Diffusion PySONIC (old) (master) History

R4670/PointNICE
master5011ac8891a539f4b9a9b87…

Jul 5 2018

added runNEURON method to run US simulation with NEURON (to be ctd).
5011ac8891a5
·tlemaire on Jul 5 2018, 23:50.

Jul 4 2018

added int64 handling in si_format.
320fafe51ff9
·tlemaire on Jul 4 2018, 17:25.
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.

Jun 18 2018

minor modifications to plotEffVars, rescale and test_intermolecular_pressure.py
3b9d8b293e8a
·tlemaire on Jun 18 2018, 17:02.

May 25 2018

added automatic y-scaling of effective variables in plotEffVars.
bd1e86dc1591
·tlemaire on May 25 2018, 22:25.
renamed plotEffCoeffs to plotEffVariables with lots of improvements.
00baa42adf67
·tlemaire on May 25 2018, 22:11.
added script to test intermoleulcar pressure approximation.
7d33ab6ec1f9
·tlemaire on May 25 2018, 15:45.

May 22 2018

minor modifications to plotActivationMap function, added plotTraces function…
e238a7caa389
·tlemaire on May 22 2018, 16:36.

May 15 2018

minor corrections to plotComp and si_format.
532e76eaa491
·tlemaire on May 15 2018, 19:04.
corrected minor mistakes in call to vectorized functions.
5232ea010459
·tlemaire on May 15 2018, 11:29.

May 11 2018

adapted plot settings (font and dimensions) for paper figures.
ddd04f71a3b3
·tlemaire on May 11 2018, 14:26.

May 8 2018

added method to find neuron-specific rheobase US amplitudes (findRheobaseAmps)…
383a6cb2fc75
·tlemaire on May 8 2018, 15:19.
divided 3D -> 1D lookups projection into 2 distinct steps (defined…
a148e58c0951
·tlemaire on May 8 2018, 10:40.

May 6 2018

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

May 4 2018

added plotActivationMap to pltutils.
75b8e9964108
·tlemaire on May 4 2018, 17:39.
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.
modified si_format to work also on tuples and lists.
7624ecfb5947
·tlemaire on May 4 2018, 11:13.

May 3 2018

solved minor issue in getPatchesLoc. replaced Rectangle by axvspan instances…
ea14e67aae6f
·tlemaire on May 3 2018, 17:09.
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.
vecotrized tauu method of LTS and TC neurons
9435cc4aff31
·tlemaire on May 2 2018, 15:46.
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 24 2018

added PmCompMethod as a parameter for all relevant methods of the…
5e84496cf5e0
·tlemaire on Apr 24 2018, 19:06.

Apr 22 2018

added __str__ method to BilayerSonophore class that prints values of class and…
a7922aa5b6ad
·tlemaire on Apr 22 2018, 23:54.

Apr 18 2018

added lookups for IB neuron
3f620b0c56a0
·tlemaire on Apr 18 2018, 18:04.
replaced assertion error by warning statement in case of peaks vs valleys…
f6e428f6c231
·tlemaire on Apr 18 2018, 11:36.

Apr 17 2018

validated IB neuron gating kinetics for E-STIM
487fd2f0db0a
·tlemaire on Apr 17 2018, 17:11.
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.
removed dependency on colorlover in plotComp
a5aaa17fbd90
·tlemaire on Apr 14 2018, 18:38.

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

corrected few mistakes in IB neuron implementation
8b637407388b
·tlemaire on Mar 30 2018, 18:17.
added better inset handling in plotComp
cf2846af1ead
·tlemaire on Mar 30 2018, 18:09.
modified plotComp to take only 1 input variable and added option to plot inset
1ac82339eaf3
·tlemaire on Mar 30 2018, 16:58.
automatic detection of time vector uniformity in detectPeaksTime
6ec806aa90d6
·tlemaire on Mar 30 2018, 13:02.

Mar 29 2018

renamed matlab utils function more explicitely.
19a21b2ee66b
·tlemaire on Mar 29 2018, 19:00.
added prominence threshold constant for spike detection. added skeleton for IB…
377594fb12b0
·tlemaire on Mar 29 2018, 18:04.

Mar 27 2018

added method to extract compuation times in utils module
c916dd9c8f25
·tlemaire on Mar 27 2018, 14:49.

Mar 22 2018

minor improvements to pltutils module
e59db772ab09
·tlemaire on Mar 22 2018, 01:45.
removed italic for latex style labelling in plotComp
80b620b50b12
·tlemaire on Mar 22 2018, 00:27.
added option to change linestyle of legend handles (dashed -> straight)
d7f0d2a86ee2
·tlemaire on Mar 22 2018, 00:17.

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 19 2018

corrected TOFF integration error in SolverElec. added PW tests to test_basic.py
dd51b4283191
·tlemaire on Mar 19 2018, 20:03.
changes to plotComp function allowing to customize linestyles, colors and…
1c8f0234e7e7
·tlemaire on Mar 19 2018, 17:36.

Mar 18 2018

corrected initial conditions error in pulsed protocols integration of…
900de6e3aa75
·Theo Lemaire on Mar 18 2018, 19:58.
removed erroneous use of y_pulse_off in runClassic method
708bc9223628
·Theo Lemaire on Mar 18 2018, 11:47.

