- r - Variable in class simulation.dynamics.Walker
-
current coords
- r0 - Variable in class simulation.dynamics.Walker
-
initial coords
- random(int, int) - Static method in class Jama.Matrix
-
Generate matrix with random elements
- randomRotMat() - Static method in class numerics.Rotations
-
Generates a random rotation matrix with random seed taken from the clock
time.
- randomRotMat(int) - Static method in class numerics.Rotations
-
Generates a seeded random rotation matrix.
- randomRotMat(Random) - Static method in class numerics.Rotations
-
Generates a random rotation matrix drawing using the random number
generator provided.
- rank() - Method in class Jama.Matrix
-
Matrix rank
- rank() - Method in class Jama.SingularValueDecomposition
-
Effective numerical matrix rank
- rbf(double, double, double, double[]) - Method in class sphfunc.RBF_Sum
-
The radial basis function itself is abstract and defined in subclasses.
- rbf(double, double, double, double[], double) - Static method in class sphfunc.TuchRBF
-
Evaluates the function at (x,y,z) assuming the centre of the
radial basis function is p.
- rbf(double, double, double, double[]) - Method in class sphfunc.TuchRBF_Sum
-
Tuch's radial basis function.
- RBF_Sum - Class in sphfunc
-
Purpose:
Function of the sphere represented using radial basis functions.
- RBF_Sum(double[]) - Constructor for class sphfunc.RBF_Sum
-
The constructor takes an array containing the coefficients.
- read(BufferedReader) - Static method in class Jama.Matrix
-
Read a matrix from a stream.
- read() - Method in class tools.BufferedInflaterInputStream
-
- read(byte[]) - Method in class tools.BufferedInflaterInputStream
-
- read(byte[], int, int) - Method in class tools.BufferedInflaterInputStream
-
- readBoolean() - Method in class tools.EndianNeutralDataInputStream
-
Reads a boolean
from the underlying input stream by
reading a single byte.
- readBoolean() - Method in class tools.LEFilterInputStream
-
Reads a boolean
from the underlying input stream by
reading a single byte.
- readByte() - Method in class tools.EndianNeutralDataInputStream
-
Reads a signed byte
from the underlying input stream
with value between -128 and 127
- readByte() - Method in class tools.LEFilterInputStream
-
Reads a signed byte
from the underlying input stream
with value between -128 and 127.
- readChar() - Method in class tools.EndianNeutralDataInputStream
-
Reads a two byte Unicode char
from the underlying
input stream.
- readChar() - Method in class tools.LEFilterInputStream
-
Reads a two byte Unicode char
from the underlying
input stream in little-endian order, low byte first.
- readCharacter() - Method in class tools.FileInput
-
Read a char value from file.
- readCharacter() - Method in class tools.KeyboardInput
-
Read a char value from keyboard input.
- readData() - Method in class imaging.Nifti1Dataset
-
Read all the data into one byte array.
- readDouble() - Method in class tools.EndianNeutralDataInputStream
-
Reads an eight byte double
from the underlying
input stream.
- readDouble() - Method in class tools.FileInput
-
Read a double value from file.
- readDouble() - Method in class tools.KeyboardInput
-
Read a double value from keyboard input.
- readDouble() - Method in class tools.LEFilterInputStream
-
- readDoubleCorrect() - Method in class imaging.EndianCorrectInputStream
-
readDoubleCorrect will return a double from the stream
- readDoubleTmcrs(short, short, short) - Method in class imaging.Nifti1Dataset
-
Read one 1D timecourse from a 4D dataset, ie all T values for
a given XYZ location.
- readDoubleVol(short) - Method in class imaging.Nifti1Dataset
-
Read one 3D volume from disk and return it as 3D double array
- readFloat(DataInputStream) - Method in class imaging.AnalyzeHeader
-
- readFloat() - Method in class tools.EndianNeutralDataInputStream
-
Reads a four byte float
from the underlying
input stream.
- readFloat() - Method in class tools.FileInput
-
Read a float value from file.
- readFloat() - Method in class tools.KeyboardInput
-
Read a float value from keyboard input.
