Diffusion PySONIC (old) (master) History

plt
master7368aa8d62606e57b6ffdbd…

Jun 9 2021

added os_name as logbal variable in utils. now using it also to output LogBatch.
f456a30eea93
·tlemaire on Jun 9 2021, 17:25.

Jun 8 2021

corrected benchmarks plotting and evaluation methods
4f17c4046cf6
·tlemaire on Jun 8 2021, 21:30.

May 31 2021

added benchmark nodecolors and periodicity line patterns
1ee42570341d
·tlemaire on May 31 2021, 18:19.

May 30 2021

corrected XYMap.addInsets to work with out or range insets
aa1ff7ae0ea8
·tlemaire on May 30 2021, 17:55.

May 28 2021

adapted parser for passive lookups
b608770eae52
·tlemaire on May 28 2021, 12:56.

May 27 2021

added factor to Qnorm pltvar.
47f7640b7bcb
·tlemaire on May 27 2021, 20:49.

May 26 2021

replaced computeDiffAreaUnderCurve by computeMeanNormDifference (more robust…
417a3bd45505
·tlemaire on May 26 2021, 18:56.
corrected nan values handling in XYMap.
87ed4cd909be
·tlemaire on May 26 2021, 16:33.
improved FiberBenchmark
fde48404e155
·tlemaire on May 26 2021, 13:44.
added new divmaps module.
02b5fdf9949f
·tlemaire on May 26 2021, 10:36.

May 25 2021

improved naming, access and iterating of DriveArray objects.
c187b85f3573
·tlemaire on May 25 2021, 15:19.

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 30 2020

adjusted benchmark classes
405697583757
·tlemaire on Sep 30 2020, 19:29.

Sep 25 2020

resolved numerical errors on multicomp benchmark (npc = 100, atol = 1e-10)
6b0629b0479c
·tlemaire on Sep 25 2020, 13:10.

Sep 24 2020

added multicomp module
6aa3e623b782
·tlemaire on Sep 24 2020, 20:49.
corrected gamma map
3f27342d2675
·tlemaire on Sep 24 2020, 15:27.

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 4 2020

replaced nbls NEURONS_LOOKUP_DIR by a more general LOOKUP_DIR defined in utils
ed71c4613b28
·tlemaire on Aug 4 2020, 17:57.

Aug 3 2020

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

Jul 24 2020

added tau_pas plotting to plotGatingKinetics
1c0831f723b0
·tlemaire on Jul 24 2020, 11:36.

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.

Jul 15 2020

added LogBatch getSerlializedOutput and getEntryOutput methods.
3998f71a5a6f
·tlemaire on Jul 15 2020, 10:41.

Jun 26 2020

added log scale option for tau axis in plotGatingStates
66f49d8e6545
·tlemaire on Jun 26 2020, 17:39.

Jun 24 2020

added pairwise utils function. added GroupedTimeSeries.shareX static method.
4b2fc8c0eea5
·tlemaire on Jun 24 2020, 11:05.

Jun 3 2020

updated MANIFEST file.
bebce73d9405
·tlemaire on Jun 3 2020, 16:57.

May 7 2020

added strictbounds plotting options
bbb3a4445235
·tlemaire on May 7 2020, 16:19.

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 2 2020

added actmap NaN data post-processing to prevent numpy warning when using log z…
db1a0c16e84b
·tlemaire on May 2 2020, 14:52.

May 1 2020

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

Apr 29 2020

corrected scaling factor in actmap.addThresholdCurve
4e922dc3531c
·tlemaire on Apr 29 2020, 22:55.
corrected queue error in actmap.addTresholdCurve
efb7e6effc92
·tlemaire on Apr 29 2020, 17:09.
corrected DC scaling in actmap.addThresholdCurve
0a9b43830b05
·tlemaire on Apr 29 2020, 16:22.
added mpi feature to actmap threshold curve.
d4087b3210f3
·tlemaire on Apr 29 2020, 14:44.
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.

Apr 21 2020

placed StimObject class in a separate stimobj module. added boltons dependency…
67531a20cdce
·tlemaire on Apr 21 2020, 12:18.

Apr 19 2020

added BalancedPulsedProtocol class.
159f140dcfb0
·tlemaire on Apr 19 2020, 15:03.

Apr 18 2020

corrected units discrepancy in actmap.py
72c8577885a8
·tlemaire on Apr 18 2020, 21:00.
corrected TimSeries.getStimPulses function (no patches for zero states).
a3ca81f69d0a
·tlemaire on Apr 18 2020, 16:14.
corrected drives and protocols inputs.
0d1777407add
·tlemaire on Apr 18 2020, 13:23.

