Diffusion PySONIC (old) (master) History

R4670/PySONIC
master888fa278603f852d29aed1d…

Jun 20 2021

added full_output option to simAndSave function
888fa278603f
·tlemaire on Jun 20 2021, 16:31.

Jun 19 2021

replaced gamma indications by axvspans in FiberBenchmark.plotQm
2372e0a6dd73
·tlemaire on Jun 19 2021, 14:14.

Jun 18 2021

corrected gamma indicators plotting in FiberBenchmark.plotQm
8b1c341f8737
·tlemaire on Jun 18 2021, 20:34.
added divarea and convarea rendering modes to XYMap.render
fcc7da6f1233
·tlemaire on Jun 18 2021, 18:38.

Jun 17 2021

updated transient divergence evaluation in passive benchmark
41830bd40849
·tlemaire on Jun 17 2021, 18:45.
added XYMap.extrapolate method. modified XYMap.getOutput to return (nx, nz)…
4792bed35eeb
·tlemaire on Jun 17 2021, 13:33.

Jun 16 2021

modified exponential build up assessment in passive benchmark
1e6c565cde54
·tlemaire on Jun 16 2021, 23:08.
removed clip_on statements
d84713700744
·tlemaire on Jun 16 2021, 19:20.
added frac_format function. added inaxes check upon map clicking in XYMap
48840d13cdab
·tlemaire on Jun 16 2021, 19:05.
added getTimeStr function (now used in Batch.run)
7368aa8d6260
·tlemaire on Jun 16 2021, 12:52.

Jun 15 2021

added minimize overlap argument on protocol array initialization
d3109cf80990
·tlemaire on Jun 15 2021, 17:58.
added functionalities to optimize protocol array (minimizing overlap)
a34dc74734dc
·tlemaire on Jun 15 2021, 17:48.
removed print statement in ProtocolArray.plot
92d6fbb787e5
·tlemaire on Jun 15 2021, 14:56.

Jun 14 2021

defined StimObjArray class, niherited by DriveArray and ProtocolArray classes
c811bdc9181b
·tlemaire on Jun 14 2021, 21:47.

Jun 9 2021

modified CustomProtocol string representation, enabled robut protocol summing…
0732d479739d
·tlemaire on Jun 9 2021, 20:56.
added os_name as logbal variable in utils. now using it also to output LogBatch.
f456a30eea93
·tlemaire on Jun 9 2021, 17:25.
implemented addition between time protocols and multiplication by scalar
d660732a8200
·tlemaire on Jun 9 2021, 16:22.
added workaround to coupled_nbls simAndSave method to handle long filepaths on…
41522f45c0c7
·tlemaire on Jun 9 2021, 00:39.

Jun 8 2021

worked on benchmark plotting modularity
82b931897c27
·tlemaire on Jun 8 2021, 22:12.
corrected benchmarks plotting and evaluation methods
4f17c4046cf6
·tlemaire on Jun 8 2021, 21:30.

Jun 7 2021

added special case handling for phi-key in DriveArray
5e1899de25b9
·tlemaire on Jun 7 2021, 23:54.

Jun 6 2021

corrected sundt spike height criterion for detection
1e4c694a74a1
·tlemaire on Jun 6 2021, 15:35.

Jun 5 2021

modified sundt spike detection settings
1a8775592b0c
·tlemaire on Jun 5 2021, 15:32.

Jun 3 2021

added subset argument to FiberBenchmark.runSimsOverAmplitudeSpace in order to…
a182936772ae
·tlemaire on Jun 3 2021, 10:51.

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

updated pandas requirements (now >=1.2.4) to ensure TimeSeries object are…
0a593ebe88fb
·tlemaire on May 28 2021, 17:03.
added new passive lookups at 20kHz and 4MHz
aa3b06ccb8aa
·tlemaire on May 28 2021, 15:40.
added pneuron.is_passive property and getDefaultPassiveNeuron function
3dd0e7ca4b5c
·tlemaire on May 28 2021, 13:41.
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.
added special case handling to find lookups name
143fbd37ca59
·tlemaire on May 27 2021, 09:22.

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

added divergence computation methods to benchmarks
a4d16de1fb6a
·tlemaire on May 25 2021, 21:08.
improved naming, access and iterating of DriveArray objects.
c187b85f3573
·tlemaire on May 25 2021, 15:19.

May 20 2021

modified xscale in benchmark 2D plot
b4ccaf49772d
·tlemaire on May 20 2021, 11:20.

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.
added option to initialize passive neuron from name code. added initFromMeta…
35b4216f3b21
·tlemaire on May 19 2021, 12:22.
added workaround solution for passive generic lookup name
40ac2cbf792f
·tlemaire on May 19 2021, 11:26.

May 18 2021

added resample and interpolate methods to spatiallyextendedtimeseries class
06fa67d560c2
·tlemaire on May 18 2021, 14:58.
added dump and dumpOutputsOtherThan methods to TimeSeries classes
3d60eae04053
·tlemaire on May 18 2021, 14:25.

May 17 2021

added half-cycle offset and interpolation in timeseries cycle averaging
66afa784ef55
·tlemaire on May 17 2021, 22:21.
fixed error in run_lookups (inconsistent redimensioning for test case)
a855f3b52095
·tlemaire on May 17 2021, 21:20.
clarified terms in gamma functions
575ad8b758ee
·tlemaire on May 17 2021, 20:53.
started implementing gamma evaluation method
9b83a80b55f5
·tlemaire on May 17 2021, 20:25.

