Write out reports to individual reconstruction derivative folders

PennLINC / qsirecon

Reconstruction of preprocessed q-space images (dMRI)

https://qsirecon.readthedocs.io/

BSD 3-Clause "New" or "Revised" License

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Write out reports to individual reconstruction derivative folders #53

Closed tsalo closed 3 months ago

tsalo commented 3 months ago

Closes #51.

Changes proposed in this pull request

Create prep-style io_spec.json to control output filenames.
Replace ReconDerivativesDataSink with DerivativesDataSink for all non-folder outputs.
Start adding figures to HTML reports.
Create clean_datasinks function to define the output directory for each reconstruction workflow separately.
Refactor the AMICO workflow a bit. Sorry, I got carried away with indentation and such.

To do:

[ ] Add HTML summaries to reports. I need to figure out what info is relevant.

tsalo commented 3 months ago

My PNG-to-SVG conversion is not working very well, unfortunately. I'll probably drop that in favor of opening an issue on Nireports.

EDIT: I've opened https://github.com/nipreps/nireports/issues/124.

tsalo commented 3 months ago

I still want to see if I can reorganize the scalar datasink into a short workflow at some point, but the TSV splitter datasink and folder-based recon datasink will be harder.

mattcieslak commented 3 months ago

I always prefer workflows too. I ended up with interfaces for these because you can't predict ahead of time what might be produced in the different nodes. But there might be a way! :roadmap: