Diffusion PySONIC (old) (master) History

History
masterf23057d86a6e782c5cc760d…

Mar 26 2021

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 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.

Historymasterf23057d86a6e782c5cc760d…

Mar 26 2021

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History
masterf23057d86a6e782c5cc760d…