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

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	DSC_MRI_toolbox.diffGaussians
(package private) class	DSC_MRI_toolbox.gauss1Fitting
(package private) class	DSC_MRI_toolbox.gauss1FittingCostFunction
(package private) class	DSC_MRI_toolbox.gauss2Fitting
(package private) class	DSC_MRI_toolbox.gauss2FittingCostFunction
(package private) class	DSC_MRI_toolbox.gaussSecondStandardDeviationFittingCostFunction
(package private) class	DSC_MRI_toolbox.gaussStandardDeviationFitting
(package private) class	DSC_MRI_toolbox.gaussStandardDeviationFittingCostFunction
(package private) class	DSC_MRI_toolbox.GVFitting
(package private) class	DSC_MRI_toolbox.GVFittingCostFunction
(package private) class	DSC_MRI_toolbox.GVRecirculation
(package private) class	DSC_MRI_toolbox.GVRecirculationCostFunction

Nested classes/interfaces inherited from class gov.nih.mipav.model.algorithms.CeresSolver

CeresSolver.ArctanLoss, CeresSolver.ArmijoLineSearch, CeresSolver.AutoDiffCostFunction<CostFunctor>, CeresSolver.BadTestTerm, CeresSolver.BFGS, CeresSolver.Block, CeresSolver.BlockEvaluatePreparer, CeresSolver.BlockJacobianWriter, CeresSolver.BlockJacobiPreconditioner, CeresSolver.BlockRandomAccessDenseMatrix, CeresSolver.BlockRandomAccessDiagonalMatrix, CeresSolver.BlockRandomAccessMatrix, CeresSolver.BlockSparseMatrix, CeresSolver.BlockSparseMatrixRandomMatrixOptions, CeresSolver.CallbackReturnType, CeresSolver.CallStatistics, CeresSolver.CauchyLoss, CeresSolver.Cell, CeresSolver.CellInfo, CeresSolver.CellLessThan, CeresSolver.CgnrLinearOperator, CeresSolver.CgnrSolver, CeresSolver.Chunk, CeresSolver.ComposedLoss, CeresSolver.CompressedList, CeresSolver.CompressedRowBlockStructure, CeresSolver.CompressedRowJacobianWriter, CeresSolver.CompressedRowSparseMatrix, CeresSolver.ConjugateGradientsSolver, CeresSolver.Context, CeresSolver.CoordinateDescentMinimizer, CeresSolver.Corrector, CeresSolver.CostFunction, CeresSolver.CostFunctorExample, CeresSolver.CovarianceAlgorithmType, CeresSolver.CRSMatrix, CeresSolver.CurveFittingFunctorExample, CeresSolver.DenseJacobianWriter, CeresSolver.DenseLinearAlgebraLibraryType, CeresSolver.DenseNormalCholeskySolver, CeresSolver.DenseQRSolver, CeresSolver.DenseSchurComplementSolver, CeresSolver.DenseSparseMatrix, CeresSolver.DoglegStrategy, CeresSolver.DoglegType, CeresSolver.DumpFormatType, CeresSolver.DynamicCompressedRowJacobianFinalizer, CeresSolver.DynamicCompressedRowJacobianWriter, CeresSolver.DynamicCostFunction, CeresSolver.DynamicNumericDiffCostFunction<T>, CeresSolver.EasyCostFunction, CeresSolver.EasyFunctor, CeresSolver.EigenQuaternionParameterization, CeresSolver.EvaluateOptions, CeresSolver.EvaluateScratch, CeresSolver.EvaluationCallback, CeresSolver.Evaluator, CeresSolver.EvaluatorOptions, CeresSolver.EventLogger, CeresSolver.ExecutionSummary, CeresSolver.ExponentialCostFunction, CeresSolver.ExponentialFunctor, CeresSolver.FirstOrderFunction, CeresSolver.FunctionSample, CeresSolver.GoodTestTerm, CeresSolver.GradientChecker, CeresSolver.GradientCheckingCostFunction, CeresSolver.GradientCheckingIterationCallback, CeresSolver.GradientProblem, CeresSolver.GradientProblemEvaluator, CeresSolver.GradientProblemSolver, CeresSolver.GradientProblemSolverOptions, CeresSolver.GradientProblemSolverStateUpdatingCallback, CeresSolver.GradientProblemSolverSummary, CeresSolver.Graph<Vertex>, CeresSolver.HomogeneousVectorParameterization, CeresSolver.HuberLoss, CeresSolver.IdentityParameterization, CeresSolver.ImplicitSchurComplement, CeresSolver.indexValueItem<Vertex