R4670/PointNICEmaster
R4670/PointNICE
master
History Graph
History Graph
Commit | Author | Details | Committed | |||
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487fd2f0db0a | tlemaire | validated IB neuron gating kinetics for E-STIM | Apr 17 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 | |||
a5aaa17fbd90 | tlemaire | removed dependency on colorlover in plotComp | 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 | |||
8b637407388b | tlemaire | corrected few mistakes in IB neuron implementation | Mar 30 2018 | |||
cf2846af1ead | tlemaire | added better inset handling in plotComp | Mar 30 2018 | |||
1ac82339eaf3 | tlemaire | modified plotComp to take only 1 input variable and added option to plot inset | Mar 30 2018 | |||
6ec806aa90d6 | tlemaire | automatic detection of time vector uniformity in detectPeaksTime | Mar 30 2018 | |||
19a21b2ee66b | tlemaire | renamed matlab utils function more explicitely. | Mar 29 2018 | |||
377594fb12b0 | tlemaire | added prominence threshold constant for spike detection. added skeleton for IB… | Mar 29 2018 | |||
c916dd9c8f25 | tlemaire | added method to extract compuation times in utils module | Mar 27 2018 | |||
e59db772ab09 | tlemaire | minor improvements to pltutils module | Mar 22 2018 | |||
80b620b50b12 | tlemaire | removed italic for latex style labelling in plotComp | Mar 22 2018 | |||
d7f0d2a86ee2 | tlemaire | added option to change linestyle of legend handles (dashed -> straight) | Mar 22 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 | |||
ee3a47c57d36 | Theo Lemaire | Added new LeechP lookups | Mar 17 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 | |||
b9f08f5eaf67 | tlemaire | added new lookups except LeechP | 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 | |||
4c475209bac9 | tlemaire | corrected Z bounding for out-of-range deflections | 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 | |||
4d2d60cc96c5 | tlemaire | generated new lookups for RS and FS neurons with a wider frequency range (20kHz… | Mar 15 2018 | |||
e5a0b44e3d54 | tlemaire | renamed INPUT_CHARGE_RANGE to CHARGE_RANGE | Mar 15 2018 | |||
d350701db48c | tlemaire | added correction of deflection value in eqMech (with warning) if below critical… | 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 | |||
10fde2422c97 | tlemaire | replaced error raising by a simple warning for out-of-range deflections in… | 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 | |||
d01c70ab720e | tlemaire | prepared creation of new lookups | 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 | |||
41e27b5ece2e | tlemaire | tested and validated plotting with pandas dataframes. | 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 | |||
d12141d0c48b | tlemaire | extended installation instructions in the README file | Mar 2 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 | |||
c59a8267c97e | tlemaire | corrected LeechP implementation using dynamic Nernst potentials for Sodium and… | Jan 9 2018 | |||
33ee63af70aa | tlemaire | Lots of corrections and improvements to the LeechP model implementation. E-STIM… | Dec 12 2017 | |||
094fd25223f4 | tlemaire | added LeechPressure to channels init. added leechP variables to pltvars. tested… | Dec 1 2017 | |||
a270608c8e8c | tlemaire | implemented leechP intracellular pools evolution according to modelDB ref | Nov 29 2017 | |||
ae51b3bafaec | tlemaire | Added sonophore diameter to ASTIM files naming, and changed DF to 2 decimals… | Nov 29 2017 | |||
1bb50e8f0025 | tlemaire | validated effective method for LeechT neuron, added that neuron to test_values. | Nov 27 2017 | |||
f1fbc6e5b9bb | tlemaire | added LeechT lookup | Nov 24 2017 | |||
e5364755a2a5 | tlemaire | added lookup files and template log files to tracking | Nov 22 2017 | |||
c9dad3d35684 | tlemaire | corrected code for LeechT neuron, and validated it on electrical stimuli | Nov 22 2017 | |||
6249b5298f4c | tlemaire | debugged double printing issue of logging statements | Sep 12 2017 | |||
6be1756dda64 | tlemaire | added biomech and biophys parameters directly as BilayerSonophore class… | Sep 12 2017 | |||
c67c8c39a93b | tlemaire | added input pltvars checking to plot functions | Sep 10 2017 | |||
189a078bf8d2 | tlemaire | added color to logging statements | Sep 10 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 | |||
15cf962d7fc7 | tlemaire | added ASTIM_run script to run single ASTIM simulation from command line | 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 | |||
6688904b2a82 | tlemaire | added smart loading of derived parameters from lookup file at BLS initiation | Sep 3 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 | |||
08165e6a06f3 | tlemaire | replaced eval statements from plotGatingKinetics & plotRateConstants by getattr… | Sep 1 2017 | |||
4c66e98d971e | tlemaire | added standardized plotRateConstants method | Sep 1 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 | |||
c5cad185b222 | tlemaire | added getNeuronsDict function to utils | 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 | |||
c61b8e3492f6 | tlemaire | renamed LoadParams to load_BLS_params | Aug 28 2017 | |||
b50efb81b3cb | tlemaire | updated test_basic.py with more thorough tests. Added more thorough input… | Aug 28 2017 | |||
06127af4b669 | tlemaire | included default plotting scheme inside neuron classes definition. Modified… | Aug 25 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 | |||
788e6d1c95b2 | tlemaire | added smart labels to plotComp, smart title to plotBatch | Aug 24 2017 |
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