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DOC: Automatic flowchart #860

Merged
merged 9 commits into from
Feb 26, 2024
Merged

DOC: Automatic flowchart #860

merged 9 commits into from
Feb 26, 2024

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larsoner
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Before merging …

  • Changelog has been updated (docs/source/changes.md)

Locally produces:

Screenshot from 2024-02-23 14-52-05

@hoechenberger feel free to push directly wording changes you want. Locally you can iterate pretty easily with:

~/python/mne-bids-pipeline/docs/site$ python -m http.server
~/python/mne-bids-pipeline/docs/site$ ../build_docs.sh

then refreshting http://localhost:8000/features/overview.html in your browser.

@larsoner
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@SophieHerbst can you see if this fixes the wording issue(s) you ran into or if there is more to do?

@@ -224,7 +224,7 @@ def apply_ica_raw(
raw_fname = in_files.pop(in_key)
assert len(in_files) == 0, in_files
out_files = dict()
out_files[in_key] = raw_fname.copy().update(processing="clean")
out_files[in_key] = raw_fname.copy().update(processing="clean", split=None)
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@hoechenberger hoechenberger Feb 23, 2024

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Should we check all code that generates output filenames to ensure we set split=None everywhere?

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I think we could do it in the function that prepares the output filenames actually. I'll give it a shot

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Should be working now!

@SophieHerbst
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@larsoner is the 'temporal regression for artifact removal' a default step? I am not aware that I am using it.
If not, I think it should be marked as optional.

@hoechenberger
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most of the steps are optional though.... we'd end up with almost everything being marked as such

@SophieHerbst
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mh right. I am wondering how to make it clearer which config options trigger which steps (or their re-run)

@hoechenberger
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there are get_config() functions in every step now which cover almost all configuration options that affect this step (exceptions are I believe n_jobs, subjects and session, but i'm not 100% certain from the top of my head)

in theory this information could be used

@SophieHerbst
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Used as in informing the documentation?
(I learned about this part last week, when I forgot to mention the image_kwargs for the report there; easy to make mistakes as it needs to be added manually)

@hoechenberger
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Used as in informing the documentation?

Yes

We'd basically have to iterate over all steps and grep the arguments used in get_config() and then put that in a table or so…

@larsoner
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Opened #862 and #861 so we can iterate further in follow-up PRs. This one in the meantime is 90% a bugfix for missing / incorrect information at the moment (the other 10% being the ICA/SSP enhancement to try and make that part clearer) -- @SophieHerbst @hoechenberger happy with those parts so we can merge this?

@hoechenberger
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yes, this is great! feel free to merge whenever you feel it's ready 👍👍👍

@larsoner larsoner merged commit 61b3553 into mne-tools:main Feb 26, 2024
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@larsoner larsoner deleted the doc branch February 26, 2024 14:22
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3 participants