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History Graph
Commit | Author | Details | Committed | ||||
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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 | ||||
9c883a796eff | tlemaire | moved example script in README and updated rest of the text. | 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 | ||||
fdc484dcbe00 | Theo Lemaire | simplified run scripts | Jun 2 2019 | ||||
49e81c5ace12 | Theo Lemaire | changed marker styles for QSS plots | Jun 2 2019 | ||||
68e2fe6fd858 | Theo Lemaire | added getInDict function used to determine output directory in sim scripts | Jun 2 2019 | ||||
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 |
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