- M - Static variable in class tools.CL_Initializer
-
The number of zero measurements.
- mag() - Method in class numerics.Complex
-
Returns the magnitude.
- magic - Variable in class imaging.Nifti1Dataset
-
- magic(int) - Static method in class Jama.examples.MagicSquareExample
-
Generate magic square test matrix.
- MagicSquareExample - Class in Jama.examples
-
Example of use of Matrix Class, featuring magic squares.
- MagicSquareExample() - Constructor for class Jama.examples.MagicSquareExample
-
- main(String[]) - Static method in class apps.CombineTwoFibreLUTs
-
- main(String[]) - Static method in class apps.ConnectivityMapping
-
- main(String[]) - Static method in class apps.ConsistencyFraction
-
- main(String[]) - Static method in class apps.CountSeeds
-
- main(String[]) - Static method in class apps.CP_Stats
-
- main(String[]) - Static method in class apps.DataStats
-
- main(String[]) - Static method in class apps.DeconvToCamenoFormat
-
- main(String[]) - Static method in class apps.EntryPoint
-
unified entrypoint for all camino commands from
commandline.
- main(String[]) - Static method in class apps.F_TestThresholdSelector
-
- main(String[]) - Static method in class apps.GatherStats
-
- main(String[]) - Static method in class apps.GenerateMFR_LUT
-
- main(String[]) - Static method in class apps.ImportSH_Coeffs
-
- main(String[]) - Static method in class apps.MESD
-
- main(String[]) - Static method in class apps.MultiFibreReconStats
-
- main(String[]) - Static method in class apps.PD_OrientationViewer
-
- main(String[]) - Static method in class apps.Reorient
-
- main(String[]) - Static method in class apps.RGB_ScalarImage
-
- main(String[]) - Static method in class apps.SchemeToFSL
-
- main(String[]) - Static method in class apps.SequenceStats
-
- main(String[]) - Static method in class apps.SphFuncPICoCalibrationData
-
- main(String[]) - Static method in class apps.TargetProbsToASCII
-
- main(String[]) - Static method in class apps.ThresholdB0
-
- main(String[]) - Static method in class apps.TractCounter
-
- main(String[]) - Static method in class apps.TractShredder
-
- main(String[]) - Static method in class apps.TractStatistics
-
- main(String[]) - Static method in class apps.VoxelMean
-
reads in voxels one at a time, calculates means, outputs
mean voxel.
- main(String[]) - Static method in class apps.VTK_Streamlines
-
- main(String[]) - Static method in class apps.WriteZeros
-
- main(String[]) - Static method in class fitters.BallAndStickLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.BallAndStickLM_OffGaussFitter
-
- main(String[]) - Static method in class fitters.BallAndStickLM_RicianFitter
-
- main(String[]) - Static method in class fitters.BallAndStickMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.BallCylinderAstrocylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.BallCylinderAstrocylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallCylinderAstrosticksLM_Fitter
-
- main(String[]) - Static method in class fitters.BallCylinderAstrosticksMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallCylinderDotLM_Fitter
-
- main(String[]) - Static method in class fitters.BallCylinderDotMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallCylinderLM_Fitter
-
- main(String[]) - Static method in class fitters.BallCylinderMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallCylinderSphereLM_Fitter
-
- main(String[]) - Static method in class fitters.BallCylinderSphereMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersAstrocylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersAstrocylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersAstrosticksLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersAstrosticksMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersDotLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersDotMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersSphereLM_Fitter
-
- main(String[]) - Static method in class fitters.BallGDRCylindersSphereMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickAstrocylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickAstrocylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickAstrosticksLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickAstrosticksMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickDotLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickDotMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.BallStickMCMC_Fitter
-
- main(String[]) - Static method in class fitters.BallStickMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.BallStickSphereLM_Fitter
-
- main(String[]) - Static method in class fitters.BallStickSphereMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.BiexponLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.BiexponMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.BiZeppelinLM_Fitter
-
- main(String[]) - Static method in class fitters.BiZeppelinMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.MMWMD_BasicLM_DirectFitter
-
- main(String[]) - Static method in class fitters.MMWMD_BasicMCMC_Fitter
-
- main(String[]) - Static method in class fitters.MMWMD_BasicMultiRunLM_DirectFitter
-
- main(String[]) - Static method in class fitters.MMWMD_FixedLM_DirectFitter
-
- main(String[]) - Static method in class fitters.MMWMD_FixedMCMC_Fitter
-
- main(String[]) - Static method in class fitters.MMWMD_FixedMultiRunLM_DirectFitter
-
- main(String[]) - Static method in class fitters.MMWMD_InVivoLM_DirectFitter
-
- main(String[]) - Static method in class fitters.MMWMD_InVivoLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.MMWMD_InVivoMCMC_Fitter
-
- main(String[]) - Static method in class fitters.MMWMD_InVivoMultiRunLM_DirectFitter
-
