def test_auto_mask():
# This mostly a smoke test
data = np.zeros((9, 9, 9))
data[2:-2, 2:-2, 2:-2] = 10
img = Nifti1Image(data, np.eye(4))
masker = MultiNiftiMasker(mask_args=dict(opening=0))
# Check that if we have not fit the masker we get a intelligible
# error
assert_raises(ValueError, masker.transform, [[img, ]])
# Check error return due to bad data format
assert_raises(ValueError, masker.fit, img)
# Smoke test the fit
masker.fit([[img]])
# Test mask intersection
data2 = np.zeros((9, 9, 9))
data2[1:-3, 1:-3, 1:-3] = 10
img2 = Nifti1Image(data2, np.eye(4))
masker.fit([[img, img2]])
assert_array_equal(masker.mask_img_.get_data(),
np.logical_or(data, data2))
# Smoke test the transform
masker.transform([[img, ]])
# It should also work with a 3D image
masker.transform(img)
# check exception when transform() called without prior fit()
masker2 = MultiNiftiMasker(mask_img=img)
assert_raises_regex(
ValueError,
'has not been fitted. ', masker2.transform, img2)
def test_check_threshold():
adjacency_matrix = np.array([[1., 2.],
[2., 1.]])
name = 'edge_threshold'
calculate = 'fast_abs_percentile'
# a few not correctly formatted strings for 'edge_threshold'
wrong_edge_thresholds = ['0.1', '10', '10.2.3%', 'asdf%']
for wrong_edge_threshold in wrong_edge_thresholds:
assert_raises_regex(ValueError,
'{0}.+should be a number followed by '
'the percent sign'.format(name),
check_threshold,
wrong_edge_threshold, adjacency_matrix,
calculate, name)
threshold = object()
assert_raises_regex(TypeError,
'{0}.+should be either a number or a string'.format(name),
check_threshold,
threshold, adjacency_matrix,
calculate, name)
# To check if it also gives the score which is expected
assert_true(1. < check_threshold("50%", adjacency_matrix,
percentile_calculate=fast_abs_percentile,
name='threshold') <= 2.)
def test_plot_surf_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
# Wrong inputs for view or hemi
assert_raises_regex(ValueError, 'view must be one of',
plot_surf, mesh, view='middle')
assert_raises_regex(ValueError, 'hemi must be one of',
plot_surf, mesh, hemi='lft')
# Wrong size of background image
assert_raises_regex(ValueError,
'bg_map does not have the same number of vertices',
plot_surf, mesh,
bg_map=rng.randn(mesh[0].shape[0] - 1, ))
# Wrong size of surface data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf, mesh,
surf_map=rng.randn(mesh[0].shape[0] + 1, ))
assert_raises_regex(ValueError,
'surf_map can only have one dimension', plot_surf,
mesh, surf_map=rng.randn(mesh[0].shape[0], 2))
def test_masker_attributes_with_fit():
# Test base module at sub-class
data, mask_img, components, rng = _make_canica_test_data(n_subjects=3)
# Passing mask_img
canica = CanICA(n_components=3, mask=mask_img, random_state=0)
canica.fit(data)
assert_true(canica.mask_img_ == mask_img)
assert_true(canica.mask_img_ == canica.masker_.mask_img_)
# Passing masker
masker = MultiNiftiMasker(mask_img=mask_img)
canica = CanICA(n_components=3, mask=masker, random_state=0)
canica.fit(data)
assert_true(canica.mask_img_ == canica.masker_.mask_img_)
canica = CanICA(mask=mask_img, n_components=3)
assert_raises_regex(ValueError,
"Object has no components_ attribute. "
"This is probably because fit has not been called",
canica.transform, data)
# Test if raises an error when empty list of provided.
assert_raises_regex(ValueError,
'Need one or more Niimg-like objects as input, '
'an empty list was given.',
canica.fit, [])
# Test passing masker arguments to estimator
canica = CanICA(n_components=3,
target_affine=np.eye(4),
target_shape=(6, 8, 10),
mask_strategy='background')
canica.fit(data)
def test_load_surf_data_file_nii_gii():
# test loading of fake data from gifti file
filename_gii = tempfile.mktemp(suffix='.gii')
if LooseVersion(nb.__version__) > LooseVersion('2.0.2'):
darray = gifti.GiftiDataArray(data=np.zeros((20, )))
else:
# Avoid a bug in nibabel 1.2.0 where GiftiDataArray were not
# initialized properly:
darray = gifti.GiftiDataArray.from_array(np.zeros((20, )),
intent='t test')
gii = gifti.GiftiImage(darrays=[darray])
gifti.write(gii, filename_gii)
assert_array_equal(load_surf_data(filename_gii), np.zeros((20, )))
os.remove(filename_gii)
# test loading of data from empty gifti file
filename_gii_empty = tempfile.mktemp(suffix='.gii')
gii_empty = gifti.GiftiImage()
gifti.write(gii_empty, filename_gii_empty)
assert_raises_regex(ValueError,
'must contain at least one data array',
load_surf_data, filename_gii_empty)
os.remove(filename_gii_empty)
# test loading of fake data from nifti file
filename_nii = tempfile.mktemp(suffix='.nii')
filename_niigz = tempfile.mktemp(suffix='.nii.gz')
nii = nb.Nifti1Image(np.zeros((20, )), affine=None)
nb.save(nii, filename_nii)
nb.save(nii, filename_niigz)
assert_array_equal(load_surf_data(filename_nii), np.zeros((20, )))
assert_array_equal(load_surf_data(filename_niigz), np.zeros((20, )))
os.remove(filename_nii)
os.remove(filename_niigz)
def test_load_surf_data_file_glob():
data2D = np.ones((20, 3))
fnames = []
for f in range(3):
fnames.append(tempfile.mktemp(prefix='glob_%s_' % f, suffix='.gii'))
data2D[:, f] *= f
if LooseVersion(nb.__version__) > LooseVersion('2.0.2'):
darray = gifti.GiftiDataArray(data=data2D[:, f])
else:
# Avoid a bug in nibabel 1.2.0 where GiftiDataArray were not
# initialized properly:
darray = gifti.GiftiDataArray.from_array(data2D[:, f],
intent='t test')
gii = gifti.GiftiImage(darrays=[darray])
gifti.write(gii, fnames[f])
assert_array_equal(load_surf_data(os.path.join(os.path.dirname(fnames[0]),
"glob*.gii")), data2D)
# make one more gii file that has more than one dimension
fnames.append(tempfile.mktemp(prefix='glob_3_', suffix='.gii'))
if LooseVersion(nb.__version__) > LooseVersion('2.0.2'):
darray1 = gifti.GiftiDataArray(data=np.ones((20, )))
darray2 = gifti.GiftiDataArray(data=np.ones((20, )))
darray3 = gifti.GiftiDataArray(data=np.ones((20, )))
else:
# Avoid a bug in nibabel 1.2.0 where GiftiDataArray were not
# initialized properly:
darray1 = gifti.GiftiDataArray.from_array(np.ones((20, )),
intent='t test')
