Diffusion PySONIC (old) (master) History

History
master8573c726b48090ae5a0c6c0…

Nov 20 2018

modified getLookups2D to project along any dimensions pair in (a, f, A).
8573c726b480
·tlemaire on Nov 20 2018, 19:32.

Nov 19 2018

modified runSONIC method to use odeint solver with interpolated lookups for…
da009206a90e
·tlemaire on Nov 19 2018, 21:46.

Oct 28 2018

improved plotPhasePlane function. implemented isWithin function for loose bound…
d17615ffb4e6
·tlemaire on Oct 28 2018, 22:49.

Oct 25 2018

plotPhaseDiagram method validated on CW stimuli
35b8bf12ec49
·tlemaire on Oct 25 2018, 22:49.
implemented figtitle method for direct labeling from metadata. implemented…
d2b627754312
·tlemaire on Oct 25 2018, 14:52.

Oct 5 2018

deleted old docs files.
ea968231b9bb
·tlemaire on Oct 5 2018, 09:14.

Oct 2 2018

cleaned up figures scripts.
cb633e403bc8
·tlemaire on Oct 2 2018, 13:53.
added scripts to generate paper figures automatically.
ed0d192b377b
·tlemaire on Oct 2 2018, 02:55.

Sep 28 2018

moved run_tests.sh to tests folder
fe08c7f79e09
·tlemaire on Sep 28 2018, 14:25.
updated package documentation
73851d6ac128
·tlemaire on Sep 28 2018, 14:23.
new lookup tables for IB, LeechT and LeechP neurons.
d2bb8612b26e
·tlemaire on Sep 28 2018, 01:13.

Sep 27 2018

revmoved old TC.mod file
3ba84a26398c
·tlemaire on Sep 27 2018, 11:25.
removed print statements in run_astim
0927fba5ad55
·tlemaire on Sep 27 2018, 11:17.
added LTS and TC lookups. corrected errors in run_astim and run_estim arguments…
81ffd1c605f6
·tlemaire on Sep 27 2018, 11:16.
attempt to fix multiprocessing lookups creation.
f5f327799ad4
·tlemaire on Sep 27 2018, 03:03.

Sep 26 2018

removed pltutils file
7075d3ab7f91
·tlemaire on Sep 26 2018, 17:26.
added actmap to plt module, with command line script.
4a67049acd76
·tlemaire on Sep 26 2018, 17:06.
corrected error on lookups dict save.
7bd042cd39f7
·tlemaire on Sep 26 2018, 09:33.

Sep 25 2018

fixed call to plotBatch in run scripts
0412541be120
·tlemaire on Sep 25 2018, 18:03.
moved plotComp and plotBatch functions to separate files. created unique plot…
a35c13583071
·tlemaire on Sep 25 2018, 17:25.
cleaned up deprecated folder. added notebook about balance quasi-steady…
8819bbb0e66f
·tlemaire on Sep 25 2018, 16:13.
cleaned up utils module. removed log templates (now generated on the fly with…
610dc8472dcf
·tlemaire on Sep 25 2018, 14:46.

Sep 24 2018

turned intermolecular pressure test script into notebook. removed Input error…
954e545fa6ac
·tlemaire on Sep 24 2018, 23:54.
moved lookups into neurons folder
1951d49ccd25
·tlemaire on Sep 24 2018, 21:48.
cleaned up plot_batch and plot_comp scripts
4c4f11074ce9
·tlemaire on Sep 24 2018, 21:08.
moved relevant plot scripts to scripts folder. Turned analysis scripts into…
4d53b2a42b5e
·tlemaire on Sep 24 2018, 21:00.

Sep 23 2018

changed scripts names to lowercase
559985791c43
·tlemaire on Sep 23 2018, 16:18.
replaced SonicNeuron by NeuronalBilayerSonophore
de613ac9c35a
·tlemaire on Sep 23 2018, 15:33.
removed InputError references in core modules
2dc56eb8b91e
·tlemaire on Sep 23 2018, 14:41.
major changes to the package (PointNeuron, SonicNeuron, ...)
2a334b211bff
·tlemaire on Sep 23 2018, 14:28.

Sep 19 2018

included 4D lookup for RS neuron.
193d4adc2a5f
·tlemaire on Sep 19 2018, 20:11.
added vtrap function to compute rate constants. added selectDirDialog function…
b115baec5ab3
·tlemaire on Sep 19 2018, 16:13.
minor improvements on findPeaks function. changed Worker call method to…
06fa4e9d8465
·tlemaire on Sep 19 2018, 13:43.

Sep 15 2018

corrected generic worker call method
c0b25f676500
·tlemaire on Sep 15 2018, 18:08.
prepared getLookups2D for interpolation in 4D space. added computeTestLookups…
d481c6dc0ac6
·tlemaire on Sep 15 2018, 17:12.

