- P - Variable in class simulation.geometry.elements.BasicCylinder
-
position vector
- P - Variable in class simulation.geometry.substrates.SquashyInflammationSubstrate
-
array of cylinder positions
- p - Static variable in class tools.CL_Initializer
-
The test function to use for simulations.
- pack(byte[]) - Static method in class numerics.MTRandom
-
This simply utility method can be used in cases where a byte
array of seed data is to be used to repeatedly re-seed the
random number sequence.
- paintComponent(Graphics) - Method in class apps.F_TestThresholdSelector
-
Draws the image (and crosshairs, if needed).
- paintComponent(Graphics) - Method in class apps.PD_OrientationViewer
-
Draws the image and PDs.
- pairEnergyMatrix(double[][]) - Static method in class misc.OrderedAcqMinimizer
-
- ParallelCylinderSubstrate - Class in simulation.geometry.substrates
-
Implements a class of substrates with a single population
of parallel cylinders with a single constant thickness.
- ParallelCylinderSubstrate(SimulationParams) - Constructor for class simulation.geometry.substrates.ParallelCylinderSubstrate
-
construct a lattice of parallel simple cylinders of
given radius, orientation and spacing
- ParallelCylinderSubstrate(CylinderFactory.CylType, SimulationParams) - Constructor for class simulation.geometry.substrates.ParallelCylinderSubstrate
-
constructor for thick-walled cylinders.
- ParametricModel - Class in models
-
Purpose:
Abstract parametric model class for data synthesis or model fitting.
- ParametricModel(int) - Constructor for class models.ParametricModel
-
constructor.
- Parr - Variable in class simulation.geometry.elements.BasicCylinder
-
pos as point
- parseBinaryStatsFile(String) - Method in class simulation.measurement.StickyStatsModule
-
parses binary stats file into csv for easy excel importing
- parseIndicesFile(String) - Static method in class apps.ConnectivityMapping
-
- parseLabelFile(String, HashMap<Integer, String>) - Static method in class apps.ConnectivityMapping
-
- pathLengthFromSeed(int) - Method in class tractography.Tract
-
Gets the length of the streamline from the seed to point index
.
- PD - Class in sphfunc
-
Purpose:
Stores a direction vector with proportional magnitude.
- PD(double, double, double) - Constructor for class sphfunc.PD
-
Constructs a PD object from spherical polar coordinates.
- PD(double[], double) - Constructor for class sphfunc.PD
-
Constructs a PD object from Cartesian coordinates.
- PD_OrientationViewer - Class in apps
-
Simple tool to visualize principal directions of tensor data.
- PD_TractographyImage - Class in tractography
-
Tractography image for PD data (output of sfpeaks).
- PD_TractographyImage(VoxelOrderDataSource, int, int[], double[]) - Constructor for class tractography.PD_TractographyImage
-
Constructs an image from a data source.
- PD_TractographyImage(Vector3D[][][][], double[], int) - Constructor for class tractography.PD_TractographyImage
-
- PD_TractographyImage(int[], double[], int) - Constructor for class tractography.PD_TractographyImage
-
- pdf(Vector3D) - Method in class numerics.ACG_Distribution
-
Gets the pdf of the distribution.
- pdf(Vector3D) - Method in interface numerics.AxialDistribution
-
Gets the probability density for a given unit vector.
- pdf(Vector3D) - Method in class numerics.BinghamDistribution
-
Evaluate the pdf of the distribution.
- pdf(Vector3D[], double[], Vector3D) - Static method in class numerics.BinghamDistribution
-
Evaluate the pdf of the distribution.
- pdf(Vector3D) - Method in class numerics.WatsonDistribution
-
Evaluate the pdf of the distribution.
- pdf(Vector3D, double) - Method in class numerics.WatsonDistribution
-
Evaluate the pdf of the distribution.
- pdf(Vector3D, Vector3D, double) - Static method in class numerics.WatsonDistribution
-
Evaluate the pdf of any Watson distribution.
- pdf(int, int, int, int, Vector3D) - Method in class tractography.PICoBootstrapRandomizer
-
Evaluates the PDF for a vector at voxel (i,j,k).
- pdf(int, int, int, int, Vector3D) - Method in interface tractography.PICoRandomizer
-
Evaluates the PDF for a vector at voxel (i,j,k).
- pdf(int, int, int, int, Vector3D) - Method in class tractography.SimplePICoRandomizer
-
- PDList - Class in sphfunc
-
Purpose: Stores a list of PDs.
- PDList(double) - Constructor for class sphfunc.PDList
-
Constructs a PDList object given a threshold for the difference of dot
products from 1 below which PDs are considered the same.
- PDList() - Constructor for class sphfunc.PDList
-
Constructs a PDList object with a default threshold of zero, which means
that all added PDs remain in the list.
- PercCellularLattice - Class in simulation.geometry.substrates
-
Camino fibre reconstruction and tracking toolkit
PercCellularLattice (simulation)
Initialises a cellular lattice occupied like a using a
percolation-like technique.
