- Walker - Class in simulation.dynamics
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Camino fibre reconstruction and tracking toolkit
Walker (simulation.dynamics)
describes a single brownian walker in a diffusion simulation
each walker has an initial position, a current position and
sums of positions during each gradient block.
- Walker(double[], StepGenerator, Substrate, SyntheticScan, DataOutputStream) - Constructor for class simulation.dynamics.Walker
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public constructor.
- Walker(double[]) - Constructor for class simulation.dynamics.Walker
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initialises a walker without a step generator.
- Walker(double[], Substrate) - Constructor for class simulation.dynamics.Walker
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initialises a walker without a step generator.
- WalkerFactory - Class in simulation.dynamics
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generate walkers of the chosen type
- WalkerFactory() - Constructor for class simulation.dynamics.WalkerFactory
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- wasExtracellular - Variable in class simulation.dynamics.StickyWalker
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flag to say whether the spin was initially extracellular or intracellular
- WATSON - Static variable in class tractography.DT_LookupTableGenerator
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- WatsonD - Class in numerics
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Description: Evaluates D_3(kappa), eqn 10.3.32 in Mardia and Jupp "Directional Statistics" (2000)
- WatsonD() - Constructor for class numerics.WatsonD
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- WatsonDistribution - Class in numerics
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Watson Distribution, kind of like a Fisher but for axial data, ie p(x) == p(-x).
- WatsonDistribution(Vector3D, Random) - Constructor for class numerics.WatsonDistribution
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- WatsonDistribution(Vector3D, double, Random) - Constructor for class numerics.WatsonDistribution
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- WatsonFitter - Class in numerics
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This class implements several routines for fitting and evaluating
goodness-of-fit to a Watson distribution.
- WatsonFitter() - Constructor for class numerics.WatsonFitter
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- WeightedLinearDT_Inversion - Class in inverters
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Uses a weighted-linear least-squares algorithm to fit the diffusion tensor.
- WeightedLinearDT_Inversion(DW_Scheme) - Constructor for class inverters.WeightedLinearDT_Inversion
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The constructor requires the details of the sequence used to generate the
data that will be processed.
- weightedMean(double[], double[]) - Static method in class tools.ArrayOps
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Returns the mean value in the array.
- weightedVar(double[], double[], double) - Static method in class tools.ArrayOps
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Returns the weighted variance of the values in the array.
- width - Variable in class imaging.AnalyzeHeader
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- WildBootstrapDataSynth - Class in data
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Provides wild bootstrap data.
- WildBootstrapDataSynth(DataSource, DW_Scheme, int) - Constructor for class data.WildBootstrapDataSynth
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- WildBootstrapDataSynth(DataSource, DW_Scheme, int, int) - Constructor for class data.WildBootstrapDataSynth
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- WildBootstrapDataSynth(DataSource, DW_Scheme, int, Random) - Constructor for class data.WildBootstrapDataSynth
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This is the constructor that actually does everything, so ensure that this eventually gets
called.
- wildBootstrapModel - Static variable in class tools.CL_Initializer
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Model used in wild bootstrapping.
- WildBS_DT_DataSynth - Class in data
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Provides wild bootstrap data based on diffusion tensor reconstruction.
- WildBS_DT_DataSynth(DataSource, DW_Scheme, int) - Constructor for class data.WildBS_DT_DataSynth
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- WildBS_DT_DataSynth(DataSource, DW_Scheme, int, int) - Constructor for class data.WildBS_DT_DataSynth
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- WildBS_DT_DataSynth(DataSource, DW_Scheme, int, Random) - Constructor for class data.WildBS_DT_DataSynth
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- WildBS_DT_TractographyImage - Class in tractography
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Each call to #getPDs(int, int, int) returns a new bootstrap estimate of the PDs.
- WildBS_DT_TractographyImage(float[][][][], double[], int[][][], DW_Scheme, Random) - Constructor for class tractography.WildBS_DT_TractographyImage
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- write(int) - Method in class tools.LEFilterOutputStream
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Writes the specified byte value to the underlying output stream.
- write(byte[], int, int) - Method in class tools.LEFilterOutputStream
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Writes length
bytes from the specified byte array
starting at offset
to the underlying output stream.
- writeAnalyze(String) - Method in class misc.ScalarImage
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Write the image in analyze format.
- writeBoolean(boolean) - Method in class tools.LEFilterOutputStream
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Writes a boolean
to the underlying output stream as
a single byte.
- writeByte(int) - Method in class tools.LEFilterOutputStream
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Writes out a byte
to the underlying output stream
- writeBytes(String) - Method in class tools.LEFilterOutputStream
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Writes a string to the underlying output stream as a sequence of
bytes.
- writeChar(int) - Method in class tools.LEFilterOutputStream
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Writes a two byte char
to the underlying output stream
in little endian order, low byte first.
- writeCharacter(char) - Method in class tools.FileOutput
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Write a char value to a file.
- writeChars(String) - Method in class tools.LEFilterOutputStream
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Writes a string to the underlying output stream as a sequence of
characters.
