- cal_max - Variable in class imaging.Nifti1Dataset
-
- cal_min - Variable in class imaging.Nifti1Dataset
-
- calibratedTemp(double) - Method in class optimizers.SimulatedAnnealingOptimizer
-
Calibrates the temperature by moving to the nearest local minimum and calculating the mean
increase in energy of attempted state changes.
- calls - Static variable in class simulation.DiffusionSimulation
-
counter for the number of times the substrate initialiser function is called
- caminoDataTypeString() - Method in class imaging.AnalyzeHeader
-
- caminoDataTypeString() - Method in class imaging.MetaImageHeader
-
Gets the Camino data type string
- caminoDataTypeString() - Method in class imaging.Nifti1Dataset
-
Gets the Camino data type string, for passing to the DataSource classes.
- CellularLattice - Class in simulation.geometry.substrates
-
Abstract class that implements a general cubic lattice geometry
initialisation of the geometry is left abstract so that inheriting
classes may implement any pattern they choose.
- CellularLattice(SimulationParams) - Constructor for class simulation.geometry.substrates.CellularLattice
-
- centralMoment(int) - Method in class sphfunc.SphericalFunction
-
Computes the order-th central moment of the function over the
sphere.
- centralMoment(int, double[][]) - Method in class sphfunc.SphericalFunction
-
Computes the order-th central moment of the function over the
sphere.
- centre - Variable in class imaging.AnalyzeHeader
-
Centre of the Talairach coordinate system
- centreDist - Static variable in class tools.CL_Initializer
-
distance of centre of circle from centre of voxel grid
- channels - Variable in class imaging.MetaImageHeader
-
ElementNumberOfChannels, number of components.
- CHAR - Static variable in class data.ExternalDataSource
-
- checkDims(String, int[], double[]) - Static method in class imaging.ImageHeader
-
Checks data and voxel dimensions from a header with those given in the arrays.
- checkHeader() - Method in class imaging.Nifti1Dataset
-
Check the header fields for valid settings
- checkParsing(String[]) - Static method in class tools.CL_Initializer
-
Checks the arguments and logs any args that have not been marked as
parsed.
- checkQuaternion() - Method in class imaging.Nifti1Dataset
-
Check the qfac is consistent with the quaternion
- checkZeroRows() - Method in class numerics.RealMatrix
-
Test function to check for all-zero rows in matrix.
- chol() - Method in class Jama.Matrix
-
Cholesky Decomposition
- CholeskyDecomposition - Class in Jama
-
Cholesky Decomposition.
- CholeskyDecomposition(Matrix) - Constructor for class Jama.CholeskyDecomposition
-
Cholesky algorithm for symmetric and positive definite matrix.
- chop(int, int) - Method in class tractography.Tract
-
Chop off one or both ends of a tract.
- chords - Variable in class simulation.geometry.elements.SquashyCylinder
-
array of Chords and lengths
- chuck - Variable in class simulation.geometry.substrates.SquashyInflammationSubstrate
-
for debugging
- ChunkStats - Class in apps
-
Purpose:
Computes statistics of chunks of data.
- ChunkStats(String[]) - Constructor for class apps.ChunkStats
-
- CL_init(String[]) - Static method in class tools.CL_Initializer
-
The constructor requires only the array of command line arguments.
- CL_Initializer - Class in tools
-
Purpose:
Parses command line arguments common to many of the Camino applications
and sets up the common objects.
- ClassifiedModelFit - Class in apps
-
Purpose:
Classified model fitting program.
- ClassifiedModelFit(String[]) - Constructor for class apps.ClassifiedModelFit
-
- classifiedModelIndices - Static variable in class tools.CL_Initializer
-
Array of indices of the models in classified model fitting.
- clone() - Method in class Jama.Matrix
-
Clone the Matrix object.
- clone() - Method in class misc.DT
-
- clone() - Method in class numerics.Complex
-
- clone() - Method in class numerics.RealMatrix
-
- cloneHasStopped() - Method in class simulation.geometry.elements.SquashyCylinder
-
a stop instruction from a clone.
- close() - Method in class data.OutputManager
-
Closes and tidies up.
