A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 

L

lambda1 - Static variable in class tools.CL_Initializer
Alternative setting for lambda1 in the standard test functions.
lastStickTime - Variable in class simulation.dynamics.StickyWalker
the last time we got stuck
LEFilterInputStream - Class in tools
A little-endian input stream reads two's complement, little-endian integers, floating-point numbers, and characters and returns them as Java primitive types.
LEFilterInputStream(InputStream) - Constructor for class tools.LEFilterInputStream
Creates a new little-endian input stream and chains it to the input stream specified by the in argument.
LEFilterOutputStream - Class in tools
A little endian output stream writes primitive Java numbers and characters to an output stream in a little endian format.
LEFilterOutputStream(OutputStream) - Constructor for class tools.LEFilterOutputStream
Creates a new little endian output stream and chains it to the output stream specified by the out argument.
length() - Method in class tractography.Tract
 
Line - Class in simulation.geometry.elements
 
Line(double, double, double, double) - Constructor for class simulation.geometry.elements.Line
 
LinearADC_Inversion - Class in inverters
Purpose: Fits the apparent diffusion coefficient on the assumption of isotropic diffusion.
LinearADC_Inversion(DW_Scheme) - Constructor for class inverters.LinearADC_Inversion
The constructor requires the details of the sequence used to generate the data that will be processed.
LinearBasisFunction - Class in sphfunc
Purpose: General class for functions of the sphere used as linear basis functions.
LinearBasisFunction() - Constructor for class sphfunc.LinearBasisFunction
Default constructor
LinearBasisSum - Class in sphfunc
Purpose: General class for functions of the sphere represented as the sum of basis functions.
LinearBasisSum() - Constructor for class sphfunc.LinearBasisSum
Default constructor
LinearDT_Inversion - Class in inverters
Purpose: Fits the diffusion tensor.
LinearDT_Inversion(DW_Scheme) - Constructor for class inverters.LinearDT_Inversion
The constructor requires the details of the sequence used to generate the data that will be processed.
LinearInversion - Class in inverters
Purpose: Performs a linear inversion Description: Reads any linear transformation matrix in from a file and uses it to transform input data.
LinearInversion(DW_Scheme, String, boolean, boolean) - Constructor for class inverters.LinearInversion
The constructor requires the details of the sequence used to generate the data that will be processed and the name of the file containing the linear transformation matrix.
LinearRecon - Class in apps
Purpose: Performs a linear reconstruction in each voxel.
LinearRecon(String[]) - Constructor for class apps.LinearRecon
 
LinIntDTEulerFibreTracker - Class in tractography
Tracks through DT data using Euler's method, with linear interpolation of the tensor elements.
LinIntDTEulerFibreTracker(DT_TractographyImage, double, double) - Constructor for class tractography.LinIntDTEulerFibreTracker
 
LinIntVectorEulerFibreTracker - Class in tractography
Tracks through vector data using Euler's method, with linear interpolation of the vector elements.
LinIntVectorEulerFibreTracker(TractographyImage, double, double) - Constructor for class tractography.LinIntVectorEulerFibreTracker
 
LinIntVectorRK4FibreTracker - Class in tractography
Tracks through vector data using the fourth-rder Runge-Kutta method, with linear interpolation of the vector elements at each step or sub step.
LinIntVectorRK4FibreTracker(TractographyImage, double, double) - Constructor for class tractography.LinIntVectorRK4FibreTracker
 
ListDistributionCompartment - Class in data.compartments
 
ListDistributionCompartment(int, ParametricModel) - Constructor for class data.compartments.ListDistributionCompartment
 
ListDistributionCompartment(double[][], String, int) - Constructor for class data.compartments.ListDistributionCompartment
constructor.
ListDistributionCompartment - Class in models.compartments
 
ListDistributionCompartment(int, ParametricModel) - Constructor for class models.compartments.ListDistributionCompartment
 
ListDistributionCompartment(double[][], String, int) - Constructor for class models.compartments.ListDistributionCompartment
constructor.
LM_GaussianMinimizer - Class in optimizers
Purpose: Levenberg-Marquardt algorithm for minimizing chi-squared objective function, ie Gaussian noise model, with equal variance on each measurement.
LM_GaussianMinimizer() - Constructor for class optimizers.LM_GaussianMinimizer
Default constructor.
LM_GaussianMinimizer(DW_Scheme, ParametricModel, Codec) - Constructor for class optimizers.LM_GaussianMinimizer
Constructor needs all the following:
LM_Minimizer - Class in optimizers
 
