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S

samples - Static variable in class tools.CL_Initializer
Number of samples produced by Markov Chain Monte Carlo algorithm .
scalarGamma() - Method in class apps.RGB_ScalarImage
 
ScalarImage - Class in misc
Interpolated scalar image.
ScalarImage(double[][][], double[]) - Constructor for class misc.ScalarImage
Construct an image, default interpolation is nearest neighbour.
ScalarImage(String) - Constructor for class misc.ScalarImage
Construct an image from an Analyze or NIFTI file.
ScalarImage(String, int) - Constructor for class misc.ScalarImage
Construct an image from one component of a NIFTI file, default interpolation is nearest neighbour.
scalarMult(double) - Method in class numerics.RealMatrix
Multiplies the matrix by a scalar and returns the result leaving the original unchanged.
scale(double) - Method in class misc.DT
Scales a diffusion tensor.
scale(double) - Method in class numerics.RealMatrix
Multiplies the matrix by a scalar.
scale - Static variable in class tools.CL_Initializer
Alternative setting for scaling the standard test functions.
scaled(double) - Method in class numerics.Vector3D
Scale vector by some constant.
scaleInter - Variable in class imaging.AnalyzeHeader
 
scaleSlope - Variable in class imaging.AnalyzeHeader
 
ScanFactory - Class in simulation.measurement
factory class for creating scans (and other measurement modules).
ScanFactory() - Constructor for class simulation.measurement.ScanFactory
 
ScanFactory.ScanType - Enum in simulation.measurement
enumeration of synthetic scan types
ScannerOrderDataSource - Class in data
Purpose: Source of data from a scanner-order data file or standard input stream.
ScannerOrderDataSource(String, int, int, String) - Constructor for class data.ScannerOrderDataSource
Constructor requires the filename, the dimensions of the measurement volume, the number of values in each voxel and the data type.
ScannerOrderDataSource(String, int, int, String, boolean) - Constructor for class data.ScannerOrderDataSource
Constructor requires the filename, the dimensions of the measurement volume, the number of values in each voxel and the data type.
ScannerOrderDataSource(String, int, int, String, boolean, int) - Constructor for class data.ScannerOrderDataSource
Constructor requires the filename, the number of values in each voxel and the data type.
ScannerOrderDataSource(double[][]) - Constructor for class data.ScannerOrderDataSource
Constructs a data source from an array.
ScannerOrderScaledDataSource - Class in data
Like a regular ScannerOrderDataSource, except that it scales the input data.
ScannerOrderScaledDataSource(String, int, int, String, boolean, int, double, double) - Constructor for class data.ScannerOrderScaledDataSource
Constructor requires the filename, the number of values in each voxel and the data type.
ScannerToVoxel - Class in apps
Purpose: Converts scanner order data to the voxel order format used by the Camino suite.
ScannerToVoxel(String[]) - Constructor for class apps.ScannerToVoxel
 
scanType - Static variable in class simulation.SimulationParams
scan type
schemeFile - Static variable in class tools.CL_Initializer
Name of the imaging scheme file.
SchemeToFSL - Class in apps
Converts Camino scheme files to FSL b-vectors and b-values.
SchemeToFSL() - Constructor for class apps.SchemeToFSL
 
scl_inter - Variable in class imaging.Nifti1Dataset
 
scl_slope - Variable in class imaging.Nifti1Dataset
 
seed - Static variable in class tools.CL_Initializer
Random number generator seed.
seedPointIndex() - Method in class tractography.Tract
 
seedPointIndex() - Method in class tractography.VoxelList
 
selectModel(double[], double, double, double) - Method in class inverters.EvenSphHarmFitter
Performs a series of F-tests given the probabilities of equivalence of each pair of spherical harmonic models.
selectModel(double[], int, double, double, double) - Static method in class inverters.EvenSphHarmFitter
Performs a series of F-tests given the probabilities of equivalence of each pair of spherical harmonic models.
SequenceStats - Class in apps
Purpose: Computes statistics of a number of similar results from different random rotations.
SequenceStats() - Constructor for class apps.SequenceStats
 
session_error - Variable in class imaging.Nifti1Dataset
 
set(int, int, double) - Method in class Jama.Matrix
Set a single element.
setConvergence(double) - Method in class optimizers.MarquardtMinimiser
Sets the convergence threshold, default is 10^-8.
setCONVERGETHRESH(double) - Static method in class optimizers.MarquardtMinimiser
 
setCONVERGETHRESH(double) - Method in class optimizers.MultiRunLM_Minimizer
Sets the convergence threshold in the LM algorithm.
setConvThresh(double) - Method in class sphfunc.SphericalFunction
Sets the convergence threshold for Powell's algorithm used in getPDs.
setCount(int) - Method in class tractography.Edge
 
