R4670/scriptsmaster
R4670/scripts
master
History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
165caa8bf488 | tlemaire | moved getMeta to utils | Feb 20 2020 | |||
27d8aafffa88 | tlemaire | Created Drive objects inheritance scheme (now used in all model classes). | Feb 3 2020 | |||
9d0666784d2d | tlemaire | Created AcousticSource class to be used for US simulations. | Feb 3 2020 | |||
c995e8999df7 | tlemaire | Modified Lookup class (new properties, corrected methods). | Jan 26 2020 | |||
38dc94d61fe7 | tlemaire | added DQ_LOOKUP constant (used in run_lookups.py) | Jan 26 2020 | |||
a0b6724a45a5 | tlemaire | removed plotVarQSSDynamics function from QSS and plot_QSS | Dec 14 2019 | |||
6797e5e1f52b | tlemaire | moved pushbullet key file to package root | Nov 26 2019 | |||
6deb0da8868d | tlemaire | added internal bls.simUntilConvergence method (without decorators) to enable… | Nov 26 2019 | |||
36119dd01aec | tlemaire | moved filecode function to utils | Nov 14 2019 | |||
163afcce99af | tlemaire | renamed PhaseDiagram to SpikePlot (more appropriate). simplified Sundt model… | Nov 6 2019 | |||
a2c1e3e2eb02 | tlemaire | modified nbls.QSSderivatives and nbls.__simQSS to work with any specified… | Nov 6 2019 | |||
aee2c4e6cb21 | tlemaire | added Lookup.tile and modified SmartLookup.projectDC. modified nbls. | Oct 10 2019 | |||
20f96c135bce | tlemaire | defined Lookup algorihtmic operators. defined OnOffSimulator class. defined… | Oct 7 2019 | |||
f1092e3356eb | tlemaire | added Parser.addCheckForOutput method, now used in run_*** scripts to… | Sep 17 2019 | |||
89e117f6ffaa | tlemaire | add handling of positional and keyword arguments in Batch queues. added… | Sep 17 2019 | |||
8cf15b137151 | tlemaire | abstracted Model.simQueue method (now defined in children classes). changed… | Sep 17 2019 | |||
d2ccd21d9889 | tlemaire | corrected crucial error in nbls.spatialAverage method. corrected Cm0 and Qm0… | Sep 2 2019 | |||
1b3cffe95e7a | tlemaire | added sweeney lookups (ASTIM not working yet). added fixLookup to remove single… | Aug 29 2019 | |||
db880034dc26 | tlemaire | harmonized peaks/spikes detection process across the package. | Aug 22 2019 | |||
366c7e528105 | tlemaire | added VoltageClamp class with associated script and parser | Aug 14 2019 | |||
1b242e25ca45 | tlemaire | added plot_intensity_vs_amplitude.py script | Aug 14 2019 | |||
d50bf6119d40 | tlemaire | started implementing SonicTranslator.parseSteadyStates method. Implemented… | Jul 15 2019 | |||
d1a3fbaefd83 | tlemaire | added option to provide simAndSave or simulate to batches. implemented addMeta… | Jul 1 2019 | |||
4937955d0214 | tlemaire | adapted methods of all classes into classmethods and staticmethods when… | Jun 29 2019 | |||
4997a9f88989 | tlemaire | transformed model inputs, checkInputs and simQueue into static methods | Jun 28 2019 | |||
22abb7710105 | tlemaire | created separate test module with TestBase class. renamed test_basic into… | Jun 28 2019 | |||
b73594f4d58b | tlemaire | moved lookup to core module. moved getLookup methods to nbls class. | Jun 27 2019 | |||
dffee6926b85 | tlemaire | added fs (spatially-averaged) as input to nbls model. defined SmartLookup class… | Jun 26 2019 | |||
db8cc8e2b5ff | tlemaire | added automatic effRates function definition in pneuron.parse method. removed… | Jun 25 2019 | |||
a03eb1b35b77 | tlemaire | added custom parsing to plot_gating_kinetics.py | Jun 17 2019 | |||
3b86ec877351 | tlemaire | added custom parsing to plot_effective_variables.py | Jun 17 2019 | |||
1465c48312a6 | tlemaire | adde prettify option to timeseries plots | Jun 17 2019 | |||
