Diffusion PySONIC (old) (master) History

History
master9b03fd5152c29feb43545fe…

May 2 2020

corrected DrivenNeuronalBilayerSonophore.inputs
9b03fd5152c2
·tlemaire on May 2 2020, 17:17.
corrected error in solve_ivp call.
e1f537dcc076
·tlemaire on May 2 2020, 17:11.
added actmap NaN data post-processing to prevent numpy warning when using log z…
db1a0c16e84b
·tlemaire on May 2 2020, 14:52.
new astim titrations for figure 8
430d7c8131f0
·tlemaire on May 2 2020, 12:07.

May 1 2020

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic
6d2bc897725d
·tlemaire on May 1 2020, 22:47.
added new titrations
c8cdcf5deefc
·tlemaire on May 1 2020, 22:47.
corrected ComparativePlot and CompTimeSeries to enable taking generators as…
bd7a6ec5a477
·tlemaire on May 1 2020, 22:44.
new figure 7 titrations for high PRF low DC
5742df202a16
·tlemaire on May 1 2020, 20:24.
applied correction to ODESolver.getNsamples to make sure there are at least 2…
fa9c541d7842
·tlemaire on May 1 2020, 19:27.
new figure 7 titrations
28d338972b7c
·tlemaire on May 1 2020, 18:36.

Apr 30 2020

added new astim titrations
74c7618b792a
·tlemaire on Apr 30 2020, 16:46.
added progress bar logging to nbls.simFull at INFO level.
835803fa8d6b
·tlemaire on Apr 30 2020, 13:26.

Apr 29 2020

corrected scaling factor in actmap.addThresholdCurve
4e922dc3531c
·tlemaire on Apr 29 2020, 22:55.
defined Thresholder class for a clearer threshold search implementation.
524072855745
·tlemaire on Apr 29 2020, 22:52.
added RS 10Hz titrations.
1dd1b969d0e2
·tlemaire on Apr 29 2020, 17:57.
corrected queue error in actmap.addTresholdCurve
efb7e6effc92
·tlemaire on Apr 29 2020, 17:09.
corrected DC scaling in actmap.addThresholdCurve
0a9b43830b05
·tlemaire on Apr 29 2020, 16:22.
added mpi feature to actmap threshold curve.
d4087b3210f3
·tlemaire on Apr 29 2020, 14:44.
changed bls.inputs['a'] (factor 0, unit m).
81fe27f05196
·tlemaire on Apr 29 2020, 12:35.

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 26 2020

modified BurstProtocol default BRF such that BRI is twice burst time.
2eb3a3768e1e
·tlemaire on Apr 26 2020, 19:22.
corrected simobj.check methods (incorrect paramStr call). added BRF pre-check…
fab05bc88fea
·tlemaire on Apr 26 2020, 19:10.

Apr 24 2020

added baseline_modulation example script
20183f45302e
·tlemaire on Apr 24 2020, 11:22.
added optional tstart argument to PusledProtocol classes. corrected…
6dedc53ccbc8
·tlemaire on Apr 24 2020, 11:04.

Apr 23 2020

added TCtweak70 and TCtweak50 cases.
5b268a756bc5
·tlemaire on Apr 23 2020, 12:41.
added TC2 class
a6e6abff99bc
·tlemaire on Apr 23 2020, 12:06.

Apr 22 2020

introduced lambda function for test.execute calls
93d5100bbbce
·tlemaire on Apr 22 2020, 15:13.
additional bls lookups
9342c4bfcbda
·tlemaire on Apr 22 2020, 12:56.

Apr 21 2020

defined friendlyLogspace function
7f1709df1d92
·tlemaire on Apr 21 2020, 21:01.
placed StimObject class in a separate stimobj module. added boltons dependency…
67531a20cdce
·tlemaire on Apr 21 2020, 12:18.

Apr 19 2020

added TC lookup 80 nm 590 kHz
2a0fec5672f0
·tlemaire on Apr 19 2020, 16:40.
added few utils functions
b7a48187478a
·tlemaire on Apr 19 2020, 16:37.
added BalancedPulsedProtocol class.
159f140dcfb0
·tlemaire on Apr 19 2020, 15:03.
added 48 nm TC lookups
7fdbe8544e52
·tlemaire on Apr 19 2020, 11:53.

