physiopy / physioqc

Toolbox for physiological data (Automagic) Quality Control
Apache License 2.0
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Creating nireports #22

Open SRSteinkamp opened 4 months ago

SRSteinkamp commented 4 months ago

This PR will implement the basis for creating html output using nireports.

Proposed Changes

Change Type

Checklist before review

SRSteinkamp commented 4 months ago

This PR should be more a basis for discussion of how to go further - it now creates a report in the outputdir.

Issues to discuss

SRSteinkamp commented 4 months ago

As a very small next step, I added some clunky code to use at least some BIDS naming for outputs and removing the hardcoding of subject IDs. It's not yet querying a BIDS dataset and creating a layout etc. - but I think BIDS format is at the very least implied.

me-pic commented 2 months ago

Hey @SRSteinkamp ! I would be happy to help on that PR, if you need a second pair of eyes. Would it possible to summarize what needs to be done ?

SRSteinkamp commented 1 week ago

Just trying to put some life into this.

This PR is basically a prototype, which provides a CLI that can be pointed to a physio data file and to an output directory. It will then save the report (html), figures and metrics to that output directory.

So far it is using pybids to separate fileparts etc.

I think the general question/discussion for this PR is, is this enough for the beginning, then it would need some clean up and improvement. Alternatively, we might want to discuss how the full workflow should look like (i.e. full BIDS-app style, traversing a BIDS etc.).