Implement LFPy backend #385

alejoe91 · 2022-03-01T14:49:09Z

LFPy-related changes

Added LFPy as a backend for simulation
Added extracellular efeatures class extraFELFeature that supports computing features from extracellular "template" (avg action potential). Features include:
- "peak_to_valley": duration between negative and positive peak
- "halfwidth": full width alf maximum of negative peak
- "peak_trough_ratio": ratio between peak and trough
- "repolarization_slope": slope from the first peak to baseline
- "recovery_slope": slop from second peak to baseline
- "neg_peak_relative": relative amplitude of negative peaks with respect to max channel
- "pos_peak_relative": relative amplitude of positive peaks with respect to max channel
- "neg_peak_diff": relative timing of negative peaks with respect to max channel
- "pos_peak_diff": relative timing of positive peaks with respect to max channel
- "neg_image": normalized potential at time of negative peak
- "pos_image": normalized potential at time of positive peak

Other changes

Add param_dependancies in parameters
Add **morhp_modifiers_kwargs to Morphology
Implement NrnSegmentSectionDistanceScaler (base class also for NrnSegmentSomaDistanceScaler)

DrTaDa

The setup.py needs to be updated to include LFPy.
Also we will need tests to maintain the test coverage above 90%.

alejoe91 · 2022-07-14T10:05:12Z

The setup.py needs to be updated to include LFPy. Also we will need tests to maintain the test coverage above 90%.

It was not added on purpose to make the LFPy dependency weak. All LFPy imports are local so one can still run normal BPO without having LFPy installed

DrTaDa · 2022-07-14T10:16:00Z

The setup.py needs to be updated to include LFPy. Also we will need tests to maintain the test coverage above 90%.

It was not added on purpose to make the LFPy dependency weak. All LFPy imports are local so one can still run normal BPO without having LFPy installed

LFP needs to be in an extra require then:

extras_require={
        "LFPy": ["LFPy"]
}

alejoe91 · 2022-07-14T10:24:37Z

yeah that could work!

bluepyopt/tests/test_ephys/test_models.py

tox.ini

bluepyopt/parameters.py

wvangeit · 2022-07-25T07:19:15Z

So it seems LFPy requires mpi4py? Installation seems to fail during the tests. Can we disable mpi4py in LFPy, since I assume we don't need it?

alejoe91 · 2022-07-25T08:08:25Z

So it seems LFPy requires mpi4py? Installation seems to fail during the tests. Can we disable mpi4py in LFPy, since I assume we don't need it?

Unfortunately it's a requirement: https://github.com/LFPy/LFPy/blob/master/requirements.txt

wvangeit · 2022-07-25T08:11:11Z

Could we ask to get it removed from the hard requirements (or to make an extra that doesn't require it?). I'm a bit reluctant to make mpi4py a requirement for the bpopt tests if it is not required.

alejoe91 · 2022-07-25T10:03:08Z

Could we ask to get it removed from the hard requirements (or to make an extra that doesn't require it?). I'm a bit reluctant to make mpi4py a requirement for the bpopt tests if it is not required.

LFPy/LFPy#429

DrTaDa · 2022-07-25T11:47:56Z

@alejoe91 If you agree, I will rollback the changes to parameters,py and parameterscalers.py.
We were using them for the Hallermann model but it is not use anymore.
It will also require us to do some changes on the multimodal fitting repo such as removing https://github.com/alejoe91/multimodalfitting/blob/cb49b63d0e76433448b9e4ca6ca825cf74598ffa/multimodalfitting/models/model.py#L305

DrTaDa · 2022-07-25T11:50:11Z

@alejoe91 thinking about it more, it might be useful for someone else some day. I am not sure what should be done.

Some refactoring

DrTaDa · 2022-07-29T14:37:50Z

bluepyopt/ephys/protocols.py

        """Instantiate"""

        for stimulus in self.stimuli:
-            stimulus.instantiate(sim=sim, icell=icell)
+            if isinstance(stimulus, LFPStimulus):
+                stimulus.instantiate(lfpy_cell=cell_model.lfpy_cell)


Should be sim, lfpy_cell

@AurelienJaquier can you take care of it?

@AurelienJaquier can you take care of it?

actually I'm on it ;)

* turn print statements in eFELFeature into logger.info * change docstring description of exp_mean and exp_std in extraFELFeature * remove MEA dependency in setup * use custom lfpy from fork in setup * use lfpy from extras in tox * add test function for masked_cosine_distance

…ll-changes

Small changes

espenhgn · 2022-08-19T06:14:55Z

Hi @alejoe91, @wvangeit; as mpi4py appeared to be a problem, I've made a PR to LFPy (LFPy/LFPy#433) that removes this package dependency altogether (by using similar MPI communication provided via neuron.h.ParallelContext()). Seems to work in my own testing but it should be tested also with this PR before merging.

wvangeit · 2022-08-22T10:54:19Z

There are just some formatting issues at the moment.

AurelienJaquier · 2022-08-22T13:41:01Z

I think the formatting issues have been solved in the master branch of BlueBrain/BluePyOpt. So a merge branch 'master' into 'lfpy' should solve them.

…lfpy Conflicts: bluepyopt/ephys/parameterscalers.py

codecov-commenter · 2022-12-06T10:51:03Z

Codecov Report

Merging #385 (1e56736) into master (519b2fc) will decrease coverage by 0.69%.
The diff coverage is 86.18%.

