FIX: Fix for deprecation

mne/conftest.py

@@ -71,6 +71,7 @@ def pytest_configure(config):
     ignore:numpy.ufunc size changed:RuntimeWarning
     ignore:.*mne-realtime.*:DeprecationWarning
     ignore:.*imp.*:DeprecationWarning
+    always:.*get_data.* is deprecated in favor of.*:DeprecationWarning
     """  # noqa: E501
     for warning_line in warning_lines.split('\n'):
         warning_line = warning_line.strip()

mne/fixes.py

@@ -420,6 +420,14 @@ def minimum_phase(h):
 ###############################################################################
 # Misc utilities
 
+# Deal with nibabel 2.5 img.get_data() deprecation
+def _get_img_fdata(img):
+    try:
+        return img.get_fdata()
+    except AttributeError:
+        return img.get_data().astype(float)
+
+
 def _read_volume_info(fobj):
     """An implementation of nibabel.freesurfer.io._read_volume_info, since old
     versions of nibabel (<=2.1.0) don't have it.

mne/morph.py

@@ -10,6 +10,7 @@
 import numpy as np
 from scipy import sparse
 
+from .fixes import _get_img_fdata
 from .parallel import parallel_func
 from .source_estimate import (VolSourceEstimate, SourceEstimate,
                               VolVectorSourceEstimate, VectorSourceEstimate,
@@ -524,7 +525,7 @@ def _morphed_stc_as_volume(morph, stc, mri_resolution=False, mri_space=True,
     if new_zooms is not None:
         from dipy.align.reslice import reslice
         new_zooms = new_zooms[:3]
-        img, affine = reslice(img.get_data(),
+        img, affine = reslice(_get_img_fdata(img),
                               img.affine,  # MRI to world registration
                               zooms,  # old voxel size in mm
                               new_zooms)  # new voxel size in mm
@@ -677,7 +678,8 @@ def _interpolate_data(stc, morph, mri_resolution=True, mri_space=True,
     if voxel_size_defined:
         # reslice mri
         img, img_affine = reslice(
-            img.get_data(), img.affine, _get_zooms_orig(morph), voxel_size)
+            _get_img_fdata(img), img.affine, _get_zooms_orig(morph),
+            voxel_size)
         with warnings.catch_warnings():  # nibabel<->numpy warning
             img = NiftiImage(img, img_affine, header=header)
 
@@ -710,25 +712,25 @@ def _compute_morph_sdr(mri_from, mri_to, niter_affine=(100, 100, 10),
 
     # reslice mri_from
     mri_from_res, mri_from_res_affine = reslice(
-        mri_from.get_data(), mri_from.affine, mri_from.header.get_zooms()[:3],
-        zooms)
+        _get_img_fdata(mri_from), mri_from.affine,
+        mri_from.header.get_zooms()[:3], zooms)
 
     with warnings.catch_warnings():  # nibabel<->numpy warning
         mri_from = nib.Nifti1Image(mri_from_res, mri_from_res_affine)
 
     # reslice mri_to
     mri_to_res, mri_to_res_affine = reslice(
-        mri_to.get_data(), mri_to.affine, mri_to.header.get_zooms()[:3],
+        _get_img_fdata(mri_to), mri_to.affine, mri_to.header.get_zooms()[:3],
         zooms)
 
     with warnings.catch_warnings():  # nibabel<->numpy warning
         mri_to = nib.Nifti1Image(mri_to_res, mri_to_res_affine)
 
     affine = mri_to.affine
-    mri_to = np.array(mri_to.dataobj, float)  # to ndarray
+    mri_to = _get_img_fdata(mri_to)  # to ndarray
     mri_to /= mri_to.max()
     mri_from_affine = mri_from.affine  # get mri_from to world transform
-    mri_from = np.array(mri_from.dataobj, float)  # to ndarray
+    mri_from = _get_img_fdata(mri_from)  # to ndarray
     mri_from /= mri_from.max()  # normalize
 
     # compute center of mass
@@ -1148,7 +1150,7 @@ def _morph_one(stc_one):
 
             # reslice to match morph
             img_to, img_to_affine = reslice(
-                img_to.get_data(), morph.affine, _get_zooms_orig(morph),
+                _get_img_fdata(img_to), morph.affine, _get_zooms_orig(morph),
                 morph.zooms)
 
             # morph data

mne/source_space.py

@@ -22,6 +22,7 @@
                        write_float_matrix, write_int_matrix,
                        write_coord_trans, start_file, end_file, write_id)
 from .bem import read_bem_surfaces, ConductorModel
+from .fixes import _get_img_fdata
 from .surface import (read_surface, _create_surf_spacing, _get_ico_surface,
                       _tessellate_sphere_surf, _get_surf_neighbors,
                       _normalize_vectors, _triangle_neighbors, mesh_dist,
@@ -354,7 +355,7 @@ def export_volume(self, fname, include_surfaces=True,
                 # get the inuse array
                 if mri_resolution:
                     # read the mri file used to generate volumes
-                    aseg_data = nib.load(vs['mri_file']).get_data()
+                    aseg_data = _get_img_fdata(nib.load(vs['mri_file']))
                     # get the voxel space shape
                     shape3d = (vs['mri_height'], vs['mri_depth'],
                                vs['mri_width'])
@@ -1829,7 +1830,7 @@ def _get_volume_label_mask(mri, volume_label, rr):
 
