def test_joblib_cache():
if not LooseVersion(nibabel.__version__) > LooseVersion('1.1.0'):
# Old nibabel do not pickle
raise SkipTest
from sklearn.externals.joblib import hash, Memory
mask = np.zeros((40, 40, 40))
mask[20, 20, 20] = 1
mask_img = Nifti1Image(mask, np.eye(4))
with testing.write_tmp_imgs(mask_img, create_files=True)\
as filename:
masker = NiftiMasker(mask_img=filename)
masker.fit()
mask_hash = hash(masker.mask_img_)
masker.mask_img_.get_data()
assert_true(mask_hash == hash(masker.mask_img_))
# Test a tricky issue with memmapped joblib.memory that makes
# imgs return by inverse_transform impossible to save
cachedir = mkdtemp()
try:
masker.memory = Memory(cachedir=cachedir, mmap_mode='r',
verbose=0)
X = masker.transform(mask_img)
# inverse_transform a first time, so that the result is cached
out_img = masker.inverse_transform(X)
out_img = masker.inverse_transform(X)
out_img.to_filename(os.path.join(cachedir, 'test.nii'))
finally:
shutil.rmtree(cachedir, ignore_errors=True)
def test_mask_4d():
# Dummy mask
mask = np.zeros((10, 10, 10), dtype=int)
mask[3:7, 3:7, 3:7] = 1
mask_bool = mask.astype(bool)
mask_img = Nifti1Image(mask, np.eye(4))
# Dummy data
data = np.zeros((10, 10, 10, 3), dtype=int)
data[..., 0] = 1
data[..., 1] = 2
data[..., 2] = 3
data_img_4d = Nifti1Image(data, np.eye(4))
data_imgs = [index_img(data_img_4d, 0), index_img(data_img_4d, 1),
index_img(data_img_4d, 2)]
# check whether transform is indeed selecting niimgs subset
sample_mask = np.array([0, 2])
masker = NiftiMasker(mask_img=mask_img, sample_mask=sample_mask)
masker.fit()
data_trans = masker.transform(data_imgs)
data_trans_img = index_img(data_img_4d, sample_mask)
data_trans_direct = data_trans_img.get_data()[mask_bool, :]
data_trans_direct = np.swapaxes(data_trans_direct, 0, 1)
assert_array_equal(data_trans, data_trans_direct)
masker = NiftiMasker(mask_img=mask_img, sample_mask=sample_mask)
masker.fit()
data_trans2 = masker.transform(data_img_4d)
assert_array_equal(data_trans2, data_trans_direct)
def test_with_files():
# Standard masking
data = np.zeros((40, 40, 40, 2))
data[20, 20, 20] = 1
data_img = Nifti1Image(data, np.eye(4))
with testing.write_tmp_imgs(data_img) as filename:
masker = NiftiMasker()
masker.fit(filename)
masker.transform(filename)
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_4d_single_scan():
mask = np.zeros((10, 10, 10))
mask[3:7, 3:7, 3:7] = 1
mask_img = Nifti1Image(mask, np.eye(4))
data_5d = [np.random.random((10, 10, 10, 1)) for i in range(5)]
data_4d = [d[..., 0] for d in data_5d]
data_5d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_5d]
data_4d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_4d]
masker = NiftiMasker(mask_img=mask_img)
masker.fit()
data_trans_5d = masker.transform(data_5d)
data_trans_4d = masker.transform(data_4d)
assert_array_equal(data_trans_4d, data_trans_5d)
def test_auto_mask():
# This mostly a smoke test
data = np.zeros((9, 9, 9))
data[3:-3, 3:-3, 3:-3] = 10
img = Nifti1Image(data, np.eye(4))
masker = NiftiMasker()
# Smoke test the fit
masker.fit(img)
# Smoke test the transform
# With a 4D img
masker.transform([img, ])
# With a 3D img
masker.transform(img)
# check exception when transform() called without prior fit()
masker2 = NiftiMasker(mask_img=img)
testing.assert_raises_regex(
ValueError,
'has not been fitted. ', masker2.transform, img)
def test_4d_single_scan():
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, 1)) for i in range(5)]
data_4d = [d[..., 0] for d in data_5d]
data_5d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_5d]
data_4d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_4d]
masker = NiftiMasker(mask_img=mask_img)
masker.fit()
data_trans_5d = masker.transform(data_5d)
data_trans_4d = masker.transform(data_4d)
assert_array_equal(data_trans_4d, data_trans_5d)
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,
"Input data has incompatible dimensionality: "
"Expected dimension is 4D and you provided "
"a list of 4D images \(5D\).",
masker.transform, data_5d)
def test_nan():
data = np.ones((9, 9, 9))
data[0] = np.nan
data[:, 0] = np.nan
data[:, :, 0] = np.nan
data[-1] = np.nan
data[:, -1] = np.nan
data[:, :, -1] = np.nan
data[3:-3, 3:-3, 3:-3] = 10
img = Nifti1Image(data, np.eye(4))
masker = NiftiMasker(mask_args=dict(opening=0))
masker.fit(img)
mask = masker.mask_img_.get_data()
assert_true(mask[1:-1, 1:-1, 1:-1].all())
assert_false(mask[0].any())
assert_false(mask[:, 0].any())
assert_false(mask[:, :, 0].any())
assert_false(mask[-1].any())
assert_false(mask[:, -1].any())
assert_false(mask[:, :, -1].any())
def test_matrix_orientation():
"""Test if processing is performed along the correct axis."""
