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G

GAMMA - Static variable in class imaging.DW_Scheme
Gyromagnetic ratio of protons in water, in units of s^{-1} T^{-1}.
gamma_beta - Static variable in class tools.CL_Initializer
scale parameter for gamma distribution
gamma_k - Static variable in class tools.CL_Initializer
shape parameter for gamma distributed random numbers
GammaDistribRadiiCylinders - Class in data.compartments
 
GammaDistribRadiiCylinders() - Constructor for class data.compartments.GammaDistribRadiiCylinders
constructor with nothing
GammaDistribRadiiCylinders(double, double, double, double, double, int) - Constructor for class data.compartments.GammaDistribRadiiCylinders
constructor with specified number of bins
GammaDistribRadiiCylinders(double, double, double, double, double) - Constructor for class data.compartments.GammaDistribRadiiCylinders
constructor with default number of bins
GammaFunctions - Class in numerics
Purpose: Contains implementation of the gamma function.
GammaFunctions() - Constructor for class numerics.GammaFunctions
 
GammaRandom - Class in numerics
generates gamma-distributed random numbers using a mersienne twister and a rejection-sampling technique
GammaRandom(long, double, double) - Constructor for class numerics.GammaRandom
constructor.
gammln(double) - Static method in class numerics.GammaFunctions
The gamma function.
gammp(double, double) - Static method in class numerics.ErrorFunction
Returns the (lower) incomplete gamma function P(a, x).
gammp(double, double) - Static method in class numerics.GammaFunctions
Returns the incomplete gamma function P(a; x).
GatherStats - Class in apps
 
GatherStats() - Constructor for class apps.GatherStats
 
GaussianMixture - Class in data
Purpose: Simple model for the diffusion displacement density function .
GaussianMixture(DT[], double[]) - Constructor for class data.GaussianMixture
Constructor initializes the array of diffusion tensors and mixing parameters as well as the diffusion time.
GDRCylinders - Class in models.compartments
 
GDRCylinders() - Constructor for class models.compartments.GDRCylinders
constructor with nothing
GDRCylinders(double, double, double, double, double, int) - Constructor for class models.compartments.GDRCylinders
constructor with specified number of bins
GDRCylinders(double, double, double, double, double) - Constructor for class models.compartments.GDRCylinders
constructor with default number of bins
GenerateDTLUT - Class in apps
Makes lookup tables for PICo from diffusion tensor data.
GenerateDTLUT(String[]) - Constructor for class apps.GenerateDTLUT
 
generateEV_LUT(double, double, double, int, ModelIndex, boolean, boolean, boolean) - Method in class tractography.OneTensorLUTGenerator
Generates the LUT.
generateFA_LUT(double, double, double, int, ModelIndex, boolean, boolean, boolean) - Method in class tractography.OneTensorLUTGenerator
Generates the LUT.
generateLUT(double, double, double, int, ModelIndex, boolean, boolean, boolean) - Method in class tractography.DT_LookupTableGenerator
Generates the LUT.
generateLUT(double, double, double, int, ModelIndex, boolean, boolean, boolean) - Method in class tractography.OneTensorLUTGenerator
Generates the LUT.
generateLUT(double, double, double, int, ModelIndex, boolean, boolean, boolean) - Method in class tractography.TwoTensorLUTGenerator
Generates the LUT.
GenerateMFR_LUT - Class in apps
Purpose: Generates a LUT that is indexed using the Hessian of the peaks of multi-fibre methods.
GenerateMFR_LUT() - Constructor for class apps.GenerateMFR_LUT
 
geoMean(double[]) - Static method in class tools.ArrayOps
Returns the geometric mean value in the array.
geoMeanZeroMeas(double[]) - Method in class imaging.DW_Scheme
Computes the geometric mean of the b=0 measurements.
get(int, int) - Method in class Jama.Matrix
Get a single element.
getAcceptanceRate() - Method in class optimizers.MarkovChainMonteCarlo
Returns the acceptance rate of the previous run, ie the fraction of updates that resulted in a new current set of parameters.
getAnatomicalOrientation(String) - Static method in enum imaging.MetaImageHeader.AnatomicalOrientation
 
getArgs(AnalyzeHeader, String) - Static method in class imaging.AnalyzeHeader
Get Camino program arguments for this header.
getArray() - Method in class Jama.Matrix
Access the internal two-dimensional array.
getArrayCopy() - Method in class Jama.Matrix
Copy the internal two-dimensional array.
getAutoUpdate() - Method in class apps.F_TestThresholdSelector
Returns status of auto update
getAxis() - Method in class simulation.geometry.elements.BasicCylinder
returns the axis vector of the cylinder
getB_Matrix() - Method in class imaging.DW_Scheme
The B-matrix B is defined as follows.
getB_Value(int) - Method in class imaging.B_VectorScheme
 
getB_Value(int) - Method in class imaging.DW_Scheme
Gets the b-value for measurement i.
getB_Value(int) - Method in class imaging.GradientWaveform_Scheme
calculates the b-factor of a general waveform using Price's framework (Price, 1997).
getB_Value(int) - Method in class imaging.RectGradSteTanScheme
Gets the b-value, assuming an "effective diffusion time" of (DELTA - delta / 3).
getB_Value(int) - Method in class imaging.RectGradTRSE_Scheme
 
getBallStickTractographyImage(String, String, double[][][], double, int[], double[]) - Static method in class tractography.BallStickTractographyImage
Gets an image from the data file.
getBasisSum(int) - Static method in class sphfunc.BasisSumFactory
Returns a linear basis sum of type basisType.
getBayesDiracTractographyImage(String, String, DW_Scheme, DataModel, int[][][], double[][][], double, int[], double[], int, Random) - Static method in class tractography.BayesDiracTractographyImage
Gets an image from the data file.
getBestSolution(double[][]) - Static method in class optimizers.MultiRunMinimizer
Returns the solution with minimum MSE from an array of multirun solutions
getBinghamDistribution(Vector3D[], double[], Random) - Static method in class numerics.BinghamDistribution
 
getBinghamDistribution(Vector3D[], double, double, Random) - Static method in class numerics.BinghamDistribution
 
getBinghamDistribution(EigenSystem3D) - Static method in class numerics.BinghamFitter
Get a Bingham distribution from a scatter matrix of samples.
getBinghamDistribution(EigenSystem3D, Random) - Static method in class numerics.BinghamFitter
Get a Bingham distribution from a scatter matrix of samples, and also specify the random number generator used by the distribution.
getBipolarConfidenceCone(EigenSystem3D, Vector3D[], double) - Static method in class numerics.WatsonFitter
Get the semi-vertical angle of the 100(1 - \alpha)% confidence cone around \mu.
getBitpix() - Method in class imaging.Nifti1Dataset
Get the bitpix field
getBorder() - Method in class simulation.dynamics.CylindricalSurfaceStepGenerator
 
getBorder() - Method in class simulation.dynamics.FixedLengthStepGenerator
tells the width of the cloning border.
getBorder() - Method in class simulation.dynamics.SpatiallyVaryingStepGenerator
 
getBorder() - Method in interface simulation.dynamics.StepGenerator
get the border width for cloning
getBottomLeft(int, int, int) - Method in class simulation.geometry.substrates.Substrate
calculates the spatial coordinates of the lower corner of the subvoxel with given integer indices.
getBoundingBox() - Method in class simulation.geometry.elements.BasicCylinder
 
getBoundingBox() - Method in class simulation.geometry.elements.FacetCylinder
TODO: not implement.
getBoundingBox() - Method in class simulation.geometry.elements.MyelinatedCylinder
returns the oriented bounding box for this object
getBoundingBox() - Method in interface simulation.geometry.elements.SubstrateObject
returns the oriented bounding box for the object.
getBoundingBox() - Method in class simulation.geometry.elements.Triangle
 
