- 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.