- main(String[]) - Static method in class fitters.TensorCylinderAstrocylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorCylinderAstrocylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorCylinderAstrosticksLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorCylinderAstrosticksMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorCylinderDotLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorCylinderDotMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorCylinderLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorCylinderMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorCylinderSphereLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorCylinderSphereMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersAstrocylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersAstrocylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersAstrosticksLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersAstrosticksMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersDotLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersDotMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersSphereLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorGDRCylindersSphereMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickAstrocylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickAstrocylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickAstrosticksLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickAstrosticksMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickDotLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickDotMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickSphereLM_Fitter
-
- main(String[]) - Static method in class fitters.TensorStickSphereMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderAstrocylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderAstrocylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderAstrosticksLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderAstrosticksMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderDotCSF_LM_DirectFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderDotCSF_MultiRunLM_DirectFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderDotLM_DirectFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderDotLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderDotLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderDotMCMC_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderDotMultiRunLM_DirectFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderDotMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderDotMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderLM_DirectFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderMultiRunLM_DirectFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderSphereLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderSphereMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderSphereMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderTortLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinCylinderTortMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersAstrocylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersAstrocylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersAstrosticksLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersAstrosticksLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersAstrosticksMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersAstrosticksMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersDotLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersDotLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersDotMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersDotMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersSphereLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersSphereLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersSphereMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinGDRCylindersSphereMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickAstrocylindersLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickAstrocylindersLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickAstrocylindersMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickAstrocylindersMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickAstrosticksLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickAstrosticksLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickAstrosticksMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickAstrosticksMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickDotLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickDotLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickDotMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickDotMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickLM_DirectFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickMultiRunLM_DirectFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickSphereLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickSphereLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickSphereMultiRunLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickSphereMultiRunLM_GaussianFitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickTortLM_Fitter
-
- main(String[]) - Static method in class fitters.ZeppelinStickTortMultiRunLM_Fitter
-
- main(String[]) - Static method in class imaging.AnalyzeHeader
-
- main(String[]) - Static method in class imaging.GradientWaveform_Scheme
-
testing entrypoint.
- main(String[]) - Static method in class imaging.Nifti1Dataset
-
main routine is used only for testing
- main(String[]) - Static method in class Jama.examples.MagicSquareExample
-
- main(String[]) - Static method in class Jama.test.TestMatrix
-
- main(String[]) - Static method in class mesd.SphDeconvKernels
-
- main(String[]) - Static method in class numerics.BinghamFitter
-
- main(String[]) - Static method in class numerics.ErrorFunction
-
evaluates the error function over the interval [-4.0, 4.0] and outputs
the results to stderr
- main(String[]) - Static method in class numerics.GammaRandom
-
- main(String[]) - Static method in class numerics.TwoFibreBipolarWatsonFitter
-
- main(String[]) - Static method in class numerics.TwoFibreFixedPropWatsonFitter
-
- main(String[]) - Static method in class numerics.TwoFibreWatsonFitter
-
- main(String[]) - Static method in class optimizers.ConjGradMinimizerTest
-
Creates an object and calls minimisation routine.
- main(String[]) - Static method in class optimizers.MarquardtMinimiserTest
-
Creates an object and calls minimisation routine.
- main(String[]) - Static method in class optimizers.MCMCMinimiserTest
-
Creates an object and calls minimisation routine.
- main(String[]) - Static method in class simulation.DiffusionSimulation
-
- main(String[]) - Static method in class simulation.dynamics.CylindricalSurfaceStepGenerator
-
- main(String[]) - Static method in class simulation.dynamics.FixedLengthStepGenerator
-
- main(String[]) - Static method in class simulation.dynamics.SpatiallyVaryingStepGenerator
-
- main(String[]) - Static method in class simulation.dynamics.StickyWalker
-
- main(String[]) - Static method in class simulation.dynamics.Walker
-
main is just a test method
- main(String[]) - Static method in class simulation.geometry.elements.BasicCylinder
-
entrypoint.