getBoundingBoxFromTriangles(Triangle[]) - Static method in class simulation.geometry.elements.BoundingBox
constructs and returns the optimal bounding box for an array of triangles.
getBS_TractographyImage(String[], String, DW_Scheme, ModelIndex[], int[][][], double[][][], double, int[], double[], Random) - Static method in class tractography.RepBS_DT_TractographyImage
Gets an image from the data file.
getBS_TractographyImage(String, String, DW_Scheme, int[][][], double[][][], double, int[], double[], Random) - Static method in class tractography.WildBS_DT_TractographyImage
Gets an image from the data file.
getCell(double[]) - Method in class simulation.geometry.substrates.CellularLattice
gets the cell coords from the spatia location
getCellOccupation(int[]) - Method in class simulation.geometry.substrates.CellularLattice
check if given cell is occupied on the lattice
getChiSq() - Method in class optimizers.MarquardtChiSqFitter
Returns the value of chi-squared.
getCholParams(double[]) - Static method in class numerics.TwoFibreACGFitter
Returns the elements of the Cholesky decomposition U of the matrices A and B.
getChunk(byte[]) - Static method in class apps.Shredder
Reads in the next chunk from the standard input into the array chunk and returns a boolean indicating the success of the operation.
getClassifiedModelIndices(String[]) - Static method in enum inverters.ModelIndex
Parses the model indices from string representation in either text or numeric form.
getCoeff(int, int) - Method in class sphfunc.EvenSHS
Returns a particular coefficient given the spherical harmonic order and index.
getColumnDimension() - Method in class Jama.Matrix
Get column dimension.
getColumnPackedCopy() - Method in class Jama.Matrix
Make a one-dimensional column packed copy of the internal array.
getCompartment(String) - Static method in class data.compartments.CompartmentFactory
 
getCompartment(String) - Static method in class models.compartments.CompartmentFactory
 
getCompartmentalSignals(boolean) - Method in class simulation.measurement.AgnosticScan
 
getCompartmentalSignals(boolean) - Method in interface simulation.measurement.SyntheticScan
gets the signals from the summations of the displacements in the walkers.
getCompartmentList(String) - Static method in enum fitters.FitModel
returns the compartments array used to initialise the compartment model for fitting from commandline string.
getCompartmentModelParams(String) - Static method in enum fitters.FitModel
returns dummy params array for the compartment model used in fitting.
getCompartmentnames() - Method in class data.compartments.CompartmentModel
 
getCompartmentnames() - Method in class models.compartments.CompartmentModel
 
getCompartmentType(String) - Static method in enum data.compartments.CompartmentType
returns the type enumeration based on the string handed over.
getCompartmentType(String) - Static method in enum models.compartments.CompartmentType
returns the type enumeration based on the string handed over.
getComponents() - Method in class misc.DT
Returns an array containing the components of the diffusion tensor.
getConnectingPaths(RegionOfInterest, RegionOfInterest) - Method in class tractography.FibreTracker
Finds Tract's that enter two specified regions.
getConnectionProbabilities() - Method in class tractography.ConnectionProbabilityImage
 
getConnectionProbabilities() - Method in class tractography.TargetCP_Image
Get the connection probabilities as an image, which are the streamline counts divided by the total number of streamlines.
getCONVERGETHRESH() - Static method in class optimizers.MarquardtMinimiser
 
getCONVERGETHRESH() - Method in class optimizers.MultiRunLM_Minimizer
Returns the convergence threshold in the LM algorithm.
getCoplanarListMap() - Static method in class simulation.geometry.PLYreader
returns the map of triangle it triangle indices of triangle subdivisions that should be ignored in an interior check if the original triangle is intersected by the ray.
getCount() - Method in class tractography.Edge
 
getCylinder(double[], SimulationParams) - Static method in class simulation.geometry.elements.CylinderFactory
 
getCylinder(double[], double[], SimulationParams) - Static method in class simulation.geometry.elements.CylinderFactory
 
getCylinders() - Method in class simulation.geometry.substrates.CylinderSubstrate
 
getCylinderSpacing() - Method in class simulation.geometry.substrates.ParallelCylinderSubstrate
gets the cylinder spacing same as short axis length in hex packing cell.
getD() - Method in class Jama.EigenvalueDecomposition
Return the block diagonal eigenvalue matrix
getDataDims() - Method in class imaging.AnalyzeHeader
 
getDataDims() - Method in class imaging.ImageHeader
 
getDataDims() - Method in class imaging.MetaImageHeader
 
getDataDims() - Method in class imaging.Nifti1Dataset
 
getDataDims() - Method in class misc.DynamicScalarImage
 
getDataDims() - Method in class misc.ScalarImage
 
getDataDims() - Method in class tractography.TractographyImage
Array of data dimensions.
getDataFilename() - Method in class imaging.Nifti1Dataset
Get the filename for the dataset data file
getDataSynthesizer(ModelPDF, DW_Scheme, double, int, int, int) - Static method in class tools.CL_Initializer
Creates the source of data from options specified on the command line.
getDataType(String) - Static method in enum imaging.MetaImageHeader.DataType
 
getDatatype() - Method in class imaging.Nifti1Dataset
Get the dataset datatype.
getDataTypeCode(String) - Static method in class data.ExternalDataSource
Converts a String indicating a primitive data type to an integer code for that data type..
getDel1(int) - Method in class imaging.TRSE_Scheme
 
getDel2(int) - Method in class imaging.TRSE_Scheme
 
getDel3(int) - Method in class imaging.TRSE_Scheme
 
getDel4(int) - Method in class imaging.TRSE_Scheme
 
getDelta(int) - Method in class imaging.StejskalTannerScheme
Gets the gradient pulse duration for measurement i.
getDELTA(int) - Method in class imaging.StejskalTannerScheme
Gets the gradient pulse separation for measurement i.
getDELTA(int) - Method in class imaging.TRSE_Scheme
 
getDiffTensor() - Method in class inverters.DiffTensorFitter
Returns the diffusion tensor represented by the current parameter values.
getDiffTensor() - Method in class inverters.DiffTensorUnConFitter
Returns the diffusion tensor represented by the current parameter values.
getDiffusivityAt(double[]) - Method in class simulation.geometry.elements.BasicCylinder
 
getDiffusivityAt(double[]) - Method in class simulation.geometry.elements.FacetCylinder
 
getDiffusivityAt(double[]) - Method in class simulation.geometry.elements.MyelinatedCylinder
 
getDiffusivityAt(double[]) - Method in interface simulation.geometry.elements.SubstrateObject
returns the diffusivity at the given location.
getDiffusivityAt(double[]) - Method in class simulation.geometry.elements.Triangle
 
getDiffusivityAt(double[]) - Method in class simulation.geometry.substrates.ParallelCylinderSubstrate
overrides getDiffusivityAt method in Substrate so that we can do spatial variation in diffusivity.
getDiffusivityAt(double[]) - Method in class simulation.geometry.substrates.Substrate
returns the diffusivity at a given location on the substrate
getDirectionIndex() - Method in class fitters.Codec
Returns the first index of the theta-phi pair of parameters encoding a single fiber orientation.
getDirectionIndex() - Method in class fitters.Fitter
Returns the first index of the theta-phi pair of parameters encoding a single fiber orientation.
getDirsList() - Method in class tractography.HistBin
 
getDisplacement() - Method in class simulation.dynamics.Walker
fetches the current displacemnt vector (r - r0)
getDistanceFrom(double[]) - Method in class simulation.geometry.elements.BasicCylinder
calculates the distance d of a given point from the central axis of the cylinder using the formula d = sqrt( (Q-P)^2 - [(Q-P).V]^2)
getDistanceFrom(double[]) - Method in interface simulation.geometry.elements.Cylinder
 
getDistanceFrom(double[]) - Method in class simulation.geometry.elements.FacetCylinder
calculates the distance d of a given point from the central axis of the cylinder using the formula d = sqrt( (Q-P)^2 - [(Q-P).V]^2)
getDistanceFrom(double[]) - Method in class simulation.geometry.elements.MyelinatedCylinder
 
getDistributions(double[], Random) - Static method in class numerics.TwoFibreACGFitter
Converts output of fitEstimatedParams.
getDistributions(Random) - Method in class numerics.TwoFibreBipolarWatsonFitter
 
getDistributions() - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
getDistributions(Random) - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
getDistributions() - Method in class numerics.TwoFibreWatsonFitter
 
getDoublePivot() - Method in class Jama.LUDecomposition
Return pivot permutation vector as a one-dimensional double array
getDt() - Method in class simulation.SimulationParams
 