setCountFirstEntry(boolean) - Method in class tractography.ConnectivitySegmentedImage
The default behaviour is to count the first entry of a streamline to a target zone.
setCountFirstEntry(boolean) - Method in class tractography.TargetCP_Image
The default behaviour is to count the first entry of a streamline to a target zone.
setCountIntersect(boolean) - Method in class tractography.TractStatisticImage
By default, the tract statistic is only added to the voxel where the tract was seeded.
setCurvatureG(double) - Method in class tractography.BayesDiracRandomizer
Sets the improper curvature prior |v_i \dot v_{i-1}|^\gamma, where v_i is the current orientation and v_{i-1} is the previous orientation.
setCurvatureK(double) - Method in class tractography.BayesDiracRandomizer
Curvature prior is a Watson distribution centred on the previous direction.
setCurvePriorGamma(double) - Method in class tractography.BayesDiracTractographyImage
Sets the curvature prior concentration to |v_i \dot v_{i-1}|^\gamma given the current orientation v_i and the previous one v_{i-1}.
setCurvePriorKappa(double) - Method in class tractography.BayesDiracTractographyImage
Sets the curvature prior concentration using a Watson distribution.
setCylinder(Cylinder) - Method in class simulation.dynamics.CylindricalSurfaceStepGenerator
set the current cylinder
setDataSource(DataSource) - Static method in class tools.CL_Initializer
Specifies a specific data source object.
setDatatype(short) - Method in class imaging.Nifti1Dataset
Set the dataset datatype.
setDatatype(String) - Method in class imaging.Nifti1Dataset
Sets the data type given a Camino data type string.
setDensity(int) - Method in class apps.SphFuncPD_Stats
Set the sampling density in the peak search.
setDims(short, short, short, short, short, short, short, short) - Method in class imaging.Nifti1Dataset
Set the dataset dimensions
setDims(int, int, int, int, int, int, int, int) - Method in class imaging.Nifti1Dataset
Casts args to short and calls setDims.
setDims(short[]) - Method in class imaging.Nifti1Dataset
 
setDirectional(Vector3D) - Method in class tractography.ConnectivitySegmentedImage
Call this method to split the streamlines in two at the seed point and produce separate connection probability maps from each.
setDirectional(Vector3D) - Method in class tractography.TargetCP_Image
Call this method to split the streamlines in two at the seed point and produce separate connection probability maps from each.
setDiscardLoops(boolean) - Method in class tractography.StreamlineROI_Filter
 
setDiscardOnExclusionEntry(boolean) - Method in class tractography.StreamlineROI_Filter
 
setDT2RotationAngle(double) - Static method in class data.StandardTestFunctions
Sets the dt2 rotation angle.
setEndNode(int) - Method in class tractography.Edge
 
setEndZones(short[][][]) - Method in class tractography.StreamlineROI_Filter
Set the end zones volume.
setEntry(int, int, double) - Method in class numerics.RealMatrix
Sets a matrix entry.
setExceptionLogging(boolean) - Static method in exception misc.LoggedException
Turns exception logging on or off.
setExclusionROIs(short[][][]) - Method in class tractography.StreamlineROI_Filter
Set the exclusion volume.
setExternalPriors(PICoRandomizer) - Method in class tractography.BayesDiracRandomizer
Set external priors.
setExternalPriors(PICoTractographyImage) - Method in class tractography.BayesDiracTractographyImage
 
setF_TestThresholds(double, double, double) - Method in class inverters.EvenSphHarmFitter
Sets the f-test thresholds.
setFixedParams(boolean[]) - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
setFixedParams(boolean[]) - Method in class numerics.TwoFibreWatsonFitter
 
setFlip(int) - Method in class apps.PD_OrientationViewer
flips the x, y or z direction
setFTestThresholds(double, double, double) - Method in class apps.F_TestThresholdSelector
Sets the thresholds for the F-test.
setHC2() - Method in class data.WildBootstrapDataSynth
Set the constant used in heteroscedasticity term: HC2 = -0.5, or HC3 = -1.0.
setHC3() - Method in class data.WildBootstrapDataSynth
Set the constant used in heteroscedasticity term: HC2 = -0.5, or HC3 = -1.0.
setHeaderFile(String) - Method in class imaging.AnalyzeHeader
Sets the header file for this object.
setHeaderFilename(String) - Method in class imaging.Nifti1Dataset
Set the filename for the dataset header file.
setHeaderValue(String, String) - Method in class imaging.MetaImageHeader
Parses header values from their String representation.
setImageStatistic(String) - Method in class tractography.TractStatisticImage
Sets the image statistic, which determines how multiple values in each voxel are combined.
setInitParams(double[]) - Method in class inverters.BallStickFitter
Sets the initial values of the parameters.
setInitParams(double[]) - Method in class numerics.TwoFibreBipolarWatsonFitter
Sets the initial values of the parameters.
setInitParams(Vector3D, Vector3D, double, double) - Method in class numerics.TwoFibreBipolarWatsonFitter
Set an initial estimate of the parameters.
setInitParams(double[]) - Method in class numerics.TwoFibreFixedPropWatsonFitter
Sets the initial values of the parameters.
setInitParams(Vector3D, Vector3D, double, double) - Method in class numerics.TwoFibreFixedPropWatsonFitter
Set an initial estimate of the parameters.
setInitParams(double[]) - Method in class numerics.TwoFibreWatsonFitter
Sets the initial values of the parameters.
setInitParams(double[]) - Method in class optimizers.MarkovChainMonteCarlo
Sets the initial values of the parameters.
setInitParams(double[]) - Method in class optimizers.MarquardtMinimiser
Sets the initial values of the parameters.
setInitParams(double[]) - Method in interface optimizers.Minimizer
Sets the initial values of the optimized parameters.
setInitParams(double[]) - Method in class optimizers.MultiRunMinimizer
 
setInterpolate(boolean) - Method in class tractography.TractStatisticFilter
If interpolation is enabled, the scalar image is linearly interpolated.
setInterpolate(boolean) - Method in class tractography.TractStatisticImage
By default, the image is not interpolated.
setInterpolation(String) - Method in class misc.ScalarImage
Sets the interpolation method for this image.
setInterpolationVoxels(Point3D, double[], int[]) - Method in class tractography.EightNeighbourInterpolator
Sets values relating to the position of a point, for use in interpolatation.
setInterpolationVoxelsDX(Point3D, double[], int[]) - Method in class tractography.EightNeighbourInterpolator
As setInterpolationVoxels, but the components are now for computing the derivative with respect to x.
setInterpolationVoxelsDY(Point3D, double[], int[]) - Method in class tractography.EightNeighbourInterpolator
As setInterpolationVoxels, but the components are now for computing the derivative with respect to y.
setInterpolationVoxelsDZ(Point3D, double[], int[]) - Method in class tractography.EightNeighbourInterpolator
As setInterpolationVoxels, but the components are now for computing the derivative with respect to z.
setKappa1Variable(boolean) - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
setKappa1Variable(boolean) - Method in class numerics.TwoFibreWatsonFitter
 
