Diffusion PySONIC (old) (master) History

History
master83cf10bbf6e7f9623610b4d…

Sep 17 2019

replaced hypersampling error by warning message PWSimulator.downsample
83cf10bbf6e7
·tlemaire on Sep 17 2019, 13:39.

Sep 16 2019

updated titrations log
6d8b2b3d4804
·tlemaire on Sep 16 2019, 17:39.

Sep 13 2019

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic
1d0578736cc2
·tlemaire on Sep 13 2019, 14:28.
added vsteprange to VlcampParser. changed timeseries default onset from…
0c9e09419d16
·tlemaire on Sep 13 2019, 14:27.
Merge branch 'master' of https://c4science.ch/diffusion/4670/pointnice
9b11f9b84f6e
·tlemaire on Sep 13 2019, 14:17.
re-computed lookups of FH, FS, IB, LTS, RE, RS, STN and TC neurons
5f918009eb20
·tlemaire on Sep 13 2019, 14:16.

Sep 11 2019

implemmented inheritance scheme for PointNeuron.chooseTimeStep method
d65e74f5c30c
·tlemaire on Sep 11 2019, 15:51.
added sweeney neuron lookups
737ddddddd46
·tlemaire on Sep 11 2019, 14:03.

Sep 10 2019

corrected SweeneyNode alpham equation according to Basser and Roth, 1991.
bd840351d13f
·tlemaire on Sep 10 2019, 15:01.

Sep 6 2019

added prependDataframe method to postpro module.
01c2a27636c1
·tlemaire on Sep 6 2019, 14:44.
renamed Simulator.resample method to downsample in order to avoid confusion…
c4d24a293f93
·tlemaire on Sep 6 2019, 14:32.
corrected minor issues in spike detection functions (dt bounding for resampling…
107df2b92970
·tlemaire on Sep 6 2019, 12:56.
modified find_tpeaks to work with irregular time vectors.
ec87894d9435
·tlemaire on Sep 6 2019, 12:31.

Sep 4 2019

expanded charge range for pneuron.getLookup
614c56792d61
·tlemaire on Sep 4 2019, 13:17.
updated notebooks
fdf554e5e6ab
·tlemaire on Sep 4 2019, 11:10.

Sep 3 2019

added sweeney lookups
6f5a204770f8
·tlemaire on Sep 3 2019, 18:43.
updated SPIKE_MIN_VAMP to allow robust spike detection for sweeney model
8102e979f684
·tlemaire on Sep 3 2019, 10:58.

Sep 2 2019

parametrised Qm plot range to be neuron-specific. Solved issue with pbar update.
fd4639a4c602
·tlemaire on Sep 2 2019, 20:44.
corrected crucial error in nbls.spatialAverage method. corrected Cm0 and Qm0…
d2ccd21d9889
·tlemaire on Sep 2 2019, 20:16.

Aug 29 2019

adapted test_sims (avoiding sweeney neuron)
4c34c2a9dc9a
·tlemaire on Aug 29 2019, 20:12.
remoed sweeney lookups (need to figure out the reason for weird profiles first).
f19b1648b5ed
·tlemaire on Aug 29 2019, 19:54.
added sweeney lookups (ASTIM not working yet). added fixLookup to remove single…
1b3cffe95e7a
·tlemaire on Aug 29 2019, 10:01.

Aug 26 2019

adapted constants to enable sweeney lookups creation.
8226a9490c9b
·tlemaire on Aug 26 2019, 15:19.
implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to…
4f5fb5ee0829
·tlemaire on Aug 26 2019, 14:57.
implemented pow2Search function using an incremental power of 2 search to…
d7855a1dd087
·tlemaire on Aug 26 2019, 10:48.

Aug 24 2019

corrected minor mistake in getCommonLabel
4821f3c94b73
·tlemaire on Aug 24 2019, 22:03.
added getCommonLabel method to ComparativePlot (now used to determine figure…
fdf57ea352bd
·tlemaire on Aug 24 2019, 22:00.

Aug 22 2019

harmonized peaks/spikes detection process across the package.
db880034dc26
·tlemaire on Aug 22 2019, 15:31.

Aug 19 2019

removed paper figures folder (now in separate repo)
3c76710406c6
·tlemaire on Aug 19 2019, 09:56.

Aug 16 2019

added figtitle and getModel as GenericPlot methods
0d24b201dea4
·tlemaire on Aug 16 2019, 20:09.

Aug 15 2019

added iCap to plot variables. added colormap option for comparative plots even…
3146cab6bade
·tlemaire on Aug 15 2019, 21:38.

Aug 14 2019

added automatic solution prepending to all simulate methods (to treat initial…
2278e599a753
·tlemaire on Aug 14 2019, 17:51.
corrected minor issues in timeseries
523f8865bde3
·tlemaire on Aug 14 2019, 15:58.
added VoltageClamp class with associated script and parser
366c7e528105
·tlemaire on Aug 14 2019, 15:07.
added plot_intensity_vs_amplitude.py script
1b242e25ca45
·tlemaire on Aug 14 2019, 11:49.