- close() - Method in class inverters.DiffusionInversion
-
Perform final closing operations on the inverter.
- close() - Method in class inverters.RestoreDT_Inversion
-
Overrides the default to output the outlier histogram.
- close() - Method in class inverters.WeightedLinearDT_Inversion
-
Closes the noise map output stream, if open.
- close() - Static method in class tools.DB
-
Closes the output file.
- close() - Method in class tools.EndianNeutralDataInputStream
-
- close() - Method in class tools.FileInput
-
Close the file when finished
- close() - Method in class tools.FileOutput
-
Close the file when finished
- closedSurface - Static variable in class simulation.geometry.PLYreader
-
is the object a closed surface (specified in file header)
- closeInst() - Method in class tools.DB
-
Closes the output file for an instance of the class.
- Codec - Class in fitters
-
Purpose:
Base class for codec that maps model parameters to optimization
parameters during model fitting in order to enforce constraints on
parameter values.
- Codec() - Constructor for class fitters.Codec
-
- columns() - Method in class numerics.RealMatrix
-
Returns the number of columns.
- CombineTwoFibreLUTs - Class in apps
-
Combines LUTs with different crossing angles into one.
- CombineTwoFibreLUTs() - Constructor for class apps.CombineTwoFibreLUTs
-
- combineTwoFibreLUTs(String[], double[], double) - Static method in class apps.CombineTwoFibreLUTs
-
Combine two tensor LUTs.
- compareTo(Object) - Method in class tractography.Voxel
-
- CompartmentFactory - Class in data.compartments
-
holds factory method for generating individual compartments
for the compartment model
- CompartmentFactory() - Constructor for class data.compartments.CompartmentFactory
-
- CompartmentFactory - Class in models.compartments
-
holds factory method for generating individual compartments
for the compartment model
- CompartmentFactory() - Constructor for class models.compartments.CompartmentFactory
-
- CompartmentFitter - Class in fitters
-
Fitter class specific to compartment models.
- CompartmentFitter() - Constructor for class fitters.CompartmentFitter
-
- CompartmentModel - Class in data.compartments
-
generalised compartment model for generating data from a weighted
sum of two or more compartments.
- CompartmentModel(String[], double[]) - Constructor for class data.compartments.CompartmentModel
-
constructor.
- CompartmentModel(String[], double[], DW_Scheme) - Constructor for class data.compartments.CompartmentModel
-
constructor with scheme for use in data synthesis.
- CompartmentModel - Class in models.compartments
-
generalised compartment model for generating data from a weighted
sum of two or more compartments.
- CompartmentModel(String[], double[]) - Constructor for class models.compartments.CompartmentModel
-
constructor.
- CompartmentModel(String[], double[], DW_Scheme) - Constructor for class models.compartments.CompartmentModel
-
constructor with scheme for use in data synthesis.
- compartmentModel - Static variable in class tools.CL_Initializer
-
Indicates whether to synthesise data using a compartment model
- CompartmentModelOrientationViewer - Class in apps
-
Simple tool to visualize principal directions of compartment model data.
- CompartmentModelOrientationViewer(RGB_ScalarImage, double) - Constructor for class apps.CompartmentModelOrientationViewer
-
Creates and displays the viewer.
- compartmentNames - Static variable in class tools.CL_Initializer
-
list of names for each compartment in compartment model
- CompartmentType - Enum in data.compartments
-
enumerates all types of single compartments currently implemented.
- CompartmentType - Enum in models.compartments
-
enumerates all types of single compartments currently implemented.
- Complex - Class in numerics
-
Purpose:
Complex number class.
- Complex(double, double) - Constructor for class numerics.Complex
-
Constructor from real and imaginary parts.
- Complex() - Constructor for class numerics.Complex
-
Default constructor creates zero.
- ComplexNumberException - Exception in numerics
-
Purpose:
Exception for Complex class.
