History Graph
History Graph
Commit | Author | Details | Committed | |||
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31cc2d15993a | tlemaire | updated README (added instructions for git-lfs install) | Feb 14 2020 | |||
68961385d17e | tlemaire | added copy method to all model classes. added TI US notebook. updated… | Feb 11 2020 | |||
96d3c580ee81 | tlemaire | replaced erroneous "return NotImplementedError" statements by "raise… | Feb 5 2020 | |||
8907f78b742a | tlemaire | correctd mismatch in ElectricDrive | Feb 5 2020 | |||
892f924d6e9e | tlemaire | renamed ElectricDrive A to I | Feb 5 2020 | |||
31ef6228207a | tlemaire | introduced properties in classes of drives and protocols modules. | Feb 5 2020 | |||
073e28b388f6 | tlemaire | added xkey property to XDrive class and Arange property to pneuron and nbls… | Feb 3 2020 | |||
27d8aafffa88 | tlemaire | Created Drive objects inheritance scheme (now used in all model classes). | Feb 3 2020 | |||
dba63f835a31 | tlemaire | corrected docstring errors in pneuron Cm0 and Qm0 | Feb 3 2020 | |||
062e541857dc | tlemaire | added lookups files in separate lookups folder using LFS. | Feb 3 2020 | |||
9d0666784d2d | tlemaire | Created AcousticSource class to be used for US simulations. | Feb 3 2020 | |||
eec847e65a7a | tlemaire | added sundt fs lookups. adapted RS fs lookups. adapted nbls.getLookup2D method… | Jan 26 2020 | |||
6846298198d4 | tlemaire | added interp_method Lookup attribute to enable choice of lookup interpolation… | Jan 26 2020 | |||
c995e8999df7 | tlemaire | Modified Lookup class (new properties, corrected methods). | Jan 26 2020 | |||
38dc94d61fe7 | tlemaire | added DQ_LOOKUP constant (used in run_lookups.py) | Jan 26 2020 | |||
1919e3105ee4 | tlemaire | added toDict, toJson, fromDict and fromJson methods to Lookup class. | Jan 23 2020 | |||
f4ea3f48765e | vicari | Merge completed | Jan 22 2020 | |||
e4f4732ffbab | vicari | Extra entry in bls lookup | Jan 22 2020 | |||
8478fde7a5d4 | tlemaire | Automated getModel using automatically generated dictionary of models with… | Jan 14 2020 | |||
a0b6724a45a5 | tlemaire | removed plotVarQSSDynamics function from QSS and plot_QSS | Dec 14 2019 | |||
d0b57c5e137d | tlemaire | re-ran and completed STN notebook | Dec 6 2019 | |||
bac984960467 | tlemaire | corrected nbls fullDerivatives, simFull and simHybrid methods (removed phi… | Dec 4 2019 | |||
a29eea02e330 | tlemaire | changed Lookup repr method. added test_lkp test file. | Dec 4 2019 | |||
f8107574d0a8 | tlemaire | added threshold module with isolated threshold function (now used for all… | Dec 2 2019 | |||
6deb0da8868d | tlemaire | added internal bls.simUntilConvergence method (without decorators) to enable… | Nov 26 2019 | |||
b46ab57b16d3 | tlemaire | corrected borg-graham formalism methods | Nov 22 2019 | |||
6197f85f0709 | tlemaire | corrected Astim factor error in pneuron desc. added extra parsing methods | Nov 20 2019 | |||
456fa71d226b | tlemaire | added qss_vars and pulse-avg run options to nbls simSonic method. | Nov 20 2019 | |||
681033068b15 | tlemaire | updated titrations log | Nov 15 2019 | |||
5da540f0f401 | tlemaire | moved model.simAndSave to utils to facilitate use in ExSONIC | Nov 14 2019 | |||
36119dd01aec | tlemaire | moved filecode function to utils | Nov 14 2019 | |||
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 |
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