Concatenate mne.Reports

[sappelhoff]

Describe the new feature or enhancement

I have a pipeline that creates an mne.Report per subject and per "run". I made up my mind "after the fact" and now want to combine the "runs" per subject in a single report.

It would therefore be nice if I could simply load the reports, and concatenate them into a single report.

Describe your proposed implementation

Not sure how the specifics of this would work.

Describe possible alternatives

The alternative is, that I re-write my pipeline to write one report per subject, including all "runs", from the beginning.

Additional context

No response

[larsoner]

No opposition in principle. In practice might be tricky because of DOM stuff, templating, and dealing with potential duplicates. But first supporting the case where there are no duplicates in the DOM IDs I think it shouldn't be too bad.

[Randomidous]

Hey @larsoner and @sappelhoff ,

I was thinking about picking this up in my free time but it would help me to narrow down the functionality a bit @larsoner .
Would a function in mne/report/report.py that does nothing else but appending reports using beautifulsoup4 do the job?

[larsoner]

Unfortunately that wouldn't work to concat the mne.Report objects themselves, it would only work to concatenate the generated HTML

[Randomidous]

Sorry for the ambiguous language. I meant concatenating html files not reports.
I was thinking of something like this: #13223

I have attached the report resulting from running mne.report.tests.test_report.test_concatenate_reports():
combined.pdf

[wmvanvliet]

Wouldn't it be way easier to merge/concatenate the mne.Report objects themselves? And then call .save("big_report.html") on the result. That would enable a workflow in which you have the reports of individual subjects as .h5 files (as well as .html if that is convenient) and then at the end load all the .h5 files, concatenate them, and then save the final .html.

[Randomidous]

@wmvanvliet That would work nicely, but I think the inquiry was regarding what to do once the reports are already saved:

I made up my mind "after the fact" and now want to combine the "runs" per subject in a single report.

[sappelhoff]

When I first opened this issue, I actually DID save all reports in html and h5, so what @wmvanvliet suggests would have worked there, and I believe it is a nice way to deal with the issue.

Potentially there is a place for both functions: concatenating the HTMLs themselves, as well as the workflow that Marijn suggested? What do you all think?

[drammock]

Personally I don't feel that MNE should be doing things like munging HTML files. It feels pretty squarely out of scope for a neuroscience package. Merging report .h5 files is slightly better, but even there I'd be tempted to write a recipe for how to do it yourself, and post that as a how-to example on our doc site, rather than adding new functionality to the public API.

[wmvanvliet]

@wmvanvliet That would work nicely, but I think the inquiry was regarding what to do once the reports are already saved:

If you save them as .h5 you can read them back in as mne.Report objects. Nothing is stopping you from saving both a copy in .h5 and one in .html