- PercCellularLattice(SimulationParams) - Constructor for class simulation.geometry.substrates.PercCellularLattice
-
- PercolationSubstrate - Class in simulation.geometry.substrates
-
- PercolationSubstrate(SimulationParams) - Constructor for class simulation.geometry.substrates.PercolationSubstrate
-
constructor.
- perturb(double[], double[], Random) - Method in class fitters.FixedSTD_GaussianPerturbation
-
Generate new parameters from gaussian distribution.
- perturb(double[], double[], Random) - Method in class fitters.Perturbation
-
Generate new parameters from proposal distribution.
- Perturbation - Class in fitters
-
Purpose:
Base class for starting point perturbations (as in for example
MultiRunLM fitters) or proposal distributions required for Bayesian
fitting routines such as MCMC.
- Perturbation() - Constructor for class fitters.Perturbation
-
- phase_dim - Variable in class imaging.Nifti1Dataset
-
- PICoACGRandomizer - Class in tractography
-
Provides samples from the ACG fibre orientation PDF.
- PICoBinghamRandomizer - Class in tractography
-
Provides samples from the Bingham fibre PDF.
- PICoBootstrapRandomizer - Class in tractography
-
This class forwards bootstrap PDs, it does not do any randomization of its own.
- PICoBootstrapRandomizer(BootstrapTractographyImage) - Constructor for class tractography.PICoBootstrapRandomizer
-
- PICoPDF - Enum in tractography
-
PDF types: ACG, BINGHAM, WATSON
- PICoPDF_OrientationViewer - Class in apps
-
Simple tool to visualize principal directions of PICo data.
- PICoPDF_OrientationViewer(RGB_ScalarImage, double) - Constructor for class apps.PICoPDF_OrientationViewer
-
Creates and displays the viewer.
- PICoPDFs - Class in apps
-
Calculate PICo PDFs in each voxel.
- PICoPDFs(String[]) - Constructor for class apps.PICoPDFs
-
- PICoRandomizer - Interface in tractography
-
Provides samples from the fibre orientation distribution function (PDF).
- picoSeed - Variable in class imaging.AnalyzeHeader
-
Seed point for PICo probability maps
- PICoTractographyImage - Class in tractography
-
Tractography image with all three eigenvectors of spherical PDF(s) specified in each voxel.
- PICoTractographyImage(VoxelOrderDataSource, int, PICoPDF, int[], double[], Random) - Constructor for class tractography.PICoTractographyImage
-
Constructs an image from the data sources.
- PICoWatsonRandomizer - Class in tractography
-
Provides samples from the Watson fibre (PDF).
- pixdim - Variable in class imaging.Nifti1Dataset
-
- pixelDepth - Variable in class imaging.AnalyzeHeader
-
- pixelHeight - Variable in class imaging.AnalyzeHeader
-
- pixelWidth - Variable in class imaging.AnalyzeHeader
-
- plgndr(int, int, double) - Static method in class numerics.SphericalHarmonics
-
NRC method for computing associated Legendre polynomial values.
- plus(Matrix) - Method in class Jama.Matrix
-
C = A + B
- plus(Complex) - Method in class numerics.Complex
-
Adds complex numbers.
- plus(Vector3D) - Method in class numerics.Vector3D
-
Add another vector to this one.
- plusEquals(Matrix) - Method in class Jama.Matrix
-
A = A + B
- PLYreader - Class in simulation.geometry
-
- PLYreader() - Constructor for class simulation.geometry.PLYreader
-
- Point3D - Class in numerics
-
Purpose: To encapsulate a 3D point.
- Point3D() - Constructor for class numerics.Point3D
-
Creates a point at the origin (0,0,0).
- Point3D(double, double, double) - Constructor for class numerics.Point3D
-
Creates a point at position (xVal, yVal, zVal).
- Point3D(Point3D) - Constructor for class numerics.Point3D
-
Creates a new Point3D
that is a copy of this one.
- Point3D(double[]) - Constructor for class numerics.Point3D
-
Creates a new Point3D
at the position {x,y,z}.
- PointListROI - Class in tractography
-
An ROI for tractography.
- PointListROI(Point3D[], int, int, int, double, double, double) - Constructor for class tractography.PointListROI
-
Create an ROI from a list of points in mm coordinates.
- PointListROI(Point3D[], int[], double[]) - Constructor for class tractography.PointListROI
-
Create an ROI from a list of points in mm coordinates.
- pointSetDirectory - Static variable in class misc.SphericalPoints
-
- pointsetEnergy(double[][]) - Static method in class apps.SubsetScheme
-
Calculates the total energy of a point set.
- pointSetInd - Static variable in class tools.CL_Initializer
-
Index of the ISCodes point set to use for computing spherical integrals.
- pointSetIndSet - Static variable in class tools.CL_Initializer
-
Flag indicating that the IS codes point set index was set.
- pointSetToB_VectorScheme(double[][], boolean, double[]) - Static method in class apps.PointSetToScheme
-
Converts a point set and imaging parameters to a String representation of a
B_VectorScheme
.
- pointSetToRectGradSteTanScheme(double[][], double[]) - Static method in class apps.PointSetToScheme
-
Converts a point set and imaging parameters to a String representation of a
RectGradStejskalTannerScheme
.