setKappa2Variable(boolean) - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
setKappa2Variable(boolean) - Method in class numerics.TwoFibreWatsonFitter
 
setLambda1(double) - Static method in class data.StandardTestFunctions
Sets the largest eigenvalue of the prolate diffusion tensors.
setLength(double) - Method in class tractography.Edge
 
setMaskSource(DataSource) - Static method in class tools.CL_Initializer
Specifies a specific data source object for the background mask.
setMatrix(int, int, int, int, Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int[], int[], Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int[], int, int, Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMatrix(int, int, int[], Matrix) - Method in class Jama.Matrix
Set a submatrix.
setMAXITER(int) - Static method in class optimizers.MarquardtMinimiser
 
setMAXITER(int) - Method in class optimizers.MultiRunLM_Minimizer
Sets the maximum number of iterations in each run.
setMaxN(int) - Method in class numerics.NumericalIntegration
sets the max number of terms in the integration sum (default 10000)
setMaxTractLength(double) - Method in class tractography.StreamlineROI_Filter
Truncates tracts if their length is more than length mm before any exclusion ROIs are applied.
setMaxTractPoints(int) - Method in class tractography.StreamlineROI_Filter
Truncates tracts if they have more than p points before resampling and before any exclusion ROIs are applied.
setMeasurements(double[]) - Method in class optimizers.LM_Minimizer
Initializes the fitting procedure with a new set of measurements (dependent variables).
setMeasurements(double[]) - Method in class optimizers.MCMC_Minimizer
Initializes the fitting procedure with a new set of measurements (dependent variables).
setMeasurements(double[]) - Method in interface optimizers.Minimizer
Initializes the fitting procedure with a new set of measurements (dependent variables).
setMeasurements(double[]) - Method in class optimizers.MultiRunMinimizer
 
setMinN(int) - Method in class numerics.NumericalIntegration
 
setMinTractLength(double) - Method in class tractography.StreamlineROI_Filter
Automatically remove tracts if their length is less than length mm before any exclusion ROIs are applied.
setMinTractPoints(int) - Method in class tractography.StreamlineROI_Filter
Automatically remove tracts if they have less than p points before resampling and before any exclusion ROIs are applied.
setMix3(double) - Static method in class data.StandardTestFunctions
Sets the mixing parameters for function 3.
setMix4(double, double) - Static method in class data.StandardTestFunctions
Sets the mixing parameters for function 4.
setMixingParameterVariable(boolean) - Method in class numerics.TwoFibreWatsonFitter
 
setMu1Variable(boolean) - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
setMu1Variable(boolean) - Method in class numerics.TwoFibreWatsonFitter
 
setMu2Variable(boolean) - Method in class numerics.TwoFibreFixedPropWatsonFitter
 
setMu2Variable(boolean) - Method in class numerics.TwoFibreWatsonFitter
 
setNoOutput(boolean) - Method in class apps.SphFuncPD_Stats
Set the maximum number of peaks to output per voxel.
setNormalizedScalars(double) - Method in class apps.RGB_ScalarImage
Sets scalar range from the range present in the data, after excluding outliers.
setNormalizedScalars(double, double) - Method in class apps.RGB_ScalarImage
Sets scalar range between the specified minimum (maps to black) and maximum (maps to white).
setOutputArray(int, int, int) - Method in class data.OutputManager
Specifies that the output should be stored for collection by an external process, such as Matlab.
setOutputFile(String) - Static method in class tools.DB
Sets the output filename.
setOutputFileInst(String) - Method in class tools.DB
Sets the output filename for an instance of the class.
setPdThresh(double) - Method in class apps.SphFuncPD_Stats
Set the threshold on difference between peak directions in the consistency test.
setPerturbation(Perturbation) - Method in class optimizers.MultiRunMinimizer
Sets the perturbation object for getting starting points.
setPixDims(float, float, float, float, float, float, float, float) - Method in class imaging.Nifti1Dataset
Sets the pixel dims in order.
setPixDims(float[]) - Method in class imaging.Nifti1Dataset
Sets the pixel dims in order.
setPixDims(double, double, double, double, double, double, double, double) - Method in class imaging.Nifti1Dataset
Casts args to float and calls setPixDims.
setPoints(double[][]) - Static method in class sphfunc.RBF_Sum
Allows setting of the directions defining the radial basis.
setPointSet(int) - Method in class mesd.MESD_Fitter
Specifies the index of the point set to be used to compute the numerical integrals.
setReconDirs(double[][]) - Static method in class sphfunc.MaxEntProfile
Sets the set of reconstruction directions.
setResampleStepSize(double) - Method in class tractography.StreamlineROI_Filter
Filtered streamlines will be resampled to the specified step size.
setResampleTracts(boolean) - Method in class tractography.StreamlineROI_Filter
Determines whether tracts will be resampled.
setRGB_Gamma(double) - Method in class apps.RGB_ScalarImage
Sets the gamma constant g for the rgb component.
setScalarGamma(double) - Method in class apps.RGB_ScalarImage
Sets the gamma constant g for the scalar component.
setScale(double) - Static method in class data.StandardTestFunctions
Sets the scaling factor.
setSearchRadius(double) - Static method in class sphfunc.SphericalFunction
Sets the search radius in the random sampling principal direction extraction algorithm.
setSeed(long) - Method in class numerics.MTRandom
This method resets the state of this instance using the 64 bits of seed data provided.
setSeed(byte[]) - Method in class numerics.MTRandom
This method resets the state of this instance using the byte array of seed data provided.
setSeed(int[]) - Method in class numerics.MTRandom
This method resets the state of this instance using the integer array of seed data provided.
setSig(int, double) - Method in class optimizers.MarquardtChiSqFitter
Allows the standard deviations of the data points to be specified.
setSigma(double) - Static method in class sphfunc.TuchRBF_Sum
Allows setting of the scaling parameter.
setSlice() - Method in class apps.F_TestThresholdSelector
Called if slice is moved, the plane view is switched, or the data changes.
setSliceMarkers(MouseEvent) - Method in class apps.F_TestThresholdSelector
Called when user left-clicks in the image.
setSliceOrientation(int) - Method in class apps.F_TestThresholdSelector
Sets the slice orientation to XY, XZ, or YZ, then updates the slice list and display.
setSliceOrientation(int) - Method in class apps.PD_OrientationViewer
Sets the slice orientation to XY, XZ, or YZ, then updates the slice list and display.
setSourceData(float[]) - Method in class data.WildBootstrapDataSynth
Set the source data directly.
setSourceData(double[]) - Method in class data.WildBootstrapDataSynth
Set the source data directly.
setStartFromSingleDT(DT) - Method in class inverters.ThreeTensorFitter
Choose the starting point from a single diffusion tensor.
setStartFromSingleDT(DT) - Method in class inverters.TwoTensorFitter
Choose the starting point from a single diffusion tensor.
setStartNode(int) - Method in class tractography.Edge
 