- main(String[]) - Static method in class simulation.geometry.elements.BoundingBox
-
- main(String[]) - Static method in class simulation.geometry.elements.FacetCylinder
-
- main(String[]) - Static method in class simulation.geometry.elements.Line
-
local entrypoint.
- main(String[]) - Static method in class simulation.geometry.elements.Quad
-
entrypoint.
- main(String[]) - Static method in class simulation.geometry.elements.SquashyCylinder
-
- main(String[]) - Static method in class simulation.geometry.elements.Triangle
-
- main(String[]) - Static method in class simulation.geometry.PLYreader
-
- main(String[]) - Static method in class simulation.geometry.substrates.CellularLattice
-
- main(String[]) - Static method in class simulation.geometry.substrates.CylinderSubstrate
-
- main(String[]) - Static method in class simulation.geometry.substrates.MeshSubstrate
-
test ply substrate reading and intra cellular routine
- main(String[]) - Static method in class simulation.geometry.substrates.ParallelCylinderSubstrate
-
test code for barrier crossing with cylinders
instantiates a square lattice with R=2.0, r=0.5 and a
walker at r=(1.4,1) with a step of s=(0.2,0) which
should take it across the barrier at (1.5, 1.0)
giving t=0.1
- main(String[]) - Static method in class simulation.geometry.substrates.PercCellularLattice
-
- main(String[]) - Static method in class simulation.geometry.substrates.PercolationSubstrate
-
test construction of percolation substrate
- main(String[]) - Static method in class simulation.geometry.substrates.StripedCellularLattice
-
- main(String[]) - Static method in class simulation.geometry.substrates.Substrate
-
- main(String[]) - Static method in class simulation.geometry.substrates.SubstrateFactory
-
- main(String[]) - Static method in class simulation.measurement.AgnosticScan
-
main entrypoint.
- main(String[]) - Static method in class simulation.measurement.MSdispStatsModule
-
parse a stats file into human readable form
- main(String[]) - Static method in class simulation.measurement.StickyStatsModule
-
instead of doing the full set of stats, this entrypoint parses
an existing binary stats file into csv and does the post-simulation
stats on it.
- main(String[]) - Static method in class simulation.SimulationParams
-
- main(String[]) - Static method in class sphfunc.ImagSH
-
- main(String[]) - Static method in class tools.CL_Initializer
-
- makeStep(double[]) - Method in class simulation.dynamics.Walker
-
make a specified step
- mapDTData(VoxelOrderDataSource, LookupTable[], OutputManager) - Static method in class apps.PICoPDFs
-
Get PICo PDFs for DT data.
- mapSFData(VoxelOrderDataSource, String, boolean, String[], OutputManager) - Static method in class apps.PICoPDFs
-
Get PICo PDFs for SF data.
- mapStepIntoSubstrate(Walker, double[], double[]) - Method in class simulation.geometry.substrates.CrossingCylinderSubstrate
-
overrides the default step mapper to take account of the rotated patch
in the coordinate system.
- mapStepIntoSubstrate(Walker, double[], double[]) - Method in class simulation.geometry.substrates.Substrate
-
maps the given step into the substrate coordinates.
- markAsParsed(int) - Static method in class tools.CL_Initializer
-
Mark a single argument i
as parsed.
- markAsParsed(int, int) - Static method in class tools.CL_Initializer
-
Mark sequential arguments as parsed, from i
to
i + numArgs - 1
.
- MarkovChainMonteCarlo - Class in optimizers
-
Purpose:
General Markov Chain Monte Carlo minimisation algorithm.
- MarkovChainMonteCarlo() - Constructor for class optimizers.MarkovChainMonteCarlo
-
Constructor.
- MarkovChainMonteCarloException - Exception in optimizers
-
Purpose:
Exception class used in MCMC Minimiser.
- MarkovChainMonteCarloException() - Constructor for exception optimizers.MarkovChainMonteCarloException
-
Default constructor
- MarkovChainMonteCarloException(String) - Constructor for exception optimizers.MarkovChainMonteCarloException
-
Constructor
- MarquardtChiSqFitter - Class in optimizers
-
Purpose:
Model fitting algorithm using a Levenburg Marquardt algorithm.
- MarquardtChiSqFitter() - Constructor for class optimizers.MarquardtChiSqFitter
-
- MarquardtMinimiser - Class in optimizers
-
Purpose:
General Levenburg Marquardt minimisation algorithm.
