Description of the problem

The format used for the FIL OPM system uses a tsv file to specify channel names and statuses, so functionality to check for bad channels from the *channels.tsv metadata was implemented to automatically assign the bad channels on import without user intervention. Its taken me over a year to discover this part of read_raw_fil never worked. Sorry!

Steps to reproduce

import mne
import tempfile
import shutil
import os
import pandas as pd
import traceback

subject = "sub-002"
data_path = mne.datasets.ucl_opm_auditory.data_path()
opm_orig_path = (
data_path / subject / "ses-001" / "meg"
)

# Copy test data to temporary directory
temp_dir = tempfile.TemporaryDirectory()
base_dir_name = os.path.basename(opm_orig_path)
dest_dir = os.path.join(temp_dir.name, base_dir_name)
shutil.copytree(opm_orig_path, dest_dir)


opm_temp_data_path = os.path.join(dest_dir, 'sub-002_ses-001_task-aef_run-001_meg.bin')

# raw = mne.io.read_raw_fil(opm_temp_data_path)
# print('orignal attempt read in ok')

# read in channels tsv, set one to bad (G2-17-TAN) and write out
chans_tsv_path = os.path.join(dest_dir, 'sub-002_ses-001_task-aef_run-001_channels.tsv')

chans_df = pd.read_csv(chans_tsv_path, delimiter='\t')
index = chans_df[chans_df['name'] == 'G2-17-TAN'].index
chans_df.loc[index, 'status'] = 'bad'
chans_df.to_csv(chans_tsv_path, sep='\t', index=False)

try:
    raw = mne.io.read_raw_fil(opm_temp_data_path)
except Exception as e:
    traceback.print_tb(e.__traceback__)
    
temp_dir.cleanup()

Link to data

No response

Expected results

An instance of raw should be created with the bad channels listed in the edited *_channels.tsv (this case G2-17-TAN) being populated in raw.info['bads'].

Actual results

Instance of raw not created, the following traceback below

Refining sensor orientations...
[done]
File "c:\users\george o'neill\documents\python\bad_channel_bug_test.py", line 35, in
raw = mne.io.read_raw_fil(opm_temp_data_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 12, in read_raw_fil
File "C:\Users\goneill\miniconda3\envs\mne\Lib\site-packages\mne\io\fil\fil.py", line 51, in read_raw_fil
return RawFIL(binfile, precision=precision, preload=preload)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\goneill\miniconda3\envs\mne\Lib\site-packages\mne\io\fil\fil.py", line 120, in init
info = _compose_meas_info(meg, chans)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\goneill\miniconda3\envs\mne\Lib\site-packages\mne\io\fil\fil.py", line 274, in _compose_meas_info
info["bads"] = _read_bad_channels(chans)
~~~~^^^^^^^^
File "C:\Users\goneill\miniconda3\envs\mne\Lib\site-packages\mne_fiff\meas_info.py", line 1579, in setitem
val = self._attributes[key](
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\goneill\miniconda3\envs\mne\Lib\site-packages\mne_fiff\meas_info.py", line 992, in _check_bads
return MNEBadsList(bads=bads, info=info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\goneill\miniconda3\envs\mne\Lib\site-packages\mne_fiff\meas_info.py", line 966, in init
_check_bads_info_compat(bads, info)
File "C:\Users\goneill\miniconda3\envs\mne\Lib\site-packages\mne_fiff\meas_info.py", line 959, in _check_bads_info_compat
raise ValueError(f"bad channel(s) {missing} marked do not exist in info")

Additional information

It appears to be due to the fact the check for bad channels is specified before the ch_names has been populated. This probably can be fixed by calling info._update_redundant() before _check_bads is called.