getDT1() - Method in class inverters.ThreeTensorFitter
Returns the first component diffusion tensor.
getDT1() - Method in class inverters.TwoTensorFitter
Returns the first component diffusion tensor.
getDT2() - Method in class inverters.ThreeTensorFitter
Returns the second component diffusion tensor.
getDT2() - Method in class inverters.TwoTensorFitter
Returns the second component diffusion tensor.
getDT3() - Method in class inverters.ThreeTensorFitter
Returns the third component diffusion tensor.
getDT_TractographyImage(String, String, int, double[][][], double, int[], double[]) - Static method in class tractography.DT_TractographyImage
Gets an image from the data file.
getDTs(int, int, int) - Method in class tractography.DT_TractographyImage
 
getDuration() - Method in class imaging.GradientWaveform_Scheme
returns the duration necessary from the dynamics.
getDuration() - Method in class imaging.RectGradSteTanScheme
 
getDuration() - Method in class imaging.RectGradTRSE_Scheme
 
getDuration() - Method in interface imaging.SimulableScheme
gets the duration of the scan in seconds.
getDuration() - Method in class imaging.StejskalTannerScheme
returns the duration necessary for simulation dynamics to cover the whole specified sequence
getDuration() - Method in class imaging.TRSE_Scheme
returns the duration necessary for simulation dynamics to cover the whole specified sequence
getEigenvectors(int, int, int) - Method in class tractography.BS_DT_TractographyImage
Gets a new bootstrap estimate at every call.
getEigs() - Method in class tractography.HistBin
 
getElecPointSet(int) - Static method in class misc.SphericalPoints
Reads in a returns the electrostatic pairs point set with the specified number of pairs.
getEndNode() - Method in class tractography.Edge
 
getEntrySet() - Method in class tractography.Histogram
 
getExtensionsList() - Method in class imaging.Nifti1Dataset
Get list of extensions and return it as nx2 array
getF_TestProbabilities(double[], double[]) - Method in class inverters.EvenSphHarmFitter
Computes the set of probabilities of each pair of truncatated spherical harmonic models being equivalent.
getFitAlgorithm(String) - Static method in enum fitters.FitAlgorithm
 
getFitModel(String) - Static method in enum fitters.FitModel
get the model name from the commandline string
getFitter(FitModel, NoiseModel, FitAlgorithm) - Static method in class apps.ModelFit
assembles the combination of tissue model, noise model and fitting algorithm into a fitter object that fits the specified model to the data using the specified algorithm and noise.
getFObjVal() - Method in class optimizers.MarquardtMinimiser
Returns the value of the objective function with the current parameter settings.
getFS_Reorientation(RealMatrix) - Static method in class apps.Reorient
Computes the finite strain strategy reorientation matrix.
getFunction(int) - Static method in class data.StandardTestFunctions
Returns the indexed test function rotated by the indexed rotation, with specified mixing parameters and scaling factor on the diffusion tensors.
getG(int) - Method in class imaging.StejskalTannerScheme
Gets the gradient vector g for measurement i, which is the gradient direction scaled by the average gradient magnitude.
getG(int) - Method in class imaging.TRSE_Scheme
 
getG(double[][], int) - Static method in class inverters.DiffDataFitter
Returns the indexed gradient direction.
getG_Dir(int) - Method in class imaging.DW_Scheme
Gets a copy of the i-th gradient direction.
getGeometryType() - Method in class simulation.SimulationParams
 
getGradImpulse(int, double, double) - Method in class imaging.GradientWaveform_Scheme
calculates the net area under the gradient pulse.
getGradImpulse(int, double, double) - Method in class imaging.RectGradSteTanScheme
Gets the gradient strength at a specific time point during a measurement.
getGradImpulse(int, double, double) - Method in class imaging.RectGradTRSE_Scheme
 
getGradImpulse(int, double, double) - Method in interface imaging.SimulableScheme
Gets the average gradient strength in Tesla in effect during specific time from t to tLast during a measurement.
getGradImpulse(int, double, double) - Method in class imaging.StejskalTannerScheme
returns the gradient impulse between this and most recent call
getGradImpulse(int, double, double) - Method in class imaging.TRSE_Scheme
returns the gradient impulse between this and most recent call
getH() - Method in class Jama.QRDecomposition
Return the Householder vectors
getHeader(int[], double[], short) - Static method in class imaging.AnalyzeHeader
Creates an AnalyzeHeader object, from specified dimensions.
getHeader(double[][][], double[], short) - Static method in class imaging.AnalyzeHeader
Creates an AnalyzeHeader object, with voxel and data dims taken from data.
getHeader(float[][][], double[], short) - Static method in class imaging.AnalyzeHeader
Creates an AnalyzeHeader object, with voxel and data dims taken from data.
getHeaderFile(String) - Method in class imaging.AnalyzeHeader
Gets the header file name for this object.
getHeaderFilename() - Method in class imaging.Nifti1Dataset
Get the filename for the dataset header file
getHessian(PD) - Method in class sphfunc.SphericalFunction
Computes the Hessian of the function at the specified point.
getHessian(double[]) - Method in class sphfunc.SphericalFunction
Computes the Hessian of the function at the specified point.
getHessianEigenVals(double[][], int) - Method in class apps.MultiFibreReconStats
Returns the eigenvalues of the Hessian matrix the four elements of which are in each row of the the props array starting from element firstInd.
getIcosahedralPointSet(int, int) - Static method in class misc.SphericalPoints
Returns a list of points on the sphere which is the vertices of a number of icosahedra each having undergone a separate random rotation.
getImageDataSource() - Method in class imaging.AnalyzeHeader
Gets a data source from a Analyze header.
getImageDataSource() - Method in class imaging.ImageHeader
Gets the image data source, scaling applied if applicable.
getImageDataSource() - Method in class imaging.MetaImageHeader
 
getImageDataSource() - Method in class imaging.Nifti1Dataset
Get the data source for this header.
getImagEigenvalues() - Method in class Jama.EigenvalueDecomposition
Return the imaginary parts of the eigenvalues
getImageRoot(String) - Static method in class imaging.AnalyzeHeader
Gets the image root, such that root.hdr and root.[img | img.gz] exist.
getImageStatistic() - Method in class tractography.TractStatisticImage
Gets the tract-based statistical image.
getIMG_File(String) - Static method in class imaging.AnalyzeHeader
 
getIndex(int) - Static method in enum inverters.InversionIndex
 
getIndex(int) - Static method in enum inverters.ModelIndex
 
getIndexedDT_Inversion(ModelIndex, DW_Scheme) - Static method in class inverters.DT_Inversion
Returns an indexed DT_Inversion.
getIndexedInversion(ModelIndex[], DW_Scheme) - Static method in class apps.ModelFit
Creates and returns the indexed diffusion inversion.
getIndexedThreeTensorFitter(double[][], double[], double[], int, ModelIndex) - Static method in class inverters.ThreeTensorFitter
Returns a ThreeTensorFitter with type specified by the index and initialized with the passed parameters.
getIndexedTwoTensorFitter(double[][], double[], double[], int, ModelIndex) - Static method in class inverters.TwoTensorFitter
Returns a TwoTensorFitter with type specified by the index and initialized with the passed parameters.
getIndices(String[]) - Static method in enum inverters.InversionIndex
Gets the indices from one or more strings.
getIndices(String[]) - Static method in enum inverters.ModelIndex
Gets the indices from one or more strings.
getInformationArray() - Method in class data.BallStick
 
getInitialConditions() - Method in class simulation.SimulationParams
 
getInvRotMat() - Method in class simulation.geometry.substrates.CrossingCylinderSubstrate
get the inverse rotation matrix
getIsotropicMask() - Method in class tractography.TractographyImage
Gets a boolean mask image for tracking.
getJacobian(ScalarImage, ScalarImage, ScalarImage, double, double, double) - Static method in class apps.Reorient
Computes the Jacobian of the image transformation at point (posX, posY, posZ).
getJacobian(double[], DW_Scheme) - Method in class data.compartments.CompartmentModel
Get Jacobian for each compartment separately.
getJacobian(double[], DW_Scheme) - Method in class data.compartments.CylinderGPD
 
getJacobian(double[], DW_Scheme) - Method in class data.compartments.Tensor
 
getJacobian(double[], DW_Scheme) - Method in class data.compartments.Zeppelin
 
getJacobian(double[]) - Method in class fitters.Codec
Computes the jacobian of the encoding, specifically d(model parameters)/d(optimization parameters).
getJacobian(double[], DW_Scheme) - Method in class models.compartments.Ball
Compute the jacobian of the signal.
getJacobian(double[], DW_Scheme) - Method in class models.compartments.CompartmentModel
Get Jacobian for each compartment separately.
getJacobian(double[], DW_Scheme) - Method in class models.compartments.Stick
 
