History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
043172721a44 | tlemaire | changed package name to PySONIC. | Aug 21 2018 | |||
2267460a3b52 | tlemaire | removed NEURON related code from package (runNEURON method, NMODL folder), used… | Aug 21 2018 | |||
9a37cd335585 | tlemaire | replaced titrateEStim and titrateAStim funcitons by EStimTitrator and… | Jul 24 2018 | |||
f643971bb42f | tlemaire | replaced runMech function by MechWorker class, added multiprocessing option to… | Jul 23 2018 | |||
40ccd8272444 | tlemaire | replaced runEStim funciton by EStimWorker class, added multiprocessing option… | Jul 23 2018 | |||
b1b868c26791 | tlemaire | replaced runAStim function by AStimWorker class, added multiprocessing option… | Jul 23 2018 | |||
b2f1c0675a20 | tlemaire | removed createLookup and getEffCoeffs methods from SolverUS, deleted old… | Jul 20 2018 | |||
3c4a0aef7824 | tlemaire | added multiprocessing functionality for lookups creation (Consumer and… | Jul 20 2018 | |||
8e3d2db927b5 | tlemaire | grouped mod files in single directory. defined stimonoff procedure in separate… | Jul 18 2018 | |||
09ead26fe237 | tlemaire | corrected TC mod file (needs smaller time step to be fully accurate). | Jul 17 2018 | |||
eaed73930e7c | tlemaire | separated mod files. corrected variables outputing in runNEURON. corrected Vm… | Jul 13 2018 | |||
cca23e04187b | tlemaire | improved runNEURON method. added LTS mechanism. | Jul 6 2018 | |||
5011ac8891a5 | tlemaire | added runNEURON method to run US simulation with NEURON (to be ctd). | Jul 5 2018 | |||
c98c3d8b1f8b | tlemaire | modified si_format for py35 compatibility. | Jul 4 2018 | |||
c35ee1510e54 | tlemaire | corrected Qm computation for EL simulations | Jul 4 2018 | |||
b8be2280d700 | tlemaire | added Qm to dataframe of EL simulations | Jul 4 2018 | |||
e238a7caa389 | tlemaire | minor modifications to plotActivationMap function, added plotTraces function… | May 22 2018 | |||
5232ea010459 | tlemaire | corrected minor mistakes in call to vectorized functions. | May 15 2018 | |||
383a6cb2fc75 | tlemaire | added method to find neuron-specific rheobase US amplitudes (findRheobaseAmps)… | May 8 2018 | |||
a148e58c0951 | tlemaire | divided 3D -> 1D lookups projection into 2 distinct steps (defined… | May 8 2018 | |||
718541c73181 | tlemaire | added plotDualMaxMap to pltutils. | May 6 2018 | |||
7e6607ff1a67 | tlemaire | added getMaxMap function to simutils | May 4 2018 | |||
462acad97d14 | tlemaire | added getCycleAverage and getActivationMap functions to utils | May 4 2018 | |||
9fc6ab4cdecc | tlemaire | added si_format function to format physical numbers according to the SI unit… | May 3 2018 | |||
162cb6e67011 | tlemaire | corrected logging error in runAStimBatch | May 2 2018 | |||
6392bff9bae7 | tlemaire | solved minor issue in findPeaks function (end of signal exception). | May 2 2018 | |||
419fdbc72f8c | tlemaire | replaced numpy.vectorize by explicit definition of vectorized BLS methods. | May 2 2018 | |||
f7bc3b340b2d | tlemaire | vectorized relevant functions of the BilayerSonophore class | May 2 2018 | |||
59edb2753a52 | tlemaire | added computeMeshEdges function to utils module. | May 2 2018 | |||
74c9b13f40bf | tlemaire | added reinit method to BilayerSonophore class. added ComputeSpikeMetrics… | Apr 30 2018 | |||
5e84496cf5e0 | tlemaire | added PmCompMethod as a parameter for all relevant methods of the… | Apr 24 2018 | |||
f6e428f6c231 | tlemaire | replaced assertion error by warning statement in case of peaks vs valleys… | Apr 18 2018 | |||
e2763f9ad093 | tlemaire | corrected return error in findPeaks. added new algorithmic constant: minimal… | Apr 17 2018 | |||
