Diffusion PySONIC (old) (master) History

R4670/PySONIC
master4e96a816343e77eaf0f3561…

Mar 30 2020

added MRG fs lookup.
4e96a816343e
·tlemaire on Mar 30 2020, 13:16.

Mar 27 2020

added MRG lookup.
8a68be82c2d8
·tlemaire on Mar 27 2020, 20:40.
renamed fibers point-neuron models for better interpretability. completed fiber…
8f0bbde630a7
·tlemaire on Mar 27 2020, 20:37.

Mar 26 2020

tested MRG lookups generation
a43249c6ecf1
·tlemaire on Mar 26 2020, 21:49.
corrected typo in SweeneyNode description.
a4eafd9f8059
·tlemaire on Mar 26 2020, 21:16.

Mar 24 2020

added addExcitationInset to pltutils
cf163f8c94cb
·tlemaire on Mar 24 2020, 15:51.

Mar 23 2020

added getLogStartPoint to utils
678f3f5e229d
·tlemaire on Mar 23 2020, 21:36.

Mar 21 2020

added x axis sharing in GroupedTimeSeries
84694f9507f6
·tlemaire on Mar 21 2020, 18:51.

Mar 19 2020

added polyfit amd extrapolate capabilities to Lookup class.
066e8e416305
·tlemaire on Mar 19 2020, 12:13.

Feb 28 2020

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic
8f4b9911c0d3
·tlemaire on Feb 28 2020, 17:05.
added extra functionalities to Lookup class. continued fiber nodes notebook.
c8a9ea2beb92
·tlemaire on Feb 28 2020, 17:05.
Merge solved
7d61ef15bd3b
·vicari on Feb 28 2020, 17:03.
Correction in drives
be6c868e4e5f
·vicari on Feb 28 2020, 17:00.

Feb 27 2020

added better handling of ybounds in timeseries. added MRG neuron class.
a46f7227e040
·tlemaire on Feb 27 2020, 23:02.

Feb 20 2020

moved getMeta to utils
165caa8bf488
·tlemaire on Feb 20 2020, 18:35.
changed meta property of model classes to return solely model information.
7f8a3be5ceb4
·tlemaire on Feb 20 2020, 17:03.

Feb 18 2020

added LogBatch class
b7d520b9ed42
·tlemaire on Feb 18 2020, 22:59.
added isPickable function. corrected install_requires list in setup file.
b68fc5d800ef
·tlemaire on Feb 18 2020, 13:54.

Feb 14 2020

added gaussian function to utils.
683ec602313d
·tlemaire on Feb 14 2020, 14:56.
updated README (added instructions for git-lfs install)
31cc2d15993a
·tlemaire on Feb 14 2020, 11:12.

Feb 11 2020

added copy method to all model classes. added TI US notebook. updated…
68961385d17e
·tlemaire on Feb 11 2020, 07:55.

Feb 5 2020

adapted simAndSave function to work also with source-based titration cases.
b62507055396
·tlemaire on Feb 5 2020, 19:17.
changed erroneous calls to parseAmp to parseAmplitude in parsers module
478c17a7e098
·tlemaire on Feb 5 2020, 18:46.
replaced erroneous "return NotImplementedError" statements by "raise…
96d3c580ee81
·tlemaire on Feb 5 2020, 18:20.
correctd mismatch in ElectricDrive
8907f78b742a
·tlemaire on Feb 5 2020, 18:14.
renamed ElectricDrive A to I
892f924d6e9e
·tlemaire on Feb 5 2020, 18:13.
introduced properties in classes of drives and protocols modules.
31ef6228207a
·tlemaire on Feb 5 2020, 17:08.

Feb 3 2020

added xkey property to XDrive class and Arange property to pneuron and nbls…
073e28b388f6
·tlemaire on Feb 3 2020, 23:36.
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 FH fs lookups
a42d9f542bed
·tlemaire on Feb 3 2020, 14:36.
added lookups files in separate lookups folder using LFS.
062e541857dc
·tlemaire on Feb 3 2020, 14:35.
Initialized LFS. deleted lookup files from neuron folder.
ed7412335d9f
·tlemaire on Feb 3 2020, 14:32.
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.
added membrane area attributes to IB and STN neurons
5e77509ee19d
·tlemaire on Jan 22 2020, 15:37.

