History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
aee2c4e6cb21 | tlemaire | added Lookup.tile and modified SmartLookup.projectDC. modified nbls. | Oct 10 2019 | |||
ed57fe2edc40 | tlemaire | added rotAroundPoint2D function to utils | Sep 23 2019 | |||
43cdd51258a0 | tlemaire | added nan return in pow2Search if x > xmax. added getPow10 to utils | Sep 20 2019 | |||
d0cc76d4af6b | tlemaire | changed log level for logCache found entry | Sep 19 2019 | |||
ec466c361f8c | tlemaire | added fillLine function to utils. added Parser.addOverwrite method (opposite of… | Sep 19 2019 | |||
614c56792d61 | tlemaire | expanded charge range for pneuron.getLookup | Sep 4 2019 | |||
f19b1648b5ed | tlemaire | remoed sweeney lookups (need to figure out the reason for weird profiles first). | Aug 29 2019 | |||
d7855a1dd087 | tlemaire | implemented pow2Search function using an incremental power of 2 search to… | Aug 26 2019 | |||
fdf57ea352bd | tlemaire | added getCommonLabel method to ComparativePlot (now used to determine figure… | Aug 24 2019 | |||
3146cab6bade | tlemaire | added iCap to plot variables. added colormap option for comparative plots even… | Aug 15 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 | |||
bce60bf70097 | tlemaire | adapted findModifiedEq to work with iterables as inputs | Jul 17 2019 | |||
f113d822d4fb | tlemaire | added findModifiedEq function to utils, using brentq to find a new equilibrium… | Jul 17 2019 | |||
d50bf6119d40 | tlemaire | started implementing SonicTranslator.parseSteadyStates method. Implemented… | Jul 15 2019 | |||
a96a900ad4b4 | tlemaire | define dLookUp class to perform lookup projections and interpolations | Jun 20 2019 | |||
de8bdbc4fee0 | tlemaire | added outputdir option to simQueue methods. added automatic parsing to Parser… | Jun 14 2019 | |||
812cb5c1cb3a | tlemaire | updated README headers | Jun 13 2019 | |||
b42a0de93240 | tlemaire | updated all file headers | Jun 12 2019 | |||
2f0254ea5b53 | tlemaire | added functionality to load data directly from sim results in TimeSeriesPlot… | Jun 10 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 | |||
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 | |||
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 | |||
bc5a29bc6c9a | Theo Lemaire | added caching of QSS analysis results | Jun 3 2019 | |||
f75ca2e6e294 | Theo Lemaire | added parsers module, now used in sim scripts for more consistency. | Jun 3 2019 | |||
874f4649ec44 | Theo Lemaire | corrected QSS module to work correctly with "load" option. | Jun 2 2019 | |||
e0aa4041f3b8 | Theo Lemaire | added caching to nbls.titrate method | Jun 1 2019 | |||
10d2b5bb498e | Theo Lemaire | redefined titration procedures with binarySearch method. now single runAndSave… | Jun 1 2019 | |||
af6f9a02ed42 | Theo Lemaire | reformatted simulate methods of bls, pneuron and nbls classes to return output… | May 31 2019 | |||
e08e8c736efa | Theo Lemaire | replaced progressbar2 by tqdm | May 29 2019 | |||
4ba3212edf92 | Theo Lemaire | added simulators classes to take care of simulations | May 29 2019 | |||
1391db99409d | Theo Lemaire | added intermediate "run" method that return output data and metadata | May 27 2019 | |||
21d010292ddf | Theo Lemaire | added return_val option to isExcited and isSilenced | May 27 2019 | |||
13e29c29bbb1 | Theo Lemaire | haromized amplitude and plot_scheme parsing across simulation scripts | May 27 2019 | |||
818219348db5 | Theo Lemaire | started defining ActivationMap class | May 27 2019 | |||
71a2cddb684e | Theo Lemaire | replaced filecode functions by class methods | May 27 2019 | |||
1463cf220fbc | Theo Lemaire | modified cache to only log if function has not "history" argument to avoid… | May 27 2019 | |||
4e391806ec32 | Theo Lemaire | re-implemented csvcache as decorator | May 24 2019 | |||
0453d1e710dd | Theo Lemaire | added interface around titrate function to use memory caching | May 23 2019 | |||
1a5f9b3c215b | Theo Lemaire | implemented neuron-dependent titration to find specific thresholds (excitation… | May 22 2019 | |||
0ee058e8778d | Theo Lemaire | added max integration duration to stability analysis to avoid infinite loops in… | May 22 2019 | |||
14f3b43f5ec7 | Theo Lemaire | added negative offset to QSS perturbation | May 20 2019 | |||
a66b375c6133 | Theo Lemaire | implemented getLookupsDCavg function to compute DC-averaged lookups. nbls. | May 15 2019 | |||
ee9cf8652b7e | Theo Lemaire | simplified nbls.quasiSteadyStates method, now calling explicit quasiSeadyStates… | May 15 2019 | |||
62c6723c6e71 | Theo Lemaire | changed PointNeuron getEffrates, steadyStates, derStates and derEffStates… | May 14 2019 | |||
7a27b761d220 | Theo Lemaire | major improvements to QSS module | May 10 2019 | |||
44780023da34 | Theo Lemaire | corrected titrate function to work also with negative injected currents (for… | Apr 29 2019 | |||