Jul 29 2019

fixed error in bls.filecodes
ec01e1e58099
·tlemaire on Jul 29 2019, 17:24.

Jul 26 2019

test commit.
48fd3e1df816
·tlemaire on Jul 26 2019, 18:32.

Jul 24 2019

updated README to latest changes.
8e1403abecb9
·tlemaire on Jul 24 2019, 11:44.
set simFull, simHybrid and simSonic as private nbls methods
a70fc6312da7
·tlemaire on Jul 24 2019, 09:40.

Jul 18 2019

corrected error in getSimThresholdAmps (added default fs to 1)
9ba9ca99a89f
·tlemaire on Jul 18 2019, 21:14.
corrected error in Model logNSpikes, checkTitrate and simAndSave methods.
9e0718eb1a9b
·tlemaire on Jul 18 2019, 20:47.
interoduced derivative function to compute numerical derivatives with various…
5aa12c341577
·tlemaire on Jul 18 2019, 20:02.
improved QSS fixed points color labeling
28c94d579a04
·tlemaire on Jul 18 2019, 12:11.

Jul 17 2019

added saddle point classification to QSS analysis.
ab25e778e32f
·tlemaire on Jul 17 2019, 22:15.
removed all static quasiSteadyStates definition in neuron classes.
dc37f0afbd17
·tlemaire on Jul 17 2019, 20:05.
adapted findModifiedEq to work with iterables as inputs
bce60bf70097
·tlemaire on Jul 17 2019, 17:19.
replaced createLookupLambda by createClassLambda that can take various lambda…
bf936959e87b
·tlemaire on Jul 17 2019, 16:07.
added findModifiedEq function to utils, using brentq to find a new equilibrium…
f113d822d4fb
·tlemaire on Jul 17 2019, 15:51.

Jul 16 2019

modified TC neuron steadyStates method.
17b59c14aa75
·tlemaire on Jul 16 2019, 18:57.

Jul 15 2019

transformed pneuron qsState and quasiSteadyStates methods to return lambda…
f768f01cd891
·tlemaire on Jul 15 2019, 21:40.
cleaned up nbls
137ca70ce6a3
·tlemaire on Jul 15 2019, 21:15.
re-added file caching for QSS analysis
bed4f4a9de36
·tlemaire on Jul 15 2019, 20:39.
started implementing SonicTranslator.parseSteadyStates method. Implemented…
d50bf6119d40
·tlemaire on Jul 15 2019, 20:22.

Jul 5 2019

added more robust patterns to PointNeuronTranslator
d3de1ce856e1
·tlemaire on Jul 5 2019, 13:41.
reordered TC states. minor changes in translators.
e34dcc6d2cb9
·tlemaire on Jul 5 2019, 04:48.

Jul 4 2019

add permeability_constant_pattern to PointNeuronTranslator
6755d10c0e98
·tlemaire on Jul 4 2019, 23:41.
added new functionalities to Trnalsator class (now used in SonicTranslator).
a788320b3aae
·tlemaire on Jul 4 2019, 22:06.
added getClosure method to Translator class.
aa1ed8d9b040
·tlemaire on Jul 4 2019, 17:44.

Jul 3 2019

added getClosure to translator. added getConstantsDict function in constants.py
b427c3fd93df
·tlemaire on Jul 3 2019, 01:59.

Jul 1 2019

improved checkTitrate robustness
ffdcb43ba1d8
·tlemaire on Jul 1 2019, 17:40.
removed test lookup file
be3e09e67984
·tlemaire on Jul 1 2019, 16:53.
corrected TC neuron notebook
af0e4bd2fe9e
·tlemaire on Jul 1 2019, 16:50.
added option to provide simAndSave or simulate to batches. implemented addMeta…
d1a3fbaefd83
·tlemaire on Jul 1 2019, 16:46.

Jun 30 2019

NmodlGenerator: implemented parsing of potential class attributes used as…
270ec5466a47
·tlemaire on Jun 30 2019, 13:03.
improved SonicTranslator class
f22a47305c1e
·tlemaire on Jun 30 2019, 01:24.

Jun 29 2019

adapted methods of all classes into classmethods and staticmethods when…
4937955d0214
·tlemaire on Jun 29 2019, 20:27.

Jun 28 2019

transformed model inputs, checkInputs and simQueue into static methods
4997a9f88989
·tlemaire on Jun 28 2019, 16:15.
created separate test module with TestBase class. renamed test_basic into…
22abb7710105
·tlemaire on Jun 28 2019, 13:51.

