Diffusion PySONIC (old) (master) History

parsers.py
mastera3951dd16d9c0cf6dfc91ed…

Aug 3 2020

added nmin parameter to PeriodicSolver.solve and BilayerSonophore.simCycles.
52e16ec74047
·tlemaire on Aug 3 2020, 23:13.

Apr 17 2020

implemented simQueueBurst method in pneuron and nbls classes.
6895a19a147f
·tlemaire on Apr 17 2020, 20:16.
harmonized repr, desc and filecodes methods across protocols.
e3ca275ebe0f
·tlemaire on Apr 17 2020, 19:35.

Apr 13 2020

replaced "Ascale" parsing options by "yscale" for more clarity.
b44cc93c9915
·tlemaire on Apr 13 2020, 18:17.
corrected LogBatch class to enable correct use with mpi.
f8511250c9b8
·tlemaire on Apr 13 2020, 18:00.

Feb 5 2020

changed erroneous calls to parseAmp to parseAmplitude in parsers module
478c17a7e098
·tlemaire on Feb 5 2020, 18:46.
replaced erroneous "return NotImplementedError" statements by "raise…
96d3c580ee81
·tlemaire on Feb 5 2020, 18:20.

Feb 3 2020

Created Drive objects inheritance scheme (now used in all model classes).
27d8aafffa88
·tlemaire on Feb 3 2020, 21:45.
Created AcousticSource class to be used for US simulations.
9d0666784d2d
·tlemaire on Feb 3 2020, 14:26.

Jan 26 2020

added DQ_LOOKUP constant (used in run_lookups.py)
38dc94d61fe7
·tlemaire on Jan 26 2020, 09:51.

Nov 20 2019

corrected Astim factor error in pneuron desc. added extra parsing methods
6197f85f0709
·tlemaire on Nov 20 2019, 22:24.
added qss_vars and pulse-avg run options to nbls simSonic method.
456fa71d226b
·tlemaire on Nov 20 2019, 20:32.

Nov 14 2019

moved filecode function to utils
36119dd01aec
·tlemaire on Nov 14 2019, 18:06.

Nov 6 2019

renamed PhaseDiagram to SpikePlot (more appropriate). simplified Sundt model…
163afcce99af
·tlemaire on Nov 6 2019, 19:33.
modified nbls.QSSderivatives and nbls.__simQSS to work with any specified…
a2c1e3e2eb02
·tlemaire on Nov 6 2019, 15:46.

Oct 7 2019

defined Lookup algorihtmic operators. defined OnOffSimulator class. defined…
20f96c135bce
·tlemaire on Oct 7 2019, 20:22.

Sep 19 2019

added fillLine function to utils. added Parser.addOverwrite method (opposite of…
ec466c361f8c
·tlemaire on Sep 19 2019, 11:39.

Sep 17 2019

added Parser.addCheckForOutput method, now used in run_*** scripts to…
f1092e3356eb
·tlemaire on Sep 17 2019, 17:07.
abstracted Model.simQueue method (now defined in children classes). changed…
8cf15b137151
·tlemaire on Sep 17 2019, 15:03.

Sep 13 2019

added vsteprange to VlcampParser. changed timeseries default onset from…
0c9e09419d16
·tlemaire on Sep 13 2019, 14:27.

Sep 10 2019

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

Sep 2 2019

corrected crucial error in nbls.spatialAverage method. corrected Cm0 and Qm0…
d2ccd21d9889
·tlemaire on Sep 2 2019, 20:16.

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 VoltageClamp class with associated script and parser
366c7e528105
·tlemaire on Aug 14 2019, 15:07.

Jul 3 2019

added getClosure to translator. added getConstantsDict function in constants.py
b427c3fd93df
·tlemaire on Jul 3 2019, 01:59.

Jul 1 2019

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 20 2019

added default output directory ("dump"). cleaned up neuron classes.
6c10d4162d71
·tlemaire on Jun 20 2019, 10:09.

Jun 19 2019

corrected error in subset parsing
1a9277e6bbb4
·tlemaire on Jun 19 2019, 15:46.

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_effective_variables.py
3b86ec877351
·tlemaire on Jun 17 2019, 21:13.
defined PlotParser and TimeSeriesParser classes
e3f3982b8981
·tlemaire on Jun 17 2019, 18:52.
replaced plotPhaseDiagram by PhaseDiagram class inheriting from ComparativePlot…
e01fa72e6143
·tlemaire on Jun 17 2019, 17:55.
added custom parsing to generate_mod_file.py
9556faead02c
·tlemaire on Jun 17 2019, 10:52.
replaced no_offset by tbounds in plotting options. added custom parsing to…
75f6032d2f63
·tlemaire on Jun 17 2019, 09:34.

Jun 16 2019

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

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 outputdir option to simQueue methods. added automatic parsing to Parser…
de8bdbc4fee0
·tlemaire on Jun 14 2019, 11:34.

Jun 13 2019

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.

Jun 12 2019

updated all file headers
b42a0de93240
·tlemaire on Jun 12 2019, 23:15.
replaced "neuron" by "pneuron" for all PointNeuron instances
6e017b421f3e
·tlemaire on Jun 12 2019, 12:58.

Jun 10 2019

added functionality to load data directly from sim results in TimeSeriesPlot…
2f0254ea5b53
·tlemaire on Jun 10 2019, 20:52.

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

added getModel and getPointNeuron functions. removed deprecated scripts.
1c9c63d4ba6a
·tlemaire on Jun 6 2019, 18:29.

Jun 3 2019

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.

R4670/PySONIC/parsers.pymastera3951dd16d9c0cf6dfc91ed…

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Jun 3 2019

R4670/PySONIC/parsers.py
mastera3951dd16d9c0cf6dfc91ed…