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Add initial set of metrics #19

Merged
merged 21 commits into from
Feb 25, 2021
Merged

Add initial set of metrics #19

merged 21 commits into from
Feb 25, 2021

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tsalo
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@tsalo tsalo commented Nov 13, 2020 •
edited by smoia
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Closes #2 and closes #3 and closes #7.

Proposed Changes

  • Add duecredit and a references file to collect duecredit citations.
  • Add/draft functions for the cardiac (CRF) and respiratory (RRF) response functions.
  • Add RPV, ENV, and RV metrics.
  • Add RETROICOR.

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)
  • other

Checklist before review

  • I added everything I wanted to add to this PR.
  • [Code or tests only] I wrote/updated the necessary docstrings.
  • [Code or tests only] I ran and passed tests locally.
  • [Documentation only] I built the docs locally.
  • 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!

@tsalo tsalo marked this pull request as draft November 13, 2020 14:43
tsalo
tsalo commented Dec 30, 2020
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phys2denoise/metrics/chest_belt.py
Comment on lines +110 to +112
out_samplerate : :obj:`float`
Sampling rate for the output time series in seconds.
Corresponds to TR in fMRI data.
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Do we want to include downsampling in the individual metric functions, or have it in a separate step?

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I'm thinking that downsampling should be done somewhere else TBH.

@tsalo tsalo changed the title Add initial set of metrics Add RV, RPV, ENV, RRF, and CRF Jan 1, 2021
@tsalo tsalo mentioned this pull request Jan 4, 2021
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11 tasks
@tsalo tsalo added the Minormod This PR generally closes an "Enhancement" issue. It increments the minor version (0.+1.0) label Jan 8, 2021
@tsalo tsalo added the Enhancement New feature or request label Feb 11, 2021
@tsalo tsalo added the Skip release This PR preserves the current version when merged, and doesn't appear in the changelog label Feb 25, 2021
@tsalo tsalo marked this pull request as ready for review February 25, 2021 17:12
@tsalo tsalo changed the title Add RV, RPV, ENV, RRF, and CRF Add initial set of metrics Feb 25, 2021
@smoia smoia added Minormod-breaking For development only, this PR increments the minor version (0.+1.0) but breaks compatibility and removed Minormod This PR generally closes an "Enhancement" issue. It increments the minor version (0.+1.0) Skip release This PR preserves the current version when merged, and doesn't appear in the changelog labels Feb 25, 2021
@smoia smoia assigned smoia and tsalo Feb 25, 2021
@smoia smoia merged commit fcab9f3 into physiopy:master Feb 25, 2021
@tsalo tsalo deleted the add-metrics branch February 25, 2021 18:13
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smoia commented Feb 25, 2021

🚀 PR was released in 0.2.0 🚀

@smoia smoia added the released This issue/pull request has been released label Feb 25, 2021
rzlim08
rzlim08 reviewed Feb 25, 2021
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phys2denoise/metrics/chest_belt.py
----------
.. [1] C. Chang & G. H. Glover, "Relationship between respiration,
end-tidal CO2, and BOLD signals in resting-state fMRI," Neuroimage,
issue 4, vol. 47, pp. 1381-1393, 2009.
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A bit of a nit-pick, but I think RV was described in "Influence of heart rate on the BOLD signal: the cardiac response function" also by Chang and Glover in 2009. It may also be in this paper, but I didn't see it from a skim.

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@tsalo tsalo Feb 25, 2021 •
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I think @smoia noticed similar issues with my citations (#31). We can address in a new PR, or you can fold it into #21?

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I think we should handle it in a new PR

@tsalo tsalo mentioned this pull request Feb 26, 2021
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Successfully merging this pull request may close these issues.

Requested metric: respiratory pattern variability Requested metric: respiratory variance
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@tsalo @smoia @rzlim08 @CesarCaballeroGaudes