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History Graph
Commit | Author | Details | Committed | ||||
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73851d6ac128 | tlemaire | updated package documentation | Sep 28 2018 | ||||
d2bb8612b26e | tlemaire | new lookup tables for IB, LeechT and LeechP neurons. | Sep 28 2018 | ||||
3ba84a26398c | tlemaire | revmoved old TC.mod file | Sep 27 2018 | ||||
0927fba5ad55 | tlemaire | removed print statements in run_astim | Sep 27 2018 | ||||
81ffd1c605f6 | tlemaire | added LTS and TC lookups. corrected errors in run_astim and run_estim arguments… | Sep 27 2018 | ||||
f5f327799ad4 | tlemaire | attempt to fix multiprocessing lookups creation. | Sep 27 2018 | ||||
7075d3ab7f91 | tlemaire | removed pltutils file | Sep 26 2018 | ||||
4a67049acd76 | tlemaire | added actmap to plt module, with command line script. | Sep 26 2018 | ||||
7bd042cd39f7 | tlemaire | corrected error on lookups dict save. | Sep 26 2018 | ||||
0412541be120 | tlemaire | fixed call to plotBatch in run scripts | Sep 25 2018 | ||||
a35c13583071 | tlemaire | moved plotComp and plotBatch functions to separate files. created unique plot… | Sep 25 2018 | ||||
8819bbb0e66f | tlemaire | cleaned up deprecated folder. added notebook about balance quasi-steady… | Sep 25 2018 | ||||
610dc8472dcf | tlemaire | cleaned up utils module. removed log templates (now generated on the fly with… | Sep 25 2018 | ||||
954e545fa6ac | tlemaire | turned intermolecular pressure test script into notebook. removed Input error… | Sep 24 2018 | ||||
1951d49ccd25 | tlemaire | moved lookups into neurons folder | Sep 24 2018 | ||||
4c4f11074ce9 | tlemaire | cleaned up plot_batch and plot_comp scripts | Sep 24 2018 | ||||
4d53b2a42b5e | tlemaire | moved relevant plot scripts to scripts folder. Turned analysis scripts into… | Sep 24 2018 | ||||
559985791c43 | tlemaire | changed scripts names to lowercase | Sep 23 2018 | ||||
de613ac9c35a | tlemaire | replaced SonicNeuron by NeuronalBilayerSonophore | Sep 23 2018 | ||||
2dc56eb8b91e | tlemaire | removed InputError references in core modules | Sep 23 2018 | ||||
2a334b211bff | tlemaire | major changes to the package (PointNeuron, SonicNeuron, ...) | Sep 23 2018 | ||||
193d4adc2a5f | tlemaire | included 4D lookup for RS neuron. | Sep 19 2018 | ||||
b115baec5ab3 | tlemaire | added vtrap function to compute rate constants. added selectDirDialog function… | Sep 19 2018 | ||||
06fa4e9d8465 | tlemaire | minor improvements on findPeaks function. changed Worker call method to… | Sep 19 2018 | ||||
c0b25f676500 | tlemaire | corrected generic worker call method | Sep 15 2018 | ||||
d481c6dc0ac6 | tlemaire | prepared getLookups2D for interpolation in 4D space. added computeTestLookups… | Sep 15 2018 | ||||
66e78783dda3 | tlemaire | removed use of itrpLookupsFreq by simple scipy.interp1d call | Sep 14 2018 | ||||
0178f67d315e | tlemaire | redesigned lookups creation to work with sonophore diameter as 4th dimension | Sep 14 2018 | ||||
492f512dbaee | tlemaire | added 50nm diameter BLS lookup | Sep 12 2018 | ||||
4404c3e28711 | tlemaire | merged BLS_lookups file into 1 file with 2D (a, Qm0) lookup | Sep 12 2018 | ||||
841338ad53f6 | tlemaire | added getDefaultIndexes to utils | Sep 10 2018 | ||||
eb527762650d | tlemaire | added sequential color mode to plotSignals. updated REDAME.md | Aug 30 2018 | ||||
23060daa6da3 | tlemaire | added integer conversion for frequency checking in itrpLoouksFreq. corrected… | Aug 28 2018 | ||||
54c29644be81 | tlemaire | replaced runEffective by runSONIC and 'effective' keyword by 'sonic'. | Aug 25 2018 | ||||
8b21667afa18 | tlemaire | added checkNumBounds function to utils. | Aug 24 2018 | ||||
50542c086cc4 | tlemaire | added plotSignals function to pltutils. | Aug 22 2018 | ||||
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 | ||||
1f7dfe26adab | tlemaire | removed stimulation parameters assignment in MOD files | Jul 24 2018 | ||||
e18d135cbc54 | tlemaire | new lookups for RS, FS, LTS, RE and TC neurons with extended charge range (down… | Jul 24 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 | ||||
bf0df29c93c6 | tlemaire | cleaned up new lookups_ASTIM script | Jul 20 2018 | ||||
3c4a0aef7824 | tlemaire | added multiprocessing functionality for lookups creation (Consumer and… | Jul 20 2018 | ||||
1d72b1a13aa1 | tlemaire | removed old mod folders | Jul 18 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 | ||||
2449b629e794 | tlemaire | added FS and RE mechs. | Jul 6 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 | ||||
320fafe51ff9 | tlemaire | added int64 handling in si_format. | Jul 4 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 | ||||
3b9d8b293e8a | tlemaire | minor modifications to plotEffVars, rescale and test_intermolecular_pressure.py | Jun 18 2018 | ||||
bd1e86dc1591 | tlemaire | added automatic y-scaling of effective variables in plotEffVars. | May 25 2018 | ||||
00baa42adf67 | tlemaire | renamed plotEffCoeffs to plotEffVariables with lots of improvements. | May 25 2018 | ||||
7d33ab6ec1f9 | tlemaire | added script to test intermoleulcar pressure approximation. | May 25 2018 | ||||
e238a7caa389 | tlemaire | minor modifications to plotActivationMap function, added plotTraces function… | May 22 2018 | ||||
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 |
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