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Diffusion PySONIC (old) (master) Graph

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CommitAuthorDetailsCommitted
8e3d2db927b5tlemaire
grouped mod files in single directory. defined stimonoff procedure in separate… 
Jul 18 2018
09ead26fe237tlemaire
corrected TC mod file (needs smaller time step to be fully accurate). 
Jul 17 2018
eaed73930e7ctlemaire
separated mod files. corrected variables outputing in runNEURON. corrected Vm… 
Jul 13 2018
2449b629e794tlemaire
added FS and RE mechs. 
Jul 6 2018
cca23e04187btlemaire
improved runNEURON method. added LTS mechanism. 
Jul 6 2018
5011ac8891a5tlemaire
added runNEURON method to run US simulation with NEURON (to be ctd). 
Jul 5 2018
320fafe51ff9tlemaire
added int64 handling in si_format. 
Jul 4 2018
c98c3d8b1f8btlemaire
modified si_format for py35 compatibility. 
Jul 4 2018
c35ee1510e54tlemaire
corrected Qm computation for EL simulations 
Jul 4 2018
b8be2280d700tlemaire
added Qm to dataframe of EL simulations 
Jul 4 2018
3b9d8b293e8atlemaire
minor modifications to plotEffVars, rescale and test_intermolecular_pressure.py 
Jun 18 2018
bd1e86dc1591tlemaire
added automatic y-scaling of effective variables in plotEffVars. 
May 25 2018
00baa42adf67tlemaire
renamed plotEffCoeffs to plotEffVariables with lots of improvements. 
May 25 2018
7d33ab6ec1f9tlemaire
added script to test intermoleulcar pressure approximation. 
May 25 2018
e238a7caa389tlemaire
minor modifications to plotActivationMap function, added plotTraces function… 
May 22 2018
532e76eaa491tlemaire
minor corrections to plotComp and si_format. 
May 15 2018
5232ea010459tlemaire
corrected minor mistakes in call to vectorized functions. 
May 15 2018
ddd04f71a3b3tlemaire
adapted plot settings (font and dimensions) for paper figures. 
May 11 2018
383a6cb2fc75tlemaire
added method to find neuron-specific rheobase US amplitudes (findRheobaseAmps)… 
May 8 2018
a148e58c0951tlemaire
divided 3D -> 1D lookups projection into 2 distinct steps (defined… 
May 8 2018
718541c73181tlemaire
added plotDualMaxMap to pltutils. 
May 6 2018
75b8e9964108tlemaire
added plotActivationMap to pltutils. 
May 4 2018
7e6607ff1a67tlemaire
added getMaxMap function to simutils 
May 4 2018
462acad97d14tlemaire
added getCycleAverage and getActivationMap functions to utils 
May 4 2018
7624ecfb5947tlemaire
modified si_format to work also on tuples and lists. 
May 4 2018
ea14e67aae6ftlemaire
solved minor issue in getPatchesLoc. replaced Rectangle by axvspan instances… 
May 3 2018
9fc6ab4cdecctlemaire
added si_format function to format physical numbers according to the SI unit… 
May 3 2018
162cb6e67011tlemaire
corrected logging error in runAStimBatch 
May 2 2018
6392bff9bae7tlemaire
solved minor issue in findPeaks function (end of signal exception). 
May 2 2018
419fdbc72f8ctlemaire
replaced numpy.vectorize by explicit definition of vectorized BLS methods. 
May 2 2018
9435cc4aff31tlemaire
vecotrized tauu method of LTS and TC neurons 
May 2 2018
f7bc3b340b2dtlemaire
vectorized relevant functions of the BilayerSonophore class 
May 2 2018
120267c92007tlemaire
modified batch_ASTIM.py for activation maps 
May 2 2018
59edb2753a52tlemaire
added computeMeshEdges function to utils module. 
May 2 2018
74c9b13f40bftlemaire
added reinit method to BilayerSonophore class. added ComputeSpikeMetrics… 
Apr 30 2018
5e84496cf5e0tlemaire
added PmCompMethod as a parameter for all relevant methods of the… 
Apr 24 2018
a7922aa5b6adtlemaire
added __str__ method to BilayerSonophore class that prints values of class and… 
Apr 22 2018
70d9c59ab1d9tlemaire
added IB testing in test_values script 
Apr 18 2018
3f620b0c56a0tlemaire
added lookups for IB neuron 
Apr 18 2018
f6e428f6c231tlemaire
replaced assertion error by warning statement in case of peaks vs valleys… 
Apr 18 2018
cf488f35629btlemaire
corrected scripts names in setup.py 
Apr 17 2018
487fd2f0db0atlemaire
validated IB neuron gating kinetics for E-STIM 
Apr 17 2018
e2763f9ad093tlemaire
corrected return error in findPeaks. added new algorithmic constant: minimal… 
Apr 17 2018
bea9167abc2btlemaire
changed names of simulation scripts for more intuitive use 
Apr 17 2018
613073ed9c81tlemaire
increased amplitude precision for ESTIM and ASTIM file naming 
Apr 17 2018
27332b793c2atlemaire
changed PRF and DC format in file naming (simutils output and pltutils input) 
Apr 14 2018
a5aaa17fbd90tlemaire
removed dependency on colorlover in plotComp 
Apr 14 2018
d5e56c2f9c40tlemaire
replaced detectSpikes by the more robust findPeaks. added a plot_spikes script… 
Apr 4 2018
6d97721d9c51tlemaire
solved rendering issue with plotComp. Implemented and tested a robust peak… 
Apr 3 2018
8b637407388btlemaire
corrected few mistakes in IB neuron implementation 
Mar 30 2018
cf2846af1eadtlemaire
added better inset handling in plotComp 
Mar 30 2018
1ac82339eaf3tlemaire
modified plotComp to take only 1 input variable and added option to plot inset 
Mar 30 2018
6ec806aa90d6tlemaire
automatic detection of time vector uniformity in detectPeaksTime 
Mar 30 2018
19a21b2ee66btlemaire
renamed matlab utils function more explicitely. 