Mar 17 2018

Added new LeechP lookups
ee3a47c57d36
·Theo Lemaire on Mar 17 2018, 19:07.

Mar 16 2018

programmed classic method progress bar to show up both on DEBUG and INFO levels
c6b29afe2de9
·tlemaire on Mar 16 2018, 17:31.
corrected createLookup runMech error by calling super.run method
4b7e412bb8d6
·tlemaire on Mar 16 2018, 14:32.
added new lookups except LeechP
b9f08f5eaf67
·tlemaire on Mar 16 2018, 14:11.
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.
corrected Z bounding for out-of-range deflections
4c475209bac9
·tlemaire on Mar 16 2018, 11:52.

Mar 15 2018

added runMechSingle to simutils and MECH_run script
50e85131e3d9
·tlemaire on Mar 15 2018, 19:23.
added user input to decide whether lookup file should be overwritten in case of…
69a4e42fa766
·tlemaire on Mar 15 2018, 17:45.
introduced custom defined InputError exceptions (instead of assert statements)…
4ffaa73494ea
·tlemaire on Mar 15 2018, 17:06.
generated new lookups for RS and FS neurons with a wider frequency range (20kHz…
4d2d60cc96c5
·tlemaire on Mar 15 2018, 14:28.
renamed INPUT_CHARGE_RANGE to CHARGE_RANGE
e5a0b44e3d54
·tlemaire on Mar 15 2018, 14:02.
added correction of deflection value in eqMech (with warning) if below critical…
d350701db48c
·tlemaire on Mar 15 2018, 14:00.
addded time-step-dependent output arrays downsampling in classic simulations to…
9df57ec1684b
·tlemaire on Mar 15 2018, 12:00.
temporarily removed checking for prior lookup file existence upon new lookup…
d8a1246ad44e
·tlemaire on Mar 15 2018, 11:20.
replaced error raising by a simple warning for out-of-range deflections in…
10fde2422c97
·tlemaire on Mar 15 2018, 11:17.

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

Switched from ode (lsoda) to odeint for classic method to see if it solves…
01238213b788
·tlemaire on Mar 13 2018, 23:22.
prepared creation of new lookups
d01c70ab720e
·tlemaire on Mar 13 2018, 17:35.
implemented neuron-specific charge interval for lookup creation.
1b6d6a579519
·tlemaire on Mar 13 2018, 17:31.
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.
tested and validated plotting with pandas dataframes.
41e27b5ece2e
·tlemaire on Mar 13 2018, 12:37.
replaced DF by DC, and added pandas dataframes to store and retrieve simulation…
1edd575f6465
·Theo Lemaire on Mar 13 2018, 01:14.

Mar 12 2018

replaced channels by neurons
edd5594d9646
·Theo Lemaire on Mar 12 2018, 20:01.

Mar 8 2018

adaptive time step lowering for high-PRF protocols in Elec and effective-US…
8d85b3cb30d6
·tlemaire on Mar 8 2018, 09:53.

Mar 7 2018

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

Mar 2 2018

extended installation instructions in the README file
d12141d0c48b
·tlemaire on Mar 2 2018, 17:57.

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.

Jan 9 2018

corrected LeechP implementation using dynamic Nernst potentials for Sodium and…
c59a8267c97e
·tlemaire on Jan 9 2018, 14:53.

Dec 12 2017

Lots of corrections and improvements to the LeechP model implementation. E-STIM…
33ee63af70aa
·tlemaire on Dec 12 2017, 15:16.

Dec 1 2017

added LeechPressure to channels init. added leechP variables to pltvars. tested…
094fd25223f4
·tlemaire on Dec 1 2017, 09:01.

Nov 29 2017

implemented leechP intracellular pools evolution according to modelDB ref
a270608c8e8c
·tlemaire on Nov 29 2017, 19:28.
Added sonophore diameter to ASTIM files naming, and changed DF to 2 decimals…
ae51b3bafaec
·tlemaire on Nov 29 2017, 14:59.

Nov 27 2017

validated effective method for LeechT neuron, added that neuron to test_values.
1bb50e8f0025
·tlemaire on Nov 27 2017, 13:18.

Nov 24 2017

added LeechT lookup
f1fbc6e5b9bb
·tlemaire on Nov 24 2017, 12:32.

Nov 22 2017

added lookup files and template log files to tracking
e5364755a2a5
·tlemaire on Nov 22 2017, 14:38.
corrected code for LeechT neuron, and validated it on electrical stimuli
c9dad3d35684
·tlemaire on Nov 22 2017, 14:01.

Sep 12 2017

debugged double printing issue of logging statements
6249b5298f4c
·tlemaire on Sep 12 2017, 18:56.
added biomech and biophys parameters directly as BilayerSonophore class…
6be1756dda64
·tlemaire on Sep 12 2017, 14:46.

Sep 10 2017

added input pltvars checking to plot functions
c67c8c39a93b
·tlemaire on Sep 10 2017, 19:07.
added color to logging statements
189a078bf8d2
·tlemaire on Sep 10 2017, 18:46.

R4670/PointNICEmaster5011ac8891a539f4b9a9b87…

Jul 5 2018

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R4670/PointNICE
master5011ac8891a539f4b9a9b87…