Diffusion PySONIC (old) (master) History

utils.py
mastereb70f6afb883b04513201bc…

Oct 10 2019

added Lookup.tile and modified SmartLookup.projectDC. modified nbls.
aee2c4e6cb21
·tlemaire on Oct 10 2019, 16:48.

Sep 23 2019

added rotAroundPoint2D function to utils
ed57fe2edc40
·tlemaire on Sep 23 2019, 00:38.

Sep 20 2019

added nan return in pow2Search if x > xmax. added getPow10 to utils
43cdd51258a0
·tlemaire on Sep 20 2019, 20:00.

Sep 19 2019

changed log level for logCache found entry
d0cc76d4af6b
·tlemaire on Sep 19 2019, 11:48.
added fillLine function to utils. added Parser.addOverwrite method (opposite of…
ec466c361f8c
·tlemaire on Sep 19 2019, 11:39.

Sep 4 2019

expanded charge range for pneuron.getLookup
614c56792d61
·tlemaire on Sep 4 2019, 13:17.

Aug 29 2019

remoed sweeney lookups (need to figure out the reason for weird profiles first).
f19b1648b5ed
·tlemaire on Aug 29 2019, 19:54.

Aug 26 2019

implemented pow2Search function using an incremental power of 2 search to…
d7855a1dd087
·tlemaire on Aug 26 2019, 10:48.

Aug 24 2019

added getCommonLabel method to ComparativePlot (now used to determine figure…
fdf57ea352bd
·tlemaire on Aug 24 2019, 22:00.

Aug 15 2019

added iCap to plot variables. added colormap option for comparative plots even…
3146cab6bade
·tlemaire on Aug 15 2019, 21:38.

Jul 18 2019

interoduced derivative function to compute numerical derivatives with various…
5aa12c341577
·tlemaire on Jul 18 2019, 20:02.
improved QSS fixed points color labeling
28c94d579a04
·tlemaire on Jul 18 2019, 12:11.

Jul 17 2019

adapted findModifiedEq to work with iterables as inputs
bce60bf70097
·tlemaire on Jul 17 2019, 17:19.
added findModifiedEq function to utils, using brentq to find a new equilibrium…
f113d822d4fb
·tlemaire on Jul 17 2019, 15:51.

Jul 15 2019

started implementing SonicTranslator.parseSteadyStates method. Implemented…
d50bf6119d40
·tlemaire on Jul 15 2019, 20:22.

Jun 20 2019

define dLookUp class to perform lookup projections and interpolations
a96a900ad4b4
·tlemaire on Jun 20 2019, 17:35.

Jun 14 2019

added outputdir option to simQueue methods. added automatic parsing to Parser…
de8bdbc4fee0
·tlemaire on Jun 14 2019, 11:34.

Jun 13 2019

updated README headers
812cb5c1cb3a
·tlemaire on Jun 13 2019, 03:18.

Jun 12 2019

updated all file headers
b42a0de93240
·tlemaire on Jun 12 2019, 23:15.

Jun 10 2019

added functionality to load data directly from sim results in TimeSeriesPlot…
2f0254ea5b53
·tlemaire on Jun 10 2019, 20:52.

Jun 9 2019

added first-call check that condition changes within the interval to…
b88c300e48f0
·tlemaire on Jun 9 2019, 22:48.
added file locking to cache functions
db58a9d4e8b7
·tlemaire on Jun 9 2019, 21:55.
added nbls isStableQSS and titrateQSS methods. finished plotQSSThresholdCurve
863bdf8330f4
·tlemaire on Jun 9 2019, 19:51.

Jun 7 2019

added getSimThresholdAmps and plotQSSThresholdCurve functions to QSS module…
26fdc0bbfe8d
·tlemaire on Jun 7 2019, 18:28.
added custom parsers to plot_timeseries and plot_QSS
1f1e59762ea3
·tlemaire on Jun 7 2019, 15:56.

