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.

Jun 2 2019

changed marker styles for QSS plots
49e81c5ace12
·Theo Lemaire on Jun 2 2019, 17:55.
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.
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

added logNSpikes function to pneuron class.
c23526a0ca16
·Theo Lemaire on May 27 2019, 16:38.
haromized amplitude and plot_scheme parsing across simulation scripts
13e29c29bbb1
·Theo Lemaire on May 27 2019, 15:29.
started defining ActivationMap class
818219348db5
·Theo Lemaire on May 27 2019, 14:40.
replaced filecode functions by class methods
71a2cddb684e
·Theo Lemaire on May 27 2019, 13:46.

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

implemented neuron-dependent titration to find specific thresholds (excitation…
1a5f9b3c215b
·Theo Lemaire on May 22 2019, 19:07.
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.
implemented nbls.quasiSteadStateiNet method, used to compute Q-SFPs iteratively…
2024b001441b
·Theo Lemaire on May 22 2019, 09:36.

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 warning note about why QSS cannot be interpolated accurately and must be…
df4bf6f7892b
·Theo Lemaire on May 17 2019, 19:35.
added fixed point classification based on perturbation reaction in QSS analysis.
3e55319aff15
·Theo Lemaire on May 17 2019, 19:26.
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

added Qi-conditional graphs labeling for plotQSSVarVsAmp and plotEqChargeVsAmp
f7c982e3c3ea
·Theo Lemaire on Apr 5 2019, 21:12.
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.
replaced lookups list by lookups dict in all derStatesEff methods. added get…
8a71066a647c
·tlemaire on Mar 26 2019, 11:52.

Mar 20 2019

corrected STN lookups, comparison of temporal profiles of spontaneous activity…
6f96c02c5ecb
·tlemaire on Mar 20 2019, 11:41.

Mar 18 2019

moved membrane currents in 2rd position of neurons pltscheme. extractPltVar now…
cf921135e3f2
·tlemaire on Mar 18 2019, 17:56.

Mar 15 2019

removed old pltvars dictionary.
895dbbeb52ae
·tlemaire on Mar 15 2019, 01:32.
added rates to pneuron.getPltVars method. adapted use in plotEffectiveVariables…
6bc050dea626
·tlemaire on Mar 15 2019, 01:30.
adapted plotComp to new plot variables scheme.
ad0a33b92c3c
·tlemaire on Mar 15 2019, 01:15.
created plt.pltutils module and moved relevant plotting functions into it.
a812d7d527af
·tlemaire on Mar 15 2019, 00:20.

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.
cleaned up neurons docstring. defined PointNeuron.getPltVars method (possibly…
f6195a153a01
·tlemaire on Mar 14 2019, 13:38.

Mar 13 2019

removed all combined gating variables from pltvars schemes.
33c52c6b04a5
·tlemaire on Mar 13 2019, 15:14.
implemented PointNeuron.getCurrentPltVars method to genrate a dictionary plot…
817387c89edd
·tlemaire on Mar 13 2019, 15:00.

Mar 11 2019

adapted plotSpikingMetrics for uniform y-axis scale. adapted ASTIM_filecode…
cd145e4db3e8
·tlemaire on Mar 11 2019, 13:55.

Mar 8 2019

adapted fig9.py with corrected STN model (new traces).
a74f9c571b7d
·tlemaire on Mar 8 2019, 16:52.

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 6 2019

renamed currents for more clarity
da8e0bbde997
·tlemaire on Mar 6 2019, 17:56.

Mar 5 2019

changed nomenclature of current methods from "curr..." to "i..."
2e64aa90c325
·tlemaire on Mar 5 2019, 12:18.
implemented getLookupsOff function to retrieve US-OFF lookups. adapted…
c72b7b319ed0
·tlemaire on Mar 5 2019, 11:04.

Feb 28 2019

added RS neuron lookups with partial coverage (spatially averaged). updated…
865020d8c630
·tlemaire on Feb 28 2019, 11:41.

Jan 9 2019

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

Dec 14 2018

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

Dec 9 2018

added pltvars for STN neuron. added plotFRprofile function along with paper…
0fcd53a68ce7
·tlemaire on Dec 9 2018, 16:17.

Nov 30 2018

replaced 'L' by 'Leak' in neurons nomenclature. implemented STN neuron with…
0ebd7ae3b932
·tlemaire on Nov 30 2018, 10:37.

Nov 29 2018

added plotFRspectrum function to actmap module. updated fig7 script, and added…
850b05b61c5e
·tlemaire on Nov 29 2018, 16:00.

Nov 25 2018

added recording of computation times during lookups creation.
9f827c942524
·tlemaire on Nov 25 2018, 01:10.

Nov 22 2018

improved plotRheobaseAmps function. improved arguments parsing in command line…
2f63e4926c36
·tlemaire on Nov 22 2018, 17:58.

R4670/PySONIC/pltmaster83ff47370d86bfd8d5e8c90…

Jun 20 2019

Jun 19 2019

Jun 17 2019

Jun 16 2019

Jun 15 2019

Jun 14 2019

Jun 13 2019

Jun 12 2019

Jun 11 2019

Jun 10 2019

Jun 9 2019

Jun 7 2019

Jun 6 2019

Jun 4 2019

Jun 3 2019

Jun 2 2019

May 31 2019

May 29 2019

May 27 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

Mar 18 2019

Mar 15 2019

Mar 14 2019

Mar 13 2019

Mar 11 2019

Mar 8 2019

Mar 7 2019

Mar 6 2019

Mar 5 2019

Feb 28 2019

Jan 9 2019

Dec 14 2018

Dec 9 2018

Nov 30 2018

Nov 29 2018

Nov 25 2018

Nov 22 2018

R4670/PySONIC/plt
master83ff47370d86bfd8d5e8c90…