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History Graph
Commit | Author | Details | Committed | ||||
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e73ca2da1333 | tlemaire | corrected STN lookups. added testQSS script to analyze STN neuron plateau… | Mar 8 2019 | ||||
990c8181cf46 | tlemaire | corrected sigmaT2_b from -10 mV to 10 mV in STN implementation. started new QSS… | Mar 7 2019 | ||||
da8e0bbde997 | tlemaire | renamed currents for more clarity | Mar 6 2019 | ||||
2e64aa90c325 | tlemaire | changed nomenclature of current methods from "curr..." to "i..." | Mar 5 2019 | ||||
c72b7b319ed0 | tlemaire | implemented getLookupsOff function to retrieve US-OFF lookups. adapted… | Mar 5 2019 | ||||
865020d8c630 | tlemaire | added RS neuron lookups with partial coverage (spatially averaged). updated… | Feb 28 2019 | ||||
702446ca2ad5 | tlemaire | corrected error in getLookups2Dfs | Jan 23 2019 | ||||
957db9d021d6 | tlemaire | added getLookups2Dfs method to interpolate lookups at given membrane coverage. | Jan 23 2019 | ||||
80aa94a42257 | tlemaire | added script to compute quick lookups for a span of partial sonophore coverage… | Jan 23 2019 | ||||
69f20e7c2a18 | tlemaire | modified Qbounds to account for capacitance value in all neuron types. | Jan 11 2019 | ||||
cf20bd8f6516 | tlemaire | added lookups for FH membrane mechanism (tested) | Jan 11 2019 | ||||
8684707c3f08 | tlemaire | corrected Qbounds for lookups generation in FH neuron | Jan 10 2019 | ||||
82590fe13581 | tlemaire | changed PMAVG_STD_ERR_MAX value to allow BLS lookups generation for FH… | Jan 9 2019 | ||||
65c1d8649331 | tlemaire | implemented Frankenhaeuser-Huxley membrane mechanism (validated against data… | Jan 9 2019 | ||||
8a4719662fd9 | tlemaire | corrected error in Vm post-processing in runSONIC. added plotV option to… | Dec 27 2018 | ||||
42f56ab271e3 | tlemaire | modified plotActivationMap to plot amplitude thresholds computed from titration… | Dec 14 2018 | ||||
0fcd53a68ce7 | tlemaire | added pltvars for STN neuron. added plotFRprofile function along with paper… | Dec 9 2018 | ||||
81adcb430e9f | tlemaire | implemented notebook for validation of STN neuron (both ESTIM and ASTIM). | Dec 4 2018 | ||||
e99b70b6952c | tlemaire | added STN lookups and corrected derEffStates method. | Dec 4 2018 | ||||
7655cca494a0 | tlemaire | corrected STN getEffRates and derStatesEff methods for correct lookups creation… | Dec 3 2018 | ||||
9eca746695d1 | tlemaire | STN model validated for E-STIM by reproduction of key features (spontaneous… | Dec 3 2018 | ||||
0ebd7ae3b932 | tlemaire | replaced 'L' by 'Leak' in neurons nomenclature. implemented STN neuron with… | Nov 30 2018 | ||||
850b05b61c5e | tlemaire | added plotFRspectrum function to actmap module. updated fig7 script, and added… | Nov 29 2018 | ||||
fa4c643a5a4b | tlemaire | added spanDC argument to run_astim. removed rheobase amp preconditioning in… | Nov 27 2018 | ||||
84a00ea7e59b | tlemaire | recomputed lookups for all CNS neurons. modified figs 5 and 6 generation… | Nov 27 2018 | ||||
9f827c942524 | tlemaire | added recording of computation times during lookups creation. | Nov 25 2018 | ||||
b9f44bd89005 | tlemaire | improved methods that generate figures 5 & 6 of SONIC paper. | Nov 22 2018 | ||||
2f63e4926c36 | tlemaire | improved plotRheobaseAmps function. improved arguments parsing in command line… | Nov 22 2018 | ||||
8573c726b480 | tlemaire | modified getLookups2D to project along any dimensions pair in (a, f, A). | Nov 20 2018 | ||||
da009206a90e | tlemaire | modified runSONIC method to use odeint solver with interpolated lookups for… | Nov 19 2018 | ||||
d17615ffb4e6 | tlemaire | improved plotPhasePlane function. implemented isWithin function for loose bound… | Oct 28 2018 | ||||
35b8bf12ec49 | tlemaire | plotPhaseDiagram method validated on CW stimuli | Oct 25 2018 | ||||
d2b627754312 | tlemaire | implemented figtitle method for direct labeling from metadata. implemented… | Oct 25 2018 | ||||
ea968231b9bb | tlemaire | deleted old docs files. | Oct 5 2018 | ||||
cb633e403bc8 | tlemaire | cleaned up figures scripts. | Oct 2 2018 | ||||
ed0d192b377b | tlemaire | added scripts to generate paper figures automatically. | Oct 2 2018 | ||||
fe08c7f79e09 | tlemaire | moved run_tests.sh to tests folder | Sep 28 2018 | ||||
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 |
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