Skip to content
This repository was archived by the owner on Feb 26, 2025. It is now read-only.

Conversation

anilbey
Copy link
Contributor

@anilbey anilbey commented Apr 4, 2024

With this change the Cell object calls the recording.compute_efeatures in parallel in the extract_efeatures function.

@codecov-commenter
Copy link

Codecov Report

Attention: Patch coverage is 89.06250% with 7 lines in your changes are missing coverage. Please review.

Project coverage is 73.29%. Comparing base (b5fc0e5) to head (0b3eb99).

Files Patch % Lines
bluepyefe/cell.py 90.90% 2 Missing ⚠️
bluepyefe/rheobase.py 77.77% 2 Missing ⚠️
tests/test_efel_settings.py 66.66% 2 Missing ⚠️
bluepyefe/extract.py 66.66% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #176      +/-   ##
==========================================
- Coverage   73.76%   73.29%   -0.48%     
==========================================
  Files          38       39       +1     
  Lines        2413     2430      +17     
==========================================
+ Hits         1780     1781       +1     
- Misses        633      649      +16     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.


self.assertEqual(self.cell.recordings[0].efeatures["Spikecount"], 0.)

def test_efel_threshold(self):
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

duplicate of another test with the same name

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

the other test has more checks

@anilbey anilbey marked this pull request as ready for review April 11, 2024 09:59
recording = self.cell.recordings[0]
recording = self.cell.recordings["IDRest"][0]
self.assertEqual(recording.efeatures["Spikecount"], 0.)
self.assertLess(abs(recording.efeatures["AP1_amp"] - 66.68), 0.01)
Copy link
Contributor Author

@anilbey anilbey Apr 11, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

this code was not getting executed for a long time. The other test was shadowing it

@anilbey anilbey changed the title attempt to feature extraction in parallel use all available cores in feature extraction Apr 11, 2024
@darshanmandge
Copy link
Contributor

Thanks @anilbey !
I think we should test this with all the readers: ibw, different types of nwb, abf, etc. with a good number of ephys files to see if it works and if it improves the performance. e.g. for ibw files this bluepyemodel example would be a sufficient test.

Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants