Diffusion PySONIC (old) (master) History

core
master23adeab812fde5ce5524ea8…

May 15 2021

started working on coupled_nbls module
23adeab812fd
·tlemaire on May 15 2021, 20:47.

May 14 2021

started working on coupled_nbls module
6aadfe75ac22
·tlemaire on May 14 2021, 19:50.

Mar 26 2021

improved logging in nbls.computeEffVars
5159d5ca1d87
·tlemaire on Mar 26 2021, 20:13.
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 5 2021

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

Mar 2 2021

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

Feb 11 2021

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.

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.

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.

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.

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 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

introduced default celsius (36°C) as a PointNeuron property shared by all…
42a3be29b47b
·tlemaire on Jul 21 2020, 16:18.
added HH point neuron
4884f5695b3e
·tlemaire on Jul 21 2020, 15:28.

Jul 15 2020

removed SilentMRGNode class (now generated on-the-fly in analysis notebook)
c9894bdbd61c
·tlemaire on Jul 15 2020, 21:24.
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 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 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.
new astim titrations for figure 8
430d7c8131f0
·tlemaire on May 2 2020, 12:07.

May 1 2020

added new titrations
c8cdcf5deefc
·tlemaire on May 1 2020, 22:47.
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

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.
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 optional tstart argument to PusledProtocol classes. corrected…
6dedc53ccbc8
·tlemaire on Apr 24 2020, 11:04.

Apr 23 2020

added TC2 class
a6e6abff99bc
·tlemaire on Apr 23 2020, 12:06.

Apr 22 2020

additional bls lookups
9342c4bfcbda
·tlemaire on Apr 22 2020, 12:56.

Apr 21 2020

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

Apr 19 2020

added BalancedPulsedProtocol class.
159f140dcfb0
·tlemaire on Apr 19 2020, 15:03.

Apr 18 2020

added max_nsamples parameter to effective solver to avoid memory allocation…
108548aa8cc8
·tlemaire on Apr 18 2020, 21:25.
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.
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.
corrected error in computeFRProfile when no spikes are detected.
447a9236fa20
·tlemaire on Apr 17 2020, 14:53.

Apr 16 2020

improved solvers docstrings and clarified their use in model classes.
69892d75c503
·tlemaire on Apr 16 2020, 13:30.

Apr 15 2020

removed ambiguity around initialConditions methods to allow correct lookups…
d03caf415e89
·tlemaire on Apr 15 2020, 21:04.
implemented better solvers (now inside solvers module), including an…
b77cd9e4eb12
·tlemaire on Apr 15 2020, 20:53.

Apr 13 2020

corrected LogBatch class to enable correct use with mpi.
f8511250c9b8
·tlemaire on Apr 13 2020, 18:00.
added better fs handling in actmap
10270ea94712
·tlemaire on Apr 13 2020, 12:33.

Apr 10 2020

removed useless error instance catch in utils
a8ffc4cf6311
·tlemaire on Apr 10 2020, 18:36.

Apr 9 2020

added multiprocessing functionality to LogBatch class.
3af9c9df32cc
·tlemaire on Apr 9 2020, 15:53.
corrected ActMap class (now inheriting from LogBatch).
18480eb7bebc
·tlemaire on Apr 9 2020, 14:07.

Apr 5 2020

added TimeProtocol.stimEvents method (used in NEURON simulations).
63ef9868bbd2
·tlemaire on Apr 5 2020, 17:59.
added eventsON and eventsOFF methods to Protocol classes.
06f8250793a6
·tlemaire on Apr 5 2020, 15:22.

Apr 3 2020

added __eq__ methods to pneuron and nbls classes
cc5348bc40ca
·tlemaire on Apr 3 2020, 15:33.

Mar 31 2020

added ASTIM_REL_CONV_THR to constants file.
9239911c1f35
·tlemaire on Mar 31 2020, 18:41.

Mar 30 2020

added TC fs lookup.
9dcd3884ae33
·tlemaire on Mar 30 2020, 21:50.

Mar 27 2020

renamed fibers point-neuron models for better interpretability. completed fiber…
8f0bbde630a7
·tlemaire on Mar 27 2020, 20:37.

Mar 26 2020

tested MRG lookups generation
a43249c6ecf1
·tlemaire on Mar 26 2020, 21:49.