getJacobian(double[], DW_Scheme) - Method in class models.compartments.Tensor
 
getJacobian(double[], DW_Scheme) - Method in class models.compartments.Zeppelin
 
getJacobian(double[], DW_Scheme) - Method in class models.ParametricModel
 
getJacobian(double[], DW_Scheme, int) - Method in class models.ParametricModel
Computes the Jacobian of the model numerically.
getJacobian_old(double[], DW_Scheme) - Method in class models.ParametricModel
Computes the Jacobian of the model numerically.
getKappas() - Method in class numerics.TwoFibreBipolarWatsonFitter
 
getKappas() - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
getKappas() - Method in class numerics.TwoFibreWatsonFitter
 
getL() - Method in class Jama.CholeskyDecomposition
Return triangular factor.
getL() - Method in class Jama.LUDecomposition
Return lower triangular factor
getLambdaDirs() - Static method in class sphfunc.MaxEntProfile
Returns the array of reconstruction directions (directions for the lambdas), as distinct from gradient directions.
getLength() - Method in class tractography.Edge
 
getLogEigs() - Method in class tractography.HistBin
 
getLogMagnetisation(int) - Method in class simulation.dynamics.Walker
returns log magnetisaion for a given measurement
getLogMagnetisationChange(Walker, double, double) - Method in class simulation.geometry.substrates.StickyCylinderSubstrate
returns the change in magnetisation at a given location and time.
getLogMagnetisationChange(Walker, double, double) - Method in class simulation.geometry.substrates.Substrate
returns the change in magnetisation at a given location and time
getLogTrace() - Method in class tractography.HistBin
 
getMatrix() - Method in class inverters.LinearDT_Inversion
Returns the linear inversion matrix.
getMatrix() - Method in class inverters.LinearInversion
Returns the linear inversion matrix.
getMatrix(int, int, int, int) - Method in class Jama.Matrix
Get a submatrix.
getMatrix(int[], int[]) - Method in class Jama.Matrix
Get a submatrix.
getMatrix(int, int, int[]) - Method in class Jama.Matrix
Get a submatrix.
getMatrix(int[], int, int) - Method in class Jama.Matrix
Get a submatrix.
getMaxN() - Method in class numerics.NumericalIntegration
gets the maximum number of terms in the integration sum (default 10000)
getMaxOrder() - Method in class inverters.EvenSphHarmFitter
Returns the maximum spherical harmonic order that the fitter uses.
getMaxTargetCP() - Method in class tractography.ConnectivitySegmentedImage
 
getMaxTargetSC() - Method in class tractography.ConnectivitySegmentedImage
 
getMeanNonZeroModQ() - Method in class imaging.StejskalTannerScheme
Calculates the mean |q| in the set containing all measurements with |q| > 0.
getMeanSquareDisplacement() - Method in class simulation.DiffusionSimulation
calulate the mean square displacement of walkers at their current locations.
getMeasurementModule(SimulationParams, SimulableScheme, Substrate, Walker[]) - Static method in class simulation.measurement.ScanFactory
factory method.
getMinN() - Method in class numerics.NumericalIntegration
 
getMinParams() - Method in class optimizers.PowellMinimiser
Returns the values of the parameters at the minimum point after minimisation has been performed.
getMix() - Method in class inverters.TwoTensorFitter
Returns the mixing parameter.
getMix(int, int, int) - Method in class tractography.DT_TractographyImage
 
getMix1() - Method in class inverters.ThreeTensorFitter
Returns the mixing parameter for the first component.
getMix2() - Method in class inverters.ThreeTensorFitter
Returns the mixing parameter for the second component.
getMixingParameter() - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
getMixingParameter() - Method in class numerics.TwoFibreWatsonFitter
 
getModel(String) - Static method in enum tractography.DataModel
 
getModG(int) - Method in class imaging.StejskalTannerScheme
Gets the average gradient strength for measurement i.
getModG(int) - Method in class imaging.TRSE_Scheme
 
getModQ(int) - Method in class imaging.StejskalTannerScheme
Gets the wavenumber of measurement i.
getMREClass(double) - Method in class mesd.MESD_Inversion
Performs a threshold test on the maximum relative error of the numerical integrals obtained using two point sets.
getMus(double[]) - Static method in class numerics.TwoFibreBinghamFitter
 
getMus() - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
getMus() - Method in class numerics.TwoFibreWatsonFitter
 
getN() - Method in class simulation.geometry.substrates.Substrate
 
getN_walkers() - Method in class simulation.SimulationParams
 
getNoiseModel(String) - Static method in enum fitters.NoiseModel
 
getNonZeroB_Values() - Method in class imaging.DW_Scheme
 
getNonZeroBigDeltas() - Method in class imaging.StejskalTannerScheme
Gets DELTA (gradient pulse separation) for all non-zero measurements.
getNonZeroBigDeltas() - Method in class imaging.TRSE_Scheme
Gets DELTA (separation of the onset of the first and third pulse) for all non-zero measurements.
getNonZeroDelta1s() - Method in class imaging.TRSE_Scheme
Gets delta1 for all non-zero measurements.
getNonZeroDelta2s() - Method in class imaging.TRSE_Scheme
Gets delta2 for all non-zero measurements.
getNonZeroDelta3s() - Method in class imaging.TRSE_Scheme
Gets delta3 for all non-zero measurements.
getNonZeroDelta4s() - Method in class imaging.TRSE_Scheme
Gets delta4 for all non-zero measurements.
getNonZeroG_Dirs() - Method in class imaging.DW_Scheme
 
getNonZeroGs() - Method in class imaging.StejskalTannerScheme
Gets all non-zero gradient vectors.
getNonZeroGs() - Method in class imaging.TRSE_Scheme
 
getNonZeroModGs() - Method in class imaging.StejskalTannerScheme
Gets gradient strengths for all non-zero measurements.
getNonZeroModGs() - Method in class imaging.TRSE_Scheme
Gets all gradient strengths for non-zero measurements.
getNonZeroQs() - Method in class imaging.StejskalTannerScheme
Gets all non-zero q.
getNonZeroSmallDeltas() - Method in class imaging.StejskalTannerScheme
Gets delta (gradient pulse duration) for all non-zero measurements.
getNonZeroT_Delta1s() - Method in class imaging.TRSE_Scheme
Gets t_delta1 for all non-zero measurements.
getNonZeroT_Delta2s() - Method in class imaging.TRSE_Scheme
Gets t_delta2 for all non-zero measurements.
getNonZeroT_Delta3s() - Method in class imaging.TRSE_Scheme
Gets t_delta3 for all non-zero measurements.
getNonZeroT_Delta4s() - Method in class imaging.TRSE_Scheme
Gets t_delta4 for all non-zero measurements.
getNonZeroTEs() - Method in class imaging.StejskalTannerScheme
Gets TE for all non-zero measurements.
getNonZeroTEs() - Method in class imaging.TRSE_Scheme
Gets TE for all non-zero measurements.
getNoPDs() - Method in class sphfunc.PDList
Returns the number of principal directions stored.
getNoPointSets() - Static method in class sphfunc.ISCodes
Returns the number of available point sets.
getNoPointSetsForMaxEnt() - Static method in class sphfunc.ISCodes
Returns the number of available point sets for MEFitterTest.
getNormal() - Method in class simulation.geometry.elements.Triangle
returns the normal of the triangle
getNormNonZeroQs() - Method in class imaging.StejskalTannerScheme
Gets all non-zero q normalized by getMeanNonZeroModQ().
getNumDirs() - Method in class tractography.HistBin
 
getNumMeasurements() - Method in class simulation.measurement.AgnosticScan
number of measurements in the scan.
getNumMeasurements() - Method in interface simulation.measurement.SyntheticScan
returns number of gradient directions (including unweighted)
getNumModelParams() - Method in class fitters.Codec
 
getNumOptParams() - Method in class fitters.Codec
 
getNumParams() - Static method in class sphfunc.MaxEntProfile
Gets the number of lambdas to fit
getNumSolutions() - Method in class optimizers.LM_Minimizer
 
