R4670/PySONICmaster
R4670/PySONIC
master
History Graph
History Graph
Commit | Author | Details | Committed | |||
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ed71c4613b28 | tlemaire | replaced nbls NEURONS_LOOKUP_DIR by a more general LOOKUP_DIR defined in utils | Aug 4 2020 | |||
d5c62320c0e3 | tlemaire | added expandRange docstring | Aug 4 2020 | |||
52e16ec74047 | tlemaire | added nmin parameter to PeriodicSolver.solve and BilayerSonophore.simCycles. | Aug 3 2020 | |||
1c0831f723b0 | tlemaire | added tau_pas plotting to plotGatingKinetics | Jul 24 2020 | |||
ac56c3baa94e | tlemaire | cleaned up BilayerSonophore.getPltVars | Jul 23 2020 | |||
aaeaaeac3732 | tlemaire | removed call to unstable iax in pltvars['iax'] definition | Jul 22 2020 | |||
0d4af61c20f7 | tlemaire | corrected PointNeuron dQdt method (now calculating charge derviative by finite… | Jul 22 2020 | |||
d4364da996c8 | tlemaire | added symmetric colormaps and corrected ComparativePlot cbar levels for int… | Jul 21 2020 | |||
fd4b6531e872 | tlemaire | specified logger handler stream to sys.stdout to avoid red background in… | Jul 21 2020 | |||
42a3be29b47b | tlemaire | introduced default celsius (36°C) as a PointNeuron property shared by all… | Jul 21 2020 | |||
133be2f739dd | tlemaire | added celsius parameter (36.0) to cortical and thalamic neurons. | Jul 21 2020 | |||
4884f5695b3e | tlemaire | added HH point neuron | Jul 21 2020 | |||
de400ab21db3 | tlemaire | corrected gaussian formula so that sigma matches definition of standard… | Jul 20 2020 | |||
c9894bdbd61c | tlemaire | removed SilentMRGNode class (now generated on-the-fly in analysis notebook) | Jul 15 2020 | |||
a8ba89d095f5 | tlemaire | implemented passiveNeuron wrapper function to generate PassiveNeuron class… | Jul 15 2020 | |||
3998f71a5a6f | tlemaire | added LogBatch getSerlializedOutput and getEntryOutput methods. | Jul 15 2020 | |||
095a41517e86 | tlemaire | added pneuron.tau_pas property | Jul 3 2020 | |||
66f49d8e6545 | tlemaire | added log scale option for tau axis in plotGatingStates | Jun 26 2020 | |||
4b2fc8c0eea5 | tlemaire | added pairwise utils function. added GroupedTimeSeries.shareX static method. | Jun 24 2020 | |||
64ec46ae1392 | tlemaire | corrected Lookup and TimeSeries division operators. | Jun 4 2020 | |||
bebce73d9405 | tlemaire | updated MANIFEST file. | Jun 3 2020 | |||
bbb3a4445235 | tlemaire | added strictbounds plotting options | May 7 2020 | |||
0c7bff925bd5 | tlemaire | corrected index offset error in GenericPlot.addCmap | May 5 2020 | |||
2c0253a46427 | tlemaire | added extractCommonPrefix utils function. | May 4 2020 | |||
9b03fd5152c2 | tlemaire | corrected DrivenNeuronalBilayerSonophore.inputs | May 2 2020 | |||
e1f537dcc076 | tlemaire | corrected error in solve_ivp call. | May 2 2020 | |||
db1a0c16e84b | tlemaire | added actmap NaN data post-processing to prevent numpy warning when using log z… | May 2 2020 | |||
430d7c8131f0 | tlemaire | new astim titrations for figure 8 | May 2 2020 | |||
6d2bc897725d | tlemaire | Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic | May 1 2020 | |||
c8cdcf5deefc | tlemaire | added new titrations | May 1 2020 | |||
bd7a6ec5a477 | tlemaire | corrected ComparativePlot and CompTimeSeries to enable taking generators as… | May 1 2020 | |||