setStartPoint(double[]) - Method in class inverters.DiffTensorFitter
Sets the parameters to an alternative starting point.
setStartPoint(double[]) - Method in class inverters.DiffTensorUnConFitter
 
setStdsFromMeanF(double) - Method in class apps.SphFuncPD_Stats
Adjust the threshold on small peaks to ignore.
setStepParams(double[]) - Method in class simulation.SimulationParams
sets the parameters for the step generator
setSubstrateDims(double[]) - Method in class simulation.geometry.substrates.CylinderSubstrate
change the substrate dimensions
setTemperature(double) - Method in class optimizers.SimulatedAnnealingOptimizer
 
setThreshold(double) - Method in class numerics.NumericalIntegration
 
setTraceD(double) - Static method in class data.StandardTestFunctions
Sets the trace of the components diffusion tensors.
setTractStatistic(String) - Method in class tractography.TractStatisticFilter
Sets the statistic to be computed for each tract.
setTractStatistic(String) - Method in class tractography.TractStatisticImage
Sets the tract statistic.
setTransformation(RealMatrix) - Static method in class data.StandardTestFunctions
Sets the transformation.
setTransIntoSeedSpace(RealMatrix) - Method in class tractography.StreamlineROI_Filter
Sets the transformation that warps the streamlines from diffusion space into seed space.
setTruncateLoops(boolean) - Method in class tractography.StreamlineROI_Filter
 
setVerbosity(int) - Static method in class tools.DB
Sets the verbosity level.
setVerbosityInst(int) - Method in class tools.DB
Sets the verbosity level for an instance of the class.
setVertex(int, double[]) - Method in class simulation.geometry.elements.Triangle
reset vertex i with the given vector
setVertices(double[][]) - Method in class simulation.geometry.elements.Triangle
replaces all vertices with the values given
setWaypoints(short[][][]) - Method in class tractography.StreamlineROI_Filter
Set the waypoint volume.
setWeight(double) - Method in class tractography.Edge
 
setZoomedSlice() - Method in class apps.PD_OrientationViewer
Called if zoomed section is moved, the slice is changed, or the plane view is switched.
sform_code - Variable in class imaging.Nifti1Dataset
 
SFPD_PARAMSCALE - Static variable in class sphfunc.SphericalFunction
Parameter scale used in the Powell routine for finding principal directions.
SHORT - Static variable in class data.ExternalDataSource
 
Shredder - Class in apps
Extracts periodic chunks from binary data.
Shredder(String[]) - Constructor for class apps.Shredder
 
sigma - Static variable in class tools.CL_Initializer
The expected standard deviation of the noise in the data.
sigmas() - Method in class numerics.ACG_Distribution
 
SIGN(double, double) - Static method in class optimizers.ConjGradMinimizer
Translation of the nrutil function SIGN.
signalAt(double[], double, double) - Method in class data.CylinderModel
 
sim_amender_type - Static variable in class simulation.SimulationParams
type of step amender
sim_cAngle - Static variable in class simulation.SimulationParams
angle between crossing fibres on crossing substrate.
sim_compartmentSignal - Static variable in class simulation.SimulationParams
compartmental signal output? default no
sim_crossSectionImageSize - Static variable in class simulation.SimulationParams
size of cross section image in pixels
sim_cyl_D1 - Static variable in class simulation.SimulationParams
core diffusivity of myelinated cylinders
sim_cyl_D2 - Static variable in class simulation.SimulationParams
sheath diffusivity in meylinated cyliners
sim_cyl_dist_size - Static variable in class simulation.SimulationParams
number of cylinders along a side of square distributed radius cylinder substrate
sim_cyl_max_r - Static variable in class simulation.SimulationParams
distributed cylinder max radius (meters)
sim_cyl_min_r - Static variable in class simulation.SimulationParams
distributed cylinder min radius (meters)
sim_cyl_pack - Static variable in class simulation.SimulationParams
cylinder packing
sim_cyl_r - Static variable in class simulation.SimulationParams
fixed cylinder radius (meters)
sim_cyl_R - Static variable in class simulation.SimulationParams
fixed cylinder separation (meters)
sim_cyl_r1 - Static variable in class simulation.SimulationParams
outer radius of myelinated cylinders
sim_delta - Static variable in class simulation.SimulationParams
simulation delta value
sim_DELTA - Static variable in class simulation.SimulationParams
simulation diffusion time
sim_delta_set - Static variable in class simulation.SimulationParams
has the simualtion set delta?
sim_DELTA_set - Static variable in class simulation.SimulationParams
has the simulation set DELTA?
sim_drawCrossSection - Static variable in class simulation.SimulationParams
flag to set drawing of cross section of cylinder substrate (TODO: squashy cyls only)
sim_G - Static variable in class simulation.SimulationParams
simulation G value
sim_G_set - Static variable in class simulation.SimulationParams
has the simulation set gradient strength?
sim_geomType - Static variable in class simulation.SimulationParams
the default geometry type
sim_inflamm_increments - Static variable in class simulation.SimulationParams
 
