Diffusion PySONIC (old) (master) History

core
mastered7412335d9f9d7e57266f5…

Feb 3 2020

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.
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.

R4670/PySONIC/coremastered7412335d9f9d7e57266f5…

Feb 3 2020

Jan 26 2020

Jan 23 2020

Jan 22 2020

Jan 14 2020

Dec 14 2019

Dec 6 2019

Dec 4 2019

Dec 2 2019

Nov 26 2019

Nov 22 2019

Nov 20 2019

Nov 15 2019

Nov 14 2019

Nov 13 2019

Nov 7 2019

Nov 6 2019

Oct 10 2019

Oct 7 2019

Oct 2 2019

Oct 1 2019

Sep 30 2019

Sep 18 2019

Sep 17 2019

Sep 16 2019

Sep 11 2019

Sep 10 2019

Sep 6 2019

Sep 4 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

R4670/PySONIC/core
mastered7412335d9f9d7e57266f5…