R4670/PySONICmaster
R4670/PySONIC
master
History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
e01fa72e6143 | tlemaire | replaced plotPhaseDiagram by PhaseDiagram class inheriting from ComparativePlot… | Jun 17 2019 | |||
0efc60073f8b | tlemaire | moved nmodl generator to ExSONIC package | Jun 17 2019 | |||
9556faead02c | tlemaire | added custom parsing to generate_mod_file.py | Jun 17 2019 | |||
4ce5e074ca4c | tlemaire | solved issue with ActivationMap Ascale | Jun 17 2019 | |||
75f6032d2f63 | tlemaire | replaced no_offset by tbounds in plotting options. added custom parsing to… | Jun 17 2019 | |||
cf146fbc835e | tlemaire | removed plotFRProfile from init file | Jun 16 2019 | |||
63faa327c865 | tlemaire | finished implmenting Firing Rate as plot variable (now replacing plotFRProfile). | Jun 16 2019 | |||
1329e50433cd | tlemaire | added consistent time bounding to plotters | Jun 16 2019 | |||
b461503582fb | tlemaire | added firing rate to plot variables | Jun 16 2019 | |||
012f2603c5d7 | tlemaire | added colormap functionality to CompPlot, with lin or log scale. | Jun 15 2019 | |||
c14fa0da1fd7 | tlemaire | added simkey to meta dictionary. added automatic parsing and labeling of… | Jun 15 2019 | |||
fb7c07fee5cb | tlemaire | added spike details plotting options to TimeSeriesPlot | Jun 14 2019 | |||
bdf8ef51d3db | tlemaire | added frequency and mark_spikes option to both CompPlot and SchemePlot classes | Jun 14 2019 | |||
de8bdbc4fee0 | tlemaire | added outputdir option to simQueue methods. added automatic parsing to Parser… | Jun 14 2019 | |||
b0f51febd195 | tlemaire | updated constants | Jun 13 2019 | |||
bd54da55cc7c | tlemaire | removed extra line in EStimParser | Jun 13 2019 | |||
af7294977045 | tlemaire | adapted MechSimParser for use in run_lookups.py | Jun 13 2019 | |||
812cb5c1cb3a | tlemaire | updated README headers | Jun 13 2019 | |||
b42a0de93240 | tlemaire | updated all file headers | Jun 12 2019 | |||
0ab79b08684a | tlemaire | adapted README recipe to cleaned up neuron classes | Jun 12 2019 | |||
cc309fa78cd9 | tlemaire | cleaned-up all neuron classes | Jun 12 2019 | |||
6e017b421f3e | tlemaire | replaced "neuron" by "pneuron" for all PointNeuron instances | Jun 12 2019 | |||
0028dbdfe69f | tlemaire | added neuron templyte class. added procedure to follow to add new neuron types… | Jun 11 2019 | |||
3accccc91cbe | tlemaire | added plotting of real QS SFPs and UFPs in plotQSSdynamics and plotQSSVarVsQm… | Jun 10 2019 | |||
ed095e030274 | tlemaire | minor change to getCycleProfiles | Jun 10 2019 | |||
2f0254ea5b53 | tlemaire | added functionality to load data directly from sim results in TimeSeriesPlot… | Jun 10 2019 | |||
1354c6f9d2e9 | tlemaire | switched back to old evaluateStability version | Jun 10 2019 | |||
dd32fc0479b4 | tlemaire | first attempt at replacing custom integration in nbls.evaluateStability by call… | Jun 10 2019 | |||
84c54a491722 | tlemaire | removed STN temporary fix in nbls.titrate | Jun 9 2019 | |||
b88c300e48f0 | tlemaire | added first-call check that condition changes within the interval to… | Jun 9 2019 | |||
db58a9d4e8b7 | tlemaire | added file locking to cache functions | Jun 9 2019 | |||
2e0f97a8baaf | tlemaire | added solve_ivp optional use to Simulator.integrate method | Jun 9 2019 | |||
c7f94b320ba7 | tlemaire | set t first in all derivatives function | Jun 9 2019 | |||
b46a8cd85a73 | tlemaire | removed ng and Z explicit computation in runSONIC (replaced by nan arrays) | Jun 9 2019 | |||
