MAINT: Properly check nibabel (mne-tools#11578)

Author: larsoner

.github/workflows/compat_minimal.yml

@@ -19,8 +19,7 @@ jobs:
       run:
         shell: bash
     env:
-      # TODO: Revert nibabel here pending https://github.com/mne-tools/mne-python/issues/11564
-      CONDA_DEPENDENCIES: 'numpy scipy matplotlib nibabel'
+      CONDA_DEPENDENCIES: 'numpy scipy matplotlib'
       DEPS: 'minimal'
       DISPLAY: ':99.0'
       MNE_DONTWRITE_HOME: true

mne/_freesurfer.py

@@ -17,7 +17,7 @@
                          _ensure_trans, read_ras_mni_t, Transform)
 from .surface import read_surface, _read_mri_surface
 from .utils import (verbose, _validate_type, _check_fname, _check_option,
-                    get_subjects_dir, _require_version, logger)
+                    get_subjects_dir, _import_nibabel, logger)
 
 
 def _check_subject_dir(subject, subjects_dir):
@@ -33,9 +33,7 @@ def _check_subject_dir(subject, subjects_dir):
 
 def _get_aseg(aseg, subject, subjects_dir):
     """Check that the anatomical segmentation file exists and load it."""
-    _require_version('nibabel', 'load aseg', '2.1.0')
-    import nibabel as nib
-
+    nib = _import_nibabel('load aseg')
     subjects_dir = Path(get_subjects_dir(subjects_dir, raise_error=True))
     if not aseg.endswith('aseg'):
         raise RuntimeError(
@@ -50,18 +48,6 @@ def _get_aseg(aseg, subject, subjects_dir):
     return aseg, aseg_data
 
 
-def _import_nibabel(why='use MRI files'):
-    try:
-        import nibabel as nib
-    except ImportError as exp:
-        msg = 'nibabel is required to %s, got:\n%s' % (why, exp)
-    else:
-        msg = ''
-    if msg:
-        raise ImportError(msg)
-    return nib
-
-
 def _reorient_image(img, axcodes='RAS'):
     """Reorient an image to a given orientation.
 
@@ -84,7 +70,7 @@ def _reorient_image(img, axcodes='RAS'):
     -----
     .. versionadded:: 0.24
     """
-    import nibabel as nib
+    nib = _import_nibabel('reorient MRI image')
     orig_data = np.array(img.dataobj).astype(np.float32)
     # reorient data to RAS
     ornt = nib.orientations.axcodes2ornt(
@@ -229,8 +215,7 @@ def get_volume_labels_from_aseg(mgz_fname, return_colors=False,
 
     .. versionadded:: 0.9.0
     """
-    import nibabel as nib
-
+    nib = _import_nibabel('load MRI atlas data')
     mgz_fname = _check_fname(
         mgz_fname, overwrite="read", must_exist=True, name="mgz_fname"
     )
@@ -486,7 +471,7 @@ def estimate_head_mri_t(subject, subjects_dir=None, verbose=None):
 
 def _ensure_image_in_surface_RAS(image, subject, subjects_dir):
     """Check if the image is in Freesurfer surface RAS space."""
-    import nibabel as nib
+    nib = _import_nibabel('load a volume image')
     if not isinstance(image, nib.spatialimages.SpatialImage):
         image = nib.load(image)
     image = nib.MGHImage(image.dataobj.astype(np.float32), image.affine)
@@ -614,8 +599,8 @@ def _read_mri_info(path, units='m', return_img=False, use_nibabel=False):
     # This is equivalent but 100x slower, so only use nibabel if we need to
     # (later):
     if use_nibabel:
-        import nibabel
-        hdr = nibabel.load(path).header
+        nib = _import_nibabel()
+        hdr = nib.load(path).header
         n_orig = hdr.get_vox2ras()
         t_orig = hdr.get_vox2ras_tkr()
         dims = hdr.get_data_shape()

mne/beamformer/tests/test_dics.py

@@ -58,6 +58,7 @@ def _load_forward():
 
 def _simulate_data(fwd, idx):  # Somewhere on the frontal lobe by default
     """Simulate an oscillator on the cortex."""
+    pytest.importorskip('nibabel')
     source_vertno = fwd['src'][0]['vertno'][idx]
 
     sfreq = 50.  # Hz.

mne/bem.py

@@ -36,7 +36,7 @@
 from .transforms import _ensure_trans, apply_trans, Transform
 from .utils import (verbose, logger, run_subprocess, get_subjects_dir, warn,
                     _pl, _validate_type, _TempDir, _check_freesurfer_home,
-                    _check_fname, has_nibabel, _check_option, path_like,
+                    _check_fname, _check_option, path_like, _import_nibabel,
                     _on_missing, _import_h5io_funcs, _ensure_int,
                     _path_like, _verbose_safe_false, _check_head_radius)
 
