Diffusion PySONIC (old) (master) History

R4670/PySONIC/plt/pltutils.py
masterd84713700744eb12dbe4c2c…

Jun 16 2021

removed clip_on statements
d84713700744
·tlemaire on Jun 16 2021, 19:20.

May 26 2021

improved FiberBenchmark
fde48404e155
·tlemaire on May 26 2021, 13:44.

May 19 2021

modified coupled_nbls.simAndSave to just simulate if no output directory is…
41fde2c39385
·tlemaire on May 19 2021, 22:07.
added plot utility functions
f4282fb16d90
·tlemaire on May 19 2021, 16:55.

Sep 15 2020

latest changes for morphoSONIC paper
bb9f2c79c74a
·tlemaire on Sep 15 2020, 12:24.

Aug 6 2020

added mirrorProp and mirrorAxis functions to pltutils.
0526b07ebff9
·tlemaire on Aug 6 2020, 17:56.

Aug 3 2020

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

Jul 22 2020

corrected PointNeuron dQdt method (now calculating charge derviative by finite…
0d4af61c20f7
·tlemaire on Jul 22 2020, 11:02.

Jul 21 2020

added symmetric colormaps and corrected ComparativePlot cbar levels for int…
d4364da996c8
·tlemaire on Jul 21 2020, 22:13.

May 5 2020

corrected index offset error in GenericPlot.addCmap
0c7bff925bd5
·tlemaire on May 5 2020, 14:40.

May 4 2020

added extractCommonPrefix utils function.
2c0253a46427
·tlemaire on May 4 2020, 12:34.

May 1 2020

corrected ComparativePlot and CompTimeSeries to enable taking generators as…
bd7a6ec5a477
·tlemaire on May 1 2020, 22:44.

Apr 29 2020

changed bls.inputs['a'] (factor 0, unit m).
81fe27f05196
·tlemaire on Apr 29 2020, 12:35.

Apr 28 2020

added input-ouput match pre-check in LogBatch.run method to avoid unnecessary…
fcb5a387a33e
·tlemaire on Apr 28 2020, 21:21.

Mar 24 2020

added addExcitationInset to pltutils
cf163f8c94cb
·tlemaire on Mar 24 2020, 15:51.

Feb 5 2020

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 14 2020

Automated getModel using automatically generated dictionary of models with…
8478fde7a5d4
·tlemaire on Jan 14 2020, 17:18.

Nov 20 2019

corrected Astim factor error in pneuron desc. added extra parsing methods
6197f85f0709
·tlemaire on Nov 20 2019, 22:24.

Nov 15 2019

implemented GenericPlot.wraptitle method
d14a124a4078
·tlemaire on Nov 15 2019, 16:46.

Nov 14 2019

moved model.simAndSave to utils to facilitate use in ExSONIC
5da540f0f401
·tlemaire on Nov 14 2019, 19:42.
moved filecode function to utils
36119dd01aec
·tlemaire on Nov 14 2019, 18:06.
Major update:
de255e65bccc
·tlemaire on Nov 14 2019, 16:39.
added equality operators to TimeProtocol and PulsedProtocol classes.
a26469ca67dc
·tlemaire on Nov 14 2019, 11:37.

Nov 13 2019

improved filecodes generation from meta dictionary in Model.filecode
4a5626da478c
·tlemaire on Nov 13 2019, 19:43.
created Timeprotocol and PulsedProtocol classes, now used in pneuron, nbls and…
bc1800471252
·tlemaire on Nov 13 2019, 18:11.

Nov 6 2019

modified nbls.QSSderivatives and nbls.__simQSS to work with any specified…
a2c1e3e2eb02
·tlemaire on Nov 6 2019, 15:46.

Sep 30 2019

updated ActivationMap (removed correctAmp method). corrected TimeSeriesPlot.
21401e741886
·tlemaire on Sep 30 2019, 19:48.

Aug 24 2019

corrected minor mistake in getCommonLabel
4821f3c94b73
·tlemaire on Aug 24 2019, 22:03.
added getCommonLabel method to ComparativePlot (now used to determine figure…
fdf57ea352bd
·tlemaire on Aug 24 2019, 22:00.