- MarquardtMinimiser() - Constructor for class optimizers.MarquardtMinimiser
-
- MarquardtMinimiserException - Exception in optimizers
-
Purpose:
Exception class used in Marquardt Minimiser.
- MarquardtMinimiserException() - Constructor for exception optimizers.MarquardtMinimiserException
-
- MarquardtMinimiserException(String) - Constructor for exception optimizers.MarquardtMinimiserException
-
- MarquardtMinimiserNonConvergenceException - Exception in optimizers
-
Purpose:
Exception class used in Marquardt Minimiser.
- MarquardtMinimiserNonConvergenceException() - Constructor for exception optimizers.MarquardtMinimiserNonConvergenceException
-
- MarquardtMinimiserNonConvergenceException(String) - Constructor for exception optimizers.MarquardtMinimiserNonConvergenceException
-
- MarquardtMinimiserTest - Class in optimizers
-
Purpose:
Simple test example for Marquardt minimiser class.
- MarquardtMinimiserTest() - Constructor for class optimizers.MarquardtMinimiserTest
-
Basic constructor.
- Maths - Class in Jama.util
-
- Maths() - Constructor for class Jama.util.Maths
-
- MatlabArrayDataSource - Class in data
-
Purpose:
Base class for data sources of data from files and input streams.
- MatlabArrayDataSource(double[][][][]) - Constructor for class data.MatlabArrayDataSource
-
Constructor receives a data array from matlab process.
- Matrix - Class in Jama
-
Jama = Java Matrix class.
- Matrix(int, int) - Constructor for class Jama.Matrix
-
Construct an m-by-n matrix of zeros.
- Matrix(int, int, double) - Constructor for class Jama.Matrix
-
Construct an m-by-n constant matrix.
- Matrix(double[][]) - Constructor for class Jama.Matrix
-
Construct a matrix from a 2-D array.
- Matrix(double[][], int, int) - Constructor for class Jama.Matrix
-
Construct a matrix quickly without checking arguments.
- Matrix(double[], int) - Constructor for class Jama.Matrix
-
Construct a matrix from a one-dimensional packed array
- matrixFile - Static variable in class tools.CL_Initializer
-
Name of the matrix file for linear reconstructions.
- max(double[]) - Static method in class tools.ArrayOps
-
Returns the largest value in the array.
- MaxCP - Class in tractography
-
Computes the maximum connection probability to each voxel in the image from any seed point in an ROI.
- MaxCP(int, int, int) - Constructor for class tractography.MaxCP
-
- MaxEntProfile - Class in sphfunc
-
Purpose:
Function of the sphere represented using the maximum entropy
multiplicative basis.
- MaxEntProfile(double[], double[]) - Constructor for class sphfunc.MaxEntProfile
-
Creates a max.
- maxOrder - Static variable in class tools.CL_Initializer
-
The maximum order in the fitted spherical harmonic series.
- maxTensorComponents - Static variable in class tools.CL_Initializer
-
Maximum number of components in classified model fitting.
- MCMC_Fitter - Class in fitters
-
Purpose:
General purpose MCMC fitter with implementations of various
features of all fitters that use MCMC.
- MCMC_Fitter() - Constructor for class fitters.MCMC_Fitter
-
Default constructor.
- MCMC_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.MCMC_Fitter
-
Constructor sets up various required objects for MCMC.
- MCMC_GaussianMinimizer - Class in optimizers
-
Purpose:
This class is used by fitter classes.
- MCMC_GaussianMinimizer() - Constructor for class optimizers.MCMC_GaussianMinimizer
-
Default constructor.
- MCMC_GaussianMinimizer(DW_Scheme, ParametricModel, Codec, Prior, Perturbation, double) - Constructor for class optimizers.MCMC_GaussianMinimizer
-
Constructor needs all the following:
- MCMC_Minimizer - Class in optimizers
-
Purpose:
Abstract MCMC class implementing Minimizer interfase.
- MCMC_Minimizer() - Constructor for class optimizers.MCMC_Minimizer
-
- MCMC_OffGaussMinimizer - Class in optimizers
-
Purpose:
This class is used by fitter classes.
- MCMC_OffGaussMinimizer() - Constructor for class optimizers.MCMC_OffGaussMinimizer
-
Default constructor.
- MCMC_OffGaussMinimizer(DW_Scheme, ParametricModel, Codec, Prior, Perturbation, double) - Constructor for class optimizers.MCMC_OffGaussMinimizer
-
Constructor needs all the following:
- MCMC_RicianMinimizer - Class in optimizers
-
Purpose:
This class is used by fitter classes.
