Diffusion PySONIC (old) (master) History

nbls.py
masterffdcb43ba1d8a49740c433a…

Jul 1 2019

improved checkTitrate robustness
ffdcb43ba1d8
·tlemaire on Jul 1 2019, 17:40.
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.

Jun 27 2019

added Model.description method. added nbls.getLookup2D method with correct fs…
a0db776b7966
·tlemaire on Jun 27 2019, 16:10.
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.
cleaned up model classes. defined mandatory derivatives method for model…
3528fa81b6d1
·tlemaire on Jun 26 2019, 13:38.

Jun 25 2019

improved steadyStates definition in TC and STN neurons. corrected dQdt pltvar…
9965ddc0005d
·tlemaire on Jun 25 2019, 23:21.
removed unnecessary functions from pneuron
acf299185987
·tlemaire on Jun 25 2019, 18:17.
added automatic effRates function definition in pneuron.parse method. removed…
db8cc8e2b5ff
·tlemaire on Jun 25 2019, 17:57.
finished implementing pneuron.buildDerEffStates method to automatically create…
4742d6a43494
·tlemaire on Jun 25 2019, 14:59.

Jun 24 2019

defined separate lookup decorator for bls.computePMparams method. updated…
83ff47370d86
·tlemaire on Jun 24 2019, 20:21.

Jun 20 2019

define dLookUp class to perform lookup projections and interpolations
a96a900ad4b4
·tlemaire on Jun 20 2019, 17:35.
added default output directory ("dump"). cleaned up neuron classes.
6c10d4162d71
·tlemaire on Jun 20 2019, 10:09.

Jun 19 2019

refefined derEffstates construction to return a dictionary of function.
fdebb58e8442
·tlemaire on Jun 19 2019, 19:12.
added getSteadyStates and getDerStates methods to pneuron to call steadyStates…
f719dddee9f0
·tlemaire on Jun 19 2019, 15:39.
cleaned up neuron classes. redefined currents to return functions instead of…
26fe1e08a408
·tlemaire on Jun 19 2019, 11:05.

Jun 18 2019

started implementation of buildDerEffStates to contruct the derEffStates…
40b5a09c46c2
·tlemaire on Jun 18 2019, 23:14.
replaced obscur states list by explicit dictionary in all currents methods
7b2aee9851af
·tlemaire on Jun 18 2019, 18:21.
replaced obscur states list by explicit states dictionary in derStates and…
00f57af96cfb
·tlemaire on Jun 18 2019, 16:04.

Jun 17 2019

corrected y, t order error in nbls.fullDerivatives. added custom parsing in…
66eaf2f41fba
·tlemaire on Jun 17 2019, 21:43.

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 10 2019

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.
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 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 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 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 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.

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.

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.

Jan 23 2019

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

Dec 27 2018

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

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.

Nov 19 2018

modified runSONIC method to use odeint solver with interpolated lookups for…
da009206a90e
·tlemaire on Nov 19 2018, 21:46.

Oct 28 2018

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

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.

R4670/PySONIC/core/nbls.pymasterffdcb43ba1d8a49740c433a…

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R4670/PySONIC/core/nbls.py
masterffdcb43ba1d8a49740c433a…