Generate graphic reports for phys2bids outputs

[me-pic]

Closes #131, #407

The PR solved the issues in #407 with the proposed changes mentioned below.
The PR #407 was itself a follow-up of #243

Proposed Changes

• Restrict bokeh version
• Match bokehJS version to bokeh version
• Remove x axes constraints

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!

[codecov]

Codecov Report

❌ Patch coverage is 98.82353% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 91.75%. Comparing base (4261d19) to head (0144d8c).

Files with missing lines	Patch %	Lines
phys2bids/reporting/html_report.py	98.76%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #464      +/-   ##
==========================================
+ Coverage   91.15%   91.75%   +0.59%     
==========================================
  Files           8        9       +1     
  Lines        1006     1091      +85     
==========================================
+ Hits          917     1001      +84     
- Misses         89       90       +1     

Files with missing lines	Coverage Δ
phys2bids/cli/run.py	96.55% <100.00%> (+0.12%)	⬆️
phys2bids/phys2bids.py	87.36% <100.00%> (+0.20%)	⬆️
phys2bids/reporting/html_report.py	98.76% <98.76%> (ø)

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[smoia]

@me-pic this is awesome!!! Can you look into the readthedocs failure, please?

[me-pic]

@smoia Not sure exactly what is happening with the doc... Been able to build it locally without any error using sphinx-build. Any hint on what I could check ?

[smoia]

No idea - I think it's happening also in #462. It seems to be something about the phys2bids.phys2bids module import?

[smoia]

@me-pic probably the best option is to update the documentation configuration (as well as sphinx packages version). Maybe we can open a new PR, trying to fit phys2bids docs into nigsp's configuration (it's more recent): https://github.com/MIPLabCH/nigsp/tree/master/docs

[me-pic]

@smoia Thank you ! Will take a look next week.

[smoia]

@me-pic do you still have problems with the docs?

[me-pic]

@smoia Yes.. I can't figure why, and I don't have any problem building it locally :(

[m-miedema]

I tested this with the data I'm using for the Repronim demo and it is mostly working - looks great! However, for this data there are four channels being saved, but only the first two generate plots in the report (the next two are completely missing). As well, I'm puzzled by the "phys2BIDS Output Directory" column. Is it meant to show the structure of the BIDS-ified files? Right now, it shows some assets (a bit confusing/distracting) and then the files in the folder that I ran phys2bids from (not the output directory or the files therein).

[smoia]

Can you post a screenshot please?

[m-miedema]

Can you post a screenshot please?

[me-pic]

For the phys2bids output directory, is that better ?

[smoia]

@m-miedema do you still want changes on this PR?

[m-miedema]

I don't think the issue with only the first two channel plots appearing was solved yet, but the output directory tree is better!

[me-pic]

@m-miedema regarding the plots including the first two channels, I believe the issue comes from the fact that the physio channels have different sampling frequency, and the generate_report function is called after the uniq_freq loop outside of it (see L545).

So from there we could either change the function so that all the channels, regardless of their sampling frequency, will be plotted in the same report, or do different report for different sampling frequency. I think it will be better to have all the information at the same place and perhaps just adding the sampling frequency in the plot title (e.g. currently: Channel 2: resp2, could be instead Channel 2: resp2 (100Hz)).

@m-miedema @smoia WDYT ? I'll wait for your feedback on that before making the changes !

[smoia]

Crazy idea, but what if we had two reports that link to each others through the folder list?
In that case, you could make a report for each BIDS file and even run QA/QC on it.

[m-miedema]

I think one report for every produced _physio file makes the most sense?

[me-pic]

@m-miedema @smoia I have made the changes to have one report per physio file (so one per sampling freq).

@smoia I'm not completely sure how to link the reports to each other..