def test_annot_with_different_orig_ids_settings():
vertex_labels_orig, label_colors_orig, label_names_orig, meta_data_orig = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='both', orig_ids=True)
vertex_labels, label_colors, label_names, meta_data = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='both', orig_ids=False)
assert len(vertex_labels_orig) <= len(vertex_labels)
assert label_colors_orig.shape == label_colors.shape
assert len(label_names_orig) == len(label_names)
assert_array_equal(label_names_orig, label_names)
assert_array_equal(label_colors_orig, label_colors)
assert vertex_labels[
0] == 11 # the proper index into the label_colors and label_names datastructures for this vertex, pre-computed for us.
assert vertex_labels_orig[0] == 9182740 # the original ID
def test_annot_aparc_orig_ids():
vertex_labels_mod, label_colors_mod, label_names_mod, meta_data_mod = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='both')
vertex_labels_orig, label_colors_orig, label_names_orig, meta_data_orig = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='both', orig_ids=True)
# these should not diff
assert label_colors_mod.shape == (NUM_LABELS_APARC, 5)
assert label_colors_mod.shape == label_colors_orig.shape
assert label_names_mod == label_names_orig
assert meta_data_mod == meta_data_orig
assert vertex_labels_mod.shape == vertex_labels_orig.shape
# now for the parts that should be different between the two
assert_raises(AssertionError, assert_array_equal, vertex_labels_mod,
vertex_labels_orig)
def test_annot_metadata_single_hemi_lh():
vertex_labels, label_colors, label_names, meta_data = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='lh')
assert len(meta_data) == 1
assert len(label_names) == NUM_LABELS_APARC
assert vertex_labels.shape == (SUBJECT1_SURF_LH_WHITE_NUM_VERTICES, )
assert label_colors.shape == (NUM_LABELS_APARC, 5)
def test_annot_metadata_both_hemispheres():
vertex_labels, label_colors, label_names, meta_data = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='both', orig_ids=True)
assert len(meta_data) == 2
assert len(label_names) == NUM_LABELS_APARC
assert vertex_labels.shape == (SUBJECT1_SURF_LH_WHITE_NUM_VERTICES +
SUBJECT1_SURF_RH_WHITE_NUM_VERTICES, )
assert label_colors.shape == (NUM_LABELS_APARC, 5)
def test_annot_get_label_indices():
vertex_labels, label_colors, label_names, meta_data = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='both', orig_ids=True)
assert vertex_labels[0] == 9182740
idx_map = an._get_indices_for_unique_vertex_labels(vertex_labels,
label_colors)
assert len(idx_map) == len(label_colors) - 1
assert len(idx_map) == len(label_names) - 1
assert idx_map[9182740] == 11
def test_annot_get_label_index():
vertex_labels, label_colors, label_names, meta_data = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='both', orig_ids=True)
assert vertex_labels[0] == 9182740
idx = an._get_annot_label_index(vertex_labels[0], label_colors)
assert idx == 11
# this index can now be used to retrieve the color and the label name:
color_rgbt = (label_colors[idx, 0], label_colors[idx, 1],
label_colors[idx, 2], label_colors[idx, 3])
assert color_rgbt == (20, 30, 140, 0)
label_name = label_names[idx]
assert label_name == "lateraloccipital"
def test_annot_aparc_data_makes_sense():
vertex_labels, label_colors, label_names, meta_data = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='both', orig_ids=False)
assert len(np.unique(vertex_labels)) == NUM_LABELS_APARC - 1
index_for_first_vertex = vertex_labels[0]
assert index_for_first_vertex > 0 # make sure it has a valid ID (-1 means has no label and color)
assert index_for_first_vertex == 11
color = (label_colors[index_for_first_vertex,
0], label_colors[index_for_first_vertex, 1],
label_colors[index_for_first_vertex,
2], label_colors[index_for_first_vertex, 3])
assert color == (20, 30, 140, 0)
def test_annot_metadata_single_hemi_rh_and_keep_metadata():
vertex_labels, label_colors, label_names, meta_data = an.annot(
'subject1',
TEST_DATA_DIR,
'aparc',
hemi='rh',
meta_data={'todo': 'keep_this'})
expected_annot_file = os.path.join(TEST_DATA_DIR, 'subject1', 'label',
'rh.aparc.annot')
assert len(meta_data) == 2
assert meta_data['rh.annotation_file'] == expected_annot_file
assert meta_data['todo'] == 'keep_this'
assert len(label_names) == NUM_LABELS_APARC
assert vertex_labels.shape == (SUBJECT1_SURF_RH_WHITE_NUM_VERTICES, )
assert label_colors.shape == (NUM_LABELS_APARC, 5)
def test_annot_raises_on_invalid_hemisphere():
with pytest.raises(ValueError) as exc_info:
vertex_labels, label_colors, label_names, meta_data = an.annot(
'subject1', TEST_DATA_DIR, 'aparc', hemi='invalid_hemisphere')
assert 'hemi must be one of' in str(exc_info.value)
assert 'invalid_hemisphere' in str(exc_info.value)
def test_annot_aparc():
vertex_labels, label_colors, label_names, meta_data = an.annot(
'subject1', TEST_DATA_DIR, 'aparc.DKTatlas', hemi='both')
assert label_colors.shape == (NUM_LABELS_APARC_DKTATLAS, 5)