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Channel adjacency improvements #12292

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mscheltienne opened this issue Dec 12, 2023 · 1 comment · May be fixed by #12293
Open

Channel adjacency improvements #12292

mscheltienne opened this issue Dec 12, 2023 · 1 comment · May be fixed by #12293
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@mscheltienne
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mscheltienne commented Dec 12, 2023 •
edited

Proposed documentation enhancement

The docstring of the picks argument in read_ch_adjacency is wrong as there is no info provided to this function.

Also, find_ch_adjacency could benefit from an extra argument similar to pick in read_ch_adjacency to select channels to include in the adjacency matrix. I see 2 options forward:

  • (1) Keep ch_type and add exclude=() which can be set to exclude="bads"
  • (2) Deprecate ch_type in favor of the traditional picks argument, with an adapted docstring mentioning that the channel selection provided must yield a single channel type (+ check and appropriate error message)

I'm in favor of (2) as it offers more flexibility to find_ch_adjacency.

Correspond to this forum post: https://mne.discourse.group/t/find-ch-adjacency-not-accounting-for-bad-channels/7968/
@larsoner
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Given ch_type is in second position and we easily can do something like:

def find_ch_adjacency(info, picks, *, ch_type=None):
    if ch_type is not None:
        warn(...)
        picks = ch_type

that will avoid breaking code for some folks, I'm in favor of (2)

@mscheltienne mscheltienne linked a pull request Dec 13, 2023 that will close this issue
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Improve find_ch_adjacency and read_ch_adjacency mscheltienne/mne-python
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@larsoner @mscheltienne