getNumSolutions() - Method in class optimizers.MCMC_Minimizer
 
getNumSolutions() - Method in interface optimizers.Minimizer
Returns the number of candidate solutions each run returns.
getNumSolutions() - Method in class optimizers.MultiRunMinimizer
 
getNumValuesPerRun() - Method in class fitters.Fitter
Returns the number of parameters the fitter returns for each voxel.
getNumValuesPerSolution() - Method in class fitters.Fitter
Returns the number of parameters the fitter returns for each individual solution (there may be lots of these per run/voxel).
getObjectType(String) - Static method in enum imaging.MetaImageHeader.ObjectType
 
getOneTensorBlock(double[], Random) - Static method in class apps.SphFuncPICoCalibrationData
 
getOrigin() - Method in class imaging.AnalyzeHeader
 
getOrigin() - Method in class imaging.MetaImageHeader
 
getOutputArray() - Method in class data.OutputManager
Returns the output array.
getOutputStream() - Method in class data.OutputManager
Returns the output stream.
getP() - Method in class simulation.SimulationParams
 
getPacking() - Method in class simulation.geometry.substrates.ParallelCylinderSubstrate
gets the packing type
getPackingString() - Method in class simulation.geometry.substrates.ParallelCylinderSubstrate
 
getParameters() - Method in class inverters.BallStickFitter
 
getParameters() - Method in class numerics.TwoFibreBipolarWatsonFitter
 
getParameters() - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
getParameters() - Method in class numerics.TwoFibreWatsonFitter
 
getParameters() - Method in class optimizers.MarkovChainMonteCarlo
Returns the values of the current parameters.
getParameters() - Method in class optimizers.MarquardtMinimiser
Returns the values of the parameters.
getParams(Vector3D[], double[]) - Method in class numerics.TwoFibreBinghamFitter
Gets the parameter array for fObj.
getPD() - Method in class misc.DT
Returns the principal direction.
getPD(int) - Method in class sphfunc.PDList
Returns the i-th PD in the list.
getPD_TractographyImage(String, String, int, double[][][], double, int[], double[]) - Static method in class tractography.PD_TractographyImage
Gets an image from the data file.
getPDF(String) - Static method in enum tractography.PICoPDF
 
getPDs() - Method in class data.BallStick
Returns a list of principal directions.
getPDs() - Method in class data.CylinderModel
 
getPDs() - Method in class data.GaussianMixture
Returns a list of principal directions of the test function.
getPDs() - Method in interface data.ModelPDF
Returns a list of principal directions of the test function.
getPDs(double[][], PDList) - Method in class sphfunc.SphericalFunction
Puts a list of peak directions found through sampling followed by local optimization in pdsOpt.
getPDs(int, int, int) - Method in class tractography.BayesDiracTractographyImage
 
getPDs(int, int, int, Vector3D) - Method in class tractography.BayesDiracTractographyImage
 
getPDs(int, int, int) - Method in class tractography.BootstrapTractographyImage
Gets a new bootstrap estimate at every call.
getPDs(int, int, int) - Method in class tractography.DT_TractographyImage
 
getPDs(int, int, int) - Method in class tractography.PICoTractographyImage
Gets a new sample from each PICo PDF in this voxel.
getPDs(int, int, int) - Method in class tractography.TractographyImage
 
getPDs(int, int, int, Vector3D) - Method in class tractography.TractographyImage
 
getPDsRS(double[][]) - Method in class sphfunc.SphericalFunction
Samples the function at each point and returns a list of points that are maximal with a fixed radius.
getPDX() - Method in class sphfunc.PD
Returns the x-component of the PD.
getPDY() - Method in class sphfunc.PD
Returns the y-component of the PD.
getPDZ() - Method in class sphfunc.PD
Returns the z-component of the PD.
getPeakCoord() - Method in class simulation.geometry.substrates.CellularLattice
the reason for this is to avoid initialising everyone on top of a membrane on lattices with even L.
getPeakCoord() - Method in class simulation.geometry.substrates.CrossingCylinderSubstrate
returns the peak coordinate (the place where the spike sits on each axis for delta-peaked initial conditions)
getPeakCoord() - Method in class simulation.geometry.substrates.CylinderSubstrate
 
getPeakCoord() - Method in class simulation.geometry.substrates.DistributedRadiusCylinderSubstrate
returns the coord for the delta peak (centre of substrate)
getPeakCoord() - Method in class simulation.geometry.substrates.EmptySubstrate
 
getPeakCoord() - Method in class simulation.geometry.substrates.MeshSubstrate
return peak coord, used as the ncentre of the object
getPeakCoord() - Method in class simulation.geometry.substrates.ParallelCylinderSubstrate
 
getPeakCoord() - Method in class simulation.geometry.substrates.SquashyInflammationSubstrate
returns the centra of a square substrate
getPeakCoord() - Method in class simulation.geometry.substrates.Substrate
 
getPermeability(int) - Method in class simulation.geometry.elements.Triangle
 
getPhaseShift(int) - Method in class simulation.dynamics.Walker
returns the phase shift due to diffusion weighting in a specified direction.
getPhaseShift(Walker, double, int, double) - Method in class simulation.measurement.AgnosticScan
calculates a phase shift for the given spin at the given time in the given direction
getPhaseShift(Walker, double, int, double) - Method in interface simulation.measurement.SyntheticScan
returns the phase shift at a given location at a given time
getPhi() - Method in class sphfunc.PD
Returns the angle of longitude.
getPhysicalToVoxelTransform() - Method in class imaging.ImageHeader
Gets the transformation matrix R that is the inverse of the voxel to physical space transformation.
getPICoTractographyImage(String, String, int, PICoPDF, double[][][], double, int[], double[], Random) - Static method in class tractography.PICoTractographyImage
Gets an image from the data file.
getPICoTracts(Point3D, int) - Method in class tractography.FibreTracker
Track a path from a single seed point, for many monte-carlo iterations and wrap result in a TractCollection.
getPivot() - Method in class Jama.LUDecomposition
Return pivot permutation vector
getPoint(int) - Method in class tractography.Tract
Get a point.
getPointModulus(double[][]) - Static method in class apps.PointSetToScheme
Gets the modulus of the vector from (0, 0, 0) to the point.
getPoints() - Method in class misc.OrderedAcqMinimizer
 
getPoints() - Method in class tractography.Tract
 
getPointSet(int) - Static method in class sphfunc.ISCodes
Returns the i-th point set.
getPointSetForMaxEnt(int) - Static method in class sphfunc.ISCodes
Returns the i-th point set in a smaller set of pointsets chosen for doing integration in MEFitterTest.
getPosition() - Method in class simulation.geometry.elements.BasicCylinder
returns the position vector for the cylinder.
getPosition() - Method in interface simulation.geometry.elements.Cylinder
 
getPosition() - Method in class simulation.geometry.elements.FacetCylinder
 
getPosition() - Method in class simulation.geometry.elements.MyelinatedCylinder
 
getPostSimulationStats() - Method in class simulation.measurement.MSdispStatsModule
overrides the post simulation abstract method.
getPostSimulationStats() - Method in class simulation.measurement.StatisticsModule
abstract method that is called after the end of the simulation so that stats can be calculated that accumulate over the entire duration of the simulation
getPostSimulationStats() - Method in class simulation.measurement.StickyStatsModule
calculates the mean occupation time of walkers.
getPredErrClass(double) - Method in class mesd.MESD_Inversion
Performs a threshold test on the predicted error of the numerical integrals obtained using the test point set.
getProp() - Method in class sphfunc.PD
Returns the value of the function at the PD.
getPropSum() - Method in class sphfunc.PDList
Returns the sum of the strengths of all the pds in the list.
getQ(int) - Method in class imaging.StejskalTannerScheme
Gets the radial wavenumber q for measurement i.
getQ() - Method in class Jama.QRDecomposition
Generate and return the (economy-sized) orthogonal factor
getR() - Method in class Jama.QRDecomposition
Return the upper triangular factor
getRadius() - Method in class simulation.geometry.elements.BasicCylinder
returns the radius of the cylinder
getRadius() - Method in interface simulation.geometry.elements.Cylinder
 
