Diffusion PySONIC (old) (master) History

utils.py
masterdba63f835a31dbec94c08b2…

Feb 3 2020

Created AcousticSource class to be used for US simulations.
9d0666784d2d
·tlemaire on Feb 3 2020, 14:26.

Jan 26 2020

Modified Lookup class (new properties, corrected methods).
c995e8999df7
·tlemaire on Jan 26 2020, 19:15.

Jan 14 2020

Automated getModel using automatically generated dictionary of models with…
8478fde7a5d4
·tlemaire on Jan 14 2020, 17:18.

Dec 2 2019

added threshold module with isolated threshold function (now used for all…
f8107574d0a8
·tlemaire on Dec 2 2019, 20:07.

Nov 27 2019

mofified SPIKE_MIN_QAMP and SPIKE_MIN_VAMP from 5 (nC/cm2 - mV) to 3
19881e729753
·tlemaire on Nov 27 2019, 19:48.

Nov 26 2019

moved pushbullet key file to package root
6797e5e1f52b
·tlemaire on Nov 26 2019, 18:52.

Nov 14 2019

moved model.simAndSave to utils to facilitate use in ExSONIC
5da540f0f401
·tlemaire on Nov 14 2019, 19:42.
moved filecode function to utils
36119dd01aec
·tlemaire on Nov 14 2019, 18:06.
Major update:
de255e65bccc
·tlemaire on Nov 14 2019, 16:39.

Nov 13 2019

improved filecodes generation from meta dictionary in Model.filecode
4a5626da478c
·tlemaire on Nov 13 2019, 19:43.
created Timeprotocol and PulsedProtocol classes, now used in pneuron, nbls and…
bc1800471252
·tlemaire on Nov 13 2019, 18:11.

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.

R4670/PySONIC/utils.pymasterdba63f835a31dbec94c08b2…

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R4670/PySONIC/utils.py
masterdba63f835a31dbec94c08b2…