Diffusion PySONIC (old) (master) History

R4670/PySONIC
master7a48bab581761dd037bc4c6…

Nov 5 2019

renamed iKm to iM and kmk gate to p in Sundt to match formalism ot Cortical…
7a48bab58176
·tlemaire on Nov 5 2019, 22:35.
parametrized Caiinf in sundt model (checked for correct equivalence at Vm0)
54b7854b35c3
·tlemaire on Nov 5 2019, 18:16.
corrected error in effvars for plotGatingKinetics
15f0e82253ac
·tlemaire on Nov 5 2019, 17:17.
corrected Ikd kinetics (n and l zeta signs matching those of Borg-Graham 1991…
7a4a9166c1ad
·tlemaire on Nov 5 2019, 16:14.
Sign correction and comments
58e5ce4415c8
·vicari on Nov 5 2019, 14:31.
Correction in potassium kinetics
fc00bf556d5f
·vicari on Nov 5 2019, 13:29.
Correction of the delayed rectifier potassium kinetics
a35753429a7e
·vicari on Nov 5 2019, 13:15.

Nov 1 2019

added time step reduction to sundt class. code is running but simulations and…
83ea55354a98
·tlemaire on Nov 1 2019, 17:49.
debugged sundt class (estim now running)
894410e31f4a
·tlemaire on Nov 1 2019, 17:38.
further corrections to the sundt class, and implementation of Eleak computation…
3d652adfb7ce
·tlemaire on Nov 1 2019, 17:36.
identified parameters in Sundt expressions and highlighted discrepancies with…
5a508487f9f1
·tlemaire on Nov 1 2019, 17:08.
corrected errors in sundt class (now compiling). minf and taum both seem off…
eb70f6afb883
·tlemaire on Nov 1 2019, 14:54.
implemented Sundt model
1a18aaa3abec
·vicari on Nov 1 2019, 14:40.

Oct 15 2019

added sundt import to neurons. corrected pushbullet requirement in setup
0638d724be40
·tlemaire on Oct 15 2019, 17:33.

Oct 10 2019

added Lookup.tile and modified SmartLookup.projectDC. modified nbls.
aee2c4e6cb21
·tlemaire on Oct 10 2019, 16:48.

Oct 7 2019

defined Lookup algorihtmic operators. defined OnOffSimulator class. defined…
20f96c135bce
·tlemaire on Oct 7 2019, 20:22.

Oct 2 2019

commented out numdifftools import. updated README.md
d992992a3693
·tlemaire on Oct 2 2019, 08:59.

Oct 1 2019

corrected addThresholdCurve. updated astim_titrations.log with latest batch
06580e30545f
·tlemaire on Oct 1 2019, 00:05.

Sep 30 2019

updated ActivationMap (removed correctAmp method). corrected TimeSeriesPlot.
21401e741886
·tlemaire on Sep 30 2019, 19:48.

Sep 27 2019

changed TimeSeriesPlot.addLegend from static method to instance method
fedd732d1290
·tlemaire on Sep 27 2019, 13:43.

Sep 23 2019

added rotAroundPoint2D function to utils
ed57fe2edc40
·tlemaire on Sep 23 2019, 00:38.

Sep 20 2019

added nan return in pow2Search if x > xmax. added getPow10 to utils
43cdd51258a0
·tlemaire on Sep 20 2019, 20:00.

Sep 19 2019

changed log level for logCache found entry
d0cc76d4af6b
·tlemaire on Sep 19 2019, 11:48.
added fillLine function to utils. added Parser.addOverwrite method (opposite of…
ec466c361f8c
·tlemaire on Sep 19 2019, 11:39.

Sep 18 2019

added method type in nbls.simulate logging
dd102470b272
·tlemaire on Sep 18 2019, 18:13.
corrected tirations log file
6fb96a1716d1
·tlemaire on Sep 18 2019, 18:05.

Sep 17 2019

in PWSimulator.compute: added division of offset interval in several slices if…
69faba51e2c1
·tlemaire on Sep 17 2019, 18:18.
changed outputdir to keyword argument in queue items in Model.checkOutputDir…
133c0ab1ac73
·tlemaire on Sep 17 2019, 17:28.
added Parser.addCheckForOutput method, now used in run_*** scripts to…
f1092e3356eb
·tlemaire on Sep 17 2019, 17:07.
add handling of positional and keyword arguments in Batch queues. added…
89e117f6ffaa
·tlemaire on Sep 17 2019, 16:15.
abstracted Model.simQueue method (now defined in children classes). changed…
8cf15b137151
·tlemaire on Sep 17 2019, 15:03.
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.

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

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.
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.
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.

R4670/PySONICmaster7a48bab581761dd037bc4c6…

Nov 5 2019

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R4670/PySONIC
master7a48bab581761dd037bc4c6…