History Graph
History Graph
| Commit | Author | Details | Committed | |||
|---|---|---|---|---|---|---|
| de255e65bccc | tlemaire | Major update: | Nov 14 2019 | |||
| a26469ca67dc | tlemaire | added equality operators to TimeProtocol and PulsedProtocol classes. | Nov 14 2019 | |||
| 4a5626da478c | tlemaire | improved filecodes generation from meta dictionary in Model.filecode | Nov 13 2019 | |||
| bc1800471252 | tlemaire | created Timeprotocol and PulsedProtocol classes, now used in pneuron, nbls and… | Nov 13 2019 | |||
| f1d2ab4cfb4b | tlemaire | added PointNeuron alphaBorgGaham and betaBorgGraham methods, now used for sundt… | Nov 7 2019 | |||
| a2c1e3e2eb02 | tlemaire | modified nbls.QSSderivatives and nbls.__simQSS to work with any specified… | Nov 6 2019 | |||
| aee2c4e6cb21 | tlemaire | added Lookup.tile and modified SmartLookup.projectDC. modified nbls. | Oct 10 2019 | |||
| 20f96c135bce | tlemaire | defined Lookup algorihtmic operators. defined OnOffSimulator class. defined… | Oct 7 2019 | |||
| d992992a3693 | tlemaire | commented out numdifftools import. updated README.md | Oct 2 2019 | |||
| 06580e30545f | tlemaire | corrected addThresholdCurve. updated astim_titrations.log with latest batch | Oct 1 2019 | |||
| 21401e741886 | tlemaire | updated ActivationMap (removed correctAmp method). corrected TimeSeriesPlot. | Sep 30 2019 | |||
| dd102470b272 | tlemaire | added method type in nbls.simulate logging | Sep 18 2019 | |||
| 6fb96a1716d1 | tlemaire | corrected tirations log file | Sep 18 2019 | |||
| 69faba51e2c1 | tlemaire | in PWSimulator.compute: added division of offset interval in several slices if… | Sep 17 2019 | |||
| 133c0ab1ac73 | tlemaire | changed outputdir to keyword argument in queue items in Model.checkOutputDir… | Sep 17 2019 | |||
| 89e117f6ffaa | tlemaire | add handling of positional and keyword arguments in Batch queues. added… | Sep 17 2019 | |||
| 8cf15b137151 | tlemaire | abstracted Model.simQueue method (now defined in children classes). changed… | Sep 17 2019 | |||
| 83cf10bbf6e7 | tlemaire | replaced hypersampling error by warning message PWSimulator.downsample | Sep 17 2019 | |||
| 6d8b2b3d4804 | tlemaire | updated titrations log | Sep 16 2019 | |||
| d65e74f5c30c | tlemaire | implemmented inheritance scheme for PointNeuron.chooseTimeStep method | Sep 11 2019 | |||
| bd840351d13f | tlemaire | corrected SweeneyNode alpham equation according to Basser and Roth, 1991. | Sep 10 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 | |||
| 614c56792d61 | tlemaire | expanded charge range for pneuron.getLookup | Sep 4 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 | |||
| 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 | |||
| 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 | |||
| 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 | |||
| 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 | |||
| 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 | |||
| dffee6926b85 | tlemaire | added fs (spatially-averaged) as input to nbls model. defined SmartLookup class… | 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 | |||
| 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 | |||
| 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 | |||
| 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 | |||
| 66eaf2f41fba | tlemaire | corrected y, t order error in nbls.fullDerivatives. added custom parsing in… | 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 | |||
| 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 |
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