Diffusion PySONIC (old) (master) History

R4670/scripts
master062e541857dc24b7fbc530d…

Feb 3 2020

Created AcousticSource class to be used for US simulations.
9d0666784d2d
·tlemaire on Feb 3 2020, 14:26.

Jan 26 2020

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.

Dec 14 2019

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

Nov 26 2019

moved pushbullet key file to package root
6797e5e1f52b
·tlemaire on Nov 26 2019, 18:52.
added internal bls.simUntilConvergence method (without decorators) to enable…
6deb0da8868d
·tlemaire on Nov 26 2019, 15:41.

Nov 14 2019

moved filecode function to utils
36119dd01aec
·tlemaire on Nov 14 2019, 18:06.

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.

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.

Sep 17 2019

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.

Sep 2 2019

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 22 2019

harmonized peaks/spikes detection process across the package.
db880034dc26
·tlemaire on Aug 22 2019, 15:31.

Aug 14 2019

added VoltageClamp class with associated script and parser
366c7e528105
·tlemaire on Aug 14 2019, 15:07.
added plot_intensity_vs_amplitude.py script
1b242e25ca45
·tlemaire on Aug 14 2019, 11:49.

Jul 15 2019

started implementing SonicTranslator.parseSteadyStates method. Implemented…
d50bf6119d40
·tlemaire on Jul 15 2019, 20:22.

Jul 1 2019

added option to provide simAndSave or simulate to batches. implemented addMeta…
d1a3fbaefd83
·tlemaire on Jul 1 2019, 16:46.

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.
created separate test module with TestBase class. renamed test_basic into…
22abb7710105
·tlemaire on Jun 28 2019, 13:51.

Jun 27 2019

moved lookup to core module. moved getLookup methods to nbls class.
b73594f4d58b
·tlemaire on Jun 27 2019, 14:34.

Jun 26 2019

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

Jun 25 2019

added automatic effRates function definition in pneuron.parse method. removed…
db8cc8e2b5ff
·tlemaire on Jun 25 2019, 17:57.

Jun 17 2019

added custom parsing to plot_gating_kinetics.py
a03eb1b35b77
·tlemaire on Jun 17 2019, 21:19.
added custom parsing to plot_effective_variables.py
3b86ec877351
·tlemaire on Jun 17 2019, 21:13.
adde prettify option to timeseries plots
1465c48312a6
·tlemaire on Jun 17 2019, 20:43.
defined PlotParser and TimeSeriesParser classes
e3f3982b8981
·tlemaire on Jun 17 2019, 18:52.
added colormap functionality to PhaseDiagram
9e96cf6ee947
·tlemaire on Jun 17 2019, 18:29.
replaced plotPhaseDiagram by PhaseDiagram class inheriting from ComparativePlot…
e01fa72e6143
·tlemaire on Jun 17 2019, 17:55.
moved nmodl generator to ExSONIC package
0efc60073f8b
·tlemaire on Jun 17 2019, 10:58.
added custom parsing to generate_mod_file.py
9556faead02c
·tlemaire on Jun 17 2019, 10:52.
solved issue with ActivationMap Ascale
4ce5e074ca4c
·tlemaire on Jun 17 2019, 10:24.
replaced no_offset by tbounds in plotting options. added custom parsing to…
75f6032d2f63
·tlemaire on Jun 17 2019, 09:34.

Jun 16 2019

finished implmenting Firing Rate as plot variable (now replacing plotFRProfile).
63faa327c865
·tlemaire on Jun 16 2019, 22:47.

Jun 15 2019

added colormap functionality to CompPlot, with lin or log scale.
012f2603c5d7
·tlemaire on Jun 15 2019, 19:15.
added simkey to meta dictionary. added automatic parsing and labeling of…
c14fa0da1fd7
·tlemaire on Jun 15 2019, 18:32.

Jun 14 2019

added spike details plotting options to TimeSeriesPlot
fb7c07fee5cb
·tlemaire on Jun 14 2019, 16:06.
added frequency and mark_spikes option to both CompPlot and SchemePlot classes
bdf8ef51d3db
·tlemaire on Jun 14 2019, 11:53.
added outputdir option to simQueue methods. added automatic parsing to Parser…
de8bdbc4fee0
·tlemaire on Jun 14 2019, 11:34.

Jun 13 2019

removed extra line in run_lookups.py
da542f2db42b
·tlemaire on Jun 13 2019, 15:24.
adapted MechSimParser for use in run_lookups.py
af7294977045
·tlemaire on Jun 13 2019, 15:22.