darray2 = gifti.GiftiDataArray.from_array(np.ones((20, )),
intent='t test')
darray3 = gifti.GiftiDataArray.from_array(np.ones((20, )),
intent='t test')
gii = gifti.GiftiImage(darrays=[darray1, darray2, darray3])
gifti.write(gii, fnames[-1])
data2D = np.concatenate((data2D, np.ones((20, 3))), axis=1)
assert_array_equal(load_surf_data(os.path.join(os.path.dirname(fnames[0]),
"glob*.gii")), data2D)
# make one more gii file that has a different shape in axis=0
fnames.append(tempfile.mktemp(prefix='glob_4_', suffix='.gii'))
if LooseVersion(nb.__version__) > LooseVersion('2.0.2'):
darray = gifti.GiftiDataArray(data=np.ones((15, 1)))
else:
# Avoid a bug in nibabel 1.2.0 where GiftiDataArray were not
# initialized properly:
darray = gifti.GiftiDataArray.from_array(np.ones(15, 1),
intent='t test')
gii = gifti.GiftiImage(darrays=[darray])
gifti.write(gii, fnames[-1])
assert_raises_regex(ValueError,
'files must contain data with the same shape',
load_surf_data,
os.path.join(os.path.dirname(fnames[0]), "*.gii"))
for f in fnames:
os.remove(f)
def test_design_matrix0c():
# test design matrix creation when regressors are provided manually
tr = 1.0
frame_times = np.linspace(0, 127 * tr, 128)
ax = np.random.randn(128, 4)
_, X, names = check_design_matrix(
make_design_matrix(frame_times, drift_model="polynomial", drift_order=3, add_regs=ax)
)
assert_almost_equal(X[:, 0], ax[:, 0])
ax = np.random.randn(127, 4)
assert_raises_regex(
AssertionError,
"Incorrect specification of additional regressors:.",
make_design_matrix,
frame_times,
add_regs=ax,
)
ax = np.random.randn(128, 4)
assert_raises_regex(
ValueError,
"Incorrect number of additional regressor names.",
make_design_matrix,
frame_times,
add_regs=ax,
add_reg_names="",
)
def test_index_img():
img_3d = nibabel.Nifti1Image(np.ones((3, 4, 5)), np.eye(4))
testing.assert_raises_regex(TypeError,
"Input data has incompatible dimensionality: "
"Expected dimension is 4D and you provided "
"a 3D image.",
image.index_img, img_3d, 0)
affine = np.array([[1., 2., 3., 4.],
[5., 6., 7., 8.],
[9., 10., 11., 12.],
[0., 0., 0., 1.]])
img_4d, _ = data_gen.generate_fake_fmri(affine=affine)
fourth_dim_size = img_4d.shape[3]
tested_indices = (list(range(fourth_dim_size)) +
[slice(2, 8, 2), [1, 2, 3, 2], [],
(np.arange(fourth_dim_size) % 3) == 1])
for i in tested_indices:
this_img = image.index_img(img_4d, i)
expected_data_3d = img_4d.get_data()[..., i]
assert_array_equal(this_img.get_data(),
expected_data_3d)
assert_array_equal(this_img.affine, img_4d.affine)
for i in [fourth_dim_size, - fourth_dim_size - 1,
[0, fourth_dim_size],
np.repeat(True, fourth_dim_size + 1)]:
testing.assert_raises_regex(
IndexError,
'out of bounds|invalid index|out of range|boolean index',
image.index_img, img_4d, i)
def test_index_img():
img_3d = nibabel.Nifti1Image(np.ones((3, 4, 5)), np.eye(4))
testing.assert_raises_regex(TypeError, '4D Niimg-like',
image.index_img, img_3d, 0)
affine = np.array([[1., 2., 3., 4.],
[5., 6., 7., 8.],
[9., 10., 11., 12.],
[0., 0., 0., 1.]])
img_4d, _ = testing.generate_fake_fmri(affine=affine)
fourth_dim_size = img_4d.shape[3]
tested_indices = (list(range(fourth_dim_size)) +
[slice(2, 8, 2), [1, 2, 3, 2], [],
(np.arange(fourth_dim_size) % 3) == 1])
for i in tested_indices:
this_img = image.index_img(img_4d, i)
expected_data_3d = img_4d.get_data()[..., i]
assert_array_equal(this_img.get_data(),
expected_data_3d)
assert_array_equal(this_img.get_affine(),
img_4d.get_affine())
for i in [fourth_dim_size, - fourth_dim_size - 1,
[0, fourth_dim_size],
np.repeat(True, fourth_dim_size + 1)]:
testing.assert_raises_regex(
IndexError,
'out of bounds|invalid index|out of range',
image.index_img, img_4d, i)
def test_base_decomposition():
shape = (6, 8, 10, 5)
affine = np.eye(4)
rng = np.random.RandomState(0)
data = []
for i in range(8):
this_data = rng.normal(size=shape)
# Create fake activation to get non empty mask
this_data[2:4, 2:4, 2:4, :] += 10
data.append(nibabel.Nifti1Image(this_data, affine))
mask = nibabel.Nifti1Image(np.ones(shape[:3], dtype=np.int8), affine)
masker = MultiNiftiMasker(mask_img=mask)
base_decomposition = BaseDecomposition(mask=masker, n_components=3)
base_decomposition.fit(data)
assert_true(base_decomposition.mask_img_ == mask)
assert_true(base_decomposition.mask_img_ ==
base_decomposition.masker_.mask_img_)
# Testing fit on data
masker = MultiNiftiMasker()
base_decomposition = BaseDecomposition(mask=masker, n_components=3)
base_decomposition.fit(data)
assert_true(base_decomposition.mask_img_ ==
base_decomposition.masker_.mask_img_)
assert_raises_regex(ValueError,
"Object has no components_ attribute. "
"This may be because "
"BaseDecomposition is directly "
"being used.",
base_decomposition.transform, data)
assert_raises_regex(ValueError,
'Need one or more Niimg-like objects as input, '
'an empty list was given.',
base_decomposition.fit, [])
def test_iter_check_niimgs():
no_file_matching = "No files matching path: %s"
affine = np.eye(4)
img_4d = Nifti1Image(np.ones((10, 10, 10, 4)), affine)
img_2_4d = [[img_4d, img_4d]]
for empty in ((), [], (i for i in ()), [i for i in ()]):
assert_raises_regex(ValueError,
"Input niimgs list is empty.",
list, _iter_check_niimg(empty))
nofile_path = "/tmp/nofile"
assert_raises_regex(ValueError,
no_file_matching % nofile_path,
list, _iter_check_niimg(nofile_path))
# Create a test file
filename = tempfile.mktemp(prefix="nilearn_test",
suffix=".nii",
dir=None)
img_4d.to_filename(filename)
niimgs = list(_iter_check_niimg([filename]))
assert_array_equal(niimgs[0].get_data(),
_utils.check_niimg(img_4d).get_data())
del img_4d
del niimgs
os.remove(filename)
# Regular case
niimgs = list(_iter_check_niimg(img_2_4d))
assert_array_equal(niimgs[0].get_data(),
_utils.check_niimg(img_2_4d).get_data())
def test_nifti_maps_masker_overlap():
# Test resampling in NiftiMapsMasker
affine = np.eye(4)
shape = (5, 5, 5)
length = 10
fmri_img, _ = generate_random_img(shape, affine=affine,
length=length)
non_overlapping_maps = np.zeros(shape + (2,))
non_overlapping_maps[:2, :, :, 0] = 1.
