R4670/scriptsmaster
R4670/scripts
master
History Graph
History Graph
Commit | Author | Details | Committed | |||
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63faa327c865 | tlemaire | finished implmenting Firing Rate as plot variable (now replacing plotFRProfile). | 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 | |||
da542f2db42b | tlemaire | removed extra line in run_lookups.py | Jun 13 2019 | |||
af7294977045 | tlemaire | adapted MechSimParser for use in run_lookups.py | Jun 13 2019 | |||
b42a0de93240 | tlemaire | updated all file headers | 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 | |||
3accccc91cbe | tlemaire | added plotting of real QS SFPs and UFPs in plotQSSdynamics and plotQSSVarVsQm… | 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 | |||
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 | |||
1f1e59762ea3 | tlemaire | added custom parsers to plot_timeseries and plot_QSS | Jun 7 2019 | |||
50103226d72b | tlemaire | moved getLowIntensitiesSTN to STN class | Jun 6 2019 | |||
3556a765fe5c | tlemaire | created ActivationMap class | Jun 6 2019 | |||
1c9c63d4ba6a | tlemaire | added getModel and getPointNeuron functions. removed deprecated scripts. | Jun 6 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 | |||
68e2fe6fd858 | Theo Lemaire | added getInDict function used to determine output directory in sim scripts | 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 | |||
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 | |||
4ba3212edf92 | Theo Lemaire | added simulators classes to take care of simulations | May 29 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 | |||
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 | |||
678bec02c372 | Theo Lemaire | added "PI" type control of convergence in nbls.evaluateStability method | May 23 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 | |||
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 | |||
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 | |||
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 | |||
ad0a33b92c3c | tlemaire | adapted plotComp to new plot variables scheme. | 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 | |||
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 | |||
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 | |||
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 | |||
c72b7b319ed0 | tlemaire | implemented getLookupsOff function to retrieve US-OFF lookups. adapted… | Mar 5 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 | |||
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 | |||
42f56ab271e3 | tlemaire | modified plotActivationMap to plot amplitude thresholds computed from titration… | Dec 14 2018 | |||
0fcd53a68ce7 | tlemaire | added pltvars for STN neuron. added plotFRprofile function along with paper… | Dec 9 2018 | |||
9eca746695d1 | tlemaire | STN model validated for E-STIM by reproduction of key features (spontaneous… | Dec 3 2018 | |||
0ebd7ae3b932 | tlemaire | replaced 'L' by 'Leak' in neurons nomenclature. implemented STN neuron with… | Nov 30 2018 | |||
850b05b61c5e | tlemaire | added plotFRspectrum function to actmap module. updated fig7 script, and added… | Nov 29 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 | |||
d17615ffb4e6 | tlemaire | improved plotPhasePlane function. implemented isWithin function for loose bound… | Oct 28 2018 | |||
35b8bf12ec49 | tlemaire | plotPhaseDiagram method validated on CW stimuli | Oct 25 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 |
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