Mar 19 2020

added polyfit amd extrapolate capabilities to Lookup class.
066e8e416305
·tlemaire on Mar 19 2020, 12:13.

Feb 28 2020

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic
8f4b9911c0d3
·tlemaire on Feb 28 2020, 17:05.
added extra functionalities to Lookup class. continued fiber nodes notebook.
c8a9ea2beb92
·tlemaire on Feb 28 2020, 17:05.
Merge solved
7d61ef15bd3b
·vicari on Feb 28 2020, 17:03.
Correction in drives
be6c868e4e5f
·vicari on Feb 28 2020, 17:00.

Feb 20 2020

moved getMeta to utils
165caa8bf488
·tlemaire on Feb 20 2020, 18:35.
changed meta property of model classes to return solely model information.
7f8a3be5ceb4
·tlemaire on Feb 20 2020, 17:03.

Feb 18 2020

added LogBatch class
b7d520b9ed42
·tlemaire on Feb 18 2020, 22:59.

Feb 14 2020

updated README (added instructions for git-lfs install)
31cc2d15993a
·tlemaire on Feb 14 2020, 11:12.

Feb 11 2020

added copy method to all model classes. added TI US notebook. updated…
68961385d17e
·tlemaire on Feb 11 2020, 07:55.

Feb 5 2020

replaced erroneous "return NotImplementedError" statements by "raise…
96d3c580ee81
·tlemaire on Feb 5 2020, 18:20.
correctd mismatch in ElectricDrive
8907f78b742a
·tlemaire on Feb 5 2020, 18:14.
renamed ElectricDrive A to I
892f924d6e9e
·tlemaire on Feb 5 2020, 18:13.
introduced properties in classes of drives and protocols modules.
31ef6228207a
·tlemaire on Feb 5 2020, 17:08.

Feb 3 2020

added xkey property to XDrive class and Arange property to pneuron and nbls…
073e28b388f6
·tlemaire on Feb 3 2020, 23:36.
Created Drive objects inheritance scheme (now used in all model classes).
27d8aafffa88
·tlemaire on Feb 3 2020, 21:45.
corrected docstring errors in pneuron Cm0 and Qm0
dba63f835a31
·tlemaire on Feb 3 2020, 15:11.
added lookups files in separate lookups folder using LFS.
062e541857dc
·tlemaire on Feb 3 2020, 14:35.
Created AcousticSource class to be used for US simulations.
9d0666784d2d
·tlemaire on Feb 3 2020, 14:26.

Jan 26 2020

added sundt fs lookups. adapted RS fs lookups. adapted nbls.getLookup2D method…
eec847e65a7a
·tlemaire on Jan 26 2020, 23:37.
added interp_method Lookup attribute to enable choice of lookup interpolation…
6846298198d4
·tlemaire on Jan 26 2020, 20:42.
Modified Lookup class (new properties, corrected methods).
c995e8999df7
·tlemaire on Jan 26 2020, 19:15.
added DQ_LOOKUP constant (used in run_lookups.py)
38dc94d61fe7
·tlemaire on Jan 26 2020, 09:51.

R4670/PySONIC/coremaster23adeab812fde5ce5524ea8…

May 15 2021

May 14 2021

Mar 26 2021

Mar 23 2021

Mar 5 2021

Mar 2 2021

Feb 11 2021

Nov 2 2020

Sep 30 2020

Sep 24 2020

Sep 23 2020

Sep 15 2020

Aug 8 2020

Aug 5 2020

Aug 4 2020

Aug 3 2020

Jul 23 2020

Jul 22 2020

Jul 21 2020

Jul 15 2020

Jul 3 2020

Jun 24 2020

Jun 4 2020

Jun 3 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

Apr 16 2020

Apr 15 2020

Apr 13 2020

Apr 10 2020

Apr 9 2020

Apr 5 2020

Apr 3 2020

Mar 31 2020

Mar 30 2020

Mar 27 2020

Mar 26 2020

Mar 19 2020

Feb 28 2020

Feb 20 2020

Feb 18 2020

Feb 14 2020

Feb 11 2020

Feb 5 2020

Feb 3 2020

Jan 26 2020

R4670/PySONIC/core
master23adeab812fde5ce5524ea8…