def get_data(keys):
"""Get the example data to be used.
Use MarsAtlas as it only contains 1 image for quick download and
that image is parcellated.
"""
cache_dir = os.environ.get("MONAI_DATA_DIRECTORY") or tempfile.mkdtemp()
fname = "MarsAtlas-MNI-Colin27.zip"
url = "https://www.dropbox.com/s/ndz8qtqblkciole/" + fname + "?dl=1"
out_path = os.path.join(cache_dir, "MarsAtlas-MNI-Colin27")
zip_path = os.path.join(cache_dir, fname)
download_and_extract(url, zip_path, out_path)
image, label = sorted(glob(os.path.join(out_path, "*.nii")))
data = {CommonKeys.IMAGE: image, CommonKeys.LABEL: label}
transforms = Compose([
LoadImaged(keys),
AddChanneld(keys),
ScaleIntensityd(CommonKeys.IMAGE),
Rotate90d(keys, spatial_axes=[0, 2])
])
data = transforms(data)
max_size = max(data[keys[0]].shape)
padder = SpatialPadd(keys, (max_size, max_size, max_size))
return padder(data)
def test_prob_k_spatial_axes(self):
key = 'test'
rotate = Rotate90d(keys=key, k=2, spatial_axes=(0, 1))
rotated = rotate({key: self.imt[0]})
expected = list()
for channel in self.imt[0]:
expected.append(np.rot90(channel, 2, (0, 1)))
expected = np.stack(expected)
self.assertTrue(np.allclose(rotated[key], expected))
def test_k(self):
key = None
rotate = Rotate90d(keys=key, k=2)
rotated = rotate({key: self.imt[0]})
expected = list()
for channel in self.imt[0]:
expected.append(np.rot90(channel, 2, (0, 1)))
expected = np.stack(expected)
self.assertTrue(np.allclose(rotated[key], expected))
def test_rotate90_default(self):
key = 'test'
rotate = Rotate90d(keys=key)
rotated = rotate({key: self.imt[0]})
expected = list()
for channel in self.imt[0]:
expected.append(np.rot90(channel, 1, (0, 1)))
expected = np.stack(expected)
self.assertTrue(np.allclose(rotated[key], expected))
def test_spatial_axes(self):
key = "test"
rotate = Rotate90d(keys=key, spatial_axes=(0, 1))
rotated = rotate({key: self.imt[0]})
expected = []
for channel in self.imt[0]:
expected.append(np.rot90(channel, 1, (0, 1)))
expected = np.stack(expected)
self.assertTrue(np.allclose(rotated[key], expected))
def test_prob_k_spatial_axes(self):
key = "test"
rotate = Rotate90d(keys=key, k=2, spatial_axes=(0, 1))
for p in TEST_NDARRAYS:
rotated = rotate({key: p(self.imt[0])})
expected = [
np.rot90(channel, 2, (0, 1)) for channel in self.imt[0]
]
expected = np.stack(expected)
assert_allclose(rotated[key], p(expected))
def test_k(self):
key = None
rotate = Rotate90d(keys=key, k=2)
for p in TEST_NDARRAYS:
rotated = rotate({key: p(self.imt[0])})
expected = [
np.rot90(channel, 2, (0, 1)) for channel in self.imt[0]
]
expected = np.stack(expected)
assert_allclose(rotated[key], p(expected))
def test_rotate90_default(self):
key = "test"
rotate = Rotate90d(keys=key)
for p in TEST_NDARRAYS:
rotated = rotate({key: p(self.imt[0])})
expected = [
np.rot90(channel, 1, (0, 1)) for channel in self.imt[0]
]
expected = np.stack(expected)
assert_allclose(rotated[key], p(expected))
def test_prob_k_spatial_axes(self):
key = "test"
rotate = Rotate90d(keys=key, k=2, spatial_axes=(0, 1))
for p in TEST_NDARRAYS_ALL:
im = p(self.imt[0])
rotated = rotate({key: im})
test_local_inversion(rotate, rotated, {key: im}, key)
expected = [
np.rot90(channel, 2, (0, 1)) for channel in self.imt[0]
]
expected = np.stack(expected)
assert_allclose(rotated[key], p(expected), type_test="tensor")
def test_rotate90_default(self):
key = "test"
rotate = Rotate90d(keys=key)
for p in TEST_NDARRAYS_ALL:
im = p(self.imt[0])
set_track_meta(True)
rotated = rotate({key: im})
test_local_inversion(rotate, rotated, {key: im}, key)
expected = [
np.rot90(channel, 1, (0, 1)) for channel in self.imt[0]
]
expected = np.stack(expected)
assert_allclose(rotated[key], p(expected), type_test="tensor")
set_track_meta(False)
rotated = rotate({key: im})
self.assertNotIsInstance(rotated[key], MetaTensor)
set_track_meta(True)
RandAxisFlipd(KEYS, 1),
))
for acc in [True, False]:
TESTS.append((
"Orientationd 3d",
"3D",
0,
Orientationd(KEYS, "RAS", as_closest_canonical=acc),
))
TESTS.append((
"Rotate90d 2d",
"2D",
0,
Rotate90d(KEYS),
))
TESTS.append((
"Rotate90d 3d",
"3D",
0,
Rotate90d(KEYS, k=2, spatial_axes=(1, 2)),
))
TESTS.append((
"RandRotate90d 3d",
"3D",
0,
RandRotate90d(KEYS, prob=1, spatial_axes=(1, 2)),
))
def test_no_key(self):
key = 'unknown'
rotate = Rotate90d(keys=key)
with self.assertRaisesRegex(KeyError, ''):
rotate({'test': self.imt[0]})
def test_no_key(self):
key = "unknown"
rotate = Rotate90d(keys=key)
with self.assertRaisesRegex(KeyError, ""):
rotate({"test": self.imt[0]})
TESTS.append(("ResizeWithPadOrCropd 3d", "3D", 0, True,
ResizeWithPadOrCropd(KEYS, [201, 150, 105])))
TESTS.append(("Flipd 3d", "3D", 0, True, Flipd(KEYS, [1, 2])))
TESTS.append(("Flipd 3d", "3D", 0, True, Flipd(KEYS, [1, 2])))
TESTS.append(("RandFlipd 3d", "3D", 0, True, RandFlipd(KEYS, 1, [1, 2])))
TESTS.append(("RandAxisFlipd 3d", "3D", 0, True, RandAxisFlipd(KEYS, 1)))
TESTS.append(("RandAxisFlipd 3d", "3D", 0, True, RandAxisFlipd(KEYS, 1)))
for acc in [True, False]:
TESTS.append(("Orientationd 3d", "3D", 0, True,
Orientationd(KEYS, "RAS", as_closest_canonical=acc)))
TESTS.append(("Rotate90d 2d", "2D", 0, True, Rotate90d(KEYS)))
TESTS.append(
("Rotate90d 3d", "3D", 0, True, Rotate90d(KEYS, k=2, spatial_axes=(1, 2))))
TESTS.append(("RandRotate90d 3d", "3D", 0, True,
RandRotate90d(KEYS, prob=1, spatial_axes=(1, 2))))
TESTS.append(("Spacingd 3d", "3D", 3e-2, True,
Spacingd(KEYS, [0.5, 0.7, 0.9], diagonal=False)))
TESTS.append(("Resized 2d", "2D", 2e-1, True, Resized(KEYS, [50, 47])))
TESTS.append(("Resized 3d", "3D", 5e-2, True, Resized(KEYS, [201, 150, 78])))
TESTS.append(("Resized longest 2d", "2D", 2e-1, True,