@@ -1283,7 +1283,7 @@ def make_watershed_bem(subject, subjects_dir=None, overwrite=False,
     run_subprocess_env(cmd)
     del tempdir  # clean up directory
     if op.isfile(T1_mgz):
-        new_info = _extract_volume_info(T1_mgz) if has_nibabel() else dict()
+        new_info = _extract_volume_info(T1_mgz)
         if not new_info:
             warn('nibabel is not available or the volume info is invalid.'
                  'Volume info not updated in the written surface.')
@@ -1339,8 +1339,8 @@ def make_watershed_bem(subject, subjects_dir=None, overwrite=False,
 
 def _extract_volume_info(mgz):
     """Extract volume info from a mgz file."""
-    import nibabel
-    header = nibabel.load(mgz).header
+    nib = _import_nibabel()
+    header = nib.load(mgz).header
     version = header['version']
     vol_info = dict()
     if version == 1:
@@ -1855,7 +1855,7 @@ def _prepare_env(subject, subjects_dir):
 
 
 def _write_echos(mri_dir, flash_echos, angle):
-    import nibabel as nib
+    nib = _import_nibabel('write echoes')
     from nibabel.spatialimages import SpatialImage
     if _path_like(flash_echos):
         flash_echos = nib.load(flash_echos)
@@ -2077,7 +2077,7 @@ def make_flash_bem(subject, overwrite=False, show=True, subjects_dir=None,
             raise ValueError(f'Flash 5 image cannot be found at {flash5}.')
     else:
         logger.info(f"Writing flash 5 image at {flash5}")
-        import nibabel as nib
+        nib = _import_nibabel('write an MRI image')
         nib.save(flash5_img, flash5)
 
     if register:

mne/commands/tests/test_commands.py

@@ -24,8 +24,7 @@
                           mne_prepare_bem_model, mne_sys_info)
 from mne.datasets import testing
 from mne.io import read_raw_fif, read_info
-from mne.utils import (requires_mne, requires_freesurfer,
-                       requires_nibabel, ArgvSetter,
+from mne.utils import (requires_mne, requires_freesurfer, ArgvSetter,
                        _stamp_to_dt, _record_warnings)
 
 base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
@@ -220,11 +219,11 @@ def test_surf2bem():
 @pytest.mark.timeout(900)  # took ~400 s on a local test
 @pytest.mark.slowtest
 @pytest.mark.ultraslowtest
-@requires_nibabel()
 @requires_freesurfer('mri_watershed')
 @testing.requires_testing_data
 def test_watershed_bem(tmp_path):
     """Test mne watershed bem."""
+    pytest.importorskip('nibabel')
     check_usage(mne_watershed_bem)
     # from T1.mgz
     Mdc = np.array([[-1, 0, 0], [0, 0, -1], [0, 1, 0]])
@@ -338,6 +337,7 @@ def test_flash_bem(tmp_path):
 @testing.requires_testing_data
 def test_setup_source_space(tmp_path):
     """Test mne setup_source_space."""
+    pytest.importorskip('nibabel')
     check_usage(mne_setup_source_space, force_help=True)
     # Using the sample dataset
     use_fname = op.join(tmp_path, "sources-src.fif")
@@ -367,6 +367,7 @@ def test_setup_source_space(tmp_path):
 @testing.requires_testing_data
 def test_setup_forward_model(tmp_path):
     """Test mne setup_forward_model."""
+    pytest.importorskip('nibabel')
     check_usage(mne_setup_forward_model, force_help=True)
     # Using the sample dataset
     use_fname = op.join(tmp_path, "model-bem.fif")

mne/coreg.py

@@ -26,7 +26,6 @@
 # namespace, too)
 from ._freesurfer import (_read_mri_info, get_mni_fiducials,  # noqa: F401
                           estimate_head_mri_t)  # noqa: F401
-from ._freesurfer import _import_nibabel
 from .label import read_label, Label
 from .source_space import (add_source_space_distances, read_source_spaces,  # noqa: E501,F401
                            write_source_spaces)
@@ -41,8 +40,8 @@
                          rot_to_quat, _angle_between_quats)
 from .channels import make_dig_montage
 from .utils import (get_config, get_subjects_dir, logger, pformat, verbose,
-                    warn, has_nibabel, fill_doc, _validate_type,
-                    _check_subject, _check_option)
+                    warn, fill_doc, _validate_type,
+                    _check_subject, _check_option, _import_nibabel)
 from .viz._3d import _fiducial_coords
 
