def test_image_to_file(self):
for img_path in self.img_paths:
img = ants.image_read(img_path)
new_path = img_path.replace('.nii.gz', '_write.nii.gz')
img.to_file(new_path)
new_img = ants.image_read(new_path)
self.assertEqual(img.pixeltype, new_img.pixeltype)
self.assertEqual(img.dimension, new_img.dimension)
self.assertEqual(img.components, new_img.components)
self.assertEqual(img.spacing, new_img.spacing)
self.assertEqual(img.origin, new_img.origin)
nptest.assertEqual(img.direction, new_img.direction)
nptest.assert_allclose(img.numpy(), new_img.numpy())
def setUp(self):
self.datadir = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data')
img_paths = []
for dtype in ['CHAR', 'DOUBLE', 'FLOAT', 'INT', 'SHORT',
'UNSIGNEDCHAR', 'UNSIGNEDINT', 'UNSIGNEDSHORT']:
for dim in [2,3]:
img_paths.append('image_%s_%iD.nii.gz' % (dtype, dim))
self.img_paths = [os.path.join(self.datadir, img_path) for img_path in img_paths]
self.imgs = [ants.image_read(ip) for ip in self.img_paths]
def test_image_read_then_to_numpy_WrapITK_equality(self):
"""
Test that reading an image then converting it to numpy
is the same in ANTsPy and the python version of ITK
"""
for img_path in self.img_paths:
# my itk doesnt wrap integer or unsigned integer...
if 'INT' not in img_path:
ants_array = ants.image_read(img_path).numpy()
itk_array = itk.GetArrayViewFromImage(itk.imread(img_path))
self.assertEqual(ants_array.sum(), itk_array.sum())
self.assertEqual(ants_array.dtype, itk_array.dtype)
def test_image_read(self):
"""
reading images from file
"""
for img_path in self.img_paths:
img = ants.image_read(img_path)
ptype = _parse_pixeltype_from_string(img_path)
dim = _parse_dim_from_string(img_path)
self.assertEqual(img.pixeltype, ptype)
self.assertEqual(img.dimension, dim)
self.assertEqual(img.components, 1)
def test_image_read_then_to_numpy(self):
"""
convert ANTsImage's to numpy arrays
"""
for img_path in self.img_paths:
img = ants.image_read(img_path)
img_array = img.numpy()
npy_dtype = _parse_numpy_pixeltype_from_string(img_path)
dim = _parse_dim_from_string(img_path)
self.assertGreater(img_array.sum(), 0)
self.assertGreater(len(img_array), 0)
self.assertEqual(img_array.dtype, npy_dtype)
self.assertEqual(img_array.ndim, dim)
self.assertEqual(tuple(img_array.shape), tuple(img.shape))
def test_get_and_set_direction(self):
for img_path in self.img_paths:
ndim = _parse_dim_from_string(img_path)
img = ants.image_read(img_path)
direction = img.direction
self.assertTrue(isinstance(direction, np.ndarray))
self.assertEqual(direction.shape, (ndim, ndim))
# try to set neworigin
set_direction = np.eye(ndim) * 3.6
img.set_direction(set_direction)
get_direction = img.direction
nptest.assert_allclose(set_direction, get_direction)
def test_get_and_set_spacing(self):
"""
test get and set of spacing
"""
for img_path in self.img_paths:
ndim = _parse_dim_from_string(img_path)
img = ants.image_read(img_path)
spacing = img.spacing
# assert that there is one spacing value for each dimension
self.assertEqual(len(spacing), ndim)
# try to set neworigin
img.set_spacing(tuple([3.6] * ndim))
new_spacing = img.spacing
self.assertEqual(new_spacing, tuple([3.6] * ndim))
def test_get_and_set_origin(self):
"""
test get and set of origin
"""
for img_path in self.img_paths:
ndim = _parse_dim_from_string(img_path)
img = ants.image_read(img_path)
origin = img.origin
# assert that there is one origin value for each dimension
self.assertEqual(len(origin), ndim)
# try to set neworigin
img.set_origin(tuple([3.6] * ndim))
new_origin = img.origin
self.assertEqual(new_origin, tuple([3.6] * ndim))