Jun 12 2019

updated all file headers
b42a0de93240
·tlemaire on Jun 12 2019, 23:15.
cleaned-up all neuron classes
cc309fa78cd9
·tlemaire on Jun 12 2019, 16:35.
replaced "neuron" by "pneuron" for all PointNeuron instances
6e017b421f3e
·tlemaire on Jun 12 2019, 12:58.

Jun 10 2019

added plotting of real QS SFPs and UFPs in plotQSSdynamics and plotQSSVarVsQm…
3accccc91cbe
·tlemaire on Jun 10 2019, 22:27.
moved example script in README and updated rest of the text.
9c883a796eff
·tlemaire on Jun 10 2019, 21:45.
added functionality to load data directly from sim results in TimeSeriesPlot…
2f0254ea5b53
·tlemaire on Jun 10 2019, 20:52.

Jun 9 2019

added nbls isStableQSS and titrateQSS methods. finished plotQSSThresholdCurve
863bdf8330f4
·tlemaire on Jun 9 2019, 19:51.

Jun 7 2019

added getSimThresholdAmps and plotQSSThresholdCurve functions to QSS module…
26fdc0bbfe8d
·tlemaire on Jun 7 2019, 18:28.
added custom parsers to plot_timeseries and plot_QSS
1f1e59762ea3
·tlemaire on Jun 7 2019, 15:56.

Jun 6 2019

moved getLowIntensitiesSTN to STN class
50103226d72b
·tlemaire on Jun 6 2019, 21:30.
created ActivationMap class
3556a765fe5c
·tlemaire on Jun 6 2019, 21:04.
added getModel and getPointNeuron functions. removed deprecated scripts.
1c9c63d4ba6a
·tlemaire on Jun 6 2019, 18:29.

Jun 3 2019

added caching of QSS analysis results
bc5a29bc6c9a
·Theo Lemaire on Jun 3 2019, 20:23.
corrected plot_QSS inputdir error
6cbf141d9754
·Theo Lemaire on Jun 3 2019, 17:02.
added custom parser to plot_QSS_IQ.py
1295ce41f2c3
·Theo Lemaire on Jun 3 2019, 15:58.
added parsers module, now used in sim scripts for more consistency.
f75ca2e6e294
·Theo Lemaire on Jun 3 2019, 15:11.

Jun 2 2019

removed unnecessary script
b21bb388bb20
·Theo Lemaire on Jun 2 2019, 22:42.
simplified run scripts
fdc484dcbe00
·Theo Lemaire on Jun 2 2019, 22:15.
added getInDict function used to determine output directory in sim scripts
68e2fe6fd858
·Theo Lemaire on Jun 2 2019, 15:50.
corrected QSS module to work correctly with "load" option.
874f4649ec44
·Theo Lemaire on Jun 2 2019, 15:40.
major cleanup of all core classes.
88811f7a8aa5
·Theo Lemaire on Jun 2 2019, 14:22.

May 31 2019

moved batches to core module
de01bc8b1676
·Theo Lemaire on May 31 2019, 17:09.
implemented abstract Model class to be inherit by bls, pneuron and nbls
25d498c21187
·Theo Lemaire on May 31 2019, 16:56.
added toffset to args list of pneuron and nbls filecode methods
4dd95ba1d83c
·Theo Lemaire on May 31 2019, 15:27.
moved createAStimQueue and createEStimQueue to their respective classes
6cb5dac16172
·Theo Lemaire on May 31 2019, 15:16.

May 29 2019

added simulators classes to take care of simulations
4ba3212edf92
·Theo Lemaire on May 29 2019, 03:15.

May 27 2019

haromized amplitude and plot_scheme parsing across simulation scripts
13e29c29bbb1
·Theo Lemaire on May 27 2019, 15:29.
replaced filecode functions by class methods
71a2cddb684e
·Theo Lemaire on May 27 2019, 13:46.

May 24 2019

added better plot handling to run_astim.py
de4dc186176b
·Theo Lemaire on May 24 2019, 16:36.
added Araneg and Irange args to run_astim.py
3a8d7d040f27
·Theo Lemaire on May 24 2019, 16:26.

May 23 2019

added "PI" type control of convergence in nbls.evaluateStability method
678bec02c372
·Theo Lemaire on May 23 2019, 19:03.

May 22 2019

added max integration duration to stability analysis to avoid infinite loops in…
0ee058e8778d
·Theo Lemaire on May 22 2019, 15:48.
implemented quasiSteadyStateFixedPoints as part of nbls class. Added…
3addfe632329
·Theo Lemaire on May 22 2019, 11:42.
added Amin and Amax command line arguments to plot_QSS_IQ.py
2de6d3d26717
·Theo Lemaire on May 22 2019, 10:02.