Aug 22 2019

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

Aug 19 2019

removed paper figures folder (now in separate repo)
3c76710406c6
·tlemaire on Aug 19 2019, 09:56.

Aug 16 2019

added figtitle and getModel as GenericPlot methods
0d24b201dea4
·tlemaire on Aug 16 2019, 20:09.

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.
corrected minor issues in timeseries
523f8865bde3
·tlemaire on Aug 14 2019, 15:58.
added VoltageClamp class with associated script and parser
366c7e528105
·tlemaire on Aug 14 2019, 15:07.

Jul 18 2019

corrected error in Model logNSpikes, checkTitrate and simAndSave methods.
9e0718eb1a9b
·tlemaire on Jul 18 2019, 20:47.

Jun 29 2019

adapted methods of all classes into classmethods and staticmethods when…
4937955d0214
·tlemaire on Jun 29 2019, 20:27.

Jun 26 2019

added fs (spatially-averaged) as input to nbls model. defined SmartLookup class…
dffee6926b85
·tlemaire on Jun 26 2019, 19:50.

Jun 25 2019

improved steadyStates definition in TC and STN neurons. corrected dQdt pltvar…
9965ddc0005d
·tlemaire on Jun 25 2019, 23:21.

Jun 19 2019

cleaned up neuron classes. redefined currents to return functions instead of…
26fe1e08a408
·tlemaire on Jun 19 2019, 11:05.

Jun 17 2019

adde prettify option to timeseries plots
1465c48312a6
·tlemaire on Jun 17 2019, 20:43.
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.
replaced no_offset by tbounds in plotting options. added custom parsing to…
75f6032d2f63
·tlemaire on Jun 17 2019, 09:34.

Jun 16 2019

added firing rate to plot variables
b461503582fb
·tlemaire on Jun 16 2019, 13:05.

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.
replaced "neuron" by "pneuron" for all PointNeuron instances
6e017b421f3e
·tlemaire on Jun 12 2019, 12:58.

Jun 6 2019

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

May 10 2019

major improvements to QSS module
7a27b761d220
·Theo Lemaire on May 10 2019, 18:09.

Mar 26 2019

implemented new QSS plot module with generic plotVarDynamics, plotVarsQSS and…
a2726a130bec
·tlemaire on Mar 26 2019, 19:35.

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

removed old pltvars dictionary.
895dbbeb52ae
·tlemaire on Mar 15 2019, 01:32.
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.

Sep 26 2018

removed pltutils file
7075d3ab7f91
·tlemaire on Sep 26 2018, 17:26.
added actmap to plt module, with command line script.
4a67049acd76
·tlemaire on Sep 26 2018, 17:06.

Sep 25 2018

moved plotComp and plotBatch functions to separate files. created unique plot…
a35c13583071
·tlemaire on Sep 25 2018, 17:25.
cleaned up utils module. removed log templates (now generated on the fly with…
610dc8472dcf
·tlemaire on Sep 25 2018, 14:46.

Sep 24 2018

turned intermolecular pressure test script into notebook. removed Input error…
954e545fa6ac
·tlemaire on Sep 24 2018, 23:54.
moved relevant plot scripts to scripts folder. Turned analysis scripts into…
4d53b2a42b5e
·tlemaire on Sep 24 2018, 21:00.

Sep 23 2018

major changes to the package (PointNeuron, SonicNeuron, ...)
2a334b211bff
·tlemaire on Sep 23 2018, 14:28.

Sep 14 2018

removed use of itrpLookupsFreq by simple scipy.interp1d call
66e78783dda3
·tlemaire on Sep 14 2018, 17:32.

Aug 30 2018

added sequential color mode to plotSignals. updated REDAME.md
eb527762650d
·tlemaire on Aug 30 2018, 20:10.

Aug 28 2018

added integer conversion for frequency checking in itrpLoouksFreq. corrected…
23060daa6da3
·tlemaire on Aug 28 2018, 15:40.

Aug 22 2018

added plotSignals function to pltutils.
50542c086cc4
·tlemaire on Aug 22 2018, 02:39.

Aug 21 2018

changed package name to PySONIC.
043172721a44
·tlemaire on Aug 21 2018, 16:19.