CHANGES.txt

1.3.9
  Removed random crap file ibis.mat
  Added option 'discountNegativeDeriv' to GetSpikes.m, which defaults to false
    normally but true when 'findMinis' is true. It decreases the strictness
    of required negative derivatives to detect a mini (which have slow
    repolarization).
  Corrected legend in PlotGetSpikes.m
  Added legend to dV/dt plot in GetSpikes.m
  Updated help documentation

1.3.8
  GetSpikes.m:
    Use DerivFilter instead of WienerDeriv
    Added options 'minSpikeHeight', 'minSpikeAspect'
    Changed spike search so that a negative derivative must quickly follow the
      maximum positive derivative
    Added .height, .width to output structure
  TestWaveform:
    better 1-1 matching between test and saved spike data

1.3.7
  AnalyzeWaveform.m:
    Changed how options were passed to GetSpikes
    Updated default options
  GetOptions.m:
    Improved guessing key-value pair vs list of options (still not perfect)
  TestWaveform:
    Quantitative system almost complete:
      need to get Lamont directory in the system
      Still must develop F-I specific and AnalyzeWaveform specific tests

1.3.6
  GetSpikes.m:
    Added findMinis option
  GetOptions.m:
    Added optional output argument "modified", which lists whether or not each
      option has been modified from default
  TestWaveform.m:
    Building quantitative testing system
      Maria and Jon directories are handled
      Tilman and Lamont) still must be transistioned
      Still must develop F-I specific and AnalyzeWaveform specific tests

1.3.5
  GetSpikes.m:
    Made filtering more aggressive
    Removed plot of curvature
    Tied output of some information to debugPlots
  TestWaveform.m:
    Preliminary work to make testing more quantitative, less graph-based

1.3.4
  LoadAbf:
    Fixed error condition parsing header information from some .abf files

1.3.3
  GetFICurve:
    If IIntercept is too large, produce error instead of warning, and move
      notification to fitCurve() instead of plotFI()

1.3.2
  Removed GetFICurveOld.m

1.3.1
  GetFICurve:
    updated help
    Bugfix: fI.fitInfo was computed incorrectly in some situations
    Improved smoothness of graph from plotFI

1.3.0
  GetFICurve:
    Bugfix: previously reported spike rates in kHz instead of Hz
    Organized output into struct
    Curve fit to f-I curve is now a function of f, not I
    Better estimates of standard error of mean f, I
  GetOptions:
    ignoreExtra -> allowExtra (cause extra options to be set, rather than
      completely ignored)
  TestWaveform:
    adjust determination of path so that users other than ted can run tests!

1.2.2
  Bugfix: GetFICurve had some string processing errors
  Updated TestWaveForm('Maria') to call GetFICurve

1.2.1
  Vastly improved/modernized GetFICurve.m

1.2.0
  In GetSpikes.m
    Added option 'removeOutliers'
    Corrected undesirable behavior in how spikes were bracketed
    Improved filtering strength for very noisy data
    Moved measurement of "typical" derivative noise to consider data within
      +- 1/2 sigma of median
    Altered computation of pFalseSpike to reflect that filtering decreases the
      odds that a large positive will be followed by a large negative

1.1.0
  Slight speed up to GetSpikes.m main detection loop
  Added option 'recursive' to GetSpikes.m
  For very noisy data, derivative smoothing increases
  Spike height must be at least 10 * digitization noise
  In test suite:
    Some simplification of test
    Ability to specify which tests are performed by passing name
    Some decrease in data size
    Removal of inappropriate data

1.0.6
  bugfix: in GetSpikes.m::getSpikeShape, sometimes maxDeriv or minDeriv could
    be found on the wrong side of the spike peak.

1.0.5
  bugfix: AnalyzeSlowWave.m::RemoveSpikes crashed when there were no spikes

1.0.4
  Partially cleaned up AnalyzeSlowWave.m
  Updated AnalyzeExtracellular.m
  Messing about with test functions

1.0.3
  increased resilience of GetSpikes.m::getSpikeShape in the face of very noisy
    data
  in Spectrum.m:
    included standard GetOptions interface with new options
    simplified to one method (spec = fft(correlation(0.25:0.75)))
    de-trend instead of de-mean

1.0.2
  in GetSpikes.m:
    updated plotting
      added some debugging plots
    updated method of setting spike thresholds
      chosen to match estimated probability of finding spurious spikes
    added some extra start-up options
      only plot debug plots when options.debugPlots is true
      can set pFalseSpike
  in WienerDeriv.m:  (improved quality of derivatives for noisy traces)
    Detrend input signal instead of just subtracting mean
    Changed method of estimating noise
      -remove frequencies above 1/4 Nyquist instead of 1/2
      -set noise level at 90th percentile instead of max
    Allow requesting multiple derivative orders
  in PlotGetSpikes.m:
    Don't draw vertical red lines when shape information is present
    Plot curvature information instead of minV
    Add legend
    return plot handle if requested

1.0.1
  GetSpikes.m times in spike object were off by equivalent of one index
  Changed computation of preMaxCurve and postMaxCurve to be more reliable