- MCMC_RicianMinimizer() - Constructor for class optimizers.MCMC_RicianMinimizer
-
Default constructor.
- MCMC_RicianMinimizer(DW_Scheme, ParametricModel, Codec, Prior, Perturbation, double) - Constructor for class optimizers.MCMC_RicianMinimizer
-
Constructor needs all the following:
- MCMCMinimiserTest - Class in optimizers
-
Purpose:
Simple test example for MarkovChainMonteCarlo minimiser class.
- MCMCMinimiserTest() - Constructor for class optimizers.MCMCMinimiserTest
-
Basic constructor.
- mcmcStatsFile - Static variable in class tools.CL_Initializer
-
Name of a file to output MCMC statistics.
- mean() - Method in class sphfunc.SphericalFunction
-
The mean of the function is the order 1 moment.
- mean(double[][]) - Method in class sphfunc.SphericalFunction
-
The mean of the function is the order 1 moment.
- mean(double[]) - Static method in class tools.ArrayOps
-
Returns the mean value in the array.
- meanAxis() - Method in class numerics.WatsonDistribution
-
- MeanCP - Class in tractography
-
Computes the mean connection probability to all voxels in the image.
- MeanCP(int, int, int) - Constructor for class tractography.MeanCP
-
- MeanDiff - Class in apps
-
Purpose:
Computes the mean diffusivity (trace/3) of each diffusion tensor.
- MeanDiff(String[]) - Constructor for class apps.MeanDiff
-
- meanSTDMaxAndMin(double[][], int) - Static method in class apps.InversionStats
-
Computes the mean, standard deviation, maximum and minimum of a column of
a 2D array.
- median(double[]) - Static method in class tools.ArrayOps
-
Returns the median value in the array.
- MedianCP - Class in tractography
-
Computes the median connection probability to all voxels in the image.
- MedianCP(int, int, int) - Constructor for class tractography.MedianCP
-
- mePointSet - Static variable in class tools.CL_Initializer
-
Specifies the set of reconstruction directions for maximum entropy
deconvolution if it is different from the direction set specified in the
scheme file.
- mesd - package mesd
-
- MESD - Class in apps
-
Purpose:
Runs maximum entropy spherical deconvolution on each voxel's worth of
data on the input stream.
- MESD() - Constructor for class apps.MESD
-
- MESD_Fitter - Class in mesd
-
Purpose:
Non-linear least squares fitter of the maximum entropy representation of
the spherical deconvolution.
- MESD_Fitter(double[][], int, double[], int) - Constructor for class mesd.MESD_Fitter
-
Constructor.
- MESD_Inversion - Class in mesd
-
Purpose:
Provides methods for fitting max.
- MESD_Inversion(DW_Scheme, double[], int) - Constructor for class mesd.MESD_Inversion
-
This constructor sets up the default fitter.
- mesdf - Variable in class mesd.MESD_Inversion
-
Does the MESD fitting.
- MeshSubstrate - Class in simulation.geometry.substrates
-
- MeshSubstrate(SimulationParams) - Constructor for class simulation.geometry.substrates.MeshSubstrate
-
read a substrate from the named PLY file and scale it to the
specified length.
- MetaImageHeader - Class in imaging
-
Meta image header, provides support for a common ITK file format.
- MetaImageHeader() - Constructor for class imaging.MetaImageHeader
-
Sets all values to their default.
- MetaImageHeader.AnatomicalOrientation - Enum in imaging
-
Supported anatomical orientations [L|R] [A|P] [I|S].
- MetaImageHeader.DataType - Enum in imaging
-
Data type enum.
- MetaImageHeader.ObjectType - Enum in imaging
-
Object type enum.
- mfrStats(double[][], int, double) - Static method in class apps.SequenceStats
-
Computes the statistics for data from a multiple-fibre reconstruction and
outputs them.
- midpoint() - Method in class simulation.geometry.elements.Line
-
returns the midpoint of the line in new array
- min(double[]) - Static method in class tools.ArrayOps
-
Returns the smallest value in the array.
- MinCP - Class in tractography
-
Computes the minimum connection probability to all voxels in the image.
- MinCP(int, int, int) - Constructor for class tractography.MinCP
-
- minimise(double[], double) - Method in class optimizers.ConjGradMinimizer
-
Runs the minimization.
- minimise() - Method in class optimizers.LM_Minimizer
-
- minimise() - Method in class optimizers.MarkovChainMonteCarlo
-
Runs the minimization.
- minimise() - Method in class optimizers.MarquardtMinimiser
-
Runs the minimization.
