Change Log for Previous Versions of Chronux

• October 10, 2006: chronux_1_50.zip
  • Many changes made for the SFN workshop.
  • Tested extensively under Matlab R13, R14, 2006a, 2006b.
  • Bugfixes throughout.
• August 16, 2006: chronux_1_15.zip
  • Updated comments in many functions throughout.
  • Added required f0 argument which specifies how to do line removal in rmlinesc.
  • Fixed dimensional bug in mtspecgrampt.m.
  • Changed naming of isvector.m to isavector.m to avoid conflict introduced in Matlab R2006a.
• August 13, 2006: chronux_1_1.zip
  • Added spike-sorting module in the spikesort directory.
  • Added the wave_browser and classify_spectra programs which interactively segment and classify syllables in audio wav files.
• March 28, 2006: chronux_1_0.zip
  • Added a tutorial folder with examples of common electrophysiology data analysis tasks.
  • The entire C Locfit library by Catherine Loader is now available directly to your Matlab scripts through mex functions. Locfit allows you to fit smooth curves and surfaces to data using the local regression and likelihood methods. The prior functions rscb and locfitraw are now deprecated but are still available in the old directory.
  • Better comments particularly in the coherency calculations - We now explain that the coherency routines return the standard deviation of phi in the variable phierr. However, in order to ensure that the calling sequence remains the same when Jackknife calculations are put in, the first dimension of phierr can be 1 or 2 corresponding to upper and lower confidence bands. Thus phierr(1,...)=phierr(2,...)=standard deviation of phi. For p=0.05 band one should then take phi+/- phierr(1,...). When Jackknife calculations are introduced, we will eventually have phierr(1,...) not equal to phierr(2,...). In that case the correct confidence intervals will be given by phi-phierr(1,...) and phi+phierr(2,...).
  • There was a problem with previous calculations of the derivatives. In particular, an approximate formula for the derivatives is given by X' A X where X=(x(1),x(2),...,x(k)) are the k fourier transforms (each a function of frequency), X' is the adjoint of X and A is a bidiagonal matrix of the form A(i,j)=sqrt(i) for j=i+1; A(i,j)=sqrt(j) for j=i-1, and A(i,j)=0, otherwise. The previous formula assumed A was bidiagonal but with the off diagonal terms all being 1.
  • We have introduced routines for doing the non-stationarity test a la Thomson (2000). These routines are currently available only for continuous data.
  • We have now put in routines doing the two group comparison of coherences and spectra (Bokil et al, to be submitted, 2006). These are applicable to point as well as continuous processes and allow you to compute a test statistic \Delta z, and its Jackknife variance. The test statistic is distributed as N(0,1) under the null hypothesis of equal population coherences or spectra when the underlying data are non-Gaussian. The routine also returns a variable that contains information about the frequencies at which the null can be rejected. In addition,large deviations of the Jackknife variance from 1 occurs at frequencies where the data shows non-gaussian fluctuations. The test should be treated with considerable caution at these frequencies. These routines are in the directory chronux/statistical_tests.
  • New routines have been written to compute the cross-spectral matrix, its singular values and leading singular vectors, as well as the Wiener entropy for point process data. The routine for continuous valued data is now names CrossSpecMatc.m with the old routine CrossSpecMat.m avalable in the directory chronux/old.
  • Fixed an error in binspikes.m that caused some problems with the time window specified was smaller than the maximum duration of the spikes.
• September 21, 2005: chronux_0_51.zip
  • Updated plotsigdiff.m - this routine was previously overly conservative in displaying regions of significant difference. It now corrects this problem by displaying regions in the t-f plane for which one of the inputs is outside the confidence bands of the other input. In addition, it returns two variables: (i) mask is zero for regions in the t-f plane for which no significant differences were found, it is +1 for regions where X1 is significantly greater than X2, and -1 for regions where it is significantly less than X2, (ii) Xdiff=X1-X2.
  • Updated rmlinesc.m - this routine now sets the default p value to 0.05/N. The new setting is motivated by a calculation of the false detect rate and the requirement of setting this rate to be approximately 0.05.
  • Added rmlinesmovingwinc.m - this is a new routine that extends rmlinesc.m to perform harmonic analysis with sliding windows.
• Aug 15, 2005: chronux_0_5.zip
  • Spectroscope script added which displays real-time audio (and other) data.
  • Wrapper to the R function Locfit added, and is called "locfitraw". This function implements local smoothing.
  • Help material checked both by hand and automatically for consistency to new function signatures.
  • Verified functionality under Matlab R13 and R14.
  • Assorted bugs found and fixed.
  • Calling sequence simplified by combining the arguments tapers, pad, Fs, fpass, err and trialave into a single structure params.
  • Parameter setting transferred to a single routine getparams.m
  • Added new routines for doing segmented spectral computations - mtspectrumsegc.m, coherencysegc.m etc.
  • Directory structure simplified so that Chronux is now organized into just a few directories, organized, for the most part according type of data.
  • Changes have occured in most of the coherence calculations involving spikes - we now return a variable zerosp that keeps track of situations in which there are no spikes.
  • Now released under the GNU Public License.
• Aug 1, 2005: chronux_code_0_15.zip
  • Coherence routines now ouput cross-spectra and individual spectra in addition to the coherency - separate cross-spec routines are now dropped.
  • Added new routines to compute segmented averages of the spectrum and coherence for single channel data.
  • Added routines to compute correlations in the log spectrum <log S(f) log S(f')> given a single time series. This first computes spectra on segments and then evaluates the above.
  • Comments in the coherence routines changed to so that data is of the form time x trials instead of time x channels/trials.
• May 20, 2005: chronux_code_0_14.zip
• May 18, 2005: chronux_code_0_13.zip
• Nov 24, 2004: chronux_code_0_12.zip
• Aug 26, 2004: chronux_code_0_11.zip
• Aug 24, 2004: chronux_code_0_1.zip