def test_probabilistic_labels():
"""Test plotting of probabilistic labels."""
_set_backend()
brain = Brain("fsaverage", "lh", "inflated", cortex="low_contrast")
extra, subj_dir = _get_extra()
brain.add_label("BA1" + extra, color="darkblue")
brain.add_label("BA1" + extra, color="dodgerblue", scalar_thresh=.5)
brain.add_label("BA45" + extra, color="firebrick", borders=True)
brain.add_label("BA45" + extra,
color="salmon",
borders=True,
scalar_thresh=.5)
label_file = pjoin(subj_dir, "fsaverage", "label",
"lh.BA6%s.label" % (extra, ))
prob_field = np.zeros_like(brain.geo['lh'].x)
ids, probs = nib.freesurfer.read_label(label_file, read_scalars=True)
prob_field[ids] = probs
brain.add_data(prob_field, thresh=1e-5)
with warnings.catch_warnings(record=True):
brain.data["colorbar"].number_of_colors = 10
brain.data["colorbar"].number_of_labels = 11
brain.close()
def test_label():
"""Test plotting of label."""
_set_backend()
subject_id = "fsaverage"
hemi = "lh"
surf = "inflated"
brain = Brain(subject_id, hemi, surf)
view = get_view(brain)
extra, subj_dir = _get_extra()
brain.add_label("BA1" + extra)
check_view(brain, view)
brain.add_label("BA1" + extra, color="blue", scalar_thresh=.5)
label_file = pjoin(subj_dir, subject_id, "label",
"%s.MT%s.label" % (hemi, extra))
brain.add_label(label_file)
brain.add_label("BA44" + extra, borders=True)
brain.add_label("BA6" + extra, alpha=.7)
brain.show_view("medial")
brain.add_label("V1" + extra, color="steelblue", alpha=.6)
brain.add_label("V2" + extra, color="#FF6347", alpha=.6)
brain.add_label("entorhinal" + extra, color=(.2, 1, .5), alpha=.6)
brain.set_surf('white')
brain.show_view(dict(elevation=40, distance=430), distance=430)
with pytest.raises(ValueError, match='!='):
brain.show_view(dict(elevation=40, distance=430), distance=431)
# remove labels
brain.remove_labels('V1' + extra)
assert 'V2' + extra in brain.labels_dict
assert 'V1' + extra not in brain.labels_dict
brain.remove_labels()
assert 'V2' + extra not in brain.labels_dict
brain.close()
def test_surface():
"""Test IO for Surface class"""
extra, subj_dir = utils._get_extra()
for subjects_dir in [None, subj_dir]:
surface = utils.Surface('fsaverage', 'lh', 'inflated',
subjects_dir=subjects_dir)
surface.load_geometry()
surface.load_label('BA1' + extra)
surface.load_curvature()
xfm = np.eye(4)
xfm[:3, -1] += 2 # translation
x = surface.x
surface.apply_xfm(xfm)
x_ = surface.x
assert_array_almost_equal(x + 2, x_)
# normals
nn = _slow_compute_normals(surface.coords, surface.faces[:10000])
nn_fast = utils._compute_normals(surface.coords, surface.faces[:10000])
assert_array_almost_equal(nn, nn_fast)
assert 50 < np.linalg.norm(surface.coords, axis=-1).mean() < 100 # mm
surface = utils.Surface('fsaverage', 'lh', 'inflated',
subjects_dir=subj_dir, units='m')
surface.load_geometry()
assert 0.05 < np.linalg.norm(surface.coords, axis=-1).mean() < 0.1 # m
def test_surface():
"""Test IO for Surface class"""
extra, subj_dir = utils._get_extra()
for subjects_dir in [None, subj_dir]:
surface = utils.Surface('fsaverage', 'lh', 'inflated',
subjects_dir=subjects_dir)
surface.load_geometry()
surface.load_label('BA1' + extra)
surface.load_curvature()
xfm = np.eye(4)
xfm[:3, -1] += 2 # translation
x = surface.x
surface.apply_xfm(xfm)
x_ = surface.x
assert_allclose(x + 2, x_)
# normals
nn = _slow_compute_normals(surface.coords, surface.faces[:10000])
nn_fast = utils._compute_normals(surface.coords, surface.faces[:10000])
assert_allclose(nn, nn_fast)
assert 50 < np.linalg.norm(surface.coords, axis=-1).mean() < 100 # mm
surface = utils.Surface('fsaverage', 'lh', 'inflated',
subjects_dir=subj_dir, units='m')
surface.load_geometry()
assert 0.05 < np.linalg.norm(surface.coords, axis=-1).mean() < 0.1 # m
def test_label():
"""Test plotting of label."""
_set_backend()
subject_id = "fsaverage"
hemi = "lh"
surf = "inflated"
brain = Brain(subject_id, hemi, surf)
view = get_view(brain)
extra, subj_dir = _get_extra()
brain.add_label("BA1" + extra)
check_view(brain, view)
brain.add_label("BA1" + extra, color="blue", scalar_thresh=.5)
label_file = pjoin(subj_dir, subject_id,
"label", "%s.MT%s.label" % (hemi, extra))
brain.add_label(label_file)
brain.add_label("BA44" + extra, borders=True)
brain.add_label("BA6" + extra, alpha=.7)
brain.show_view("medial")
brain.add_label("V1" + extra, color="steelblue", alpha=.6)
brain.add_label("V2" + extra, color="#FF6347", alpha=.6)
brain.add_label("entorhinal" + extra, color=(.2, 1, .5), alpha=.6)
brain.set_surf('white')
brain.show_view(dict(elevation=40, distance=430), distance=430)
with pytest.raises(ValueError, match='!='):
brain.show_view(dict(elevation=40, distance=430), distance=431)
# remove labels
brain.remove_labels('V1' + extra)
assert 'V2' + extra in brain.labels_dict
assert 'V1' + extra not in brain.labels_dict
brain.remove_labels()
assert 'V2' + extra not in brain.labels_dict
brain.close()
def test_probabilistic_labels():
"""Test plotting of probabilistic labels."""
_set_backend()
brain = Brain("fsaverage", "lh", "inflated",
cortex="low_contrast")
extra, subj_dir = _get_extra()
brain.add_label("BA1" + extra, color="darkblue")
brain.add_label("BA1" + extra, color="dodgerblue", scalar_thresh=.5)
brain.add_label("BA45" + extra, color="firebrick", borders=True)
brain.add_label("BA45" + extra, color="salmon", borders=True,
scalar_thresh=.5)
label_file = pjoin(subj_dir, "fsaverage", "label",
"lh.BA6%s.label" % (extra,))
prob_field = np.zeros_like(brain.geo['lh'].x)
ids, probs = nib.freesurfer.read_label(label_file, read_scalars=True)
prob_field[ids] = probs
brain.add_data(prob_field, thresh=1e-5)
with warnings.catch_warnings(record=True):
brain.data["colorbar"].number_of_colors = 10
brain.data["colorbar"].number_of_labels = 11
brain.close()