non_overlapping_maps[2:, :, :, 1] = 1.
non_overlapping_maps_img = nibabel.Nifti1Image(non_overlapping_maps,
affine)
overlapping_maps = np.zeros(shape + (2,))
overlapping_maps[:3, :, :, 0] = 1.
overlapping_maps[2:, :, :, 1] = 1.
overlapping_maps_img = nibabel.Nifti1Image(overlapping_maps, affine)
overlapping_masker = NiftiMapsMasker(non_overlapping_maps_img,
allow_overlap=True)
overlapping_masker.fit_transform(fmri_img)
overlapping_masker = NiftiMapsMasker(overlapping_maps_img,
allow_overlap=True)
overlapping_masker.fit_transform(fmri_img)
non_overlapping_masker = NiftiMapsMasker(non_overlapping_maps_img,
allow_overlap=False)
non_overlapping_masker.fit_transform(fmri_img)
non_overlapping_masker = NiftiMapsMasker(overlapping_maps_img,
allow_overlap=False)
assert_raises_regex(ValueError, 'Overlap detected',
non_overlapping_masker.fit_transform, fmri_img)
def test_check_parameters_transform():
rng = np.random.RandomState(0)
data = np.ones((10, 11, 12, 10))
data[6, 7, 8] = 2
data[9, 10, 11] = 3
# single image
fmri_img = nibabel.Nifti1Image(data, affine=np.eye(4))
# single confound
confounds = rng.randn(*(10, 3))
# Tests to check whether imgs, confounds returned are
# list or not. Pre-check in parameters to work for list
# of multi images and multi confounds
imgs, confounds, single_subject = _check_parameters_transform(fmri_img,
confounds)
assert_true(isinstance(imgs, (list, tuple)))
assert_true(isinstance(confounds, (list, tuple)))
assert_true(single_subject, True)
# multi images
fmri_imgs = [fmri_img, fmri_img, fmri_img]
confounds_list = [confounds, confounds, confounds]
imgs, confounds, _ = _check_parameters_transform(fmri_imgs, confounds_list)
assert_equal(imgs, fmri_imgs)
assert_equal(confounds_list, confounds)
# Test the error when length of images and confounds are not same
msg = ("Number of confounds given does not match with the "
"given number of images")
not_match_confounds_list = [confounds, confounds]
assert_raises_regex(ValueError, msg, _check_parameters_transform,
fmri_imgs, not_match_confounds_list)
def test_fail_fetch_atlas_harvard_oxford():
# specify non-existing atlas item
assert_raises_regex(ValueError, "Invalid atlas name", atlas.fetch_atlas_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(tmpdir, "fsl", "data", "atlases")
os.makedirs(ho_dir)
nifti_dir = os.path.join(ho_dir, "HarvardOxford")
os.makedirs(nifti_dir)
target_atlas_nii = os.path.join(nifti_dir, target_atlas_fname)
struct.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()
ho = atlas.fetch_atlas_harvard_oxford(target_atlas, data_dir=tmpdir)
assert_true(isinstance(nibabel.load(ho.maps), nibabel.Nifti1Image))
assert_true(isinstance(ho.labels, np.ndarray))
assert_true(len(ho.labels) > 0)
def test_vec_to_sym_matrix():
# Check error if unsuitable size
vec = np.ones(31)
assert_raises_regex(ValueError, 'Vector of unsuitable shape',
vec_to_sym_matrix, vec)
# Check error if given diagonal shape incompatible with vec
vec = np.ones(3)
diagonal = np.zeros(4)
assert_raises_regex(ValueError, 'incompatible with vector',
vec_to_sym_matrix, vec, diagonal)
# Check output value is correct
vec = np.ones(6, )
sym = np.array([[sqrt(2), 1., 1.], [1., sqrt(2), 1.],
[1., 1., sqrt(2)]])
assert_array_almost_equal(vec_to_sym_matrix(vec), sym)
# Check output value is correct with seperate diagonal
vec = np.ones(3, )
diagonal = np.ones(3)
assert_array_almost_equal(vec_to_sym_matrix(vec, diagonal=diagonal), sym)
# Check vec_to_sym_matrix is the inverse function of sym_matrix_to_vec
# when diagonal is included
assert_array_almost_equal(vec_to_sym_matrix(sym_matrix_to_vec(sym)), sym)
# when diagonal is discarded
vec = sym_matrix_to_vec(sym, discard_diagonal=True)
diagonal = np.diagonal(sym) / sqrt(2)
assert_array_almost_equal(vec_to_sym_matrix(vec, diagonal=diagonal), sym)
def test_get_dataset_dir():
# testing folder creation under different environments, enforcing
# a custom clean install
os.environ.pop('NILEARN_DATA', None)
os.environ.pop('NILEARN_SHARED_DATA', None)
expected_base_dir = os.path.expanduser('~/nilearn_data')
data_dir = datasets._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_nilearn_data')
os.environ['NILEARN_DATA'] = expected_base_dir
data_dir = datasets._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 = datasets._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 = datasets._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 = datasets._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',
datasets._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',
datasets._get_dataset_dir, 'test', test_file,
verbose=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(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=tmpdir)
assert_true(isinstance(nibabel.load(out_nii), nibabel.Nifti1Image))
assert_true(isinstance(arr, np.ndarray))
assert_true(len(arr) > 0)
def test_plot_surf_error():
# Axes3DSubplot has no attribute 'plot_trisurf' for older versions of
# matplotlib
if LooseVersion(matplotlib.__version__) <= LooseVersion('1.3.1'):
raise SkipTest
mesh = _generate_surf()
rng = np.random.RandomState(0)
# Wrong inputs for view or hemi
assert_raises_regex(ValueError, 'view must be one of',
plot_surf, mesh, view='middle')
assert_raises_regex(ValueError, 'hemi must be one of',
plot_surf, mesh, hemi='lft')
# Wrong size of background image
assert_raises_regex(ValueError,
'bg_map does not have the same number of vertices',
plot_surf, mesh,
bg_map=rng.randn(mesh[0].shape[0] - 1, ))
# Wrong size of surface data
assert_raises_regex(ValueError,
'surf_map does not have the same number of vertices',
plot_surf, mesh,
surf_map=rng.randn(mesh[0].shape[0] + 1, ))
assert_raises_regex(ValueError,
'surf_map can only have one dimension', plot_surf,
mesh, surf_map=rng.randn(mesh[0].shape[0], 2))
def test_small_radius():
affine = np.eye(4)
shape = (3, 3, 3)
data = np.random.random(shape)
mask = np.zeros(shape)
mask[1, 1, 1] = 1
mask[2, 2, 2] = 1
affine = np.eye(4) * 1.2
seed = (1.4, 1.4, 1.4)
masker = NiftiSpheresMasker([seed], radius=0.1,
mask_img=nibabel.Nifti1Image(mask, affine))
masker.fit_transform(nibabel.Nifti1Image(data, affine))
# Test if masking is taken into account
mask[1, 1, 1] = 0
mask[1, 1, 0] = 1
masker = NiftiSpheresMasker([seed], radius=0.1,
mask_img=nibabel.Nifti1Image(mask, affine))