Apr 18 2020

added max_nsamples parameter to effective solver to avoid memory allocation…
108548aa8cc8
·tlemaire on Apr 18 2020, 21:25.
added more TC lookups.
a72a071b87d0
·tlemaire on Apr 18 2020, 21:03.
corrected units discrepancy in actmap.py
72c8577885a8
·tlemaire on Apr 18 2020, 21:00.
corrected TimSeries.getStimPulses function (no patches for zero states).
a3ca81f69d0a
·tlemaire on Apr 18 2020, 16:14.
updated README
83d7d8df16fa
·tlemaire on Apr 18 2020, 15:52.
defined protocols copy methods.
00f6aa560a10
·tlemaire on Apr 18 2020, 15:10.
corrected drives and protocols inputs.
0d1777407add
·tlemaire on Apr 18 2020, 13:23.

Apr 17 2020

simplified drives and protocols
241946f34fa2
·tlemaire on Apr 17 2020, 23:28.
updated inputs precision in protocols
5e4003f785f9
·tlemaire on Apr 17 2020, 20:48.
updated README
b80a24a22518
·tlemaire on Apr 17 2020, 20:46.
cleand-up run_astim.py
5fe7fba7ad8c
·tlemaire on Apr 17 2020, 20:25.
added 64nm 590 kHz fs-dependent TC lookup
420b1c0ceb3e
·tlemaire on Apr 17 2020, 20:18.
implemented simQueueBurst method in pneuron and nbls classes.
6895a19a147f
·tlemaire on Apr 17 2020, 20:16.
harmonized repr, desc and filecodes methods across protocols.
e3ca275ebe0f
·tlemaire on Apr 17 2020, 19:35.
added update interval argument to HybridSolve.solve method.
e62423f9469d
·tlemaire on Apr 17 2020, 15:27.
cleaned-up find_tpeaks function
e775528e1afc
·tlemaire on Apr 17 2020, 15:18.
corrected error in computeFRProfile when no spikes are detected.
447a9236fa20
·tlemaire on Apr 17 2020, 14:53.

Apr 16 2020

improved solvers docstrings and clarified their use in model classes.
69892d75c503
·tlemaire on Apr 16 2020, 13:30.

Apr 15 2020

added 2 MHz 32nm TC lookup.
81c3d55cddff
·tlemaire on Apr 15 2020, 21:07.
removed ambiguity around initialConditions methods to allow correct lookups…
d03caf415e89
·tlemaire on Apr 15 2020, 21:04.
implemented better solvers (now inside solvers module), including an…
b77cd9e4eb12
·tlemaire on Apr 15 2020, 20:53.

Apr 13 2020

added TC fs lookup at 1 MHz.
7ae0b7961ae4
·tlemaire on Apr 13 2020, 18:29.
replaced "Ascale" parsing options by "yscale" for more clarity.
b44cc93c9915
·tlemaire on Apr 13 2020, 18:17.
corrected LogBatch class to enable correct use with mpi.
f8511250c9b8
·tlemaire on Apr 13 2020, 18:00.
added better fs handling in actmap
10270ea94712
·tlemaire on Apr 13 2020, 12:33.

Apr 10 2020

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

Apr 9 2020

added example actmap script
077023563760
·tlemaire on Apr 9 2020, 16:17.
changed default actmap tstim from 1s to 200 ms
4907be82d296
·tlemaire on Apr 9 2020, 16:13.
added multiprocessing functionality to LogBatch class.
3af9c9df32cc
·tlemaire on Apr 9 2020, 15:53.
corrected ActMap class (now inheriting from LogBatch).
18480eb7bebc
·tlemaire on Apr 9 2020, 14:07.

Apr 5 2020

added TimeProtocol.stimEvents method (used in NEURON simulations).
63ef9868bbd2
·tlemaire on Apr 5 2020, 17:59.
added eventsON and eventsOFF methods to Protocol classes.
06f8250793a6
·tlemaire on Apr 5 2020, 15:22.

Apr 4 2020

moved example scripts to examples folder and defined README.mdpp markdown…
afdde67646ea
·tlemaire on Apr 4 2020, 16:40.

