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https://github.com/cvnlab/knkutils

MATLAB utility functions written by Kendrick Kay
https://github.com/cvnlab/knkutils

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MATLAB utility functions written by Kendrick Kay

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README 

        
This is a collection of MATLAB utilities developed by Kendrick Kay ([email protected], http://kendrickkay.net).  The philosophy of the code is to maximize power (i.e. the ability to perform many different things) and generality (i.e. the ability to re-use code for many different situations).  Let me know if you have comments.



Some of the code uses random-number generation, so it is recommended that you have something like

  rand('state',sum(100*clock));

  randn('state',sum(100*clock));

in your MATLAB startup.m file.



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% CHANGE HISTORY



Below we document major code changes.  Minor code changes and tweaks that have no significant impact are not mentioned here (e.g. things like cosmetic adjustments, code speed-ups, making functions more general by adding optional input arguments, fixing bugs that would have result in code crashes, etc.).  Major changes include things that make the code backwards-incompatible and things that change actual analysis results.



History of major code changes:

2019/09/23 - major bug fix to matchfiles.m.  previously the order of cell vector elements was not respected.  now order is respected.

2018/12/22 - matchfiles.m now RETURNS any duplicate filename matches. This changes past behavior.

2018/12/22 - to resolve function naming conflicts, we have done the following: (1) completely removed the function called count.m, (2) completely removed the function called discretize.m, (3) renamed the function strsplit.m to strsplitalt.m

2014/07/31 - in constructpolynomialmatrix.m, we now make the polynomials orthogonal and unit length. this changes previous behavior!

2013/11/18 - use a smoother canonical HRF in getcanonicalhrf.m

2013/09/07 - fix bug in fitnonlinearmodel (if polynomials or extra regressors were used in multiple runs, then they were not getting fit properly).

2013/08/18 - in makedirid.m, occurrences of '-' are now replaced with '_'

2013/08/18 - in projectionmatrix.m, in the cases of empty , we now return 1 instead of [].

2012/06/14 - in constructpolynomialmatrix2d.m and constructpolynomialmatrix3d.m, we now sort the char representation of the basis functions.  the reason is that previously, different machine architectures would give different orders for the basis functions.  this is horrible, as it means that different machines would have different parameter orders.  the fix (which hopefully is robust) is to sort the basis function character-wise, explicitly.  please be aware of this change!

2012/01/23 - in viewimage.m, no longer make a new window and no longer return the figure number

2011/12/10 - in applymultiscalegaussianfilters.m, we now make the default mode to be 0 (center on pixels).  this changes previous behavior.

2011/10/13 - in pton.m, now always generate a CLUT at 8-bit (256 rows)

2011/10/09 - in fitprfstatic.m,  no longer accepts all those special inputs; it is now a usual OutputFcn.

2011/09/22 - add required argument to copyxform_nii

2011/09/16 - the default behavior in dicomloaddir has changed.  we now match all files and perform numerical sorting.

2011/09/13 - make the yellow color in cmapdistinct slightly darker

2011/08/30 - in fitprf.m, we now use stepwise fitting in the nonlinear case (i.e.  is not 0 nor {0}).  this should improve the avoidance of local minima problems, but does change previous behavior!!

2011/07/11 - in dicomloaddir.m, we now have the extra assumption that all files are DICOM files when  is supplied

2011/07/01 - we now use nanmedian and nanmean in calcmdse.m

2011/06/29 - in printnice.m, we now temporarily change PaperPositionMode to auto before printing.  this should make rasterized image output better (in terms of getting the resolution right).

2011/06/27 - in olsmatrix.m, we now explicitly handle the case of all-zero regressors.  previously, NaNs would result.  now, we just ensure that these all-zero regressors get returned a zero weight.

2011/05/26 - in scatterb.m, we weren't drawing the main line.  weird.  we have changed it now to do the right thing.  this modifies old behavior.

2011/04/26 - in constructorientationfilter.m, fixed major bug. orientation was interpreted wrongly and filters were peaked at the wrong orientation.

2011/04/02 - in matchfiles.m, time-sorting behavior did not work (it would always give alphabetical order).  fixed now.

2011/03/09 - in defineellipse3d.m, we now show a maximum of 25 slices.

2011/03/08 - for alignvolumedata.m, make much faster (using ba_interp3), take less memory, remove spline interpolation option, ensure that the alignvolumedata_auto_outputfcn runs at optimization completion.

2011/03/08 - smoothvolumes handles NaNs intelligently now.  this changes old behavior.

2011/03/06 - complete revamp of calcnoiseceiling.m.