- writeConnectionMatrix(ArrayList<Integer>, ArrayList<Edge>, HashMap<Integer, String>) - Static method in class apps.ConnectivityMapping
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Creates a file "ConnectionMatrix.txt" at the current location
containing a matrix of connecting tracts between the ROIs
- writeData(byte[]) - Method in class imaging.Nifti1Dataset
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Write a byte array of data to disk, starting at vox_offset,
beginning of image data.
- writeDouble(double) - Method in class tools.FileOutput
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Write a double value to a file.
- writeDouble(double) - Method in class tools.LEFilterOutputStream
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Writes an 8 byte Java double to the underlying output stream in
little endian order.
- writeDoubleCorrect(double) - Method in class imaging.EndianCorrectOutputStream
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writeDoubleCorrect will write a double to the stream
- writeFloat(float) - Method in class tools.FileOutput
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Write a float value to a file.
- writeFloat(float) - Method in class tools.LEFilterOutputStream
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Writes a 4 byte Java float to the underlying output stream in
little endian order.
- writeFloatCorrect(float) - Method in class imaging.EndianCorrectOutputStream
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writeFloatCorrect will write a float to the stream
- writeHeader() - Method in class imaging.AnalyzeHeader
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Writes header to the file.
- writeHeader(String) - Method in class imaging.MetaImageHeader
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Writes header to a file.
- writeHeader(DataOutput) - Method in class imaging.MetaImageHeader
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- writeHeader() - Method in class imaging.Nifti1Dataset
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Write header information to disk file
- writeImage(String) - Method in class apps.RGB_ScalarImage
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Writes this image, determines output type from extension (either .mha, .mhd or .vtk).
- writeImage(int[][][], int[][][], int[][][], AnalyzeHeader, String, boolean) - Static method in class imaging.AnalyzeHeader
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Writes file.hdr and file.img.
- writeImage(short[][][], AnalyzeHeader, String, boolean) - Static method in class imaging.AnalyzeHeader
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Writes file.hdr and file.img.
- writeImage(int[][][], AnalyzeHeader, String, boolean) - Static method in class imaging.AnalyzeHeader
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Writes file.hdr and file.img.
- writeImage(float[][][], AnalyzeHeader, String, boolean) - Static method in class imaging.AnalyzeHeader
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Writes file.hdr and file.img.
- writeImage(double[][][], AnalyzeHeader, String, boolean) - Static method in class imaging.AnalyzeHeader
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Writes file.hdr and file.img.
- writeInt(int) - Method in class tools.LEFilterOutputStream
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Writes a four-byte int
to the underlying output stream
in little endian order, low byte first, high byte last
- writeIntCorrect(int) - Method in class imaging.EndianCorrectOutputStream
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writeIntCorrect will write an int to the stream
- writeInteger(int) - Method in class tools.FileOutput
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Write an int value to a file.
- writeLong(long) - Method in class tools.FileOutput
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Write a long value to a file.
- writeLong(long) - Method in class tools.LEFilterOutputStream
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Writes an eight-byte long
to the underlying output stream
in little endian order, low byte first, high byte last
- writeLongCorrect(long) - Method in class imaging.EndianCorrectOutputStream
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writeLongCorrect will write a long to the stream
- writeMeta(String) - Method in class apps.RGB_ScalarImage
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Writes the RGB image in Meta I/O format.
- writeNewline() - Method in class tools.FileOutput
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Write a newline to a file.
- writeOOGL_BinaryVECT(DataOutputStream) - Method in class tractography.Tract
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Output as a binary OOGL vector, suitable for display in Geomview.
- writeRaw(DataOutputStream) - Method in class tractography.Tract
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Writes tract so that it can be read later by a TractSource.
- writeRawTracts(DataOutputStream) - Method in class tractography.TractCollection
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Writes tracts so that they can be read later with readTracts
.
- writeRGB() - Method in class apps.PD_OrientationViewer
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- writeScheme() - Method in class apps.PD_OrientationViewer
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- writeShort(int) - Method in class tools.LEFilterOutputStream
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Writes a two byte short
to the underlying output stream in
little endian order, low byte first.
- writeShortCorrect(short) - Method in class imaging.EndianCorrectOutputStream
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writeShortCorrect will write a short to the stream
- writeString(String) - Method in class tools.FileOutput
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Write a String value to a file.
- writeUTF(String) - Method in class tools.LEFilterOutputStream
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Writes a string of no more than 65,535 characters
to the underlying output stream using UTF-8
encoding.
- writeVol(double[][][], short) - Method in class imaging.Nifti1Dataset
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Write one 3D double array to disk.
- writeVoxelList(DataOutputStream) - Method in class tractography.VoxelList
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- writeVTK(String) - Method in class apps.RGB_ScalarImage
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Writes a VTK 2.0 (ie, not the new XML) file.
- WriteZeros - Class in apps
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Purpose:
Write binary zeros (or any other number) to the standard
output.
- WriteZeros() - Constructor for class apps.WriteZeros
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