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History Graph
Commit | Author | Details | Committed | ||||
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84c6a191108c | Theo Lemaire | updated package requirements | 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 | ||||
de4dc186176b | Theo Lemaire | added better plot handling to run_astim.py | May 24 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 | ||||
2de6d3d26717 | Theo Lemaire | added Amin and Amax command line arguments to plot_QSS_IQ.py | 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 | ||||
f7c982e3c3ea | Theo Lemaire | added Qi-conditional graphs labeling for plotQSSVarVsAmp and plotEqChargeVsAmp | Apr 5 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 | ||||
178930fa846c | tlemaire | added generic plot_QSS_IQ.py script to plot the IQ phase-plane diagram for a… | Mar 26 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 | ||||
d06d82b80840 | tlemaire | added rmse evaluation for Q-stab comparison between sims and QSS approx. in… | Mar 20 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 | ||||
895dbbeb52ae | tlemaire | removed old pltvars dictionary. | 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 | ||||
d744944eba53 | tlemaire | major reformatting of neuron classes. | Mar 13 2019 | ||||
db85dec73950 | tlemaire | implemented PointNeuron.currentToConcentrationRate method for a common way to… | Mar 13 2019 | ||||
b178c1dca3c9 | tlemaire | replaced CCa_out by Cao and KCa by 1 / taur_Cai in STN class for more clarity. | Mar 13 2019 | ||||
ce5a9df84ba1 | tlemaire | added Qbounds as a PointNeuron class method. cleaned up use of Cai in TC class. | Mar 13 2019 | ||||
33c52c6b04a5 | tlemaire | removed all combined gating variables from pltvars schemes. | 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 | ||||
2b5b9cf5a78b | tlemaire | corrected error in STN.derD1. lookup tables to re-run. | Mar 12 2019 | ||||
7082d86bf3da | tlemaire | added get_dCCa and findCaeq methods ot STN neuron (iterative search to find… | Mar 12 2019 | ||||
2979d8329c88 | tlemaire | added detection of stabilization (time and value) from charge density profiles… | Mar 11 2019 | ||||
d99d9eb144b6 | tlemaire | implemented NeuronalBilayerSonophore.getQSSvars method to compute QSS… | Mar 11 2019 | ||||
cd145e4db3e8 | tlemaire | adapted plotSpikingMetrics for uniform y-axis scale. adapted ASTIM_filecode… | Mar 11 2019 | ||||
c5433b2c448c | tlemaire | added currents methods to Cortical, Thalamic and STN classes, that returns a… | Mar 10 2019 | ||||
a74f9c571b7d | tlemaire | adapted fig9.py with corrected STN model (new traces). | Mar 8 2019 | ||||
e73ca2da1333 | tlemaire | corrected STN lookups. added testQSS script to analyze STN neuron plateau… | Mar 8 2019 | ||||
990c8181cf46 | tlemaire | corrected sigmaT2_b from -10 mV to 10 mV in STN implementation. started new QSS… | Mar 7 2019 | ||||
da8e0bbde997 | tlemaire | renamed currents for more clarity | Mar 6 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 | ||||
865020d8c630 | tlemaire | added RS neuron lookups with partial coverage (spatially averaged). updated… | Feb 28 2019 | ||||
702446ca2ad5 | tlemaire | corrected error in getLookups2Dfs | Jan 23 2019 | ||||
957db9d021d6 | tlemaire | added getLookups2Dfs method to interpolate lookups at given membrane coverage. | Jan 23 2019 | ||||
80aa94a42257 | tlemaire | added script to compute quick lookups for a span of partial sonophore coverage… | Jan 23 2019 | ||||
69f20e7c2a18 | tlemaire | modified Qbounds to account for capacitance value in all neuron types. | Jan 11 2019 |
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