Apr 13 2020

corrected LogBatch class to enable correct use with mpi.
f8511250c9b8
·tlemaire on Apr 13 2020, 18:00.
added better fs handling in actmap
10270ea94712
·tlemaire on Apr 13 2020, 12:33.

Apr 9 2020

added multiprocessing functionality to LogBatch class.
3af9c9df32cc
·tlemaire on Apr 9 2020, 15:53.
corrected ActMap class (now inheriting from LogBatch).
18480eb7bebc
·tlemaire on Apr 9 2020, 14:07.

Apr 5 2020

added eventsON and eventsOFF methods to Protocol classes.
06f8250793a6
·tlemaire on Apr 5 2020, 15:22.

Mar 24 2020

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

Mar 23 2020

added getLogStartPoint to utils
678f3f5e229d
·tlemaire on Mar 23 2020, 21:36.

Mar 21 2020

added x axis sharing in GroupedTimeSeries
84694f9507f6
·tlemaire on Mar 21 2020, 18:51.

Feb 27 2020

added better handling of ybounds in timeseries. added MRG neuron class.
a46f7227e040
·tlemaire on Feb 27 2020, 23:02.

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 26 2020

Modified Lookup class (new properties, corrected methods).
c995e8999df7
·tlemaire on Jan 26 2020, 19:15.
added DQ_LOOKUP constant (used in run_lookups.py)
38dc94d61fe7
·tlemaire on Jan 26 2020, 09:51.

Jan 14 2020

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

Dec 14 2019

removed plotVarQSSDynamics function from QSS and plot_QSS
a0b6724a45a5
·tlemaire on Dec 14 2019, 11:46.

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

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.

Nov 5 2019

corrected error in effvars for plotGatingKinetics
15f0e82253ac
·tlemaire on Nov 5 2019, 17:17.

Oct 10 2019

added Lookup.tile and modified SmartLookup.projectDC. modified nbls.
aee2c4e6cb21
·tlemaire on Oct 10 2019, 16:48.

Oct 1 2019

corrected addThresholdCurve. updated astim_titrations.log with latest batch
06580e30545f
·tlemaire on Oct 1 2019, 00:05.

Sep 30 2019

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

Sep 27 2019

changed TimeSeriesPlot.addLegend from static method to instance method
fedd732d1290
·tlemaire on Sep 27 2019, 13:43.

Sep 13 2019

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

Sep 6 2019

modified find_tpeaks to work with irregular time vectors.
ec87894d9435
·tlemaire on Sep 6 2019, 12:31.

Aug 29 2019

added sweeney lookups (ASTIM not working yet). added fixLookup to remove single…
1b3cffe95e7a
·tlemaire on Aug 29 2019, 10:01.

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.
added plot_intensity_vs_amplitude.py script
1b242e25ca45
·tlemaire on Aug 14 2019, 11:49.

Jul 18 2019

corrected error in getSimThresholdAmps (added default fs to 1)
9ba9ca99a89f
·tlemaire on Jul 18 2019, 21:14.
corrected error in Model logNSpikes, checkTitrate and simAndSave methods.
9e0718eb1a9b
·tlemaire on Jul 18 2019, 20:47.
interoduced derivative function to compute numerical derivatives with various…
5aa12c341577
·tlemaire on Jul 18 2019, 20:02.
improved QSS fixed points color labeling
28c94d579a04
·tlemaire on Jul 18 2019, 12:11.

Jul 17 2019

added saddle point classification to QSS analysis.
ab25e778e32f
·tlemaire on Jul 17 2019, 22:15.

Jul 15 2019

transformed pneuron qsState and quasiSteadyStates methods to return lambda…
f768f01cd891
·tlemaire on Jul 15 2019, 21:40.
re-added file caching for QSS analysis
bed4f4a9de36
·tlemaire on Jul 15 2019, 20:39.
started implementing SonicTranslator.parseSteadyStates method. Implemented…
d50bf6119d40
·tlemaire on Jul 15 2019, 20:22.

Jun 29 2019

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

Jun 27 2019

moved lookup to core module. moved getLookup methods to nbls class.
b73594f4d58b
·tlemaire on Jun 27 2019, 14:34.

Jun 26 2019

changed TimeSeries.getStimPulses to class method
b7e75610c1d2
·tlemaire on Jun 26 2019, 20:03.
added fs (spatially-averaged) as input to nbls model. defined SmartLookup class…
dffee6926b85
·tlemaire on Jun 26 2019, 19:50.

R4670/PySONIC/pltmaster7368aa8d62606e57b6ffdbd…

Jun 9 2021

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R4670/PySONIC/plt
master7368aa8d62606e57b6ffdbd…