Diffusion PySONIC (old) (master) History

History
master7d732f9d2c25403f1843225…

Mar 23 2021

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 18 2021

small corrections in demo notebook
215b15082b72
·tlemaire on Mar 18 2021, 15:01.

Mar 16 2021

updated setup file. corrected some imports in notebooks (AcousticSource ->…
1b7cf6045963
·tlemaire on Mar 16 2021, 18:32.

Mar 5 2021

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

Mar 3 2021

added emphasis on git-lfs requirement in REAMDE.
0df71d46a8b6
·tlemaire on Mar 3 2021, 15:50.

Mar 2 2021

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

Feb 11 2021

updated pandas requirements in setup.py
573f1807c8e3
·tlemaire on Feb 11 2021, 12:42.
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 18 2020

updated README.
ef08cb208ad1
·tlemaire on May 18 2020, 15:22.

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

corrected DrivenNeuronalBilayerSonophore.inputs
9b03fd5152c2
·tlemaire on May 2 2020, 17:17.
corrected error in solve_ivp call.
e1f537dcc076
·tlemaire on May 2 2020, 17:11.
added actmap NaN data post-processing to prevent numpy warning when using log z…
db1a0c16e84b
·tlemaire on May 2 2020, 14:52.
new astim titrations for figure 8
430d7c8131f0
·tlemaire on May 2 2020, 12:07.

May 1 2020

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic
6d2bc897725d
·tlemaire on May 1 2020, 22:47.
added new titrations
c8cdcf5deefc
·tlemaire on May 1 2020, 22:47.
corrected ComparativePlot and CompTimeSeries to enable taking generators as…
bd7a6ec5a477
·tlemaire on May 1 2020, 22:44.
new figure 7 titrations for high PRF low DC
5742df202a16
·tlemaire on May 1 2020, 20:24.
applied correction to ODESolver.getNsamples to make sure there are at least 2…
fa9c541d7842
·tlemaire on May 1 2020, 19:27.
new figure 7 titrations
28d338972b7c
·tlemaire on May 1 2020, 18:36.

Apr 30 2020

added new astim titrations
74c7618b792a
·tlemaire on Apr 30 2020, 16:46.
added progress bar logging to nbls.simFull at INFO level.
835803fa8d6b
·tlemaire on Apr 30 2020, 13:26.

Apr 29 2020

corrected scaling factor in actmap.addThresholdCurve
4e922dc3531c
·tlemaire on Apr 29 2020, 22:55.
defined Thresholder class for a clearer threshold search implementation.
524072855745
·tlemaire on Apr 29 2020, 22:52.
added RS 10Hz titrations.
1dd1b969d0e2
·tlemaire on Apr 29 2020, 17:57.
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 26 2020

modified BurstProtocol default BRF such that BRI is twice burst time.
2eb3a3768e1e
·tlemaire on Apr 26 2020, 19:22.
corrected simobj.check methods (incorrect paramStr call). added BRF pre-check…
fab05bc88fea
·tlemaire on Apr 26 2020, 19:10.

Apr 24 2020

added baseline_modulation example script
20183f45302e
·tlemaire on Apr 24 2020, 11:22.
added optional tstart argument to PusledProtocol classes. corrected…
6dedc53ccbc8
·tlemaire on Apr 24 2020, 11:04.

Apr 23 2020

added TCtweak70 and TCtweak50 cases.
5b268a756bc5
·tlemaire on Apr 23 2020, 12:41.
added TC2 class
a6e6abff99bc
·tlemaire on Apr 23 2020, 12:06.

Apr 22 2020

introduced lambda function for test.execute calls
93d5100bbbce
·tlemaire on Apr 22 2020, 15:13.
additional bls lookups
9342c4bfcbda
·tlemaire on Apr 22 2020, 12:56.

Apr 21 2020

defined friendlyLogspace function
7f1709df1d92
·tlemaire on Apr 21 2020, 21:01.
placed StimObject class in a separate stimobj module. added boltons dependency…
67531a20cdce
·tlemaire on Apr 21 2020, 12:18.

Apr 19 2020

added TC lookup 80 nm 590 kHz
2a0fec5672f0
·tlemaire on Apr 19 2020, 16:40.
added few utils functions
b7a48187478a
·tlemaire on Apr 19 2020, 16:37.
added BalancedPulsedProtocol class.
159f140dcfb0
·tlemaire on Apr 19 2020, 15:03.
added 48 nm TC lookups
7fdbe8544e52
·tlemaire on Apr 19 2020, 11:53.

Apr 18 2020

added max_nsamples parameter to effective solver to avoid memory allocation…
108548aa8cc8
·tlemaire on Apr 18 2020, 21:25.
added more TC lookups.
a72a071b87d0
·tlemaire on Apr 18 2020, 21:03.
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.
updated README
83d7d8df16fa
·tlemaire on Apr 18 2020, 15:52.
defined protocols copy methods.
00f6aa560a10
·tlemaire on Apr 18 2020, 15:10.
corrected drives and protocols inputs.
0d1777407add
·tlemaire on Apr 18 2020, 13:23.

Apr 17 2020

simplified drives and protocols
241946f34fa2
·tlemaire on Apr 17 2020, 23:28.
updated inputs precision in protocols
5e4003f785f9
·tlemaire on Apr 17 2020, 20:48.
updated README
b80a24a22518
·tlemaire on Apr 17 2020, 20:46.
cleand-up run_astim.py
5fe7fba7ad8c
·tlemaire on Apr 17 2020, 20:25.
added 64nm 590 kHz fs-dependent TC lookup
420b1c0ceb3e
·tlemaire on Apr 17 2020, 20:18.
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.
added update interval argument to HybridSolve.solve method.
e62423f9469d
·tlemaire on Apr 17 2020, 15:27.

Historymaster7d732f9d2c25403f1843225…

Mar 23 2021

Mar 18 2021

Mar 16 2021

Mar 5 2021

Mar 3 2021

Mar 2 2021

Feb 11 2021

Nov 2 2020

Sep 30 2020

Sep 25 2020

Sep 24 2020

Sep 23 2020

Sep 15 2020

Aug 8 2020

Aug 6 2020

Aug 5 2020

Aug 4 2020

Aug 3 2020

Jul 24 2020

Jul 23 2020

Jul 22 2020

Jul 21 2020

Jul 20 2020

Jul 15 2020

Jul 3 2020

Jun 26 2020

Jun 24 2020

Jun 4 2020

Jun 3 2020

May 18 2020

May 7 2020

May 5 2020

May 4 2020

May 2 2020

May 1 2020

Apr 30 2020

Apr 29 2020

Apr 28 2020

Apr 26 2020

Apr 24 2020

Apr 23 2020

Apr 22 2020

Apr 21 2020

Apr 19 2020

Apr 18 2020

Apr 17 2020

History
master7d732f9d2c25403f1843225…