2011/02/24 - in matchfiles.m, we now properly match patterns that have spaces in them (since we now escape the spaces using \).  previous behavior was to simply not match those cases.

2011/02/02 - in zerodiv.m, in the case that y is not a scalar and wantcaution is set to 0, we were allowing division by 0 to result in Inf and *notreplaced with val as desired.  big mistake.  we have now fixed this.  utilities that could have used this buggy behavior of zerodiv include calccod, calccorrelation, calcentropy, calcsparseness, calczscore, l1unitlength, unitlength.

2011/01/21 - in matchfiles.m, we explicitly use MATLAB's sort function (for alphabetical ordering) to ensure consistency across platforms.  this might change the alphabetical ordering of matches!

2010/01/17 - completely change cmapdistinct.m; leave JVM on by default in runmatlabinbg.pl

2010/01/05 - in scatterline.m, we now attempt to use nanmean and nanstd to allow more cases in.  see code for details.

2010/12/27 - in divnorm.m, we now explicitly handle cases where the numerator is Inf.  the goal is to try to keep outputs finite when possible.

2010/12/16 - circlewithin.m changed from binary (all within or not) to a graded response

2010/12/06 - in fitprf.m, change initial seeds for certain basis function cases (in particular, we no longer force weights to 1. it seems that nonlinear fitting can operate successfully even if there is a gain ambiguity)

2010/12/03 - in fitprf.m, changed the form of the input  (this requires changes to how the function is called); 

2010/12/02 - in fitprf.m and fitprfmulti.m, a number of significant changes: [ input has been deprecated;  input has been removed; the ,,, outputs have been removed (I no longer think they are useful); fix bug --- the signal and drift outputs were not getting assigned in the re-do calls of the [A B C] case of ]; removed evaluateprfmodel.m

2010/11/24 - remove hrfsample1, remove hrfsample2 [these were obsolete]

2010/11/23 - in calccod.m, change the output range to percentages (R^2).  thus the range is (-Inf,100]. also, we removed the  input since it was dumb. also, please note that many functions that rely on calccod.m inherit this change to percentages. thus, this was a big global code change.

2010/10/24 - we now impose assumption in rowfun.m that each result has the same size

2010/10/22 - in fitprf.m, fix bug concerning exitflag and maxiters.  if there were multiple resamplings, then we were checking only the last exitflag when deciding to re-do the fitting process.  now, we do the right thing --- we check to see if any of the resamplings stopped because they reached the max number of iterations.

2010/10/22 - in fitprf.m, change initial seed for prfmodel and hrfmodel basis functions to 0!

2010/10/09 - remove showmulticlass.m

2010/10/05 - fixed bugs in sortnumerical.m.  previous calls may have crashed or failed to produce correct answer.

2010/10/02 - fot defineellipse3d.m, change initial visualization state

2010/10/02 - for fitgaussian3d.m, new default initial seed. more liberal tolerance. explicitly guard against nans.

2010/10/02 - in defineellipse3d.m, the fitted Gaussian no longer has a dc fixed to 0 but has an exponent now.

2010/09/27 - zerodiv.m no longer issues warnings when not 

2010/08/25 - explicitly put /home/knk in queuedaemon.  this should be revisited eventually...

2010/08/25 - for outputfcnplot, we revamped this function [hack out ratio check; hack out ; hack out NaN case for ]

2010/08/11 - queuedaemon, runme have been revamped and are not backwards-compatible.

2010/06/22 - unix_wrapper.m now reports status and result to the command window.

2010/06/15 - start using calccod.m instead of calccorrelation.m where appropriate (see subspaceapprox, fitprf, fitprfmulti, fitgabor2d, fitorientedgaussian2d, fitrbf2d)



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% SUMMARY OF FUNCTIONS



Here is a short summary of each function so that you can do a simple text search to see if there is a function that already does what you need.



matrix/

  addvectors - add vectors of unequal sizes

  blob - sum over successive groups along a certain dimension of a matrix

  catcell - concatenate elements of a cell matrix

  catmatrix - concatenate matrices (possibly unequal in size)

  cellfunfirst - apply function to first element of a cell matrix (or the matrix itself)

  cropvalidvolume - extract a subvolume of a matrix based on valid values

  equalizematrixdimensions - make two matrices the same dimensions by expanding

  fillout - repeat a matrix to fill a desired size

  filterout - remove elements of a matrix according to a simple boolean operation

  flatten - make into a row vector

  fillmatrix - take a vector and fill a matrix with it

  flipdims - flip some dimensions of a matrix

  insertelt - insert element(s) in a vector

  placematrix - place a 2D matrix inside another 2D matrix at an arbitrary position

