MAINT: Work around MNE change

doc/whats_new.rst

@@ -29,6 +29,7 @@ The following authors contributed for the first time. Thank you so much! 🤩
 The following authors had contributed before. Thank you for sticking around! 🤘
 
 * `Richard Höchenberger`_
+* `Eric Larson`_
 
 Detailed list of changes
 ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -54,6 +55,7 @@ Detailed list of changes
 - Amending a dataset now works in cases where the newly-written data contains additional participant properties (new columns in ``participants.tsv``) not found in the existing dataset, by `Richard Höchenberger`_ (:gh:`1113`)
 - Fix ``raw_to_bids`` CLI tool to properly recognize boolean and numeric values for the ``line_freq`` and ``overwrite`` parameters, by `Stefan Appelhoff`_ (:gh:`1125`)
 - Fix :func:`~mne_bids.copyfiles.copyfile_eeglab` to prevent data type conversion leading to an ``eeg_checkset`` failure when trying to load the file in EEGLAB, by `Laetitia Fesselier`_ (:gh:`1122`)
+- Improve compatibility with latest MNE-Python, by `Eric Larson`_ (:gh:`1128`)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

mne_bids/dig.py

@@ -15,7 +15,7 @@
 import numpy as np
 from mne.io.constants import FIFF
 from mne.utils import (logger, _validate_type, _check_option,
-                       has_nibabel, get_subjects_dir)
+                       get_subjects_dir)
 from mne.io.pick import _picks_to_idx
 
 from mne_bids.config import (ALLOWED_SPACES, BIDS_COORDINATE_UNITS,
@@ -25,7 +25,7 @@
                              BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS)
 from mne_bids.tsv_handler import _from_tsv
 from mne_bids.utils import (_scale_coord_to_meters, _write_json, _write_tsv,
-                            verbose, warn)
+                            verbose, warn, _import_nibabel)
 from mne_bids.path import BIDSPath
 
 data_dir = Path(__file__).parent / 'data'
@@ -667,9 +667,7 @@ def convert_montage_to_ras(montage, subject, subjects_dir=None, verbose=None):
     %(subjects_dir)s
     %(verbose)s
     """
-    if not has_nibabel():  # pragma: no cover
-        raise ImportError('This function requires nibabel.')
-    import nibabel as nib
+    nib = _import_nibabel('converting a montage to RAS')
 
     subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
     T1_fname = op.join(subjects_dir, subject, 'mri', 'T1.mgz')
@@ -712,9 +710,7 @@ def convert_montage_to_mri(montage, subject, subjects_dir=None, verbose=None):
         The transformation matrix from ``'ras'`` (``scanner RAS``) to
         ``'mri'`` (``surface RAS``).
     """
-    if not has_nibabel():  # pragma: no cover
-        raise ImportError('This function requires nibabel.')
-    import nibabel as nib
+    nib = _import_nibabel('converting a montage to MRI')
 
     subjects_dir = get_subjects_dir(subjects_dir, raise_error=True)
     T1_fname = op.join(subjects_dir, subject, 'mri', 'T1.mgz')

mne_bids/read.py

@@ -18,7 +18,7 @@
 import mne
 from mne import io, read_events, events_from_annotations
 from mne.io.pick import pick_channels_regexp
-from mne.utils import has_nibabel, logger, get_subjects_dir
+from mne.utils import logger, get_subjects_dir
 from mne.coreg import fit_matched_points
 from mne.transforms import apply_trans
 
@@ -27,7 +27,7 @@
 from mne_bids.config import (ALLOWED_DATATYPE_EXTENSIONS,
                              ANNOTATIONS_TO_KEEP,
                              reader, _map_options)
-from mne_bids.utils import _get_ch_type_mapping, verbose, warn
+from mne_bids.utils import _get_ch_type_mapping, verbose, warn, _import_nibabel
 from mne_bids.path import (BIDSPath, _parse_ext, _find_matching_sidecar,
                            _infer_datatype, get_bids_path_from_fname)
 
