def test_fetch_oasis_vbm():
local_url = "file://" + get_datadir()
ids = np.asarray(['OAS1_%4d' % i for i in range(457)])
ids = ids.view(dtype=[('ID', 'S9')])
get_file_mock().add_csv('oasis_cross-sectional.csv', ids)
# Disabled: cannot be tested without actually fetching covariates CSV file
dataset = datasets.fetch_oasis_vbm(data_dir=get_tmpdir(), url=local_url,
verbose=0)
assert_equal(len(dataset.gray_matter_maps), 403)
assert_equal(len(dataset.white_matter_maps), 403)
assert_true(isinstance(dataset.gray_matter_maps[0], _basestring))
assert_true(isinstance(dataset.white_matter_maps[0], _basestring))
assert_true(isinstance(dataset.ext_vars, np.recarray))
assert_true(isinstance(dataset.data_usage_agreement, _basestring))
assert_equal(len(get_url_request().urls), 3)
dataset = datasets.fetch_oasis_vbm(data_dir=get_tmpdir(), url=local_url,
dartel_version=False, verbose=0)
assert_equal(len(dataset.gray_matter_maps), 415)
assert_equal(len(dataset.white_matter_maps), 415)
assert_true(isinstance(dataset.gray_matter_maps[0], _basestring))
assert_true(isinstance(dataset.white_matter_maps[0], _basestring))
assert_true(isinstance(dataset.ext_vars, np.recarray))
assert_true(isinstance(dataset.data_usage_agreement, _basestring))
assert_equal(len(get_url_request().urls), 4)
def test_fetch_haxby():
for i in range(1, 6):
haxby = datasets.fetch_haxby(data_dir=get_tmpdir(), n_subjects=i,
verbose=0)
assert_equal(len(get_url_request().urls), 1 + (i == 1)) # subject_data + md5
assert_equal(len(haxby.func), i)
assert_equal(len(haxby.anat), i)
assert_equal(len(haxby.session_target), i)
assert_equal(len(haxby.mask_vt), i)
assert_equal(len(haxby.mask_face), i)
assert_equal(len(haxby.mask_house), i)
assert_equal(len(haxby.mask_face_little), i)
assert_equal(len(haxby.mask_house_little), i)
get_url_request().reset()
def test_miyawaki2008():
dataset = datasets.fetch_miyawaki2008(data_dir=get_tmpdir(), verbose=0)
assert_equal(len(dataset.func), 32)
assert_equal(len(dataset.label), 32)
assert_true(isinstance(dataset.mask, _basestring))
assert_equal(len(dataset.mask_roi), 38)
assert_equal(len(get_url_request().urls), 1)
def test_fetch_yeo_2011_atlas():
dataset = datasets.fetch_yeo_2011_atlas(data_dir=get_tmpdir(), verbose=0)
assert_true(isinstance(dataset.anat, _basestring))
assert_true(isinstance(dataset.colors_17, _basestring))
assert_true(isinstance(dataset.colors_7, _basestring))
assert_true(isinstance(dataset.thick_17, _basestring))
assert_true(isinstance(dataset.thick_7, _basestring))
assert_true(isinstance(dataset.thin_17, _basestring))
assert_true(isinstance(dataset.thin_7, _basestring))
assert_equal(len(get_url_request().urls), 1)
def test_fetch_yeo_2011_atlas():
dataset = datasets.fetch_yeo_2011_atlas(data_dir=get_tmpdir(), verbose=0)
assert_true(isinstance(dataset.anat, _basestring))
assert_true(isinstance(dataset.colors_17, _basestring))
assert_true(isinstance(dataset.colors_7, _basestring))
assert_true(isinstance(dataset.thick_17, _basestring))
assert_true(isinstance(dataset.thick_7, _basestring))
assert_true(isinstance(dataset.thin_17, _basestring))
assert_true(isinstance(dataset.thin_7, _basestring))
assert_equal(len(get_url_request().urls), 1)
def test_fetch_icbm152_2009():
dataset = datasets.fetch_icbm152_2009(data_dir=get_tmpdir(), verbose=0)
assert_true(isinstance(dataset.csf, _basestring))
assert_true(isinstance(dataset.eye_mask, _basestring))
assert_true(isinstance(dataset.face_mask, _basestring))