Jan 17 2020

improved modularity of TestBase class
fdde4affcc90
·tlemaire on Jan 17 2020, 18:24.

Jan 14 2020

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

Dec 14 2019

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic
382b41779471
·tlemaire on Dec 14 2019, 11:47.
removed plotVarQSSDynamics function from QSS and plot_QSS
a0b6724a45a5
·tlemaire on Dec 14 2019, 11:46.

Dec 13 2019

Merge solved
dd4bcd97ad83
·vicari on Dec 13 2019, 16:00.
Correction in of the find_tpeaks function in postpro.py
cad5a41a29b0
·vicari on Dec 13 2019, 15:56.

Dec 10 2019

updated STN neuron notebook with correct model parameters and enabled…
5c9777d249d7
·tlemaire on Dec 10 2019, 17:14.

Dec 9 2019

added boundDataframe method to postpro module
4a918211cc11
·tlemaire on Dec 9 2019, 08:14.

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 27 2019

mofified SPIKE_MIN_QAMP and SPIKE_MIN_VAMP from 5 (nC/cm2 - mV) to 3
19881e729753
·tlemaire on Nov 27 2019, 19:48.
added sundt lookups
d27e95459175
·tlemaire on Nov 27 2019, 15:23.

Nov 26 2019

moved pushbullet key file to package root
6797e5e1f52b
·tlemaire on Nov 26 2019, 18:52.
commented useless parameters in Sundt class
977bea19e55e
·tlemaire on Nov 26 2019, 18:40.
added internal bls.simUntilConvergence method (without decorators) to enable…
6deb0da8868d
·tlemaire on Nov 26 2019, 15:41.

Nov 25 2019

added Eleak logging upon Sundt class creation.
647c007ad5d7
·tlemaire on Nov 25 2019, 12:22.

Nov 22 2019

cleaned up Sundt class
974a5f7d7fef
·tlemaire on Nov 22 2019, 18:42.
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

implemented GenericPlot.wraptitle method
d14a124a4078
·tlemaire on Nov 15 2019, 16:46.
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

checked iM taup against ref. (Yamada 1989)
fa8f94b4198c
·tlemaire on Nov 7 2019, 14:43.
added PointNeuron alphaBorgGaham and betaBorgGraham methods, now used for sundt…
f1d2ab4cfb4b
·tlemaire on Nov 7 2019, 12:44.

Nov 6 2019

renamed PhaseDiagram to SpikePlot (more appropriate). simplified Sundt model…
163afcce99af
·tlemaire on Nov 6 2019, 19:33.
modified nbls.QSSderivatives and nbls.__simQSS to work with any specified…
a2c1e3e2eb02
·tlemaire on Nov 6 2019, 15:46.

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.

R4670/PySONICmaster4e96a816343e77eaf0f3561…

Mar 30 2020

Mar 27 2020

Mar 26 2020

Mar 24 2020

Mar 23 2020

Mar 21 2020

Mar 19 2020

Feb 28 2020

Feb 27 2020

Feb 20 2020

Feb 18 2020

Feb 14 2020

Feb 11 2020

Feb 5 2020

Feb 3 2020

Jan 26 2020

Jan 23 2020

Jan 22 2020

Jan 17 2020

Jan 14 2020

Dec 14 2019

Dec 13 2019

Dec 10 2019

Dec 9 2019

Dec 6 2019

Dec 4 2019

Dec 2 2019

Nov 27 2019

Nov 26 2019

Nov 25 2019

Nov 22 2019

Nov 20 2019

Nov 15 2019

Nov 14 2019

Nov 13 2019

Nov 7 2019

Nov 6 2019

Nov 5 2019

Nov 1 2019

Oct 15 2019

Oct 10 2019

Oct 7 2019

Oct 2 2019

Oct 1 2019

Sep 30 2019

Sep 27 2019

Sep 23 2019

Sep 20 2019

Sep 19 2019

R4670/PySONIC
master4e96a816343e77eaf0f3561…