May 15 2021

started working on coupled_nbls module
23adeab812fd
·tlemaire on May 15 2021, 20:47.

May 14 2021

started working on coupled_nbls module
6aadfe75ac22
·tlemaire on May 14 2021, 19:50.

Mar 26 2021

improved logging in nbls.computeEffVars
5159d5ca1d87
·tlemaire on Mar 26 2021, 20:13.
improved error logging in bls.balancedefQS.
f23057d86a6e
·tlemaire on Mar 26 2021, 20:05.

Mar 23 2021

improved lookup naming system (and renamed all lookups accordingly).
b4233b34e678
·tlemaire on Mar 23 2021, 21:36.
adapted nbls.computeEffVars method to accomodate for Fourier Fourier overtones…
7d732f9d2c25
·tlemaire on Mar 23 2021, 19:10.
added array-typed charge input (i.e. US-periodic profile) option to…
e7842427f677
·tlemaire on Mar 23 2021, 13:46.

Mar 5 2021

corrected Cm lkp extension
cbeb67523b66
·tlemaire on Mar 5 2021, 13:36.

Mar 2 2021

added transition handling in computeTimeStep.
28b9ed25d674
·tlemaire on Mar 2 2021, 15:03.

Feb 11 2021

added stimProfile and plot methods to TimeProtocol class
35b0a5fef28a
·tlemaire on Feb 11 2021, 12:20.

Nov 2 2020

new bls lookups
5f4e38528e1a
·tlemaire on Nov 2 2020, 12:09.

Sep 30 2020

added getPulseTrainProtocol function
9b2552960a06
·tlemaire on Sep 30 2020, 22:35.
adjusted benchmark classes
405697583757
·tlemaire on Sep 30 2020, 19:29.

Sep 25 2020

added SonicBenchmark.phaseplotQnorm method
b89adb5fba58
·tlemaire on Sep 25 2020, 19:54.
removed OldDriveDivergenceMap, added GammaDivergenceMap
3e45a355b863
·tlemaire on Sep 25 2020, 14:43.
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.
added multicomp_benchmark module (cleaned-up version).
190d52832d89
·tlemaire on Sep 24 2020, 18:44.
corrected gamma map
3f27342d2675
·tlemaire on Sep 24 2020, 15:27.

Sep 23 2020

added plot_Zprofiles.py script
fe5b0a532e32
·tlemaire on Sep 23 2020, 12:36.

Sep 15 2020

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

Aug 8 2020

added Lookup.reduce method to compute bls gamma_lkp on-the-fly (removed…
e54883c44689
·tlemaire on Aug 8 2020, 16:35.
added postpro.filtfilt function and plot_Cm_filtering script
a3951dd16d9c
·tlemaire on Aug 8 2020, 15:49.

Aug 6 2020

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

Aug 5 2020

corrected error in bls.logRelGap. Re-computed Cm_lkp
aa8497513a7a
·tlemaire on Aug 5 2020, 21:24.
simplified bls.capacitance expresion
e57b064d8f70
·tlemaire on Aug 5 2020, 20:43.
added FHnode fs lookup at 36 celsius.
bf832e749cbd
·tlemaire on Aug 5 2020, 11:23.

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.
added expandRange docstring
d5c62320c0e3
·tlemaire on Aug 4 2020, 14:05.

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 23 2020

cleaned up BilayerSonophore.getPltVars
ac56c3baa94e
·tlemaire on Jul 23 2020, 11:17.

Jul 22 2020

removed call to unstable iax in pltvars['iax'] definition
aaeaaeac3732
·tlemaire on Jul 22 2020, 16:45.
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.
specified logger handler stream to sys.stdout to avoid red background in…
fd4b6531e872
·tlemaire on Jul 21 2020, 20:03.
introduced default celsius (36°C) as a PointNeuron property shared by all…
42a3be29b47b
·tlemaire on Jul 21 2020, 16:18.
added celsius parameter (36.0) to cortical and thalamic neurons.
133be2f739dd
·tlemaire on Jul 21 2020, 15:41.
added HH point neuron
4884f5695b3e
·tlemaire on Jul 21 2020, 15:28.

Jul 20 2020

corrected gaussian formula so that sigma matches definition of standard…
de400ab21db3
·tlemaire on Jul 20 2020, 21:30.

Jul 15 2020

removed SilentMRGNode class (now generated on-the-fly in analysis notebook)
c9894bdbd61c
·tlemaire on Jul 15 2020, 21:24.
implemented passiveNeuron wrapper function to generate PassiveNeuron class…
a8ba89d095f5
·tlemaire on Jul 15 2020, 12:18.
added LogBatch getSerlializedOutput and getEntryOutput methods.
3998f71a5a6f
·tlemaire on Jul 15 2020, 10:41.

Jul 3 2020

added pneuron.tau_pas property
095a41517e86
·tlemaire on Jul 3 2020, 11:22.

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 4 2020

corrected Lookup and TimeSeries division operators.
64ec46ae1392
·tlemaire on Jun 4 2020, 22:07.

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.

R4670/PySONICmaster888fa278603f852d29aed1d…

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R4670/PySONIC
master888fa278603f852d29aed1d…