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Thank you @maestroque for working on that ! It's really nice to have doc for phys2denoise 🎉 Just left some comments in my review. Let me know if you have any question / want to discuss them !
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| .. _basic_installation: | ||
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| Developer installation |
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Wondering if there is a reason to only have the dev installation here
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| # Load the physiological data | ||
| sample_rate = 1000 | ||
| physio = io.load_physio('path/to/physiological/data', fs=sample_rate) |
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At some point it would be nice to provide actual data for people to play around
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| Contents | |||
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I think for now it is ok, but at some point it would be necessary to provide a bit more context/use cases for that package. You can check peakdet doc for an example
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| The benefit of using a Physio object other than the encapsulation of all the desired parameters in a single object is the fact that | ||
| the object retains a history of all the operations performed on it. This allows for easy debugging and reproducibility of the results. | ||
| For further information refer to the :py:mod:`physutils` documentation. |
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Maybe I'm not aware of it, but it looks like for the moment there is not physutils documentation. So since you are referring to it, I'm wondering if we should work on the physutils docs before merging that PR.
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I can generate some docs only including API for the time being.
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| from phys2denoise.metrics.chest_belt import respiratory_variance_time | ||
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| # Given that the respiratory signal is stored in `data`, the peaks in `peaks`, the troughs in `troughs` |
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Here do you mean the respiratory signal is stored in physio ? However I think it might be less confusing to keep the name you used in the comment and use data in the function i.e. respiratory_variance_time(data, peaks, troughs, sample_rate)
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Also do you think it would be a good idea to show in that example how users would load their data ?
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thanks, good catch
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I think loading the data is really dependent on the format the user is using, idk if it would be fitting here
docs/user_guide/metrics.rst
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| Without using a Physio object | ||
| ############################# | ||
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| However, if the use of :py:mod:`physutils` is not preferred, the metrics can be also computed without it. The following |
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Wondering if it would make more sense to say if the use of the physio object rather than if the use of physutils. What do you think ?
| from phys2denoise.metrics.utils import export_metric | ||
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| RVT = respiratory_variance_time( | ||
| resp.data, resp.peaks, resp.troughs, resp.fs, lags=(0, 4, 8, 12) |
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I might have missed it but I don't see where resp was defined previously
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@me-pic I implemented your suggestions, it should hopefully be gtg |
for more information, see https://pre-commit.ci
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@maestroque Thank you ! I've pushed some changes directly on your branch. Just changed some sentence formulation and added the warning about the potential installation issue regarding matplotlib versioning
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Closes #
Generate a documentation page for
phys2denoise, including showcase of the utilization of the Physio object within the packageChange 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