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A

a - Variable in class simulation.geometry.substrates.Substrate
fraction of substrate size to distance of test boundary from actual
abutts(SquashyCylinder) - Method in class simulation.geometry.elements.SquashyCylinder
checks if this cylinder abuts another
ACG - Static variable in class tractography.DT_LookupTableGenerator
 
ACG_Distribution - Class in numerics
Angular Central Gaussian Distribution on a 3D sphere.
ACG_Distribution(RealMatrix, Random) - Constructor for class numerics.ACG_Distribution
 
ACG_Distribution(Vector3D[], double[], Random) - Constructor for class numerics.ACG_Distribution
 
ACG_Fitter - Class in numerics
This class implements several routines for fitting an ACG distribution.
add(RealMatrix) - Method in class numerics.RealMatrix
Adds matrices.
add(Vector3D, double, double) - Method in class tractography.Histogram
 
addDirToList(Vector3D) - Method in class tractography.HistBin
 
addExtension(int, String) - Method in class imaging.Nifti1Dataset
Add an extension stored in a file to a header
addGaussianNoise(double[], double, Random) - Static method in class data.DataSynthesizer
Adds Gaussian noise to each measurement.
addImage(double[][][]) - Method in class tractography.CP_StatMap
Adds an image.
addIntersectionWith(SquashyCylinder) - Method in class simulation.geometry.elements.SquashyCylinder
adds a new intersection with the given cylinder
AddNoise - Class in apps
app for adding rician noise to noiseless synthetic noiseless measurements given SNR and scheme file
AddNoise(String[]) - Constructor for class apps.AddNoise
 
addNoise(double[], double, Random) - Static method in class data.DataSynthesizer
Adds isotropic complex Gaussian noise to each measurement and takes the modulus resulting in Rician noise.
addPD(PD) - Method in class sphfunc.PDList
Adds the new PD to the list provided the list does not already contain an entry close to the new PD.
addPoint(Point3D) - Method in class tractography.Tract
Add a point.
addPoint(Point3D, double) - Method in class tractography.Tract
Adds a point.
addToMyClones(SquashyCylinder) - Method in class simulation.geometry.elements.SquashyCylinder
add a clone to the list.
addTract(Tract) - Method in class tractography.TractCollection
Adds a tract to this collection.
addTractCollection(TractCollection) - Method in class tractography.TractCollection
Adds all tracts from another TractCollection to this TractCollection.
addValue(int, int, int, double) - Method in class misc.DynamicScalarImage
Adds a value to the voxel (i,j,k), with unit weight.
addValue(int, int, int, double, double) - Method in class misc.DynamicScalarImage
Add a value to the voxel (i,j,k), with custom weight.
addValue(Point3D, double) - Method in class misc.DynamicScalarImage
Add a value to the voxel containing the point, with unit weight.
addValue(Point3D, double, double) - Method in class misc.DynamicScalarImage
Add a value to the voxel containing the point, with custom weight.
addValue(int, int, int, double) - Method in class misc.SparseVectorImage
Add a value to the voxel (i,j,k), with unit weight.
addValue(int, int, int, double, double) - Method in class misc.SparseVectorImage
Add a value to the voxel (i,j,k), with custom weight.
addValue(Point3D, double) - Method in class misc.SparseVectorImage
Add a value to the voxel containing the point, with unit weight.
addValue(Point3D, double, double) - Method in class misc.SparseVectorImage
Add a value to the voxel containing the point, with custom weight.
addValue(int, int, int, double) - Method in interface misc.VoxelwiseStatisticalImage
Add a value to the voxel (i,j,k).
addValue(Point3D, double) - Method in interface misc.VoxelwiseStatisticalImage
Add a value to the voxel containing the point.
addValue(int, int, int, double, double) - Method in interface misc.VoxelwiseStatisticalImage
Add a value to the voxel (i,j,k), with an associated weight.
addValue(Point3D, double, double) - Method in interface misc.VoxelwiseStatisticalImage
Add a value to the voxel containing the point, with an associated weight.
adjoint() - Method in class numerics.RealMatrix
Computes the adjoint matrix.
AgnosticScan - Class in simulation.measurement
agnostic scan is a passive scan module that is completely agnostic towards the actual pulse-sequence defined in the scheme file.
AgnosticScan(SimulableScheme, Walker[], Substrate) - Constructor for class simulation.measurement.AgnosticScan
constructor.
ALLCOMPS - Static variable in class simulation.SimulationParams
flag for compartmental signal: output for each component
amend(Walker, double[], double, int) - Method in class simulation.geometry.substrates.Substrate
 