sim_initial - Static variable in class simulation.SimulationParams
initial conditions flag
sim_L - Static variable in class simulation.SimulationParams
the substrate size
sim_l - Static variable in class simulation.SimulationParams
cell size for cellular lattice
sim_N_walkers - Static variable in class simulation.SimulationParams
number of walkers in the simulation
sim_num_cylinders - Static variable in class simulation.SimulationParams
number of cylinders on substrate
sim_num_facets - Static variable in class simulation.SimulationParams
number of facets on a facetted cylinder
sim_onlyRun - Static variable in class simulation.SimulationParams
only run a single iteration of the substrate? -1 if no.
sim_p - Static variable in class simulation.SimulationParams
membrane transition probability
sim_p_perc - Static variable in class simulation.SimulationParams
percolation prob for perc lattic
sim_p_stick - Static variable in class simulation.SimulationParams
probability for sticking to a membrane
sim_p_unstick - Static variable in class simulation.SimulationParams
probability for a spin unsticking itself from a membrane
sim_plyfile - Static variable in class simulation.SimulationParams
name of PLY file to read
sim_postproStatsFname - Static variable in class simulation.SimulationParams
name of post-processing stats file
sim_separate_runs - Static variable in class simulation.SimulationParams
indicates whether to run a separate simulation for each voxel (true) or generate all voxels from the same simulation
sim_spatial_grid_size - Static variable in class simulation.SimulationParams
density of square grid used for sptial sorting
sim_statsfile - Static variable in class simulation.SimulationParams
name of stats output file
sim_StatsModType - Static variable in class simulation.SimulationParams
type of statistics to generate
sim_stepType - Static variable in class simulation.SimulationParams
the type of step distibution
sim_stripethickness - Static variable in class simulation.SimulationParams
stripe width for striped substrate
sim_surfaceDiffusivity - Static variable in class simulation.SimulationParams
diffusivity on surface of an object for sticky walks (default is one order of magnitude lower than free diffusivity)
sim_T2 - Static variable in class simulation.SimulationParams
compartmental T2 in seconds (default vals: 2.28s for bulk CSF, 10% of that on surface)
sim_tmax - Static variable in class simulation.SimulationParams
number of timesteps in the diffusion simulation
sim_voxelSize - Static variable in class simulation.SimulationParams
the size of the central voxel
sim_voxelSizeFrac - Static variable in class simulation.SimulationParams
fraction of outer voxel voxel on mesh substrate used to generate data
simParams - Static variable in class tools.CL_Initializer
diffusion simulation parameters object
SimplePICoRandomizer - Class in tractography
Provides samples from the fibre orientation PDF.
SimulableScheme - Interface in imaging
 
SimulatedAnnealingOptimizer - Class in optimizers
General superclass for simulated annealing optimization.
SimulatedAnnealingOptimizer(double, int, long, String, Random) - Constructor for class optimizers.SimulatedAnnealingOptimizer
 
simulation - package simulation
 
simulation.dynamics - package simulation.dynamics
 
simulation.geometry - package simulation.geometry
 
simulation.geometry.elements - package simulation.geometry.elements
 
simulation.geometry.substrates - package simulation.geometry.substrates
 
simulation.measurement - package simulation.measurement
 
SimulationParams - Class in simulation
Camino fibre reconstruction and tracking toolkit SimulationParams (simulation) contains extra parameters for simulations not contained in imaging params.
SimulationParams(int, int, double, int, SubstrateFactory.SubstrateType, StepGeneratorFactory.StepType, double, SimulableScheme) - Constructor for class simulation.SimulationParams
 
SimulationParams(int, int, double, int, SubstrateFactory.SubstrateType, StepGeneratorFactory.StepType, double, double) - Constructor for class simulation.SimulationParams
alternate constructor with no scheme object.
sin() - Method in class numerics.Complex
Returns the sine.
singleDT_Stats(double[][]) - Static method in class apps.SequenceStats
Computes the statistics for single DT data and outputs them.
SingularValueDecomposition - Class in Jama
Singular Value Decomposition.
SingularValueDecomposition(Matrix) - Constructor for class Jama.SingularValueDecomposition
Construct the singular value decomposition
sinh(double) - Static method in class numerics.Complex
 
sinh() - Method in class numerics.Complex
 
size() - Method in class tools.LEFilterOutputStream
Returns the number of bytes written to this little endian output stream.
size() - Method in class tractography.VoxelList
 
sizeof_hdr - Variable in class imaging.Nifti1Dataset
 
skewness() - Method in class sphfunc.SphericalFunction
The skewness is the cube root of order 3 normalised moment.
skip(int) - Static method in class apps.Shredder
Skip bytes from the input stream.
skip(long) - Method in class tools.BufferedInflaterInputStream
Inefficiently skips bytes by reading them, but faster than the superclass method, which seems to take forever.
skipBytes(int) - Method in class tools.EndianNeutralDataInputStream
Skip exactly n bytes of input in the underlying input stream.
skipBytes(int) - Method in class tools.LEFilterInputStream
Skip exactly n bytes of input in the underlying input stream.
slice_code - Variable in class imaging.Nifti1Dataset
 
