Diffusion PySONIC (old) (master) History

simutils.py
master043172721a44fb57010eeab…

Aug 21 2018

changed package name to PySONIC.
043172721a44
·tlemaire on Aug 21 2018, 16:19.

Jul 24 2018

replaced titrateEStim and titrateAStim funcitons by EStimTitrator and…
9a37cd335585
·tlemaire on Jul 24 2018, 12:03.

Jul 23 2018

replaced runMech function by MechWorker class, added multiprocessing option to…
f643971bb42f
·tlemaire on Jul 23 2018, 14:40.
replaced runEStim funciton by EStimWorker class, added multiprocessing option…
40ccd8272444
·tlemaire on Jul 23 2018, 13:41.
replaced runAStim function by AStimWorker class, added multiprocessing option…
b1b868c26791
·tlemaire on Jul 23 2018, 11:40.

Jul 20 2018

added multiprocessing functionality for lookups creation (Consumer and…
3c4a0aef7824
·tlemaire on Jul 20 2018, 18:05.

Jul 4 2018

modified si_format for py35 compatibility.
c98c3d8b1f8b
·tlemaire on Jul 4 2018, 17:18.
corrected Qm computation for EL simulations
c35ee1510e54
·tlemaire on Jul 4 2018, 11:49.
added Qm to dataframe of EL simulations
b8be2280d700
·tlemaire on Jul 4 2018, 11:47.

May 15 2018

corrected minor mistakes in call to vectorized functions.
5232ea010459
·tlemaire on May 15 2018, 11:29.

May 6 2018

added plotDualMaxMap to pltutils.
718541c73181
·tlemaire on May 6 2018, 22:21.

May 4 2018

added getMaxMap function to simutils
7e6607ff1a67
·tlemaire on May 4 2018, 16:40.
added getCycleAverage and getActivationMap functions to utils
462acad97d14
·tlemaire on May 4 2018, 16:16.

May 3 2018

added si_format function to format physical numbers according to the SI unit…
9fc6ab4cdecc
·tlemaire on May 3 2018, 12:42.

May 2 2018

corrected logging error in runAStimBatch
162cb6e67011
·tlemaire on May 2 2018, 22:26.
solved minor issue in findPeaks function (end of signal exception).
6392bff9bae7
·tlemaire on May 2 2018, 22:10.
replaced numpy.vectorize by explicit definition of vectorized BLS methods.
419fdbc72f8c
·tlemaire on May 2 2018, 21:15.
vectorized relevant functions of the BilayerSonophore class
f7bc3b340b2d
·tlemaire on May 2 2018, 15:40.
added computeMeshEdges function to utils module.
59edb2753a52
·tlemaire on May 2 2018, 11:38.

Apr 30 2018

added reinit method to BilayerSonophore class. added ComputeSpikeMetrics…
74c9b13f40bf
·tlemaire on Apr 30 2018, 13:55.

Apr 18 2018

replaced assertion error by warning statement in case of peaks vs valleys…
f6e428f6c231
·tlemaire on Apr 18 2018, 11:36.

Apr 17 2018

corrected return error in findPeaks. added new algorithmic constant: minimal…
e2763f9ad093
·tlemaire on Apr 17 2018, 11:45.
increased amplitude precision for ESTIM and ASTIM file naming
613073ed9c81
·tlemaire on Apr 17 2018, 11:08.

Apr 14 2018

changed PRF and DC format in file naming (simutils output and pltutils input)
27332b793c2a
·tlemaire on Apr 14 2018, 19:41.

Apr 4 2018

replaced detectSpikes by the more robust findPeaks. added a plot_spikes script…
d5e56c2f9c40
·tlemaire on Apr 4 2018, 17:55.

Apr 3 2018

solved rendering issue with plotComp. Implemented and tested a robust peak…
6d97721d9c51
·tlemaire on Apr 3 2018, 20:30.

Mar 30 2018

automatic detection of time vector uniformity in detectPeaksTime
6ec806aa90d6
·tlemaire on Mar 30 2018, 13:02.

Mar 29 2018

added prominence threshold constant for spike detection. added skeleton for IB…
377594fb12b0
·tlemaire on Mar 29 2018, 18:04.

Mar 21 2018

added extra options to plotComp (custom ticks, black legend with colored plots)
3bee78ffb4bc
·tlemaire on Mar 21 2018, 18:34.

Mar 20 2018

added detailed docstring to detectPeaks
3fabf680de73
·tlemaire on Mar 20 2018, 21:49.