e3f3982b8981 | tlemaire | defined PlotParser and TimeSeriesParser classes | Jun 17 2019 | |||
9e96cf6ee947 | tlemaire | added colormap functionality to PhaseDiagram | Jun 17 2019 | |||
e01fa72e6143 | tlemaire | replaced plotPhaseDiagram by PhaseDiagram class inheriting from ComparativePlot… | Jun 17 2019 | |||
0efc60073f8b | tlemaire | moved nmodl generator to ExSONIC package | Jun 17 2019 | |||
9556faead02c | tlemaire | added custom parsing to generate_mod_file.py | Jun 17 2019 | |||
4ce5e074ca4c | tlemaire | solved issue with ActivationMap Ascale | Jun 17 2019 | |||
75f6032d2f63 | tlemaire | replaced no_offset by tbounds in plotting options. added custom parsing to… | Jun 17 2019 | |||
63faa327c865 | tlemaire | finished implmenting Firing Rate as plot variable (now replacing plotFRProfile). | Jun 16 2019 | |||
012f2603c5d7 | tlemaire | added colormap functionality to CompPlot, with lin or log scale. | Jun 15 2019 | |||
c14fa0da1fd7 | tlemaire | added simkey to meta dictionary. added automatic parsing and labeling of… | Jun 15 2019 | |||
fb7c07fee5cb | tlemaire | added spike details plotting options to TimeSeriesPlot | Jun 14 2019 | |||
bdf8ef51d3db | tlemaire | added frequency and mark_spikes option to both CompPlot and SchemePlot classes | Jun 14 2019 | |||
de8bdbc4fee0 | tlemaire | added outputdir option to simQueue methods. added automatic parsing to Parser… | Jun 14 2019 | |||
da542f2db42b | tlemaire | removed extra line in run_lookups.py | Jun 13 2019 | |||
af7294977045 | tlemaire | adapted MechSimParser for use in run_lookups.py | Jun 13 2019 | |||
b42a0de93240 | tlemaire | updated all file headers | Jun 12 2019 | |||
cc309fa78cd9 | tlemaire | cleaned-up all neuron classes | Jun 12 2019 | |||
6e017b421f3e | tlemaire | replaced "neuron" by "pneuron" for all PointNeuron instances | Jun 12 2019 | |||
3accccc91cbe | tlemaire | added plotting of real QS SFPs and UFPs in plotQSSdynamics and plotQSSVarVsQm… | Jun 10 2019 | |||
9c883a796eff | tlemaire | moved example script in README and updated rest of the text. | Jun 10 2019 | |||
2f0254ea5b53 | tlemaire | added functionality to load data directly from sim results in TimeSeriesPlot… | Jun 10 2019 | |||
863bdf8330f4 | tlemaire | added nbls isStableQSS and titrateQSS methods. finished plotQSSThresholdCurve | Jun 9 2019 | |||
26fdc0bbfe8d | tlemaire | added getSimThresholdAmps and plotQSSThresholdCurve functions to QSS module… | Jun 7 2019 | |||
1f1e59762ea3 | tlemaire | added custom parsers to plot_timeseries and plot_QSS | Jun 7 2019 | |||
50103226d72b | tlemaire | moved getLowIntensitiesSTN to STN class | Jun 6 2019 | |||
3556a765fe5c | tlemaire | created ActivationMap class | Jun 6 2019 | |||
1c9c63d4ba6a | tlemaire | added getModel and getPointNeuron functions. removed deprecated scripts. | Jun 6 2019 | |||
bc5a29bc6c9a | Theo Lemaire | added caching of QSS analysis results | Jun 3 2019 | |||
6cbf141d9754 | Theo Lemaire | corrected plot_QSS inputdir error | Jun 3 2019 | |||
1295ce41f2c3 | Theo Lemaire | added custom parser to plot_QSS_IQ.py | Jun 3 2019 | |||
f75ca2e6e294 | Theo Lemaire | added parsers module, now used in sim scripts for more consistency. | Jun 3 2019 | |||
b21bb388bb20 | Theo Lemaire | removed unnecessary script | Jun 2 2019 | |||
fdc484dcbe00 | Theo Lemaire | simplified run scripts | Jun 2 2019 | |||
68e2fe6fd858 | Theo Lemaire | added getInDict function used to determine output directory in sim scripts | Jun 2 2019 | |||
874f4649ec44 | Theo Lemaire | corrected QSS module to work correctly with "load" option. | Jun 2 2019 | |||
88811f7a8aa5 | Theo Lemaire | major cleanup of all core classes. | Jun 2 2019 | |||
de01bc8b1676 | Theo Lemaire | moved batches to core module | May 31 2019 | |||
