Diffusion PySONIC (old) (master) History

core
master27d8aafffa88e49079f3995…

Feb 3 2020

Created Drive objects inheritance scheme (now used in all model classes).
27d8aafffa88
·tlemaire on Feb 3 2020, 21:45.
corrected docstring errors in pneuron Cm0 and Qm0
dba63f835a31
·tlemaire on Feb 3 2020, 15:11.
added lookups files in separate lookups folder using LFS.
062e541857dc
·tlemaire on Feb 3 2020, 14:35.
Created AcousticSource class to be used for US simulations.
9d0666784d2d
·tlemaire on Feb 3 2020, 14:26.

Jan 26 2020

added sundt fs lookups. adapted RS fs lookups. adapted nbls.getLookup2D method…
eec847e65a7a
·tlemaire on Jan 26 2020, 23:37.
added interp_method Lookup attribute to enable choice of lookup interpolation…
6846298198d4
·tlemaire on Jan 26 2020, 20:42.
Modified Lookup class (new properties, corrected methods).
c995e8999df7
·tlemaire on Jan 26 2020, 19:15.
added DQ_LOOKUP constant (used in run_lookups.py)
38dc94d61fe7
·tlemaire on Jan 26 2020, 09:51.

Jan 23 2020

added toDict, toJson, fromDict and fromJson methods to Lookup class.
1919e3105ee4
·tlemaire on Jan 23 2020, 12:10.

Jan 22 2020

Merge completed
f4ea3f48765e
·vicari on Jan 22 2020, 17:04.
Extra entry in bls lookup
e4f4732ffbab
·vicari on Jan 22 2020, 17:01.

Jan 14 2020

Automated getModel using automatically generated dictionary of models with…
8478fde7a5d4
·tlemaire on Jan 14 2020, 17:18.

Dec 14 2019

removed plotVarQSSDynamics function from QSS and plot_QSS
a0b6724a45a5
·tlemaire on Dec 14 2019, 11:46.

Dec 6 2019

re-ran and completed STN notebook
d0b57c5e137d
·tlemaire on Dec 6 2019, 17:43.

Dec 4 2019

corrected nbls fullDerivatives, simFull and simHybrid methods (removed phi…
bac984960467
·tlemaire on Dec 4 2019, 15:46.
changed Lookup repr method. added test_lkp test file.
a29eea02e330
·tlemaire on Dec 4 2019, 15:37.

Dec 2 2019

added threshold module with isolated threshold function (now used for all…
f8107574d0a8
·tlemaire on Dec 2 2019, 20:07.

Nov 26 2019

added internal bls.simUntilConvergence method (without decorators) to enable…
6deb0da8868d
·tlemaire on Nov 26 2019, 15:41.

Nov 22 2019

corrected borg-graham formalism methods
b46ab57b16d3
·tlemaire on Nov 22 2019, 18:36.

Nov 20 2019

corrected Astim factor error in pneuron desc. added extra parsing methods
6197f85f0709
·tlemaire on Nov 20 2019, 22:24.
added qss_vars and pulse-avg run options to nbls simSonic method.
456fa71d226b
·tlemaire on Nov 20 2019, 20:32.

Nov 15 2019

updated titrations log
681033068b15
·tlemaire on Nov 15 2019, 01:12.

Nov 14 2019

moved model.simAndSave to utils to facilitate use in ExSONIC
5da540f0f401
·tlemaire on Nov 14 2019, 19:42.
moved filecode function to utils
36119dd01aec
·tlemaire on Nov 14 2019, 18:06.
Major update:
de255e65bccc
·tlemaire on Nov 14 2019, 16:39.
added equality operators to TimeProtocol and PulsedProtocol classes.
a26469ca67dc
·tlemaire on Nov 14 2019, 11:37.

Nov 13 2019

improved filecodes generation from meta dictionary in Model.filecode
4a5626da478c
·tlemaire on Nov 13 2019, 19:43.
created Timeprotocol and PulsedProtocol classes, now used in pneuron, nbls and…
bc1800471252
·tlemaire on Nov 13 2019, 18:11.

Nov 7 2019

added PointNeuron alphaBorgGaham and betaBorgGraham methods, now used for sundt…
f1d2ab4cfb4b
·tlemaire on Nov 7 2019, 12:44.

Nov 6 2019

modified nbls.QSSderivatives and nbls.__simQSS to work with any specified…
a2c1e3e2eb02
·tlemaire on Nov 6 2019, 15:46.

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 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.
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 11 2019

implemmented inheritance scheme for PointNeuron.chooseTimeStep method
d65e74f5c30c
·tlemaire on Sep 11 2019, 15:51.

Sep 10 2019

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

Sep 6 2019

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.

Sep 4 2019

expanded charge range for pneuron.getLookup
614c56792d61
·tlemaire on Sep 4 2019, 13:17.

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

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.

Aug 24 2019

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.

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.
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.

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.

Jun 26 2019

added fs (spatially-averaged) as input to nbls model. defined SmartLookup class…
dffee6926b85
·tlemaire on Jun 26 2019, 19:50.
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.

R4670/PySONIC/coremaster27d8aafffa88e49079f3995…

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R4670/PySONIC/core
master27d8aafffa88e49079f3995…