def test_metadata(self):
field, field_val = "EchoTime", 4.0
volume = np.random.rand(10, 20, 30, 40)
headers = ututils.build_dummy_headers(volume.shape[2:],
{field: field_val})
mv_no_headers = MedicalVolume(volume, self._AFFINE)
mv = MedicalVolume(volume, self._AFFINE, headers=headers)
assert mv_no_headers.headers() is None
assert mv_no_headers.headers(flatten=True) is None
with self.assertRaises(ValueError):
mv.get_metadata("foobar")
assert mv.get_metadata("foobar", default=0) == 0
echo_time = mv.get_metadata(field)
assert echo_time == field_val
new_val = 5.0
mv2 = mv.clone(headers=True)
mv2.set_metadata(field, new_val)
assert mv.get_metadata(field, type(field_val)) == field_val
assert mv2.get_metadata(field, type(new_val)) == new_val
for h in mv2.headers(flatten=True):
assert h[field].value == new_val
new_val = 6.0
mv2 = mv.clone(headers=True)
mv2[..., 1].set_metadata(field, new_val)
assert mv2[..., 0].get_metadata(field) == field_val
assert mv2[..., 1].get_metadata(field) == new_val
headers = mv2.headers()
for h in headers[..., 0].flatten():
assert h[field].value == field_val
for h in headers[..., 1].flatten():
assert h[field].value == new_val
# Set metadata when volume has no headers.
mv_nh = MedicalVolume(volume, self._AFFINE, headers=None)
with self.assertRaises(ValueError):
mv_nh.set_metadata("EchoTime", 40.0)
with self.assertWarns(UserWarning):
mv_nh.set_metadata("EchoTime", 40.0, force=True)
assert mv_nh._headers.shape == (1, ) * len(mv_nh.shape)
assert mv_nh.get_metadata("EchoTime") == 40.0
assert mv_nh[:1, :2, :3]._headers.shape == (1, ) * len(mv_nh.shape)
def test_comparison(self):
mv1 = MedicalVolume(np.ones((10, 20, 30)), self._AFFINE)
mv2 = MedicalVolume(2 * np.ones((10, 20, 30)), self._AFFINE)
assert np.all((mv1 == mv1.clone()).volume)
assert np.all((mv1 != mv2).volume)
assert np.all((mv1 < mv2).volume)
assert np.all((mv1 <= mv2).volume)
assert np.all((mv2 > mv1).volume)
assert np.all((mv2 >= mv1).volume)
def test_clone(self):
mv = MedicalVolume(np.random.rand(10, 20, 30), self._AFFINE)
mv2 = mv.clone()
assert mv.is_identical(mv2) # expected identical volumes
mv = MedicalVolume(
np.random.rand(10, 20, 30),
self._AFFINE,
headers=ututils.build_dummy_headers((1, 1, 30)),
)
mv2 = mv.clone(headers=False)
assert mv.is_identical(mv2) # expected identical volumes
assert id(mv.headers(flatten=True)[0]) == id(
mv2.headers(flatten=True)
[0]), "headers not cloned, expected same memory address"
mv3 = mv.clone(headers=True)
assert mv.is_identical(mv3) # expected identical volumes
assert id(mv.headers(flatten=True)[0]) != id(
mv3.headers(flatten=True)
[0]), "headers cloned, expected different memory address"
def test_reformat_header(self):
volume = np.random.rand(10, 20, 30, 40)
headers = ututils.build_dummy_headers(volume.shape[2:])
mv = MedicalVolume(volume, self._AFFINE, headers=headers)
new_orientation = tuple(x[::-1] for x in mv.orientation[::-1])
mv2 = mv.reformat(new_orientation)
assert mv2._headers.shape == (30, 1, 1, 40)
mv2 = mv.clone()
mv2.reformat(new_orientation, inplace=True)
assert mv2._headers.shape == (30, 1, 1, 40)
volume = np.random.rand(10, 20, 30, 40)
headers = ututils.build_dummy_headers((volume.shape[2], 1))
mv = MedicalVolume(volume, self._AFFINE, headers=headers)
new_orientation = tuple(x[::-1] for x in mv.orientation[::-1])
mv2 = mv.reformat(new_orientation)
assert mv2._headers.shape == (30, 1, 1, 1)
def test_math(self):
mv1 = MedicalVolume(np.ones((10, 20, 30)), self._AFFINE)
mv2 = MedicalVolume(2 * np.ones((10, 20, 30)), self._AFFINE)
out = mv1 + mv2
assert np.all(mv1._volume == 1)
assert np.all(mv2._volume == 2)
assert np.all(out._volume == 3)
out = mv1 - mv2
assert np.all(mv1._volume == 1)
assert np.all(mv2._volume == 2)
assert np.all(out._volume == -1)
out = mv1 * mv2
assert np.all(mv1._volume == 1)
assert np.all(mv2._volume == 2)
assert np.all(out._volume == 2)
out = mv1 / mv2
assert np.all(mv1._volume == 1)
assert np.all(mv2._volume == 2)
assert np.all(out._volume == 0.5)
out = mv1 // mv2
assert np.all(mv1._volume == 1)
assert np.all(mv2._volume == 2)
assert np.all(out._volume == 0)
out = mv1**mv2
assert np.all(mv1._volume == 1)
assert np.all(mv2._volume == 2)
assert np.all(out._volume == 1)
out = mv1.clone()
out += mv2
assert np.all(out._volume == 3)
out = mv1.clone()
out -= mv2
assert np.all(out._volume == -1)
out = mv1.clone()
out *= mv2
assert np.all(out._volume == 2)
out = mv1.clone()
out /= mv2
assert np.all(out._volume == 0.5)
out = mv1.clone()
out //= mv2
assert np.all(out._volume == 0)
out = mv1.clone()
out **= mv2
assert np.all(out._volume == 1)
mv3 = mv1.clone().reformat(mv1.orientation[::-1])
with self.assertRaises(ValueError):
mv3 + mv2