mne.channels.read_ch_adjacency 'picks' argument does not function as described

[aaronjnewman]

Proposed documentation enhancement

The explanation of the picks for mne.channels.read_ch_adjacency reads:

Channels to include. Slices and lists of integers will be interpreted as channel indices. In lists, channel type strings (e.g., ['meg', 'eeg']) will pick channels of those types, channel name strings (e.g., ['MEG0111', 'MEG2623'] will pick the given channels. Can also be the string values “all” to pick all channels, or “data” to pick data channels. None (default) will pick all channels. Note that channels in info['bads'] will be included if their names or indices are explicitly provided. Picks must match the template.

However, mne.channels.read_ch_adjacency('elec1005', picks=['eeg']) generates an error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-81-6e28f3bd522a> in <module>
----> 1 mne.channels.read_ch_adjacency('elec1005', picks=['eeg'])

/opt/conda/lib/python3.9/site-packages/mne/channels/channels.py in read_ch_adjacency(fname, picks)
   1504     nb = loadmat(fname)['neighbours']
   1505     ch_names = _recursive_flatten(nb['label'], str)
-> 1506     picks = _picks_to_idx(len(ch_names), picks)
   1507     neighbors = [_recursive_flatten(c, str) for c in
   1508                  nb['neighblabel'].flatten()]

/opt/conda/lib/python3.9/site-packages/mne/io/pick.py in _picks_to_idx(info, picks, none, exclude, allow_empty, with_ref_meg, return_kind)
   1011         raise ValueError('picks must be 1D, got %sD' % (picks.ndim,))
   1012     if picks.dtype.char in ('S', 'U'):
-> 1013         picks = _picks_str_to_idx(info, picks, exclude, with_ref_meg,
   1014                                   return_kind, extra_repr, allow_empty,
   1015                                   orig_picks)

/opt/conda/lib/python3.9/site-packages/mne/io/pick.py in _picks_str_to_idx(info, picks, exclude, with_ref_meg, return_kind, extra_repr, allow_empty, orig_picks)
   1046     # special case for _picks_to_idx w/no info: shouldn't really happen
   1047     if isinstance(info, int):
-> 1048         raise ValueError('picks as str can only be used when measurement '
   1049                          'info is available')
   1050 

ValueError: picks as str can only be used when measurement info is available

The same error is generated if I provide a list of channel names, e.g.:

chs = ['Fp1', 'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'FC5', 'FC1', 'FC2', 'FC6', 'T7', 'C3', 'Cz', 'C4', 'T8', 'TP9', 'CP5', 'CP1', 'CP2', 'CP6', 'TP10', 'P7', 'P3', 'Pz', 'P4', 'P8', 'PO9', 'O1', 'Oz', 'O2', 'PO10']
mne.channels.read_ch_adjacency('elec1005', picks=chs)

Am I mis-reading the docs, or is this an error either in the code or the docs?

[drammock]

I think the docstring is wrong. The built-in neighbor files don't keep track of channel type information, so picking by channel type can't work. The second case (giving a list of channel names) could work though... easiest might be to create a fake Info from the ch_names present in the neighbors file, and pass that to _picks_to_idx instead of passing len(ch_names). @aaronjnewman do you feel up to making a PR that does that?

[sappelhoff]

Note: @dominikwelke is working on this

[dominikwelke]

actually, I just see that this has already been adressed (also the docstring was changed, I just missed this as I first looked at the stable doc).

so this can be closed I guess
@larsoner - you did this, right? anything still open about this?