getRadius() - Method in class simulation.geometry.elements.FacetCylinder
 
getRadius() - Method in class simulation.geometry.elements.MyelinatedCylinder
 
getRadius(double, double) - Method in class sphfunc.EvenSHS
Overridden to sum the spherical harmonics at the specified point.
getRadius(double, double, double) - Method in class sphfunc.EvenSHS
Overridden to convert the Cartesian parameters to spherical polars and call the getRadius(theta, phi).
getRadius(double, double) - Method in class sphfunc.ImagSH
Overridden to return the imaginary part rather than the real part.
getRadius(double, double, double) - Method in class sphfunc.MaxEntProfile
 
getRadius(double, double, double) - Method in class sphfunc.RBF_Sum
Overridden to sum the weighted radial basis functions at the specified point.
getRadius(double, double) - Method in class sphfunc.RealSH
Overridden to evaluate the function directly as it is simpler in polar coordinates.
getRadius(double, double, double) - Method in class sphfunc.RealSH
Overridden to convert the Cartesian parameters to spherical polars and call the getRadius(theta, phi).
getRadius(double, double) - Method in class sphfunc.SphericalFunction
Return the radius of the function at a specified latitude and longitude.
getRadius(double, double, double) - Method in class sphfunc.SphericalFunction
Return the radius along a specified vector.
getRadius(double, double, double) - Method in class sphfunc.TuchRBF
Evaluates the function at (x,y,z).
getRandomizedPDs(int, int, int) - Method in class tractography.BayesDiracRandomizer
Samples from the likelihood function in this voxel, does not consider the prior fibre orientation.
getRandomizedPDs(int, int, int, Vector3D) - Method in class tractography.BayesDiracRandomizer
Samples from the posterior distribution in this voxel.
getRandomizedPDs(int, int, int) - Method in class tractography.PICoBootstrapRandomizer
 
getRandomizedPDs(int, int, int) - Method in interface tractography.PICoRandomizer
Randomizes the PDs in the voxel (i,j,k) and returns them.
getRandomizedPDs(int, int, int) - Method in class tractography.SimplePICoRandomizer
 
getRandomizer(PICoTractographyImage, Random) - Method in enum tractography.PICoPDF
 
getRandomPoint(Random) - Static method in class misc.SphericalPoints
Get a single random point on the unit sphere, drawn from a uniform distribution over its surface.
getRandomSubset(double[][], int, Random) - Static method in class apps.SubsetScheme
Gets a randomly chosen subset of points.
getRandomSubsetEnergy(double[][], int, int, Random) - Static method in class apps.SubsetScheme
Gets a sample of random subsets, and returns their energy.
getRealEigenvalues() - Method in class Jama.EigenvalueDecomposition
Return the real parts of the eigenvalues
getRegion(int) - Method in class tractography.FreeFormROI
Get a specific ROI.
getRegion(int) - Method in class tractography.PointListROI
There is only one ROI in this class, so the index must be 0 and the returned reference is this.
getRegion(int) - Method in interface tractography.RegionOfInterest
Get a specific ROI.
getRegionLabels() - Method in class tractography.FreeFormROI
Get the list of unique region labels in this ROI, ordered from smallest to largest intensity.
getRegionLabels() - Method in class tractography.PointListROI
Get the list of unique region labels in this ROI, ordered from smallest to largest intensity.
getRegionLabels() - Method in interface tractography.RegionOfInterest
Get the list of unique region labels in this ROI, ordered from smallest to largest intensity.
getRegions(short[][][], double, double, double) - Static method in class tractography.FreeFormROI
Get all regions in the volume with a nonzero index.
getRelativeResidual() - Method in class optimizers.MarquardtChiSqFitter
Returns the mean squared relative error given the current values in a.
getResidErrClass(double) - Method in class mesd.MESD_Inversion
Performs a threshold test on the RMS fitting error.
getResidual() - Method in class optimizers.MarquardtChiSqFitter
Returns the average residual squared error given the current values in a.
getResiduals() - Method in class optimizers.MarquardtChiSqFitter
Returns the residual error (absolute difference from fitted value) for each data point.
getRotationMatrix() - Static method in class data.StandardTestFunctions
returns the rotation matrix transform
getRotMat(double, double, double) - Static method in class numerics.Rotations
Computes the rotation matrix that rotates by angle theta about axis (alpha, beta).
getRotMat(double[], double) - Static method in class numerics.Rotations
Computes the rotation matrix that rotates by angle theta about axis r = (rx, ry, rz).
getRotMat(Vector3D, double) - Static method in class numerics.Rotations
Computes the rotation matrix that rotates by angle theta about axis r = (rx, ry, rz).
getRotMat(Vector3D, Vector3D) - Static method in class numerics.Rotations
Get rotation matrix of one vector onto another vector.
getRotMat() - Method in class simulation.geometry.substrates.CrossingCylinderSubstrate
get the rotation matrix
getRowDimension() - Method in class Jama.Matrix
Get row dimension.
getRowPackedCopy() - Method in class Jama.Matrix
Make a one-dimensional row packed copy of the internal array.
getRuntimeStats(double) - Method in class simulation.measurement.MSdispStatsModule
overrides abstract runtime stats method.
getRuntimeStats(double) - Method in class simulation.measurement.StatisticsModule
 
getRuntimeStats(double) - Method in class simulation.measurement.StickyStatsModule
 
getS() - Method in class Jama.SingularValueDecomposition
Return the diagonal matrix of singular values
getScanType() - Method in class simulation.measurement.AgnosticScan
returns an agnostic identifier
getScanType() - Method in interface simulation.measurement.SyntheticScan
returns the scan type
getSearchRadius() - Static method in class sphfunc.SphericalFunction
Returns the value of the search radius in the random sampling principal direction extraction algorithm.
getSeedPoints() - Method in class tractography.FreeFormROI
 
getSeedPoints() - Method in class tractography.PointListROI
 
getSeedPoints() - Method in interface tractography.RegionOfInterest
 
getSegmentedSeeds() - Method in class tractography.ConnectivitySegmentedImage
 
getSettings() - Method in class sphfunc.EvenSHS
Returns the parameters used in the basis sum as a string
getSettings() - Method in class sphfunc.LinearBasisSum
Returns the parameters used in the basis sum as a string
getSettings() - Method in class sphfunc.TuchRBF_Sum
Returns the parameters used in the basis sum as a string
getSigma() - Static method in class sphfunc.TuchRBF_Sum
Returns the value of the scaling parameter
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.Astrocylinders
generates signals from this compartment for the given line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.Astrosticks
generates signals from this compartment for each line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.Ball
generates signals from this compartment for each line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.CompartmentModel
sum up the signals from each compartment
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.CylinderGPD
generates signals from this compartment for each line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.Dot
return a single signal from the scheme from the dot model
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.GammaDistribRadiiCylinders
 
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.ListDistributionCompartment
 
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.SphereGPD
 
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.Stick
 
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.Tensor
generates signals from this compartment for each line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class data.compartments.Zeppelin
 
getSignal(double[], DW_Scheme, int) - Method in class models.BallAndStickModel
 
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.Astrocylinders
generates signals from this compartment for the given line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.Astrosticks
generates signals from this compartment for each line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.Ball
generates signals from this compartment for each line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.CompartmentModel
sum up the signals from each compartment
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.CylinderGPD
generates signals from this compartment for one particular line in the scheme given.
getSignal(double[], double, double, double[]) - Method in class models.compartments.CylinderGPD
generates signals from this compartment for one particular line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.Dot
return a single signal from the scheme from the dot model
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.GDRCylinders
 
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.ListDistributionCompartment
 
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.SphereGPD
generates signals from this compartment for one particular line in the scheme given.
getSignal(double[], double, double, double[]) - Method in class models.compartments.SphereGPD
generates signals from this compartment for one particular line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.Stick
 
