Diffusion PySONIC (old) (master) History

History
mastera812d7d527af43c35726b03…

Mar 15 2019

created plt.pltutils module and moved relevant plotting functions into it.
a812d7d527af
·tlemaire on Mar 15 2019, 00:20.

Mar 14 2019

removed states0 attribute from neuron classes (now calling steadyStates method…
81554e5d4d67
·tlemaire on Mar 14 2019, 23:52.
generalized the use of getPltVars and getPltScheme with inheritance scheme…
453f896987ce
·tlemaire on Mar 14 2019, 23:35.
major reformatting of plotBatch function
9d1a2fc5cd08
·tlemaire on Mar 14 2019, 19:09.
cleaned up neurons docstring. defined PointNeuron.getPltVars method (possibly…
f6195a153a01
·tlemaire on Mar 14 2019, 13:38.

Mar 13 2019

major reformatting of neuron classes.
d744944eba53
·tlemaire on Mar 13 2019, 18:35.
implemented PointNeuron.currentToConcentrationRate method for a common way to…
db85dec73950
·tlemaire on Mar 13 2019, 16:08.
replaced CCa_out by Cao and KCa by 1 / taur_Cai in STN class for more clarity.
b178c1dca3c9
·tlemaire on Mar 13 2019, 15:51.
added Qbounds as a PointNeuron class method. cleaned up use of Cai in TC class.
ce5a9df84ba1
·tlemaire on Mar 13 2019, 15:44.
removed all combined gating variables from pltvars schemes.
33c52c6b04a5
·tlemaire on Mar 13 2019, 15:14.
implemented PointNeuron.getCurrentPltVars method to genrate a dictionary plot…
817387c89edd
·tlemaire on Mar 13 2019, 15:00.
replaced iNet method by currents method in all neuron classes (iNet now defined…
09ec0decb4bd
·tlemaire on Mar 13 2019, 10:17.

Mar 12 2019

corrected error in STN.derD1. lookup tables to re-run.
2b5b9cf5a78b
·tlemaire on Mar 12 2019, 12:51.
added get_dCCa and findCaeq methods ot STN neuron (iterative search to find…
7082d86bf3da
·tlemaire on Mar 12 2019, 01:29.

Mar 11 2019

added detection of stabilization (time and value) from charge density profiles…
2979d8329c88
·tlemaire on Mar 11 2019, 21:51.
implemented NeuronalBilayerSonophore.getQSSvars method to compute QSS…
d99d9eb144b6
·tlemaire on Mar 11 2019, 20:39.
adapted plotSpikingMetrics for uniform y-axis scale. adapted ASTIM_filecode…
cd145e4db3e8
·tlemaire on Mar 11 2019, 13:55.

Mar 10 2019

added currents methods to Cortical, Thalamic and STN classes, that returns a…
c5433b2c448c
·tlemaire on Mar 10 2019, 19:36.

Mar 8 2019

adapted fig9.py with corrected STN model (new traces).
a74f9c571b7d
·tlemaire on Mar 8 2019, 16:52.
corrected STN lookups. added testQSS script to analyze STN neuron plateau…
e73ca2da1333
·tlemaire on Mar 8 2019, 15:38.

Mar 7 2019

corrected sigmaT2_b from -10 mV to 10 mV in STN implementation. started new QSS…
990c8181cf46
·tlemaire on Mar 7 2019, 16:00.

Mar 6 2019

renamed currents for more clarity
da8e0bbde997
·tlemaire on Mar 6 2019, 17:56.

Mar 5 2019

changed nomenclature of current methods from "curr..." to "i..."
2e64aa90c325
·tlemaire on Mar 5 2019, 12:18.
implemented getLookupsOff function to retrieve US-OFF lookups. adapted…
c72b7b319ed0
·tlemaire on Mar 5 2019, 11:04.

Feb 28 2019

added RS neuron lookups with partial coverage (spatially averaged). updated…
865020d8c630
·tlemaire on Feb 28 2019, 11:41.

Jan 23 2019

corrected error in getLookups2Dfs
702446ca2ad5
·tlemaire on Jan 23 2019, 19:05.
added getLookups2Dfs method to interpolate lookups at given membrane coverage.
957db9d021d6
·tlemaire on Jan 23 2019, 18:15.
added script to compute quick lookups for a span of partial sonophore coverage…
80aa94a42257
·tlemaire on Jan 23 2019, 16:00.

Jan 11 2019

modified Qbounds to account for capacitance value in all neuron types.
69f20e7c2a18
·tlemaire on Jan 11 2019, 08:50.
added lookups for FH membrane mechanism (tested)
cf20bd8f6516
·tlemaire on Jan 11 2019, 08:26.

Jan 10 2019

corrected Qbounds for lookups generation in FH neuron
8684707c3f08
·tlemaire on Jan 10 2019, 12:31.

Jan 9 2019

changed PMAVG_STD_ERR_MAX value to allow BLS lookups generation for FH…
82590fe13581
·tlemaire on Jan 9 2019, 18:05.
implemented Frankenhaeuser-Huxley membrane mechanism (validated against data…
65c1d8649331
·tlemaire on Jan 9 2019, 17:59.

Dec 27 2018

corrected error in Vm post-processing in runSONIC. added plotV option to…
8a4719662fd9
·tlemaire on Dec 27 2018, 19:08.

Dec 14 2018

modified plotActivationMap to plot amplitude thresholds computed from titration…
42f56ab271e3
·tlemaire on Dec 14 2018, 18:16.

Dec 9 2018

added pltvars for STN neuron. added plotFRprofile function along with paper…
0fcd53a68ce7
·tlemaire on Dec 9 2018, 16:17.

Dec 4 2018

implemented notebook for validation of STN neuron (both ESTIM and ASTIM).
81adcb430e9f
·tlemaire on Dec 4 2018, 17:11.
added STN lookups and corrected derEffStates method.
e99b70b6952c
·tlemaire on Dec 4 2018, 01:20.

Dec 3 2018

corrected STN getEffRates and derStatesEff methods for correct lookups creation…
7655cca494a0
·tlemaire on Dec 3 2018, 21:52.
STN model validated for E-STIM by reproduction of key features (spontaneous…
9eca746695d1
·tlemaire on Dec 3 2018, 17:46.

Nov 30 2018

replaced 'L' by 'Leak' in neurons nomenclature. implemented STN neuron with…
0ebd7ae3b932
·tlemaire on Nov 30 2018, 10:37.

Nov 29 2018

added plotFRspectrum function to actmap module. updated fig7 script, and added…
850b05b61c5e
·tlemaire on Nov 29 2018, 16:00.

Nov 27 2018

added spanDC argument to run_astim. removed rheobase amp preconditioning in…
fa4c643a5a4b
·tlemaire on Nov 27 2018, 16:18.
recomputed lookups for all CNS neurons. modified figs 5 and 6 generation…
84a00ea7e59b
·tlemaire on Nov 27 2018, 11:28.

Nov 25 2018

added recording of computation times during lookups creation.
9f827c942524
·tlemaire on Nov 25 2018, 01:10.

Nov 22 2018

improved methods that generate figures 5 & 6 of SONIC paper.
b9f44bd89005
·tlemaire on Nov 22 2018, 19:15.
improved plotRheobaseAmps function. improved arguments parsing in command line…
2f63e4926c36
·tlemaire on Nov 22 2018, 17:58.

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.

Historymastera812d7d527af43c35726b03…

Mar 15 2019

Mar 14 2019

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Mar 12 2019

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Sep 15 2018

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Jul 23 2018

History
mastera812d7d527af43c35726b03…