Diffusion PySONIC (old) (master) History

R4670/scripts
master71a2cddb684eb3ad713c253…

May 27 2019

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.

Dec 9 2018

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

Dec 3 2018

STN model validated for E-STIM by reproduction of key features (spontaneous…
9eca746695d1
·tlemaire on Dec 3 2018, 17:46.

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 27 2018

added spanDC argument to run_astim. removed rheobase amp preconditioning in…
fa4c643a5a4b
·tlemaire on Nov 27 2018, 16:18.

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.

Nov 20 2018

modified getLookups2D to project along any dimensions pair in (a, f, A).
8573c726b480
·tlemaire on Nov 20 2018, 19:32.

Oct 28 2018

improved plotPhasePlane function. implemented isWithin function for loose bound…
d17615ffb4e6
·tlemaire on Oct 28 2018, 22:49.

Oct 25 2018

plotPhaseDiagram method validated on CW stimuli
35b8bf12ec49
·tlemaire on Oct 25 2018, 22:49.
implemented figtitle method for direct labeling from metadata. implemented…
d2b627754312
·tlemaire on Oct 25 2018, 14:52.

Oct 2 2018

added scripts to generate paper figures automatically.
ed0d192b377b
·tlemaire on Oct 2 2018, 02:55.

Sep 28 2018

updated package documentation
73851d6ac128
·tlemaire on Sep 28 2018, 14:23.

Sep 27 2018

removed print statements in run_astim
0927fba5ad55
·tlemaire on Sep 27 2018, 11:17.
added LTS and TC lookups. corrected errors in run_astim and run_estim arguments…
81ffd1c605f6
·tlemaire on Sep 27 2018, 11:16.
attempt to fix multiprocessing lookups creation.
f5f327799ad4
·tlemaire on Sep 27 2018, 03:03.

Sep 26 2018

added actmap to plt module, with command line script.
4a67049acd76
·tlemaire on Sep 26 2018, 17:06.
corrected error on lookups dict save.
7bd042cd39f7
·tlemaire on Sep 26 2018, 09:33.

Sep 25 2018

fixed call to plotBatch in run scripts
0412541be120
·tlemaire on Sep 25 2018, 18:03.
moved plotComp and plotBatch functions to separate files. created unique plot…
a35c13583071
·tlemaire on Sep 25 2018, 17:25.
cleaned up utils module. removed log templates (now generated on the fly with…
610dc8472dcf
·tlemaire on Sep 25 2018, 14:46.

Sep 24 2018

turned intermolecular pressure test script into notebook. removed Input error…
954e545fa6ac
·tlemaire on Sep 24 2018, 23:54.
moved lookups into neurons folder
1951d49ccd25
·tlemaire on Sep 24 2018, 21:48.
cleaned up plot_batch and plot_comp scripts
4c4f11074ce9
·tlemaire on Sep 24 2018, 21:08.
moved relevant plot scripts to scripts folder. Turned analysis scripts into…
4d53b2a42b5e
·tlemaire on Sep 24 2018, 21:00.

R4670/scriptsmaster71a2cddb684eb3ad713c253…

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

Mar 18 2019

Mar 15 2019

Mar 14 2019

Mar 13 2019

Mar 12 2019

Mar 11 2019

Mar 10 2019

Mar 8 2019

Mar 7 2019

Mar 5 2019

Jan 23 2019

Jan 9 2019

Dec 27 2018

Dec 14 2018

Dec 9 2018

Dec 3 2018

Nov 30 2018

Nov 29 2018

Nov 27 2018

Nov 25 2018

Nov 22 2018

Nov 20 2018

Oct 28 2018

Oct 25 2018

Oct 2 2018

Sep 28 2018

Sep 27 2018

Sep 26 2018

Sep 25 2018

Sep 24 2018

R4670/scripts
master71a2cddb684eb3ad713c253…