Mar 29 2018
377594fb12b0tlemaire
added prominence threshold constant for spike detection. added skeleton for IB… 
Mar 29 2018
c916dd9c8f25tlemaire
added method to extract compuation times in utils module 
Mar 27 2018
e59db772ab09tlemaire
minor improvements to pltutils module 
Mar 22 2018
80b620b50b12tlemaire
removed italic for latex style labelling in plotComp 
Mar 22 2018
d7f0d2a86ee2tlemaire
added option to change linestyle of legend handles (dashed -> straight) 
Mar 22 2018
3bee78ffb4bctlemaire
added extra options to plotComp (custom ticks, black legend with colored plots) 
Mar 21 2018
3fabf680de73tlemaire
added detailed docstring to detectPeaks 
Mar 20 2018
dd51b4283191tlemaire
corrected TOFF integration error in SolverElec. added PW tests to test_basic.py 
Mar 19 2018
1c8f0234e7e7tlemaire
changes to plotComp function allowing to customize linestyles, colors and… 
Mar 19 2018
900de6e3aa75Theo Lemaire
corrected initial conditions error in pulsed protocols integration of… 
Mar 18 2018
708bc9223628Theo Lemaire
removed erroneous use of y_pulse_off in runClassic method 
Mar 18 2018
ee3a47c57d36Theo Lemaire
Added new LeechP lookups 
Mar 17 2018
c6b29afe2de9tlemaire
programmed classic method progress bar to show up both on DEBUG and INFO levels 
Mar 16 2018
4b7e412bb8d6tlemaire
corrected createLookup runMech error by calling super.run method 
Mar 16 2018
b9f08f5eaf67tlemaire
added new lookups except LeechP 
Mar 16 2018
5049e821acd8tlemaire
Added user input to decide whether to continue batch after assertion error or… 
Mar 16 2018
5b8f09fbd295tlemaire
renamed BilayerSonophore.runMech to BilayerSonophore.run, and runMechSingle to… 
Mar 16 2018
cf2459c7182etlemaire
removed unwanted data files from sim directory 
Mar 16 2018
4c475209bac9tlemaire
corrected Z bounding for out-of-range deflections 
Mar 16 2018
50e85131e3d9tlemaire
added runMechSingle to simutils and MECH_run script 
Mar 15 2018
69a4e42fa766tlemaire
added user input to decide whether lookup file should be overwritten in case of… 
Mar 15 2018
4ffaa73494eatlemaire
introduced custom defined InputError exceptions (instead of assert statements)… 
Mar 15 2018
4d2d60cc96c5tlemaire
generated new lookups for RS and FS neurons with a wider frequency range (20kHz… 
Mar 15 2018
e5a0b44e3d54tlemaire
renamed INPUT_CHARGE_RANGE to CHARGE_RANGE 
Mar 15 2018
d350701db48ctlemaire
added correction of deflection value in eqMech (with warning) if below critical… 
Mar 15 2018
9df57ec1684btlemaire
addded time-step-dependent output arrays downsampling in classic simulations to… 
Mar 15 2018
d8a1246ad44etlemaire
temporarily removed checking for prior lookup file existence upon new lookup… 
Mar 15 2018
10fde2422c97tlemaire
replaced error raising by a simple warning for out-of-range deflections in… 
Mar 15 2018
b65f7bad637ctlemaire
general optimization of integration methods (elec, mech and US classic) using… 
Mar 14 2018
01238213b788tlemaire
Switched from ode (lsoda) to odeint for classic method to see if it solves… 
Mar 13 2018
d01c70ab720etlemaire
prepared creation of new lookups 
Mar 13 2018
1b6d6a579519tlemaire
implemented neuron-specific charge interval for lookup creation. 
Mar 13 2018
acab28778569tlemaire
changed "ch_mech" by "neuron" 
Mar 13 2018
0c7107d859aatlemaire
added neuron name to meta dictionary for ESTIM and ASTIM simulations 
Mar 13 2018
d2ee8d2274d4tlemaire
added tcomp to "meta" dictionary. 
Mar 13 2018
41e27b5ece2etlemaire
tested and validated plotting with pandas dataframes. 
Mar 13 2018
1edd575f6465Theo Lemaire
replaced DF by DC, and added pandas dataframes to store and retrieve simulation… 
Mar 13 2018
edd5594d9646Theo Lemaire
replaced channels by neurons 
Mar 12 2018
34958bd21f55tlemaire
adapted batch files for LeechP 
Mar 8 2018
8d85b3cb30d6tlemaire
adaptive time step lowering for high-PRF protocols in Elec and effective-US… 
Mar 8 2018
6e5878fe0ecftlemaire
corrected PRF display issues in command line scripts ESTIM_run and ASTIM_run 
Mar 7 2018
63c842041ef8tlemaire
updated README and LICENCSE files. added extra BLS lookups. corrected titration… 
Mar 7 2018
063d417bd20ctlemaire
added pre-commit hook and adapted run_tests.sh command 
Mar 2 2018
d12141d0c48btlemaire
extended installation instructions in the README file 
Mar 2 2018
89d20f6d2cb6tlemaire
updated titration methods and generated LeechP lookups 
Feb 28 2018
bf5a88531d4btlemaire
tried to adapt pre-commit hook after Anaconda re-install to call python with… 
Jan 18 2018
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