[ENH, MRG] Simplify reading dig (#979)

* Simplify reading dig [skip ci]

* update whatsnew

* Update doc/whats_new.rst

Co-authored-by: Adam Li <[email protected]>

Co-authored-by: Richard Höchenberger <[email protected]>
Co-authored-by: Adam Li <[email protected]>

Author: 3 people

doc/whats_new.rst

@@ -54,6 +54,8 @@ Enhancements
 
 - :func:`mne_bids.update_anat_landmarks` can now directly work with fiducials saved from the MNE-Python coregistration GUI or :func:`mne.io.write_fiducials`, by Richard Höchenberger`_ (:gh:`977`)
 
+- All non-MNE-Python BIDS coordinate frames are now set to ``'unknown'`` on reading, by `Alex Rockhill`_ (:gh:`979`)
+
 API and behavior changes
 ^^^^^^^^^^^^^^^^^^^^^^^^
 

mne_bids/config.py

@@ -205,18 +205,27 @@
     'UNCInfant2V23',
 ]
 
-coordsys_meg = ['CTF', 'ElektaNeuromag', '4DBti', 'KitYokogawa', 'ChietiItab']
-coordsys_eeg = ['CapTrak']
-coordsys_ieeg = ['Pixels', 'ACPC']
+# accepted BIDS formats, which may be subject to change
+# depending on the specification
+BIDS_IEEG_COORDINATE_FRAMES = ['ACPC', 'Pixels']
+BIDS_MEG_COORDINATE_FRAMES = ['CTF', 'ElektaNeuromag',
+                              '4DBti', 'KitYokogawa',
+                              'ChietiItab']
+BIDS_EEG_COORDINATE_FRAMES = ['CapTrak']
+
+# accepted coordinate SI units
+BIDS_COORDINATE_UNITS = ['m', 'cm', 'mm']
 coordsys_wildcard = ['Other']
-coordsys_shared = (coordsys_standard_template +
-                   coordsys_standard_template_deprecated +
-                   coordsys_wildcard)
+BIDS_SHARED_COORDINATE_FRAMES = (coordsys_standard_template +
+                                 coordsys_standard_template_deprecated +
+                                 coordsys_wildcard)
 
 ALLOWED_SPACES = dict()
-ALLOWED_SPACES['meg'] = coordsys_shared + coordsys_meg + coordsys_eeg
-ALLOWED_SPACES['eeg'] = coordsys_shared + coordsys_meg + coordsys_eeg
-ALLOWED_SPACES['ieeg'] = coordsys_shared + coordsys_ieeg
+ALLOWED_SPACES['meg'] = ALLOWED_SPACES['eeg'] = \
+    BIDS_SHARED_COORDINATE_FRAMES + BIDS_MEG_COORDINATE_FRAMES + \
+    BIDS_EEG_COORDINATE_FRAMES
+ALLOWED_SPACES['ieeg'] = \
+    BIDS_SHARED_COORDINATE_FRAMES + BIDS_IEEG_COORDINATE_FRAMES
 ALLOWED_SPACES['anat'] = None
 ALLOWED_SPACES['beh'] = None
 
@@ -235,17 +244,6 @@
     'extension': 'label'
 }
 
-# accepted BIDS formats, which may be subject to change
-# depending on the specification
-BIDS_IEEG_COORDINATE_FRAMES = ['ACPC', 'Pixels', 'Other']
-BIDS_MEG_COORDINATE_FRAMES = ['CTF', 'ElektaNeuromag',
-                              '4DBti', 'KitYokogawa',
-                              'ChietiItab', 'Other']
-BIDS_EEG_COORDINATE_FRAMES = ['CapTrak']
-
-# accepted coordinate SI units
-BIDS_COORDINATE_UNITS = ['m', 'cm', 'mm']
-
 # mapping from supported BIDs coordinate frames -> MNE
 BIDS_TO_MNE_FRAMES = {
     'CTF': 'ctf_head',
@@ -256,8 +254,7 @@
     'CapTrak': 'head',
     'ACPC': 'mri',  # assumes T1 is ACPC-aligned, if not the coordinates are lost  # noqa
     'fsaverage': 'mni_tal',  # XXX: note fsaverage and MNI305 are the same  # noqa
-    'MNI305': 'mni_tal',
-    'Other': 'unknown'
+    'MNI305': 'mni_tal'
 }
 