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.Tensor
generates signals from this compartment for each line in the scheme given.
getSignal(double[], DW_Scheme, int) - Method in class models.compartments.Zeppelin
 
getSignal(double[], DW_Scheme, int) - Method in class models.ParametricModel
Returns the signals for the i-th measurement of specified scheme from the model using the specified model parameters.
getSignals(double[], DW_Scheme) - Method in class data.compartments.Astrocylinders
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class data.compartments.Astrosticks
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class data.compartments.Ball
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class data.compartments.CompartmentModel
sum up the signals from each compartment
getSignals(double[], DW_Scheme) - Method in class data.compartments.CylinderGPD
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class data.compartments.Dot
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class data.compartments.GammaDistribRadiiCylinders
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class data.compartments.ListDistributionCompartment
 
getSignals(double[], DW_Scheme) - Method in class data.compartments.SphereGPD
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class data.compartments.Stick
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class data.compartments.Tensor
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class data.compartments.Zeppelin
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.BallAndStickModel
 
getSignals(double[], DW_Scheme) - Method in class models.compartments.Astrocylinders
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.compartments.Astrosticks
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.compartments.Ball
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.compartments.CompartmentModel
sum up the signals from each compartment
getSignals(double[], DW_Scheme) - Method in class models.compartments.CylinderGPD
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.compartments.Dot
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.compartments.GDRCylinders
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.compartments.ListDistributionCompartment
 
getSignals(double[], DW_Scheme) - Method in class models.compartments.SphereGPD
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.compartments.Stick
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.compartments.Tensor
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.compartments.Zeppelin
generates signals from this compartment for each line in the scheme given.
getSignals(double[], DW_Scheme) - Method in class models.ParametricModel
Returns a list of signals for the specified scheme from the model using the specified model parameters.
getSignals() - Method in class simulation.measurement.AgnosticScan
 
getSignals() - Method in interface simulation.measurement.SyntheticScan
gets the signals from the summations of the displacements in the walkers.
getSingularValues() - Method in class Jama.SingularValueDecomposition
Return the one-dimensional array of singular values
getSolutions() - Method in class optimizers.LM_Minimizer
Returns the single minimum found by one run of the gradient descent.
getSolutions() - Method in class optimizers.MCMC_Minimizer
Returns the list of M samples from the MCMC.
getSolutions() - Method in interface optimizers.Minimizer
Returns the list of candidate solutions.
getSolutions() - Method in class optimizers.MultiRunMinimizer
 
getSphHarmAnisotropy(double[]) - Method in class apps.SphHarmFitter
Computes the spherical harmonic anisotropy.
getSphPolars(double[]) - Static method in class misc.SphericalPoints
Converts an xyz vector to spherical polar coordinates: r, theta, phi.
getStartNode() - Method in class tractography.Edge
 
getStats() - Method in class sphfunc.SphericalFunction
Computes the mean, variance, max and min of the spherical function and returns them in an array.
getStatsModule(Walker[]) - Static method in class simulation.measurement.StatisticsModuleFactory
factory method
getStep(Walker) - Method in class simulation.dynamics.CylindricalSurfaceStepGenerator
Generates steps confined to the surface of the given cylinder.
getStep(Walker) - Method in class simulation.dynamics.FixedLengthStepGenerator
generates a step of fixed length and uniformly distributed orientation in D<4 dimensions
getStep(Walker) - Method in class simulation.dynamics.SpatiallyVaryingStepGenerator
queries the substrate for the diffusivity at the current location, the constructs a step of the appropriate length.
getStep(Walker) - Method in interface simulation.dynamics.StepGenerator
returns a step vector as array of doubles
getStepAmender(StepAmenderFactory.AmenderType, Substrate) - Static method in class simulation.dynamics.StepAmenderFactory
 
getStepGenerator() - Method in class simulation.DiffusionSimulation
 
getStepGenerator(SimulationParams) - Static method in class simulation.dynamics.StepGeneratorFactory
factory method
getStepParams() - Method in class simulation.SimulationParams
 
getStepParamsArray(StepGeneratorFactory.StepType, SimulationParams) - Static method in class simulation.dynamics.StepGeneratorFactory
parameters array generator
getStepType() - Method in class simulation.SimulationParams
 
getStreamlineCounts() - Method in class tractography.ConnectionProbabilityImage
 
getStreamlineCounts() - Method in class tractography.TargetCP_Image
Get the streamline counts as an image.
getSubsCoords(double[]) - Method in class simulation.dynamics.StickyWalker
 
getSubsetScheme(int[]) - Method in class imaging.B_VectorScheme
Gets a scheme composed of a subset of the measurements.
getSubsetScheme(int[]) - Method in class imaging.DW_Scheme
Gets a scheme composed of a subset of the measurements in this scheme.
getSubsetScheme(int[]) - Method in class imaging.GradientWaveform_Scheme
generates a new scheme from a specified subset of the acquisitions in the current scheme.
getSubsetScheme(int[]) - Method in class imaging.RectGradSteTanScheme
 
getSubsetScheme(int[]) - Method in class imaging.RectGradTRSE_Scheme
 
getSubsObj() - Method in class simulation.geometry.substrates.Substrate
 
getSubstrate() - Method in class simulation.DiffusionSimulation
 
getSubstrate(SubstrateFactory.SubstrateType, SimulationParams) - Static method in class simulation.geometry.substrates.SubstrateFactory
factory method for making geometries.
getSubstrateCoords(double[], double[], double[]) - Method in class simulation.geometry.substrates.CrossingCylinderSubstrate
override the get substrate coords method from substrate
getSubstrateCoords(double[], double[], double[]) - Method in class simulation.geometry.substrates.ParallelCylinderSubstrate
transforms the walker coords into the cell
getSubstrateCoords(double[], double[], double[]) - Method in class simulation.geometry.substrates.Substrate
maps physical walker location into substrate cell.
getSubstrateSize() - Method in class simulation.geometry.substrates.CellularLattice
returns the size of the substrate
getSubstrateSize() - Method in class simulation.geometry.substrates.CrossingCylinderSubstrate
return the size of the unit cell
getSubstrateSize() - Method in class simulation.geometry.substrates.CylinderSubstrate
 
getSubstrateSize() - Method in class simulation.geometry.substrates.DistributedRadiusCylinderSubstrate
returns the size of the substrate (N*R)
getSubstrateSize() - Method in class simulation.geometry.substrates.EmptySubstrate
 
getSubstrateSize() - Method in class simulation.geometry.substrates.MeshSubstrate
returns the size of the unit cell
getSubstrateSize() - Method in class simulation.geometry.substrates.ParallelCylinderSubstrate
 
getSubstrateSize() - Method in class simulation.geometry.substrates.SquashyInflammationSubstrate
 
getSubstrateSize() - Method in class simulation.geometry.substrates.Substrate
 
getSubVoxelIndex(int, int, int) - Method in class simulation.geometry.substrates.Substrate
calculates linear index from three subvoxel coordinates.
getT_Del1(int) - Method in class imaging.TRSE_Scheme
 
getT_Del2(int) - Method in class imaging.TRSE_Scheme
 
getT_Del3(int) - Method in class imaging.TRSE_Scheme
 
getT_Del4(int) - Method in class imaging.TRSE_Scheme
 
getTE(int) - Method in class imaging.StejskalTannerScheme
Gets the echo time for measurement i.
getTE(int) - Method in class imaging.TRSE_Scheme
 
getTensorList(double[], String) - Static method in class apps.FracAnis
Constructs a list of diffusion tensors from the input data in a single voxel.
getTensors() - Method in class data.GaussianMixture
 
getTheta() - Method in class sphfunc.PD
Returns the angle of colatitude.
getThreshold() - Method in class numerics.NumericalIntegration
 
getTmax() - Method in class simulation.SimulationParams
 
getTrace() - Method in class tractography.HistBin
 
getTrackingDirection(Point3D, Vector3D) - Method in class tractography.DT_LinearInterpolator
 
getTrackingDirection(Point3D, int, boolean) - Method in class tractography.DT_LinearInterpolator
Get the initial tracking direction, given a pdIndex and a seed point.
getTrackingDirection(Point3D, Vector3D) - Method in interface tractography.ImageInterpolator
Gets tracking direction at some point.
getTrackingDirection(Point3D, int, boolean) - Method in interface tractography.ImageInterpolator
Gets the initial tracking direction, given a pdIndex and a seed point.
getTrackingDirection(Point3D, Vector3D) - Method in class tractography.NeighbourChoiceInterpolator
Get the tracking direction at some point.
getTrackingDirection(Point3D, int, boolean) - Method in class tractography.NeighbourChoiceInterpolator
Get the initial tracking direction, given a pdIndex and a seed point.
getTrackingDirection(Point3D, Vector3D) - Method in class tractography.TendInterpolator
 
getTrackingDirection(int, int, int, Vector3D) - Method in class tractography.TendInterpolator
 
getTrackingDirection(Point3D, int, boolean) - Method in class tractography.TendInterpolator
Get the initial tracking direction, given a pdIndex and a seed point.
getTrackingDirection(Point3D, Vector3D) - Method in class tractography.VectorLinearInterpolator
 
