Diffusion PySONIC (old) (master) History

R4670/PySONIC
masterd03caf415e89146c4837c75…

Apr 15 2020

removed ambiguity around initialConditions methods to allow correct lookups…
d03caf415e89
·tlemaire on Apr 15 2020, 21:04.
implemented better solvers (now inside solvers module), including an…
b77cd9e4eb12
·tlemaire on Apr 15 2020, 20:53.

Apr 13 2020

added TC fs lookup at 1 MHz.
7ae0b7961ae4
·tlemaire on Apr 13 2020, 18:29.
replaced "Ascale" parsing options by "yscale" for more clarity.
b44cc93c9915
·tlemaire on Apr 13 2020, 18:17.
corrected LogBatch class to enable correct use with mpi.
f8511250c9b8
·tlemaire on Apr 13 2020, 18:00.
added better fs handling in actmap
10270ea94712
·tlemaire on Apr 13 2020, 12:33.

Apr 10 2020

removed useless error instance catch in utils
a8ffc4cf6311
·tlemaire on Apr 10 2020, 18:36.

Apr 9 2020

added multiprocessing functionality to LogBatch class.
3af9c9df32cc
·tlemaire on Apr 9 2020, 15:53.
corrected ActMap class (now inheriting from LogBatch).
18480eb7bebc
·tlemaire on Apr 9 2020, 14:07.

Apr 5 2020

added TimeProtocol.stimEvents method (used in NEURON simulations).
63ef9868bbd2
·tlemaire on Apr 5 2020, 17:59.
added eventsON and eventsOFF methods to Protocol classes.
06f8250793a6
·tlemaire on Apr 5 2020, 15:22.

Apr 3 2020

added __eq__ methods to pneuron and nbls classes
cc5348bc40ca
·tlemaire on Apr 3 2020, 15:33.

Mar 31 2020

added ASTIM_REL_CONV_THR to constants file.
9239911c1f35
·tlemaire on Mar 31 2020, 18:41.

Mar 30 2020

added TC fs lookup.
9dcd3884ae33
·tlemaire on Mar 30 2020, 21:50.
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.

R4670/PySONICmasterd03caf415e89146c4837c75…

Apr 15 2020

Apr 13 2020

Apr 10 2020

Apr 9 2020

Apr 5 2020

Apr 3 2020

Mar 31 2020

Mar 30 2020

Mar 27 2020

Mar 26 2020

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Feb 11 2020

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Jan 14 2020

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Nov 27 2019

Nov 26 2019

Nov 25 2019

Nov 22 2019

Nov 20 2019

Nov 15 2019

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Nov 6 2019

Nov 5 2019

Nov 1 2019

R4670/PySONIC
masterd03caf415e89146c4837c75…