DRAFT PR - Add cardiac and respiratory quality metrics (from the OHBM 2024 hackathon) by bbfrederick · Pull Request #44 · physiopy/physioqc

bbfrederick · 2025-01-19T17:29:01Z

Closes #

This PR adds in the quality metric code that I wrote at the OHBM 2024

Proposed Changes

metrics/cardiac.py is now fully fleshed out out from a stub.
metrics/chest_belt.py is now fully fleshed out out from a stub.
There are two test scripts and some test data at the root level of the package (they don't belong there, but I wasn't sure where they should live). They exercise the preprocessing and quality metric processing for respiratory and cardiac data.
metrics/utils.py has several filtering support routines added.

Change Type

Checklist before review

I added everything I wanted to add to this PR.
[Code or tests only] I wrote/updated the necessary docstrings.
[x ] [Code or tests only] I ran and passed tests locally.
[Documentation only] I built the docs locally.
[x ] My contribution is harmonious with the rest of the code: I'm not introducing repetitions.
My code respects the adopted style, especially linting conventions.
The title of this PR is explanatory on its own, enough to be understood as part of a changelog.
I added or indicated the right labels.

I added information regarding the timeline of completion for this PR.

Please, comment on my PR while it's a draft and give me feedback on the development!

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smoia · 2025-01-20T06:38:04Z

@me-pic do you want to have a look at this one?

me-pic · 2025-01-20T21:01:59Z

@smoia Can try to have a look at it by the end of the month !

@bbfrederick Thanks a lot for getting the ball rolling on that 🥳

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me-pic

Thank you so much @bbfrederick for opening that PR ! It is a big push for the development of physioqc. Super exciting 🤩

I quickly went through the changes, and left a few comments to discuss. Will take a closer in the next week or two. Happy to help wherever I can !

physioqc/metrics/utils.py

me-pic · 2025-01-20T21:22:51Z

physioqc/metrics/utils.py

+    return signal.sosfiltfilt(sos, inputdata).real
+
+
+def readbidstsv(inputfilename, colspec=None, warn=True, debug=False):


Really happy to see physioqc supporting BIDS dataset !!! 😸

I'm wondering if there is a reason not to add pybids as a dependency, which might facilitate the loading data from a bids dataset part

I can check that out - I just pulled in a routine I wrote a while back to use in one of my packages to read BIDS files, but I can use a standard routine.

me-pic · 2025-01-20T21:26:45Z

physioqc/metrics/cardiac.py

+    return thefit
+
+
+def detrend(inputdata, order=1, demean=False):


@smoia What do you think about the idea of integrating that function in the peakdet operations module instead ?

Detrend? Sure. When I went to fork peakdet, I saw that the description says "Former toolbox for physiological peak detection analyses. Deprecated in favour of prep4phys". So should I be using that instead?

That's a good question ! @smoia @m-miedema WDYT ?

I would say let's keep working on peakdet and we'll project the changes to prep4phys. I'm surprised peakdet didn't have detrending options before!

me-pic · 2025-01-20T21:33:18Z

physioqc/metrics/cardiac.py

+    return heartbeatlist
+
+
+def plotheartbeatqualities(heartbeatlist, totaltime=None):


I'm wondering if all the plotting functions (or just lines related to plotting in general) should not be integrated in the visualizations script ?

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bbfrederick added 3 commits January 19, 2025 12:19

Merge in quality metrics from OHBM 2024 brainhack

006b4ca

Remove plots

fbb75a5

Update .gitignore

30a7dcc

github-actions bot assigned bbfrederick Jan 19, 2025

github-actions bot added the Internal Changes affect the internal API. It doesn't increase the version, but produces a changelog label Jan 19, 2025

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bbfrederick added 2 commits January 20, 2025 15:57

Added legends to plots

bd39278

Added legends to plots, tweaked envelope filtering

02e9592

me-pic self-requested a review January 20, 2025 21:02

bbfrederick and others added 4 commits January 20, 2025 16:32

Added docstrings

1d425de

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Update chest_belt.py

3bc84d5

Merge branch 'master' of https://github.com/bbfrederick/physioqc

b41c04e

me-pic reviewed Jan 20, 2025

View reviewed changes

bbfrederick and others added 9 commits January 20, 2025 22:51

Switched filters and interpolation ops to use peakdet routines.

d96c1a5

Finished converting to physio inputs

cbc63ff

[pre-commit.ci] auto fixes from pre-commit.com hooks

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Updated cardiac to match respiratory code

00609bf

Merge branch 'master' of https://github.com/bbfrederick/physioqc

d1f983f

[pre-commit.ci] auto fixes from pre-commit.com hooks

bc0d87b

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Update chest_belt.py

ffc60e0

Merge branch 'master' of https://github.com/bbfrederick/physioqc

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DRAFT PR - Add cardiac and respiratory quality metrics (from the OHBM 2024 hackathon)#44

DRAFT PR - Add cardiac and respiratory quality metrics (from the OHBM 2024 hackathon)#44
bbfrederick wants to merge 19 commits intophysiopy:masterfrom
bbfrederick:master

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		return signal.sosfiltfilt(sos, inputdata).real


		def readbidstsv(inputfilename, colspec=None, warn=True, debug=False):

		return heartbeatlist


		def plotheartbeatqualities(heartbeatlist, totaltime=None):

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bbfrederick commented Jan 19, 2025

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