- readFloat() - Method in class tools.LEFilterInputStream
-
- readFloatCorrect() - Method in class imaging.EndianCorrectInputStream
-
readFloatCorrect will return a float from the stream
- readFromFile(String) - Static method in class misc.SphericalPoints
-
Loads a spherical point set from a file converted by PointSetReformat
from the format output by the ElecPairsOnSphere program.
- readFSL_Affine(String) - Static method in class apps.Reorient
-
Reads an affine transformation from a file in the format output
by FSL's flirt program into a matrix object.
- readFully(byte[]) - Method in class tools.EndianNeutralDataInputStream
-
- readFully(byte[], int, int) - Method in class tools.EndianNeutralDataInputStream
-
- readFully(byte[]) - Method in class tools.LEFilterInputStream
-
- readFully(byte[], int, int) - Method in class tools.LEFilterInputStream
-
- readFunctions(String) - Static method in class numerics.PolynomialFunction
-
Reads a function from a file.
- readFunctions(String) - Static method in class numerics.PolynomialFunction1D
-
Reads a function from a file.
- readFunctions(String) - Static method in class numerics.PolynomialFunction2D
-
Reads a function from a file.
- readHeader(String) - Static method in class imaging.AnalyzeHeader
-
Reads a header from the given file.
- readHeader(String) - Static method in class imaging.ImageHeader
-
Returns the appropriate header based on the given file name.
- readHeader(String) - Static method in class imaging.MetaImageHeader
-
Read the text header from a file.
- readHeader(DataInput) - Static method in class imaging.MetaImageHeader
-
Read the text header from an input stream.
- readHeader() - Method in class imaging.Nifti1Dataset
-
Read header information into memory
- readHeader(String) - Static method in class imaging.Nifti1Dataset
-
- readInt(DataInputStream) - Method in class imaging.AnalyzeHeader
-
- readInt() - Method in class tools.EndianNeutralDataInputStream
-
Reads a four byte signed int
from the underlying
input stream.
- readInt() - Method in class tools.LEFilterInputStream
-
Reads a four byte signed int
from the underlying
input stream in little-endian order, low byte first.
- readIntCorrect() - Method in class imaging.EndianCorrectInputStream
-
readIntCorrect will return an int from the stream
- readInteger() - Method in class tools.FileInput
-
Read an int value from file.
- readInteger() - Method in class tools.KeyboardInput
-
Read an int value from keyboard input.
- readLine() - Method in class tools.EndianNeutralDataInputStream
-
Deprecated.
This method does not properly convert bytes to characters.
Use a Reader instead with a little-endian encoding.
- readLine() - Method in class tools.LEFilterInputStream
-
Deprecated.
This method does not properly convert bytes to characters.
Use a Reader instead with a little-endian encoding.
- readLong() - Method in class tools.EndianNeutralDataInputStream
-
Reads an eight byte signed long
from the underlying
input stream.
- readLong() - Method in class tools.FileInput
-
Read a long value from file.
- readLong() - Method in class tools.KeyboardInput
-
Read a long value from keyboard input.
- readLong() - Method in class tools.LEFilterInputStream
-
Reads an eight byte signed long
from the underlying
input stream in little-endian order, low byte first.
- readLongCorrect() - Method in class imaging.EndianCorrectInputStream
-
readLongCorrect will return a long from the stream
- readLUT(String) - Static method in class tractography.LookupTable
-
LUT Format: xMin xMax yMin yMax zMin zMax xStep yStep zStep valuesPerPosition .
- readNext(String, Object[]) - Static method in class apps.BinaryToText
-
Reads the next value and places it in the first element of array o
.
- readPLYfile(String, double, double) - Static method in class simulation.geometry.PLYreader
-
static method to read a named PLY format file, parse the
contents and return a Collection
of
Triangle
objects.
- readPoints(String) - Static method in class apps.PointSetToScheme
-
Reads points in the format
numPoints
x y z
x y z
...
- readPoints(String, boolean, boolean, boolean) - Static method in class apps.PointSetToScheme
-
Reads points in the format
numPoints
x y z
x y z
...
- readPoints(String, int[], double[]) - Static method in class tractography.PointListROI
-
Create an ROI from a list of points, in mm coordinates, stored as text in the format
x y z\nx y z\n...
.
- readScheme(String) - Static method in class imaging.DW_Scheme
-
Reads a scheme from a scheme file.