- minimise() - Method in interface optimizers.Minimizer
-
Runs the minimization.
- minimise() - Method in class optimizers.MultiRunMinimizer
-
Run the minimizer repeatedly from perturbed starting points and
concatenate the result.
- minimise(double[], double) - Method in class optimizers.PowellMinimiser
-
Performs the actual minimisation given a starting point and convergence
threshold.
- minimize() - Method in class optimizers.SimulatedAnnealingOptimizer
-
Runs the minimization.
- Minimizer - Interface in optimizers
-
Purpose:
Interface for objects that act as minimizers for model fitting.
- MinimizerException - Exception in optimizers
-
Purpose:
General Exception class for Minimizer objects.
- MinimizerException() - Constructor for exception optimizers.MinimizerException
-
- MinimizerException(String) - Constructor for exception optimizers.MinimizerException
-
- minus(Matrix) - Method in class Jama.Matrix
-
C = A - B
- minus(Vector3D) - Method in class numerics.Vector3D
-
Subtract another vector from this one.
- minusEquals(Matrix) - Method in class Jama.Matrix
-
A = A - B
- misc - package misc
-
- MMWMD_BasicLM_DirectFitter - Class in fitters
-
Purpose:
Fits the most basic minimal model of white matter diffusion, as
used for the simulations in Alexander et al NIMG 2010, using one run
of a Levenburg Marquardt with any specified noise model.
- MMWMD_BasicLM_DirectFitter() - Constructor for class fitters.MMWMD_BasicLM_DirectFitter
-
Default constructor required for derived classes.
- MMWMD_BasicLM_DirectFitter(DW_Scheme) - Constructor for class fitters.MMWMD_BasicLM_DirectFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_BasicLM_DirectFitter(DW_Scheme, String[], double[]) - Constructor for class fitters.MMWMD_BasicLM_DirectFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_BasicMCMC_Fitter - Class in fitters
-
Purpose:
Fits the basic MMWMD model using MCMC and with a specified
noise model.
- MMWMD_BasicMCMC_Fitter() - Constructor for class fitters.MMWMD_BasicMCMC_Fitter
-
Default constructor required for derived classes.
- MMWMD_BasicMCMC_Fitter(DW_Scheme) - Constructor for class fitters.MMWMD_BasicMCMC_Fitter
-
Basic constructor extracts model particulars and calls
full constructor.
- MMWMD_BasicMCMC_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.MMWMD_BasicMCMC_Fitter
-
Constructor sets up various required objects for MCMC.
- MMWMD_BasicMultiRunLM_DirectFitter - Class in fitters
-
Purpose:
Fits the basic MMWMD model using multiple runs of a Levenburg
Marquardt and a specified noise model.
- MMWMD_BasicMultiRunLM_DirectFitter(DW_Scheme, int, int) - Constructor for class fitters.MMWMD_BasicMultiRunLM_DirectFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_FixedLM_DirectFitter - Class in fitters
-
Purpose:
Fits the minimal model of white matter diffusion, as described
in Alexander et al NIMG 2010, with fixed tissue settings using one
run of a Levenburg Marquardt with any specified noise model.
- MMWMD_FixedLM_DirectFitter() - Constructor for class fitters.MMWMD_FixedLM_DirectFitter
-
Default constructor required for derived classes.
- MMWMD_FixedLM_DirectFitter(DW_Scheme) - Constructor for class fitters.MMWMD_FixedLM_DirectFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_FixedLM_DirectFitter(DW_Scheme, String[], double[]) - Constructor for class fitters.MMWMD_FixedLM_DirectFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_FixedMCMC_Fitter - Class in fitters
-
Purpose:
Fits the MMWMD fixed tissue model using MCMC and with a
specified noise model.
- MMWMD_FixedMCMC_Fitter() - Constructor for class fitters.MMWMD_FixedMCMC_Fitter
-
Default constructor required for derived classes.
- MMWMD_FixedMCMC_Fitter(DW_Scheme) - Constructor for class fitters.MMWMD_FixedMCMC_Fitter
-
Basic constructor extracts model particulars and calls
full constructor.
- MMWMD_FixedMCMC_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.MMWMD_FixedMCMC_Fitter
-
Constructor sets up various required objects for MCMC.
- MMWMD_FixedMultiRunLM_DirectFitter - Class in fitters
-
Purpose:
Fits the MMWMD fixed tissue model using multiple runs of a
Levenburg Marquardt and a specified noise model.