assert_raises_regex(ValueError, 'Sphere around seed #0 is empty',
masker.fit_transform,
nibabel.Nifti1Image(data, affine))
masker = NiftiSpheresMasker([seed], radius=1.6,
mask_img=nibabel.Nifti1Image(mask, affine))
masker.fit_transform(nibabel.Nifti1Image(data, affine))
def test_fail_fetch_atlas_harvard_oxford():
# specify non-existing atlas item
assert_raises_regex(ValueError, 'Invalid atlas name',
atlas.fetch_atlas_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(tst.tmpdir, 'fsl', 'data', 'atlases')
os.makedirs(ho_dir)
nifti_dir = os.path.join(ho_dir, 'HarvardOxford')
os.makedirs(nifti_dir)
target_atlas_nii = os.path.join(nifti_dir, target_atlas_fname)
struct.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()
ho = atlas.fetch_atlas_harvard_oxford(target_atlas,
data_dir=tst.tmpdir)
assert_true(isinstance(nibabel.load(ho.maps), nibabel.Nifti1Image))
assert_true(isinstance(ho.labels, np.ndarray))
assert_true(len(ho.labels) > 0)
def test_check_niimg():
affine = np.eye(4)
img_3d = Nifti1Image(np.ones((10, 10, 10)), affine)
img_4d = Nifti1Image(np.ones((10, 10, 10, 4)), affine)
img_3_3d = [[[img_3d, img_3d]]]
img_2_4d = [[img_4d, img_4d]]
assert_raises_regex(
DimensionError,
"Input data has incompatible dimensionality: "
"Expected dimension is 2D and you provided "
"a list of list of list of 3D images \(6D\)",
_utils.check_niimg, img_3_3d, ensure_ndim=2)
assert_raises_regex(
DimensionError,
"Input data has incompatible dimensionality: "
"Expected dimension is 4D and you provided "
"a list of list of 4D images \(6D\)",
_utils.check_niimg, img_2_4d, ensure_ndim=4)
# check data dtype equal with dtype='auto'
img_3d_check = _utils.check_niimg(img_3d, dtype='auto')
assert_equal(img_3d.get_data().dtype.kind, img_3d_check.get_data().dtype.kind)
img_4d_check = _utils.check_niimg(img_4d, dtype='auto')
assert_equal(img_4d.get_data().dtype.kind, img_4d_check.get_data().dtype.kind)
def test_get_dataset_dir():
# testing folder creation under different environments, enforcing
# a custom clean install
os.environ.pop('NILEARN_DATA', None)
os.environ.pop('NILEARN_SHARED_DATA', None)
expected_base_dir = os.path.expanduser('~/nilearn_data')
data_dir = utils._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(tst.tmpdir, 'test_nilearn_data')
os.environ['NILEARN_DATA'] = expected_base_dir
data_dir = utils._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(tst.tmpdir, 'nilearn_shared_data')
os.environ['NILEARN_SHARED_DATA'] = expected_base_dir
data_dir = utils._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(tst.tmpdir, 'env_data')
expected_dataset_dir = os.path.join(expected_base_dir, 'test')
data_dir = utils._get_dataset_dir(
'test', default_paths=[expected_dataset_dir], 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(tst.tmpdir, 'no_write')
os.makedirs(no_write)
os.chmod(no_write, 0o400)
expected_base_dir = os.path.join(tst.tmpdir, 'nilearn_shared_data')
os.environ['NILEARN_SHARED_DATA'] = expected_base_dir
data_dir = utils._get_dataset_dir('test',
default_paths=[no_write],
verbose=0)
# Non writeable dir is returned because dataset may be in there.
assert_equal(data_dir, no_write)
assert os.path.exists(data_dir)
# Set back write permissions in order to be able to remove the file
os.chmod(no_write, 0o600)
shutil.rmtree(data_dir)
# Verify exception for a path which exists and is a file
test_file = os.path.join(tst.tmpdir, 'some_file')
with open(test_file, 'w') as out:
out.write('abcfeg')
assert_raises_regex(OSError,
'Nilearn tried to store the dataset '
'in the following directories, but',
utils._get_dataset_dir,
'test', test_file, verbose=0)
def test_invalid_threshold_strategies():
maps, _ = generate_maps((6, 8, 10), n_regions=1)
extract_strategy_check = RegionExtractor(maps, thresholding_strategy='n_')
valid_strategies = ['ratio_n_voxels', 'img_value', 'percentile']
assert_raises_regex(ValueError,
"'thresholding_strategy' should be either of "
"these".format(valid_strategies),
extract_strategy_check.fit)
def test_concat_niimgs():
# create images different in affine and 3D/4D shape
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
shape2 = (12, 11, 10)
img1b = Nifti1Image(np.ones(shape2), affine)
shape3 = (11, 22, 33)
img1c = Nifti1Image(np.ones(shape3), affine)
# check basic concatenation with equal shape/affine
concatenated = _utils.concat_niimgs((img1, img3, img1),
accept_4d=False)
concatenate_true = np.ones(shape + (3,))
# Smoke-test the accept_4d
assert_raises_regex(ValueError, 'image',
_utils.concat_niimgs, [img1, img4d])
concatenated = _utils.concat_niimgs([img1, img4d], accept_4d=True)
np.testing.assert_equal(concatenated.get_data(), concatenate_true,
verbose=0)
# smoke-test auto_resample
concatenated = _utils.concat_niimgs((img1, img1b, img1c), accept_4d=False,
auto_resample=True)
assert_true(concatenated.shape == img1.shape + (3, ))
# check error for non-forced but necessary resampling
assert_raises_regex(ValueError, 'different from reference affine',
_utils.concat_niimgs, [img1, img2],
accept_4d=False)
# Smoke-test the 4d parsing
concatenated = _utils.concat_niimgs([img1, img4d], accept_4d=True)
assert_equal(concatenated.shape[3], 3)
# test list of 4D niimgs as input
_, tmpimg1 = tempfile.mkstemp(suffix='.nii')
_, tmpimg2 = tempfile.mkstemp(suffix='.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img3, tmpimg2)
concatenated = _utils.concat_niimgs([tmpimg1, tmpimg2],
accept_4d=False)
assert_array_equal(
concatenated.get_data()[..., 0], img1.get_data())
assert_array_equal(
concatenated.get_data()[..., 1], img3.get_data())
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
def test_invalid_in_display_mode_cut_coords_all_plots():
img = _generate_img()
for plot_func in [plot_img, plot_anat, plot_roi, plot_epi,
plot_stat_map, plot_prob_atlas, plot_glass_brain]:
assert_raises_regex(ValueError,
"The input given for display_mode='ortho' needs to "
"be a list of 3d world coordinates.",
plot_func,
img, display_mode='ortho', cut_coords=2)
def test_get_colorbar_and_data_ranges_with_vmin():
data = np.array([[-.5, 1., np.nan],
[0., np.nan, -.2],
[1.5, 2.5, 3.]])
assert_raises_regex(ValueError,
'does not accept a "vmin" argument',
_get_colorbar_and_data_ranges,
data, vmax=None,
symmetric_cbar=True, kwargs={'vmin': 1.})
def test_space_net_no_crash_not_fitted():
"""Regression test."""