assert_true(isinstance(dataset.gm, _basestring))
assert_true(isinstance(dataset.mask, _basestring))
assert_true(isinstance(dataset.pd, _basestring))
assert_true(isinstance(dataset.t1, _basestring))
assert_true(isinstance(dataset.t2, _basestring))
assert_true(isinstance(dataset.t2_relax, _basestring))
assert_true(isinstance(dataset.wm, _basestring))
assert_equal(len(get_url_request().urls), 1)
def test_fetch_icbm152_2009():
dataset = datasets.fetch_icbm152_2009(data_dir=get_tmpdir(), verbose=0)
assert_true(isinstance(dataset.csf, _basestring))
assert_true(isinstance(dataset.eye_mask, _basestring))
assert_true(isinstance(dataset.face_mask, _basestring))
assert_true(isinstance(dataset.gm, _basestring))
assert_true(isinstance(dataset.mask, _basestring))
assert_true(isinstance(dataset.pd, _basestring))
assert_true(isinstance(dataset.t1, _basestring))
assert_true(isinstance(dataset.t2, _basestring))
assert_true(isinstance(dataset.t2_relax, _basestring))
assert_true(isinstance(dataset.wm, _basestring))
assert_equal(len(get_url_request().urls), 1)
def test_fetch_craddock_2012_atlas():
bunch = datasets.fetch_craddock_2012_atlas(data_dir=get_tmpdir(), verbose=0)
keys = ("scorr_mean", "tcorr_mean",
"scorr_2level", "tcorr_2level",
"random")
filenames = [
"scorr05_mean_all.nii.gz",
"tcorr05_mean_all.nii.gz",
"scorr05_2level_all.nii.gz",
"tcorr05_2level_all.nii.gz",
"random_all.nii.gz",
]
assert_equal(len(get_url_request().urls), 1)
for key, fn in zip(keys, filenames):
assert_equal(bunch[key], os.path.join(get_tmpdir(), 'craddock_2012', fn))
def test_fetch_smith_2009_atlas():
bunch = datasets.fetch_smith_2009(data_dir=get_tmpdir(), verbose=0)
keys = ("rsn20", "rsn10", "rsn70", "bm20", "bm10", "bm70")
filenames = [
"rsn20.nii.gz",
"PNAS_Smith09_rsn10.nii.gz",
"rsn70.nii.gz",
"bm20.nii.gz",
"PNAS_Smith09_bm10.nii.gz",
"bm70.nii.gz",
]
assert_equal(len(get_url_request().urls), 6)
for key, fn in zip(keys, filenames):
assert_equal(bunch[key], os.path.join(get_tmpdir(), 'smith_2009', fn))
def test_fetch_smith_2009_atlas():
bunch = datasets.fetch_smith_2009(data_dir=get_tmpdir(), verbose=0)
keys = ("rsn20", "rsn10", "rsn70",
"bm20", "bm10", "bm70")
filenames = [
"rsn20.nii.gz",
"PNAS_Smith09_rsn10.nii.gz",
"rsn70.nii.gz",
"bm20.nii.gz",
"PNAS_Smith09_bm10.nii.gz",
"bm70.nii.gz",
]
assert_equal(len(get_url_request().urls), 6)
for key, fn in zip(keys, filenames):
assert_equal(bunch[key], os.path.join(get_tmpdir(), 'smith_2009', fn))
def test_fetch_craddock_2012_atlas():
bunch = datasets.fetch_craddock_2012_atlas(data_dir=get_tmpdir(),
verbose=0)
keys = ("scorr_mean", "tcorr_mean", "scorr_2level", "tcorr_2level",
"random")
filenames = [
"scorr05_mean_all.nii.gz",
"tcorr05_mean_all.nii.gz",
"scorr05_2level_all.nii.gz",
"tcorr05_2level_all.nii.gz",
"random_all.nii.gz",
]
assert_equal(len(get_url_request().urls), 1)
for key, fn in zip(keys, filenames):
assert_equal(bunch[key], os.path.join(get_tmpdir(), 'craddock_2012',
fn))
def test_fetch_msdl_atlas():
dataset = datasets.fetch_msdl_atlas(data_dir=get_tmpdir(), verbose=0)
assert_true(isinstance(dataset.labels, _basestring))
assert_true(isinstance(dataset.maps, _basestring))
assert_equal(len(get_url_request().urls), 1)
def test_fetch_msdl_atlas():
dataset = datasets.fetch_msdl_atlas(data_dir=get_tmpdir(), verbose=0)
assert_true(isinstance(dataset.labels, _basestring))
assert_true(isinstance(dataset.maps, _basestring))
assert_equal(len(get_url_request().urls), 1)