613073ed9c81 | tlemaire | increased amplitude precision for ESTIM and ASTIM file naming | Apr 17 2018 | |||
27332b793c2a | tlemaire | changed PRF and DC format in file naming (simutils output and pltutils input) | Apr 14 2018 | |||
d5e56c2f9c40 | tlemaire | replaced detectSpikes by the more robust findPeaks. added a plot_spikes script… | Apr 4 2018 | |||
6d97721d9c51 | tlemaire | solved rendering issue with plotComp. Implemented and tested a robust peak… | Apr 3 2018 | |||
6ec806aa90d6 | tlemaire | automatic detection of time vector uniformity in detectPeaksTime | Mar 30 2018 | |||
377594fb12b0 | tlemaire | added prominence threshold constant for spike detection. added skeleton for IB… | Mar 29 2018 | |||
3bee78ffb4bc | tlemaire | added extra options to plotComp (custom ticks, black legend with colored plots) | Mar 21 2018 | |||
3fabf680de73 | tlemaire | added detailed docstring to detectPeaks | Mar 20 2018 | |||
dd51b4283191 | tlemaire | corrected TOFF integration error in SolverElec. added PW tests to test_basic.py | Mar 19 2018 | |||
1c8f0234e7e7 | tlemaire | changes to plotComp function allowing to customize linestyles, colors and… | Mar 19 2018 | |||
900de6e3aa75 | Theo Lemaire | corrected initial conditions error in pulsed protocols integration of… | Mar 18 2018 | |||
708bc9223628 | Theo Lemaire | removed erroneous use of y_pulse_off in runClassic method | Mar 18 2018 | |||
c6b29afe2de9 | tlemaire | programmed classic method progress bar to show up both on DEBUG and INFO levels | Mar 16 2018 | |||
4b7e412bb8d6 | tlemaire | corrected createLookup runMech error by calling super.run method | Mar 16 2018 | |||
5049e821acd8 | tlemaire | Added user input to decide whether to continue batch after assertion error or… | Mar 16 2018 | |||
5b8f09fbd295 | tlemaire | renamed BilayerSonophore.runMech to BilayerSonophore.run, and runMechSingle to… | Mar 16 2018 | |||
50e85131e3d9 | tlemaire | added runMechSingle to simutils and MECH_run script | Mar 15 2018 | |||
69a4e42fa766 | tlemaire | added user input to decide whether lookup file should be overwritten in case of… | Mar 15 2018 | |||
4ffaa73494ea | tlemaire | introduced custom defined InputError exceptions (instead of assert statements)… | Mar 15 2018 | |||
9df57ec1684b | tlemaire | addded time-step-dependent output arrays downsampling in classic simulations to… | Mar 15 2018 | |||
d8a1246ad44e | tlemaire | temporarily removed checking for prior lookup file existence upon new lookup… | Mar 15 2018 | |||
b65f7bad637c | tlemaire | general optimization of integration methods (elec, mech and US classic) using… | Mar 14 2018 | |||
01238213b788 | tlemaire | Switched from ode (lsoda) to odeint for classic method to see if it solves… | Mar 13 2018 | |||
1b6d6a579519 | tlemaire | implemented neuron-specific charge interval for lookup creation. | Mar 13 2018 | |||
acab28778569 | tlemaire | changed "ch_mech" by "neuron" | Mar 13 2018 | |||
0c7107d859aa | tlemaire | added neuron name to meta dictionary for ESTIM and ASTIM simulations | Mar 13 2018 | |||
d2ee8d2274d4 | tlemaire | added tcomp to "meta" dictionary. | Mar 13 2018 | |||
1edd575f6465 | Theo Lemaire | replaced DF by DC, and added pandas dataframes to store and retrieve simulation… | Mar 13 2018 | |||
edd5594d9646 | Theo Lemaire | replaced channels by neurons | Mar 12 2018 | |||
8d85b3cb30d6 | tlemaire | adaptive time step lowering for high-PRF protocols in Elec and effective-US… | Mar 8 2018 | |||
63c842041ef8 | tlemaire | updated README and LICENCSE files. added extra BLS lookups. corrected titration… | Mar 7 2018 | |||
89d20f6d2cb6 | tlemaire | updated titration methods and generated LeechP lookups | Feb 28 2018 | |||
