- 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.