MAINT: Fix Azure (mne-tools#11815)

doc/changes/latest.inc

@@ -52,6 +52,7 @@ Bugs
 - Fix bug with :func:`mne.io.read_raw_fil` where datasets without sensor positions would not import (:gh:`11733` by `George O'Neill`_)
 - Fix bug with :func:`mne.chpi.compute_chpi_snr` where cHPI being off for part of the recording or bad channels being defined led to an error or incorrect behavior (:gh:`11754`, :gh:`11755` by `Eric Larson`_)
 - Allow int-like for the argument ``id`` of `~mne.make_fixed_length_events` (:gh:`11748` by `Mathieu Scheltienne`_)
+- Fix bug where :func:`mne.io.read_raw_egi` did not properly set the EEG reference location for the reference channel itself (:gh:`11822` by `Eric Larson`_)
 - Fix bug with legacy :meth:`~mne.io.Raw.plot_psd` method where passed axes were not used (:gh:`11778` by `Daniel McCloy`_)
 - blink :class:`mne.Annotations` read in by :func:`mne.io.read_raw_eyelink` now begin with ``'BAD_'``, i.e. ``'BAD_blink'``, because ocular data are missing during blinks. (:gh:`11746` by `Scott Huberty`_)
 - Fix bug where :ref:`mne show_fiff` could fail with an ambiguous error if the file is corrupt (:gh:`11800` by `Eric Larson`_)

mne/channels/montage.py

@@ -1171,25 +1171,22 @@ def _backcompat_value(pos, ref_pos):
     chs = [info["chs"][ii] for ii in picks]
     non_names = [info["chs"][ii]["ch_name"] for ii in non_picks]
     del picks
-    ref_pos = [ch["loc"][3:6] for ch in chs]
+    ref_pos = np.array([ch["loc"][3:6] for ch in chs])
 
     # keep reference location from EEG-like channels if they
     # already exist and are all the same.
-    custom_eeg_ref_dig = False
     # Note: ref position is an empty list for fieldtrip data
-    if ref_pos:
-        if (
-            all([np.equal(ref_pos[0], pos).all() for pos in ref_pos])
-            and not np.equal(ref_pos[0], [0, 0, 0]).all()
-        ):
-            eeg_ref_pos = ref_pos[0]
-            # since we have an EEG reference position, we have
-            # to add it into the info['dig'] as EEG000
-            custom_eeg_ref_dig = True
-    if not custom_eeg_ref_dig:
+    if len(ref_pos) and ref_pos[0].any() and (ref_pos[0] == ref_pos).all():
+        eeg_ref_pos = ref_pos[0]
+        # since we have an EEG reference position, we have
+        # to add it into the info['dig'] as EEG000
+        custom_eeg_ref_dig = True
+    else:
         refs = set(ch_pos) & {"EEG000", "REF"}
         assert len(refs) <= 1
         eeg_ref_pos = np.zeros(3) if not refs else ch_pos.pop(refs.pop())
+        custom_eeg_ref_dig = False
+    del ref_pos
 
     # This raises based on info being subset/superset of montage
     info_names = [ch["ch_name"] for ch in chs]
@@ -1306,6 +1303,7 @@ def _backcompat_value(pos, ref_pos):
 
     # determine if needed to add an extra EEG REF DigPoint
     if custom_eeg_ref_dig:
+        print(len(digpoints))
         # ref_name = 'EEG000' if match_case else 'eeg000'
         ref_dig_dict = {
             "kind": FIFF.FIFFV_POINT_EEG,
@@ -1318,6 +1316,7 @@ def _backcompat_value(pos, ref_pos):
         # in the old dig
         if ref_dig_point in old_dig:
             digpoints.append(ref_dig_point)
+        print(len(digpoints))
     # Next line modifies info['dig'] in place
     with info._unlock():
         info["dig"] = _format_dig_points(digpoints, enforce_order=True)

mne/io/egi/egimff.py

@@ -575,14 +575,9 @@ def __init__(
             ref_idx = ref_idx.item()
             ref_coords = info["chs"][int(ref_idx)]["loc"][:3]
             for chan in info["chs"]:
-                is_eeg = chan["kind"] == FIFF.FIFFV_EEG_CH
-                is_not_ref = chan["ch_name"] not in REFERENCE_NAMES
-                if is_eeg and is_not_ref:
+                if chan["kind"] == FIFF.FIFFV_EEG_CH:
                     chan["loc"][3:6] = ref_coords
 