>, CeresSolver.IterationCallback, CeresSolver.IterationSummary, CeresSolver.IterativeSchurComplementSolver, CeresSolver.LBFGS, CeresSolver.LevenbergMarquardtStrategy, CeresSolver.LinearCostFunction, CeresSolver.LinearLeastSquaresProblem, CeresSolver.LinearOperator, CeresSolver.LinearSolver, CeresSolver.LinearSolverOptions, CeresSolver.LinearSolverPerSolveOptions, CeresSolver.LinearSolverSummary, CeresSolver.LinearSolverTerminationType, CeresSolver.LinearSolverType, CeresSolver.LineSearch, CeresSolver.LineSearchDirection, CeresSolver.LineSearchDirectionOptions, CeresSolver.LineSearchDirectionType, CeresSolver.LineSearchFunction, CeresSolver.LineSearchInterpolationType, CeresSolver.LineSearchMinimizer, CeresSolver.LineSearchOptions, CeresSolver.LineSearchPreprocessor, CeresSolver.LineSearchSummary, CeresSolver.LineSearchType, CeresSolver.LocalParameterization, CeresSolver.LoggingCallback, CeresSolver.LoggingType, CeresSolver.LossFunction, CeresSolver.LossFunctionWrapper, CeresSolver.LowRankInverseHessian, CeresSolver.Minimizer, CeresSolver.MinimizerOptions, CeresSolver.MinimizerType, CeresSolver.MyCostFunctor, CeresSolver.MyThreeParameterCostFunctor, CeresSolver.NonlinearConjugateGradient, CeresSolver.NonlinearConjugateGradientType, CeresSolver.NormalPrior, CeresSolver.NullJacobianFinalizer, CeresSolver.NumericDiffCostFunction<CostFunctor>, CeresSolver.NumericDiffMethodType, CeresSolver.NumericDiffOptions, CeresSolver.OnlyFillsOneOutputFunctor, CeresSolver.OrderedGroups<T>, CeresSolver.Ownership, CeresSolver.Pair<T,U>, CeresSolver.ParameterBlock, CeresSolver.PartitionedMatrixView, CeresSolver.Preconditioner, CeresSolver.PreconditionerOptions, CeresSolver.PreconditionerType, CeresSolver.PreprocessedProblem, CeresSolver.Preprocessor, CeresSolver.ProbeResults, CeresSolver.ProblemImpl, CeresSolver.ProblemOptions, CeresSolver.ProductParameterization, CeresSolver.Program, CeresSolver.ProgramEvaluator<EvaluatePreparer,JacobianWriter,JacobianFinalizer>, CeresSolver.QuaternionParameterization, CeresSolver.RandomizedCostFunction, CeresSolver.RandomizedFunctor, CeresSolver.ResidualBlock, CeresSolver.ScaledLoss, CeresSolver.SchurComplementSolver, CeresSolver.SchurEliminator, CeresSolver.SchurEliminatorBase, CeresSolver.SchurJacobiPreconditioner, CeresSolver.ScopedExecutionTimer, CeresSolver.ScratchEvaluatePreparer, CeresSolver.SizedCostFunction, CeresSolver.SizeTestingCostFunction, CeresSolver.SoftLOneLoss, CeresSolver.Solver, CeresSolver.SolverOptions, CeresSolver.SolverSummary, CeresSolver.SparseLinearAlgebraLibraryType, CeresSolver.SparseMatrix, CeresSolver.SparseMatrixPreconditionerWrapper, CeresSolver.StateUpdatingCallback, CeresSolver.SteepestDescent, CeresSolver.SubsetParameterization, CeresSolver.TerminationType, CeresSolver.TestTerm, CeresSolver.TolerantLoss, CeresSolver.TranscendentalCostFunction, CeresSolver.TranscendentalFunctor, CeresSolver.TripletSparseMatrix, CeresSolver.TripletSparseMatrixRandomMatrixOptions, CeresSolver.TrivialLoss, CeresSolver.TrustRegionMinimizer, CeresSolver.TrustRegionPreprocessor, CeresSolver.TrustRegionStepEvaluator, CeresSolver.TrustRegionStrategy, CeresSolver.TrustRegionStrategyOptions, CeresSolver.TrustRegionStrategyPerSolveOptions, CeresSolver.TrustRegionStrategySummary, CeresSolver.TrustRegionStrategyType, CeresSolver.TukeyLoss, CeresSolver.TypedLinearSolver<MatrixType>, CeresSolver.TypedPreconditioner<MatrixType>, CeresSolver.VertexDegreeLessThan<Vertex>, CeresSolver.VertexTotalOrdering<Vertex>, CeresSolver.VisibilityClusteringType, CeresSolver.WeightedGraph<Vertex>, CeresSolver.WolfeLineSearch