5eed591ede6e | tlemaire | corrected errors in nbls interpEFFVariable and runSONIC methods | Jun 9 2019 | |||
863bdf8330f4 | tlemaire | added nbls isStableQSS and titrateQSS methods. finished plotQSSThresholdCurve | Jun 9 2019 | |||
26fdc0bbfe8d | tlemaire | added getSimThresholdAmps and plotQSSThresholdCurve functions to QSS module… | Jun 7 2019 | |||
86564c193a65 | tlemaire | added multiprocessing for runAndGetStab function | Jun 7 2019 | |||
1f1e59762ea3 | tlemaire | added custom parsers to plot_timeseries and plot_QSS | Jun 7 2019 | |||
50103226d72b | tlemaire | moved getLowIntensitiesSTN to STN class | Jun 6 2019 | |||
0984b86caa8f | tlemaire | moved lookups utilities into separate lookups module (in neurons folder) | Jun 6 2019 | |||
3556a765fe5c | tlemaire | created ActivationMap class | Jun 6 2019 | |||
1c9c63d4ba6a | tlemaire | added getModel and getPointNeuron functions. removed deprecated scripts. | Jun 6 2019 | |||
01bf73a48e1a | Theo Lemaire | minodr edits | Jun 4 2019 | |||
bc5a29bc6c9a | Theo Lemaire | added caching of QSS analysis results | Jun 3 2019 | |||
6cbf141d9754 | Theo Lemaire | corrected plot_QSS inputdir error | Jun 3 2019 | |||
1295ce41f2c3 | Theo Lemaire | added custom parser to plot_QSS_IQ.py | Jun 3 2019 | |||
f75ca2e6e294 | Theo Lemaire | added parsers module, now used in sim scripts for more consistency. | Jun 3 2019 | |||
b21bb388bb20 | Theo Lemaire | removed unnecessary script | Jun 2 2019 | |||
49e81c5ace12 | Theo Lemaire | changed marker styles for QSS plots | Jun 2 2019 | |||
874f4649ec44 | Theo Lemaire | corrected QSS module to work correctly with "load" option. | Jun 2 2019 | |||
88811f7a8aa5 | Theo Lemaire | major cleanup of all core classes. | Jun 2 2019 | |||
c49110f6c3cf | Theo Lemaire | added isAsymptoticallyStable method to PeriodicSolver | Jun 1 2019 | |||
7c909ad7dbbd | Theo Lemaire | added convfunc attribute to PeriodicSimulator class | Jun 1 2019 | |||
e0aa4041f3b8 | Theo Lemaire | added caching to nbls.titrate method | Jun 1 2019 | |||
10d2b5bb498e | Theo Lemaire | redefined titration procedures with binarySearch method. now single runAndSave… | Jun 1 2019 | |||
de01bc8b1676 | Theo Lemaire | moved batches to core module | May 31 2019 | |||
25d498c21187 | Theo Lemaire | implemented abstract Model class to be inherit by bls, pneuron and nbls | May 31 2019 | |||
4dd95ba1d83c | Theo Lemaire | added toffset to args list of pneuron and nbls filecode methods | May 31 2019 | |||
6cb5dac16172 | Theo Lemaire | moved createAStimQueue and createEStimQueue to their respective classes | May 31 2019 | |||
aae3bfea421b | Theo Lemaire | moved "amp" parameter back to appropriate in args list of runAndSave functions | May 31 2019 | |||
42ef7cb1063a | Theo Lemaire | added "meta" method to core classes | May 31 2019 | |||
af6f9a02ed42 | Theo Lemaire | reformatted simulate methods of bls, pneuron and nbls classes to return output… | May 31 2019 | |||
19a9b2f737fd | Theo Lemaire | cleaned up simulators classes | May 31 2019 | |||
f713b8d85160 | Theo Lemaire | added appendSolution method to simulators | May 30 2019 | |||
17f1482bc336 | Theo Lemaire | added docstring to simulators classes | May 30 2019 | |||
e08e8c736efa | Theo Lemaire | replaced progressbar2 by tqdm | May 29 2019 | |||
440f5459adf4 | Theo Lemaire | added HybridSimulator used for nbls.runHybrid | May 29 2019 | |||
370f27746bca | Theo Lemaire | added use of PWSimulator in pneuron | May 29 2019 | |||
4ba3212edf92 | Theo Lemaire | added simulators classes to take care of simulations | May 29 2019 | |||
