DRAFT PR - Add cardiac and respiratory quality metrics (from the OHBM 2024 hackathon) #44
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@me-pic do you want to have a look at this one? |
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@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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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 !
| return signal.sosfiltfilt(sos, inputdata).real | ||
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| def readbidstsv(inputfilename, colspec=None, warn=True, debug=False): |
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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
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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.
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| def detrend(inputdata, order=1, demean=False): |
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@smoia What do you think about the idea of integrating that function in the peakdet operations module instead ?
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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?
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That's a good question ! @smoia @m-miedema WDYT ?
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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!
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| def plotheartbeatqualities(heartbeatlist, totaltime=None): |
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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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Closes #
This PR adds in the quality metric code that I wrote at the OHBM 2024
Proposed Changes
Change Type
bugfix(+0.0.1)minor(+0.1.0)major(+1.0.0)refactoring(no version update)test(no version update)infrastructure(no version update)documentation(no version update)otherChecklist before review