- pointSetToRectGradTRSE_Scheme(double[][], double[]) - Static method in class apps.PointSetToScheme
-
Converts a point set and imaging parameters to a String representation of a
RectGradTRSE_Scheme
.
- PointSetToScheme - Class in apps
-
Converts point sets to scheme files, given additional imaging parameters.
- PointSetToScheme(String[]) - Constructor for class apps.PointSetToScheme
-
- PolynomialFunction - Class in numerics
-
Represents a polynomial function of any degree.
- PolynomialFunction() - Constructor for class numerics.PolynomialFunction
-
- PolynomialFunction1D - Class in numerics
-
Represents a polynomial function of any degree with one variable {x}.
- PolynomialFunction1D(int, double[]) - Constructor for class numerics.PolynomialFunction1D
-
Construct a function with a specified order and associated coefficients.
- PolynomialFunction2D - Class in numerics
-
Represents a polynomial function of any degree with two variables {x, y}.
- PolynomialFunction2D(int, double[]) - Constructor for class numerics.PolynomialFunction2D
-
Construct a function with a specified order and associated coefficients.
- positive() - Method in class numerics.Complex
-
Makes both components positive.
- PowellMinimiser - Class in optimizers
-
Description:
Minimises a function objfunc of n variables.
- PowellMinimiserException - Exception in optimizers
-
Description:
Minimises a function objfunc of n variables.
- ppd(RealMatrix) - Method in class misc.DT
-
Reorients the tensor using the PPD algorithm.
- predErrThresh - Static variable in class mesd.MESD_Inversion
-
The threshold on the predicted error of the numerical integrals obtained
using the test point set.
- print(int, int) - Method in class Jama.Matrix
-
Print the matrix to stdout.
- print(PrintWriter, int, int) - Method in class Jama.Matrix
-
Print the matrix to the output stream.
- print(NumberFormat, int) - Method in class Jama.Matrix
-
Print the matrix to stdout.
- print(PrintWriter, NumberFormat, int) - Method in class Jama.Matrix
-
Print the matrix to the output stream.
- printDoubleTmcrs(double[]) - Method in class imaging.Nifti1Dataset
-
Print a voxel timecourse to standard out.
- printHeader() - Method in class imaging.Nifti1Dataset
-
Print header information to standard out.
- printIfVerbose(Object, int) - Static method in class tools.DB
-
Prints the object if vLevel is less than or equal to the specified
verbosity.
- printIfVerboseInst(Object, int) - Method in class tools.DB
-
Prints the object if vLevel is less than or equal to the specified
verbosity.
- Prior - Class in fitters
-
Purpose:
Base class for prior probability distributions required for
Bayesian fitting routines such as MCMC.
- Prior() - Constructor for class fitters.Prior
-
- prior(double[]) - Method in class fitters.Prior
-
Returns the prior probability of the specified list of
optimization parameters.
- ProbabilisticInterpolator - Interface in tractography
-
Purpose: Interface for probabilistic interpolators.
- ProcessStreamlines - Class in apps
-
Processes streamline output from StreamlineTractography or from a previous invocation of this
program.
- ProcessStreamlines(String[]) - Constructor for class apps.ProcessStreamlines
-
- processTract(Tract) - Method in class tractography.ConnectionProbabilityImage
-
Add a single streamline to the image.
- processTract(Tract) - Method in class tractography.StreamlineROI_Filter
-
- processTract(Tract) - Method in class tractography.TargetCP_Image
-
Add a single streamline to the image.
- processTract(Tract) - Method in class tractography.TractStatisticFilter
-
Process a tract.
- processTract(Tract) - Method in class tractography.TractStatisticImage
-
Processes a single tract.
- processTracts(TractCollection) - Method in class tractography.ConnectionProbabilityImage
-
Add some streamlines to the image.
- processTracts(int, TractCollection) - Method in class tractography.ConnectivitySegmentedImage
-
apply some tracts to a specified seed point.
- processTracts(TractCollection) - Method in class tractography.StreamlineROI_Filter
-
- processTracts(TractCollection) - Method in class tractography.TargetCP_Image
-
Add some streamlines to the image.
- processTracts(TractCollection) - Method in class tractography.TractStatisticImage
-
Add all of the tracts in the collection to the image.
- product(RealMatrix) - Method in class numerics.RealMatrix
-
Multiplies matrices.
- propagateCloneRelationships() - Method in class simulation.geometry.elements.SquashyCylinder
-
before this is called, the orginal cylinder knows about its clones
but the clones don't know about each other, or about the original.
- ProtArr - Variable in class simulation.geometry.elements.BasicCylinder
-
pos as point
- prune(double) - Method in class sphfunc.PDList
-
Prunes from the list of PDs all of those whose strength is less than the
specified fraction of the sum of the strengths of all the PDs in the
list.
- pruneByValue(double) - Method in class sphfunc.PDList
-
Prunes from the list of PDs by removing all those with value less than
the threshold.
- pseudoInv(double) - Method in class numerics.RealMatrix
-
- pseudoInv() - Method in class numerics.RealMatrix
-