- MMWMD_FixedMultiRunLM_DirectFitter(DW_Scheme, int, int) - Constructor for class fitters.MMWMD_FixedMultiRunLM_DirectFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_InVivoLM_DirectFitter - Class in fitters
-
Purpose:
Fits the minimal model of white matter diffusion, as described
in Alexander et al NIMG 2010, with in-vivo settings using one run
of a Levenburg Marquardt with any specified noise model.
- MMWMD_InVivoLM_DirectFitter() - Constructor for class fitters.MMWMD_InVivoLM_DirectFitter
-
Default constructor required for derived classes.
- MMWMD_InVivoLM_DirectFitter(DW_Scheme) - Constructor for class fitters.MMWMD_InVivoLM_DirectFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_InVivoLM_DirectFitter(DW_Scheme, String[], double[]) - Constructor for class fitters.MMWMD_InVivoLM_DirectFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_InVivoLM_GaussianFitter - Class in fitters
-
Purpose:
Fits the minimal model of white matter diffusion, as described
in Alexander et al NIMG 2010, with in-vivo settings using one run
of a Levenburg Marquardt and assuming a Gaussian noise model.
- MMWMD_InVivoLM_GaussianFitter() - Constructor for class fitters.MMWMD_InVivoLM_GaussianFitter
-
Default constructor required for derived classes.
- MMWMD_InVivoLM_GaussianFitter(DW_Scheme) - Constructor for class fitters.MMWMD_InVivoLM_GaussianFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_InVivoLM_GaussianFitter(DW_Scheme, String[], double[]) - Constructor for class fitters.MMWMD_InVivoLM_GaussianFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- MMWMD_InVivoMCMC_Fitter - Class in fitters
-
Purpose:
Fits the MMWMD in-vivo model using MCMC and with a specified
noise model.
- MMWMD_InVivoMCMC_Fitter() - Constructor for class fitters.MMWMD_InVivoMCMC_Fitter
-
Default constructor required for derived classes.
- MMWMD_InVivoMCMC_Fitter(DW_Scheme) - Constructor for class fitters.MMWMD_InVivoMCMC_Fitter
-
Basic constructor extracts model particulars and calls
full constructor.
- MMWMD_InVivoMCMC_Fitter(DW_Scheme, String[], double[]) - Constructor for class fitters.MMWMD_InVivoMCMC_Fitter
-
Constructor sets up various required objects for MCMC.
- MMWMD_InVivoMultiRunLM_DirectFitter - Class in fitters
-
Purpose:
Fits the MMWMD in-vivo model using multiple runs of a Levenburg
Marquardt and a specified noise model.
- MMWMD_InVivoMultiRunLM_DirectFitter(DW_Scheme, int, int) - Constructor for class fitters.MMWMD_InVivoMultiRunLM_DirectFitter
-
Constructor implements the mapping between model and optimized
parameters in the Codec object.
- mmwmddiff - Static variable in class tools.CL_Initializer
-
Intrinsic diffusivity in the MMWMD models.
- mod() - Method in class numerics.Complex
-
Returns the modulus.
- mod() - Method in class numerics.Vector3D
-
- ModelFit - Class in apps
-
Purpose:
Diffusion data inversion application using model fitting.
- ModelFit(String[]) - Constructor for class apps.ModelFit
-
- modelfitting - Static variable in class tools.CL_Initializer
-
indicates if we are using our compartment model for fitting or not
- ModelIndex - Enum in inverters
-
Codes for model-based inversions.
- ModelPDF - Interface in data
-
Purpose:
General interface for models for the diffusion displacement density
function.
- models - package models
-
- models.compartments - package models.compartments
-
- modelToOpt(double[]) - Method in class fitters.Codec
-
Maps the model parameters to the optimized parameters.
- modSquared() - Method in class numerics.Vector3D
-
- moment(int) - Method in class sphfunc.SphericalFunction
-
Computes the order-th moment of the function over the
sphere.
- moment(int, double[][]) - Method in class sphfunc.SphericalFunction
-
Computes the order-th moment of the function over the
sphere.
- more() - Method in class data.BootstrapDataSynthesizer
-
- more() - Method in class data.compartments.CompartmentModel
-
have we done all the voxels we've been asked for?
- more() - Method in interface data.DataSource
-
Tests whether there are unprocessed voxels in the data source.