Apr 3 2020

added __eq__ methods to pneuron and nbls classes
cc5348bc40ca
·tlemaire on Apr 3 2020, 15:33.

Mar 31 2020

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

Mar 30 2020

added TC fs lookup.
9dcd3884ae33
·tlemaire on Mar 30 2020, 21:50.
added MRG fs lookup.
4e96a816343e
·tlemaire on Mar 30 2020, 13:16.

Mar 27 2020

added MRG lookup.
8a68be82c2d8
·tlemaire on Mar 27 2020, 20:40.
renamed fibers point-neuron models for better interpretability. completed fiber…
8f0bbde630a7
·tlemaire on Mar 27 2020, 20:37.

Mar 26 2020

tested MRG lookups generation
a43249c6ecf1
·tlemaire on Mar 26 2020, 21:49.
corrected typo in SweeneyNode description.
a4eafd9f8059
·tlemaire on Mar 26 2020, 21:16.

Mar 24 2020

added addExcitationInset to pltutils
cf163f8c94cb
·tlemaire on Mar 24 2020, 15:51.

Mar 23 2020

added getLogStartPoint to utils
678f3f5e229d
·tlemaire on Mar 23 2020, 21:36.

Mar 21 2020

added x axis sharing in GroupedTimeSeries
84694f9507f6
·tlemaire on Mar 21 2020, 18:51.

Mar 19 2020

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

Feb 28 2020

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic
8f4b9911c0d3
·tlemaire on Feb 28 2020, 17:05.
added extra functionalities to Lookup class. continued fiber nodes notebook.
c8a9ea2beb92
·tlemaire on Feb 28 2020, 17:05.
Merge solved
7d61ef15bd3b
·vicari on Feb 28 2020, 17:03.
Correction in drives
be6c868e4e5f
·vicari on Feb 28 2020, 17:00.

Feb 27 2020

added fiber ndoes analysis notebook
edc36b1686d6
·tlemaire on Feb 27 2020, 23:06.
added better handling of ybounds in timeseries. added MRG neuron class.
a46f7227e040
·tlemaire on Feb 27 2020, 23:02.

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 18 2020

added LogBatch class
b7d520b9ed42
·tlemaire on Feb 18 2020, 22:59.
added isPickable function. corrected install_requires list in setup file.
b68fc5d800ef
·tlemaire on Feb 18 2020, 13:54.

Feb 14 2020

added gaussian function to utils.
683ec602313d
·tlemaire on Feb 14 2020, 14:56.
updated README (added instructions for git-lfs install)
31cc2d15993a
·tlemaire on Feb 14 2020, 11:12.

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

adapted simAndSave function to work also with source-based titration cases.
b62507055396
·tlemaire on Feb 5 2020, 19:17.
changed erroneous calls to parseAmp to parseAmplitude in parsers module
478c17a7e098
·tlemaire on Feb 5 2020, 18:46.
replaced erroneous "return NotImplementedError" statements by "raise…
96d3c580ee81
·tlemaire on Feb 5 2020, 18:20.
correctd mismatch in ElectricDrive
8907f78b742a
·tlemaire on Feb 5 2020, 18:14.
renamed ElectricDrive A to I
892f924d6e9e
·tlemaire on Feb 5 2020, 18:13.
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.

Historymaster9b03fd5152c29feb43545fe…

May 2 2020

May 1 2020

Apr 30 2020

Apr 29 2020

Apr 28 2020

Apr 26 2020

Apr 24 2020

Apr 23 2020

Apr 22 2020

Apr 21 2020

Apr 19 2020

Apr 18 2020

Apr 17 2020

Apr 16 2020

Apr 15 2020

Apr 13 2020

Apr 10 2020

Apr 9 2020

Apr 5 2020

Apr 4 2020

Apr 3 2020

Mar 31 2020

Mar 30 2020

Mar 27 2020

Mar 26 2020

Mar 24 2020

Mar 23 2020

Mar 21 2020

Mar 19 2020

Feb 28 2020

Feb 27 2020

Feb 20 2020

Feb 18 2020

Feb 14 2020

Feb 11 2020

Feb 5 2020

Feb 3 2020

History
master9b03fd5152c29feb43545fe…