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History Graph
History Graph
Commit | Author | Details | Committed | ||||
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01c2a27636c1 | tlemaire | added prependDataframe method to postpro module. | Sep 6 2019 | ||||
c4d24a293f93 | tlemaire | renamed Simulator.resample method to downsample in order to avoid confusion… | Sep 6 2019 | ||||
107df2b92970 | tlemaire | corrected minor issues in spike detection functions (dt bounding for resampling… | Sep 6 2019 | ||||
ec87894d9435 | tlemaire | modified find_tpeaks to work with irregular time vectors. | Sep 6 2019 | ||||
614c56792d61 | tlemaire | expanded charge range for pneuron.getLookup | Sep 4 2019 | ||||
fdf554e5e6ab | tlemaire | updated notebooks | Sep 4 2019 | ||||
6f5a204770f8 | tlemaire | added sweeney lookups | Sep 3 2019 | ||||
8102e979f684 | tlemaire | updated SPIKE_MIN_VAMP to allow robust spike detection for sweeney model | Sep 3 2019 | ||||
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 | ||||
4c34c2a9dc9a | tlemaire | adapted test_sims (avoiding sweeney neuron) | Aug 29 2019 | ||||
f19b1648b5ed | tlemaire | remoed sweeney lookups (need to figure out the reason for weird profiles first). | Aug 29 2019 | ||||
1b3cffe95e7a | tlemaire | added sweeney lookups (ASTIM not working yet). added fixLookup to remove single… | Aug 29 2019 | ||||
8226a9490c9b | tlemaire | adapted constants to enable sweeney lookups creation. | Aug 26 2019 | ||||
4f5fb5ee0829 | tlemaire | implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to… | Aug 26 2019 | ||||
d7855a1dd087 | tlemaire | implemented pow2Search function using an incremental power of 2 search to… | Aug 26 2019 | ||||
4821f3c94b73 | tlemaire | corrected minor mistake in getCommonLabel | Aug 24 2019 | ||||
fdf57ea352bd | tlemaire | added getCommonLabel method to ComparativePlot (now used to determine figure… | Aug 24 2019 | ||||
db880034dc26 | tlemaire | harmonized peaks/spikes detection process across the package. | Aug 22 2019 | ||||
3c76710406c6 | tlemaire | removed paper figures folder (now in separate repo) | Aug 19 2019 | ||||
0d24b201dea4 | tlemaire | added figtitle and getModel as GenericPlot methods | Aug 16 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 | ||||
523f8865bde3 | tlemaire | corrected minor issues in timeseries | Aug 14 2019 | ||||
366c7e528105 | tlemaire | added VoltageClamp class with associated script and parser | Aug 14 2019 | ||||
1b242e25ca45 | tlemaire | added plot_intensity_vs_amplitude.py script | Aug 14 2019 | ||||
ec01e1e58099 | tlemaire | fixed error in bls.filecodes | Jul 29 2019 | ||||
48fd3e1df816 | tlemaire | test commit. | Jul 26 2019 | ||||
8e1403abecb9 | tlemaire | updated README to latest changes. | Jul 24 2019 | ||||
a70fc6312da7 | tlemaire | set simFull, simHybrid and simSonic as private nbls methods | Jul 24 2019 | ||||
9ba9ca99a89f | tlemaire | corrected error in getSimThresholdAmps (added default fs to 1) | Jul 18 2019 | ||||
9e0718eb1a9b | tlemaire | corrected error in Model logNSpikes, checkTitrate and simAndSave methods. | Jul 18 2019 | ||||
5aa12c341577 | tlemaire | interoduced derivative function to compute numerical derivatives with various… | Jul 18 2019 | ||||
28c94d579a04 | tlemaire | improved QSS fixed points color labeling | Jul 18 2019 | ||||
ab25e778e32f | tlemaire | added saddle point classification to QSS analysis. | Jul 17 2019 | ||||
dc37f0afbd17 | tlemaire | removed all static quasiSteadyStates definition in neuron classes. | Jul 17 2019 | ||||
bce60bf70097 | tlemaire | adapted findModifiedEq to work with iterables as inputs | Jul 17 2019 | ||||
bf936959e87b | tlemaire | replaced createLookupLambda by createClassLambda that can take various lambda… | 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 | ||||
137ca70ce6a3 | tlemaire | cleaned up nbls | Jul 15 2019 | ||||
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 | ||||
af0e4bd2fe9e | tlemaire | corrected TC neuron notebook | 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 | ||||
9ac705d6dbee | tlemaire | updated README | 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 | ||||
d909927fd268 | tlemaire | defined TestBase class with smart subset handling (inherited by TestSims) | Jun 27 2019 | ||||
eb0324a5cd27 | tlemaire | rewrote test_basic into a class | 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 | ||||
65a9529c2978 | tlemaire | updated 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 | ||||
21dda94243b8 | tlemaire | added precisions about derStates requirements in README | 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 |
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