@@ -900,9 +900,7 @@ def get_head_mri_trans(bids_path, extra_params=None, t1_bids_path=None,
     trans : mne.transforms.Transform
         The data transformation matrix from head to MRI coordinates.
     """
-    if not has_nibabel():  # pragma: no cover
-        raise ImportError('This function requires nibabel.')
-    import nibabel as nib
+    nib = _import_nibabel('get a head to MRI transform')
 
     if not isinstance(bids_path, BIDSPath):
         raise RuntimeError('"bids_path" must be a BIDSPath object. Please '

mne_bids/tests/test_read.py

@@ -20,7 +20,7 @@
 import mne
 from mne.datasets import testing
 from mne.io.constants import FIFF
-from mne.utils import requires_nibabel, object_diff, requires_version
+from mne.utils import object_diff, requires_version
 from mne.utils import assert_dig_allclose, check_version
 
 from mne_bids import BIDSPath
@@ -209,12 +209,11 @@ def test_read_participants_handedness_and_sex_mapping(hand_bids, hand_mne,
     assert raw.info['subject_info']['sex'] is sex_mne
 
 
-@requires_nibabel()
 @pytest.mark.filterwarnings(warning_str['channel_unit_changed'])
 @testing.requires_testing_data
 def test_get_head_mri_trans(tmp_path):
     """Test getting a trans object from BIDS data."""
-    import nibabel as nib
+    nib = pytest.importorskip('nibabel')
 
     event_id = {'Auditory/Left': 1, 'Auditory/Right': 2, 'Visual/Left': 3,
                 'Visual/Right': 4, 'Smiley': 5, 'Button': 32}
@@ -1009,13 +1008,12 @@ def test_handle_ieeg_coords_reading(bids_path, tmp_path):
             assert ch['ch_name'] not in raw.info['bads']
 
 
-@requires_nibabel()
 @pytest.mark.filterwarnings(warning_str['channel_unit_changed'])
 @pytest.mark.parametrize('fname', ['testdata_ctf.ds', 'catch-alp-good-f.ds'])
 @testing.requires_testing_data
 def test_get_head_mri_trans_ctf(fname, tmp_path):
     """Test getting a trans object from BIDS data in CTF."""
-    import nibabel as nib
+    nib = pytest.importorskip('nibabel')
 
     ctf_data_path = op.join(data_path, 'CTF')
     raw_ctf_fname = op.join(ctf_data_path, fname)

mne_bids/tests/test_update.py

@@ -12,7 +12,6 @@
 import mne
 from mne.io.constants import FIFF
 from mne.datasets import testing
-from mne.utils import requires_nibabel
 
 from mne_bids import (BIDSPath, write_raw_bids,
                       write_meg_calibration, write_meg_crosstalk,
@@ -136,10 +135,10 @@ def test_update_sidecar_jsons(_get_bids_test_dir, _bids_validate,
             error_bids_path, _get_sidecar_json_update_file)
 
 
-@requires_nibabel()
 @testing.requires_testing_data
 def test_update_anat_landmarks(tmp_path):
     """Test updating the anatomical landmarks of an MRI scan."""
+    pytest.importorskip('nibabel')
     raw_path = data_path / 'MEG' / 'sample' / 'sample_audvis_trunc_raw.fif'
     trans_path = Path(str(raw_path).replace('_raw.fif', '-trans.fif'))
     t1_path = data_path / 'subjects' / 'sample' / 'mri' / 'T1.mgz'

mne_bids/tests/test_write.py

@@ -30,7 +30,7 @@
 
 import mne
 from mne.datasets import testing
-from mne.utils import check_version, requires_nibabel, requires_version
+from mne.utils import check_version, requires_version
 from mne.io import anonymize_info
 from mne.io.constants import FIFF
 from mne.io.kit.kit import get_kit_info
@@ -1983,12 +1983,11 @@ def test_get_anat_landmarks():
         mri_voxel_landmarks, landmarks, decimal=5)
 
 
-@requires_nibabel()
 @testing.requires_testing_data
 def test_write_anat(_bids_validate, tmp_path):
     """Test writing anatomical data."""
+    nib = pytest.importorskip('nibabel')
     # Get the MNE testing sample data
-    import nibabel as nib
     bids_root = tmp_path / 'bids1'
 
     # Get the T1 weighted MRI data file
@@ -2199,10 +2198,10 @@ def test_write_raw_no_dig(tmp_path):
     assert bids_path_.extension == '.fif'
 