slice_dim - Variable in class imaging.Nifti1Dataset
 
slice_duration - Variable in class imaging.Nifti1Dataset
 
slice_end - Variable in class imaging.Nifti1Dataset
 
slice_start - Variable in class imaging.Nifti1Dataset
 
SNR - Static variable in class tools.CL_Initializer
The signal to noise ratio in synthetic data.
snrDiff(double[][]) - Static method in class apps.EstimateSNR
Computes SNR from a single ROI, imaged twice.
snrMult(double[][]) - Static method in class apps.EstimateSNR
Computes SNR from a single ROI, imaged many times.
snrStdv(double[][], double[]) - Static method in class apps.EstimateSNR
Computes SNR from a single ROI with noise variance estimated from background.
solve(Matrix) - Method in class Jama.CholeskyDecomposition
Solve A*X = B
solve(Matrix) - Method in class Jama.LUDecomposition
Solve A*X = B
solve(Matrix) - Method in class Jama.Matrix
Solve A*X = B
solve(Matrix) - Method in class Jama.QRDecomposition
Least squares solution of A*X = B
solve(SVAnalyticalFunction, double, double, double) - Static method in class numerics.NewtonRaphsonSolver
Solve the function f(x) - c = 0.
solveTranspose(Matrix) - Method in class Jama.Matrix
Solve X*A = B, which is also A'*X' = B'
sort(EigenvalueDecomposition) - Static method in class numerics.EigenSystem3D
Sorts eigen system by eigenvalue, greatest first.
sort(RealMatrix) - Static method in class numerics.EigenSystem3D
Sorts eigen system by eigenvalue, greatest first.
sortedEigenSystem() - Method in class misc.DT
Returns a sorted eigensystem, with the largest eigenvalue and corresponding eigenvector in column 0.
spacing - Variable in class imaging.MetaImageHeader
Voxel dimensions.
SparseVectorImage - Class in misc
Sparsely populated 3D image.
SparseVectorImage(int[], double[]) - Constructor for class misc.SparseVectorImage
Construct an image, default interpolation is nearest neighbour.
SpatiallyVaryingStepGenerator - Class in simulation.dynamics
step generator for substrates where the diffusivity can vary spatially.
SpatiallyVaryingStepGenerator(SimulationParams, Substrate) - Constructor for class simulation.dynamics.SpatiallyVaryingStepGenerator
constructor.
spatialOptInitialised - Variable in class simulation.geometry.substrates.Substrate
flag indicating if spatial opt grid has been set or not
SPECIAL - Static variable in class simulation.SimulationParams
flag for special (debug) initial conditions.
SphDeconvKernels - Class in mesd
Purpose: Container class for deconvolution kernels.
SphDeconvKernels() - Constructor for class mesd.SphDeconvKernels
 
SphereGPD - Class in data.compartments
implents the compartment interface for an isotropic restricted compartment, Spherical boundary compartment using the GPD approximation.
SphereGPD() - Constructor for class data.compartments.SphereGPD
constructor.
SphereGPD - Class in models.compartments
Implements the compartment interface for an isotropic restricted compartment, Spherical boundary compartment using the GPD approximation.
SphereGPD() - Constructor for class models.compartments.SphereGPD
constructor.
SPHERICAL_HARMONICS - Static variable in class sphfunc.BasisSumFactory
Creates an EvenSHS object
SphericalDistributionFitter - Class in numerics
Superclass for classes that fit parametric distributions to vectors or axes on the sphere.
SphericalDistributionFitter() - Constructor for class numerics.SphericalDistributionFitter
 
SphericalFunction - Class in sphfunc
Purpose: General spherical function representation.
SphericalFunction() - Constructor for class sphfunc.SphericalFunction
 
SphericalHarmonicException - Exception in numerics
Purpose: Exception class used by the SphericalHarmonics class.
SphericalHarmonics - Class in numerics
Purpose: Spherical harmonic functions and associated Legendre polynomials.
SphericalHarmonics() - Constructor for class numerics.SphericalHarmonics
 
SphericalPoints - Class in misc
Purpose: Library of functions concerning points on the sphere.
SphericalPoints() - Constructor for class misc.SphericalPoints
 
SphericalPointSet - Class in sphfunc
Purpose: Implements a storage class for sets of points on the sphere that can read arrays out of the files downloaded from Hardin Sloane and Smith.
SphericalPointSet(String) - Constructor for class sphfunc.SphericalPointSet
Constructor reads the data from the file and stores it in data.
sphfunc - package sphfunc
 
SphFuncAnisotropy - Class in apps
Purpose: Computes the anisotropy of an input stream of spherical functions.
SphFuncAnisotropy(String[]) - Constructor for class apps.SphFuncAnisotropy
Output manager
SphFuncBitMap - Class in apps
Purpose: Generates a bitmap showing the spherical function in each voxel of a region of the input data.
SphFuncBitMap(String[]) - Constructor for class apps.SphFuncBitMap
 
SphFuncKurtosis - Class in apps
Purpose: Computes the kurtosis (fourth root of normalized fourth moment: \sqrt[4]{\int (f(x) - m)^4/\int f^4(x) dx) normalized by the anisotropy (see SphFuncAnisotropy) of an input stream of spherical functions.
SphFuncKurtosis(String[]) - Constructor for class apps.SphFuncKurtosis
Output manager
SphFuncPD_Stats - Class in apps
Purpose: Computes the peak directions of spherical functions.
SphFuncPD_Stats(String[]) - Constructor for class apps.SphFuncPD_Stats
 