7497a2150a6b | tlemaire | corrected computation of firing rate in detectSpikes function | Jan 16 2018 | |||
ae51b3bafaec | tlemaire | Added sonophore diameter to ASTIM files naming, and changed DF to 2 decimals… | Nov 29 2017 | |||
c9dad3d35684 | tlemaire | corrected code for LeechT neuron, and validated it on electrical stimuli | Nov 22 2017 | |||
6be1756dda64 | tlemaire | added biomech and biophys parameters directly as BilayerSonophore class… | Sep 12 2017 | |||
6cd8d175ad7b | tlemaire | improved error handling | Sep 10 2017 | |||
43647159e654 | tlemaire | replaced print statements with logging statements in internal modules | Sep 10 2017 | |||
ffed8b864bbf | tlemaire | replaced getopt with argparse in test scripts | Sep 6 2017 | |||
14d95d317eeb | tlemaire | replaced neurons object lists by neurons name list in batch functions input | Sep 6 2017 | |||
151337217cab | tlemaire | introduced default arguments in batch functions for bls_params and geom | Sep 6 2017 | |||
7fff2117cd10 | tlemaire | replaced printPct by progressbar | Sep 6 2017 | |||
63f20548155d | tlemaire | separated checkBatchLog function into setBatchDir and checkBatchLog functions | Sep 6 2017 | |||
8680bc7dccaf | tlemaire | added runEStim and runAStim functions. added locker to xlslog | Sep 4 2017 | |||
f51d67fdf64a | tlemaire | updated test_values | Sep 3 2017 | |||
92e2cd326a4e | tlemaire | added profiling option for each method inside test_basic.py, using cProfile and… | Sep 3 2017 | |||
b0a231289d69 | tlemaire | added standardized plotEffCoeffs function to pltutils | Sep 2 2017 | |||
3f5921510ae9 | tlemaire | added plotGatingKinetics method to plot the steady-sate and time constant… | Sep 1 2017 | |||
32c77b1353fa | tlemaire | added temporary code to delay last pulse during PW stimuli in runEffective… | Sep 1 2017 | |||
e2ff032a6759 | tlemaire | added option to specify labels in plotComp | Sep 1 2017 | |||
cf8e6794b04c | tlemaire | debugged and validated new runEffective method: interpolation datasets at… | Aug 30 2017 | |||
7da392ae7e7a | tlemaire | added 2nd version of runEffective where 3D (f, A, Q) interpolation datasets are… | Aug 29 2017 | |||
071e81993e19 | tlemaire | modified data validation on Adrive for MECH and ASTIM simulations (strictly… | Aug 29 2017 | |||
0f69714e39ec | tlemaire | modified createLookup method to create, for each coefficient, a 3D array of… | Aug 29 2017 | |||
1ea422ad10eb | tlemaire | optimized effective method: 2D (amp, charge) coefficients interpolators are… | Aug 28 2017 | |||
90c71fb8d8e5 | tlemaire | updated run functions to deal with zero offset. updated test_graphs | Aug 28 2017 | |||
b50efb81b3cb | tlemaire | updated test_basic.py with more thorough tests. Added more thorough input… | Aug 28 2017 | |||
c30d03edb7cc | tlemaire | adapted plotComp to deal with pulsed ESTIM outputs and MECH outputs. corrected… | Aug 25 2017 | |||
0a89dde7f847 | tlemaire | implemented runMechBatch function. adapted plotBatch function to deal with MECH… | Aug 25 2017 | |||
c9053e689690 | tlemaire | added titrateEStim and titrateEStimBatch functions | Aug 25 2017 | |||
3c218a52595b | tlemaire | Added pulsed stimuli handling to SolverElec. Implemented moved titration… | Aug 25 2017 | |||
2c7de2047898 | tlemaire | introduced standardized workflow for both E-STIM and A-STIM simulations and… | Aug 24 2017 | |||
4f9a8fd2aed4 | tlemaire | moved some utils functions into simutils & pltutils modules | Aug 23 2017 | |||
af10a48546b7 | tlemaire | created plotting module inside package, with plotComp and plotBatch functions | Aug 23 2017 | |||
abfba2e921d7 | tlemaire | first commit to c4science | Aug 23 2017 |
c4science · Help