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C

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
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