iris = load_iris()
X, y = iris.data, iris.target
X, mask = to_niimgs(X, [2, 2, 2])
for model in [SpaceNetRegressor, SpaceNetClassifier]:
assert_raises_regex(RuntimeError,
"This %s instance is not fitted yet" % (
model.__name__), model().predict, X)
model(mask=mask, alphas=1.).fit(X, y).predict(X)
def test_filter_and_mask():
data = np.zeros([20, 30, 40, 5])
mask = np.zeros([20, 30, 40, 2])
mask[10, 15, 20, :] = 1
data_img = nibabel.Nifti1Image(data, np.eye(4))
mask_img = nibabel.Nifti1Image(mask, np.eye(4))
assert_raises_regex(DimensionError, "Data must be a 3D", filter_and_mask,
data_img, mask_img, {})
def test_space_net_no_crash_not_fitted():
"""Regression test."""
iris = load_iris()
X, y = iris.data, iris.target
X, mask = to_niimgs(X, [2, 2, 2])
for model in [SpaceNetRegressor, SpaceNetClassifier]:
assert_raises_regex(RuntimeError,
"This %s instance is not fitted yet" % (
model.__name__), model().predict, X)
model(mask=mask, alphas=1.).fit(X, y).predict(X)
def test_filter_and_mask():
data = np.zeros([20, 30, 40, 5])
mask = np.zeros([20, 30, 40, 2])
mask[10, 15, 20, :] = 1
data_img = nibabel.Nifti1Image(data, np.eye(4))
mask_img = nibabel.Nifti1Image(mask, np.eye(4))
assert_raises_regex(TypeError, "A 3D image is expected", filter_and_mask,
data_img, mask_img, {})
def test_invalid_in_display_mode_tiled_cut_coords_single_all_plots():
img = _generate_img()
for plot_func in [plot_img, plot_anat, plot_roi, plot_epi,
plot_stat_map,plot_prob_atlas]:
assert_raises_regex(ValueError,
"The input given for display_mode='tiled' needs to "
"be a list of 3d world coordinates.",
plot_func,
img, display_mode='tiled', cut_coords=2)
def test_invalid_in_display_mode_tiled_cut_coords_all_plots():
img = _generate_img()
for plot_func in [plot_img, plot_anat, plot_roi, plot_epi,
plot_stat_map,plot_prob_atlas]:
assert_raises_regex(ValueError,
"The number cut_coords passed does not "
"match the display_mode",
plot_func,
img, display_mode='tiled', cut_coords=(2,2))
def test_invalid_in_display_mode_tiled_cut_coords_all_plots():
img = _generate_img()
for plot_func in [plot_img, plot_anat, plot_roi, plot_epi,
plot_stat_map,plot_prob_atlas]:
assert_raises_regex(ValueError,
"The number cut_coords passed does not "
"match the display_mode",
plot_func,
img, display_mode='tiled', cut_coords=(2,2))
def test_get_colorbar_and_data_ranges_with_vmin():
data = np.array([[-.5, 1., np.nan],
[0., np.nan, -.2],
[1.5, 2.5, 3.]])
assert_raises_regex(ValueError,
'does not accept a "vmin" argument',
_get_colorbar_and_data_ranges,
data, vmax=None,
symmetric_cbar=True, kwargs={'vmin': 1.})
def test_find_parcellation_cut_coords():
data = np.zeros((100, 100, 100))
x_map_a, y_map_a, z_map_a = (10, 10, 10)
x_map_b, y_map_b, z_map_b = (30, 30, 30)
x_map_c, y_map_c, z_map_c = (50, 50, 50)
# Defining 3 parcellations
data[x_map_a - 10:x_map_a + 10, y_map_a - 10:y_map_a + 10, z_map_a - 10: z_map_a + 10] = 1
data[x_map_b - 10:x_map_b + 10, y_map_b - 10:y_map_b + 10, z_map_b - 10: z_map_b + 10] = 2
data[x_map_c - 10:x_map_c + 10, y_map_c - 10:y_map_c + 10, z_map_c - 10: z_map_c + 10] = 3
# Number of labels
labels = np.unique(data)
labels = labels[labels != 0]
n_labels = len(labels)
# identity affine
affine = np.eye(4)
img = nibabel.Nifti1Image(data, affine)
# find coordinates with return label names is True
coords, labels_list = find_parcellation_cut_coords(img,
return_label_names=True)
# Check outputs
assert_equal((n_labels, 3), coords.shape)
# number of labels in data should equal number of labels list returned
assert_equal(n_labels, len(labels_list))
# Labels numbered should match the numbers in returned labels list
assert_equal(list(labels), labels_list)
# Match with the number of non-overlapping labels
np.testing.assert_allclose((coords[0][0], coords[0][1], coords[0][2]),
(x_map_a, y_map_a, z_map_a), rtol=6e-2)
np.testing.assert_allclose((coords[1][0], coords[1][1], coords[1][2]),
(x_map_b, y_map_b, z_map_b), rtol=6e-2)
np.testing.assert_allclose((coords[2][0], coords[2][1], coords[2][2]),
(x_map_c, y_map_c, z_map_c), rtol=6e-2)
# non-trivial affine
affine = np.diag([1 / 2., 1 / 3., 1 / 4., 1.])
img = nibabel.Nifti1Image(data, affine)
coords = find_parcellation_cut_coords(img)
assert_equal((n_labels, 3), coords.shape)
np.testing.assert_allclose((coords[0][0], coords[0][1], coords[0][2]),
(x_map_a / 2., y_map_a / 3., z_map_a / 4.),
rtol=6e-2)
np.testing.assert_allclose((coords[1][0], coords[1][1], coords[1][2]),
(x_map_b / 2., y_map_b / 3., z_map_b / 4.),
rtol=6e-2)
np.testing.assert_allclose((coords[2][0], coords[2][1], coords[2][2]),
(x_map_c / 2., y_map_c / 3., z_map_c / 4.),
rtol=6e-2)
# test raises an error with wrong label_hemisphere name with 'lft'
error_msg = ("Invalid label_hemisphere name:lft. Should be one of "
"these 'left' or 'right'.")
assert_raises_regex(ValueError, error_msg, find_parcellation_cut_coords,
labels_img=img, label_hemisphere='lft')
def test_get_dataset_dir():
# testing folder creation under different environments, enforcing
# a custom clean install
os.environ.pop('NILEARN_DATA', None)
os.environ.pop('NILEARN_SHARED_DATA', None)
expected_base_dir = os.path.expanduser('~/nilearn_data')
data_dir = utils._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_nilearn_data')
os.environ['NILEARN_DATA'] = expected_base_dir
data_dir = utils._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 = utils._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')
expected_dataset_dir = os.path.join(expected_base_dir, 'test')
data_dir = utils._get_dataset_dir(
'test', default_paths=[expected_dataset_dir], 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)
expected_base_dir = os.path.join(tmpdir, 'nilearn_shared_data')
os.environ['NILEARN_SHARED_DATA'] = expected_base_dir
data_dir = utils._get_dataset_dir('test',
default_paths=[no_write],
verbose=0)
