def surface():
return fetch_desikan_killiany(native=False, surface=True)
import pandas as pd
from nilearn._utils import check_niimg
from nilearn.image import new_img_like
from abagen import allen
from abagen.datasets import fetch_desikan_killiany
ATLAS = fetch_desikan_killiany()
def test_label_samples(testfiles):
out = allen.label_samples(testfiles.annotation[0], ATLAS.image)
assert isinstance(out, pd.DataFrame)
assert out.index.name == 'sample_id'
assert out.columns == ['label']
def test_vanilla_get_expression_data(testdir, testfiles):
out = allen.get_expression_data(ATLAS.image, data_dir=testdir,
donors=['12876', '15496'])
assert isinstance(out, pd.DataFrame)
assert out.index.name == 'label'
assert out.columns.name == 'gene_symbol'
def test_extra_get_expression_data(testdir, testfiles):
for opts in [{'atlas_info': ATLAS.info},
{'exact': False},
{'reannotated': False},
{'atlas_info': ATLAS.info, 'exact': False}]:
out = allen.get_expression_data(ATLAS.image, data_dir=testdir,
donors=['12876', '15496'], **opts)
def atlas():
return fetch_desikan_killiany(native=False, surface=False)
def atlas():
return fetch_desikan_killiany()