 # mapping from supported MNE coordinate frames -> BIDS

mne_bids/dig.py

@@ -15,9 +15,7 @@
 from mne.utils import logger, warn
 from mne.io.pick import _picks_to_idx
 
-from mne_bids.config import (BIDS_IEEG_COORDINATE_FRAMES,
-                             BIDS_MEG_COORDINATE_FRAMES,
-                             BIDS_EEG_COORDINATE_FRAMES,
+from mne_bids.config import (ALLOWED_SPACES,
                              BIDS_COORDINATE_UNITS,
                              MNE_TO_BIDS_FRAMES, BIDS_TO_MNE_FRAMES,
                              MNE_FRAME_TO_STR, BIDS_COORD_FRAME_DESCRIPTIONS)
@@ -535,57 +533,17 @@ def _read_dig_bids(electrodes_fpath, coordsystem_fpath,
     bids_coord_frame, bids_coord_unit = _handle_coordsystem_reading(
         coordsystem_fpath, datatype)
 
-    if datatype == 'meg':
-        if bids_coord_frame not in BIDS_MEG_COORDINATE_FRAMES:
-            warn(f'MEG coordinate frame "{bids_coord_frame}" is not '
-                 f'supported. The supported coordinate frames are: '
-                 f'{BIDS_MEG_COORDINATE_FRAMES}')
-            coord_frame = None
-        elif bids_coord_frame == 'Other':
-            warn("Coordinate frame of MEG data can't be determined "
-                 "when 'other'. The currently accepted keywords are: "
-                 "{}".format(BIDS_MEG_COORDINATE_FRAMES))
-            coord_frame = None
-        else:
-            coord_frame = BIDS_TO_MNE_FRAMES.get(bids_coord_frame, None)
-    elif datatype == 'ieeg':
-        # iEEG datatype for BIDS only supports
-        # acpc, pixels and then standard templates
-        # iEEG datatype for mne-python only supports
-        # mni_tal == fsaverage == MNI305
-        if bids_coord_frame == 'Pixels':
-            warn("Coordinate frame of iEEG data in pixels is not "
-                 "recognized by mne-python, the coordinate frame "
-                 "of the montage will be set to 'unknown'")
-            coord_frame = 'unknown'
-        elif bids_coord_frame == 'ACPC':
-            coord_frame = BIDS_TO_MNE_FRAMES.get(bids_coord_frame, None)
-        elif bids_coord_frame == 'Other':
-            # default coordinate frames to available ones in mne-python
-            # noqa: see https://bids-specification.readthedocs.io/en/stable/99-appendices/08-coordinate-systems.html
-            warn(f"Defaulting coordinate frame to unknown "
-                 f"from coordinate system input {bids_coord_frame}")
-            coord_frame = BIDS_TO_MNE_FRAMES.get(bids_coord_frame, None)
-        else:
-            coord_frame = BIDS_TO_MNE_FRAMES.get(bids_coord_frame, None)
-
-            # XXX: if the coordinate frame is not recognized, then
-            # coordinates are stored in a system that we cannot
-            # recognize yet.
-            if coord_frame is None:
-                warn(f"iEEG Coordinate frame {bids_coord_frame} is not a "
-                     f"readable BIDS keyword by mne-bids yet. The allowed "
-                     f"keywords are: {BIDS_IEEG_COORDINATE_FRAMES}")
-                coord_frame = 'unknown'
-    elif datatype == 'eeg':
-        # only accept captrak
-        if bids_coord_frame not in BIDS_EEG_COORDINATE_FRAMES:
-            warn("EEG Coordinate frame is not accepted "
-                 "BIDS keyword. The allowed keywords are: "
-                 "{}".format(BIDS_IEEG_COORDINATE_FRAMES))
-            coord_frame = None
-        else:
-            coord_frame = BIDS_TO_MNE_FRAMES.get(bids_coord_frame, None)
+    if bids_coord_frame not in ALLOWED_SPACES[datatype]:
+        warn(f'"{bids_coord_frame}" is not a BIDS-acceptable coordinate frame '
+             f'for {datatype.upper()}. The supported coordinate frames are: '
+             '{}'.format(ALLOWED_SPACES[datatype]))
+        coord_frame = None
+    elif bids_coord_frame in BIDS_TO_MNE_FRAMES:
+        coord_frame = BIDS_TO_MNE_FRAMES.get(bids_coord_frame, None)
+    else:
+        warn(f"{bids_coord_frame} is not an MNE-Python coordinate frame "
+             f"for {datatype.upper()} data and so will be set to 'unknown'")
+        coord_frame = 'unknown'
 