5742df202a16 | tlemaire | new figure 7 titrations for high PRF low DC | May 1 2020 | |||
fa9c541d7842 | tlemaire | applied correction to ODESolver.getNsamples to make sure there are at least 2… | May 1 2020 | |||
28d338972b7c | tlemaire | new figure 7 titrations | May 1 2020 | |||
74c7618b792a | tlemaire | added new astim titrations | Apr 30 2020 | |||
835803fa8d6b | tlemaire | added progress bar logging to nbls.simFull at INFO level. | Apr 30 2020 | |||
4e922dc3531c | tlemaire | corrected scaling factor in actmap.addThresholdCurve | Apr 29 2020 | |||
524072855745 | tlemaire | defined Thresholder class for a clearer threshold search implementation. | Apr 29 2020 | |||
1dd1b969d0e2 | tlemaire | added RS 10Hz titrations. | Apr 29 2020 | |||
efb7e6effc92 | tlemaire | corrected queue error in actmap.addTresholdCurve | Apr 29 2020 | |||
0a9b43830b05 | tlemaire | corrected DC scaling in actmap.addThresholdCurve | Apr 29 2020 | |||
d4087b3210f3 | tlemaire | added mpi feature to actmap threshold curve. | Apr 29 2020 | |||
81fe27f05196 | tlemaire | changed bls.inputs['a'] (factor 0, unit m). | Apr 29 2020 | |||
fcb5a387a33e | tlemaire | added input-ouput match pre-check in LogBatch.run method to avoid unnecessary… | Apr 28 2020 | |||
2eb3a3768e1e | tlemaire | modified BurstProtocol default BRF such that BRI is twice burst time. | Apr 26 2020 | |||
fab05bc88fea | tlemaire | corrected simobj.check methods (incorrect paramStr call). added BRF pre-check… | Apr 26 2020 | |||
6dedc53ccbc8 | tlemaire | added optional tstart argument to PusledProtocol classes. corrected… | Apr 24 2020 | |||
5b268a756bc5 | tlemaire | added TCtweak70 and TCtweak50 cases. | Apr 23 2020 | |||
a6e6abff99bc | tlemaire | added TC2 class | Apr 23 2020 | |||
93d5100bbbce | tlemaire | introduced lambda function for test.execute calls | Apr 22 2020 | |||
9342c4bfcbda | tlemaire | additional bls lookups | Apr 22 2020 | |||
7f1709df1d92 | tlemaire | defined friendlyLogspace function | Apr 21 2020 | |||
67531a20cdce | tlemaire | placed StimObject class in a separate stimobj module. added boltons dependency… | Apr 21 2020 | |||
2a0fec5672f0 | tlemaire | added TC lookup 80 nm 590 kHz | Apr 19 2020 | |||
b7a48187478a | tlemaire | added few utils functions | Apr 19 2020 | |||
159f140dcfb0 | tlemaire | added BalancedPulsedProtocol class. | Apr 19 2020 | |||
7fdbe8544e52 | tlemaire | added 48 nm TC lookups | Apr 19 2020 | |||
108548aa8cc8 | tlemaire | added max_nsamples parameter to effective solver to avoid memory allocation… | Apr 18 2020 | |||
a72a071b87d0 | tlemaire | added more TC lookups. | Apr 18 2020 | |||
72c8577885a8 | tlemaire | corrected units discrepancy in actmap.py | Apr 18 2020 | |||
a3ca81f69d0a | tlemaire | corrected TimSeries.getStimPulses function (no patches for zero states). | Apr 18 2020 | |||
00f6aa560a10 | tlemaire | defined protocols copy methods. | Apr 18 2020 | |||
0d1777407add | tlemaire | corrected drives and protocols inputs. | Apr 18 2020 | |||
241946f34fa2 | tlemaire | simplified drives and protocols | Apr 17 2020 | |||
5e4003f785f9 | tlemaire | updated inputs precision in protocols | Apr 17 2020 | |||
420b1c0ceb3e | tlemaire | added 64nm 590 kHz fs-dependent TC lookup | Apr 17 2020 | |||