  placematrix2 - place a matrix inside another matrix

  placematrixmulti - repeatedly randomly place a 2D matrix inside another 2D matrix

  reshape2D - get into 2D for convenient manipulation

  reshape2D_undo - undo what reshape2D does

  reshapesquare - reshape a vector into a square matrix

  rotatematrix - 2D rotation for an arbitrary matrix

  sizefull - get size of a matrix for a certain number of dimensions

  splitmatrix - take slices of a matrix and put them into a cell vector

  splitruns - find runs of non-NaN numbers in a vector

  squeezedim - remove a specific dimension that has only one element

  squish - squish together the first n dimensions of a matrix

  upsamplematrix - change the dimensionality of a matrix by upsampling

  vflatten - make into a column vector



indexing/

  calcposition - calculate the position of elements relative to a list

  chunking - split a vector into chunks

  firstel - return first element of a matrix

  firstelc - return first element of a cell matrix

  indexall - return an indexing helper for cell vectors

  lastel - return last element of a matrix

  linspacecircular - get equally spaced points in a circular domain

  linspacefixeddiff - get equally spaced points given a fixed difference

  linspacepixels - get equally spaced points that can be treated as centers of pixels

  matrixindex - return different slices through a matrix based on an indexing matrix

  permutedim - shuffle a matrix along a certain dimension or globally

  picksubset - return a random subset of the elements in a matrix

  removerepeats - get rid of runs of consecutive items

  resamplingindices - get indices corresponding to the process of resampling

  slicematrix - return a slice from a matrix

  subscript - get elements using a vector or cell vector of indices

  vectorsplit - split a vector into chunks



programming/

  allocatememory - force allocation of a certain amount of memory (to induce swapping)

  alwaysone - always return 1

  alwayszero - always return 0

  assignseparatevars - split a matrix and assign it to multiple variables

  assigntobaseworkspace - assign all variables to the base workspace

  checkmemoryworkspace - figure how much memory is being used in the caller's workspace

  checkpathconflicts - check for .m file conflicts

  choose - functional form of if-else

  copymatrix - make a copy of a matrix with a subscript assignment on-the-fly

  consolidatemat - consolidate results from multiple .mat files into a single .mat file

  consolidatematdir - consolidate results from .mat files in a directory

  decodenum - undo encodenum.m

  defaultoptimset - return a default optimset options structure

  encapsulate - evaluate a function at multiple values and encapsulate results into a cell vector

  encodenum - encode a number as a string of uppercase letters

  enforcenan - set cases with all 0 to NaN

  evalme - evaluate multi-line input in the MATLAB workspace

  gethostname - get the hostname

  getpid - get the process ID for this instance of MATLAB

  gettimestring - return the current date/time as a simple integer string

  GPUconv - convert to GPU format

  GPUok - return whether we should try to use the GPU

  gunziptemp - gunzip a file on the fly

  identity - return an argument unchanged

  infiniteloop - do nothing forever

  inputmulti - take multi-line string input from stdin

  isfinitenum - evaluate whether each element is finite and numeric

  isint - evaluate whether each element is an integer

  isrowvector - evaluate whether matrix is 1 x n (where n >= 0)

  maketempdir - make a new empty temporary directory and return the path to it.

  mergestructs - merge one struct into another

  mkdirquiet - make a directory, suppressing warnings

  mtimesmulti - multiply arguments together

  passmulti - pass multiple arguments to a function from a cell vector

  pause2 - pause but also return an output

  playalarm - play an alarm to get the user's attention

  plusmulti - add arguments together

  processchunks - perform an operation on successive chunks of a big matrix to save on memory usage

  promptforfile - get a .mat file name from the user

  repeatuntil - call a function until a condition is satisfied

  reportmemoryandtime - use a warning to report the current memory usage and the current time

  rmdirquiet - remove a file or directory, suppressing warnings

  rowfun - apply a function to each row of a 2D matrix

  runmatlabinbg.pl - run MATLAB in the background for a single function/script call

  sanitycheck - print out some fprintf statements about values in a matrix

  saveemptymat - save an empty .mat file

  setrandstate - induce randomness by (randomly) setting the seed of rand and randn

  sgerun2 - run MATLAB code using the Sun Grid Engine (SGE)

  statusdots - write out dots (.) indicating progress of code execution

  subsetfun - apply a function to successive subsets of a vector

  swap - swap two arguments

  unix_wrapper - a nice wrapper for unix.m



string/

  cell2str - convert 2D cell matrix into string representation

  cell2str2 - convert cell vector of strings into a single string that names each string

  fixstr - fix string for use with MATLAB's figure functions

  makedirid - return a string with elements of a path joined with '_'

