Diffusion PySONIC (old) (master) History

History
master1951d49ccd25614064ea13b…

Sep 24 2018

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.
changed names of simulation scripts for more intuitive use
bea9167abc2b
·tlemaire on Apr 17 2018, 11:12.
increased amplitude precision for ESTIM and ASTIM file naming
613073ed9c81
·tlemaire on Apr 17 2018, 11:08.

Apr 14 2018

changed PRF and DC format in file naming (simutils output and pltutils input)
27332b793c2a
·tlemaire on Apr 14 2018, 19:41.
removed dependency on colorlover in plotComp
a5aaa17fbd90
·tlemaire on Apr 14 2018, 18:38.

Apr 4 2018

replaced detectSpikes by the more robust findPeaks. added a plot_spikes script…
d5e56c2f9c40
·tlemaire on Apr 4 2018, 17:55.

Apr 3 2018

solved rendering issue with plotComp. Implemented and tested a robust peak…
6d97721d9c51
·tlemaire on Apr 3 2018, 20:30.

Mar 30 2018

corrected few mistakes in IB neuron implementation
8b637407388b
·tlemaire on Mar 30 2018, 18:17.
added better inset handling in plotComp
cf2846af1ead
·tlemaire on Mar 30 2018, 18:09.
modified plotComp to take only 1 input variable and added option to plot inset
1ac82339eaf3
·tlemaire on Mar 30 2018, 16:58.
automatic detection of time vector uniformity in detectPeaksTime
6ec806aa90d6
·tlemaire on Mar 30 2018, 13:02.

Mar 29 2018

renamed matlab utils function more explicitely.
19a21b2ee66b
·tlemaire on Mar 29 2018, 19:00.
added prominence threshold constant for spike detection. added skeleton for IB…
377594fb12b0
·tlemaire on Mar 29 2018, 18:04.

Mar 27 2018

added method to extract compuation times in utils module
c916dd9c8f25
·tlemaire on Mar 27 2018, 14:49.

Mar 22 2018

minor improvements to pltutils module
e59db772ab09
·tlemaire on Mar 22 2018, 01:45.
removed italic for latex style labelling in plotComp
80b620b50b12
·tlemaire on Mar 22 2018, 00:27.
added option to change linestyle of legend handles (dashed -> straight)
d7f0d2a86ee2
·tlemaire on Mar 22 2018, 00:17.

Mar 21 2018

added extra options to plotComp (custom ticks, black legend with colored plots)
3bee78ffb4bc
·tlemaire on Mar 21 2018, 18:34.

Mar 20 2018

added detailed docstring to detectPeaks
3fabf680de73
·tlemaire on Mar 20 2018, 21:49.

Mar 19 2018

corrected TOFF integration error in SolverElec. added PW tests to test_basic.py
dd51b4283191
·tlemaire on Mar 19 2018, 20:03.
changes to plotComp function allowing to customize linestyles, colors and…
1c8f0234e7e7
·tlemaire on Mar 19 2018, 17:36.

Mar 18 2018

corrected initial conditions error in pulsed protocols integration of…
900de6e3aa75
·Theo Lemaire on Mar 18 2018, 19:58.
removed erroneous use of y_pulse_off in runClassic method
708bc9223628
·Theo Lemaire on Mar 18 2018, 11:47.

Mar 17 2018

Added new LeechP lookups
ee3a47c57d36
·Theo Lemaire on Mar 17 2018, 19:07.

Historymaster1951d49ccd25614064ea13b…

Sep 24 2018

Sep 23 2018

Sep 19 2018

Sep 15 2018

Sep 14 2018

Sep 12 2018

Sep 10 2018

Aug 30 2018

Aug 28 2018

Aug 25 2018

Aug 24 2018

Aug 22 2018

Aug 21 2018

Jul 24 2018

Jul 23 2018

Jul 20 2018

Jul 18 2018

Jul 17 2018

Jul 13 2018

Jul 6 2018

Jul 5 2018

Jul 4 2018

Jun 18 2018

May 25 2018

May 22 2018

May 15 2018

May 11 2018

May 8 2018

May 6 2018

May 4 2018

May 3 2018

May 2 2018

Apr 30 2018

Apr 24 2018

Apr 22 2018

Apr 18 2018

Apr 17 2018

Apr 14 2018

Apr 4 2018

Apr 3 2018

Mar 30 2018

Mar 29 2018

Mar 27 2018

Mar 22 2018

Mar 21 2018

Mar 20 2018

Mar 19 2018

Mar 18 2018

Mar 17 2018

History
master1951d49ccd25614064ea13b…