Diffusion PySONIC (old) (master) History

History
master68961385d17ec3ff6a7c2e7…

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

updated README with instructions on how to cite.
82b1e406d267
·tlemaire on Dec 4 2019, 16:15.
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.
Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic
ab186ad4e8bf
·tlemaire on Nov 1 2019, 14:42.
modified README
0394f06c57fd
·tlemaire on Nov 1 2019, 14:42.
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 26 2019

corrected unwanted changes to sublime-project file
a4e909590831
·tlemaire on Sep 26 2019, 11:35.

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.

Historymaster68961385d17ec3ff6a7c2e7…

Feb 11 2020

Feb 5 2020

Feb 3 2020

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History
master68961385d17ec3ff6a7c2e7…