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TODO.md

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ToDo

General

  • logging module + log file, beware only import/manipulate logging module for our module

  • change logging to load config from file -> here take care not to overwrite existing loggers

  • use python 3.5 for development and minimal reqs check matplotlib

  • test suite to check min dependencies through to latest

  • import modules into _variables? No: check what numpy does via all

  • check that input_handler is fast when getting data in the right format. Yeah: checked 1k trials with length 1e6 in the right format 100 times in 60sec

  • add date to log file

  • draw fits behind coefficients but in legend data still first, matplotlib z-index? For dense/heavily fluctuating data, better fits in front

  • add all function arguments to log/resulting container

  • ask Jens to link our repo from nat comm url

  • How do we want to seed the rng per default?

  • Disentangle spaghetti code, probably along with all fix

  • log.status or log.progress that does not appear in files. maybe we can have this guy as console logger only with \r by default!

  • custom Fitfunction crashes fit due to call for default args?

  • Outputhandler rasterization and upper limit for exported stuff -> timeseries plots easily grow to hundreds of mb

  • try abs exp amplitude-> always positive without bounds

  • check if integrated autocorrelation time works, too -> only m < 1

  • sometimes saving from outputhandler crops labels -> tight_layout(), but this shoud only take place if external figure was not provided.

  • bug: calling coefficients with steps=np.arange(0,2000,10) crashes 0 -> invalid step

  • bug: breaking printout (probably \r if is not reset)

  • bug: crash on import if logfile cannot be overwritten.

  • bug: crash if no fit converges is inconvenient when running scripts

  • bug: wrapper crashes if substract trial average is used on activity of integers

  • important: set decent default maxstep for coefficients. at the moment it is 1500

  • check if inputhandler changes passed arrays in place or returns a copy

  • python deconstructor to close figures when outputhandler variables are overwritten.

Tipps and Tricks Documentation Section

  • Note: OutputHandler create a huge amount of figures when scripted (and matplotlib interactive is true). Kindoff solved via deconstructor.
>>> import matplotlib
>>> matplotlib.use('Agg')
>>> mre.plt.close('all')
>>> mre.plt.close(2) # figure 2
  • handling different trial lentgh: input_handler on each file. then v-stack
  • Customizing plots, Rasterization, axis label, size, logscale

Wrapper Function

  • propper required argument printout + errors with confusing stack traces in the right place
  • less args
  • plot
  • replace member samples with bootsamples and trials; kept samples for now
  • previous point has to change a bit more:
    • trials -> trialcr: list of CoefficientResults 'cr';
    • trialactivites: list of mean trial activities, always length 'numtrials'
    • bootsamples -> bootstrapcr: list of 'cr'
    • ndarray behaves a bit weird when adding objects (e.g. prints the sub arrays of the contained 'cr')
    • this should allow to fit() and plot on resampled data and individual trials
    • maybe drop 'namedtuple' inheritence for cr and fr, some functions we take over dont work well.
      • reimplement useful ones _asdict (if child != None)
      • _fields
      • _index? no!
  • function call parameters as dict in result of wrapper, coefficients and fit
  • coefficients(): bootstrap for ts method, too
  • just do the bootstrapping for coefficients and make bs of fit optional (fitting takes ages) fit use numboots from wrapper, if none only do bs for ceoffs
  • numboot doesnt do anything so far
  • results file mit function pars of all called steps
  • target dir optional and how to deal with log file/console/function isolated?
  • remove mean trial activity plot and 'average' if only a single trial
  • adaptive maxfev in fit()
  • loglevel argument should be the console handler, i would say. we have a default log file anyway.
  • plot zorder is hardcoded, check if args set. removed shaded areas of fits
  • add qunatil labels to fit results -> use 25% for fiterr instead of variance

Test Script

  • single trial | trial structure
  • sm | ts
  • numboots = 0 | > 0