R4670/PySONICmaster
R4670/PySONIC
master
History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
58e5ce4415c8 | vicari | Sign correction and comments | Nov 5 2019 | |||
fc00bf556d5f | vicari | Correction in potassium kinetics | Nov 5 2019 | |||
a35753429a7e | vicari | Correction of the delayed rectifier potassium kinetics | Nov 5 2019 | |||
83ea55354a98 | tlemaire | added time step reduction to sundt class. code is running but simulations and… | Nov 1 2019 | |||
894410e31f4a | tlemaire | debugged sundt class (estim now running) | Nov 1 2019 | |||
3d652adfb7ce | tlemaire | further corrections to the sundt class, and implementation of Eleak computation… | Nov 1 2019 | |||
5a508487f9f1 | tlemaire | identified parameters in Sundt expressions and highlighted discrepancies with… | Nov 1 2019 | |||
eb70f6afb883 | tlemaire | corrected errors in sundt class (now compiling). minf and taum both seem off… | Nov 1 2019 | |||
1a18aaa3abec | vicari | implemented Sundt model | Nov 1 2019 | |||
0638d724be40 | tlemaire | added sundt import to neurons. corrected pushbullet requirement in setup | Oct 15 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 | |||
fedd732d1290 | tlemaire | changed TimeSeriesPlot.addLegend from static method to instance method | Sep 27 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 | |||
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 | |||
f1092e3356eb | tlemaire | added Parser.addCheckForOutput method, now used in run_*** scripts to… | 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 | |||
1d0578736cc2 | tlemaire | Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic | Sep 13 2019 | |||
0c9e09419d16 | tlemaire | added vsteprange to VlcampParser. changed timeseries default onset from… | Sep 13 2019 | |||
9b11f9b84f6e | tlemaire | Merge branch 'master' of https://c4science.ch/diffusion/4670/pointnice | Sep 13 2019 | |||
5f918009eb20 | tlemaire | re-computed lookups of FH, FS, IB, LTS, RE, RS, STN and TC neurons | Sep 13 2019 | |||
d65e74f5c30c | tlemaire | implemmented inheritance scheme for PointNeuron.chooseTimeStep method | Sep 11 2019 | |||
737ddddddd46 | tlemaire | added sweeney neuron lookups | Sep 11 2019 | |||
bd840351d13f | tlemaire | corrected SweeneyNode alpham equation according to Basser and Roth, 1991. | Sep 10 2019 | |||
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 | |||
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 | |||
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 | |||
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 | |||
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 | |||
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 |
c4science · Help