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M

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
 
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