Diffusion PySONIC (old) (master) History

core
master7368aa8d62606e57b6ffdbd…

Jun 16 2021

added getTimeStr function (now used in Batch.run)
7368aa8d6260
·tlemaire on Jun 16 2021, 12:52.

Jun 15 2021

added minimize overlap argument on protocol array initialization
d3109cf80990
·tlemaire on Jun 15 2021, 17:58.
added functionalities to optimize protocol array (minimizing overlap)
a34dc74734dc
·tlemaire on Jun 15 2021, 17:48.
removed print statement in ProtocolArray.plot
92d6fbb787e5
·tlemaire on Jun 15 2021, 14:56.

Jun 14 2021

defined StimObjArray class, niherited by DriveArray and ProtocolArray classes
c811bdc9181b
·tlemaire on Jun 14 2021, 21:47.

Jun 9 2021

modified CustomProtocol string representation, enabled robut protocol summing…
0732d479739d
·tlemaire on Jun 9 2021, 20:56.
added os_name as logbal variable in utils. now using it also to output LogBatch.
f456a30eea93
·tlemaire on Jun 9 2021, 17:25.
implemented addition between time protocols and multiplication by scalar
d660732a8200
·tlemaire on Jun 9 2021, 16:22.

Jun 8 2021

corrected benchmarks plotting and evaluation methods
4f17c4046cf6
·tlemaire on Jun 8 2021, 21:30.

Jun 7 2021

added special case handling for phi-key in DriveArray
5e1899de25b9
·tlemaire on Jun 7 2021, 23:54.

May 28 2021

updated pandas requirements (now >=1.2.4) to ensure TimeSeries object are…
0a593ebe88fb
·tlemaire on May 28 2021, 17:03.
added pneuron.is_passive property and getDefaultPassiveNeuron function
3dd0e7ca4b5c
·tlemaire on May 28 2021, 13:41.

May 27 2021

added factor to Qnorm pltvar.
47f7640b7bcb
·tlemaire on May 27 2021, 20:49.
added special case handling to find lookups name
143fbd37ca59
·tlemaire on May 27 2021, 09:22.

May 26 2021

replaced computeDiffAreaUnderCurve by computeMeanNormDifference (more robust…
417a3bd45505
·tlemaire on May 26 2021, 18:56.

May 25 2021

improved naming, access and iterating of DriveArray objects.
c187b85f3573
·tlemaire on May 25 2021, 15:19.

May 19 2021

modified coupled_nbls.simAndSave to just simulate if no output directory is…
41fde2c39385
·tlemaire on May 19 2021, 22:07.
added plot utility functions
f4282fb16d90
·tlemaire on May 19 2021, 16:55.
added workaround solution for passive generic lookup name
40ac2cbf792f
·tlemaire on May 19 2021, 11:26.

May 18 2021

added resample and interpolate methods to spatiallyextendedtimeseries class
06fa67d560c2
·tlemaire on May 18 2021, 14:58.
added dump and dumpOutputsOtherThan methods to TimeSeries classes
3d60eae04053
·tlemaire on May 18 2021, 14:25.

May 17 2021

added half-cycle offset and interpolation in timeseries cycle averaging
66afa784ef55
·tlemaire on May 17 2021, 22:21.
fixed error in run_lookups (inconsistent redimensioning for test case)
a855f3b52095
·tlemaire on May 17 2021, 21:20.
started implementing gamma evaluation method
9b83a80b55f5
·tlemaire on May 17 2021, 20:25.

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.

R4670/PySONIC/coremaster7368aa8d62606e57b6ffdbd…

Jun 16 2021

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R4670/PySONIC/core
master7368aa8d62606e57b6ffdbd…