  makeletters - generate a cell vector of letter characters

  mat2cellstr - convert a matrix of numbers into a cell matrix of strings

  matchword - return the first word found in a string

  randomword - generate a random word consisting of capital letters

  sortnumerical - sort a cell vector of strings according to trailing integers

  strsplitalt - split a string based on a pattern



io/

  absolutepath - return the absolute path to a given file

  clearexcept - clear all variables except certain variables

  getextension - get the extension (e.g. '.txt') of a filename

  loadbinary - load numbers from a binary file

  loadexcept - load variables from a .mat file, excluding certain variables

  loadmaybe - load variable from a .mat file, but failing gracefully

  loadmulti - concatenate or merge a single variable from multiple .mat files

  loadmulti2 - load multiple variables from one .mat file

  loadtext - load strings from a text file

  matchfiles - return strings containing paths to matched files and/or directories

  multifile - apply a function to multiple files

  niiload - load specific voxels from NIFTI files containing 4D data

  raw2dload - load specific columns from binary files containing 2D data

  savebinary - save numbers to a binary file

  saveexcept - save all variables to a .mat file, excluding certain variables

  savetext - save strings to a text file

  shuffletext - shuffle lines in a text file

  stripext - remove the extension from a file name

  stripfile - remove the file name from a string



math/

  addnoise - add some noise to a matrix

  allzero - check whether all elements are equal to zero within some tolerance

  ang2complex - convert angles to unit-magnitude complex numbers

  chunkfun - apply a function to successive chunks of a vector

  chunknormalize - subtract mean of successive chunks of a matrix

  calccod - calculate coefficient of determination (R^2)

  calccodcell - calccod for cell vectors of matrices

  calccorrelation - calculate Pearson's correlation coefficient (r)

  calcmdse - calculate the median and the standard error on the median

  calcmdsepct - calculate the median and percentiles on bootstraps of the median

  calcsparseness - calculate sparseness

  calczscore - convert to z-scores

  circularavg - average numbers, respecting circularity

  circulardiff - difference between two values defined in a circular domain

  circularshiftandsum - take a vector, circularly shift it multiple times, and sum

  clipoutliers - clip the outliers of a matrix

  constructpathonsphere - connect points on the unit sphere

  countinstances - count how many 1s, 2s, etc. are in a matrix

  divnorm - apply divisive normalization to a matrix

  matchgain - figure out scalar factor to match one set of data to another

  meanandse - calculate the mean and standard error

  meancell - take the mean for data that are split into cell matrices

  mod2 - like mod.m but return 0 outputs as the modulus itself

  mod4 - like mod.m but restrict outputs to the range [-modulus/2,modulus/2]

  mtimescell - do matrix multiplication but with an argument split into a cell vector

  nanreplace - replace NaNs with a specified value

  nanreplace2 - replace NaNs with a specified value (alternative mode of operation)

  nantoclosest - replace NaNs with the nearest valid values

  negrect - negative-rectify

  negreplace - replace negative values with a specified value

  normalizerange - scale to fit within a specific range

  normalizemax - scale such that max value is 1

  posnegrect - positive- and negative-rectify

  posrect - positive-rectify

  restrictrange - truncate values to fit within a range

  robustrange - calculate a robust range of a set of values

  signedarraypower - take the array power but preserve sign

  signforce - return +1 for positive or zero elements; -1 for negative elements

  stdquartile - return something like std but in the percentile sense

  unitlength - normalize to have unit length (L2-norm is 1)

  unitlengthfast - normalize to have unit length (L2-norm is 1)

  l1unitlength - normalize to have unit length (L1-norm is 1)

  vectorlength - calculate vector length (L2-norm)

  l1vectorlength - calculate vector length (L1-norm)

  zerodiv - divide but with special handling for division by zero

  zeromean - subtract off the mean



stats/

  applyfiltermultidim - apply filters for the case of images with multiple features

  bootstrap - apply a function to bootstrap samples drawn from a vector (useful for computing standard error)

  bootstrapdim - more general version of bootstrap

  calcconfusionmatrix - calculate a confusion matrix (i.e. covariance, cross-product, etc.)