     # check coordinate units
     if bids_coord_unit not in BIDS_COORDINATE_UNITS:

mne_bids/tests/test_read.py

@@ -20,7 +20,8 @@
 from mne.datasets import testing, somato
 
 from mne_bids import BIDSPath
-from mne_bids.config import MNE_STR_TO_FRAME
+from mne_bids.config import (MNE_STR_TO_FRAME, BIDS_SHARED_COORDINATE_FRAMES,
+                             BIDS_TO_MNE_FRAMES)
 from mne_bids.read import (read_raw_bids,
                            _read_raw, get_head_mri_trans,
                            _handle_events_reading)
@@ -733,8 +734,8 @@ def test_handle_eeg_coords_reading(tmp_path):
                                                suffix='coordsystem',
                                                extension='.json')
     _update_sidecar(coordsystem_fname, 'EEGCoordinateSystem', 'besa')
-    with pytest.warns(RuntimeWarning, match='EEG Coordinate frame is not '
-                                            'accepted BIDS keyword'):
+    with pytest.warns(RuntimeWarning, match='is not a BIDS-acceptable '
+                                            'coordinate frame for EEG'):
         raw_test = read_raw_bids(bids_path)
         assert raw_test.info['dig'] is None
 
@@ -842,25 +843,25 @@ def test_handle_ieeg_coords_reading(bids_path, tmp_path):
         _update_sidecar(coordsystem_fname, 'iEEGCoordinateSystem', coord_frame)
         # read in raw file w/ updated coordinate frame
         # and make sure all digpoints are MRI coordinate frame
-        with pytest.warns(RuntimeWarning, match="Defaulting coordinate "
-                                                "frame to unknown"):
+        with pytest.warns(RuntimeWarning, match="not an MNE-Python "
+                                                "coordinate frame"):
             raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
             assert raw_test.info['dig'] is not None
 
     # check that standard template identifiers that are unsupported in
     # mne-python coordinate frames, still get read in, but produce a warning
-    coordinate_frames = ['individual', 'fsnative', 'scanner',
-                         'ICBM452AirSpace', 'NIHPD']
-    for coord_frame in coordinate_frames:
+    for coord_frame in BIDS_SHARED_COORDINATE_FRAMES:
         # update coordinate units
         _update_sidecar(coordsystem_fname, 'iEEGCoordinateSystem', coord_frame)
         # read in raw file w/ updated coordinate frame
         # and make sure all digpoints are MRI coordinate frame
-        with pytest.warns(
-                RuntimeWarning, match=f"iEEG Coordinate frame {coord_frame} "
-                                      f"is not a readable BIDS keyword "):
+        if coord_frame in BIDS_TO_MNE_FRAMES:
             raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
-            assert raw_test.info['dig'] is not None
+        else:
+            with pytest.warns(RuntimeWarning, match="not an MNE-Python "
+                                                    "coordinate frame"):
+                raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
+        assert raw_test.info['dig'] is not None
 
     # ACPC should be read in as RAS for iEEG
     _update_sidecar(coordsystem_fname, 'iEEGCoordinateSystem', 'ACPC')

mne_bids/tests/test_write.py

@@ -3642,7 +3642,7 @@ def test_write_dig(tmpdir):
     coordsystem_path = bids_path.copy().update(
         task=None, run=None, suffix='coordsystem', extension='.json')
     with pytest.warns(RuntimeWarning,
-                      match='recognized by mne-python'):
+                      match='not an MNE-Python coordinate frame'):
         _read_dig_bids(electrodes_path, coordsystem_path,
                        bids_path.datatype, raw)
     montage2 = raw.get_montage()