def test_read_labels_from_annot():
"""Test reading labels from FreeSurfer parcellation
"""
# test some invalid inputs
assert_raises(ValueError, read_labels_from_annot, 'sample', hemi='bla',
subjects_dir=subjects_dir)
assert_raises(ValueError, read_labels_from_annot, 'sample',
annot_fname='bla.annot', subjects_dir=subjects_dir)
# read labels using hemi specification
labels_lh = read_labels_from_annot('sample', hemi='lh',
subjects_dir=subjects_dir)
for label in labels_lh:
assert_true(label.name.endswith('-lh'))
assert_true(label.hemi == 'lh')
# XXX fails on 2.6 for some reason...
if sys.version_info[:2] > (2, 6):
assert_is_not(label.color, None)
# read labels using annot_fname
annot_fname = op.join(subjects_dir, 'sample', 'label', 'rh.aparc.annot')
labels_rh = read_labels_from_annot('sample', annot_fname=annot_fname,
subjects_dir=subjects_dir)
for label in labels_rh:
assert_true(label.name.endswith('-rh'))
assert_true(label.hemi == 'rh')
# XXX doesn't work on py26 for some reason
if sys.version_info[:2] > (2, 6):
assert_is_not(label.color, None)
# combine the lh, rh, labels and sort them
labels_lhrh = list()
labels_lhrh.extend(labels_lh)
labels_lhrh.extend(labels_rh)
names = [label.name for label in labels_lhrh]
labels_lhrh = [label for (name, label) in sorted(zip(names, labels_lhrh))]
# read all labels at once
labels_both = read_labels_from_annot('sample', subjects_dir=subjects_dir)
# we have the same result
_assert_labels_equal(labels_lhrh, labels_both)
# aparc has 68 cortical labels
assert_true(len(labels_both) == 68)
# test regexp
label = read_labels_from_annot('sample', parc='aparc.a2009s',
regexp='Angu', subjects_dir=subjects_dir)[0]
assert_true(label.name == 'G_pariet_inf-Angular-lh')
# silly, but real regexp:
label = read_labels_from_annot('sample', 'aparc.a2009s',
regexp='.*-.{4,}_.{3,3}-L',
subjects_dir=subjects_dir)[0]
assert_true(label.name == 'G_oc-temp_med-Lingual-lh')
assert_raises(RuntimeError, read_labels_from_annot, 'sample', parc='aparc',
annot_fname=annot_fname, regexp='JackTheRipper',
subjects_dir=subjects_dir)
def test_read_labels_from_annot():
"""Test reading labels from FreeSurfer parcellation
"""
# test some invalid inputs
assert_raises(ValueError, read_labels_from_annot, 'sample', hemi='bla',
subjects_dir=subjects_dir)
assert_raises(ValueError, read_labels_from_annot, 'sample',
annot_fname='bla.annot', subjects_dir=subjects_dir)
# read labels using hemi specification
labels_lh = read_labels_from_annot('sample', hemi='lh',
subjects_dir=subjects_dir)
for label in labels_lh:
assert_true(label.name.endswith('-lh'))
assert_true(label.hemi == 'lh')
# XXX fails on 2.6 for some reason...
if sys.version_info[:2] > (2, 6):
assert_is_not(label.color, None)
# read labels using annot_fname
annot_fname = op.join(subjects_dir, 'sample', 'label', 'rh.aparc.annot')
labels_rh = read_labels_from_annot('sample', annot_fname=annot_fname,
subjects_dir=subjects_dir)
for label in labels_rh:
assert_true(label.name.endswith('-rh'))
assert_true(label.hemi == 'rh')
# XXX doesn't work on py26 for some reason
if sys.version_info[:2] > (2, 6):
assert_is_not(label.color, None)
# combine the lh, rh, labels and sort them
labels_lhrh = list()
labels_lhrh.extend(labels_lh)
labels_lhrh.extend(labels_rh)
names = [label.name for label in labels_lhrh]
labels_lhrh = [label for (name, label) in sorted(zip(names, labels_lhrh))]
# read all labels at once
labels_both = read_labels_from_annot('sample', subjects_dir=subjects_dir)
# we have the same result
_assert_labels_equal(labels_lhrh, labels_both)
# aparc has 68 cortical labels
assert_true(len(labels_both) == 68)
# test regexp
label = read_labels_from_annot('sample', parc='aparc.a2009s',
regexp='Angu', subjects_dir=subjects_dir)[0]
assert_true(label.name == 'G_pariet_inf-Angular-lh')
# silly, but real regexp:
label = read_labels_from_annot('sample', 'aparc.a2009s',
regexp='.*-.{4,}_.{3,3}-L',
subjects_dir=subjects_dir)[0]
assert_true(label.name == 'G_oc-temp_med-Lingual-lh')
assert_raises(RuntimeError, read_labels_from_annot, 'sample', parc='aparc',
annot_fname=annot_fname, regexp='JackTheRipper',
subjects_dir=subjects_dir)
def test_read_labels_from_annot():
"""Test reading labels from FreeSurfer parcellation
"""
# test some invalid inputs
assert_raises(ValueError, read_labels_from_annot, "sample", hemi="bla", subjects_dir=subjects_dir)
assert_raises(ValueError, read_labels_from_annot, "sample", annot_fname="bla.annot", subjects_dir=subjects_dir)
# read labels using hemi specification
labels_lh = read_labels_from_annot("sample", hemi="lh", subjects_dir=subjects_dir)
for label in labels_lh:
assert_true(label.name.endswith("-lh"))
assert_true(label.hemi == "lh")
# XXX fails on 2.6 for some reason...
if sys.version_info[:2] > (2, 6):
assert_is_not(label.color, None)
# read labels using annot_fname
annot_fname = op.join(subjects_dir, "sample", "label", "rh.aparc.annot")
labels_rh = read_labels_from_annot("sample", annot_fname=annot_fname, subjects_dir=subjects_dir)
for label in labels_rh:
assert_true(label.name.endswith("-rh"))
assert_true(label.hemi == "rh")
assert_is_not(label.color, None)
# combine the lh, rh, labels and sort them
labels_lhrh = list()
labels_lhrh.extend(labels_lh)
labels_lhrh.extend(labels_rh)
names = [label.name for label in labels_lhrh]
labels_lhrh = [label for (name, label) in sorted(zip(names, labels_lhrh))]
# read all labels at once
labels_both = read_labels_from_annot("sample", subjects_dir=subjects_dir)
# we have the same result
_assert_labels_equal(labels_lhrh, labels_both)
# aparc has 68 cortical labels
assert_true(len(labels_both) == 68)
# test regexp
label = read_labels_from_annot("sample", parc="aparc.a2009s", regexp="Angu", subjects_dir=subjects_dir)[0]
assert_true(label.name == "G_pariet_inf-Angular-lh")
# silly, but real regexp:
label = read_labels_from_annot("sample", "aparc.a2009s", regexp=".*-.{4,}_.{3,3}-L", subjects_dir=subjects_dir)[0]
assert_true(label.name == "G_oc-temp_med-Lingual-lh")
assert_raises(
RuntimeError,
read_labels_from_annot,
"sample",
parc="aparc",
annot_fname=annot_fname,
regexp="JackTheRipper",
subjects_dir=subjects_dir,
)
