Diffusion PySONIC (old) (master) History

R4670/PySONIC
masteracf299185987f8bd08d48f4…

Jun 25 2019

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.
corrected error in subset parsing
1a9277e6bbb4
·tlemaire on Jun 19 2019, 15:46.
added getSteadyStates and getDerStates methods to pneuron to call steadyStates…
f719dddee9f0
·tlemaire on Jun 19 2019, 15:39.
corrected Cinf error in ThalamoCortical neuron
becd2527f268
·tlemaire on Jun 19 2019, 15:19.
redefined derStates and steadyStates as dictionary of lambda functions
98942bac6b56
·tlemaire on Jun 19 2019, 15:16.
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

added custom parsing to paper figure scripts
d4798d527ccc
·tlemaire on Jun 17 2019, 22:08.
corrected y, t order error in nbls.fullDerivatives. added custom parsing in…
66eaf2f41fba
·tlemaire on Jun 17 2019, 21:43.
added custom parsing to plot_gating_kinetics.py
a03eb1b35b77
·tlemaire on Jun 17 2019, 21:19.
added custom parsing to plot_effective_variables.py
3b86ec877351
·tlemaire on Jun 17 2019, 21:13.
adde prettify option to timeseries plots
1465c48312a6
·tlemaire on Jun 17 2019, 20:43.
defined PlotParser and TimeSeriesParser classes
e3f3982b8981
·tlemaire on Jun 17 2019, 18:52.
added colormap functionality to PhaseDiagram
9e96cf6ee947
·tlemaire on Jun 17 2019, 18:29.
replaced plotPhaseDiagram by PhaseDiagram class inheriting from ComparativePlot…
e01fa72e6143
·tlemaire on Jun 17 2019, 17:55.
moved nmodl generator to ExSONIC package
0efc60073f8b
·tlemaire on Jun 17 2019, 10:58.
added custom parsing to generate_mod_file.py
9556faead02c
·tlemaire on Jun 17 2019, 10:52.
solved issue with ActivationMap Ascale
4ce5e074ca4c
·tlemaire on Jun 17 2019, 10:24.
replaced no_offset by tbounds in plotting options. added custom parsing to…
75f6032d2f63
·tlemaire on Jun 17 2019, 09:34.

Jun 16 2019

removed plotFRProfile from init file
cf146fbc835e
·tlemaire on Jun 16 2019, 22:52.
finished implmenting Firing Rate as plot variable (now replacing plotFRProfile).
63faa327c865
·tlemaire on Jun 16 2019, 22:47.
added consistent time bounding to plotters
1329e50433cd
·tlemaire on Jun 16 2019, 20:42.
added firing rate to plot variables
b461503582fb
·tlemaire on Jun 16 2019, 13:05.

Jun 15 2019

added colormap functionality to CompPlot, with lin or log scale.
012f2603c5d7
·tlemaire on Jun 15 2019, 19:15.
added simkey to meta dictionary. added automatic parsing and labeling of…
c14fa0da1fd7
·tlemaire on Jun 15 2019, 18:32.

Jun 14 2019

added spike details plotting options to TimeSeriesPlot
fb7c07fee5cb
·tlemaire on Jun 14 2019, 16:06.
added frequency and mark_spikes option to both CompPlot and SchemePlot classes
bdf8ef51d3db
·tlemaire on Jun 14 2019, 11:53.
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.
removed extra line in EStimParser
bd54da55cc7c
·tlemaire on Jun 13 2019, 15:24.
adapted MechSimParser for use in run_lookups.py
af7294977045
·tlemaire on Jun 13 2019, 15:22.
updated README headers
812cb5c1cb3a
·tlemaire on Jun 13 2019, 03:18.

Jun 12 2019

updated all file headers
b42a0de93240
·tlemaire on Jun 12 2019, 23:15.
adapted README recipe to cleaned up neuron classes
0ab79b08684a
·tlemaire on Jun 12 2019, 17:16.
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

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.
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.
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.

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 Araneg and Irange args to run_astim.py
3a8d7d040f27
·Theo Lemaire on May 24 2019, 16:26.

R4670/PySONICmasteracf299185987f8bd08d48f4…

Jun 25 2019

Jun 24 2019

Jun 20 2019

Jun 19 2019

Jun 18 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

Jun 1 2019

May 31 2019

May 30 2019

May 29 2019

May 27 2019

May 24 2019

R4670/PySONIC
masteracf299185987f8bd08d48f4…