def get_FS_from_paths(path_list, masker):
print "Loading first-level images from subjects data..."
l = []
niis = check_niimgs(path_list)
data4d = niis.get_data()
for iimg in range(data4d.shape[3]):
masked = masker.transform(
nib.Nifti1Image(data4d[..., iimg], niis.get_affine()))[0]
l.append(masked)
FS_org = np.asarray(l)
return FS_org
def test_check_niimgs():
assert_raises(TypeError, _utils.check_niimgs, 0)
affine = np.eye(4)
niimg = Nifti1Image(np.ones((10, 10, 10)), affine)
_utils.check_niimgs([niimg, niimg])
# This should raise an error: a 3D niimg is given and we want a 4D
assert_raises(TypeError, _utils.check_niimgs, niimg)
# This shouldn't raise an error
_utils.check_niimgs(niimg, accept_3d=True)
# Test a Niimage that does not hold a shape attribute
phony_niimg = PhonyNiimage()
_utils.check_niimgs(phony_niimg)
def test_check_niimgs():
assert_raises(TypeError, _utils.check_niimgs, 0)
assert_raises(TypeError, _utils.check_niimgs, [])
affine = np.eye(4)
niimg = Nifti1Image(np.ones((10, 10, 10)), affine)
_utils.check_niimgs([niimg, niimg])
# This should raise an error: a 3D niimg is given and we want a 4D
assert_raises(TypeError, _utils.check_niimgs, niimg)
# This shouldn't raise an error
_utils.check_niimgs(niimg, accept_3d=True)
# Test a Niimage that does not hold a shape attribute
phony_niimg = PhonyNiimage()
_utils.check_niimgs(phony_niimg)
def test_check_niimgs():
assert_raises_regexp(TypeError, 'image', _utils.check_niimgs, 0)
assert_raises_regexp(TypeError, 'image', _utils.check_niimgs, [])
affine = np.eye(4)
img_3d = Nifti1Image(np.ones((10, 10, 10)), affine)
# Tests with return_iterator=False
img_4d_1 = _utils.check_niimgs([img_3d, img_3d])
assert_true(img_4d_1.get_data().shape == (10, 10, 10, 2))
assert_array_equal(img_4d_1.get_affine(), affine)
img_4d_2 = _utils.check_niimgs(img_4d_1)
assert_array_equal(img_4d_2.get_data(), img_4d_2.get_data())
assert_array_equal(img_4d_2.get_affine(), img_4d_2.get_affine())
# Tests with return_iterator=True
img_3d_iterator = _utils.check_niimgs([img_3d, img_3d],
return_iterator=True)
img_3d_iterator_length = sum(1 for _ in img_3d_iterator)
assert_true(img_3d_iterator_length == 2)
img_3d_iterator_1 = _utils.check_niimgs([img_3d, img_3d],
return_iterator=True)
img_3d_iterator_2 = _utils.check_niimgs(img_3d_iterator_1,
return_iterator=True)
for img_1, img_2 in itertools.izip(img_3d_iterator_1, img_3d_iterator_2):
assert_true(img_1.get_data().shape == (10, 10, 10))
assert_array_equal(img_1.get_data(), img_2.get_data())
assert_array_equal(img_1.get_affine(), img_2.get_affine())
img_3d_iterator_1 = _utils.check_niimgs([img_3d, img_3d],
return_iterator=True)
img_3d_iterator_2 = _utils.check_niimgs(img_4d_1, return_iterator=True)
for img_1, img_2 in itertools.izip(img_3d_iterator_1, img_3d_iterator_2):
assert_true(img_1.get_data().shape == (10, 10, 10))
assert_array_equal(img_1.get_data(), img_2.get_data())
assert_array_equal(img_1.get_affine(), img_2.get_affine())
# This should raise an error: a 3D img is given and we want a 4D
assert_raises_regexp(TypeError, 'image', _utils.check_niimgs, img_3d)
# This shouldn't raise an error
_utils.check_niimgs(img_3d, accept_3d=True)
# Test a Niimage that does not hold a shape attribute
phony_img = PhonyNiimage()
_utils.check_niimgs(phony_img)
def test_check_niimgs():
with assert_raises(TypeError) as cm:
_utils.check_niimgs(0)