May 21 2019

added nA command line argument to plot_QSS_IQ.py
6b55fdb84a7a
·Theo Lemaire on May 21 2019, 19:08.
implemented specific nbls evaluateStability method to evaluate FP stability by…
8a17ab2f8c11
·Theo Lemaire on May 21 2019, 18:06.

May 20 2019

added negative offset to QSS perturbation
14f3b43f5ec7
·Theo Lemaire on May 20 2019, 18:02.

May 17 2019

added isTitratable method to neuron classes. improved QSS SFP stability…
4d8fa0caef5b
·Theo Lemaire on May 17 2019, 16:22.

May 16 2019

replaced linear interpolation of QSS at Q-SFPs (inaccurate) by full…
3ad8ad914eec
·Theo Lemaire on May 16 2019, 17:18.
added np.nan bounding to all np.interp uses in the code. implemented…
3f4135902bdc
·Theo Lemaire on May 16 2019, 15:30.

May 15 2019

implemented getLookupsDCavg function to compute DC-averaged lookups. nbls.
a66b375c6133
·Theo Lemaire on May 15 2019, 16:36.
simplified nbls.quasiSteadyStates method, now calling explicit quasiSeadyStates…
ee9cf8652b7e
·Theo Lemaire on May 15 2019, 13:53.

May 14 2019

changed PointNeuron getEffrates, steadyStates, derStates and derEffStates…
62c6723c6e71
·Theo Lemaire on May 14 2019, 19:21.

May 10 2019

major improvements to QSS module
7a27b761d220
·Theo Lemaire on May 10 2019, 18:09.

May 6 2019

added ref mode to QSSvar with phase plot arrows.
536de29806e2
·Theo Lemaire on May 6 2019, 19:15.

Apr 29 2019

corrected titrate function to work also with negative injected currents (for…
44780023da34
·Theo Lemaire on Apr 29 2019, 12:09.

Apr 8 2019

adapted plotQSSVarVsAmp and plotEqChargeVsAmp functions for ESTIM use (not…
ddab2a4571ea
·Theo Lemaire on Apr 8 2019, 23:07.

Apr 5 2019

corrected nbls.quasiSteadyStates to return DC-averaged Vmeff, and adapted nbls.
490706425b05
·Theo Lemaire on Apr 5 2019, 21:04.
improved titrate function with nSpikes methods pneuron and nbls classes. added…
6ffd825273a4
·Theo Lemaire on Apr 5 2019, 17:47.

Apr 4 2019

Changed titration functions (now using generic titrate), Implemented Xinf…
9f09f2fdc039
·Theo Lemaire on Apr 4 2019, 13:38.

Mar 26 2019

added generic plot_QSS_IQ.py script to plot the IQ phase-plane diagram for a…
178930fa846c
·tlemaire on Mar 26 2019, 23:29.
implemented new QSS plot module with generic plotVarDynamics, plotVarsQSS and…
a2726a130bec
·tlemaire on Mar 26 2019, 19:35.
corrected the nbls.quasiSteadyStates method to compute QSS values of slow…
b6c44fad8f0a
·tlemaire on Mar 26 2019, 14:53.
replaced lookups list by lookups dict in all derStatesEff methods. added get…
8a71066a647c
·tlemaire on Mar 26 2019, 11:52.

Mar 20 2019

added rmse evaluation for Q-stab comparison between sims and QSS approx. in…
d06d82b80840
·tlemaire on Mar 20 2019, 17:59.

R4670/scriptsmaster062e541857dc24b7fbc530d…

Feb 3 2020

Jan 26 2020

Dec 14 2019

Nov 26 2019

Nov 14 2019

Nov 6 2019

Oct 10 2019

Oct 7 2019

Sep 17 2019

Sep 2 2019

Aug 29 2019

Aug 22 2019

Aug 14 2019

Jul 15 2019

Jul 1 2019

Jun 29 2019

Jun 28 2019

Jun 27 2019

Jun 26 2019

Jun 25 2019

Jun 17 2019

Jun 16 2019

Jun 15 2019

Jun 14 2019

Jun 13 2019

Jun 12 2019

Jun 10 2019

Jun 9 2019

Jun 7 2019

Jun 6 2019

Jun 3 2019

Jun 2 2019

May 31 2019

May 29 2019

May 27 2019

May 24 2019

May 23 2019

May 22 2019

May 21 2019

May 20 2019

May 17 2019

May 16 2019

May 15 2019

May 14 2019

May 10 2019

May 6 2019

Apr 29 2019

Apr 8 2019

Apr 5 2019

Apr 4 2019

Mar 26 2019

Mar 20 2019

R4670/scripts
master062e541857dc24b7fbc530d…