[Feature] Add Fast Visibility Graph Based ECG R-peak Detector

[JonasEmrich]

Adding the accelerated visbility-graph-based R-peak detector (https://ieeexplore.ieee.org/document/10290007, https://github.com/JonasEmrich/vg-beat-detectors) #938

[welcome]

Thanks for opening this pull request! We'll make sure it's perfect before merging 🤗
Make sure to read the contributing guide. Also, if you think that your contribution is worthy of it, you can consider adding yourself to the Contributors list (feel free to ask us if you have any doubts).

[codecov-commenter]

Codecov Report

Attention: 101 lines in your changes are missing coverage. Please review.

Comparison is base (87c8c60) 54.82% compared to head (72e7601) 54.60%.

Files	Patch %	Lines
neurokit2/ecg/ecg_findpeaks.py	14.91%	97 Missing ⚠️
neurokit2/ecg/ecg_clean.py	50.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #939      +/-   ##
==========================================
- Coverage   54.82%   54.60%   -0.22%     
==========================================
  Files         304      304              
  Lines       14269    14333      +64     
==========================================
+ Hits         7823     7827       +4     
- Misses       6446     6506      +60     

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

[JonasEmrich]

Now, I should have adapted the package at all the required places. Together with the authors of the koka2022 method, we decided to remove it in favor of this more advanced method.

I tested the implementation briefly on two databases, and it appears that it procures results comparable to the original FastNVG algorithm (https://github.com/JonasEmrich/vg-beat-detectors)

[DominiqueMakowski]

Amazing job! Thanks

Together with the authors of the koka2022 method, we decided to remove it in favor of this more advanced method.

In that case, could we leave the "koka2022" input to then run your udpated method, throwing a warning that "The 'koka2022' method has been replaced by XX. Please replace method='koka2022' by ..." (so that we don't break potential user code just yet)

[JonasEmrich]

In that case, could we leave the "koka2022" input to then run your udpated method, throwing a warning that "The 'koka2022' method has been replaced by XX. Please replace method='koka2022' by ..." (so that we don't break potential user code just yet)

Thanks for pointing this out! Now, I added a warning in ecg_clean() and ecg_findpeaks().

[DominiqueMakowski]

I think we can just add it in ecg_findpeaks() because it's there that the switch happens

[JonasEmrich]

I think we can just add it in ecg_findpeaks() because it's there that the switch happens

Although the emrich2023 method uses the same cleaning as koka2022 (points to the same function), I think that perhaps users also should use emrich2023 here instead of koka2022. It's just the naming but makes it more consistent, since the koka2022 method is deprecated/removed. Or what are your thoughts?

[DominiqueMakowski]

It's just the naming but makes it more consistent, since the koka2022 method is deprecated/removed

makes sense!

[DominiqueMakowski]

@JonasEmrich is it good for me to merge?

[JonasEmrich]

@JonasEmrich is it good for me to merge?

@DominiqueMakowski yes, from my side it is ready to merge

[DominiqueMakowski]

Amazing, thanks again for all the work :)

[welcome]

Congrats on merging your first pull request! 🎉🍾 We're looking forward to your next one!

[NikkiNgombe]

Hello @JonasEmrich and @DominiqueMakowski ,
I'm working with some ECG and wanted to use "emrich2023" for the peak detection. However, I get the following error:

ValueError: NeuroKit error: ecg_findpeaks(): 'emrich2023' not implemented.

After installing ts2vg, I was able to use koka2022, but I am still unable to run ecg_findpeaks() using the Emrich 2023 method. Is this emrich2023 method actually implemented in NeuroKit2? When I checked the source code for ecg_findpeaks(), I also noticed, that emrich2023 wasn't listed in the available methods.

Any help would be greatly appreciated, thank you!
Nikki

[DominiqueMakowski]

I can see the lines in the current version:

NeuroKit/neurokit2/ecg/ecg_clean.py

Lines 126 to 127 in 1aa8dee

	elif method in ["vg", "vgraph", "fastnvg", "emrich", "emrich2023"]:
	clean = _ecg_clean_vgraph(ecg_signal, sampling_rate)

Do you have the latest version of NK installed?

[NikkiNgombe]

Thank you for the quick response! I was using version 0.2.7. I have now updated to version 0.2.9 and can now use the emrich2023 option. Thank you so much! :)