# Non writeable dir is returned because dataset may be in there.
assert_equal(data_dir, no_write)
assert os.path.exists(data_dir)
shutil.rmtree(data_dir)
# 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',
utils._get_dataset_dir, 'test', test_file,
verbose=0)
def test_load_surf_data_file_error():
# test if files with unexpected suffixes raise errors
data = np.zeros((20, ))
wrong_suff = ['.vtk', '.obj', '.mnc', '.txt']
for suff in wrong_suff:
filename_wrong = tempfile.mktemp(suffix=suff)
np.savetxt(filename_wrong, data)
assert_raises_regex(ValueError,
'input type is not recognized',
load_surf_data, filename_wrong)
os.remove(filename_wrong)
def test_fail_fetch_atlas_harvard_oxford():
# specify non-existing atlas item
assert_raises_regex(ValueError, 'Invalid atlas name',
atlas.fetch_atlas_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(tst.tmpdir, 'fsl', 'data', 'atlases')
os.makedirs(ho_dir)
nifti_dir = os.path.join(ho_dir, 'HarvardOxford')
os.makedirs(nifti_dir)
target_atlas_nii = os.path.join(nifti_dir, target_atlas_fname)
# Create false atlas
atlas_data = np.zeros((10, 10, 10), dtype=int)
# Create an interhemispheric map
atlas_data[:, :2, :] = 1
# Create a left map
atlas_data[:5, 3:5, :] = 2
# Create a right map, with one voxel on the left side
atlas_data[5:, 7:9, :] = 3
atlas_data[4, 7, 0] = 3
nibabel.Nifti1Image(atlas_data, np.eye(4) * 3).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'?>\n"
"<data>\n"
'<label index="0" x="48" y="94" z="35">R1</label>\n'
'<label index="1" x="25" y="70" z="32">R2</label>\n'
'<label index="2" x="33" y="73" z="63">R3</label>\n'
"</data>")
dummy.close()
ho = atlas.fetch_atlas_harvard_oxford(target_atlas,
data_dir=tst.tmpdir,
symmetric_split=True)
assert_true(isinstance(ho.maps, nibabel.Nifti1Image))
assert_true(isinstance(ho.labels, list))
assert_equal(len(ho.labels), 5)
assert_equal(ho.labels[0], "Background")
assert_equal(ho.labels[1], "R1, left part")
assert_equal(ho.labels[2], "R1, right part")
assert_equal(ho.labels[3], "R2")
assert_equal(ho.labels[4], "R3")
def test_raises_upon_3x3_affine_and_no_shape():
img = Nifti1Image(np.zeros([8, 9, 10]),
affine=np.eye(4))
exception = ValueError
message = ("Given target shape without anchor "
"vector: Affine shape should be \(4, 4\) and "
"not \(3, 3\)")
testing.assert_raises_regex(
exception, message,
resample_img, img, target_affine=np.eye(3) * 2,
target_shape=(10, 10, 10))
def test_multi_pca():
# Smoke test the MultiPCA
# XXX: this is mostly a smoke test
shape = (6, 8, 10, 5)
affine = np.eye(4)
rng = np.random.RandomState(0)
# Create a "multi-subject" dataset
data = []
for i in range(8):
this_data = rng.normal(size=shape)
# Create fake activation to get non empty mask
this_data[2:4, 2:4, 2:4, :] += 10
data.append(nibabel.Nifti1Image(this_data, affine))
mask_img = nibabel.Nifti1Image(np.ones(shape[:3], dtype=np.int8), affine)
multi_pca = MultiPCA(mask=mask_img, n_components=3, random_state=0)
# Test that the components are the same if we put twice the same data, and
# that fit output is deterministic
components1 = multi_pca.fit(data).components_
components2 = multi_pca.fit(data).components_
components3 = multi_pca.fit(2 * data).components_
np.testing.assert_array_equal(components1, components2)
np.testing.assert_array_almost_equal(components1, components3)
# Smoke test fit with 'confounds' argument
confounds = [np.arange(10).reshape(5, 2)] * 8
multi_pca.fit(data, confounds=confounds)
# Smoke test that multi_pca also works with single subject data
multi_pca.fit(data[0])
# Check that asking for too little components raises a ValueError
multi_pca = MultiPCA()
assert_raises(ValueError, multi_pca.fit, data[:2])
# Smoke test the use of a masker and without CCA
multi_pca = MultiPCA(mask=MultiNiftiMasker(mask_args=dict(opening=0)),
do_cca=False,
n_components=3)
multi_pca.fit(data[:2])
# Smoke test the transform and inverse_transform
multi_pca.inverse_transform(multi_pca.transform(data[-2:]))
# Smoke test to fit with no img
assert_raises(TypeError, multi_pca.fit)
multi_pca = MultiPCA(mask=mask_img, n_components=3)
assert_raises_regex(
ValueError, "Object has no components_ attribute. "
"This is probably because fit has not been called",
multi_pca.transform, data)
def test_plot_surf_roi_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi_idx = rng.randint(0, mesh[0].shape[0], size=5)
# Wrong input
assert_raises_regex(ValueError,
'roi_map does not have the same number of vertices',
plot_surf_roi,
mesh,
roi_map=roi_idx)
def test_invalid_thresholds_in_threshold_maps_ratio():
maps, _ = generate_maps((10, 11, 12), n_regions=2)
for invalid_threshold in ['80%', 'auto', -1.0]:
assert_raises_regex(ValueError,
"threshold given as ratio to the number of voxels must "
"be Real number and should be positive and between 0 and "
"total number of maps i.e. n_maps={0}. "
"You provided {1}".format(maps.shape[-1], invalid_threshold),
_threshold_maps_ratio,
maps, threshold=invalid_threshold)
def test_threshold_as_none_and_string_cases():
maps, _ = generate_maps((6, 8, 10), n_regions=1)
extract_thr_none_check = RegionExtractor(maps, threshold=None)
assert_raises_regex(ValueError,
"The given input to threshold is not valid.",
extract_thr_none_check.fit)
extract_thr_string_check = RegionExtractor(maps, threshold='30%')
assert_raises_regex(ValueError,
"The given input to threshold is not valid.",
extract_thr_string_check.fit)
def test_get_colorbar_and_data_ranges_with_vmin():
affine = np.eye(4)
data = np.array([[-.5, 1., np.nan], [0., np.nan, -.2], [1.5, 2.5, 3.]])