- components() - Method in class imaging.AnalyzeHeader
-
- components() - Method in class imaging.ImageHeader
-
Analyze : nImages
Meta : channels
NIFTI-1 : DIM5
- components() - Method in class imaging.MetaImageHeader
-
- components() - Method in class imaging.Nifti1Dataset
-
- compParams - Static variable in class tools.CL_Initializer
-
list of parsed parameters for compartmentModel
- compressedData - Variable in class imaging.MetaImageHeader
-
CompressedData, if true, data is compressed with zlib.
- computeEdges(ArrayList<Edge>, ArrayList<Tract>, HashMap<Integer, ArrayList<Tract>>) - Static method in class apps.ConnectivityMapping
-
Computes the number of tracts connecting any two ROI and their length and weight
- computeIsotropicMask(double) - Method in class tractography.DT_TractographyImage
-
Computes boolean mask, a voxel is true if the voxel contains one DT, and the DT's
FA is below the threshold.
- computeIsotropicMask() - Method in class tractography.TractographyImage
-
Computes mask for tracking.
- computeIsotropicMask(double[][][], double) - Method in class tractography.TractographyImage
-
Computes mask for tracking.
- computeNoiseVariance(RealMatrix[]) - Method in class inverters.WeightedLinearDT_Inversion
-
Computes the noise variance \sigma^2 = (Y - XB)^T W^2 (Y - XB) / (DOF), where
DOF is the number of degrees of freedom in the model.
- computeResidualVector(RealMatrix[]) - Method in class inverters.WeightedLinearDT_Inversion
-
- computeStat(double[], String) - Static method in class apps.DT_ShapeStatistics
-
- computeStatistic(double[][], String) - Method in class optimizers.MCMCMinimiserTest
-
Because MCMC produces set of samples for each parameter instead of one fixed value,
we can choose different statistics of that set of samples.
- computeStrength(ArrayList<Edge>, HashMap<Integer, Integer>) - Static method in class apps.ConnectivityMapping
-
Creates a hashmap of the node intensities and the number of tracts
reaching a node.
- computeWeightedFit(double[]) - Method in class inverters.WeightedLinearDT_Inversion
-
Solves W*Y = W*X*B for B.
- computeWeightedFit(double[], double[]) - Method in class inverters.WeightedLinearDT_Inversion
-
Solves W*Y = W*X*B for B.
- concentration() - Method in class numerics.WatsonDistribution
-
- cond() - Method in class Jama.Matrix
-
Matrix condition (2 norm)
- cond() - Method in class Jama.SingularValueDecomposition
-
Two norm condition number
- ConjGradMinimizer - Class in optimizers
-
Purpose:
General Conjugate Gradients minimisation algorithm.
- ConjGradMinimizer() - Constructor for class optimizers.ConjGradMinimizer
-
- ConjGradMinimizerException - Exception in optimizers
-
Purpose:
Exception class used in ConjGradMinimizer.
- ConjGradMinimizerTest - Class in optimizers
-
Purpose:
Simple test example for conjugate gradients minimiser class.
- ConjGradMinimizerTest() - Constructor for class optimizers.ConjGradMinimizerTest
-
Basic constructor.
- conjugate() - Method in class numerics.Complex
-
Returns the complex conjugate.
- ConnectionProbabilityImage - Class in tractography
-
Connection probability image.
- ConnectionProbabilityImage(int, int, int, double, double, double) - Constructor for class tractography.ConnectionProbabilityImage
-
Initializes the filter with the dimensions of the seed space.
- ConnectivityMapping - Class in apps
-
- ConnectivityMapping() - Constructor for class apps.ConnectivityMapping
-
- ConnectivitySegmentedImage - Class in tractography
-
Labels a seed image with the target that has the maximum connection probability to each seed.
- ConnectivitySegmentedImage(FreeFormROI, short[][][], double, double, double) - Constructor for class tractography.ConnectivitySegmentedImage
-
Initializes the image with the dimensions of the seed space.
- ConsistencyFraction - Class in apps
-
Purpose:
Computes the consistency fraction from multiple-fibre reconstruction
outputs.
- constructTestFunction(double[]) - Static method in class tools.CL_Initializer
-
Constructs a test function from an array of values given on the command
line.
- constructWithCopy(double[][]) - Static method in class Jama.Matrix
-
Construct a matrix from a copy of a 2-D array.