Field Summary

Fields

Modifier and Type	Field	Description
(package private) double	A_init
(package private) double[]	AIF_conc
private double	aif_diffPeak
private int	aif_enable
(package private) double[]	AIF_fit_cv_est_parGV
(package private) double[]	AIF_fit_gv
(package private) double[]	AIF_fit_parameters
(package private) double[]	AIF_fit_weights
private int	aif_nSlice
private int	aif_nVoxelMax
private int	aif_nVoxelMin
private double	aif_pArea
private double	aif_pReg
private double	aif_pTTP
private int	aif_recirculation
(package private) byte[][]	AIF_ROI
(package private) double[]	AIF_ROI_x
(package private) double[]	AIF_ROI_y
private double	aif_semiMajorAxis
private double	aif_semiMinorAxis
(package private) int[][]	AIF_voxels
private double[][][]	AIFslice
(package private) double	alpha_init
(package private) double	beta_init
(package private) int[]	bolus
(package private) double	c1
(package private) double	c2
(package private) double[][][]	cbf_csvd
(package private) double[][][][]	cbf_csvd_residual
(package private) double[][][]	cbf_osvd
(package private) double[][][]	cbf_osvd_OI
(package private) double[][][][]	cbf_osvd_residual
(package private) double[][][]	cbf_svd
(package private) double[][][][]	cbf_svd_residual
(package private) double[][][]	cbv
(package private) double[][][]	cbv_lc
private double[][][][]	conc
(package private) double[]	cv_est_parGV_peak1
(package private) double[]	cv_est_parGV_peak2
(package private) double[]	data_peak1
(package private) double[]	dati_peak2
private int	deconv_cSVD_residual
private double	deconv_cSVD_threshold
private java.lang.String[]	deconv_method
private double	deconv_oSVD_OIthres
private int	deconv_oSVD_residual
private int	deconv_SS_residual
private int	deconv_SVD_residual
private double	deconv_SVD_threshold
private int	display
(package private) boolean	doAIFTransfer
(package private) boolean	doCurveIntersect
private boolean	doSaveAllOutputs
(package private) boolean	equalTimeSpacing
(package private) boolean	errorInMaskRoutine
private int[]	extents2D
private int[]	extents3D
private int[]	extents4D
private FileIO	fileIO
(package private) double	firstGaussianAmplitude
(package private) double	firstGaussianMean
(package private) int	firstGaussianMeanBin
(package private) double	firstGaussianStandardDeviation
(package private) double[]	fitParameters_peak1
(package private) double[]	fitParameters_peak2
(package private) double[][][]	fwhm
(package private) boolean	gauss1FittingCheck
(package private) boolean	gauss2FittingCheck
private double[]	gauss2FittingData
private int	gauss2FittingObservations
(package private) boolean	gaussStandardDeviationCheck
(package private) boolean	GVFittingCheck
(package private) boolean	GVRecirculationCheck
private double[]	GxData
private double[]	GxxData
private java.lang.String	inputFileName
(package private) double[]	intensity
(package private) double	K_init
private int	length
private byte[][][]	mask_aif
private byte[][]	mask_aif_slice
private byte[][][]	mask_data
private int	mask_npixel
(package private) double	maxSum
(package private) double	minSum
(package private) double[][][]	mtt_csvd
(package private) double[][][]	mtt_osvd
(package private) double[][][]	mtt_svd
private int	nC
private int	nR
private int	nS
private int	nT
(package private) int	nTfine
private int	options_conc
private java.lang.String	outputFilePath
private java.lang.String	outputPrefix
private double	par_kh
private double	par_kvoi
private double	par_rho
(package private) double[]	probDouble
private double	qr_a
private double	qr_b
private int	qr_enable
private double	qr_r
(package private) boolean	readTestImage
(package private) float[]	resolutions3D
(package private) float[]	resolutions4D
private int	S0_nSamplesMax
private int	S0_nSamplesMin
private double	S0_thresh
(package private) double[][][]	S0map
private int	saveFileFormat
(package private) double	secondGaussianAmplitude
(package private) double	secondGaussianMean
(package private) int	secondGaussianMeanBin
(package private) double	secondGaussianStandardDeviation
private double[]	sigmas
private ModelImage	srcImage
(package private) double	t0_init
(package private) double	tao_init
(package private) double	td_init
private double	te
(package private) boolean	test2PerfectGaussians
(package private) double[]	tGrid
private double[]	time
(package private) double	Tmax
(package private) double	Tmin
private double	tr
(package private) double	TR
(package private) double	TRfine
(package private) short[][][]	ttp
private ViewUserInterface	UI
(package private) int[]	units3D
(package private) int[]	units4D
private int	volume
private double[][][][]	volumes
private int	waitbar
(package private) double[]	weights_peak1
(package private) double[]	weights_peak2
(package private) double[]	x_loc
(package private) double[]	x_out
(package private) double[]	y_loc
(package private) double[]	y_out

