gauss2FittingCheck

      boolean gauss2FittingCheck

    • GVFittingCheck

      boolean GVFittingCheck

    • GVRecirculationCheck

      boolean GVRecirculationCheck

    • doAIFTransfer

      boolean doAIFTransfer

    • errorInMaskRoutine

      boolean errorInMaskRoutine

    • intensity

      double[] intensity

    • probDouble

      double[] probDouble

    • cbv

      double[][][] cbv

    • cbv_lc

      double[][][] cbv_lc

    • cbf_svd

      double[][][] cbf_svd

    • cbf_svd_residual

      double[][][][] cbf_svd_residual

    • cbf_csvd

      double[][][] cbf_csvd

    • cbf_csvd_residual

      double[][][][] cbf_csvd_residual

    • cbf_osvd

      double[][][] cbf_osvd

    • cbf_osvd_OI

      double[][][] cbf_osvd_OI

    • cbf_osvd_residual

      double[][][][] cbf_osvd_residual

    • mtt_svd

      double[][][] mtt_svd

    • mtt_csvd

      double[][][] mtt_csvd

    • mtt_osvd

      double[][][] mtt_osvd

    • ttp

      short[][][] ttp

    • fwhm

      double[][][] fwhm

    • sliceAifFile

      File sliceAifFile

  • Constructor Details

    • DSC_MRI_toolbox

      public DSC_MRI_toolbox()

    • DSC_MRI_toolbox

      public DSC_MRI_toolbox(ModelImage srcImage, String outputFilePath, double te, double tr, int aif_nSlice, String[] deconv_method)

    • DSC_MRI_toolbox

      public DSC_MRI_toolbox(double[][][][] volumes, double te, double tr, int aif_nSlice, String outputFilePath)

  • Method Details

    • runAlgorithm

      public void runAlgorithm()

    • getAIF_voxels

      public int[][] getAIF_voxels()

    • DSC_mri_core

      public void DSC_mri_core()

    • DSC_mri_mask

      public void DSC_mri_mask()

    • backupSecondGaussianRoutine

      private void backupSecondGaussianRoutine()

    • DSC_mri_conc

      public void DSC_mri_conc()

    • DSC_mri_S0

      public void DSC_mri_S0()

    • DSC_mri_aif

      public void DSC_mri_aif()

    • DSC_mri_slice_selection_figure

      public int DSC_mri_slice_selection_figure()

    • extractAIF

      public void extractAIF()

    • DSC_mri_cbv

      public void DSC_mri_cbv()

    • DSC_mri_cbv_lc

      public void DSC_mri_cbv_lc()

    • DSC_mri_cbf

      public void DSC_mri_cbf()

    • DSC_mri_SVD

      public void DSC_mri_SVD()

    • DSC_mri_cSVD

      public void DSC_mri_cSVD()

    • DSC_mri_oSVD

      public void DSC_mri_oSVD()

    • DSC_mri_mtt

      public void DSC_mri_mtt()

    • DSC_mri_ttp

      public void DSC_mri_ttp()

    • DSC_mri_fwhm

      public void DSC_mri_fwhm()

    • fwhm

      double fwhm(double[] x, double[] yorg)

    • vol2mat

      private double[][] vol2mat(double[][][][] data, byte[][][] selected)

    • GVfunction

      private double[] GVfunction(double[] p)

    • fitGV_peak1

      private void fitGV_peak1(double[] dati, double[] orgWeights)

    • fitGV_peak2

      private void fitGV_peak2(double[] dati, double[] weights)

    • GVfunction_recirculation

      private double[] GVfunction_recirculation(double[] p)

    • GVfunction_peak1

      private double[] GVfunction_peak1(double[] p)

    • clusterHierarchical

      private void clusterHierarchical(double[][] dati, int nCluster, double[][] centroidi)

    • calculateREG

      private double[][] calculateREG(byte[][] mask)

    • cumtrapz

      private double[] cumtrapz(double[] f)

    • trapz

      private double trapz(double[] f)

    • trapz

      private double[][] trapz(double[][][] f)

    • saveImageFile

      private File saveImageFile(ModelImage img, String dir, String fileBasename, int fileType)

    • saveImageFile

      private File saveImageFile(ModelImage img, String dir, String fileBasename, int fileType, boolean alwaysSave)

    • calcZeroX

      public byte[] calcZeroX(double[] buffer)

    • edgeDetect

      public byte[] edgeDetect(double[] secondDerivBuffer)

    • makeGxxKernels1D

      private void makeGxxKernels1D()
      Creates Gaussian derivative kernels.

    • makeGxKernels1D

      private void makeGxKernels1D()

    • convolve

      private void convolve(double[] imageBuffer, double[] kernelBuffer, double[] resultBuffer)
      Perform one-dimension convolution.
      Parameters:
      imageBuffer -
      kernelBuffer -
      resultBuffer - Problem is huge border effects. Convolution uses kernels of length going from 9 to 801 on buffer of length 100.

    • curveIntersect

      public void curveIntersect(double[] x, double[] param)

    • curveintersect_local

      public void curveintersect_local(double[] x1, double[] y1, double[] x2, double[] y2)

    • mminvinterp

      public void mminvinterp(double[] x, double[] y, double yo)

    • interp1

      public double[] interp1(double[] x, double[] y, double[] x_loc)

    • fitToExternalFunction

      public boolean fitToExternalFunction(double[] x, double[] residuals, double[][] jacobian)
      Specified by:
      fitToExternalFunction in class CeresSolver

    • getSliceAifFile

      public File getSliceAifFile()