- more() - Method in class data.DataSynthesizer
-
- more() - Method in class data.DataSynthFromInput
-
- more() - Method in class data.MatlabArrayDataSource
-
- more() - Method in class data.ScannerOrderDataSource
-
- more() - Method in class data.SyntheticBootstrapper
-
- more() - Method in class data.VoxelOrderDataSource
-
- more() - Method in class data.WildBootstrapDataSynth
-
- more() - Method in class models.compartments.CompartmentModel
-
have we done all the voxels we've been asked for?
- more() - Method in class simulation.DiffusionSimulation
-
- more() - Method in class tractography.TractSource
-
- moreCandidates() - Method in class simulation.geometry.substrates.Substrate
-
are there more candidates to check?
- MSdispStatsModule - Class in simulation.measurement
-
generates mean-squared displacements
- MSdispStatsModule(Walker[]) - Constructor for class simulation.measurement.MSdispStatsModule
-
constructor, takes array of walkers
- MTRandom - Class in numerics
-
- MTRandom() - Constructor for class numerics.MTRandom
-
The default constructor for an instance of MTRandom.
- MTRandom(boolean) - Constructor for class numerics.MTRandom
-
This version of the constructor can be used to implement identical
behaviour to the original C code version of this algorithm including
exactly replicating the case where the seed value had not been set
prior to calling genrand_int32.
- MTRandom(long) - Constructor for class numerics.MTRandom
-
This version of the constructor simply initialises the class with
the given 64 bit seed value.
- MTRandom(byte[]) - Constructor for class numerics.MTRandom
-
This version of the constructor initialises the class with the
given byte array.
- MTRandom(int[]) - Constructor for class numerics.MTRandom
-
This version of the constructor initialises the class with the
given integer array.
- MultiFibreReconStats - Class in apps
-
Purpose:
Computes statistics of properties of the multiple-fibre
reconstruction outputs.
- multiply(double[]) - Method in class misc.DT
-
Multiplies the vector by the diffusion tensor.
- MultiRunLM_GaussianMinimizer - Class in optimizers
-
Purpose:
Runs the LM_Gaussian minimizer multiple times from different starting
points and concatenates the results.
- MultiRunLM_GaussianMinimizer(DW_Scheme, ParametricModel, Codec, Perturbation, int, int) - Constructor for class optimizers.MultiRunLM_GaussianMinimizer
-
- MultiRunLM_Minimizer - Class in optimizers
-
Purpose:
Multi-run minimizer specifically for LM minimization.
- MultiRunLM_Minimizer() - Constructor for class optimizers.MultiRunLM_Minimizer
-
- MultiRunLM_Minimizer(DW_Scheme, ParametricModel, Codec, Perturbation, int, int) - Constructor for class optimizers.MultiRunLM_Minimizer
-
- MultiRunLM_OffGaussMinimizer - Class in optimizers
-
Purpose:
Runs the LM minimizer with offset Gaussian noise model multiple
times from different starting points and concatenates the results.
- MultiRunLM_OffGaussMinimizer(DW_Scheme, ParametricModel, Codec, Perturbation, int, int, double) - Constructor for class optimizers.MultiRunLM_OffGaussMinimizer
-
- MultiRunLM_RicianMinimizer - Class in optimizers
-
Purpose:
Runs the LM minimizer with Rician noise model multiple
times from different starting points and concatenates the results.
- MultiRunLM_RicianMinimizer(DW_Scheme, ParametricModel, Codec, Perturbation, int, int, double) - Constructor for class optimizers.MultiRunLM_RicianMinimizer
-
- MultiRunMinimizer - Class in optimizers
-
Purpose:
Runs another minimizer multiple times from different starting
points and concatenates the results.
- MultiRunMinimizer() - Constructor for class optimizers.MultiRunMinimizer
-
Basic constructor required for inheritance.
- MultiRunMinimizer(DW_Scheme, ParametricModel, Codec, Perturbation, int, int) - Constructor for class optimizers.MultiRunMinimizer
-
Constructor needs all the following:
- MultiTensorInversion - Class in inverters
-
Purpose:
Fits models selected according to an input voxel
classification.
- MultiTensorInversion(DW_Scheme, String, ModelIndex[][], int) - Constructor for class inverters.MultiTensorInversion
-
This constructor requires the details of the sequence, the name
of the file containing the voxel classification and the list of
indices of the inverters.
- MyelinatedCylinder - Class in simulation.geometry.elements
-
Thick-walled cylinder.
- MyelinatedCylinder(double[], double, double, double, double, double) - Constructor for class simulation.geometry.elements.MyelinatedCylinder
-
- MyelinatedCylinder(double[], double[], double, double, double, double, double) - Constructor for class simulation.geometry.elements.MyelinatedCylinder
-