def test_fail_fetch_harvard_oxford():
# specify non-existing atlas item
assert_raises_regex(ValueError, 'Invalid atlas name',
datasets.fetch_harvard_oxford, 'not_inside')
# specify existing atlas item
target_atlas = 'cort-maxprob-thr0-1mm'
target_atlas_fname = 'HarvardOxford-' + target_atlas + '.nii.gz'
HO_dir = os.path.join(get_tmpdir(), 'harvard_oxford')
os.mkdir(HO_dir)
nifti_dir = os.path.join(HO_dir, 'HarvardOxford')
os.mkdir(nifti_dir)
target_atlas_nii = os.path.join(nifti_dir, target_atlas_fname)
datasets.load_mni152_template().to_filename(target_atlas_nii)
dummy = open(os.path.join(HO_dir, 'HarvardOxford-Cortical.xml'), 'w')
dummy.write("<?xml version='1.0' encoding='us-ascii'?> "
"<metadata>"
"</metadata>")
dummy.close()
out_nii, arr = datasets.fetch_harvard_oxford(target_atlas, data_dir=get_tmpdir())
assert_true(isinstance(nibabel.load(out_nii), nibabel.Nifti1Image))
assert_true(isinstance(arr, np.ndarray))
assert_true(len(arr) > 0)
def test_fail_fetch_harvard_oxford():
# specify non-existing atlas item
assert_raises_regex(ValueError, 'Invalid atlas name',
datasets.fetch_harvard_oxford, 'not_inside')
# specify existing atlas item
target_atlas = 'cort-maxprob-thr0-1mm'
target_atlas_fname = 'HarvardOxford-' + target_atlas + '.nii.gz'
HO_dir = os.path.join(get_tmpdir(), 'harvard_oxford')
os.mkdir(HO_dir)
nifti_dir = os.path.join(HO_dir, 'HarvardOxford')
os.mkdir(nifti_dir)
target_atlas_nii = os.path.join(nifti_dir, target_atlas_fname)
datasets.load_mni152_template().to_filename(target_atlas_nii)
dummy = open(os.path.join(HO_dir, 'HarvardOxford-Cortical.xml'), 'w')
dummy.write("<?xml version='1.0' encoding='us-ascii'?> "
"<metadata>"
"</metadata>")
dummy.close()
out_nii, arr = datasets.fetch_harvard_oxford(target_atlas,
data_dir=get_tmpdir())
assert_true(isinstance(nibabel.load(out_nii), nibabel.Nifti1Image))
assert_true(isinstance(arr, np.ndarray))
assert_true(len(arr) > 0)
def testget_dataset_dir():
# testing folder creation under different environments, enforcing
# a custom clean install
os.environ.pop('NIDATA_PATH', None)
os.environ.pop('NILEARN_SHARED_DATA', None)
expected_base_dir = os.path.expanduser('~/NIDATA_PATH')
data_dir = fetchers.get_dataset_dir('test', verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
expected_base_dir = os.path.join(tmpdir, 'test_NIDATA_PATH')
os.environ['NIDATA_PATH'] = expected_base_dir
data_dir = fetchers.get_dataset_dir('test', verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
expected_base_dir = os.path.join(tmpdir, 'nilearn_shared_data')
os.environ['NILEARN_SHARED_DATA'] = expected_base_dir
data_dir = fetchers.get_dataset_dir('test', verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
expected_base_dir = os.path.join(tmpdir, 'env_data')
os.environ['MY_DATA'] = expected_base_dir
data_dir = fetchers.get_dataset_dir('test', env_vars=['MY_DATA'],
verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
no_write = os.path.join(tmpdir, 'no_write')
os.makedirs(no_write)
os.chmod(no_write, 0o400)
# Verify that default is used if non writeable dir
os.environ['MY_DATA'] = no_write
expected_base_dir = os.path.join(tmpdir, 'nilearn_shared_data')
os.environ['NILEARN_SHARED_DATA'] = expected_base_dir
data_dir = fetchers.get_dataset_dir('test', env_vars=['MY_DATA'],
verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
# Verify exception is raised on read-only directories
assert_raises_regex(OSError, 'Permission denied',
fetchers.get_dataset_dir, 'test', no_write,
verbose=0)
# Verify exception for a path which exists and is a file
test_file = os.path.join(tmpdir, 'some_file')
with open(test_file, 'w') as out:
out.write('abcfeg')
assert_raises_regex(OSError, 'Not a directory',
fetchers.get_dataset_dir, 'test', test_file,
verbose=0)
def testget_dataset_dir():
# testing folder creation under different environments, enforcing
# a custom clean install
os.environ.pop('NIDATA_PATH', None)
os.environ.pop('NILEARN_SHARED_DATA', None)
expected_base_dir = os.path.expanduser('~/NIDATA_PATH')
data_dir = fetchers.get_dataset_dir('test', verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
expected_base_dir = os.path.join(tmpdir, 'test_NIDATA_PATH')
os.environ['NIDATA_PATH'] = expected_base_dir
data_dir = fetchers.get_dataset_dir('test', verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
expected_base_dir = os.path.join(tmpdir, 'nilearn_shared_data')
os.environ['NILEARN_SHARED_DATA'] = expected_base_dir
data_dir = fetchers.get_dataset_dir('test', verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
expected_base_dir = os.path.join(tmpdir, 'env_data')
os.environ['MY_DATA'] = expected_base_dir
data_dir = fetchers.get_dataset_dir('test',
env_vars=['MY_DATA'],
verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
no_write = os.path.join(tmpdir, 'no_write')
os.makedirs(no_write)
os.chmod(no_write, 0o400)
# Verify that default is used if non writeable dir
os.environ['MY_DATA'] = no_write
expected_base_dir = os.path.join(tmpdir, 'nilearn_shared_data')
os.environ['NILEARN_SHARED_DATA'] = expected_base_dir
data_dir = fetchers.get_dataset_dir('test',
env_vars=['MY_DATA'],
verbose=0)
assert_equal(data_dir, os.path.join(expected_base_dir, 'test'))
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
# Verify exception is raised on read-only directories
assert_raises_regex(OSError,
'Permission denied',
fetchers.get_dataset_dir,
'test',
no_write,
verbose=0)
# Verify exception for a path which exists and is a file
test_file = os.path.join(tmpdir, 'some_file')
with open(test_file, 'w') as out:
out.write('abcfeg')
assert_raises_regex(OSError,
'Not a directory',
fetchers.get_dataset_dir,
'test',
test_file,
verbose=0)