NDLUTIL software Version 0.163 Sunday 17 Jun 2012 at 08:11 This toolbox implements some generic functions used by other toolboxes. Originally it was spun out of the IVM 0.221 toolbox. Version 0.163 ------------- Added plotMatrix for visualizing matrices on figure axes. Version 0.162 ------------- Added files for printing to latex plots from Octave. Version 0.161 ------------- Antti updated lnDiffErfs. Added readBinaryDoubles and printPlot. Version 0.16 ------------ Release for ICML tutorial. Added cumGamma and gammaPdf. Also added isoctave and several matlab helper files for reading from file IDs. Version 0.159 ------------- Minor release for dimensional reduction demos. Added centeringMatrix.m. Version 0.158 ------------- Antti Honkela provided the files lnDiffErfs and gradLnDiffErfs to assist in computing the DISIM kernel from the kernel toolbox stably. Version 0.157 ------------- Added treeFindLeaves. Version 0.156 ------------- Moved treeFindParents, treeFindChildren and treeSwapNode into this toolbox from MOCAP toolbox. Version 0.155 ------------- Moved lnCumGaussSum from NCNM toolbox to this toolbox as part of merge of NCNM toolbox into NOISE and IVM toolboxes. Version 0.154 ------------- Added code for checking Hessian matrices. Version 0.153 ------------- Added comments to files and changed jitChol, pdinv and logdet so that they can return any jitter added. If the return the jitter then they don't emit a warning. Version 0.152 ------------- There was a sign error in lnDiffCumGaussian. This has been fixed. The sign error was replicated in the NOISE and PRIOR toolboxes (a case of two wrongs making a 'right'). This means that earlier versions of this toolbox are incompatible with versions of PRIOR before 0.131 and versions of NOISE before 0.131. Version 0.151 ------------- Sped up the sparseDiag command using spdiag, this makes the FGPLVM code run much faster. Version 0.15 ------------ Fixed inconsistencies in logdet and pdinv and corrected the amount of jitter that is added at first try. Placed the jitter addition in a new file jitChol which is called by both functions. Added kldivGaussian for computing Gaussian Kullback-Leibler divergences. Added deg2rad for converting degrees to radians. Version 0.142 ------------- Added sparseDiag and moved data loading methods into the new DATASETS toolbox. Version 0.14 ------------ Moved in lvmLoadData and mappingLoadData as generic methods of loading in data sets. Version 0.131 Release Notes --------------------------- Added files getline.m and tokenise.m which are string utilities for reading and processing files. Version 0.13 Release Notes -------------------------- pdinv now adds jitter which is proportional to the mean of the diagonal elements of the matrix. MATLAB Files ------------ Matlab files associated with the toolbox are: readDoubleFromFID.m: Read a double from an FID. readBinaryDoubles.m: Read information from a binary file in as doubles. cumGaussian.m: Cumulative distribution for Gaussian. plotMatrixOptions.m: Default options for plot matrix. traceProduct.m: Returns the trace of the product of two matrices. stringSplit.m: Return separate parts of a string. lnDiffErfs.m: Helper function for computing the log of difference treeGetWidths.m: give width of each level of tree. printPlot.m: Print a plot to eps and png files. ngaussian.m: Compute a Gaussian with mean 0 and variance 1. xgamrnd.m: Draw a sample from the gamma distribution. lnCumGaussSum.m: The log of the weighted sum of two cumulative Gaussians. writeIntToFID.m: Writes an integer to an FID. printLatexOptions.m: Options for printing a plot to LaTeX. treeFindLeaves.m: Return indices of all leaf nodes in a tree structure. defaultOptions.m: The default options for optimisation. hessianCheck.m: Check Hessian of objective function. writeStringToFID.m: Writes a string to an FID. gradLnDiffErfs.m: Compute the gradient of the log difference of two erfs. deg2rad.m: Transform degrees to radians. negLogLogit.m: Function which returns the negative log of the logistic function. pdinv.m: Invert a positive definite matrix. preparePlot.m: Helper function for tidying up the plot before printing. plotMatrix.m: Fill a given axis with a matrix plot. tokenise.m: Split a string into separate tokens. readStringFromFID.m: Read an boolean from an FID. gradientCheck.m: Check gradients of objective function. printLatexPlot.m: Print a plot to LaTeX. lnDiffCumGaussian.m: Log of the difference between two cumulative Gaussians. readBoolFromFID.m: Read a boolean from an FID. tableRead.m: Read in data which has column titles in the first line and separated values in each other line. invCumGaussian.m: Computes inverse of the cumulative Gaussian. scatterPlot.m: 2-D scatter plot of labelled points. rayleighSamp.m: Sample from a Rayleigh with a given sigma. sparseDiag.m: Create a diagonal matrix that is sparse from a vector. gradLogCumGaussian.m: Gradient of the log of the cumulative Gaussian. cell2num.m: Converts a cell array of strings to numbers. readIntFromFID.m: Read an integer from an FID. printLatexText.m: Print a text string to file for latex input. safeSave.m: Safe save timeseriesdata.m: make a time series data set with the given window length. treeFindRoots.m: Return indices of all root nodes in a tree structure. cumGamma.m: Cumulative distribution for gamma. writeVersionToFID.m: Writes a version to an FID. treeSwapNode.m: Swap two nodes in the tree structure array. readVersionFromFID.m: Read version number from an FID. jitChol.m: Do a Cholesky decomposition with jitter. gaussOverDiffCumGaussian.m: A Gaussian over difference of cumulative Gaussians. lnCumGaussian.m: log cumulative distribution for the normalised Gaussian. sigmoid.m: The sigmoid function isoctave.m: Returns true if the software running is Octave. stringSigFigs.m: Convert number to a string with a number of significant digits. gaussSamp.m: Sample from a Gaussian with a given covariance. writeDoubleToFID.m: Writes a double to an FID. centeringMatrix.m: returns the centering matrix for the given dimensionality. invSigmoid.m: The inverse of the sigmoid function. numsf2str.m: Convert number to a string with a number of significant digits. treeFindChildren.m: Given a tree that lists only parents, add children. rocCurve.m: Draw ROC curve and return labels. getline.m: Get a line from a file. logdet.m: The log of the determinant when argument is positive definite. zeroAxes.m: A function to move the axes crossing point to the origin. writeBoolToFID.m: Writes a boolean to an FID. getSymbols.m: Get a cell array of different plot symbols. dist1.m: Calculates absolute distance (i.e. L1 norm) between two sets of xlogy.m: z = x*log(y) returns zero if x=y=0 ndlutilToolboxes.m: Loads in toolboxes for NDLUTIL. kldivGaussian.m: Give the KL divergence between two Gaussians. treeFindParents.m: Given a tree that lists only children, add parents. stack.m: Return column stacked vector of given matrix. escapeText.m: Add back slashes to escape existing backslashes in a text. gammaPdf.m: PDF for the Gamma distribution.