- 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.