getTrackingDirection(Point3D, int, boolean) - Method in class tractography.VectorLinearInterpolator
Get the initial tracking direction, given a pdIndex and a seed point.
getTract(int) - Method in class tractography.TractCollection
Get a Tract.
getTwoTensorBlock(double[], double[], double, Random) - Static method in class apps.SphFuncPICoCalibrationData
Compute two tensors over a range of anisotropy, with a fixed crossing angle.
getType() - Method in class simulation.dynamics.CylindricalSurfaceStepGenerator
 
getType() - Method in class simulation.dynamics.FixedLengthStepGenerator
 
getType() - Method in class simulation.dynamics.SpatiallyVaryingStepGenerator
returns the type code of the generator
getType() - Method in interface simulation.dynamics.StepGenerator
get the step generator type
getU() - Method in class Jama.LUDecomposition
Return upper triangular factor
getU() - Method in class Jama.SingularValueDecomposition
Return the left singular vectors
getUpperRight(int, int, int) - Method in class simulation.geometry.substrates.Substrate
calculates the spatial coordinates of the upper right corner of the subvoxel given.
getV() - Method in class Jama.EigenvalueDecomposition
Return the eigenvector matrix
getV() - Method in class Jama.SingularValueDecomposition
Return the right singular vectors
getValues(double, double, double, boolean, boolean) - Method in class tractography.LookupTable
Get the value(s) of the LUT at the point x,y.
getValues(double, boolean, boolean) - Method in class tractography.LookupTable
Get the value(s) of the LUT at the point z.
getValues(double, double, boolean, boolean) - Method in class tractography.LookupTable
Get the value(s) of the LUT at the point y,z.
getVerbosity() - Static method in class tools.DB
Returns the current verbosity level.
getVerbosityInst() - Method in class tools.DB
Returns the current verbosity level for an instance of the class.
getVertex(int) - Method in class simulation.geometry.elements.Triangle
 
getVoxel(int) - Method in class tractography.VoxelList
 
getVoxelDims() - Method in class apps.RGB_ScalarImage
 
getVoxelDims() - Method in class imaging.AnalyzeHeader
 
getVoxelDims() - Method in class imaging.ImageHeader
Voxel dims may be negative for Analyze, use checkDims to get the absolute values.
getVoxelDims() - Method in class imaging.MetaImageHeader
 
getVoxelDims() - Method in class imaging.Nifti1Dataset
 
getVoxelDims() - Method in class misc.DynamicScalarImage
 
getVoxelDims() - Method in class misc.ScalarImage
 
getVoxelDims() - Method in class tractography.TractographyImage
Array of voxel dimensions in mm.
getVoxelDims() - Method in class tractography.VoxelList
 
getVoxelPathLengths(double[]) - Method in class tractography.Tract
Divides the streamline into line segments.
getVoxelPathLengths(double, double, double) - Method in class tractography.Tract
Divides the streamline into line segments.
getVoxels() - Method in class tractography.FreeFormROI
 
getVoxels() - Method in class tractography.PointListROI
 
getVoxels() - Method in interface tractography.RegionOfInterest
 
getVoxels() - Method in class tractography.VoxelList
 
getVoxelSize() - Method in class simulation.SimulationParams
 
getVoxelStatistic(String) - Method in class misc.DynamicScalarImage
Computes a 3D image, where each voxel intensity is some statistic of the data in each voxel.
getVoxelStatistic(String) - Method in class misc.SparseVectorImage
Computes a 3D image, where each voxel intensity is some statistic of the associated vector.
getVoxelStatistic(String) - Method in interface misc.VoxelwiseStatisticalImage
Computes a 3D image, where each voxel intensity is some statistic of the values in the voxel.
getVoxelToPhysicalTransform() - Method in class imaging.AnalyzeHeader
Gets the transformation matrix R that provides a transformation from a = (i, j, k, 1) in voxel space to b = (x, y, z, 1) in physical space.
getVoxelToPhysicalTransform() - Method in class imaging.ImageHeader
Gets the transformation matrix R that provides a transformation from a = (i, j, k, 1) in voxel space to b = (x, y, z, 1) in physical space
getVoxelToPhysicalTransform() - Method in class imaging.MetaImageHeader
Will use TransformMatrix + Offset, because it's not clear what coordinates CenterOfRotation uses
getVoxelToPhysicalTransform() - Method in class imaging.Nifti1Dataset
Gets the transformation matrix R that provides a transformation from a = (i, j, k, 1) in voxel space to b = (x, y, z, 1) in physical space.
getWalker(double[], StepGenerator, Substrate, SyntheticScan, DataOutputStream, SimulationParams) - Static method in class simulation.dynamics.WalkerFactory
constructs the correct type of walker for the desired simulation
getWalkers() - Method in class simulation.DiffusionSimulation
 
getWeight() - Method in class tractography.Edge
 
getWindingNumbers(double[]) - Method in class simulation.geometry.substrates.CellularLattice
constructs the array of "winding numbers" for walker positions.
getWindingNumbers(Walker) - Method in class simulation.geometry.substrates.CellularLattice
wrapper for winding nimber routine using walker instead of position
getX() - Method in class numerics.Point3D
 
getY() - Method in class numerics.Point3D
 
getZ() - Method in class numerics.Point3D
 
getZPhiXs(int) - Static method in class misc.SphericalPoints
Returns an array of unit vectors obtained by sampling z and phi evenly at the resolution specified.
glmax - Variable in class imaging.AnalyzeHeader
 
glmax - Variable in class imaging.Nifti1Dataset
 
glmin - Variable in class imaging.AnalyzeHeader
 
glmin - Variable in class imaging.Nifti1Dataset
 
GLOBALSTATS - Static variable in class apps.SphFuncPD_Stats
The total number global statistics of the input function output before the list of PDs
GradientWaveform_Scheme - Class in imaging
scheme object for general gradient waveforms.
gradOrder(int[]) - Method in class imaging.B_VectorScheme
Re-orders the components of the gradient vectors.
gradOrder(int[]) - Method in class imaging.DW_Scheme
Reorders the gradient directions.
gradOrder(int[]) - Method in class imaging.GradientWaveform_Scheme
constructs a new set of waveforms in an order specified by the given array of indices.
gradOrder(int[]) - Method in class imaging.RectGradSteTanScheme
 
gradOrder(int[]) - Method in class imaging.RectGradTRSE_Scheme
 
gradXYZ - Static variable in class imaging.DW_Scheme
may be passed to gradOrder method to get X, Y, Z ordering of the gradient directions.
gradXZY - Static variable in class imaging.DW_Scheme
may be passed to gradOrder method to get X, Z, Y ordering of the gradient directions.
gradYXZ - Static variable in class imaging.DW_Scheme
may be passed to gradOrder method to get Y, X, Z ordering of the gradient directions.
gradYZX - Static variable in class imaging.DW_Scheme
may be passed to gradOrder method to get Y, Z, X ordering of the gradient directions.
gradZXY - Static variable in class imaging.DW_Scheme
may be passed to gradOrder method to get Z, X, Y ordering of the gradient directions.
gradZYX - Static variable in class imaging.DW_Scheme
may be passed to gradOrder method to get Z, Y, X ordering of the gradient directions.
Graph - Class in tractography
 
Graph(ArrayList<Integer>, HashMap<Integer, Integer>, HashMap<Integer, Integer>, ArrayList<Edge>, HashMap<Integer, String>, HashMap<Integer, Integer>, int) - Constructor for class tractography.Graph
 
greatCircleCentralMoment(double[], double) - Method in class sphfunc.SphericalFunction
returns the central moment of order pow of the spherical function given a vector normal to the plane of the great circle.
greatCircleIntegral(double[]) - Method in class sphfunc.ImagSH
overridden great circle integral calculation.
greatCircleIntegral(double[]) - Method in class sphfunc.RealSH
overridden great circle integral calculation.
greatCircleIntegral(double[]) - Method in class sphfunc.SphericalFunction
returns the great circle integral given a vector normal to the plane of the great circle.
greatCirclePowerIntegral(double[], double) - Method in class sphfunc.SphericalFunction
returns the great circle integral of the spherical function raised to power pow given a vector normal to the plane of the great circle.
GZIP_EXT - Static variable in class imaging.Nifti1Dataset
 
gzipOut - Static variable in class data.OutputManager
Write GZIP output.
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