R4670/PySONICmaster
R4670/PySONIC
master
History Graph
History Graph
Commit | Author | Details | Committed | |||
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bed4f4a9de36 | tlemaire | re-added file caching for QSS analysis | Jul 15 2019 | |||
d50bf6119d40 | tlemaire | started implementing SonicTranslator.parseSteadyStates method. Implemented… | Jul 15 2019 | |||
d3de1ce856e1 | tlemaire | added more robust patterns to PointNeuronTranslator | Jul 5 2019 | |||
e34dcc6d2cb9 | tlemaire | reordered TC states. minor changes in translators. | Jul 5 2019 | |||
6755d10c0e98 | tlemaire | add permeability_constant_pattern to PointNeuronTranslator | Jul 4 2019 | |||
a788320b3aae | tlemaire | added new functionalities to Trnalsator class (now used in SonicTranslator). | Jul 4 2019 | |||
aa1ed8d9b040 | tlemaire | added getClosure method to Translator class. | Jul 4 2019 | |||
b427c3fd93df | tlemaire | added getClosure to translator. added getConstantsDict function in constants.py | Jul 3 2019 | |||
ffdcb43ba1d8 | tlemaire | improved checkTitrate robustness | Jul 1 2019 | |||
be3e09e67984 | tlemaire | removed test lookup file | Jul 1 2019 | |||
d1a3fbaefd83 | tlemaire | added option to provide simAndSave or simulate to batches. implemented addMeta… | Jul 1 2019 | |||
270ec5466a47 | tlemaire | NmodlGenerator: implemented parsing of potential class attributes used as… | Jun 30 2019 | |||
f22a47305c1e | tlemaire | improved SonicTranslator class | Jun 30 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 | |||
22abb7710105 | tlemaire | created separate test module with TestBase class. renamed test_basic into… | Jun 28 2019 | |||
0fe23305b3ad | tlemaire | re-introduced derivatives as mandatory model method | Jun 27 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 | |||
b7e75610c1d2 | tlemaire | changed TimeSeries.getStimPulses to class method | Jun 26 2019 | |||
dffee6926b85 | tlemaire | added fs (spatially-averaged) as input to nbls model. defined SmartLookup class… | Jun 26 2019 | |||
07c34eeed0f7 | tlemaire | added test at bottom of lookups module | Jun 26 2019 | |||
4d047c49f50d | tlemaire | added paper url to setup.py | Jun 26 2019 | |||
4ebf9fe64023 | tlemaire | replaced multiprocessing import by multiprocess import in batches.py to enable… | Jun 26 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 | |||
f83e0e973bd3 | tlemaire | corrected README | 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 | |||
83ff47370d86 | tlemaire | defined separate lookup decorator for bls.computePMparams method. updated… | Jun 24 2019 | |||
a96a900ad4b4 | tlemaire | define dLookUp class to perform lookup projections and interpolations | Jun 20 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 | |||
1a9277e6bbb4 | tlemaire | corrected error in subset parsing | Jun 19 2019 | |||
f719dddee9f0 | tlemaire | added getSteadyStates and getDerStates methods to pneuron to call steadyStates… | Jun 19 2019 | |||
becd2527f268 | tlemaire | corrected Cinf error in ThalamoCortical neuron | 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 | |||
40b5a09c46c2 | tlemaire | started implementation of buildDerEffStates to contruct the derEffStates… | Jun 18 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 | |||
d4798d527ccc | tlemaire | added custom parsing to paper figure scripts | Jun 17 2019 | |||
66eaf2f41fba | tlemaire | corrected y, t order error in nbls.fullDerivatives. added custom parsing in… | Jun 17 2019 | |||
a03eb1b35b77 | tlemaire | added custom parsing to plot_gating_kinetics.py | Jun 17 2019 | |||
3b86ec877351 | tlemaire | added custom parsing to plot_effective_variables.py | Jun 17 2019 | |||
1465c48312a6 | tlemaire | adde prettify option to timeseries plots | Jun 17 2019 | |||
e3f3982b8981 | tlemaire | defined PlotParser and TimeSeriesParser classes | Jun 17 2019 | |||
9e96cf6ee947 | tlemaire | added colormap functionality to PhaseDiagram | Jun 17 2019 | |||
e01fa72e6143 | tlemaire | replaced plotPhaseDiagram by PhaseDiagram class inheriting from ComparativePlot… | Jun 17 2019 | |||
0efc60073f8b | tlemaire | moved nmodl generator to ExSONIC package | Jun 17 2019 | |||
9556faead02c | tlemaire | added custom parsing to generate_mod_file.py | Jun 17 2019 | |||
4ce5e074ca4c | tlemaire | solved issue with ActivationMap Ascale | Jun 17 2019 | |||
75f6032d2f63 | tlemaire | replaced no_offset by tbounds in plotting options. added custom parsing to… | Jun 17 2019 | |||
cf146fbc835e | tlemaire | removed plotFRProfile from init file | Jun 16 2019 | |||
63faa327c865 | tlemaire | finished implmenting Firing Rate as plot variable (now replacing plotFRProfile). | Jun 16 2019 | |||
1329e50433cd | tlemaire | added consistent time bounding to plotters | Jun 16 2019 | |||
b461503582fb | tlemaire | added firing rate to plot variables | 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 | |||
b0f51febd195 | tlemaire | updated constants | Jun 13 2019 | |||
bd54da55cc7c | tlemaire | removed extra line in EStimParser | Jun 13 2019 | |||
af7294977045 | tlemaire | adapted MechSimParser for use in run_lookups.py | Jun 13 2019 | |||
812cb5c1cb3a | tlemaire | updated README headers | Jun 13 2019 | |||
b42a0de93240 | tlemaire | updated all file headers | Jun 12 2019 | |||
0ab79b08684a | tlemaire | adapted README recipe to cleaned up neuron classes | 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 | |||
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 | |||
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 |
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