SphFuncPeaksOrientationViewer - Class in apps
Simple tool to visualize principal directions of spherical function data.
SphFuncPeaksOrientationViewer(RGB_ScalarImage, double) - Constructor for class apps.SphFuncPeaksOrientationViewer
Creates and displays the viewer.
SphFuncPICoCalibrationData - Class in apps
Generates data for Hessian-based PICo calibration.
SphFuncPICoCalibrationData() - Constructor for class apps.SphFuncPICoCalibrationData
 
SphFuncSkewness - Class in apps
Purpose: Computes the skewness (cube root of normalized third moment: \sqrt[3]{\int (f(x) - m)^3/\int f^3(x) dx) of an input stream of spherical functions.
SphFuncSkewness(String[]) - Constructor for class apps.SphFuncSkewness
Output manager
SphHarmFitter - Class in apps
Purpose: Computes the anisotropy based on the spherical harmonic fit.
SphHarmFitter(String[]) - Constructor for class apps.SphHarmFitter
 
SphPDF_Fit - Class in apps
Fits a spherical PDF to a collection of axes, and outputs a result in the same format as PICoPDFs (number of PDs is assumed to be 1).
SphPDF_Fit(String[]) - Constructor for class apps.SphPDF_Fit
Output manager
SPIKE - Static variable in class simulation.SimulationParams
flag for delta-peaked initially posiitoned walkers
Split4D_NiiImage - Class in apps
Splits a 4D Nifti image into 3D component volumes.
Split4D_NiiImage(String[]) - Constructor for class apps.Split4D_NiiImage
 
sqrt() - Method in class numerics.Complex
Returns the square root.
SQUARE - Static variable in class simulation.geometry.substrates.ParallelCylinderSubstrate
 
SquashyCylinder - Class in simulation.geometry.elements
A squashy cylinder is one that deforms when it abutts another cylinder.
SquashyCylinder(double[], double, double) - Constructor for class simulation.geometry.elements.SquashyCylinder
instantiates a cylinder with no squishes parallel to z-axis
SquashyCylinder(double[], double[], double, double) - Constructor for class simulation.geometry.elements.SquashyCylinder
 
SquashyCylinder.Chord - Class in simulation.geometry.elements
little class containing the chord
SquashyInflammationSubstrate - Class in simulation.geometry.substrates
 
SquashyInflammationSubstrate(SimulationParams) - Constructor for class simulation.geometry.substrates.SquashyInflammationSubstrate
constructor.
srow_x - Variable in class imaging.Nifti1Dataset
 
srow_y - Variable in class imaging.Nifti1Dataset
 
srow_z - Variable in class imaging.Nifti1Dataset
 
StandardTestFunctions - Class in data
Purpose: Implements standard test functions.
StandardTestFunctions() - Constructor for class data.StandardTestFunctions
 
state() - Method in class misc.OrderedAcqSingleSubsetMinimizer
Gets a String representation of the current state of the system.
state() - Method in class misc.OrderedAcqSubsetMinimizer
Gets a String representation of the current state of the system.
state() - Method in class misc.OrderedAcqWeightedMinimizer
Gets a String representation of the current state of the system.
state() - Method in class optimizers.SimulatedAnnealingOptimizer
Gets a String representation of the current state of the system.
StatisticsModule - Class in simulation.measurement
derives statistical measures from the walkers directly, without recourse to a synthetic scan.
StatisticsModule(Walker[]) - Constructor for class simulation.measurement.StatisticsModule
constructor.
StatisticsModuleFactory - Class in simulation.measurement
constructs stats modules of a specified type from simulation params and walkers array.
StatisticsModuleFactory() - Constructor for class simulation.measurement.StatisticsModuleFactory
 
StatisticsModuleFactory.StatsModuleType - Enum in simulation.measurement
enum for stats module types
STATSPERPD - Static variable in class apps.SphFuncPD_Stats
The total number of values output for each direction.
StejskalTannerScheme - Class in imaging
Superclass for Stejskal-Tanner imaging schemes.
step - Variable in class simulation.dynamics.Walker
space to store next step
StepAmender - Interface in simulation.dynamics
interface describing a step amendment object.
StepAmenderFactory - Class in simulation.dynamics
factory class for producing step amender objects
StepAmenderFactory() - Constructor for class simulation.dynamics.StepAmenderFactory
 
StepAmenderFactory.AmenderType - Enum in simulation.dynamics
 
StepGenerator - Interface in simulation.dynamics
Camino fibre reconstruction and tracking toolkit Step (simulation) Contains a method protottype to get a step vector for a Walker ro use during walker update
StepGeneratorFactory - Class in simulation.dynamics
Camino fibre reconstruction and tracking toolkit StepGeneratorFactory (simulation) build step generators from given list of types.
StepGeneratorFactory() - Constructor for class simulation.dynamics.StepGeneratorFactory
 
StepGeneratorFactory.StepType - Enum in simulation.dynamics
enumerator for step generator types
stepSize() - Method in class tractography.EulerFibreTracker
 
stepSize() - Method in class tractography.RK4FibreTracker
 
Stick - Class in data.compartments
implements the compartment interface for a restricted compartment (according to Behren's ball and stick model) the Stick compartment
Stick() - Constructor for class data.compartments.Stick
constructor.
Stick - Class in models.compartments
implements the compartment interface for a restricted compartment (according to Behren's ball and stick model) the Stick compartment
Stick() - Constructor for class models.compartments.Stick
constructor.
StickAndDiffuse - Class in simulation.dynamics
 
StickAndDiffuse(Substrate) - Constructor for class simulation.dynamics.StickAndDiffuse
constructor.
StickyCylinderSubstrate - Class in simulation.geometry.substrates
 