Jun 6 2019

moved getLowIntensitiesSTN to STN class
50103226d72b
·tlemaire on Jun 6 2019, 21:30.
moved lookups utilities into separate lookups module (in neurons folder)
0984b86caa8f
·tlemaire on Jun 6 2019, 21:25.
created ActivationMap class
3556a765fe5c
·tlemaire on Jun 6 2019, 21:04.
added getModel and getPointNeuron functions. removed deprecated scripts.
1c9c63d4ba6a
·tlemaire on Jun 6 2019, 18:29.

Jun 3 2019

added caching of QSS analysis results
bc5a29bc6c9a
·Theo Lemaire on Jun 3 2019, 20:23.
added parsers module, now used in sim scripts for more consistency.
f75ca2e6e294
·Theo Lemaire on Jun 3 2019, 15:11.

Jun 2 2019

corrected QSS module to work correctly with "load" option.
874f4649ec44
·Theo Lemaire on Jun 2 2019, 15:40.

Jun 1 2019

added caching to nbls.titrate method
e0aa4041f3b8
·Theo Lemaire on Jun 1 2019, 16:50.
redefined titration procedures with binarySearch method. now single runAndSave…
10d2b5bb498e
·Theo Lemaire on Jun 1 2019, 16:41.

May 31 2019

reformatted simulate methods of bls, pneuron and nbls classes to return output…
af6f9a02ed42
·Theo Lemaire on May 31 2019, 14:43.

May 29 2019

replaced progressbar2 by tqdm
e08e8c736efa
·Theo Lemaire on May 29 2019, 18:35.
added simulators classes to take care of simulations
4ba3212edf92
·Theo Lemaire on May 29 2019, 03:15.

May 27 2019

added intermediate "run" method that return output data and metadata
1391db99409d
·Theo Lemaire on May 27 2019, 20:13.
added return_val option to isExcited and isSilenced
21d010292ddf
·Theo Lemaire on May 27 2019, 19:50.
haromized amplitude and plot_scheme parsing across simulation scripts
13e29c29bbb1
·Theo Lemaire on May 27 2019, 15:29.
started defining ActivationMap class
818219348db5
·Theo Lemaire on May 27 2019, 14:40.
replaced filecode functions by class methods
71a2cddb684e
·Theo Lemaire on May 27 2019, 13:46.
modified cache to only log if function has not "history" argument to avoid…
1463cf220fbc
·Theo Lemaire on May 27 2019, 12:07.

May 24 2019

re-implemented csvcache as decorator
4e391806ec32
·Theo Lemaire on May 24 2019, 13:13.

May 23 2019

added interface around titrate function to use memory caching
0453d1e710dd
·Theo Lemaire on May 23 2019, 21:01.

May 22 2019

implemented neuron-dependent titration to find specific thresholds (excitation…
1a5f9b3c215b
·Theo Lemaire on May 22 2019, 19:07.
added max integration duration to stability analysis to avoid infinite loops in…
0ee058e8778d
·Theo Lemaire on May 22 2019, 15:48.

May 20 2019

added negative offset to QSS perturbation
14f3b43f5ec7
·Theo Lemaire on May 20 2019, 18:02.

May 15 2019

implemented getLookupsDCavg function to compute DC-averaged lookups. nbls.
a66b375c6133
·Theo Lemaire on May 15 2019, 16:36.
simplified nbls.quasiSteadyStates method, now calling explicit quasiSeadyStates…
ee9cf8652b7e
·Theo Lemaire on May 15 2019, 13:53.

May 14 2019

changed PointNeuron getEffrates, steadyStates, derStates and derEffStates…
62c6723c6e71
·Theo Lemaire on May 14 2019, 19:21.

May 10 2019

major improvements to QSS module
7a27b761d220
·Theo Lemaire on May 10 2019, 18:09.