  calcentropy - calculate entropy based on a matrix with counts

  calcggaussianlikelihood - calculate likelihood of a set of points assuming independent generalized Gaussian distributions

  calcintrinsicdim - calculate number of eigenvectors needed to achieve a certain amount of the variance in a matrix

  calcmutualinformation - calculate mutual information between two matrices

  calcmutualinformationcontinuous - calculate mutual information between two matrices in a continuous way

  calcmvgaussianpdf - calculate multivarate Gaussian probability density function

  calcnoiseceiling - calculate how well a set of data can be predicted, taking into account the intrinsic noisiness of the data

  calcoptimalhistbins - calculate the optimum number of bins to use for hist.m

  calcrbflikelihood - calculate likelihood of a set of points given a collection of RBFs

  calcrectlikelihood - calculate likelihood of a set of points given a collection of directions (half-squared responses)

  calcrobustsummary - calculate the median and one-half of the central 68% range

  calcshrunkencovariance - use shrinkage and cross-validation to obtain more robust estimates of covariance

  calcsurfaceareanball - calculate surface area of a unit n-ball

  centerofmass - calculate the center-of-mass of a matrix

  constructdctmatrix - construct a matrix with DCT-II basis functions in the columns

  constructdftmatrix - construct a matrix with DFT basis functions in the columns

  constructfiltersubsample - construct 2D filters according to a subsampling scheme

  constructfiltertiling - construct filters by tiling a single 2D filter

  constructnearestpsdcovariance - find the nearest positive semidefinite matrix

  constructpolynomialmatrix - construct a matrix with polynomials in the columns

  constructpolynomialmatrix2d - evaluate polynomial basis functions defined in 2D at some locations

  constructpolynomialmatrix3d - evaluate polynomial basis functions defined in 3D at some locations

  convertcovariancetocorrelation - convert a covariance matrix to a correlation matrix

  evaldivnorm - evaluate divisive-normalization function at some values

  evalgaussian1d - evaluate 1D Gaussian function at some coordinates

  evalgaussian2d - evaluate 2D Gaussian function at some coordinates

  evalgaussian2doriented - evaluate 2D Gaussian function (that can be rotated) at some coordinates

  evalgaussian3d - evaluate 3D Gaussian function at some coordinates

  evalgeneralizedgaussian - evaluate generalized Gaussian pdf

  filter2subsample - apply filter2 and then subsample the result

  findlocal - find points that are close to a given point

  findtailthreshold - determine a threshold for a distribution of data using a GMM with 2 Gaussians

  fit2dpolynomialmodel - use polynomial basis functions to fit a surface defined in 2D, allowing scale factor for different cases

  fit3dpolynomialmodel - use polynomial basis functions to fit a surface defined in 3D, allowing scale factor for different cases

  fit3dpolynomialmodel2 - use polynomial basis functions to fit a surface defined in 3D, allowing DC offset for different cases

  fitdivnorm - fit divisive-normalization function

  fitgaussian1d - fit 1D Gaussian function

  fitgaussian2d - fit 2D Gaussian function

  fitgaussian2doriented - fit 2D Gaussian function that can be rotated

  fitgaussian3d - fit 3D Gaussian function

  fitl1line - perform linear regression but use an L1-error metric 

  fitline2derror - fit a line to a set of 2D points using an error metric that is sensitive to both x and y

  fitnonlinearmodel - a useful wrapper around MATLAB's lsqcurvefit.m function

  fitnonlinearmodel_consolidate - consolidate .mat files written by fitnonlinearmodel

  fitnonlinearmodel_helper - a helper function for fitnonlinearmodel.m

  fitrbfpdf - fit a simplified mixture-of-Gaussians probability density function model using k-means

  fitrectpdf - fit a rectified squared model using k-means and interpret as a PDF

  fitrectdensity - fit a rectified squared model using k-means and interpret more like ANN

  gradientdescent - perform gradient descent or forward stagewise regression

  gradientdescent_wrapper - perform n-fold averaging technique for gradientdescent.m

  localregression - given a degree, kernel, and bandwidth, use local regression to predict values (surface defined on one dimension)

  localregression2d - given a degree, kernel, and bandwidth, use local regression to predict values (surface defined on two dimensions)

  localregression3d - given a degree, kernel, and bandwidth, use local regression to predict values (surface defined on three dimensions)

  localregression4d - given a degree, kernel, and bandwidth, use local regression to predict values (surface defined on four dimensions)

  localregressionbandwidth - cross-validate to determine the optimal bandwidth for local regression

  olscontrol - perform ordinary least-squares regression while controlling for some given regressors

  olsmatrix - perform ordinary least-squares regression

  olsmatrix2 - perform ordinary least-squares regression (fast mode)

  outputfcnplot - plot parameter history during an optimization

  outputfcnsanitycheck - explicit check on the size of the residuals to prevent infinite computation

  performfreqwhitening - flatten the average amplitude spectra of a set of images

  performpcawhitening - whiten a matrix in the PCA sense

  projectionmatrix - project out a linear subspace using ordinary least-squares regression

