Diffusion PySONIC (old) (master) History

R4670/PySONIC/core/model.py
master7d732f9d2c25403f1843225…

Jun 3 2020

updated MANIFEST file.
bebce73d9405
·tlemaire on Jun 3 2020, 16:57.

Apr 28 2020

added input-ouput match pre-check in LogBatch.run method to avoid unnecessary…
fcb5a387a33e
·tlemaire on Apr 28 2020, 21:21.

Apr 21 2020

placed StimObject class in a separate stimobj module. added boltons dependency…
67531a20cdce
·tlemaire on Apr 21 2020, 12:18.

Apr 17 2020

harmonized repr, desc and filecodes methods across protocols.
e3ca275ebe0f
·tlemaire on Apr 17 2020, 19:35.
corrected error in computeFRProfile when no spikes are detected.
447a9236fa20
·tlemaire on Apr 17 2020, 14:53.

Apr 10 2020

removed useless error instance catch in utils
a8ffc4cf6311
·tlemaire on Apr 10 2020, 18:36.

Apr 9 2020

corrected ActMap class (now inheriting from LogBatch).
18480eb7bebc
·tlemaire on Apr 9 2020, 14:07.

Mar 31 2020

added ASTIM_REL_CONV_THR to constants file.
9239911c1f35
·tlemaire on Mar 31 2020, 18:41.

Mar 19 2020

added polyfit amd extrapolate capabilities to Lookup class.
066e8e416305
·tlemaire on Mar 19 2020, 12:13.

Feb 20 2020

moved getMeta to utils
165caa8bf488
·tlemaire on Feb 20 2020, 18:35.
changed meta property of model classes to return solely model information.
7f8a3be5ceb4
·tlemaire on Feb 20 2020, 17:03.

Feb 11 2020

added copy method to all model classes. added TI US notebook. updated…
68961385d17e
·tlemaire on Feb 11 2020, 07:55.

Feb 5 2020

replaced erroneous "return NotImplementedError" statements by "raise…
96d3c580ee81
·tlemaire on Feb 5 2020, 18:20.
introduced properties in classes of drives and protocols modules.
31ef6228207a
·tlemaire on Feb 5 2020, 17:08.

Feb 3 2020

added xkey property to XDrive class and Arange property to pneuron and nbls…
073e28b388f6
·tlemaire on Feb 3 2020, 23:36.
Created Drive objects inheritance scheme (now used in all model classes).
27d8aafffa88
·tlemaire on Feb 3 2020, 21:45.
Created AcousticSource class to be used for US simulations.
9d0666784d2d
·tlemaire on Feb 3 2020, 14:26.

Nov 26 2019

added internal bls.simUntilConvergence method (without decorators) to enable…
6deb0da8868d
·tlemaire on Nov 26 2019, 15:41.

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.

Sep 17 2019

changed outputdir to keyword argument in queue items in Model.checkOutputDir…
133c0ab1ac73
·tlemaire on Sep 17 2019, 17:28.
add handling of positional and keyword arguments in Batch queues. added…
89e117f6ffaa
·tlemaire on Sep 17 2019, 16:15.
abstracted Model.simQueue method (now defined in children classes). changed…
8cf15b137151
·tlemaire on Sep 17 2019, 15:03.

Aug 26 2019

adapted constants to enable sweeney lookups creation.
8226a9490c9b
·tlemaire on Aug 26 2019, 15:19.

Aug 24 2019

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

Aug 19 2019

removed paper figures folder (now in separate repo)
3c76710406c6
·tlemaire on Aug 19 2019, 09:56.

Aug 16 2019

added figtitle and getModel as GenericPlot methods
0d24b201dea4
·tlemaire on Aug 16 2019, 20:09.

Aug 14 2019

added automatic solution prepending to all simulate methods (to treat initial…
2278e599a753
·tlemaire on Aug 14 2019, 17:51.

Jul 29 2019

fixed error in bls.filecodes
ec01e1e58099
·tlemaire on Jul 29 2019, 17:24.

Jul 18 2019

corrected error in getSimThresholdAmps (added default fs to 1)
9ba9ca99a89f
·tlemaire on Jul 18 2019, 21:14.
corrected error in Model logNSpikes, checkTitrate and simAndSave methods.
9e0718eb1a9b
·tlemaire on Jul 18 2019, 20:47.

Jul 15 2019

re-added file caching for QSS analysis
bed4f4a9de36
·tlemaire on Jul 15 2019, 20:39.

Jul 1 2019

improved checkTitrate robustness
ffdcb43ba1d8
·tlemaire on Jul 1 2019, 17:40.
added option to provide simAndSave or simulate to batches. implemented addMeta…
d1a3fbaefd83
·tlemaire on Jul 1 2019, 16:46.

Jun 29 2019

adapted methods of all classes into classmethods and staticmethods when…
4937955d0214
·tlemaire on Jun 29 2019, 20:27.

Jun 28 2019

transformed model inputs, checkInputs and simQueue into static methods
4997a9f88989
·tlemaire on Jun 28 2019, 16:15.

Jun 27 2019

re-introduced derivatives as mandatory model method
0fe23305b3ad
·tlemaire on Jun 27 2019, 19:13.
added Model.description method. added nbls.getLookup2D method with correct fs…
a0db776b7966
·tlemaire on Jun 27 2019, 16:10.

Jun 26 2019

added fs (spatially-averaged) as input to nbls model. defined SmartLookup class…
dffee6926b85
·tlemaire on Jun 26 2019, 19:50.
cleaned up model classes. defined mandatory derivatives method for model…
3528fa81b6d1
·tlemaire on Jun 26 2019, 13:38.

Jun 15 2019

added simkey to meta dictionary. added automatic parsing and labeling of…
c14fa0da1fd7
·tlemaire on Jun 15 2019, 18:32.

Jun 14 2019

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

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 solve_ivp optional use to Simulator.integrate method
2e0f97a8baaf
·tlemaire on Jun 9 2019, 21:36.
added nbls isStableQSS and titrateQSS methods. finished plotQSSThresholdCurve
863bdf8330f4
·tlemaire on Jun 9 2019, 19:51.

Jun 6 2019

added getModel and getPointNeuron functions. removed deprecated scripts.
1c9c63d4ba6a
·tlemaire on Jun 6 2019, 18:29.

Jun 2 2019

corrected QSS module to work correctly with "load" option.
874f4649ec44
·Theo Lemaire on Jun 2 2019, 15:40.
major cleanup of all core classes.
88811f7a8aa5
·Theo Lemaire on Jun 2 2019, 14:22.

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

implemented abstract Model class to be inherit by bls, pneuron and nbls
25d498c21187
·Theo Lemaire on May 31 2019, 16:56.