1391db99409d | Theo Lemaire | added intermediate "run" method that return output data and metadata | May 27 2019 | |||
21d010292ddf | Theo Lemaire | added return_val option to isExcited and isSilenced | May 27 2019 | |||
c23526a0ca16 | Theo Lemaire | added logNSpikes function to pneuron class. | May 27 2019 | |||
13e29c29bbb1 | Theo Lemaire | haromized amplitude and plot_scheme parsing across simulation scripts | May 27 2019 | |||
818219348db5 | Theo Lemaire | started defining ActivationMap class | May 27 2019 | |||
71a2cddb684e | Theo Lemaire | replaced filecode functions by class methods | May 27 2019 | |||
1463cf220fbc | Theo Lemaire | modified cache to only log if function has not "history" argument to avoid… | May 27 2019 | |||
3a8d7d040f27 | Theo Lemaire | added Araneg and Irange args to run_astim.py | May 24 2019 | |||
4e391806ec32 | Theo Lemaire | re-implemented csvcache as decorator | May 24 2019 | |||
0453d1e710dd | Theo Lemaire | added interface around titrate function to use memory caching | May 23 2019 | |||
678bec02c372 | Theo Lemaire | added "PI" type control of convergence in nbls.evaluateStability method | May 23 2019 | |||
1a5f9b3c215b | Theo Lemaire | implemented neuron-dependent titration to find specific thresholds (excitation… | May 22 2019 | |||
0ee058e8778d | Theo Lemaire | added max integration duration to stability analysis to avoid infinite loops in… | May 22 2019 | |||
3addfe632329 | Theo Lemaire | implemented quasiSteadyStateFixedPoints as part of nbls class. Added… | May 22 2019 | |||
2024b001441b | Theo Lemaire | implemented nbls.quasiSteadStateiNet method, used to compute Q-SFPs iteratively… | May 22 2019 | |||
6b55fdb84a7a | Theo Lemaire | added nA command line argument to plot_QSS_IQ.py | May 21 2019 | |||
8a17ab2f8c11 | Theo Lemaire | implemented specific nbls evaluateStability method to evaluate FP stability by… | May 21 2019 | |||
14f3b43f5ec7 | Theo Lemaire | added negative offset to QSS perturbation | May 20 2019 | |||
df4bf6f7892b | Theo Lemaire | added warning note about why QSS cannot be interpolated accurately and must be… | May 17 2019 | |||
3e55319aff15 | Theo Lemaire | added fixed point classification based on perturbation reaction in QSS analysis. | May 17 2019 | |||
4d8fa0caef5b | Theo Lemaire | added isTitratable method to neuron classes. improved QSS SFP stability… | May 17 2019 | |||
3ad8ad914eec | Theo Lemaire | replaced linear interpolation of QSS at Q-SFPs (inaccurate) by full… | May 16 2019 | |||
3f4135902bdc | Theo Lemaire | added np.nan bounding to all np.interp uses in the code. implemented… | May 16 2019 | |||
a66b375c6133 | Theo Lemaire | implemented getLookupsDCavg function to compute DC-averaged lookups. nbls. | May 15 2019 | |||
ee9cf8652b7e | Theo Lemaire | simplified nbls.quasiSteadyStates method, now calling explicit quasiSeadyStates… | May 15 2019 | |||
62c6723c6e71 | Theo Lemaire | changed PointNeuron getEffrates, steadyStates, derStates and derEffStates… | May 14 2019 | |||
7a27b761d220 | Theo Lemaire | major improvements to QSS module | May 10 2019 | |||
536de29806e2 | Theo Lemaire | added ref mode to QSSvar with phase plot arrows. | May 6 2019 | |||
44780023da34 | Theo Lemaire | corrected titrate function to work also with negative injected currents (for… | Apr 29 2019 | |||
ddab2a4571ea | Theo Lemaire | adapted plotQSSVarVsAmp and plotEqChargeVsAmp functions for ESTIM use (not… | Apr 8 2019 |
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