History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
e54883c44689 | tlemaire | added Lookup.reduce method to compute bls gamma_lkp on-the-fly (removed… | Aug 8 2020 | |||
aa8497513a7a | tlemaire | corrected error in bls.logRelGap. Re-computed Cm_lkp | Aug 5 2020 | |||
e57b064d8f70 | tlemaire | simplified bls.capacitance expresion | Aug 5 2020 | |||
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 | |||
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 | |||
42a3be29b47b | tlemaire | introduced default celsius (36°C) as a PointNeuron property shared by all… | Jul 21 2020 | |||
4884f5695b3e | tlemaire | added HH point neuron | Jul 21 2020 | |||
c9894bdbd61c | tlemaire | removed SilentMRGNode class (now generated on-the-fly in analysis notebook) | Jul 15 2020 | |||
3998f71a5a6f | tlemaire | added LogBatch getSerlializedOutput and getEntryOutput methods. | Jul 15 2020 | |||
095a41517e86 | tlemaire | added pneuron.tau_pas property | Jul 3 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 | |||
9b03fd5152c2 | tlemaire | corrected DrivenNeuronalBilayerSonophore.inputs | May 2 2020 | |||
e1f537dcc076 | tlemaire | corrected error in solve_ivp call. | May 2 2020 | |||
430d7c8131f0 | tlemaire | new astim titrations for figure 8 | May 2 2020 | |||
c8cdcf5deefc | tlemaire | added new titrations | 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 | |||
524072855745 | tlemaire | defined Thresholder class for a clearer threshold search implementation. | Apr 29 2020 | |||
1dd1b969d0e2 | tlemaire | added RS 10Hz titrations. | 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 | |||
a6e6abff99bc | tlemaire | added TC2 class | Apr 23 2020 | |||
9342c4bfcbda | tlemaire | additional bls lookups | Apr 22 2020 | |||
67531a20cdce | tlemaire | placed StimObject class in a separate stimobj module. added boltons dependency… | Apr 21 2020 | |||
159f140dcfb0 | tlemaire | added BalancedPulsedProtocol class. | Apr 19 2020 | |||
108548aa8cc8 | tlemaire | added max_nsamples parameter to effective solver to avoid memory allocation… | 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 | |||
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 | |||
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 | |||
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 | |||
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 | |||
8f0bbde630a7 | tlemaire | renamed fibers point-neuron models for better interpretability. completed fiber… | Mar 27 2020 | |||
a43249c6ecf1 | tlemaire | tested MRG lookups generation | Mar 26 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 | |||
165caa8bf488 | tlemaire | moved getMeta to utils | Feb 20 2020 | |||
7f8a3be5ceb4 | tlemaire | changed meta property of model classes to return solely model information. | Feb 20 2020 | |||
b7d520b9ed42 | tlemaire | added LogBatch class | Feb 18 2020 | |||
31cc2d15993a | tlemaire | updated README (added instructions for git-lfs install) | Feb 14 2020 | |||
68961385d17e | tlemaire | added copy method to all model classes. added TI US notebook. updated… | Feb 11 2020 | |||
96d3c580ee81 | tlemaire | replaced erroneous "return NotImplementedError" statements by "raise… | Feb 5 2020 | |||
8907f78b742a | tlemaire | correctd mismatch in ElectricDrive | Feb 5 2020 | |||
892f924d6e9e | tlemaire | renamed ElectricDrive A to I | Feb 5 2020 | |||
31ef6228207a | tlemaire | introduced properties in classes of drives and protocols modules. | Feb 5 2020 | |||
073e28b388f6 | tlemaire | added xkey property to XDrive class and Arange property to pneuron and nbls… | Feb 3 2020 | |||
27d8aafffa88 | tlemaire | Created Drive objects inheritance scheme (now used in all model classes). | Feb 3 2020 | |||
dba63f835a31 | tlemaire | corrected docstring errors in pneuron Cm0 and Qm0 | Feb 3 2020 | |||
062e541857dc | tlemaire | added lookups files in separate lookups folder using LFS. | Feb 3 2020 | |||
9d0666784d2d | tlemaire | Created AcousticSource class to be used for US simulations. | Feb 3 2020 | |||
eec847e65a7a | tlemaire | added sundt fs lookups. adapted RS fs lookups. adapted nbls.getLookup2D method… | Jan 26 2020 | |||
6846298198d4 | tlemaire | added interp_method Lookup attribute to enable choice of lookup interpolation… | Jan 26 2020 | |||
c995e8999df7 | tlemaire | Modified Lookup class (new properties, corrected methods). | Jan 26 2020 | |||
38dc94d61fe7 | tlemaire | added DQ_LOOKUP constant (used in run_lookups.py) | Jan 26 2020 | |||
1919e3105ee4 | tlemaire | added toDict, toJson, fromDict and fromJson methods to Lookup class. | Jan 23 2020 | |||
f4ea3f48765e | vicari | Merge completed | Jan 22 2020 | |||
e4f4732ffbab | vicari | Extra entry in bls lookup | Jan 22 2020 | |||
8478fde7a5d4 | tlemaire | Automated getModel using automatically generated dictionary of models with… | Jan 14 2020 | |||
a0b6724a45a5 | tlemaire | removed plotVarQSSDynamics function from QSS and plot_QSS | Dec 14 2019 | |||
d0b57c5e137d | tlemaire | re-ran and completed STN notebook | Dec 6 2019 | |||
bac984960467 | tlemaire | corrected nbls fullDerivatives, simFull and simHybrid methods (removed phi… | Dec 4 2019 | |||
a29eea02e330 | tlemaire | changed Lookup repr method. added test_lkp test file. | Dec 4 2019 | |||
f8107574d0a8 | tlemaire | added threshold module with isolated threshold function (now used for all… | Dec 2 2019 | |||
6deb0da8868d | tlemaire | added internal bls.simUntilConvergence method (without decorators) to enable… | Nov 26 2019 | |||
b46ab57b16d3 | tlemaire | corrected borg-graham formalism methods | Nov 22 2019 | |||
6197f85f0709 | tlemaire | corrected Astim factor error in pneuron desc. added extra parsing methods | Nov 20 2019 | |||
456fa71d226b | tlemaire | added qss_vars and pulse-avg run options to nbls simSonic method. | Nov 20 2019 | |||
681033068b15 | tlemaire | updated titrations log | Nov 15 2019 | |||
5da540f0f401 | tlemaire | moved model.simAndSave to utils to facilitate use in ExSONIC | Nov 14 2019 | |||
36119dd01aec | tlemaire | moved filecode function to utils | Nov 14 2019 |
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