# the "step" kind generate heavyside-like signals for each voxel.
# all signals being identical, standardizing along the wrong axis
# would leave a null signal. Along the correct axis, the step remains.
fmri, mask = testing.generate_fake_fmri(shape=(40, 41, 42), kind="step")
masker = NiftiMasker(mask_img=mask, standardize=True, detrend=True)
timeseries = masker.fit_transform(fmri)
assert(timeseries.shape[0] == fmri.shape[3])
assert(timeseries.shape[1] == mask.get_data().sum())
std = timeseries.std(axis=0)
assert(std.shape[0] == timeseries.shape[1]) # paranoid
assert(not np.any(std < 0.1))
# Test inverse transform
masker = NiftiMasker(mask_img=mask, standardize=False, detrend=False)
masker.fit()
timeseries = masker.transform(fmri)
recovered = masker.inverse_transform(timeseries)
np.testing.assert_array_almost_equal(recovered.get_data(), fmri.get_data())
def test_compute_gray_matter_mask():
# Check masker for template masking strategy
img = np.random.rand(9, 9, 5)
img = Nifti1Image(img, np.eye(4))
masker = NiftiMasker(mask_strategy='template')
masker.fit(img)
mask1 = masker.mask_img_
masker2 = NiftiMasker(mask_strategy='template',
mask_args=dict(threshold=0.))
masker2.fit(img)
mask2 = masker2.mask_img_
mask_ref = np.zeros((9, 9, 5))
mask_ref[2:7, 2:7, 2] = 1
np.testing.assert_array_equal(mask1.get_data(), mask_ref)
np.testing.assert_array_equal(mask2.get_data(), mask_ref)
def test_compute_epi_mask():
# Taken from test_masking.py, but used to test that the masker class
# is passing parameters appropriately.
mean_image = np.ones((9, 9, 3))
mean_image[3:-2, 3:-2, :] = 10
mean_image[5, 5, :] = 11
mean_image = Nifti1Image(mean_image.astype(float), np.eye(4))
masker = NiftiMasker(mask_strategy='epi',
mask_args=dict(opening=False))
masker.fit(mean_image)
mask1 = masker.mask_img_
masker2 = NiftiMasker(mask_strategy='epi',
mask_args=dict(opening=False, exclude_zeros=True))
masker2.fit(mean_image)
mask2 = masker2.mask_img_
# With an array with no zeros, exclude_zeros should not make
# any difference
np.testing.assert_array_equal(mask1.get_data(), mask2.get_data())
# Check that padding with zeros does not change the extracted mask
mean_image2 = np.zeros((30, 30, 3))
mean_image2[3:12, 3:12, :] = mean_image.get_data()
mean_image2 = Nifti1Image(mean_image2, np.eye(4))
masker3 = NiftiMasker(mask_strategy='epi',
mask_args=dict(opening=False, exclude_zeros=True))
masker3.fit(mean_image2)
mask3 = masker3.mask_img_
np.testing.assert_array_equal(mask1.get_data(),
mask3.get_data()[3:12, 3:12])
# However, without exclude_zeros, it does
masker4 = NiftiMasker(mask_strategy='epi', mask_args=dict(opening=False))
masker4.fit(mean_image2)
mask4 = masker4.mask_img_
assert_false(np.allclose(mask1.get_data(),
mask4.get_data()[3:12, 3:12]))
def test_compute_epi_mask():
# Taken from test_masking.py, but used to test that the masker class
# is passing parameters appropriately.
mean_image = np.ones((9, 9, 3))
mean_image[3:-2, 3:-2, :] = 10
mean_image[5, 5, :] = 11
mean_image = Nifti1Image(mean_image.astype(float), np.eye(4))
masker = NiftiMasker(mask_strategy='epi', mask_args=dict(opening=False))
masker.fit(mean_image)
mask1 = masker.mask_img_
masker2 = NiftiMasker(mask_strategy='epi',
mask_args=dict(opening=False, exclude_zeros=True))
masker2.fit(mean_image)
mask2 = masker2.mask_img_
# With an array with no zeros, exclude_zeros should not make
# any difference
np.testing.assert_array_equal(mask1.get_data(), mask2.get_data())
# Check that padding with zeros does not change the extracted mask
mean_image2 = np.zeros((30, 30, 3))
mean_image2[3:12, 3:12, :] = mean_image.get_data()
mean_image2 = Nifti1Image(mean_image2, np.eye(4))
masker3 = NiftiMasker(mask_strategy='epi',
mask_args=dict(opening=False, exclude_zeros=True))
masker3.fit(mean_image2)
mask3 = masker3.mask_img_
np.testing.assert_array_equal(mask1.get_data(),
mask3.get_data()[3:12, 3:12])
# However, without exclude_zeros, it does
masker4 = NiftiMasker(mask_strategy='epi', mask_args=dict(opening=False))
masker4.fit(mean_image2)
mask4 = masker4.mask_img_
assert_false(np.allclose(mask1.get_data(), mask4.get_data()[3:12, 3:12]))
def test_mask_init_errors():
# Errors that are caught in init
mask = NiftiMasker(mask_strategy='oops')
with pytest.raises(ValueError,
match="Unknown value of mask_strategy 'oops'"):
mask.fit()
def test_compute_brain_mask(strategy, mask_args, expected_mask):
# Check masker for template masking strategy
img = _get_random_img((9, 9, 5))
masker = NiftiMasker(mask_strategy=strategy, mask_args=mask_args)
masker.fit(img)
np.testing.assert_array_equal(get_data(masker.mask_img_), expected_mask)