Jun 27 2019

re-introduced derivatives as mandatory model method
0fe23305b3ad
·tlemaire on Jun 27 2019, 19:13.
updated README
9ac705d6dbee
·tlemaire on Jun 27 2019, 19:12.
added Model.description method. added nbls.getLookup2D method with correct fs…
a0db776b7966
·tlemaire on Jun 27 2019, 16:10.
moved lookup to core module. moved getLookup methods to nbls class.
b73594f4d58b
·tlemaire on Jun 27 2019, 14:34.
moved effRates vectorization into pneuron.getEffRates method
8f1ea1a16339
·tlemaire on Jun 27 2019, 12:59.
defined TestBase class with smart subset handling (inherited by TestSims)
d909927fd268
·tlemaire on Jun 27 2019, 10:59.
rewrote test_basic into a class
eb0324a5cd27
·tlemaire on Jun 27 2019, 10:47.

Jun 26 2019

changed TimeSeries.getStimPulses to class method
b7e75610c1d2
·tlemaire on Jun 26 2019, 20:03.
added fs (spatially-averaged) as input to nbls model. defined SmartLookup class…
dffee6926b85
·tlemaire on Jun 26 2019, 19:50.
added test at bottom of lookups module
07c34eeed0f7
·tlemaire on Jun 26 2019, 16:50.
added paper url to setup.py
4d047c49f50d
·tlemaire on Jun 26 2019, 13:51.
replaced multiprocessing import by multiprocess import in batches.py to enable…
4ebf9fe64023
·tlemaire on Jun 26 2019, 13:49.
cleaned up model classes. defined mandatory derivatives method for model…
3528fa81b6d1
·tlemaire on Jun 26 2019, 13:38.

Jun 25 2019

improved steadyStates definition in TC and STN neurons. corrected dQdt pltvar…
9965ddc0005d
·tlemaire on Jun 25 2019, 23:21.
corrected README
f83e0e973bd3
·tlemaire on Jun 25 2019, 19:19.
updated README
65a9529c2978
·tlemaire on Jun 25 2019, 18:52.
corrected labeling error in GroupedTimeSeries
8b3f49b0bac4
·tlemaire on Jun 25 2019, 18:26.
removed unnecessary functions from pneuron
acf299185987
·tlemaire on Jun 25 2019, 18:17.
added automatic effRates function definition in pneuron.parse method. removed…
db8cc8e2b5ff
·tlemaire on Jun 25 2019, 17:57.
added precisions about derStates requirements in README
21dda94243b8
·tlemaire on Jun 25 2019, 15:09.
finished implementing pneuron.buildDerEffStates method to automatically create…
4742d6a43494
·tlemaire on Jun 25 2019, 14:59.

Jun 24 2019

defined separate lookup decorator for bls.computePMparams method. updated…
83ff47370d86
·tlemaire on Jun 24 2019, 20:21.

Jun 20 2019

define dLookUp class to perform lookup projections and interpolations
a96a900ad4b4
·tlemaire on Jun 20 2019, 17:35.
added default output directory ("dump"). cleaned up neuron classes.
6c10d4162d71
·tlemaire on Jun 20 2019, 10:09.

Jun 19 2019

refefined derEffstates construction to return a dictionary of function.
fdebb58e8442
·tlemaire on Jun 19 2019, 19:12.
corrected error in subset parsing
1a9277e6bbb4
·tlemaire on Jun 19 2019, 15:46.
added getSteadyStates and getDerStates methods to pneuron to call steadyStates…
f719dddee9f0
·tlemaire on Jun 19 2019, 15:39.
corrected Cinf error in ThalamoCortical neuron
becd2527f268
·tlemaire on Jun 19 2019, 15:19.
redefined derStates and steadyStates as dictionary of lambda functions
98942bac6b56
·tlemaire on Jun 19 2019, 15:16.
cleaned up neuron classes. redefined currents to return functions instead of…
26fe1e08a408
·tlemaire on Jun 19 2019, 11:05.

Jun 18 2019

started implementation of buildDerEffStates to contruct the derEffStates…
40b5a09c46c2
·tlemaire on Jun 18 2019, 23:14.
replaced obscur states list by explicit dictionary in all currents methods
7b2aee9851af
·tlemaire on Jun 18 2019, 18:21.

Historymaster83cf10bbf6e7f9623610b4d…

Sep 17 2019

Sep 16 2019

Sep 13 2019

Sep 11 2019

Sep 10 2019

Sep 6 2019

Sep 4 2019

Sep 3 2019

Sep 2 2019

Aug 29 2019

Aug 26 2019

Aug 24 2019

Aug 22 2019

Aug 19 2019

Aug 16 2019

Aug 15 2019

Aug 14 2019

Jul 29 2019

Jul 26 2019

Jul 24 2019

Jul 18 2019

Jul 17 2019

Jul 16 2019

Jul 15 2019

Jul 5 2019

Jul 4 2019

Jul 3 2019

Jul 1 2019

Jun 30 2019

Jun 29 2019

Jun 28 2019

Jun 27 2019

Jun 26 2019

Jun 25 2019

Jun 24 2019

Jun 20 2019

Jun 19 2019

Jun 18 2019

History
master83cf10bbf6e7f9623610b4d…