Fields inherited from class gov.nih.mipav.model.algorithms.CeresSolver

BAD_TEST_TERM_EXAMPLE, COST_FUNCTOR_EXAMPLE, CURVE_FITTING_EXAMPLE, curveFittingData, curveFittingObservations, default_relstep, DYNAMIC, EASY_COST_FUNCTION, EASY_FUNCTOR_EXAMPLE, epsilon, ERROR, EXPONENTIAL_COST_FUNCTION, EXPONENTIAL_FUNCTOR, FATAL, GOOD_TEST_TERM_EXAMPLE, INFO, LINEAR_COST_FUNCTION_EXAMPLE, m, MAX_LOG_LEVEL, MY_COST_FUNCTOR, MY_THREE_PARAMETER_COST_FUNCTOR, N0, ONLY_FILLS_ONE_OUTPUT_FUNCTOR, optionsValid, RANDOMIZED_COST_FUNCTION, RANDOMIZED_FUNCTOR, SIZE_TESTING_COST_FUNCTION, svd, TEST_TERM_EXAMPLE, testCase, testMode, TRANSCENDENTAL_COST_FUNCTION, TRANSCENDENTAL_FUNCTOR, WARNING

Constructor Summary

Constructors

Constructor	Description
DSC_MRI_toolbox()
DSC_MRI_toolbox(double[][][][] volumes, double te, double tr, int aif_nSlice, java.lang.String outputFilePath)
DSC_MRI_toolbox(ModelImage srcImage, java.lang.String outputFilePath, double te, double tr, int aif_nSlice, java.lang.String[] deconv_method)

Method Summary

Modifier and Type	Method	Description
private void	backupSecondGaussianRoutine()
private double[][]	calculateREG(byte[][] mask)
byte[]	calcZeroX(double[] buffer)
private void	clusterHierarchical(double[][] dati, int nCluster, double[][] centroidi)
private void	convolve(double[] imageBuffer, double[] kernelBuffer, double[] resultBuffer)	Perform one-dimension convolution.
private double[]	cumtrapz(double[] f)
void	curveIntersect(double[] x, double[] param)
void	curveintersect_local(double[] x1, double[] y1, double[] x2, double[] y2)
void	DSC_mri_aif()
void	DSC_mri_cbf()
void	DSC_mri_cbv()
void	DSC_mri_cbv_lc()
void	DSC_mri_conc()
void	DSC_mri_core()
void	DSC_mri_cSVD()
void	DSC_mri_fwhm()
void	DSC_mri_mask()
void	DSC_mri_mtt()
void	DSC_mri_oSVD()
void	DSC_mri_S0()
int	DSC_mri_slice_selection_figure()
void	DSC_mri_SVD()
void	DSC_mri_ttp()
byte[]	edgeDetect(double[] secondDerivBuffer)
void	extractAIF()
private void	fitGV_peak1(double[] dati, double[] orgWeights)
private void	fitGV_peak2(double[] dati, double[] weights)
boolean	fitToExternalFunction(double[] x, double[] residuals, double[][] jacobian)
(package private) double	fwhm(double[] x, double[] yorg)
int[][]	getAIF_voxels()
private double[]	GVfunction(double[] p)
private double[]	GVfunction_peak1(double[] p)
private double[]	GVfunction_recirculation(double[] p)
double[]	interp1(double[] x, double[] y, double[] x_loc)
private void	makeGxKernels1D()
private void	makeGxxKernels1D()	Creates Gaussian derivative kernels.
void	mminvinterp(double[] x, double[] y, double yo)
void	runAlgorithm()
private java.io.File	saveImageFile(ModelImage img, java.lang.String dir, java.lang.String fileBasename, int fileType)
private java.io.File	saveImageFile(ModelImage img, java.lang.String dir, java.lang.String fileBasename, int fileType, boolean alwaysSave)
private double	trapz(double[] f)
private double[][]	trapz(double[][][] f)
private double[][]	vol2mat(double[][][][] data, byte[][][] selected)