Mar 16 2018

Added user input to decide whether to continue batch after assertion error or…
5049e821acd8
·tlemaire on Mar 16 2018, 13:30.
renamed BilayerSonophore.runMech to BilayerSonophore.run, and runMechSingle to…
5b8f09fbd295
·tlemaire on Mar 16 2018, 12:06.

Mar 15 2018

added runMechSingle to simutils and MECH_run script
50e85131e3d9
·tlemaire on Mar 15 2018, 19:23.
introduced custom defined InputError exceptions (instead of assert statements)…
4ffaa73494ea
·tlemaire on Mar 15 2018, 17:06.

Mar 14 2018

general optimization of integration methods (elec, mech and US classic) using…
b65f7bad637c
·tlemaire on Mar 14 2018, 19:30.

Mar 13 2018

changed "ch_mech" by "neuron"
acab28778569
·tlemaire on Mar 13 2018, 14:33.
added neuron name to meta dictionary for ESTIM and ASTIM simulations
0c7107d859aa
·tlemaire on Mar 13 2018, 12:49.
added tcomp to "meta" dictionary.
d2ee8d2274d4
·tlemaire on Mar 13 2018, 12:42.
replaced DF by DC, and added pandas dataframes to store and retrieve simulation…
1edd575f6465
·Theo Lemaire on Mar 13 2018, 01:14.

Mar 7 2018

updated README and LICENCSE files. added extra BLS lookups. corrected titration…
63c842041ef8
·tlemaire on Mar 7 2018, 15:28.

Feb 28 2018

updated titration methods and generated LeechP lookups
89d20f6d2cb6
·tlemaire on Feb 28 2018, 16:53.

Jan 16 2018

corrected computation of firing rate in detectSpikes function
7497a2150a6b
·tlemaire on Jan 16 2018, 20:07.

Nov 29 2017

Added sonophore diameter to ASTIM files naming, and changed DF to 2 decimals…
ae51b3bafaec
·tlemaire on Nov 29 2017, 14:59.

Nov 22 2017

corrected code for LeechT neuron, and validated it on electrical stimuli
c9dad3d35684
·tlemaire on Nov 22 2017, 14:01.

Sep 12 2017

added biomech and biophys parameters directly as BilayerSonophore class…
6be1756dda64
·tlemaire on Sep 12 2017, 14:46.

Sep 10 2017

improved error handling
6cd8d175ad7b
·tlemaire on Sep 10 2017, 17:53.

Sep 6 2017

replaced neurons object lists by neurons name list in batch functions input
14d95d317eeb
·tlemaire on Sep 6 2017, 16:14.
introduced default arguments in batch functions for bls_params and geom
151337217cab
·tlemaire on Sep 6 2017, 15:03.
separated checkBatchLog function into setBatchDir and checkBatchLog functions
63f20548155d
·tlemaire on Sep 6 2017, 13:42.

Sep 4 2017

added runEStim and runAStim functions. added locker to xlslog
8680bc7dccaf
·tlemaire on Sep 4 2017, 17:00.

Sep 3 2017

updated test_values
f51d67fdf64a
·tlemaire on Sep 3 2017, 17:23.

Sep 1 2017

added option to specify labels in plotComp
e2ff032a6759
·tlemaire on Sep 1 2017, 15:55.

Aug 25 2017

adapted plotComp to deal with pulsed ESTIM outputs and MECH outputs. corrected…
c30d03edb7cc
·tlemaire on Aug 25 2017, 17:54.
implemented runMechBatch function. adapted plotBatch function to deal with MECH…
0a89dde7f847
·tlemaire on Aug 25 2017, 17:20.
added titrateEStim and titrateEStimBatch functions
c9053e689690
·tlemaire on Aug 25 2017, 14:59.
Added pulsed stimuli handling to SolverElec. Implemented moved titration…
3c218a52595b
·tlemaire on Aug 25 2017, 13:06.

Aug 24 2017

introduced standardized workflow for both E-STIM and A-STIM simulations and…
2c7de2047898
·tlemaire on Aug 24 2017, 17:49.

Aug 23 2017

moved some utils functions into simutils & pltutils modules
4f9a8fd2aed4
·tlemaire on Aug 23 2017, 16:28.
created plotting module inside package, with plotComp and plotBatch functions
af10a48546b7
·tlemaire on Aug 23 2017, 15:45.

R4670/PointNICE/solvers/simutils.pymaster043172721a44fb57010eeab…

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Aug 23 2017

R4670/PointNICE/solvers/simutils.py
master043172721a44fb57010eeab…