- containsMMPoint(Point3D) - Method in class tractography.FreeFormROI
-
Tests to see if a point measured in MM coordinates is in this region.
- containsMMPoint(Point3D) - Method in class tractography.PointListROI
-
Tests to see if point
is within a voxel that contains one or more seed
points.
- containsMMPoint(Point3D) - Method in interface tractography.RegionOfInterest
-
Tests if a point is within a voxel that contains one or more seed points.
- containsVoxel(int, int, int) - Method in class tractography.FreeFormROI
-
Tests to see if a specific voxel is in this region.
- containsVoxel(int, int, int) - Method in class tractography.PointListROI
-
Tests to see if a specific voxel is in this region.
- containsVoxel(int, int, int) - Method in interface tractography.RegionOfInterest
-
Tests to see if a specific voxel is in this region.
- contractBy(double[]) - Method in class misc.DT
-
Contracts the diffusion tensor by a vector.
- ConvergenceException - Exception in numerics
-
- ConvergenceException(String) - Constructor for exception numerics.ConvergenceException
-
- convertTo3D(String, String, String) - Static method in class imaging.Nifti1Dataset
-
Convert a 4D nii file to a series of 3D NIFTI volumes.
- convt - Static variable in class mesd.MESD_Inversion
-
Convergence threshold in Lev.
- copy() - Method in class Jama.Matrix
-
Make a deep copy of a matrix
- copyHeader(Nifti1Dataset) - Method in class imaging.Nifti1Dataset
-
- copyTransforms(Nifti1Dataset) - Method in class imaging.Nifti1Dataset
-
Sets the transform information: pixdims, qform, qoffset, quaternion, sform
Sets the transform fields of this header equal to those of the source.
- cos() - Method in class numerics.Complex
-
Returns the cosine.
- cosh(double) - Static method in class numerics.Complex
-
- cosh() - Method in class numerics.Complex
-
- CountSeeds - Class in apps
-
Counts the number of seed voxels (voxels with values > 0).
- CountSeeds() - Constructor for class apps.CountSeeds
-
- CP_StatMap - Class in tractography
-
Superclass for memory-efficient storage of multiple scalar images.
- CP_StatMap(int, int, int) - Constructor for class tractography.CP_StatMap
-
- CP_Stats - Class in apps
-
Reads PICo probability maps and computes a voxel-based statistic of them.
- CP_Stats() - Constructor for class apps.CP_Stats
-
- cross(Vector3D) - Method in class numerics.Vector3D
-
Gives vector (cross) product of this with another vector.
- crossedBy(double[], double[], double[], double[], boolean, double, double[]) - Method in class simulation.geometry.elements.Line
-
- crosses(double[], double[], double[], double[], boolean, double, double[], boolean[], double[]) - Method in class simulation.geometry.elements.BasicCylinder
-
checks if step will intersect the cylinder.
- crosses(double[], double[], double[], double[], boolean, double, double[], boolean[], double[]) - Method in class simulation.geometry.elements.FacetCylinder
-
checks cylinder crossing by identifying candidate facet
and checking line-line intersection.
- crosses(double[], double[], double[], double[], boolean, double, double[], boolean[], double[]) - Method in class simulation.geometry.elements.MyelinatedCylinder
-
- crosses(double[], double[], double[], double[], boolean, double, double[], boolean[], double[]) - Method in class simulation.geometry.elements.SquashyCylinder
-
checks if a given step crosses this cylinder, taking account
of all current chords where the cylinder abutts others
- crosses(double[], double[], double[], double[], boolean, double, double[], boolean[], double[]) - Method in interface simulation.geometry.elements.SubstrateObject
-
checks if a given step will cross a membrane in the object
- crosses(double[], double[], double[], double[], boolean, double, double[], boolean[], double[]) - Method in class simulation.geometry.elements.Triangle
-
checks intersection of a given step with the triangle.
- crossesMembrane(Walker, double[], double[], double[], double[], boolean, double, boolean[], double[]) - Method in class simulation.geometry.substrates.CellularLattice
-
checks if a step will take a walker across a membrane or not
by comparing the cell coords before and after the step.
