RF Use nibabel.freesurfer.read_ functions in test_viz and examples

Author: effigies

examples/plot_foci.py

@@ -13,8 +13,8 @@
 import os.path as op
 from numpy import arange
 from numpy.random import permutation
+import nibabel as nib
 from surfer import Brain
-from surfer import io
 
 subject_id = "fsaverage"
 subjects_dir = os.environ["SUBJECTS_DIR"]
@@ -61,7 +61,7 @@
 and find 10 random vertices within the STS.
 """
 annot_path = op.join(subjects_dir, subject_id, "label/lh.aparc.a2009s.annot")
-ids, ctab, names = io.read_annot(annot_path)
+ids, ctab, names = nib.freesurfer.read_annot(annot_path)
 verts = arange(0, len(ids))
 coords = permutation(verts[ids == 74])[:10]
 

examples/plot_parc_values.py

@@ -12,7 +12,8 @@
 import os
 import os.path as op
 import numpy as np
-from surfer import io, Brain
+import nibabel as nib
+from surfer import Brain
 
 subject_id = "fsaverage"
 hemi = "lh"
@@ -31,7 +32,7 @@
 aparc_file = op.join(os.environ["SUBJECTS_DIR"],
                      subject_id, "label",
                      hemi + ".aparc.a2009s.annot")
-labels, ctab, names = io.read_annot(aparc_file)
+labels, ctab, names = nib.freesurfer.read_annot(aparc_file)
 
 """
 Make a random vector of scalar data corresponding to

surfer/tests/test_viz.py

@@ -3,6 +3,7 @@
 from os.path import join as pjoin
 from numpy.testing import assert_raises
 from tempfile import mktemp
+import nibabel as nib
 
 from surfer import Brain
 from surfer import io
@@ -99,7 +100,7 @@ def test_foci():
     brain.add_foci(coords, map_surface="white", color="gold")
 
     annot_path = pjoin(subj_dir, subject_id, 'label', 'lh.aparc.a2009s.annot')
-    ids, ctab, names = io.read_annot(annot_path)
+    ids, ctab, names = nib.freesurfer.read_annot(annot_path)
     verts = np.arange(0, len(ids))
     coords = np.random.permutation(verts[ids == 74])[:10]
     scale_factor = 0.7