assert_true('image' in cm.exception.message
or 'affine' in cm.exception.message)
with assert_raises(TypeError) as cm:
_utils.check_niimgs([])
assert_true('image' in cm.exception.message
or 'affine' in cm.exception.message)
affine = np.eye(4)
niimg = Nifti1Image(np.ones((10, 10, 10)), affine)
_utils.check_niimgs([niimg, niimg])
with assert_raises(TypeError) as cm:
# This should raise an error: a 3D niimg is given and we want a 4D
_utils.check_niimgs(niimg)
assert_true('image' in cm.exception.message)
# This shouldn't raise an error
_utils.check_niimgs(niimg, accept_3d=True)
# Test a Niimage that does not hold a shape attribute
phony_niimg = PhonyNiimage()
_utils.check_niimgs(phony_niimg)
def test_check_niimgs():
with assert_raises(TypeError) as cm:
_utils.check_niimgs(0)
assert_true('image' in cm.exception.message
or 'affine' in cm.exception.message)
with assert_raises(TypeError) as cm:
_utils.check_niimgs([])
assert_true('image' in cm.exception.message
or 'affine' in cm.exception.message)
affine = np.eye(4)
niimg = Nifti1Image(np.ones((10, 10, 10)), affine)
_utils.check_niimgs([niimg, niimg])
with assert_raises(TypeError) as cm:
# This should raise an error: a 3D niimg is given and we want a 4D
_utils.check_niimgs(niimg)
assert_true('image' in cm.exception.message)
# This shouldn't raise an error
_utils.check_niimgs(niimg, accept_3d=True)
# Test a Niimage that does not hold a shape attribute
phony_niimg = PhonyNiimage()
_utils.check_niimgs(phony_niimg)
def test_check_niimgs():
assert_raises_regexp(TypeError, 'image',
_utils.check_niimgs, 0)
assert_raises_regexp(TypeError, 'image',
_utils.check_niimgs, [])
affine = np.eye(4)
img_3d = Nifti1Image(np.ones((10, 10, 10)), affine)
# Tests with return_iterator=False
img_4d_1 = _utils.check_niimgs([img_3d, img_3d])
assert_true(img_4d_1.get_data().shape == (10, 10, 10, 2))
assert_array_equal(img_4d_1.get_affine(), affine)
img_4d_2 = _utils.check_niimgs(img_4d_1)
assert_array_equal(img_4d_2.get_data(), img_4d_2.get_data())
assert_array_equal(img_4d_2.get_affine(), img_4d_2.get_affine())
# Tests with return_iterator=True
img_3d_iterator = _utils.check_niimgs([img_3d, img_3d],
return_iterator=True)
img_3d_iterator_length = sum(1 for _ in img_3d_iterator)
assert_true(img_3d_iterator_length == 2)
img_3d_iterator_1 = _utils.check_niimgs([img_3d, img_3d],
return_iterator=True)
img_3d_iterator_2 = _utils.check_niimgs(img_3d_iterator_1,
return_iterator=True)
for img_1, img_2 in itertools.izip(img_3d_iterator_1, img_3d_iterator_2):
assert_true(img_1.get_data().shape == (10, 10, 10))
assert_array_equal(img_1.get_data(), img_2.get_data())
assert_array_equal(img_1.get_affine(), img_2.get_affine())
img_3d_iterator_1 = _utils.check_niimgs([img_3d, img_3d],
return_iterator=True)
img_3d_iterator_2 = _utils.check_niimgs(img_4d_1,
return_iterator=True)
for img_1, img_2 in itertools.izip(img_3d_iterator_1, img_3d_iterator_2):
assert_true(img_1.get_data().shape == (10, 10, 10))
assert_array_equal(img_1.get_data(), img_2.get_data())
assert_array_equal(img_1.get_affine(), img_2.get_affine())
# This should raise an error: a 3D img is given and we want a 4D
assert_raises_regexp(TypeError, 'image',
_utils.check_niimgs, img_3d)
# This shouldn't raise an error
_utils.check_niimgs(img_3d, accept_3d=True)
# Test a Niimage that does not hold a shape attribute
phony_img = PhonyNiimage()
_utils.check_niimgs(phony_img)