StickyCylinderSubstrate(SimulationParams) - Constructor for class simulation.geometry.substrates.StickyCylinderSubstrate
constructor from superclass
StickyStatsModule - Class in simulation.measurement
statistics module that calculates sticky stats as well as mean-squared displacements.
StickyStatsModule(Walker[]) - Constructor for class simulation.measurement.StickyStatsModule
constructor, takes array of walkers
StickyWalker - Class in simulation.dynamics
This is a kind of Walker that stick to barriers and diffuse around on the surface for a while.
StickyWalker(double[], StepGenerator, StepGenerator, Substrate, SyntheticScan, DataOutputStream, boolean, double) - Constructor for class simulation.dynamics.StickyWalker
main constructor.
StickyWalker(double[], StepGenerator, Substrate, boolean) - Constructor for class simulation.dynamics.StickyWalker
test constructor with specified stick state.
StickyWalker(double[]) - Constructor for class simulation.dynamics.StickyWalker
test constructor with unspecified stick state, assumes unstuck.
stopExpanding() - Method in class simulation.geometry.elements.SquashyCylinder
stops this cylinder and all clones expanding due to pressure from another one.
StreamlineROI_Filter - Class in tractography
Takes as input the streamline output from a FibreTracker.
StreamlineROI_Filter(int[], double[]) - Constructor for class tractography.StreamlineROI_Filter
Initializes the filter with the dimensions of the seed space.
StreamlineROI_Filter(int, int, int, double, double, double) - Constructor for class tractography.StreamlineROI_Filter
Initializes the filter with the dimensions of the seed space.
StreamlineTractography - Class in apps
Does tractography.
StreamlineTractography(String[]) - Constructor for class apps.StreamlineTractography
 
StreamlineTractography.ImageType - Enum in apps
 
StripedCellularLattice - Class in simulation.geometry.substrates
Camino fibre reconstruction and tracking toolkit StripedCellularLattice (simulation)
StripedCellularLattice(SimulationParams) - Constructor for class simulation.geometry.substrates.StripedCellularLattice
initialises stripes of occupied cells of given thickness (given in number of cells) stripes will be parallel to the second coordinate direction.
sub(RealMatrix) - Method in class numerics.RealMatrix
Subtracts matrices.
SubsetScheme - Class in apps
Produces information about the quality of electrostatic subsets, and produces scheme files for those subsets given the scheme file for the full set.
SubsetScheme(String[]) - Constructor for class apps.SubsetScheme
 
Substrate - Class in simulation.geometry.substrates
Abstract root class of all substrates.
Substrate(SimulationParams, double[]) - Constructor for class simulation.geometry.substrates.Substrate
constructor with p specified
Substrate(double[]) - Constructor for class simulation.geometry.substrates.Substrate
constructor for testing.
SubstrateFactory - Class in simulation.geometry.substrates
Camino fibre reconstruction and tracking toolkit SubstrateFactory (simulation)
SubstrateFactory() - Constructor for class simulation.geometry.substrates.SubstrateFactory
 
SubstrateFactory.SubstrateType - Enum in simulation.geometry.substrates
 
substrateInfo - Static variable in class simulation.SimulationParams
flag to read out cylinder info
SubstrateObject - Interface in simulation.geometry.elements
substrate objects are sub-units of a substrate geometry such as a cylinder, a triangle or a complete mesh.
subtract(Complex) - Method in class numerics.Complex
Subtracts complex numbers.
sum(double[]) - Static method in class tools.ArrayOps
Returns the sum of the values in the array.
SumCP - Class in tractography
Computes the minimum connection probability to all voxels in the image.
SumCP(int, int, int) - Constructor for class tractography.SumCP
 
sumLogPDF(Vector3D, Vector3D[], double) - Static method in class numerics.WatsonDistribution
Calculate the log likelihood of a set of axes.
SVAnalyticalFunction - Class in numerics
A mathematical function that returns a single value from a single variable.
SVAnalyticalFunction(boolean) - Constructor for class numerics.SVAnalyticalFunction
 
svd() - Method in class Jama.Matrix
Singular Value Decomposition
svd() - Method in class numerics.RealMatrix
Computes the singular value decomposition U, S and V of the matrix A, so that A = U S V^T.
SVD_Exception - Exception in numerics
Purpose: Exception class used in the SVD method of RealMatrix.
SVD_Exception(String) - Constructor for exception numerics.SVD_Exception
 
swapColumns(int, int) - Method in class numerics.RealMatrix
Switches two columns of the matrix.
swapDirs(int[]) - Method in class apps.PD_OrientationViewer
 
swapRows(int, int) - Method in class numerics.RealMatrix
Switches two rows of the matrix.
symmetric() - Method in class numerics.RealMatrix
Tests whether the matrix is symmetric.
SyntheticBootstrapper - Class in data
Purpose: Source of synthetic data bootstrapped from a small number of samples.
SyntheticBootstrapper(ModelPDF, DW_Scheme, double, int, int) - Constructor for class data.SyntheticBootstrapper
Constructor includes the number of voxels in the synthetic data source.
SyntheticBootstrapper(ModelPDF, DW_Scheme, double, int, int, int) - Constructor for class data.SyntheticBootstrapper
Constructor includes the number of voxels in the synthetic data source.
SyntheticBootstrapper(ModelPDF, DW_Scheme, double, int, int, Random) - Constructor for class data.SyntheticBootstrapper
Constructor includes the number of voxels in the synthetic data source.
SyntheticData - Class in apps
Purpose: Creates a stream of synthetic data Description: Outputs a specified number of voxels worth of data synthesized from the specified test function with the specified imaging parameters and noise level.
SyntheticData(String[]) - Constructor for class apps.SyntheticData
 
SyntheticScan - Interface in simulation.measurement
Camino fibre reconstruction and tracking toolkit SyntheticScan (simulation) the object that constructs the final readings from the simulation.
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