img = nibabel.Nifti1Image(data, affine)
assert_raises_regex(ValueError,
'does not accept a "vmin" argument',
_get_colorbar_and_data_ranges,
img,
vmax=None,
symmetric_cbar=True,
kwargs={'vmin': 1.})
def test_targets_in_y_space_net_regressor():
# This tests whether raises an error when unique targets given in y
# are single.
iris = load_iris()
X, _ = iris.data, iris.target
y = np.ones((iris.target.shape))
imgs, mask = to_niimgs(X, (2, 2, 2))
regressor = SpaceNetRegressor(mask=mask)
assert_raises_regex(ValueError,
"The given input y must have atleast 2 targets",
regressor.fit, imgs, y)
def test_invalids_extract_types_in_connected_regions():
maps, _ = generate_maps((10, 11, 12), n_regions=2)
valid_names = ['connected_components', 'local_regions']
# test whether same error raises as expected when invalid inputs
# are given to extract_type in connected_regions function
message = ("'extract_type' should be {0}")
for invalid_extract_type in ['connect_region', 'local_regios']:
assert_raises_regex(ValueError,
message.format(valid_names),
connected_regions,
maps, extract_type=invalid_extract_type)
def test_load_surf_mesh_file_error():
if LooseVersion(nb.__version__) <= LooseVersion('1.2.0'):
raise SkipTest
# test if files with unexpected suffixes raise errors
mesh = _generate_surf()
wrong_suff = ['.vtk', '.obj', '.mnc', '.txt']
for suff in wrong_suff:
filename_wrong = tempfile.mktemp(suffix=suff)
nb.freesurfer.write_geometry(filename_wrong, mesh[0], mesh[1])
assert_raises_regex(ValueError, 'input type is not recognized',
load_surf_data, filename_wrong)
os.remove(filename_wrong)
def test_filter_and_mask():
data = np.zeros([20, 30, 40, 5])
mask = np.zeros([20, 30, 40, 2])
mask[10, 15, 20, :] = 1
data_img = nibabel.Nifti1Image(data, np.eye(4))
mask_img = nibabel.Nifti1Image(mask, np.eye(4))
masker = NiftiMasker()
params = get_params(NiftiMasker, masker)
assert_raises_regex(DimensionError, "Data must be a 3D", filter_and_mask,
data_img, mask_img, params)
def test_coregister():
anat_file = os.path.join(os.path.dirname(testing_data.__file__),
'anat.nii.gz')
func_file = os.path.join(os.path.dirname(testing_data.__file__),
'func.nii.gz')
mean_func_file = os.path.join(tst.tmpdir, 'mean_func.nii.gz')
mean_img(func_file).to_filename(mean_func_file)
bunch = func.coregister(anat_file,
mean_func_file,
tst.tmpdir,
slice_timing=False,
verbose=False,
reorient_only=True)
assert_true(
_check_same_fov(nibabel.load(bunch.coreg_func_),
nibabel.load(bunch.coreg_anat_)))
assert_true(_check_same_obliquity(bunch.coreg_anat_, bunch.coreg_func_))
assert_true(os.path.isfile(bunch.coreg_transform_))
assert_less(0, len(bunch.coreg_warps_))
assert_true(bunch.coreg_warps_[-1] is None) # Last slice in functional
# is without signal
for warp_file in bunch.coreg_warps_[:-1]:
assert_true(os.path.isfile(warp_file))
# Check environement variables setting
assert_raises_regex(RuntimeError,
"3dcopy",
func.coregister,
anat_file,
mean_func_file,
tst.tmpdir,
slice_timing=False,
verbose=False,
reorient_only=True,
AFNI_DECONFLICT='NO')
# Check caching does not change the paths
bunch2 = func.coregister(anat_file,
mean_func_file,
tst.tmpdir,
slice_timing=False,
verbose=False,
caching=True,
reorient_only=True,
AFNI_DECONFLICT='OVERWRITE')
assert_equal(bunch.coreg_func_, bunch2.coreg_func_)
assert_equal(bunch.coreg_anat_, bunch2.coreg_anat_)
assert_equal(bunch.coreg_transform_, bunch2.coreg_transform_)
for warp_file, warp_file2 in zip(bunch.coreg_warps_, bunch2.coreg_warps_):
assert_equal(warp_file, warp_file2)
def test_resampling_error_checks():
shape = (3, 2, 5, 2)
target_shape = (5, 3, 2)
affine = np.eye(4)
data = np.random.randint(0, 10, shape)
img = Nifti1Image(data, affine)
# Correct parameters: no exception
resample_img(img, target_shape=target_shape, target_affine=affine)
resample_img(img, target_affine=affine)
with testing.write_tmp_imgs(img) as filename:
resample_img(filename, target_shape=target_shape, target_affine=affine)
# Missing parameter
assert_raises(ValueError, resample_img, img, target_shape=target_shape)
# Invalid shape
assert_raises(ValueError, resample_img, img, target_shape=(2, 3),
target_affine=affine)
# Invalid interpolation
interpolation = 'an_invalid_interpolation'
pattern = "interpolation must be either.+{0}".format(interpolation)
testing.assert_raises_regex(ValueError, pattern,
resample_img, img, target_shape=target_shape,
target_affine=affine,
interpolation="an_invalid_interpolation")
# Noop
target_shape = shape[:3]
img_r = resample_img(img, copy=False)
assert_equal(img_r, img)
img_r = resample_img(img, copy=True)
assert_false(np.may_share_memory(img_r.get_data(), img.get_data()))
np.testing.assert_almost_equal(img_r.get_data(), img.get_data())
np.testing.assert_almost_equal(img_r.affine, img.affine)
img_r = resample_img(img, target_affine=affine, target_shape=target_shape,
copy=False)
assert_equal(img_r, img)
img_r = resample_img(img, target_affine=affine, target_shape=target_shape,
copy=True)
assert_false(np.may_share_memory(img_r.get_data(), img.get_data()))
np.testing.assert_almost_equal(img_r.get_data(), img.get_data())
np.testing.assert_almost_equal(img_r.affine, img.affine)
def test_error_messages_connected_label_regions():
shape = (13, 11, 12)
affine = np.eye(4)
n_regions = 2
labels_img = testing.generate_labeled_regions(shape, affine=affine,
n_regions=n_regions)
assert_raises_regex(ValueError,
"Expected 'min_size' to be specified as integer.",
connected_label_regions,
labels_img=labels_img, min_size='a')
assert_raises_regex(ValueError,
"'connect_diag' must be specified as True or False.",
connected_label_regions,
labels_img=labels_img, connect_diag=None)
def test_check_niimg_3d():
# check error for non-forced but necessary resampling
assert_raises_regex(TypeError, 'nibabel format', _utils.check_niimg, 0)
# check error for non-forced but necessary resampling
assert_raises_regex(TypeError, 'empty object', _utils.check_niimg, [])
# Check that a filename does not raise an error
data = np.zeros((40, 40, 40, 1))
data[20, 20, 20] = 1
data_img = Nifti1Image(data, np.eye(4))
with testing.write_tmp_imgs(data_img, create_files=True) as filename:
_utils.check_niimg_3d(filename)
def test_concat_niimgs():
# create images different in affine and 3D/4D shape
shape = (10, 11, 12)
affine = np.eye(4)
img1 = Nifti1Image(np.ones(shape), affine)
img2 = Nifti1Image(np.ones(shape), 2 * affine)
img3 = Nifti1Image(np.zeros(shape), affine)