6895a19a147f | tlemaire | implemented simQueueBurst method in pneuron and nbls classes. | Apr 17 2020 | |||
e3ca275ebe0f | tlemaire | harmonized repr, desc and filecodes methods across protocols. | Apr 17 2020 | |||
e62423f9469d | tlemaire | added update interval argument to HybridSolve.solve method. | Apr 17 2020 | |||
e775528e1afc | tlemaire | cleaned-up find_tpeaks function | Apr 17 2020 | |||
447a9236fa20 | tlemaire | corrected error in computeFRProfile when no spikes are detected. | Apr 17 2020 | |||
69892d75c503 | tlemaire | improved solvers docstrings and clarified their use in model classes. | Apr 16 2020 | |||
81c3d55cddff | tlemaire | added 2 MHz 32nm TC lookup. | Apr 15 2020 | |||
d03caf415e89 | tlemaire | removed ambiguity around initialConditions methods to allow correct lookups… | Apr 15 2020 | |||
b77cd9e4eb12 | tlemaire | implemented better solvers (now inside solvers module), including an… | Apr 15 2020 | |||
7ae0b7961ae4 | tlemaire | added TC fs lookup at 1 MHz. | Apr 13 2020 | |||
b44cc93c9915 | tlemaire | replaced "Ascale" parsing options by "yscale" for more clarity. | Apr 13 2020 | |||
f8511250c9b8 | tlemaire | corrected LogBatch class to enable correct use with mpi. | Apr 13 2020 | |||
10270ea94712 | tlemaire | added better fs handling in actmap | Apr 13 2020 | |||
a8ffc4cf6311 | tlemaire | removed useless error instance catch in utils | Apr 10 2020 | |||
3af9c9df32cc | tlemaire | added multiprocessing functionality to LogBatch class. | Apr 9 2020 | |||
18480eb7bebc | tlemaire | corrected ActMap class (now inheriting from LogBatch). | Apr 9 2020 | |||
63ef9868bbd2 | tlemaire | added TimeProtocol.stimEvents method (used in NEURON simulations). | Apr 5 2020 | |||
06f8250793a6 | tlemaire | added eventsON and eventsOFF methods to Protocol classes. | Apr 5 2020 | |||
cc5348bc40ca | tlemaire | added __eq__ methods to pneuron and nbls classes | Apr 3 2020 | |||
9239911c1f35 | tlemaire | added ASTIM_REL_CONV_THR to constants file. | Mar 31 2020 | |||
9dcd3884ae33 | tlemaire | added TC fs lookup. | Mar 30 2020 | |||
4e96a816343e | tlemaire | added MRG fs lookup. | Mar 30 2020 | |||
8a68be82c2d8 | tlemaire | added MRG lookup. | Mar 27 2020 | |||
8f0bbde630a7 | tlemaire | renamed fibers point-neuron models for better interpretability. completed fiber… | Mar 27 2020 | |||
a43249c6ecf1 | tlemaire | tested MRG lookups generation | Mar 26 2020 | |||
a4eafd9f8059 | tlemaire | corrected typo in SweeneyNode description. | Mar 26 2020 | |||
cf163f8c94cb | tlemaire | added addExcitationInset to pltutils | Mar 24 2020 | |||
678f3f5e229d | tlemaire | added getLogStartPoint to utils | Mar 23 2020 | |||
84694f9507f6 | tlemaire | added x axis sharing in GroupedTimeSeries | Mar 21 2020 | |||
066e8e416305 | tlemaire | added polyfit amd extrapolate capabilities to Lookup class. | Mar 19 2020 | |||
8f4b9911c0d3 | tlemaire | Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic | Feb 28 2020 | |||
c8a9ea2beb92 | tlemaire | added extra functionalities to Lookup class. continued fiber nodes notebook. | Feb 28 2020 | |||
7d61ef15bd3b | vicari | Merge solved | Feb 28 2020 | |||
be6c868e4e5f | vicari | Correction in drives | Feb 28 2020 |
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