@@            Coverage Diff             @@
##           master     #385      +/-   ##
==========================================
- Coverage   89.53%   88.84%   -0.70%     
==========================================
  Files          34       35       +1     
  Lines        2361     2977     +616     
==========================================
+ Hits         2114     2645     +531     
- Misses        247      332      +85

Impacted Files	Coverage Δ
bluepyopt/ephys/morphologies.py	`96.51% <75.00%> (+0.12%)`	⬆️
bluepyopt/ephys/stimuli.py	`95.23% <76.66%> (-4.77%)`	⬇️
bluepyopt/ephys/models.py	`86.36% <78.81%> (-4.74%)`	⬇️
bluepyopt/ephys/simulators.py	`86.95% <80.64%> (-2.33%)`	⬇️
bluepyopt/ephys/efeatures.py	`85.45% <83.06%> (-4.09%)`	⬇️
bluepyopt/ephys/parameters.py	`88.46% <83.33%> (-1.34%)`	⬇️
bluepyopt/ephys/responses.py	`86.66% <87.50%> (+0.30%)`	⬆️
bluepyopt/ephys/parameterscalers.py	`91.13% <88.57%> (-0.39%)`	⬇️
bluepyopt/ephys/protocols.py	`83.44% <93.33%> (+0.46%)`	⬆️
bluepyopt/ephys/recordings.py	`97.22% <94.44%> (-2.78%)`	⬇️
... and 3 more

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wvangeit · 2022-12-06T10:54:15Z

Should we merge this, @alejoe91 @DrTaDa @AurelienJaquier ?

DrTaDa · 2022-12-06T11:44:10Z

Yes !

Tanguy Pierre Louis Damart and others added 7 commits February 24, 2022 10:00

Update doctsrings and minor changes

65a4855

Clean LFPy port

1459882

docstrings

819a553

Merge with master

4547971

Merge branch 'master' into lfpy

7c4bf9d

Fix parameterscalerrs value

fba3f4f

Merge branch 'lfpy' of https://github.com/alejoe91/BluePyOpt into lfpy

dc7cf86

DrTaDa reviewed Jul 14, 2022

View reviewed changes

rm workflow

1e0275e

wvangeit reviewed Jul 22, 2022

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bluepyopt/tests/test_ephys/test_models.py Show resolved Hide resolved

wvangeit reviewed Jul 22, 2022

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tox.ini Outdated Show resolved Hide resolved

wvangeit reviewed Jul 22, 2022

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bluepyopt/parameters.py Outdated Show resolved Hide resolved

Merge branch 'master' into lfpy

ac16ef2

Add Dummy LFPy Cell and add lfpy stimuli tests

4b510a9

Jaquier Aurélien Tristan added 5 commits July 25, 2022 10:54

add lfpy simulator tests

2f64d53

Add more lfpy model tests

34e1167

add objectives tests

bf5e7b7

fix typo

e4724be

add recording tests

0749d97

alejoe91 mentioned this pull request Jul 25, 2022

Make mpi4py an optional dependency LFPy/LFPy#429

Closed

Add protocols tests

00b7139

Jaquier Aurélien Tristan added 7 commits July 29, 2022 10:49

Turn pkl data file into npy file for py37 compatibility

1d4a64c

Fix expected value in test_lfpy_evaluator

eda3976

Fix lfpy evaluator and lfpy test

cc39eef

improve lfpy evaluator example

3206e0d

Improve lfpy example scripts

1dbebd4

Add LFPStimulus base class for lfp stimuli

9de5202

small fix

2212a7a

wvangeit added the dontmerge label Jul 29, 2022

Jaquier Aurélien Tristan and others added 3 commits July 29, 2022 15:29

Fix instantiate arguments of LFPStimulus

84802f0

Merge pull request #31 from alejoe91/cleaning

efeb84a

Some refactoring

Merge branch 'master' into lfpy

b139c64

DrTaDa reviewed Jul 29, 2022

View reviewed changes

alejoe91 and others added 7 commits July 29, 2022 16:57

Add sim to LFPstimulus instantiate

bf60eaa

Merge branch 'lfpy' of github.com:alejoe91/BluePyOpt into lfpy

c192c6a

Merge branch 'lfpy' of https://github.com/alejoe91/BluePyOpt into sma…

d9bb8e5

…ll-changes

lint fixes

306c905

fix stimuli test

1363f71

Merge pull request #33 from alejoe91/small-changes

d12dd08

Small changes

Jaquier Aurélien Tristan and others added 3 commits August 22, 2022 15:45

Merge branch 'master' of https://github.com/BlueBrain/BluePyOpt into …

46dbc84

…lfpy Conflicts: bluepyopt/ephys/parameterscalers.py

Install LFPy from master (no MPI needed)

2ab0c58

Merge branch 'master' into lfpy

1e56736

wvangeit approved these changes Dec 6, 2022

View reviewed changes

wvangeit merged commit 3440402 into BlueBrain:master Dec 8, 2022

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Implement LFPy backend #385

Implement LFPy backend #385

alejoe91 commented Mar 1, 2022

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alejoe91 commented Jul 14, 2022

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espenhgn commented Aug 19, 2022

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wvangeit commented Dec 6, 2022

DrTaDa commented Dec 6, 2022

Implement LFPy backend #385

Implement LFPy backend #385

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alejoe91 commented Mar 1, 2022

LFPy-related changes

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