  randgg - generate random numbers from a generalized Gaussian

  randintrange,randintrange2 - randomly choose integers within a given range

  randnmulti - generate random numbers from a multivariate Gaussian

  randomization - calculate p-values using randomization

  randomorthogonalbasis - generate a random set of orthogonal basis functions

  resamplingtransform - a utility function to deal with cross-validation ordering as used in fitnonlinearmodel.m

  roundpvalue - round p-value up to have the form Xe-Y

  runkmeans - run the k-means clustering algorithm

  subspaceapprox - calculate correlation between a subspace and a vector



timeseries/

  calcpeak - calculate the peak of some time-series data (using interpolation)

  constructbutterfilter1D - construct a Fourier-domain Butterworth filter

  conv2run - convolve but keep runs separate

  deconvolvevectors - deconvolve one vector from another vector

  fouriertospace1D - convert magnitude filter in Fourier domain to the space domain

  generatepinknoise1D - generate samples of pink noise

  processmulti1D - apply a function that expects a single vector to multiple vectors

  sincshift - shift time-series data using sinc interpolation and padding

  tseriesinterp - interpolate time-series to achieve a new sampling rate

  tsfilter - filter time-series data with a Fourier-defined magnitude-based filter



imageprocessing/

  applymultiscalegaborfilters - filter images with a set of multi-scale Gabor filters

  applymultiscalegaussianfilters - filter images with a set of multi-scale Gaussian or Difference-of-Gaussians filters

  ba_interp3_wrapper - convenient wrapper for the 3D interpolation toolbox ba_interp3

  calcamplitudespectrum - calculate a smooth function relating spatial frequency to amplitude

  calccpfov - return number of cycles per FOV associated with fft2 after fftshifting

  calccpfov1D - return number of cycles per FOV associated with fft after fftshifting

  calccpfov3D - return number of cycles per FOV associated with fftn (in three dimensions) after fftshifting

  calcimagecoordinates - return coordinates of the pixels of an image

  calcpositiondifferentfov - determine the coordinates of a new image with respect to an original image

  calcunitcoordinates - return coordinates of points equally spaced within the square bounded by -.5 and .5

  checkimagesize - inspect pixel dimensions of a batch of image files

  chtoim - reshape image(s) from images x res*res to res x res x images

  concatimages - concatenate multiple images together

  constructbutterfilter - construct a Fourier-domain Butterworth filter (for images)

  constructbutterfilter3D - construct a Fourier-domain Butterworth filter (for volumes)

  constructcosinefilter - construct a Fourier-domain cosine-tapered filter

  constructorientationfilter - construct a Fourier-domain orientation filter (von Mises distribution)

  constructsmoothingfilter - construct a space-domain 2D or 3D Gaussian filter

  constructwhiteningfilter - construct a Fourier-domain whitening filter

  detectedges - detect edges in an image using simple scheme

  evaldog2d - evaluate 2D Difference-of-Gaussians function at some coordinates

  evalgabor2d - evaluate 2D Gabor function at some coordinates

  evalgrating2d - evaluate 2D sinusoidal grating function at some coordinates

  evalorientedgaussian2d - evaluate oriented 2D Gaussian at some coordinates

  evalrbf2d - evaluate 2D radial basis function at some coordinates

  extractwindow - easily pull out different chunks of an image

  fitgabor2d - fit 2D Gabor function

  fitorientedgaussian2d - fit oriented 2D Gaussian

  fitrbf2d - fit 2D radial basis function

  fftshift2 - apply fftshift along the first two dimensions

  flattenspectra - apply spatial frequency filtering to flatten the spectra of some images

  fouriertospace - convert magnitude filter in Fourier domain to the space domain

  gabortransform - perform Gabor transformation on one or more images

  generatepinknoise - generate samples of pink noise

  generaterandomphase - generate random phases suitable for multiplication with output of fft2

  generatewinnermap - compress multidimensional data by using hue and brightness to represent the maximum value along a dimension

  getsamplebrain - return a brain volume

  getsampleimage - return a 500x500 grayscale natural image

  ifftshift2 - apply ifftshift along the first two dimensions

  imagefilter - filter images with a Fourier-defined magnitude-based filter

  imagefilter3D - filter volumes with a Fourier-defined magnitude-based filter

  imagesearch - search through image space to minimize some cost function

  imagesequenceconcatenate - concatenate multiple image files together

  imagesequencetomovie - make a QT movie from images

  imaveragefiles - average multiple image files together

  imcropfiles - manually define a crop region and then apply to one or more image files

