- 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.