Diffusion PySONIC (old) (master) History

core
masterb461503582fb4f3a1e07494…

Jun 16 2019

added firing rate to plot variables
b461503582fb
·tlemaire on Jun 16 2019, 13:05.

Jun 15 2019

added simkey to meta dictionary. added automatic parsing and labeling of…
c14fa0da1fd7
·tlemaire on Jun 15 2019, 18:32.

Jun 14 2019

added outputdir option to simQueue methods. added automatic parsing to Parser…
de8bdbc4fee0
·tlemaire on Jun 14 2019, 11:34.

Jun 13 2019

updated constants
b0f51febd195
·tlemaire on Jun 13 2019, 23:54.

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 11 2019

added neuron templyte class. added procedure to follow to add new neuron types…
0028dbdfe69f
·tlemaire on Jun 11 2019, 16:56.

Jun 10 2019

minor change to getCycleProfiles
ed095e030274
·tlemaire on Jun 10 2019, 21:56.
added functionality to load data directly from sim results in TimeSeriesPlot…
2f0254ea5b53
·tlemaire on Jun 10 2019, 20:52.
switched back to old evaluateStability version
1354c6f9d2e9
·tlemaire on Jun 10 2019, 16:34.
first attempt at replacing custom integration in nbls.evaluateStability by call…
dd32fc0479b4
·tlemaire on Jun 10 2019, 00:06.

Jun 9 2019

removed STN temporary fix in nbls.titrate
84c54a491722
·tlemaire on Jun 9 2019, 23:00.
added first-call check that condition changes within the interval to…
b88c300e48f0
·tlemaire on Jun 9 2019, 22:48.
added file locking to cache functions
db58a9d4e8b7
·tlemaire on Jun 9 2019, 21:55.
added solve_ivp optional use to Simulator.integrate method
2e0f97a8baaf
·tlemaire on Jun 9 2019, 21:36.
set t first in all derivatives function
c7f94b320ba7
·tlemaire on Jun 9 2019, 21:16.
removed ng and Z explicit computation in runSONIC (replaced by nan arrays)
b46a8cd85a73
·tlemaire on Jun 9 2019, 20:47.
corrected errors in nbls interpEFFVariable and runSONIC methods
5eed591ede6e
·tlemaire on Jun 9 2019, 20:10.
added nbls isStableQSS and titrateQSS methods. finished plotQSSThresholdCurve
863bdf8330f4
·tlemaire on Jun 9 2019, 19:51.

Jun 7 2019

added multiprocessing for runAndGetStab function
86564c193a65
·tlemaire on Jun 7 2019, 16:41.
added custom parsers to plot_timeseries and plot_QSS
1f1e59762ea3
·tlemaire on Jun 7 2019, 15:56.

Jun 6 2019

moved lookups utilities into separate lookups module (in neurons folder)
0984b86caa8f
·tlemaire on Jun 6 2019, 21:25.
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

corrected plot_QSS inputdir error
6cbf141d9754
·Theo Lemaire on Jun 3 2019, 17:02.
added parsers module, now used in sim scripts for more consistency.
f75ca2e6e294
·Theo Lemaire on Jun 3 2019, 15:11.

Jun 2 2019

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.

Jun 1 2019

added isAsymptoticallyStable method to PeriodicSolver
c49110f6c3cf
·Theo Lemaire on Jun 1 2019, 20:00.
added convfunc attribute to PeriodicSimulator class
7c909ad7dbbd
·Theo Lemaire on Jun 1 2019, 17:19.
added caching to nbls.titrate method
e0aa4041f3b8
·Theo Lemaire on Jun 1 2019, 16:50.
redefined titration procedures with binarySearch method. now single runAndSave…
10d2b5bb498e
·Theo Lemaire on Jun 1 2019, 16:41.

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.
moved "amp" parameter back to appropriate in args list of runAndSave functions
aae3bfea421b
·Theo Lemaire on May 31 2019, 15:04.
added "meta" method to core classes
42ef7cb1063a
·Theo Lemaire on May 31 2019, 14:56.
reformatted simulate methods of bls, pneuron and nbls classes to return output…
af6f9a02ed42
·Theo Lemaire on May 31 2019, 14:43.
cleaned up simulators classes
19a9b2f737fd
·Theo Lemaire on May 31 2019, 10:52.

May 30 2019

added appendSolution method to simulators
f713b8d85160
·Theo Lemaire on May 30 2019, 23:42.
added docstring to simulators classes
17f1482bc336
·Theo Lemaire on May 30 2019, 23:32.

May 29 2019

replaced progressbar2 by tqdm
e08e8c736efa
·Theo Lemaire on May 29 2019, 18:35.
added HybridSimulator used for nbls.runHybrid
440f5459adf4
·Theo Lemaire on May 29 2019, 16:17.
added use of PWSimulator in pneuron
370f27746bca
·Theo Lemaire on May 29 2019, 09:59.
added simulators classes to take care of simulations
4ba3212edf92
·Theo Lemaire on May 29 2019, 03:15.

May 27 2019

added intermediate "run" method that return output data and metadata
1391db99409d
·Theo Lemaire on May 27 2019, 20:13.
added return_val option to isExcited and isSilenced
21d010292ddf
·Theo Lemaire on May 27 2019, 19:50.
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.
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

implemented specific nbls evaluateStability method to evaluate FP stability by…
8a17ab2f8c11
·Theo Lemaire on May 21 2019, 18:06.

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.

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

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

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

Mar 15 2019

cleaned up neurons docstring. added getDesc method to PointNeurons class.
8623752f128f
·tlemaire on Mar 15 2019, 02:20.
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

implemented PointNeuron.currentToConcentrationRate method for a common way to…
db85dec73950
·tlemaire on Mar 13 2019, 16:08.
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.
replaced iNet method by currents method in all neuron classes (iNet now defined…
09ec0decb4bd
·tlemaire on Mar 13 2019, 10:17.

Mar 11 2019

implemented NeuronalBilayerSonophore.getQSSvars method to compute QSS…
d99d9eb144b6
·tlemaire on Mar 11 2019, 20:39.

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.

Jan 23 2019

added script to compute quick lookups for a span of partial sonophore coverage…
80aa94a42257
·tlemaire on Jan 23 2019, 16:00.

Jan 11 2019

added lookups for FH membrane mechanism (tested)
cf20bd8f6516
·tlemaire on Jan 11 2019, 08:26.

Jan 10 2019

corrected Qbounds for lookups generation in FH neuron
8684707c3f08
·tlemaire on Jan 10 2019, 12:31.

Jan 9 2019

changed PMAVG_STD_ERR_MAX value to allow BLS lookups generation for FH…
82590fe13581
·tlemaire on Jan 9 2019, 18:05.
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 3 2018

corrected STN getEffRates and derStatesEff methods for correct lookups creation…
7655cca494a0
·tlemaire on Dec 3 2018, 21:52.

R4670/PySONIC/coremasterb461503582fb4f3a1e07494…

Jun 16 2019

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R4670/PySONIC/core
masterb461503582fb4f3a1e07494…