25d498c21187 | Theo Lemaire | implemented abstract Model class to be inherit by bls, pneuron and nbls | May 31 2019 | |||
4dd95ba1d83c | Theo Lemaire | added toffset to args list of pneuron and nbls filecode methods | May 31 2019 | |||
6cb5dac16172 | Theo Lemaire | moved createAStimQueue and createEStimQueue to their respective classes | May 31 2019 | |||
4ba3212edf92 | Theo Lemaire | added simulators classes to take care of simulations | May 29 2019 | |||
13e29c29bbb1 | Theo Lemaire | haromized amplitude and plot_scheme parsing across simulation scripts | May 27 2019 | |||
71a2cddb684e | Theo Lemaire | replaced filecode functions by class methods | May 27 2019 | |||
de4dc186176b | Theo Lemaire | added better plot handling to run_astim.py | May 24 2019 | |||
3a8d7d040f27 | Theo Lemaire | added Araneg and Irange args to run_astim.py | May 24 2019 | |||
678bec02c372 | Theo Lemaire | added "PI" type control of convergence in nbls.evaluateStability method | May 23 2019 | |||
0ee058e8778d | Theo Lemaire | added max integration duration to stability analysis to avoid infinite loops in… | May 22 2019 | |||
3addfe632329 | Theo Lemaire | implemented quasiSteadyStateFixedPoints as part of nbls class. Added… | May 22 2019 | |||
2de6d3d26717 | Theo Lemaire | added Amin and Amax command line arguments to plot_QSS_IQ.py | May 22 2019 | |||
6b55fdb84a7a | Theo Lemaire | added nA command line argument to plot_QSS_IQ.py | May 21 2019 | |||
8a17ab2f8c11 | Theo Lemaire | implemented specific nbls evaluateStability method to evaluate FP stability by… | May 21 2019 | |||
14f3b43f5ec7 | Theo Lemaire | added negative offset to QSS perturbation | May 20 2019 | |||
4d8fa0caef5b | Theo Lemaire | added isTitratable method to neuron classes. improved QSS SFP stability… | May 17 2019 | |||
3ad8ad914eec | Theo Lemaire | replaced linear interpolation of QSS at Q-SFPs (inaccurate) by full… | May 16 2019 | |||
3f4135902bdc | Theo Lemaire | added np.nan bounding to all np.interp uses in the code. implemented… | May 16 2019 | |||
a66b375c6133 | Theo Lemaire | implemented getLookupsDCavg function to compute DC-averaged lookups. nbls. | May 15 2019 | |||
ee9cf8652b7e | Theo Lemaire | simplified nbls.quasiSteadyStates method, now calling explicit quasiSeadyStates… | May 15 2019 | |||
62c6723c6e71 | Theo Lemaire | changed PointNeuron getEffrates, steadyStates, derStates and derEffStates… | May 14 2019 | |||
7a27b761d220 | Theo Lemaire | major improvements to QSS module | May 10 2019 | |||
536de29806e2 | Theo Lemaire | added ref mode to QSSvar with phase plot arrows. | May 6 2019 | |||
44780023da34 | Theo Lemaire | corrected titrate function to work also with negative injected currents (for… | Apr 29 2019 | |||
ddab2a4571ea | Theo Lemaire | adapted plotQSSVarVsAmp and plotEqChargeVsAmp functions for ESTIM use (not… | Apr 8 2019 | |||
490706425b05 | Theo Lemaire | corrected nbls.quasiSteadyStates to return DC-averaged Vmeff, and adapted nbls. | Apr 5 2019 | |||
6ffd825273a4 | Theo Lemaire | improved titrate function with nSpikes methods pneuron and nbls classes. added… | Apr 5 2019 | |||
9f09f2fdc039 | Theo Lemaire | Changed titration functions (now using generic titrate), Implemented Xinf… | Apr 4 2019 | |||
178930fa846c | tlemaire | added generic plot_QSS_IQ.py script to plot the IQ phase-plane diagram for a… | Mar 26 2019 | |||
a2726a130bec | tlemaire | implemented new QSS plot module with generic plotVarDynamics, plotVarsQSS and… | Mar 26 2019 | |||
b6c44fad8f0a | tlemaire | corrected the nbls.quasiSteadyStates method to compute QSS values of slow… | Mar 26 2019 |
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