Apr 29 2019

corrected titrate function to work also with negative injected currents (for…
44780023da34
·Theo Lemaire on Apr 29 2019, 12:09.

Apr 5 2019

improved titrate function with nSpikes methods pneuron and nbls classes. added…
6ffd825273a4
·Theo Lemaire on Apr 5 2019, 17:47.

Apr 4 2019

Changed titration functions (now using generic titrate), Implemented Xinf…
9f09f2fdc039
·Theo Lemaire on Apr 4 2019, 13:38.

Mar 18 2019

moved membrane currents in 2rd position of neurons pltscheme. extractPltVar now…
cf921135e3f2
·tlemaire on Mar 18 2019, 17:56.

Mar 15 2019

adapted plotComp to new plot variables scheme.
ad0a33b92c3c
·tlemaire on Mar 15 2019, 01:15.
created plt.pltutils module and moved relevant plotting functions into it.
a812d7d527af
·tlemaire on Mar 15 2019, 00:20.

Mar 14 2019

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.

Mar 11 2019

adapted plotSpikingMetrics for uniform y-axis scale. adapted ASTIM_filecode…
cd145e4db3e8
·tlemaire on Mar 11 2019, 13:55.

Mar 8 2019

adapted fig9.py with corrected STN model (new traces).
a74f9c571b7d
·tlemaire on Mar 8 2019, 16:52.

Mar 5 2019

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.

Jan 9 2019

implemented Frankenhaeuser-Huxley membrane mechanism (validated against data…
65c1d8649331
·tlemaire on Jan 9 2019, 17:59.

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

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 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.

Oct 28 2018

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

Oct 25 2018

implemented figtitle method for direct labeling from metadata. implemented…
d2b627754312
·tlemaire on Oct 25 2018, 14:52.

Oct 2 2018

added scripts to generate paper figures automatically.
ed0d192b377b
·tlemaire on Oct 2 2018, 02:55.

Sep 28 2018

updated package documentation
73851d6ac128
·tlemaire on Sep 28 2018, 14:23.

Sep 27 2018

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.

Sep 23 2018

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.

Sep 15 2018

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.

Sep 12 2018

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 28 2018

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

Aug 24 2018

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

Aug 21 2018

changed package name to PySONIC.
043172721a44
·tlemaire on Aug 21 2018, 16:19.

R4670/PySONIC/utils.pymastereb70f6afb883b04513201bc…

Oct 10 2019

Sep 23 2019

Sep 20 2019

Sep 19 2019

Sep 4 2019

Aug 29 2019

Aug 26 2019

Aug 24 2019

Aug 15 2019

Jul 18 2019

Jul 17 2019

Jul 15 2019

Jun 20 2019

Jun 14 2019

Jun 13 2019

Jun 12 2019

Jun 10 2019

Jun 9 2019

Jun 7 2019

Jun 6 2019

Jun 3 2019

Jun 2 2019

Jun 1 2019

May 31 2019

May 29 2019

May 27 2019

May 24 2019

May 23 2019

May 22 2019

May 20 2019

May 15 2019

May 14 2019

May 10 2019

Apr 29 2019

Apr 5 2019

Apr 4 2019

Mar 18 2019

Mar 15 2019

Mar 14 2019

Mar 11 2019

Mar 8 2019

Mar 5 2019

Feb 28 2019

Jan 23 2019

Jan 9 2019

Nov 29 2018

Nov 27 2018

Nov 25 2018

Nov 22 2018

Nov 20 2018

Oct 28 2018

Oct 25 2018

Oct 2 2018

Sep 28 2018

Sep 27 2018

Sep 26 2018

Sep 25 2018

Sep 24 2018

Sep 23 2018

Sep 19 2018

Sep 15 2018

Sep 14 2018

Sep 12 2018

Sep 10 2018

Aug 28 2018

Aug 24 2018

Aug 21 2018

R4670/PySONIC/utils.py
mastereb70f6afb883b04513201bc…