img4d = Nifti1Image(np.ones(shape + (2, )), affine)
shape2 = (12, 11, 10)
img1b = Nifti1Image(np.ones(shape2), affine)
shape3 = (11, 22, 33)
img1c = Nifti1Image(np.ones(shape3), affine)
# Regression test for #601. Dimensionality of first image was not checked
# properly
_dimension_error_msg = ("Input data has incompatible dimensionality: "
"Expected dimension is 4D and you provided "
"a list of 4D images \(5D\)")
assert_raises_regex(DimensionError,
_dimension_error_msg,
_utils.concat_niimgs, [img4d],
ensure_ndim=4)
# check basic concatenation with equal shape/affine
concatenated = _utils.concat_niimgs((img1, img3, img1))
assert_raises_regex(DimensionError, _dimension_error_msg,
_utils.concat_niimgs, [img1, img4d])
# smoke-test auto_resample
concatenated = _utils.concat_niimgs((img1, img1b, img1c),
auto_resample=True)
assert_true(concatenated.shape == img1.shape + (3, ))
# check error for non-forced but necessary resampling
assert_raises_regex(ValueError,
'Field of view of image',
_utils.concat_niimgs, [img1, img2],
auto_resample=False)
# test list of 4D niimgs as input
tmpimg1 = tempfile.mktemp(suffix='.nii')
tmpimg2 = tempfile.mktemp(suffix='.nii')
try:
nibabel.save(img1, tmpimg1)
nibabel.save(img3, tmpimg2)
concatenated = _utils.concat_niimgs([tmpimg1, tmpimg2])
assert_array_equal(concatenated.get_data()[..., 0], img1.get_data())
assert_array_equal(concatenated.get_data()[..., 1], img3.get_data())
finally:
_remove_if_exists(tmpimg1)
_remove_if_exists(tmpimg2)
img5d = Nifti1Image(np.ones((2, 2, 2, 2, 2)), affine)
assert_raises_regex(
TypeError, 'Concatenated images must be 3D or 4D. '
'You gave a list of 5D images', _utils.concat_niimgs, [img5d, img5d])
def test_validity_of_ncuts_error_in_find_cut_slices():
data = np.zeros((50, 50, 50))
affine = np.eye(4)
x_map, y_map, z_map = 25, 5, 20
data[x_map - 15:x_map + 15, y_map - 3:y_map + 3, z_map - 10:z_map + 10] = 1
img = nibabel.Nifti1Image(data, affine)
direction = 'z'
for n_cuts in (0, -2, -10.00034, 0.999999, 0.4, 0.11111111):
message = ("Image has %d slices in direction %s. Therefore, the number "
"of cuts must be between 1 and %d. You provided n_cuts=%s " % (
data.shape[0], direction, data.shape[0], n_cuts))
assert_raises_regex(ValueError,
message,
find_cut_slices,
img, n_cuts=n_cuts)
def test_plot_surf_roi_error():
mesh = _generate_surf()
rng = np.random.RandomState(0)
roi1 = rng.randint(0, mesh[0].shape[0], size=5)
roi2 = rng.randint(0, mesh[0].shape[0], size=10)
# Wrong input
assert_raises_regex(ValueError,
'Invalid input for roi_map',
plot_surf_roi,
mesh,
roi_map={
'roi1': roi1,
'roi2': roi2
})
def test_filter_and_mask_error():
data = np.zeros([20, 30, 40, 5])
mask = np.zeros([20, 30, 40, 2])
mask[10, 15, 20, :] = 1
data_img = nibabel.Nifti1Image(data, np.eye(4))
mask_img = nibabel.Nifti1Image(mask, np.eye(4))
masker = NiftiMasker()
params = get_params(NiftiMasker, masker)
assert_raises_regex(
DimensionError, "Input data has incompatible dimensionality: "
"Expected dimension is 3D and you provided "
"a 4D image.", filter_and_mask, data_img, mask_img, params)
def test_iter_img():
img_3d = nibabel.Nifti1Image(np.ones((3, 4, 5)), np.eye(4))
testing.assert_raises_regex(TypeError,
"Input data has incompatible dimensionality: "
"Expected dimension is 4D and you provided "
"a 3D image.",
image.iter_img, img_3d)
affine = np.array([[1., 2., 3., 4.],
[5., 6., 7., 8.],
[9., 10., 11., 12.],
[0., 0., 0., 1.]])
img_4d, _ = testing.generate_fake_fmri(affine=affine)
for i, img in enumerate(image.iter_img(img_4d)):
expected_data_3d = img_4d.get_data()[..., i]
assert_array_equal(img.get_data(),
expected_data_3d)
assert_array_equal(compat.get_affine(img),
compat.get_affine(img_4d))
with testing.write_tmp_imgs(img_4d) as img_4d_filename:
for i, img in enumerate(image.iter_img(img_4d_filename)):
expected_data_3d = img_4d.get_data()[..., i]
assert_array_equal(img.get_data(),
expected_data_3d)
assert_array_equal(compat.get_affine(img),
compat.get_affine(img_4d))
# enables to delete "img_4d_filename" on windows
del img
img_3d_list = list(image.iter_img(img_4d))
for i, img in enumerate(image.iter_img(img_3d_list)):
expected_data_3d = img_4d.get_data()[..., i]
assert_array_equal(img.get_data(),
expected_data_3d)
assert_array_equal(compat.get_affine(img),
compat.get_affine(img_4d))
with testing.write_tmp_imgs(*img_3d_list) as img_3d_filenames:
for i, img in enumerate(image.iter_img(img_3d_filenames)):
expected_data_3d = img_4d.get_data()[..., i]
assert_array_equal(img.get_data(),
expected_data_3d)
assert_array_equal(compat.get_affine(img),
compat.get_affine(img_4d))
# enables to delete "img_3d_filename" on windows
del img
def test_validity_threshold_value_in_threshold_img():
shape = (6, 8, 10)
maps, _ = testing.generate_maps(shape, n_regions=2)
# testing to raise same error when threshold=None case
testing.assert_raises_regex(ValueError,
"The input parameter 'threshold' is empty. ",
threshold_img, maps, threshold=None)
invalid_threshold_values = ['90t%', 's%', 't', '0.1']
name = 'threshold'
for thr in invalid_threshold_values:
testing.assert_raises_regex(ValueError,
'{0}.+should be a number followed by '
'the percent sign'.format(name),
threshold_img, maps, threshold=thr)
def test_5d():
mask = np.zeros((10, 10, 10))
mask[3:7, 3:7, 3:7] = 1
mask_img = Nifti1Image(mask, np.eye(4))
# Test that, in list of 4d images with last dimension=1, they are
# considered as 3d
data_5d = [np.random.random((10, 10, 10, 3)) for i in range(5)]
data_5d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_5d]
masker = NiftiMasker(mask_img=mask_img)
masker.fit()
testing.assert_raises_regex(
DimensionError, 'Data must be a 4D Niimg-like object but you provided'
' a list of 4D images.', masker.transform, data_5d)
def test_3d_images():
# Test that the MultiNiftiMasker works with 3D images
mask_img = Nifti1Image(np.ones((2, 2, 2), dtype=np.int8),
affine=np.diag((4, 4, 4, 1)))
epi_img1 = Nifti1Image(np.ones((2, 2, 2)), affine=np.diag((4, 4, 4, 1)))
epi_img2 = Nifti1Image(np.ones((2, 2, 2)), affine=np.diag((2, 2, 2, 1)))
masker = MultiNiftiMasker(mask_img=mask_img)
epis = masker.fit_transform([epi_img1, epi_img2])
# This is mostly a smoke test
assert_equal(len(epis), 2)
# verify that 4D mask arguments are refused
mask_img_4d = Nifti1Image(np.ones((2, 2, 2, 2), dtype=np.int8),
affine=np.diag((4, 4, 4, 1)))
masker2 = MultiNiftiMasker(mask_img=mask_img_4d)
assert_raises_regex(DimensionError, "Data must be a 3D", masker2.fit)