Sep 14 2018

removed use of itrpLookupsFreq by simple scipy.interp1d call
66e78783dda3
·tlemaire on Sep 14 2018, 17:32.
redesigned lookups creation to work with sonophore diameter as 4th dimension
0178f67d315e
·tlemaire on Sep 14 2018, 14:49.

Sep 12 2018

added 50nm diameter BLS lookup
492f512dbaee
·tlemaire on Sep 12 2018, 18:48.
merged BLS_lookups file into 1 file with 2D (a, Qm0) lookup
4404c3e28711
·tlemaire on Sep 12 2018, 18:44.

Sep 10 2018

added getDefaultIndexes to utils
841338ad53f6
·tlemaire on Sep 10 2018, 16:29.

Aug 30 2018

added sequential color mode to plotSignals. updated REDAME.md
eb527762650d
·tlemaire on Aug 30 2018, 20:10.

Aug 28 2018

added integer conversion for frequency checking in itrpLoouksFreq. corrected…
23060daa6da3
·tlemaire on Aug 28 2018, 15:40.

Aug 25 2018

replaced runEffective by runSONIC and 'effective' keyword by 'sonic'.
54c29644be81
·tlemaire on Aug 25 2018, 02:15.

Aug 24 2018

added checkNumBounds function to utils.
8b21667afa18
·tlemaire on Aug 24 2018, 18:45.

Aug 22 2018

added plotSignals function to pltutils.
50542c086cc4
·tlemaire on Aug 22 2018, 02:39.

Aug 21 2018

changed package name to PySONIC.
043172721a44
·tlemaire on Aug 21 2018, 16:19.
removed NEURON related code from package (runNEURON method, NMODL folder), used…
2267460a3b52
·tlemaire on Aug 21 2018, 14:29.

Jul 24 2018

removed stimulation parameters assignment in MOD files
1f7dfe26adab
·tlemaire on Jul 24 2018, 15:01.
new lookups for RS, FS, LTS, RE and TC neurons with extended charge range (down…
e18d135cbc54
·tlemaire on Jul 24 2018, 12:16.
replaced titrateEStim and titrateAStim funcitons by EStimTitrator and…
9a37cd335585
·tlemaire on Jul 24 2018, 12:03.

Jul 23 2018

replaced runMech function by MechWorker class, added multiprocessing option to…
f643971bb42f
·tlemaire on Jul 23 2018, 14:40.
replaced runEStim funciton by EStimWorker class, added multiprocessing option…
40ccd8272444
·tlemaire on Jul 23 2018, 13:41.
replaced runAStim function by AStimWorker class, added multiprocessing option…
b1b868c26791
·tlemaire on Jul 23 2018, 11:40.

Jul 20 2018

removed createLookup and getEffCoeffs methods from SolverUS, deleted old…
b2f1c0675a20
·tlemaire on Jul 20 2018, 18:22.
cleaned up new lookups_ASTIM script
bf0df29c93c6
·tlemaire on Jul 20 2018, 18:09.
added multiprocessing functionality for lookups creation (Consumer and…
3c4a0aef7824
·tlemaire on Jul 20 2018, 18:05.

Jul 18 2018

removed old mod folders
1d72b1a13aa1
·tlemaire on Jul 18 2018, 15:49.
grouped mod files in single directory. defined stimonoff procedure in separate…
8e3d2db927b5
·tlemaire on Jul 18 2018, 15:44.

Jul 17 2018

corrected TC mod file (needs smaller time step to be fully accurate).
09ead26fe237
·tlemaire on Jul 17 2018, 16:29.

Jul 13 2018

separated mod files. corrected variables outputing in runNEURON. corrected Vm…
eaed73930e7c
·tlemaire on Jul 13 2018, 14:59.

Jul 6 2018

added FS and RE mechs.
2449b629e794
·tlemaire on Jul 6 2018, 18:48.
improved runNEURON method. added LTS mechanism.
cca23e04187b
·tlemaire on Jul 6 2018, 17:44.

Jul 5 2018

added runNEURON method to run US simulation with NEURON (to be ctd).
5011ac8891a5
·tlemaire on Jul 5 2018, 23:50.

Jul 4 2018

added int64 handling in si_format.
320fafe51ff9
·tlemaire on Jul 4 2018, 17:25.
modified si_format for py35 compatibility.
c98c3d8b1f8b
·tlemaire on Jul 4 2018, 17:18.
corrected Qm computation for EL simulations
c35ee1510e54
·tlemaire on Jul 4 2018, 11:49.
added Qm to dataframe of EL simulations
b8be2280d700
·tlemaire on Jul 4 2018, 11:47.

