FIX: mne.io.read_raw_fil handling of bad channels (#12597)

doc/changes/devel/12597.bugfix.rst

@@ -0,0 +1 @@
+Fix bug where :func:`mne.io.read_raw_fil` could not assign bad channels on import, by `George O'Neill`_.

mne/io/fil/fil.py

@@ -266,16 +266,14 @@ def _convert_channel_info(chans):
 def _compose_meas_info(meg, chans):
     """Create info structure."""
     info = _empty_info(meg["SamplingFrequency"])
-
     # Collect all the necessary data from the structures read
     info["meas_id"] = get_new_file_id()
     tmp = _convert_channel_info(chans)
     info["chs"] = _refine_sensor_orientation(tmp)
-    # info['chs'] = _convert_channel_info(chans)
     info["line_freq"] = meg["PowerLineFrequency"]
+    info._update_redundant()
     info["bads"] = _read_bad_channels(chans)
     info._unlocked = False
-    info._update_redundant()
     return info
 
 

mne/io/fil/tests/test_fil.py

@@ -25,6 +25,21 @@
 )
 
 
+def _set_bads_tsv(chanfile, badchan):
+    """Update channels.tsv by setting target channel to bad."""
+    data = []
+    with open(chanfile, encoding="utf-8") as f:
+        for line in f:
+            columns = line.strip().split("\t")
+            data.append(columns)
+
+    with open(chanfile, "w", encoding="utf-8") as f:
+        for row in data:
+            if badchan in row:
+                row[-1] = "bad"
+            f.write("\t".join(row) + "\n")
+
+
 def unpack_mat(matin):
     """Extract relevant entries from unstructred readmat."""
     data = matin["data"]
@@ -159,3 +174,20 @@ def test_fil_no_positions(tmp_path):
     chs = raw.info["chs"]
     locs = array([ch["loc"][:] for ch in chs])
     assert isnan(locs).all()
+
+
+@testing.requires_testing_data
+def test_fil_bad_channel_spec(tmp_path):
+    """Test FIL reader when a bad channel is specified in channels.tsv."""
+    test_path = tmp_path / "FIL"
+    shutil.copytree(fil_path, test_path)
+
+    channame = test_path / "sub-noise_ses-001_task-noise220622_run-001_channels.tsv"
+    binname = test_path / "sub-noise_ses-001_task-noise220622_run-001_meg.bin"
+    bad_chan = "G2-OG-Y"
+
+    _set_bads_tsv(channame, bad_chan)
+
+    raw = read_raw_fil(binname)
+    bads = raw.info["bads"]
+    assert bad_chan in bads