Add integrated equation of motion to ReSurfEMG

[rspwarnaar]

Summary

Add the integrated equation of motion, as described by Graßhoff 2023 to ReSurfEMG

Related Issues

N/A

Changes Introduced

List the major changes made in this PR:

• Added subpackage modelling, with modules tau_estimation, integrated_equation_of_motion, fit
• Added module pneumatic to preprocessing with methods to compute volume from flow
• Updated postprocessing.baseline moving_baseline method with an omit_nan boolean
• Updated postprocessing.event_detection find_linked_peaks method with a tolerance argument
• Added neural_expiratory_time method to postprocessing.event_detection
• Added percentile_snr method to postprocessing.features

Motivation and Context

Methods accompany a research paper and increase the robustness of EMG-based assessment of respiratory effort

Testing

Describe how you tested your changes. Include:

• Unit tests added or updated
• Notebook added showing the pipeline for the baseline profile in the paper

Checklist

• I have read the contributing guidelines
• My code follows the project's coding style
• I have added tests that prove my fix is effective or my feature works
• I have updated the documentation accordingly
• All existing and new tests pass

Additional Notes

Any other context or information reviewers should know?

[codecov]

Codecov Report

❌ Patch coverage is 96.49123% with 10 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
resurfemg/postprocessing/features.py	92.50%	6 Missing ⚠️
resurfemg/modelling/tau_estimation.py	96.72%	2 Missing ⚠️
resurfemg/postprocessing/event_detection.py	91.66%	2 Missing ⚠️

📢 Thoughts on this report? Let us know!

[ChiaraM96]

I finished going over the changes and I flagged down a few small bugs to address before merging - while they didn't seem to affect the results with the current synthetic data, they may become an issue with real data.

Other than that, it all looks nice and clean!

[rspwarnaar]

@ChiaraM96 Thanks Chiara. That was really helpful. Could you checkout the new changes?

[ChiaraM96]

Everything looks clean and merge-ready!