Jun 18 2018

minor modifications to plotEffVars, rescale and test_intermolecular_pressure.py
3b9d8b293e8a
·tlemaire on Jun 18 2018, 17:02.

May 25 2018

added automatic y-scaling of effective variables in plotEffVars.
bd1e86dc1591
·tlemaire on May 25 2018, 22:25.
renamed plotEffCoeffs to plotEffVariables with lots of improvements.
00baa42adf67
·tlemaire on May 25 2018, 22:11.
added script to test intermoleulcar pressure approximation.
7d33ab6ec1f9
·tlemaire on May 25 2018, 15:45.

May 22 2018

minor modifications to plotActivationMap function, added plotTraces function…
e238a7caa389
·tlemaire on May 22 2018, 16:36.

May 15 2018

minor corrections to plotComp and si_format.
532e76eaa491
·tlemaire on May 15 2018, 19:04.
corrected minor mistakes in call to vectorized functions.
5232ea010459
·tlemaire on May 15 2018, 11:29.

May 11 2018

adapted plot settings (font and dimensions) for paper figures.
ddd04f71a3b3
·tlemaire on May 11 2018, 14:26.

May 8 2018

added method to find neuron-specific rheobase US amplitudes (findRheobaseAmps)…
383a6cb2fc75
·tlemaire on May 8 2018, 15:19.
divided 3D -> 1D lookups projection into 2 distinct steps (defined…
a148e58c0951
·tlemaire on May 8 2018, 10:40.

May 6 2018

added plotDualMaxMap to pltutils.
718541c73181
·tlemaire on May 6 2018, 22:21.

May 4 2018

added plotActivationMap to pltutils.
75b8e9964108
·tlemaire on May 4 2018, 17:39.
added getMaxMap function to simutils
7e6607ff1a67
·tlemaire on May 4 2018, 16:40.
added getCycleAverage and getActivationMap functions to utils
462acad97d14
·tlemaire on May 4 2018, 16:16.
modified si_format to work also on tuples and lists.
7624ecfb5947
·tlemaire on May 4 2018, 11:13.

May 3 2018

solved minor issue in getPatchesLoc. replaced Rectangle by axvspan instances…
ea14e67aae6f
·tlemaire on May 3 2018, 17:09.
added si_format function to format physical numbers according to the SI unit…
9fc6ab4cdecc
·tlemaire on May 3 2018, 12:42.

May 2 2018

corrected logging error in runAStimBatch
162cb6e67011
·tlemaire on May 2 2018, 22:26.
solved minor issue in findPeaks function (end of signal exception).
6392bff9bae7
·tlemaire on May 2 2018, 22:10.
replaced numpy.vectorize by explicit definition of vectorized BLS methods.
419fdbc72f8c
·tlemaire on May 2 2018, 21:15.
vecotrized tauu method of LTS and TC neurons
9435cc4aff31
·tlemaire on May 2 2018, 15:46.
vectorized relevant functions of the BilayerSonophore class
f7bc3b340b2d
·tlemaire on May 2 2018, 15:40.
modified batch_ASTIM.py for activation maps
120267c92007
·tlemaire on May 2 2018, 12:14.
added computeMeshEdges function to utils module.
59edb2753a52
·tlemaire on May 2 2018, 11:38.

Apr 30 2018

added reinit method to BilayerSonophore class. added ComputeSpikeMetrics…
74c9b13f40bf
·tlemaire on Apr 30 2018, 13:55.

Apr 24 2018

added PmCompMethod as a parameter for all relevant methods of the…
5e84496cf5e0
·tlemaire on Apr 24 2018, 19:06.

Apr 22 2018

added __str__ method to BilayerSonophore class that prints values of class and…
a7922aa5b6ad
·tlemaire on Apr 22 2018, 23:54.

Apr 18 2018

added IB testing in test_values script
70d9c59ab1d9
·tlemaire on Apr 18 2018, 18:24.
added lookups for IB neuron
3f620b0c56a0
·tlemaire on Apr 18 2018, 18:04.
replaced assertion error by warning statement in case of peaks vs valleys…
f6e428f6c231
·tlemaire on Apr 18 2018, 11:36.

Apr 17 2018

corrected scripts names in setup.py
cf488f35629b
·tlemaire on Apr 17 2018, 18:06.
validated IB neuron gating kinetics for E-STIM
487fd2f0db0a
·tlemaire on Apr 17 2018, 17:11.
corrected return error in findPeaks. added new algorithmic constant: minimal…
e2763f9ad093
·tlemaire on Apr 17 2018, 11:45.

Historymaster8573c726b48090ae5a0c6c0…

Nov 20 2018

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History
master8573c726b48090ae5a0c6c0…