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R

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.
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