  imreadmulti - load in multiple images

  imrectsquare - enforce square and integer crop to an imrect

  imrectimagecrop - return a valid image crop from imrect

  imresizedifferentfov - resize an image but use a different field-of-view

  imresizememory - call imresize on a bunch of images, minimizing memory usage

  imwritemulti - write multiple images to multiple files

  imtoch - reshape image(s) from res x res x images to images x res*res

  makecircleimage - draw a circle as an image

  makecolorimagestack - convert a 4D matrix containing multiple color images into a 3D matrix

  makeconcentricgrating2d - make a concentric 2D sinusoidal grating

  makedog2d - make a 2D Difference-of-Gaussians

  makegabor2d - make a 2D Gabor

  makegaussian2d - make a 2D Gaussian

  makegaussian3d - make a 3D Gaussian

  makegrating2d - make a 2D sinusoidal grating

  makegratings2d - make a set of 2D sinusoidal gratings

  makeimagestack - convert a 3D matrix containing multiple images into a 2D matrix

  makeimagestack_wrapper - run makeimagestack for multiple 3D matrices

  makeimagestack3dfiles - like makeimagestack but write out some convenient .png files

  makeorientedgaussian2d - make an oriented 2D Gaussian

  makesquareimage - draw a square as an image

  maskmultiscalegaborfilters - modify results of applymultiscalegaborfilters according to a binary mask

  phasescrambleimage - blend image with random-phase image

  placeimageintosquare - place an image anywhere within another image

  processimages - perform some function on many image files

  processmulti - apply a function that expects a single image to multiple images

  scrambleimage - scramble an image, preserving chunks of a certain size

  smoothvolumes - use a Gaussian filter to smooth one or more 3D volumes

  socmodel - compute the response of the SOC model to some stimuli

  splitimages - split images into chunks

  unitlengthfft2 - unit-length-normalize a Fourier domain filter

  varycontrast - vary the contrast of an image

  viewimage - do some visualizations for a given image

  viewimages - visualize many images at once

  viewmovie - view a series of images as a movie (or write a series of image files)

  visualizemultiscalegaborfilters- visualize points associated with applymultiscalegaborfilters



figure/

  addlogticks - add logarithmic ticks to a figure whose data have already been log-transformed

  axissquarify - make axis equal-aspect, square, and origin-centered and draw unity line

  errorbar2 - draw error bars (as lines)

  errorbar3 - draw error bars (as a polygon)

  figureprep - make an invisible figure window

  figurewrite - write the invisible figure window to an image file

  getcolorchar - take an integer and get a color character

  getfigurepos - return figure position (in normalized units)

  hist1dimage - draw a histogram as a vertical 1D image

  histrobust - run hist but ensuring a robust range

  imageactual - draw an image at its native resolution

  imagescmulti - make separate figure windows for multiple images

  plotorientedbar - plot an oriented bar

  plotrectangle - plot a rectangle

  printnice - print figure window to file

  setaxispos - set axis position (without mangling the Units setting)

  setfigurepos - set figure position (without mangling the Units setting)

  scatterb - do a binned scatterplot

  scatterline - use local linear regression to summarize a scatterplot

  scattersparse - do a scatterplot but limit the number of points

  scatterimagesparse - do a image scatterplot and limit the number of points

  squarify - figure out a roughly evenly balanced number of rows and columns necessary to fit a certain number of elements

  straightline - draw horizontal or vertical lines

  subplotresize - make the subplots of a figure as big as possible



colormap/

  cmapang - hue-based colormap suitable for circular ranges (e.g. angles)

  cmapangLR - like cmapang.m but left-right flipped

  cmapangLVF - like cmapang.m but focused on the left visual field

  cmapangRVF - like cmapang.m but focused on the right visual field

  cmapdistinct - hue-based colormap for cases where you want maximally distinct colors

  cmaplookup - take values and get colors from colormap

  cmaphue - hue-based colormap suitable for circular ranges

  cmapsinglecolor - generate colormap that mixes from one color to a second color

  cmapsign - blue-black-red colormap suitable for ranges like [-X X]

  cmapsign2 - blue-white-red colormap suitable for ranges like [-X X]

  cmapsign3 - blue-lightgray-red colormap suitable for ranges like [-X X]

  cmapsign4 - cyan-blue-black-red-yellow colormap suitable for ranges like [-X X]

  cmaptab10 - a set of 10 discrete colors

  cmapturbo - jet-like colormap

  colorinterpolate - make a colormap by interpolating between key colors

  drawcolorbar - draw a colorbar on the current figure

  drawcolorbarcircular - draw a circular colorbar on the current figure



graphic/

  calcdistpointline - calculate the distance between one or more points and a line

  circlewithin - determine whether one or more circles are contained within a certain circle