- crossesMembrane(Walker, double[], double[], double[], double[], boolean, double, boolean[], double[]) - Method in class simulation.geometry.substrates.CrossingCylinderSubstrate
-
checks if a walker's step will take it across a membrane or not.
- crossesMembrane(Walker, double[], double[], double[], double[], boolean, double, boolean[], double[]) - Method in class simulation.geometry.substrates.CylinderSubstrate
-
checks if a walker's step will take it across a membrane or not.
- crossesMembrane(Walker, double[], double[], double[], double[], boolean, double, boolean[], double[]) - Method in class simulation.geometry.substrates.EmptySubstrate
-
- crossesMembrane(Walker, double[], double[], double[], double[], boolean, double, boolean[], double[]) - Method in class simulation.geometry.substrates.MeshSubstrate
-
- crossesMembrane(Walker, double[], double[], double[], double[], boolean, double, boolean[], double[]) - Method in class simulation.geometry.substrates.StickyCylinderSubstrate
-
wrapper for crosses membrane method.
- crossesMembrane(Walker, double[], double[], double[], double[], boolean, double, boolean[], double[]) - Method in class simulation.geometry.substrates.Substrate
-
checks if a step will cross a barrier or not
- CrossingCylinderSubstrate - Class in simulation.geometry.substrates
-
substrate will two principle directions.
- CrossingCylinderSubstrate(SimulationParams) - Constructor for class simulation.geometry.substrates.CrossingCylinderSubstrate
-
constructor for default crossing angle.
- crossSectionFig - Static variable in class simulation.SimulationParams
-
Name of file to output the cross section figure
- CSFTHRESHOLD - Static variable in class tools.CL_Initializer
-
Threshold on the q=0 measurements to detect CSF.
- Cylinder - Interface in simulation.geometry.elements
-
subinterface for cylinders.
- cylinder - Variable in class simulation.geometry.substrates.CylinderSubstrate
-
- cylinder - Variable in class simulation.geometry.substrates.SquashyInflammationSubstrate
-
array of cylinders
- CylinderFactory - Class in simulation.geometry.elements
-
cylinder factory class.
- CylinderFactory() - Constructor for class simulation.geometry.elements.CylinderFactory
-
- CylinderFactory.CylType - Enum in simulation.geometry.elements
-
- CylinderGPD - Class in data.compartments
-
- CylinderGPD() - Constructor for class data.compartments.CylinderGPD
-
constructor.
- CylinderGPD - Class in models.compartments
-
- CylinderGPD() - Constructor for class models.compartments.CylinderGPD
-
constructor.
- CylinderModel - Class in data
-
Purpose:
Simple model for the diffusion displacement density function in white matter with two
compartments.
- CylinderModel(double, double, double, double, double[]) - Constructor for class data.CylinderModel
-
constructor for volume fraction, specified diffusivities, axon radius and fibre
direction.
- CylinderSubstrate - Class in simulation.geometry.substrates
-
- CylinderSubstrate(double[], SimulationParams, boolean) - Constructor for class simulation.geometry.substrates.CylinderSubstrate
-
- cylinderType - Static variable in class simulation.SimulationParams
-
type of cylinders
- CylindricalSurfaceStepGenerator - Class in simulation.dynamics
-
generates steps such that all beginning and end points
are on the surface of a cylinder (assumes that initial
position is on the cylinder, if not oddness will ensue)
- CylindricalSurfaceStepGenerator(double) - Constructor for class simulation.dynamics.CylindricalSurfaceStepGenerator
-
test constructor.
- CylindricalSurfaceStepGenerator(SimulationParams) - Constructor for class simulation.dynamics.CylindricalSurfaceStepGenerator
-
- CylindricalSurfaceStepGenerator(SimulationParams, StickyCylinderSubstrate) - Constructor for class simulation.dynamics.CylindricalSurfaceStepGenerator
-
- CylindricalSurfaceStepGenerator(Substrate) - Constructor for class simulation.dynamics.CylindricalSurfaceStepGenerator
-
constructor that takes step length directly