-            # Cz ref was applied during acquisition, so mark as already set.
-            with info._unlock():
-                info["custom_ref_applied"] = FIFF.FIFFV_MNE_CUSTOM_REF_ON
         file_bin = op.join(input_fname, egi_info["eeg_fname"])
         egi_info["egi_events"] = egi_events
 

mne/io/egi/tests/test_egi.py

@@ -2,6 +2,7 @@
 #          simplified BSD-3 license
 
 
+from copy import deepcopy
 from pathlib import Path
 import os
 import shutil
@@ -12,7 +13,7 @@
 import pytest
 from scipy import io as sio
 
-from mne import find_events, pick_types, pick_channels
+from mne import find_events, pick_types
 from mne.io import read_raw_egi, read_evokeds_mff, read_raw_fif
 from mne.io.constants import FIFF
 from mne.io.egi.egi import _combine_triggers
@@ -161,14 +162,12 @@ def test_io_egi_mff():
     assert raw.info["dig"][0]["kind"] == FIFF.FIFFV_POINT_CARDINAL
     assert raw.info["dig"][3]["kind"] == FIFF.FIFFV_POINT_EEG
     assert raw.info["dig"][-1]["ident"] == 129
-    assert raw.info["custom_ref_applied"] == FIFF.FIFFV_MNE_CUSTOM_REF_ON
+    # This is not a custom reference, it's consistent across all channels
+    assert raw.info["custom_ref_applied"] == FIFF.FIFFV_MNE_CUSTOM_REF_OFF
     ref_loc = raw.info["dig"][-1]["r"]
     eeg_picks = pick_types(raw.info, eeg=True)
     assert len(eeg_picks) == n_eeg + n_ref  # 129
-    # ref channel doesn't store its own loc as ref location
-    # so don't test it
-    ref_pick = pick_channels(raw.info["ch_names"], ["VREF"])
-    eeg_picks = np.setdiff1d(eeg_picks, ref_pick)
+    # ref channel should store its own loc as ref location, so't test it
     for i in eeg_picks:
         loc = raw.info["chs"][i]["loc"]
         assert loc[:3].any(), loc[:3]
@@ -523,13 +522,25 @@ def test_meas_date(fname, timestamp, utc_offset):
         (egi_mff_pns_fname, "GSN-HydroCel-257"),  # 257 chan EGI file
     ],
 )
-def test_set_standard_montage(fname, standard_montage):
+def test_set_standard_montage_mff(fname, standard_montage):
     """Test setting a standard montage."""
     raw = read_raw_egi(fname, verbose="warning")
-    dig_before_mon = raw.info["dig"]
+    n = int(standard_montage.split("-")[-1]) + 3
+    dig_before_mon = deepcopy(raw.info["dig"])
+    assert len(dig_before_mon) == n
+    ref_loc = dig_before_mon[-1]["r"]
+    picks = pick_types(raw.info, eeg=True)
+    assert len(picks) == n
+    for pick in picks:
+        assert_allclose(raw.info["chs"][pick]["loc"][3:6], ref_loc)
 
     raw.set_montage(standard_montage, match_alias=True, on_missing="ignore")
     dig_after_mon = raw.info["dig"]
 
     # No dig entries should have been dropped while setting montage
-    assert len(dig_before_mon) == len(dig_after_mon)
+    assert len(dig_before_mon) == n
+    assert len(dig_after_mon) == n
+
+    # Check that the reference remained
+    for pick in picks:
+        assert_allclose(raw.info["chs"][pick]["loc"][3:6], ref_loc)