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History Graph
History Graph
Commit | Author | Details | Committed | ||||
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532e76eaa491 | tlemaire | minor corrections to plotComp and si_format. | May 15 2018 | ||||
5232ea010459 | tlemaire | corrected minor mistakes in call to vectorized functions. | May 15 2018 | ||||
ddd04f71a3b3 | tlemaire | adapted plot settings (font and dimensions) for paper figures. | May 11 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 | ||||
75b8e9964108 | tlemaire | added plotActivationMap to pltutils. | May 4 2018 | ||||
7e6607ff1a67 | tlemaire | added getMaxMap function to simutils | May 4 2018 | ||||
462acad97d14 | tlemaire | added getCycleAverage and getActivationMap functions to utils | May 4 2018 | ||||
7624ecfb5947 | tlemaire | modified si_format to work also on tuples and lists. | May 4 2018 | ||||
ea14e67aae6f | tlemaire | solved minor issue in getPatchesLoc. replaced Rectangle by axvspan instances… | May 3 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 | ||||
9435cc4aff31 | tlemaire | vecotrized tauu method of LTS and TC neurons | May 2 2018 | ||||
f7bc3b340b2d | tlemaire | vectorized relevant functions of the BilayerSonophore class | May 2 2018 | ||||
120267c92007 | tlemaire | modified batch_ASTIM.py for activation maps | 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 | ||||
a7922aa5b6ad | tlemaire | added __str__ method to BilayerSonophore class that prints values of class and… | Apr 22 2018 | ||||
70d9c59ab1d9 | tlemaire | added IB testing in test_values script | Apr 18 2018 | ||||
3f620b0c56a0 | tlemaire | added lookups for IB neuron | Apr 18 2018 | ||||
f6e428f6c231 | tlemaire | replaced assertion error by warning statement in case of peaks vs valleys… | Apr 18 2018 | ||||
cf488f35629b | tlemaire | corrected scripts names in setup.py | Apr 17 2018 | ||||
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 | ||||
bea9167abc2b | tlemaire | changed names of simulation scripts for more intuitive use | 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 | ||||
cf2459c7182e | tlemaire | removed unwanted data files from sim directory | 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 | ||||
34958bd21f55 | tlemaire | adapted batch files for LeechP | Mar 8 2018 | ||||
8d85b3cb30d6 | tlemaire | adaptive time step lowering for high-PRF protocols in Elec and effective-US… | Mar 8 2018 | ||||
6e5878fe0ecf | tlemaire | corrected PRF display issues in command line scripts ESTIM_run and ASTIM_run | Mar 7 2018 | ||||
63c842041ef8 | tlemaire | updated README and LICENCSE files. added extra BLS lookups. corrected titration… | Mar 7 2018 | ||||
063d417bd20c | tlemaire | added pre-commit hook and adapted run_tests.sh command | Mar 2 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 | ||||
bf5a88531d4b | tlemaire | tried to adapt pre-commit hook after Anaconda re-install to call python with… | Jan 18 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 | ||||
69e2945beb69 | tlemaire | added latest dependencies to setup file | 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 | ||||
3cb02a5f8d12 | tlemaire | emphasized code in README | Sep 12 2017 | ||||
d67a94aa1050 | tlemaire | modified README file to include installation and usage info | Sep 12 2017 | ||||
6be1756dda64 | tlemaire | added biomech and biophys parameters directly as BilayerSonophore class… | Sep 12 2017 |
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