- readShort(DataInputStream) - Method in class imaging.AnalyzeHeader
-
- readShort() - Method in class tools.EndianNeutralDataInputStream
-
Reads a two byte signed short
from the underlying
input stream.
- readShort() - Method in class tools.LEFilterInputStream
-
Reads a two byte signed short
from the underlying
input stream in little-endian order, low byte first.
- readShortCorrect() - Method in class imaging.EndianCorrectInputStream
-
readShortCorrect will return a short from the stream
- readString() - Method in class tools.FileInput
-
Read an String value from file.
- readString() - Method in class tools.KeyboardInput
-
Read an String value from keyboard input.
- readUnsignedByte() - Method in class tools.EndianNeutralDataInputStream
-
Reads an unsigned byte
from the underlying
input stream with value between 0 and 255
- readUnsignedByte() - Method in class tools.LEFilterInputStream
-
Reads an unsigned byte
from the underlying
input stream with value between 0 and 255.
- readUnsignedInt() - Method in class tools.EndianNeutralDataInputStream
-
Reads a four byte unsigned int
from the underlying
input stream.
- readUnsignedShort() - Method in class tools.EndianNeutralDataInputStream
-
Reads a two byte unsigned short
from the underlying
input stream in little endian order, low byte first.
- readUnsignedShort() - Method in class tools.LEFilterInputStream
-
Reads a two byte unsigned short
from the underlying
input stream in little-endian order, low byte first.
- readUTF() - Method in class tools.EndianNeutralDataInputStream
-
Reads a string of no more than 65,535 characters
from the underlying input stream using UTF-8
encoding.
- readUTF() - Method in class tools.LEFilterInputStream
-
Reads a string of no more than 65,535 characters
from the underlying input stream using UTF-8
encoding.
- readVolume(int) - Method in class imaging.AnalyzeHeader
-
- readVolume(int) - Method in class imaging.ImageHeader
-
Reads a 3D Analyze volume and returns the result as double.
- readVolume(int) - Method in class imaging.MetaImageHeader
-
- readVolume(int) - Method in class imaging.Nifti1Dataset
-
- readVolumeData() - Method in class imaging.AnalyzeHeader
-
Reads a 4D Analyze volume and returns the result as double.
- readVolumeData() - Method in class imaging.ImageHeader
-
Gets all the data in the image.
- readVolumeData() - Method in class imaging.MetaImageHeader
-
Reads a data array, assuming voxel-ordered data for multi-channel data.
- readVolumeData() - Method in class imaging.Nifti1Dataset
-
Reads a 4D Analyze volume and returns the result as double.
- real() - Method in class numerics.Complex
-
Returns the real part.
- RealMatrix - Class in numerics
-
Purpose:
Matrix of real numbers.
- RealMatrix() - Constructor for class numerics.RealMatrix
-
Default constructor creates an empty matrix.
- RealMatrix(int, int) - Constructor for class numerics.RealMatrix
-
Creates a matrix full of zeros with the specified size.
- RealMatrix(double[][]) - Constructor for class numerics.RealMatrix
-
Creates a matrix using the supplied array as the entries.
- RealSH - Class in sphfunc
-
Purpose:
Real part of spherical harmonic function.
- RealSH(int, int) - Constructor for class sphfunc.RealSH
-
Constructor requires order and the index.
- RealSH(int, int, double) - Constructor for class sphfunc.RealSH
-
Constructor requires order, index and a constant scaling factor.
- RectGradSteTanScheme - Class in imaging
-
Stejskal-Tanner scheme with rectangular gradient blocks.
- RectGradTRSE_Scheme - Class in imaging
-
Twice-refocused scheme with rectangular gradient pulses.
- RegionOfInterest - Interface in tractography
-
Interface for a tractography region of interest.
- regular - Variable in class imaging.Nifti1Dataset
-
- reInit() - Method in class mesd.MESD_Fitter
-
Reinitialises the parameters of the function to be minimised to the
starting position.
- relResidThresh - Static variable in class mesd.MESD_Inversion
-
The threshold on the RMS relative fitting error.
