History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
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 | |||
71a2cddb684e | Theo Lemaire | replaced filecode functions by class methods | May 27 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 | |||
8a17ab2f8c11 | Theo Lemaire | implemented specific nbls evaluateStability method to evaluate FP stability by… | May 21 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 | |||
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 | |||
490706425b05 | Theo Lemaire | corrected nbls.quasiSteadyStates to return DC-averaged Vmeff, and adapted nbls. | Apr 5 2019 | |||
6ffd825273a4 | Theo Lemaire | improved titrate function with nSpikes methods pneuron and nbls classes. added… | Apr 5 2019 | |||
9f09f2fdc039 | Theo Lemaire | Changed titration functions (now using generic titrate), Implemented Xinf… | Apr 4 2019 | |||
a2726a130bec | tlemaire | implemented new QSS plot module with generic plotVarDynamics, plotVarsQSS and… | Mar 26 2019 | |||
b6c44fad8f0a | tlemaire | corrected the nbls.quasiSteadyStates method to compute QSS values of slow… | Mar 26 2019 | |||
8a71066a647c | tlemaire | replaced lookups list by lookups dict in all derStatesEff methods. added get… | Mar 26 2019 | |||
5a5f2babbc5d | tlemaire | corrected computation of Cai_ss for STN neuron, now using voltage-gated steady… | Mar 20 2019 | |||
256a4aab9b65 | tlemaire | corrected nbls.getQSSvars method, now computing non-rate-defined QSS values… | Mar 20 2019 | |||
6f96c02c5ecb | tlemaire | corrected STN lookups, comparison of temporal profiles of spontaneous activity… | Mar 20 2019 | |||
07d55c08e109 | tlemaire | Implemented NmodlGenerator core class to automatically generate NEURON MOD file… | Mar 18 2019 | |||
cf921135e3f2 | tlemaire | moved membrane currents in 2rd position of neurons pltscheme. extractPltVar now… | Mar 18 2019 | |||
8623752f128f | tlemaire | cleaned up neurons docstring. added getDesc method to PointNeurons class. | Mar 15 2019 | |||
6bc050dea626 | tlemaire | added rates to pneuron.getPltVars method. adapted use in plotEffectiveVariables… | Mar 15 2019 | |||
ad0a33b92c3c | tlemaire | adapted plotComp to new plot variables scheme. | Mar 15 2019 | |||
a812d7d527af | tlemaire | created plt.pltutils module and moved relevant plotting functions into it. | Mar 15 2019 | |||
81554e5d4d67 | tlemaire | removed states0 attribute from neuron classes (now calling steadyStates method… | Mar 14 2019 | |||
453f896987ce | tlemaire | generalized the use of getPltVars and getPltScheme with inheritance scheme… | Mar 14 2019 | |||
9d1a2fc5cd08 | tlemaire | major reformatting of plotBatch function | Mar 14 2019 | |||
f6195a153a01 | tlemaire | cleaned up neurons docstring. defined PointNeuron.getPltVars method (possibly… | Mar 14 2019 | |||
db85dec73950 | tlemaire | implemented PointNeuron.currentToConcentrationRate method for a common way to… | Mar 13 2019 | |||
ce5a9df84ba1 | tlemaire | added Qbounds as a PointNeuron class method. cleaned up use of Cai in TC class. | Mar 13 2019 | |||
817387c89edd | tlemaire | implemented PointNeuron.getCurrentPltVars method to genrate a dictionary plot… | Mar 13 2019 | |||
09ec0decb4bd | tlemaire | replaced iNet method by currents method in all neuron classes (iNet now defined… | Mar 13 2019 | |||
d99d9eb144b6 | tlemaire | implemented NeuronalBilayerSonophore.getQSSvars method to compute QSS… | Mar 11 2019 | |||
2e64aa90c325 | tlemaire | changed nomenclature of current methods from "curr..." to "i..." | Mar 5 2019 | |||
c72b7b319ed0 | tlemaire | implemented getLookupsOff function to retrieve US-OFF lookups. adapted… | Mar 5 2019 | |||
80aa94a42257 | tlemaire | added script to compute quick lookups for a span of partial sonophore coverage… | Jan 23 2019 | |||
cf20bd8f6516 | tlemaire | added lookups for FH membrane mechanism (tested) | Jan 11 2019 | |||
8684707c3f08 | tlemaire | corrected Qbounds for lookups generation in FH neuron | Jan 10 2019 | |||
82590fe13581 | tlemaire | changed PMAVG_STD_ERR_MAX value to allow BLS lookups generation for FH… | Jan 9 2019 | |||
65c1d8649331 | tlemaire | implemented Frankenhaeuser-Huxley membrane mechanism (validated against data… | Jan 9 2019 | |||
8a4719662fd9 | tlemaire | corrected error in Vm post-processing in runSONIC. added plotV option to… | Dec 27 2018 | |||
7655cca494a0 | tlemaire | corrected STN getEffRates and derStatesEff methods for correct lookups creation… | Dec 3 2018 | |||
0ebd7ae3b932 | tlemaire | replaced 'L' by 'Leak' in neurons nomenclature. implemented STN neuron with… | Nov 30 2018 | |||
fa4c643a5a4b | tlemaire | added spanDC argument to run_astim. removed rheobase amp preconditioning in… | Nov 27 2018 | |||
9f827c942524 | tlemaire | added recording of computation times during lookups creation. | Nov 25 2018 | |||
2f63e4926c36 | tlemaire | improved plotRheobaseAmps function. improved arguments parsing in command line… | Nov 22 2018 | |||
8573c726b480 | tlemaire | modified getLookups2D to project along any dimensions pair in (a, f, A). | Nov 20 2018 | |||
da009206a90e | tlemaire | modified runSONIC method to use odeint solver with interpolated lookups for… | Nov 19 2018 | |||
d17615ffb4e6 | tlemaire | improved plotPhasePlane function. implemented isWithin function for loose bound… | Oct 28 2018 | |||
d2b627754312 | tlemaire | implemented figtitle method for direct labeling from metadata. implemented… | Oct 25 2018 | |||
ed0d192b377b | tlemaire | added scripts to generate paper figures automatically. | Oct 2 2018 | |||
73851d6ac128 | tlemaire | updated package documentation | Sep 28 2018 | |||
f5f327799ad4 | tlemaire | attempt to fix multiprocessing lookups creation. | Sep 27 2018 | |||
4a67049acd76 | tlemaire | added actmap to plt module, with command line script. | Sep 26 2018 | |||
610dc8472dcf | tlemaire | cleaned up utils module. removed log templates (now generated on the fly with… | Sep 25 2018 | |||
954e545fa6ac | tlemaire | turned intermolecular pressure test script into notebook. removed Input error… | Sep 24 2018 | |||
1951d49ccd25 | tlemaire | moved lookups into neurons folder | Sep 24 2018 | |||
de613ac9c35a | tlemaire | replaced SonicNeuron by NeuronalBilayerSonophore | Sep 23 2018 | |||
2dc56eb8b91e | tlemaire | removed InputError references in core modules | Sep 23 2018 | |||
2a334b211bff | tlemaire | major changes to the package (PointNeuron, SonicNeuron, ...) | Sep 23 2018 |
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