Diffusion PySONIC (old) (master) History

History
masterbebce73d940559dfe1966fc…

Jun 3 2020

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

May 18 2020

updated README.
ef08cb208ad1
·tlemaire on May 18 2020, 15:22.

May 7 2020

added strictbounds plotting options
bbb3a4445235
·tlemaire on May 7 2020, 16:19.

May 5 2020

corrected index offset error in GenericPlot.addCmap
0c7bff925bd5
·tlemaire on May 5 2020, 14:40.

May 4 2020

added extractCommonPrefix utils function.
2c0253a46427
·tlemaire on May 4 2020, 12:34.

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.

Historymasterbebce73d940559dfe1966fc…

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History
masterbebce73d940559dfe1966fc…