History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
fd4639a4c602 | tlemaire | parametrised Qm plot range to be neuron-specific. Solved issue with pbar update. | Sep 2 2019 | |||
d2ccd21d9889 | tlemaire | corrected crucial error in nbls.spatialAverage method. corrected Cm0 and Qm0… | Sep 2 2019 | |||
4f5fb5ee0829 | tlemaire | implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to… | Aug 26 2019 | |||
db880034dc26 | tlemaire | harmonized peaks/spikes detection process across the package. | Aug 22 2019 | |||
3146cab6bade | tlemaire | added iCap to plot variables. added colormap option for comparative plots even… | Aug 15 2019 | |||
2278e599a753 | tlemaire | added automatic solution prepending to all simulate methods (to treat initial… | Aug 14 2019 | |||
366c7e528105 | tlemaire | added VoltageClamp class with associated script and parser | Aug 14 2019 | |||
dc37f0afbd17 | tlemaire | removed all static quasiSteadyStates definition in neuron classes. | Jul 17 2019 | |||
f113d822d4fb | tlemaire | added findModifiedEq function to utils, using brentq to find a new equilibrium… | Jul 17 2019 | |||
17b59c14aa75 | tlemaire | modified TC neuron steadyStates method. | Jul 16 2019 | |||
f768f01cd891 | tlemaire | transformed pneuron qsState and quasiSteadyStates methods to return lambda… | Jul 15 2019 | |||
ffdcb43ba1d8 | tlemaire | improved checkTitrate robustness | Jul 1 2019 | |||
d1a3fbaefd83 | tlemaire | added option to provide simAndSave or simulate to batches. implemented addMeta… | Jul 1 2019 | |||
4937955d0214 | tlemaire | adapted methods of all classes into classmethods and staticmethods when… | Jun 29 2019 | |||
4997a9f88989 | tlemaire | transformed model inputs, checkInputs and simQueue into static methods | Jun 28 2019 | |||
a0db776b7966 | tlemaire | added Model.description method. added nbls.getLookup2D method with correct fs… | Jun 27 2019 | |||
b73594f4d58b | tlemaire | moved lookup to core module. moved getLookup methods to nbls class. | Jun 27 2019 | |||
8f1ea1a16339 | tlemaire | moved effRates vectorization into pneuron.getEffRates method | Jun 27 2019 | |||
3528fa81b6d1 | tlemaire | cleaned up model classes. defined mandatory derivatives method for model… | Jun 26 2019 | |||
9965ddc0005d | tlemaire | improved steadyStates definition in TC and STN neurons. corrected dQdt pltvar… | Jun 25 2019 | |||
8b3f49b0bac4 | tlemaire | corrected labeling error in GroupedTimeSeries | Jun 25 2019 | |||
acf299185987 | tlemaire | removed unnecessary functions from pneuron | Jun 25 2019 | |||
db8cc8e2b5ff | tlemaire | added automatic effRates function definition in pneuron.parse method. removed… | Jun 25 2019 | |||
4742d6a43494 | tlemaire | finished implementing pneuron.buildDerEffStates method to automatically create… | Jun 25 2019 | |||
6c10d4162d71 | tlemaire | added default output directory ("dump"). cleaned up neuron classes. | Jun 20 2019 | |||
fdebb58e8442 | tlemaire | refefined derEffstates construction to return a dictionary of function. | Jun 19 2019 | |||
f719dddee9f0 | tlemaire | added getSteadyStates and getDerStates methods to pneuron to call steadyStates… | Jun 19 2019 | |||
98942bac6b56 | tlemaire | redefined derStates and steadyStates as dictionary of lambda functions | Jun 19 2019 | |||
26fe1e08a408 | tlemaire | cleaned up neuron classes. redefined currents to return functions instead of… | Jun 19 2019 | |||
7b2aee9851af | tlemaire | replaced obscur states list by explicit dictionary in all currents methods | Jun 18 2019 | |||
00f57af96cfb | tlemaire | replaced obscur states list by explicit states dictionary in derStates and… | Jun 18 2019 | |||
63faa327c865 | tlemaire | finished implmenting Firing Rate as plot variable (now replacing plotFRProfile). | Jun 16 2019 | |||
b461503582fb | tlemaire | added firing rate to plot variables | Jun 16 2019 | |||
c14fa0da1fd7 | tlemaire | added simkey to meta dictionary. added automatic parsing and labeling of… | Jun 15 2019 | |||
de8bdbc4fee0 | tlemaire | added outputdir option to simQueue methods. added automatic parsing to Parser… | Jun 14 2019 | |||
b0f51febd195 | tlemaire | updated constants | Jun 13 2019 | |||
b42a0de93240 | tlemaire | updated all file headers | Jun 12 2019 | |||
cc309fa78cd9 | tlemaire | cleaned-up all neuron classes | Jun 12 2019 | |||
0028dbdfe69f | tlemaire | added neuron templyte class. added procedure to follow to add new neuron types… | Jun 11 2019 | |||
c7f94b320ba7 | tlemaire | set t first in all derivatives function | 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 | |||
1c9c63d4ba6a | tlemaire | added getModel and getPointNeuron functions. removed deprecated scripts. | Jun 6 2019 | |||
6cbf141d9754 | Theo Lemaire | corrected plot_QSS inputdir error | Jun 3 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 | |||
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 | |||
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 | |||
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 | |||
1a5f9b3c215b | Theo Lemaire | implemented neuron-dependent titration to find specific thresholds (excitation… | 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 | |||
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 | |||
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 | |||
6f96c02c5ecb | tlemaire | corrected STN lookups, comparison of temporal profiles of spontaneous activity… | Mar 20 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 | |||
2e64aa90c325 | tlemaire | changed nomenclature of current methods from "curr..." to "i..." | Mar 5 2019 | |||
65c1d8649331 | tlemaire | implemented Frankenhaeuser-Huxley membrane mechanism (validated against data… | Jan 9 2019 | |||
0ebd7ae3b932 | tlemaire | replaced 'L' by 'Leak' in neurons nomenclature. implemented STN neuron with… | Nov 30 2018 | |||
2f63e4926c36 | tlemaire | improved plotRheobaseAmps function. improved arguments parsing in command line… | Nov 22 2018 | |||
73851d6ac128 | tlemaire | updated package documentation | Sep 28 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 | |||
de613ac9c35a | tlemaire | replaced SonicNeuron by NeuronalBilayerSonophore | Sep 23 2018 |
c4science · Help