amendStep(Walker, double[], double[], double[], double[], double[], double, double[], double[], double[], double[], double, int) - Method in class simulation.dynamics.ElasticReflector
amends the step for the walker by relecting it elastically off the appropriate membrane.
amendStep(Walker, double[], double[], double[], double[], double[], double, double[], double[], double[], double[], double, int) - Method in interface simulation.dynamics.StepAmender
amend a step given necessary geometric information and places to store results etc
amendStep(Walker, double[], double[], double[], double[], double[], double, double[], double[], double[], double[], double, int) - Method in class simulation.dynamics.StickAndDiffuse
if a walker is free, it sticks it with a fixed prob.
AnalyzeHeader - Class in imaging
Analyze image header, provides support for the most common header fields.
AnalyzeHeader() - Constructor for class imaging.AnalyzeHeader
Creates an AnalyzeHeader object with all of its fields set to their default value.
AnalyzeHeader(AnalyzeHeader) - Constructor for class imaging.AnalyzeHeader
Copy constructor.
anatomicalOrientation - Variable in class imaging.MetaImageHeader
AnatomicalOrientation field.
anisotropy() - Method in class sphfunc.EvenSHS
We can compute the anisotropy (sqrt of normalized second moment) analytically.
anisotropy() - Method in class sphfunc.SphericalFunction
The anisotropy is the square root of the order 2 normalised moment.
ANZ_DAT_EXT - Static variable in class imaging.Nifti1Dataset
 
ANZ_HDR_EXT - Static variable in class imaging.Nifti1Dataset
 
ANZ_HDR_SIZE - Static variable in class imaging.Nifti1Dataset
 
ANZ_MAGIC_STRING - Static variable in class imaging.Nifti1Dataset
 
applyBoundaries(Walker[]) - Method in class simulation.geometry.substrates.CellularLattice
applies periodic boundary conditions to walker positions
apps - package apps
 
arrayLeftDivide(Matrix) - Method in class Jama.Matrix
Element-by-element left division, C = A.\B
arrayLeftDivideEquals(Matrix) - Method in class Jama.Matrix
Element-by-element left division in place, A = A.\B
ArrayOps - Class in tools
Purpose: Simple operations on arrays.
ArrayOps() - Constructor for class tools.ArrayOps
 
arrayRightDivide(Matrix) - Method in class Jama.Matrix
Element-by-element right division, C = A./B
arrayRightDivideEquals(Matrix) - Method in class Jama.Matrix
Element-by-element right division in place, A = A./B
arrayTimes(Matrix) - Method in class Jama.Matrix
Element-by-element multiplication, C = A.*B
arrayTimesEquals(Matrix) - Method in class Jama.Matrix
Element-by-element multiplication in place, A = A.*B
arrFlip(byte[]) - Static method in class apps.Shredder
Reverses the order of the bytes in the array.
Astrocylinders - Class in data.compartments
Implents the compartment interface for a restricted isotropic compartment, cylinders with distributed orientations.
Astrocylinders() - Constructor for class data.compartments.Astrocylinders
constructor.
Astrocylinders - Class in models.compartments
Implents the compartment interface for a restricted isotropic compartment, cylinders with distributed orientations.
Astrocylinders() - Constructor for class models.compartments.Astrocylinders
constructor.
Astrosticks - Class in data.compartments
Implements the compartment interface for a restricted isotropic compartment, sticks with distributed orientations.
Astrosticks() - Constructor for class data.compartments.Astrosticks
constructor.
Astrosticks - Class in models.compartments
Implements the compartment interface for a restricted isotropic compartment, sticks with distributed orientations.
Astrosticks() - Constructor for class models.compartments.Astrosticks
constructor.
at(double[], double) - Method in class data.BallStick
 
at(double[], double) - Method in class data.CylinderModel
 
at(double[], double) - Method in class data.GaussianMixture
 
at(double[], double) - Method in interface data.ModelPDF
Returns the value of the function at the specified point and time.
augmentArgs(String[], String) - Static method in class tools.CL_Initializer
Augments the command-line arguments array with arguments read from a config file.
aux_file - Variable in class imaging.Nifti1Dataset
 
AxialDistribution - Interface in numerics
Interface for classes that define an axial PDF on the sphere, giving p(x) == p(-x) for any unit vector x.
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