Diffusion PySONIC (old) (master) History

R4670/PySONIC/core/pneuron.py
masterf1d2ab4cfb4b105260a6809…

Nov 7 2019

added PointNeuron alphaBorgGaham and betaBorgGraham methods, now used for sundt…
f1d2ab4cfb4b
·tlemaire on Nov 7 2019, 12:44.

Sep 17 2019

add handling of positional and keyword arguments in Batch queues. added…
89e117f6ffaa
·tlemaire on Sep 17 2019, 16:15.
abstracted Model.simQueue method (now defined in children classes). changed…
8cf15b137151
·tlemaire on Sep 17 2019, 15:03.

Sep 11 2019

implemmented inheritance scheme for PointNeuron.chooseTimeStep method
d65e74f5c30c
·tlemaire on Sep 11 2019, 15:51.

Sep 10 2019

corrected SweeneyNode alpham equation according to Basser and Roth, 1991.
bd840351d13f
·tlemaire on Sep 10 2019, 15:01.

Sep 4 2019

expanded charge range for pneuron.getLookup
614c56792d61
·tlemaire on Sep 4 2019, 13:17.

Sep 2 2019

parametrised Qm plot range to be neuron-specific. Solved issue with pbar update.
fd4639a4c602
·tlemaire on Sep 2 2019, 20:44.
corrected crucial error in nbls.spatialAverage method. corrected Cm0 and Qm0…
d2ccd21d9889
·tlemaire on Sep 2 2019, 20:16.

Aug 26 2019

implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to…
4f5fb5ee0829
·tlemaire on Aug 26 2019, 14:57.

Aug 22 2019

harmonized peaks/spikes detection process across the package.
db880034dc26
·tlemaire on Aug 22 2019, 15:31.

Aug 15 2019

added iCap to plot variables. added colormap option for comparative plots even…
3146cab6bade
·tlemaire on Aug 15 2019, 21:38.

Aug 14 2019

added automatic solution prepending to all simulate methods (to treat initial…
2278e599a753
·tlemaire on Aug 14 2019, 17:51.
added VoltageClamp class with associated script and parser
366c7e528105
·tlemaire on Aug 14 2019, 15:07.

Jul 17 2019

removed all static quasiSteadyStates definition in neuron classes.
dc37f0afbd17
·tlemaire on Jul 17 2019, 20:05.
added findModifiedEq function to utils, using brentq to find a new equilibrium…
f113d822d4fb
·tlemaire on Jul 17 2019, 15:51.

Jul 16 2019

modified TC neuron steadyStates method.
17b59c14aa75
·tlemaire on Jul 16 2019, 18:57.

Jul 15 2019

transformed pneuron qsState and quasiSteadyStates methods to return lambda…
f768f01cd891
·tlemaire on Jul 15 2019, 21:40.

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.
moved effRates vectorization into pneuron.getEffRates method
8f1ea1a16339
·tlemaire on Jun 27 2019, 12:59.

Jun 26 2019

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.
corrected labeling error in GroupedTimeSeries
8b3f49b0bac4
·tlemaire on Jun 25 2019, 18:26.
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 20 2019

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.
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

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 16 2019

finished implmenting Firing Rate as plot variable (now replacing plotFRProfile).
63faa327c865
·tlemaire on Jun 16 2019, 22:47.
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.

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 9 2019

set t first in all derivatives function
c7f94b320ba7
·tlemaire on Jun 9 2019, 21:16.
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 6 2019

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.

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 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.

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.

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 22 2019

implemented neuron-dependent titration to find specific thresholds (excitation…
1a5f9b3c215b
·Theo Lemaire on May 22 2019, 19:07.

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

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

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 STN lookups, comparison of temporal profiles of spontaneous activity…
6f96c02c5ecb
·tlemaire on Mar 20 2019, 11:41.

Mar 18 2019

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 5 2019

changed nomenclature of current methods from "curr..." to "i..."
2e64aa90c325
·tlemaire on Mar 5 2019, 12:18.

Jan 9 2019

implemented Frankenhaeuser-Huxley membrane mechanism (validated against data…
65c1d8649331
·tlemaire on Jan 9 2019, 17:59.