LM_Minimizer() - Constructor for class optimizers.LM_Minimizer
 
LM_OffGaussMinimizer - Class in optimizers
Purpose: Levenberg-Marquardt algorithm for minimizing chi-squared objective function with the offset Gaussian noise model, which adds an expected offset to each measurement from Rician noise bias; see Jones and Basser MRM 2004; Alexander "Modelling fitting and sampling..." 2009.
LM_OffGaussMinimizer(DW_Scheme, ParametricModel, Codec, double) - Constructor for class optimizers.LM_OffGaussMinimizer
Constructor needs all the following:
LM_RicianMinimizer - Class in optimizers
Purpose: Levenberg-Marquardt algorithm for minimizing the log-likelihood objective function using a Rician noise model assuming equal underlying variances on the real and imaginary Gaussian models on each measurement.
LM_RicianMinimizer(DW_Scheme, ParametricModel, Codec, double) - Constructor for class optimizers.LM_RicianMinimizer
Constructor needs all the following:
loadData(String, int, int, int, int, String) - Static method in class apps.F_TestThresholdSelector
Loads the data into a 4D array.
localDataFile - Variable in class imaging.MetaImageHeader
This variable contains the absolute path to the file containing the data (which may be the same as the file containing the header).
logException(Exception, String, Level) - Static method in exception misc.LoggedException
Logs an exception.
logExceptionSevere(Exception, String, String) - Static method in exception misc.LoggedException
Logs an exception at the SEVERE level, also logs an additional message.
logExceptionSevere(Exception, String) - Static method in exception misc.LoggedException
Logs an exception at the SEVERE level.
logExceptionWarning(Exception, String, String) - Static method in exception misc.LoggedException
Logs an exception at the WARNING level, also logs an additional message.
logExceptionWarning(Exception, String) - Static method in exception misc.LoggedException
Logs an exception at the WARNING level.
LoggedException - Exception in misc
Superclass for a RuntimeException that is automatically logged at the SEVERE level upon construction.
LoggedException() - Constructor for exception misc.LoggedException
Create an exception with an empty message.
LoggedException(Throwable) - Constructor for exception misc.LoggedException
 
LoggedException(String, Throwable) - Constructor for exception misc.LoggedException
 
LoggedException(String) - Constructor for exception misc.LoggedException
 
logHyper1F1(double, double, double, double) - Static method in class numerics.WatsonDistribution
 
logNormC() - Method in class numerics.BinghamDistribution
 
logPDF(Vector3D) - Method in class numerics.ACG_Distribution
Gets the log pdf of the distribution.
logPDF(Vector3D) - Method in class numerics.BinghamDistribution
Evaluate the pdf of the distribution.
logPDF(Vector3D) - Method in class numerics.WatsonDistribution
Evaluate the pdf of the distribution.
logPDF(Vector3D, double) - Method in class numerics.WatsonDistribution
Evaluate the pdf of the distribution.
logPDF(Vector3D, Vector3D, double) - Static method in class numerics.WatsonDistribution
Evaluate the pdf of any Watson distribution.
LONG - Static variable in class data.ExternalDataSource
 
LookupTable - Class in tractography
Lookup table for PICo parameters.
LookupTable(double[][][], double[], double[], int) - Constructor for class tractography.LookupTable
 
lowestEnergyState() - Method in class misc.OrderedAcqSingleSubsetMinimizer
Gets a String representation of the lowest energy state of the system.
lowestEnergyState() - Method in class misc.OrderedAcqSubsetMinimizer
Gets a String representation of the lowest energy state of the system.
lowestEnergyState() - Method in class misc.OrderedAcqWeightedMinimizer
Gets a String representation of the lowest energy state of the system.
lowestEnergyState() - Method in class optimizers.SimulatedAnnealingOptimizer
Gets a String representation of the lowest energy state of the system.
lrLog - Static variable in class tools.CL_Initializer
Specifies whether or not the linear reconstruction should use the log measurements.
lrNormalize - Static variable in class tools.CL_Initializer
Specifies whether or not the data should be normalized before linear reconstruction.
lu() - Method in class Jama.Matrix
LU Decomposition
LUDecomposition - Class in Jama
LU Decomposition.
LUDecomposition(Matrix) - Constructor for class Jama.LUDecomposition
LU Decomposition
luinvert() - Method in class numerics.RealMatrix
Does LU inversion.
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z