 # some path templates
@@ -1194,9 +1193,6 @@ def _scale_xfm(subject_to, xfm_fname, mri_name, subject_from, scale,
     # The nibabel warning should already be there in MRI step, if applicable,
     # as we only get here if T1.mgz is present (and thus a scaling was
     # attempted) so we can silently return here.
-    if not has_nibabel():
-        return
-
     fname_from = os.path.join(
         mri_transforms_dirname.format(
             subjects_dir=subjects_dir, subject=subject_from), xfm_fname)

mne/datasets/tests/test_datasets.py

@@ -153,6 +153,7 @@ def _error_download_2(self, fname, downloader, processor):
 @requires_good_network
 def test_fetch_parcellations(tmp_path):
     """Test fetching parcellations."""
+    pytest.importorskip('nibabel')
     this_subjects_dir = str(tmp_path)
     os.mkdir(op.join(this_subjects_dir, 'fsaverage'))
     os.mkdir(op.join(this_subjects_dir, 'fsaverage', 'label'))

mne/forward/tests/test_make_forward.py

@@ -19,9 +19,8 @@
                  get_volume_labels_from_aseg)
 from mne.surface import _get_ico_surface
 from mne.transforms import Transform
-from mne.utils import (requires_mne, requires_nibabel, run_subprocess,
-                       catch_logging, requires_mne_mark,
-                       requires_openmeeg_mark)
+from mne.utils import (requires_mne, run_subprocess, catch_logging,
+                       requires_mne_mark, requires_openmeeg_mark)
 from mne.forward._make_forward import _create_meg_coils, make_forward_dipole
 from mne.forward._compute_forward import _magnetic_dipole_field_vec
 from mne.forward import Forward, _do_forward_solution, use_coil_def
@@ -234,6 +233,7 @@ def test_make_forward_solution_bti(fname_src_small):
 ])
 def test_make_forward_solution_ctf(tmp_path, fname_src_small, other):
     """Test CTF w/compensation against MNE-C or OpenMEEG."""
+    pytest.importorskip('nibabel')
     src = read_source_spaces(fname_src_small)
     raw = read_raw_fif(fname_ctf_raw)
     assert raw.compensation_grade == 3
@@ -377,6 +377,7 @@ def test_make_forward_solution_discrete(tmp_path, small_surf_src):
 @pytest.fixture(scope='module', params=[testing._pytest_param()])
 def small_surf_src():
     """Create a small surface source space."""
+    pytest.importorskip('nibabel')
     src = setup_source_space('sample', 'oct2', subjects_dir=subjects_dir,
                              add_dist=False)
     assert sum(s['nuse'] for s in src) * 3 == n_src_small
@@ -433,9 +434,9 @@ def test_make_forward_solution_sphere(tmp_path, fname_src_small):
 
 @pytest.mark.slowtest
 @testing.requires_testing_data
-@requires_nibabel()
 def test_forward_mixed_source_space(tmp_path):
     """Test making the forward solution for a mixed source space."""
+    pytest.importorskip('nibabel')
     # get the surface source space
     rng = np.random.RandomState(0)
     surf = read_source_spaces(fname_src)

mne/gui/_core.py

@@ -21,12 +21,12 @@
 from matplotlib.figure import Figure
 from matplotlib.patches import Rectangle
 
-from .._freesurfer import _import_nibabel
 from ..viz.backends.renderer import _get_renderer
 from ..viz.utils import safe_event
 from ..surface import _read_mri_surface, _marching_cubes
 from ..transforms import apply_trans, _frame_to_str
-from ..utils import logger, _check_fname, verbose, warn, get_subjects_dir
+from ..utils import (logger, _check_fname, verbose, warn, get_subjects_dir,
+                     _import_nibabel)
 from ..viz.backends._utils import _qt_safe_window
 
 _IMG_LABELS = [['I', 'P'], ['I', 'L'], ['P', 'L']]

mne/gui/tests/test_core.py

@@ -9,19 +9,18 @@
 import pytest
 
 from mne.datasets import testing
-from mne.utils import requires_nibabel, catch_logging, use_log_level
+from mne.utils import catch_logging, use_log_level
 from mne.viz.utils import _fake_click
 
 data_path = testing.data_path(download=False)
 subject = "sample"
 subjects_dir = data_path / "subjects"
 
 
-@requires_nibabel()
 @testing.requires_testing_data
 def test_slice_browser_io(renderer_interactive_pyvistaqt):
     """Test the input/output of the slice browser GUI."""
-    import nibabel as nib
+    nib = pytest.importorskip('nibabel')
     from mne.gui._core import SliceBrowser
     with pytest.raises(ValueError, match='Base image is not aligned to MRI'):
         SliceBrowser(nib.MGHImage(
@@ -34,6 +33,7 @@ def test_slice_browser_io(renderer_interactive_pyvistaqt):
 @testing.requires_testing_data
 def test_slice_browser_display(renderer_interactive_pyvistaqt):
     """Test that the slice browser GUI displays properly."""
+    pytest.importorskip('nibabel')
     from mne.gui._core import SliceBrowser
     # test no seghead, fsaverage doesn't have seghead
     with pytest.warns(RuntimeWarning, match='`seghead` not found'):