History Graph
History Graph
Commit | Author | Details | Committed | |||
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d3109cf80990 | tlemaire | added minimize overlap argument on protocol array initialization | Jun 15 2021 | |||
a34dc74734dc | tlemaire | added functionalities to optimize protocol array (minimizing overlap) | Jun 15 2021 | |||
92d6fbb787e5 | tlemaire | removed print statement in ProtocolArray.plot | Jun 15 2021 | |||
c811bdc9181b | tlemaire | defined StimObjArray class, niherited by DriveArray and ProtocolArray classes | Jun 14 2021 | |||
0732d479739d | tlemaire | modified CustomProtocol string representation, enabled robut protocol summing… | Jun 9 2021 | |||
f456a30eea93 | tlemaire | added os_name as logbal variable in utils. now using it also to output LogBatch. | Jun 9 2021 | |||
d660732a8200 | tlemaire | implemented addition between time protocols and multiplication by scalar | Jun 9 2021 | |||
4f17c4046cf6 | tlemaire | corrected benchmarks plotting and evaluation methods | Jun 8 2021 | |||
5e1899de25b9 | tlemaire | added special case handling for phi-key in DriveArray | Jun 7 2021 | |||
0a593ebe88fb | tlemaire | updated pandas requirements (now >=1.2.4) to ensure TimeSeries object are… | May 28 2021 | |||
3dd0e7ca4b5c | tlemaire | added pneuron.is_passive property and getDefaultPassiveNeuron function | May 28 2021 | |||
47f7640b7bcb | tlemaire | added factor to Qnorm pltvar. | May 27 2021 | |||
143fbd37ca59 | tlemaire | added special case handling to find lookups name | May 27 2021 | |||
417a3bd45505 | tlemaire | replaced computeDiffAreaUnderCurve by computeMeanNormDifference (more robust… | May 26 2021 | |||
c187b85f3573 | tlemaire | improved naming, access and iterating of DriveArray objects. | May 25 2021 | |||
41fde2c39385 | tlemaire | modified coupled_nbls.simAndSave to just simulate if no output directory is… | May 19 2021 | |||
f4282fb16d90 | tlemaire | added plot utility functions | May 19 2021 | |||
40ac2cbf792f | tlemaire | added workaround solution for passive generic lookup name | May 19 2021 | |||
06fa67d560c2 | tlemaire | added resample and interpolate methods to spatiallyextendedtimeseries class | May 18 2021 | |||
3d60eae04053 | tlemaire | added dump and dumpOutputsOtherThan methods to TimeSeries classes | May 18 2021 | |||
66afa784ef55 | tlemaire | added half-cycle offset and interpolation in timeseries cycle averaging | May 17 2021 | |||
a855f3b52095 | tlemaire | fixed error in run_lookups (inconsistent redimensioning for test case) | May 17 2021 | |||
9b83a80b55f5 | tlemaire | started implementing gamma evaluation method | May 17 2021 | |||
23adeab812fd | tlemaire | started working on coupled_nbls module | May 15 2021 | |||
6aadfe75ac22 | tlemaire | started working on coupled_nbls module | May 14 2021 | |||
5159d5ca1d87 | tlemaire | improved logging in nbls.computeEffVars | Mar 26 2021 | |||
f23057d86a6e | tlemaire | improved error logging in bls.balancedefQS. | Mar 26 2021 | |||
b4233b34e678 | tlemaire | improved lookup naming system (and renamed all lookups accordingly). | Mar 23 2021 | |||
7d732f9d2c25 | tlemaire | adapted nbls.computeEffVars method to accomodate for Fourier Fourier overtones… | Mar 23 2021 | |||
e7842427f677 | tlemaire | added array-typed charge input (i.e. US-periodic profile) option to… | Mar 23 2021 | |||
cbeb67523b66 | tlemaire | corrected Cm lkp extension | Mar 5 2021 | |||
28b9ed25d674 | tlemaire | added transition handling in computeTimeStep. | Mar 2 2021 | |||
35b0a5fef28a | tlemaire | added stimProfile and plot methods to TimeProtocol class | Feb 11 2021 | |||
5f4e38528e1a | tlemaire | new bls lookups | Nov 2 2020 | |||
9b2552960a06 | tlemaire | added getPulseTrainProtocol function | Sep 30 2020 | |||
6aa3e623b782 | tlemaire | added multicomp module | Sep 24 2020 | |||
190d52832d89 | tlemaire | added multicomp_benchmark module (cleaned-up version). | Sep 24 2020 | |||
fe5b0a532e32 | tlemaire | added plot_Zprofiles.py script | Sep 23 2020 | |||
bb9f2c79c74a | tlemaire | latest changes for morphoSONIC paper | Sep 15 2020 | |||
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 |
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