     # Read the segmentation data using nibabel
     mgz = nib.load(mri)
-    mgz_data = mgz.get_data()
+    mgz_data = _get_img_fdata(mgz)
 
     # Get the numeric index for this volume label
     lut = _get_lut()
@@ -2513,7 +2514,7 @@ def get_volume_labels_from_aseg(mgz_fname, return_colors=False):
     import nibabel as nib
 
     # Read the mgz file using nibabel
-    mgz_data = nib.load(mgz_fname).get_data()
+    mgz_data = _get_img_fdata(nib.load(mgz_fname))
 
     # Get the unique label names
     lut = _get_lut()

mne/tests/test_source_estimate.py

@@ -17,7 +17,7 @@
                  spatial_src_connectivity, spatial_tris_connectivity,
                  SourceSpaces, VolVectorSourceEstimate)
 from mne.datasets import testing
-from mne.fixes import fft
+from mne.fixes import fft, _get_img_fdata
 from mne.source_estimate import grade_to_tris, _get_vol_mask
 from mne.minimum_norm import (read_inverse_operator, apply_inverse,
                               apply_inverse_epochs)
@@ -948,7 +948,7 @@ def test_vol_mask():
     data = (1 + np.arange(n_vertices))[:, np.newaxis]
     stc_tmp = VolSourceEstimate(data, vertices, tmin=0., tstep=1.)
     img = stc_tmp.as_volume(src, mri_resolution=False)
-    img_data = img.get_data()[:, :, :, 0].T
+    img_data = _get_img_fdata(img)[:, :, :, 0].T
     mask_nib = (img_data != 0)
     assert_array_equal(img_data[mask_nib], data[:, 0])
     assert_array_equal(np.where(mask_nib.ravel())[0], src[0]['vertno'])

mne/viz/_3d.py

@@ -22,7 +22,7 @@
 from scipy import linalg, sparse
 
 from ..defaults import DEFAULTS
-from ..fixes import einsum, _crop_colorbar
+from ..fixes import einsum, _crop_colorbar, _get_img_fdata
 from ..io import _loc_to_coil_trans
 from ..io.pick import pick_types, _picks_to_idx
 from ..io.constants import FIFF
@@ -431,7 +431,7 @@ def _plot_mri_contours(mri_fname, surf_fnames, orientation='coronal',
 
     # Load the T1 data
     nim = nib.load(mri_fname)
-    data = nim.get_data()
+    data = _get_img_fdata(nim)
     try:
         affine = nim.affine
     except AttributeError:  # old nibabel
@@ -1928,7 +1928,7 @@ def _click_to_cut_coords(event, params):
         cut_coords = np.array((x, y, z))
 
         if params['mode'] == 'glass_brain':  # find idx for MIP
-            img_data = np.abs(params['img_idx'].get_data())
+            img_data = np.abs(_get_img_fdata(params['img_idx']))
             ijk = _cut_coords_to_ijk(cut_coords, params['img_idx'])
             if ax == 'x':
                 ijk[0] = np.argmax(img_data[:, ijk[1], ijk[2]])
@@ -2762,7 +2762,7 @@ def _plot_dipole_mri_orthoview(dipole, trans, subject, subjects_dir=None,
                         coord_frame=coord_frame)
 
     zooms = t1.header.get_zooms()
-    data = t1.get_data()
+    data = _get_img_fdata(t1)
     dims = len(data)  # Symmetric size assumed.
     dd = dims / 2.
     dd *= t1.header.get_zooms()[0]

mne/viz/tests/test_3d.py

@@ -529,7 +529,7 @@ def test_plot_volume_source_estimates_morph():
     n_time = 2
     data = np.random.RandomState(0).rand(n_verts, n_time)
     stc = VolSourceEstimate(data, vertices, 1, 1)
-    morph = compute_source_morph(sample_src, 'sample', 'fsaverage', zooms=10,
+    morph = compute_source_morph(sample_src, 'sample', 'fsaverage', zooms=5,
                                  subjects_dir=subjects_dir)
     initial_pos = (-0.05, -0.01, -0.006)
     with pytest.warns(None):  # sometimes get scalars/index warning
@@ -538,7 +538,7 @@ def test_plot_volume_source_estimates_morph():
                      initial_pos=initial_pos, verbose=True)
     log = log.getvalue()
     assert 't = 1.000 s' in log
-    assert '(-52.0, -8.0, -2.0) mm' in log
+    assert '(-52.0, -8.0, -7.0) mm' in log
 
     with pytest.raises(ValueError, match='Allowed values are'):
         stc.plot(sample_src, 'sample', subjects_dir, mode='abcd')