Diffusion PySONIC (old) (master) History

History
master0028dbdfe69feab80262140…

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

added plotting of real QS SFPs and UFPs in plotQSSdynamics and plotQSSVarVsQm…
3accccc91cbe
·tlemaire on Jun 10 2019, 22:27.
minor change to getCycleProfiles
ed095e030274
·tlemaire on Jun 10 2019, 21:56.
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.
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 getSimThresholdAmps and plotQSSThresholdCurve functions to QSS module…
26fdc0bbfe8d
·tlemaire on Jun 7 2019, 18:28.
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 getLowIntensitiesSTN to STN class
50103226d72b
·tlemaire on Jun 6 2019, 21:30.
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 4 2019

minodr edits
01bf73a48e1a
·Theo Lemaire on Jun 4 2019, 17:21.

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.
changed marker styles for QSS plots
49e81c5ace12
·Theo Lemaire on Jun 2 2019, 17:55.
added getInDict function used to determine output directory in sim scripts
68e2fe6fd858
·Theo Lemaire on Jun 2 2019, 15:50.
updated package requirements
84c6a191108c
·Theo Lemaire on Jun 2 2019, 15:46.
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.
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.
modified cache to only log if function has not "history" argument to avoid…
1463cf220fbc
·Theo Lemaire on May 27 2019, 12:07.

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.
re-implemented csvcache as decorator
4e391806ec32
·Theo Lemaire on May 24 2019, 13:13.

May 23 2019

added interface around titrate function to use memory caching
0453d1e710dd
·Theo Lemaire on May 23 2019, 21:01.
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.
added Amin and Amax command line arguments to plot_QSS_IQ.py
2de6d3d26717
·Theo Lemaire on May 22 2019, 10:02.
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.
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.
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.
removed old pltvars dictionary.
895dbbeb52ae
·tlemaire on Mar 15 2019, 01:32.

Historymaster0028dbdfe69feab80262140…

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History
master0028dbdfe69feab80262140…