 
-@requires_nibabel()
 @testing.requires_testing_data
 def test_write_anat_pathlike(tmp_path):
     """Test writing anatomical data with pathlib.Paths."""
+    pytest.importorskip('nibabel')
     raw_fname = op.join(data_path, 'MEG', 'sample',
                         'sample_audvis_trunc_raw.fif')
     trans_fname = raw_fname.replace('_raw.fif', '-trans.fif')
@@ -3521,10 +3520,10 @@ def test_write_raw_special_paths(tmp_path, dir_name):
     write_raw_bids(raw=raw, bids_path=bids_path)
 
 
-@requires_nibabel()
 @testing.requires_testing_data
 def test_anonymize_dataset(_bids_validate, tmpdir):
     """Test creating an anonymized copy of a dataset."""
+    pytest.importorskip('nibabel')
     # Create a non-anonymized dataset
     bids_root = tmpdir / 'bids'
     bids_path = _bids_path.copy().update(

mne_bids/utils.py

@@ -458,6 +458,17 @@ def _check_datatype(raw, datatype):
             'the raw object.')
 
 
+def _import_nibabel(why='work with MRI data'):
+    try:
+        import nibabel  # noqa
+    except ImportError as exc:
+        raise exc.__class__(
+            f'nibabel is required to {why} but could not be imported, '
+            f'got: {exc}') from None
+    else:
+        return nibabel
+
+
 def warn(message, category=RuntimeWarning, module='mne_bids',
          ignore_namespaces=('mne', 'mne_bids')):  # noqa: D103
     _warn(

mne_bids/write.py

@@ -30,7 +30,7 @@
 from mne.io import BaseRaw, read_fiducials
 from mne.channels.channels import (_unit2human, _get_meg_system)
 from mne.chpi import get_chpi_info
-from mne.utils import (check_version, has_nibabel, logger, Bunch,
+from mne.utils import (check_version, logger, Bunch,
                        _validate_type, get_subjects_dir, verbose,
                        ProgressBar)
 import mne.preprocessing
@@ -40,7 +40,8 @@
 from mne_bids.utils import (_write_json, _write_tsv, _write_text,
                             _age_on_date, _infer_eeg_placement_scheme,
                             _get_ch_type_mapping, _check_anonymize,
-                            _stamp_to_dt, _handle_datatype, warn)
+                            _stamp_to_dt, _handle_datatype, warn,
+                            _import_nibabel)
 from mne_bids import (BIDSPath, read_raw_bids, get_anonymization_daysback,
                       get_bids_path_from_fname)
 from mne_bids.path import _parse_ext, _mkdir_p, _path_to_str
@@ -603,9 +604,7 @@ def _scans_tsv(raw, raw_fname, fname, keep_source, overwrite=False):
 
 
 def _load_image(image, name='image'):
-    if not has_nibabel():  # pragma: no cover
-        raise ImportError('This function requires nibabel.')
-    import nibabel as nib
+    nib = _import_nibabel()
     if type(image) not in nib.all_image_classes:
         try:
             image = _path_to_str(image)
@@ -929,9 +928,7 @@ def _sidecar_json(raw, task, manufacturer, fname, datatype,
 
 
 def _deface(image, landmarks, deface):
-    if not has_nibabel():  # pragma: no cover
-        raise ImportError('This function requires nibabel.')
-    import nibabel as nib
+    nib = _import_nibabel('deface MRIs')
 
     inset, theta = (5, 15.)
     if isinstance(deface, dict):
@@ -2028,9 +2025,7 @@ def get_anat_landmarks(image, info, trans, fs_subject, fs_subjects_dir=None):
     landmarks : mne.channels.DigMontage
         A montage with the landmarks in MRI voxel space.
     """
-    if not has_nibabel():  # pragma: no cover
-        raise ImportError('This function requires nibabel.')
-    import nibabel as nib
+    nib = _import_nibabel('get anatomical landmarks')
     coords_dict, coord_frame = _get_fid_coords(info['dig'])
     if coord_frame != FIFF.FIFFV_COORD_HEAD:
         raise ValueError('Fiducial coordinates in `info` must be in '
@@ -2184,9 +2179,7 @@ def write_anat(image, bids_path, landmarks=None, deface=False, overwrite=False,
     bids_path : BIDSPath
         Path to the written MRI data.
     """
-    if not has_nibabel():  # pragma: no cover
-        raise ImportError('This function requires nibabel.')
-    import nibabel as nib
+    nib = _import_nibabel('write anatomical MRI data')
 
     write_sidecar = landmarks is not None