History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
6b0629b0479c | tlemaire | resolved numerical errors on multicomp benchmark (npc = 100, atol = 1e-10) | Sep 25 2020 | |||
6aa3e623b782 | tlemaire | added multicomp module | Sep 24 2020 | |||
3f27342d2675 | tlemaire | corrected gamma map | Sep 24 2020 | |||
bb9f2c79c74a | tlemaire | latest changes for morphoSONIC paper | Sep 15 2020 | |||
0526b07ebff9 | tlemaire | added mirrorProp and mirrorAxis functions to pltutils. | Aug 6 2020 | |||
ed71c4613b28 | tlemaire | replaced nbls NEURONS_LOOKUP_DIR by a more general LOOKUP_DIR defined in utils | Aug 4 2020 | |||
52e16ec74047 | tlemaire | added nmin parameter to PeriodicSolver.solve and BilayerSonophore.simCycles. | Aug 3 2020 | |||
1c0831f723b0 | tlemaire | added tau_pas plotting to plotGatingKinetics | Jul 24 2020 | |||
0d4af61c20f7 | tlemaire | corrected PointNeuron dQdt method (now calculating charge derviative by finite… | Jul 22 2020 | |||
d4364da996c8 | tlemaire | added symmetric colormaps and corrected ComparativePlot cbar levels for int… | Jul 21 2020 | |||
3998f71a5a6f | tlemaire | added LogBatch getSerlializedOutput and getEntryOutput methods. | Jul 15 2020 | |||
66f49d8e6545 | tlemaire | added log scale option for tau axis in plotGatingStates | Jun 26 2020 | |||
4b2fc8c0eea5 | tlemaire | added pairwise utils function. added GroupedTimeSeries.shareX static method. | Jun 24 2020 | |||
bebce73d9405 | tlemaire | updated MANIFEST file. | Jun 3 2020 | |||
bbb3a4445235 | tlemaire | added strictbounds plotting options | May 7 2020 | |||
0c7bff925bd5 | tlemaire | corrected index offset error in GenericPlot.addCmap | May 5 2020 | |||
2c0253a46427 | tlemaire | added extractCommonPrefix utils function. | May 4 2020 | |||
db1a0c16e84b | tlemaire | added actmap NaN data post-processing to prevent numpy warning when using log z… | May 2 2020 | |||
bd7a6ec5a477 | tlemaire | corrected ComparativePlot and CompTimeSeries to enable taking generators as… | May 1 2020 | |||
4e922dc3531c | tlemaire | corrected scaling factor in actmap.addThresholdCurve | Apr 29 2020 | |||
efb7e6effc92 | tlemaire | corrected queue error in actmap.addTresholdCurve | Apr 29 2020 | |||
0a9b43830b05 | tlemaire | corrected DC scaling in actmap.addThresholdCurve | Apr 29 2020 | |||
d4087b3210f3 | tlemaire | added mpi feature to actmap threshold curve. | Apr 29 2020 | |||
81fe27f05196 | tlemaire | changed bls.inputs['a'] (factor 0, unit m). | Apr 29 2020 | |||
fcb5a387a33e | tlemaire | added input-ouput match pre-check in LogBatch.run method to avoid unnecessary… | Apr 28 2020 | |||
67531a20cdce | tlemaire | placed StimObject class in a separate stimobj module. added boltons dependency… | Apr 21 2020 | |||
159f140dcfb0 | tlemaire | added BalancedPulsedProtocol class. | Apr 19 2020 | |||
72c8577885a8 | tlemaire | corrected units discrepancy in actmap.py | Apr 18 2020 | |||
a3ca81f69d0a | tlemaire | corrected TimSeries.getStimPulses function (no patches for zero states). | Apr 18 2020 | |||
0d1777407add | tlemaire | corrected drives and protocols inputs. | Apr 18 2020 | |||
f8511250c9b8 | tlemaire | corrected LogBatch class to enable correct use with mpi. | Apr 13 2020 | |||
10270ea94712 | tlemaire | added better fs handling in actmap | Apr 13 2020 | |||
3af9c9df32cc | tlemaire | added multiprocessing functionality to LogBatch class. | Apr 9 2020 | |||
18480eb7bebc | tlemaire | corrected ActMap class (now inheriting from LogBatch). | Apr 9 2020 | |||
06f8250793a6 | tlemaire | added eventsON and eventsOFF methods to Protocol classes. | Apr 5 2020 | |||
cf163f8c94cb | tlemaire | added addExcitationInset to pltutils | Mar 24 2020 | |||
678f3f5e229d | tlemaire | added getLogStartPoint to utils | Mar 23 2020 | |||
84694f9507f6 | tlemaire | added x axis sharing in GroupedTimeSeries | Mar 21 2020 | |||
a46f7227e040 | tlemaire | added better handling of ybounds in timeseries. added MRG neuron class. | Feb 27 2020 | |||
96d3c580ee81 | tlemaire | replaced erroneous "return NotImplementedError" statements by "raise… | Feb 5 2020 | |||
27d8aafffa88 | tlemaire | Created Drive objects inheritance scheme (now used in all model classes). | Feb 3 2020 | |||
9d0666784d2d | tlemaire | Created AcousticSource class to be used for US simulations. | Feb 3 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 | |||
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 | |||
6197f85f0709 | tlemaire | corrected Astim factor error in pneuron desc. added extra parsing methods | Nov 20 2019 | |||
d14a124a4078 | tlemaire | implemented GenericPlot.wraptitle method | 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 | |||
163afcce99af | tlemaire | renamed PhaseDiagram to SpikePlot (more appropriate). simplified Sundt model… | Nov 6 2019 | |||
a2c1e3e2eb02 | tlemaire | modified nbls.QSSderivatives and nbls.__simQSS to work with any specified… | Nov 6 2019 | |||
15f0e82253ac | tlemaire | corrected error in effvars for plotGatingKinetics | Nov 5 2019 | |||
aee2c4e6cb21 | tlemaire | added Lookup.tile and modified SmartLookup.projectDC. modified nbls. | Oct 10 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 | |||
fedd732d1290 | tlemaire | changed TimeSeriesPlot.addLegend from static method to instance method | Sep 27 2019 | |||
0c9e09419d16 | tlemaire | added vsteprange to VlcampParser. changed timeseries default onset from… | Sep 13 2019 | |||
ec87894d9435 | tlemaire | modified find_tpeaks to work with irregular time vectors. | Sep 6 2019 | |||
1b3cffe95e7a | tlemaire | added sweeney lookups (ASTIM not working yet). added fixLookup to remove single… | Aug 29 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 | |||
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 | |||
f768f01cd891 | tlemaire | transformed pneuron qsState and quasiSteadyStates methods to return lambda… | 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 | |||
4937955d0214 | tlemaire | adapted methods of all classes into classmethods and staticmethods when… | Jun 29 2019 | |||
b73594f4d58b | tlemaire | moved lookup to core module. moved getLookup methods to nbls 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 | |||
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 | |||
a96a900ad4b4 | tlemaire | define dLookUp class to perform lookup projections and interpolations | Jun 20 2019 | |||
26fe1e08a408 | tlemaire | cleaned up neuron classes. redefined currents to return functions instead of… | Jun 19 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 | |||
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 |
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