  coordangle - calculate coordinates of an angle

  coordpolygon - calculate coordinates of an equilateral polygon

  createrescalingmatrix - construct a transformation matrix that rescales with respect to (0.5,0.5,0.5)

  defineellipse3d - allow user to define a 3D ellipse on a 3D volume

  drawarrow - draw an arrow (in two dimensions)

  drawbar - draw an oriented bar

  drawbars - draw a set of oriented bars

  drawbartexture - draw a random array of oriented bars

  drawcheckerboard - draw an oriented checkerboard

  drawcheckerboards - draw a set of oriented checkerboards

  drawclosedcontour - draw a generic closed contour shape

  drawclosedcontours - render several closed contours

  drawdartboard - draw a radial checkerboard (dartboard)

  drawellipse - draw a complete or partial ellipse (includes circles and arcs as special cases)

  drawmultiscale - place objects at multiple scales on a pink-noise background

  drawpolargrid - draw a polar grid consisting of rings and spokes

  drawrectangle - draw a rectangle

  drawsector - draw a sector

  drawtext - draw a word

  drawtexts - render several words

  renderfigure - render the current figure into an image (assumed to be square)

  xyzscale - construct a scaling transformation matrix

  xyztranslate - construct a translating transformation matrix

  xyzrotate_* - construct a rotation transformation matrix

  xyzrotatetoz - return rotation transformation matrix to align a vector with positive z-axis



mri/

  calchrfpeak - estimate the peak (positive or negative) value of an HRF

  changevolumeres - change the resolution of a volume while preserving field-of-view

  computebrickandindices - determine a brick into a 3D binary volume

  computetemporalsnr - compute the stability of a series of 3D volumes over time

  condition_split - perform condition-splitting on a set of design matrices

  constructhrfmodeldct - return a matrix of DCT-II basis functions for modeling HRFs

  constructhrfmodeldelta - return a matrix of delta basis functions for modeling HRFs

  constructhrfmodelspline - return an spline-based HRF model

  constructstimulusmatrices - construct design matrix for a finite impulse response (FIR) model

  copyxform_nii - propagate transformation-related fields from one NII file to others

  coregistervolumes - coregister one volume to another

  createspmmatrix - return the default SPM transformation matrix

  dicomloaddir - load volumes and voxel-size information from a DICOM directory

  evaldoublegamma - evaluate double-gamma function at some x-values

  expdesignefficiency - calculate efficiency of an experimental design

  fithrfgammadouble.m - fit a double-gamma function

  fmriquality - write figures to inspect the spatial quality of fMRI volumes

  fstoint - go from FreeSurfer space to our internal space

  getcanonicalhrf - return a canonical HRF (based on empirical data) for arbitrary duration and TR

  getcanonicalhrf2 - return canonical Early and Late HRFs (based on empirical data) for arbitrary duration and TR

  getcanonicalhrflibrary - return a set of canonical HRFs (based on empirical data) for arbitrary duration and TR

  getsamplehrf - return some sample HRFs estimated from actual fMRI data

  homogenizevolumes - homogenize a set of 3D volumes by dividing by fitted 3D polynomials

  hrfgammadouble.m - evaluate a double-gamma function

  inttofs - go from our internal space to FreeSurfer space

  motioncorrectvolumes - perform motion correction for some volumes

  preconditionvolume - precondition a 3D volume by clipping outliers and removing low-frequency signal variations

  quantifymotionparameters - compute an intuitive summary metric of rigid-body motion during a run

  resliceniftitomatch - use NIFTI header information to match one volume to another

  settr_nii - set the TR in the header information of an NII structure

  surfaceslice2 - figure out information relating voxels to vertices

  undistortvolumes - resample volumes in order to correct for motion and distortion

  write3dstack - write out extracted slices in three orientations from a 3D matrix

  writespmfiles - write a series of volumes to individual SPM/ANALYZE files



pt/

  calcfixationdotchangeperformance - perform analysis of behavioral data for experiments involving dot change detection

  preparedigits - generate some digits and letters as uint8 images

  pteyelinkoff - some eye-tracking related setup

  pteyelinkon - some eye-tracking related setup

  pton - initialize PsychToolbox stuff

  ptoff - uninitialize PsychToolbox stuff

  ptviewimage - show one or more images and allow user to position the images

  ptviewmovie - show a stimulus movie

  ptviewmoviecheck - check the results of ptviewmovie.m

  runretinotopy - script for retinotopy experiment

  showmulticlass - helper function for various experiments



external/   [code obtained from elsewhere]

  hist2d.m - count histogram frequencies in two dimensions



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Copyright (c) 2013, Kendrick Kay

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