Methods inherited from class gov.nih.mipav.model.algorithms.CeresSolver

AppendArrayToString, ApplyOrdering, BuildResidualLayout, ComputeHouseholderVector, ComputeRecursiveIndependentSetOrdering, ComputeSchurOrdering, ComputeStableSchurOrdering, copyFunctionSample, Create, Create, Create, Create, Create, Create, Create, CreateDiagonalMatrix, CreateEvaluatorScratch, CreateGradientCheckingCostFunction, CreateGradientCheckingProblemImpl, CreateHessianGraph, CreateLinearLeastSquaresProblemFromId, CreateOrdering, createPartitionedMatrixView, CreatePreprocessor, CreateRandomMatrix, CreateRandomMatrix, createSchurEliminatorBase, CreateSparseDiagonalMatrix, DetectStructure, DifferentiatePolynomial, DumpLinearLeastSquaresProblem, DumpLinearLeastSquaresProblemToConsole, DumpLinearLeastSquaresProblemToTextFile, EigenQuaternionProduct, EvaluateCostFunction, EvaluateJacobianColumn, EvaluateJacobianForParameterBlock, EvaluateJacobianForParameterBlock, EvaluatePolynomial, EvaluateRiddersJacobianColumn, ExpectClose, FindInterpolatingPolynomial, FindInvalidValue, FindLinearPolynomialRoots, FindPolynomialRoots, FindQuadraticPolynomialRoots, FindWithDefault, FindWithDefault, GetBestSchurTemplateSpecialization, GradientProblemSolverOptionsToSolverOptions, IndependentSetOrdering, InvalidateArray, InvalidateArray, InvalidateArray, InvalidateArray, InvertPSDMatrix, IsArrayValid, IsArrayValid, IsArrayValid, IsArrayValid, IsClose, IsOrderingValid, IsSchurType, IsSolutionUsable, IsSolutionUsable, LexicographicallyOrderResidualBlocks, LinearLeastSquaresProblem0, LinearLeastSquaresProblem1, LinearLeastSquaresProblem2, LinearLeastSquaresProblem3, LinearLeastSquaresProblem4, LinearSolverForZeroEBlocks, LinearSolverTypeToString, LineSearchDirectionTypeToString, LineSearchInterpolationTypeToString, LineSearchTypeToString, MatrixMatrixMultiply, MatrixMatrixMultiply, MatrixMatrixMultiply, MatrixMatrixMultiply, MatrixTransposeMatrixMultiply, MatrixTransposeVectorMultiply, MatrixVectorMultiply, MaybeReorderSchurComplementColumnsUsingEigen, MaybeReorderSchurComplementColumnsUsingSuiteSparse, Minimize, MinimizeInterpolatingPolynomial, MinimizePolynomial, MinParameterBlock, NonlinearConjugateGradientTypeToString, operator, PostSolveSummarize, PreconditionerForZeroEBlocks, PreconditionerTypeToString, QuaternionProduct, RandDouble, RandDouble, RandNormal, RemoveLeadingZeros, ReorderProgramForSchurTypeLinearSolver, RunCallbacks, SchurStructureToString, SetSummaryFinalCost, SetSummaryFinalCost, SetupCommonMinimizerOptions, Solve, Solve, StableIndependentSetOrdering, SummarizeReducedProgram, swap, TerminationTypeToString, TransposeForCompressedRowSparseStructure, Uniform, WriteArrayToFileOrDie, WriteStringToFileOrDie

Methods inherited from class java.lang.Object

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

Field Detail

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 java.lang.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 java.lang.String outputFilePath

inputFileName

private java.lang.String inputFileName

outputPrefix

private java.lang.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

Constructor Detail

DSC_MRI_toolbox

public DSC_MRI_toolbox()

DSC_MRI_toolbox

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

DSC_MRI_toolbox

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

Method Detail

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 java.io.File saveImageFile(ModelImage img,
                                   java.lang.String dir,
                                   java.lang.String fileBasename,
                                   int fileType)

saveImageFile

private java.io.File saveImageFile(ModelImage img,
                                   java.lang.String dir,
                                   java.lang.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