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P

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
 
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