- removeExtension(int) - Method in class imaging.Nifti1Dataset
-
Remove an extension from a header
- removeShortTracts(TractCollection, int) - Static method in class tractography.TractCollection
-
Remove small Tracts from a collection.
- Reorient - Class in apps
-
Purpose:
Does diffusion tensor reorientation to accompany an image
transformation.
- Reorient() - Constructor for class apps.Reorient
-
- reorientation - Static variable in class tools.CL_Initializer
-
Name of the reorientation strategy to use.
- RepBS_DT_TractographyImage - Class in tractography
-
Each call to #getPDs(int, int, int) returns a new bootstrap estimate of the PDs.
- RepBS_DT_TractographyImage(float[][][][][], double[], int[][][], ModelIndex[], DW_Scheme, Random) - Constructor for class tractography.RepBS_DT_TractographyImage
-
- replaceTensorList(double[], DT[], String) - Static method in class apps.Reorient
-
Puts a list of diffusion tensors in a single voxel into a data
array for output.
- replaceTract(Tract, int) - Method in class tractography.TractCollection
-
Replace a Tract in this collection.
- resample(double) - Method in class tractography.Tract
-
Resample the points to a minimum resolution, such that the distance between
points is no more than stepSize
.
- reset() - Static method in class data.StandardTestFunctions
-
Resets all the functions' components to the defaults.
- resetRandomization() - Method in class tractography.NeighbourChoiceInterpolator
-
- resetRandomization() - Method in interface tractography.ProbabilisticInterpolator
-
Resets the PICo randomization, so that new samples will be drawn from the ODFs.
- residualVectorMapFile - Static variable in class tools.CL_Initializer
-
Name of the residual vector map file for inversions that compute it.
- RestoreDT_Inversion - Class in inverters
-
Purpose:
Fit the diffusion tensor with outlier rejection.
- RestoreDT_Inversion(DW_Scheme, double) - Constructor for class inverters.RestoreDT_Inversion
-
Default constructor.
- RestoreDT_Inversion(DW_Scheme, double, int) - Constructor for class inverters.RestoreDT_Inversion
-
This constructor takes the imaging sequence parameters and an index
specifying the type of non-linear fitting to use.
- result() - Method in class tractography.CP_StatMap
-
Do the statistical computation and return the result.
- result() - Method in class tractography.MaxCP
-
- result() - Method in class tractography.MeanCP
-
- result() - Method in class tractography.MedianCP
-
- result() - Method in class tractography.MinCP
-
- result() - Method in class tractography.SumCP
-
- RGB_ScalarImage - Class in apps
-
Produces a scalar-modulated RGB image, colored by the tensor eigenvector or ODF peak direction.
- RGB_ScalarImage(Vector3D[][][][], double[], double[][][], double, double) - Constructor for class apps.RGB_ScalarImage
-
- rgbGamma() - Method in class apps.RGB_ScalarImage
-
- RK4FibreTracker - Class in tractography
-
Superclass for trackers that use Euler's method to track through the data.
- RK4FibreTracker(TractographyImage, double, double) - Constructor for class tractography.RK4FibreTracker
-
Construct an RK4FibreTracker with additional options set.
- rotate(double, Vector3D) - Method in class numerics.Vector3D
-
- rotatePointSet(double[][], RealMatrix) - Static method in class misc.SphericalPoints
-
Rotates a list of points.
- rotateTensor(DT, Vector3D) - Static method in class numerics.Rotations
-
Rotate a tensor so that it's e1 is aligned with vector.
- rotateVector(Vector3D, Vector3D, double) - Static method in class numerics.Rotations
-
Rotate original by angle theta about axis.
- rotateVector(Vector3D, RealMatrix) - Static method in class numerics.Rotations
-
Apply a rotation matric to a vector.
- rotationCentre - Variable in class imaging.MetaImageHeader
-
CenterOfRotation
- rotationIndex - Static variable in class tools.CL_Initializer
-
Index of the random rotation index to apply to the test function.
- Rotations - Class in numerics
-
Purpose:
Various methods for generating and using rotation matrices.
- Rotations() - Constructor for class numerics.Rotations
-
- rows() - Method in class numerics.RealMatrix
-
Returns the number of rows.
- runMainLoop() - Method in class simulation.DiffusionSimulation
-
runs the simualtion.