6ffd825273a4 | Theo Lemaire | improved titrate function with nSpikes methods pneuron and nbls classes. added… | Apr 5 2019 | |||
9f09f2fdc039 | Theo Lemaire | Changed titration functions (now using generic titrate), Implemented Xinf… | Apr 4 2019 | |||
cf921135e3f2 | tlemaire | moved membrane currents in 2rd position of neurons pltscheme. extractPltVar now… | Mar 18 2019 | |||
ad0a33b92c3c | tlemaire | adapted plotComp to new plot variables scheme. | Mar 15 2019 | |||
a812d7d527af | tlemaire | created plt.pltutils module and moved relevant plotting functions into it. | Mar 15 2019 | |||
453f896987ce | tlemaire | generalized the use of getPltVars and getPltScheme with inheritance scheme… | Mar 14 2019 | |||
9d1a2fc5cd08 | tlemaire | major reformatting of plotBatch function | Mar 14 2019 | |||
cd145e4db3e8 | tlemaire | adapted plotSpikingMetrics for uniform y-axis scale. adapted ASTIM_filecode… | Mar 11 2019 | |||
a74f9c571b7d | tlemaire | adapted fig9.py with corrected STN model (new traces). | Mar 8 2019 | |||
c72b7b319ed0 | tlemaire | implemented getLookupsOff function to retrieve US-OFF lookups. adapted… | Mar 5 2019 | |||
865020d8c630 | tlemaire | added RS neuron lookups with partial coverage (spatially averaged). updated… | Feb 28 2019 | |||
702446ca2ad5 | tlemaire | corrected error in getLookups2Dfs | Jan 23 2019 | |||
957db9d021d6 | tlemaire | added getLookups2Dfs method to interpolate lookups at given membrane coverage. | Jan 23 2019 | |||
65c1d8649331 | tlemaire | implemented Frankenhaeuser-Huxley membrane mechanism (validated against data… | Jan 9 2019 | |||
850b05b61c5e | tlemaire | added plotFRspectrum function to actmap module. updated fig7 script, and added… | Nov 29 2018 | |||
84a00ea7e59b | tlemaire | recomputed lookups for all CNS neurons. modified figs 5 and 6 generation… | Nov 27 2018 | |||
9f827c942524 | tlemaire | added recording of computation times during lookups creation. | Nov 25 2018 | |||
2f63e4926c36 | tlemaire | improved plotRheobaseAmps function. improved arguments parsing in command line… | Nov 22 2018 | |||
8573c726b480 | tlemaire | modified getLookups2D to project along any dimensions pair in (a, f, A). | Nov 20 2018 | |||
d17615ffb4e6 | tlemaire | improved plotPhasePlane function. implemented isWithin function for loose bound… | Oct 28 2018 | |||
d2b627754312 | tlemaire | implemented figtitle method for direct labeling from metadata. implemented… | Oct 25 2018 | |||
ed0d192b377b | tlemaire | added scripts to generate paper figures automatically. | Oct 2 2018 | |||
73851d6ac128 | tlemaire | updated package documentation | Sep 28 2018 | |||
f5f327799ad4 | tlemaire | attempt to fix multiprocessing lookups creation. | Sep 27 2018 | |||
7075d3ab7f91 | tlemaire | removed pltutils file | Sep 26 2018 | |||
4a67049acd76 | tlemaire | added actmap to plt module, with command line script. | Sep 26 2018 | |||
7bd042cd39f7 | tlemaire | corrected error on lookups dict save. | Sep 26 2018 | |||
0412541be120 | tlemaire | fixed call to plotBatch in run scripts | Sep 25 2018 | |||
a35c13583071 | tlemaire | moved plotComp and plotBatch functions to separate files. created unique plot… | Sep 25 2018 | |||
8819bbb0e66f | tlemaire | cleaned up deprecated folder. added notebook about balance quasi-steady… | Sep 25 2018 | |||
610dc8472dcf | tlemaire | cleaned up utils module. removed log templates (now generated on the fly with… | Sep 25 2018 | |||
954e545fa6ac | tlemaire | turned intermolecular pressure test script into notebook. removed Input error… | Sep 24 2018 | |||
1951d49ccd25 | tlemaire | moved lookups into neurons folder | Sep 24 2018 | |||
2dc56eb8b91e | tlemaire | removed InputError references in core modules | Sep 23 2018 | |||
2a334b211bff | tlemaire | major changes to the package (PointNeuron, SonicNeuron, ...) | Sep 23 2018 | |||
193d4adc2a5f | tlemaire | included 4D lookup for RS neuron. | Sep 19 2018 | |||
b115baec5ab3 | tlemaire | added vtrap function to compute rate constants. added selectDirDialog function… | Sep 19 2018 | |||
d481c6dc0ac6 | tlemaire | prepared getLookups2D for interpolation in 4D space. added computeTestLookups… | Sep 15 2018 | |||
66e78783dda3 | tlemaire | removed use of itrpLookupsFreq by simple scipy.interp1d call | Sep 14 2018 | |||
4404c3e28711 | tlemaire | merged BLS_lookups file into 1 file with 2D (a, Qm0) lookup | Sep 12 2018 | |||
841338ad53f6 | tlemaire | added getDefaultIndexes to utils | Sep 10 2018 | |||
23060daa6da3 | tlemaire | added integer conversion for frequency checking in itrpLoouksFreq. corrected… | Aug 28 2018 | |||
8b21667afa18 | tlemaire | added checkNumBounds function to utils. | Aug 24 2018 | |||
043172721a44 | tlemaire | changed package name to PySONIC. | Aug 21 2018 |
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