Diffusion PySONIC (old) (master) History

R4670/scripts
masterdffee6926b857fe0d0fc584…

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.
corrected computation of Cai_ss for STN neuron, now using voltage-gated steady…
5a5f2babbc5d
·tlemaire on Mar 20 2019, 17:12.
corrected nbls.getQSSvars method, now computing non-rate-defined QSS values…
256a4aab9b65
·tlemaire on Mar 20 2019, 15:01.
corrected STN lookups, comparison of temporal profiles of spontaneous activity…
6f96c02c5ecb
·tlemaire on Mar 20 2019, 11:41.

Mar 18 2019

Implemented NmodlGenerator core class to automatically generate NEURON MOD file…
07d55c08e109
·tlemaire on Mar 18 2019, 21:21.

Mar 15 2019

adapted plotComp to new plot variables scheme.
ad0a33b92c3c
·tlemaire on Mar 15 2019, 01:15.

Mar 14 2019

removed states0 attribute from neuron classes (now calling steadyStates method…
81554e5d4d67
·tlemaire on Mar 14 2019, 23:52.
generalized the use of getPltVars and getPltScheme with inheritance scheme…
453f896987ce
·tlemaire on Mar 14 2019, 23:35.
major reformatting of plotBatch function
9d1a2fc5cd08
·tlemaire on Mar 14 2019, 19:09.

Mar 13 2019

added Qbounds as a PointNeuron class method. cleaned up use of Cai in TC class.
ce5a9df84ba1
·tlemaire on Mar 13 2019, 15:44.
implemented PointNeuron.getCurrentPltVars method to genrate a dictionary plot…
817387c89edd
·tlemaire on Mar 13 2019, 15:00.

Mar 12 2019

corrected error in STN.derD1. lookup tables to re-run.
2b5b9cf5a78b
·tlemaire on Mar 12 2019, 12:51.
added get_dCCa and findCaeq methods ot STN neuron (iterative search to find…
7082d86bf3da
·tlemaire on Mar 12 2019, 01:29.

Mar 11 2019

added detection of stabilization (time and value) from charge density profiles…
2979d8329c88
·tlemaire on Mar 11 2019, 21:51.
implemented NeuronalBilayerSonophore.getQSSvars method to compute QSS…
d99d9eb144b6
·tlemaire on Mar 11 2019, 20:39.
adapted plotSpikingMetrics for uniform y-axis scale. adapted ASTIM_filecode…
cd145e4db3e8
·tlemaire on Mar 11 2019, 13:55.

Mar 10 2019

added currents methods to Cortical, Thalamic and STN classes, that returns a…
c5433b2c448c
·tlemaire on Mar 10 2019, 19:36.

Mar 8 2019

corrected STN lookups. added testQSS script to analyze STN neuron plateau…
e73ca2da1333
·tlemaire on Mar 8 2019, 15:38.

Mar 7 2019

corrected sigmaT2_b from -10 mV to 10 mV in STN implementation. started new QSS…
990c8181cf46
·tlemaire on Mar 7 2019, 16:00.

Mar 5 2019

implemented getLookupsOff function to retrieve US-OFF lookups. adapted…
c72b7b319ed0
·tlemaire on Mar 5 2019, 11:04.

Jan 23 2019

corrected error in getLookups2Dfs
702446ca2ad5
·tlemaire on Jan 23 2019, 19:05.
added getLookups2Dfs method to interpolate lookups at given membrane coverage.
957db9d021d6
·tlemaire on Jan 23 2019, 18:15.
added script to compute quick lookups for a span of partial sonophore coverage…
80aa94a42257
·tlemaire on Jan 23 2019, 16:00.

Jan 9 2019

implemented Frankenhaeuser-Huxley membrane mechanism (validated against data…
65c1d8649331
·tlemaire on Jan 9 2019, 17:59.

Dec 27 2018

corrected error in Vm post-processing in runSONIC. added plotV option to…
8a4719662fd9
·tlemaire on Dec 27 2018, 19:08.

Dec 14 2018

modified plotActivationMap to plot amplitude thresholds computed from titration…
42f56ab271e3
·tlemaire on Dec 14 2018, 18:16.

R4670/scriptsmasterdffee6926b857fe0d0fc584…

Jun 26 2019

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R4670/scripts
masterdffee6926b857fe0d0fc584…