def test_composition_intermediate(self, interpolation, border_mode):
"""Test that composing two opposite translations results in an identity (almost)"""
shape = (400, 200)
matrix_1 = np.array([[1, 0, 1], [0, 1, 1], [0, 0, 1]])
matrix_2 = np.array([[1, 0, -1], [0, 1, -1], [0, 0, 1]])
matrix_id = np.eye(3)
df_1 = DisplacementField.generate(shape,
approach="affine",
matrix=matrix_1)
df_2 = DisplacementField.generate(shape,
approach="affine",
matrix=matrix_2)
df_id = DisplacementField.generate(shape,
approach="affine",
matrix=matrix_id)
res = df_2(df_1, interpolation=interpolation, border_mode=border_mode)
# Works only inside:D
assert np.allclose(res.delta_x[2:-2, 2:-2], df_id.delta_x[2:-2, 2:-2])
assert np.allclose(res.delta_y[2:-2, 2:-2], df_id.delta_y[2:-2, 2:-2])
def test_no_inputs_anchor_corners(self):
"""Test that can/cannot instantiate with no inputs and with/without anchoring corners."""
shape = (40, 50)
with pytest.raises(ValueError):
DisplacementField.generate(shape,
approach="control_points",
anchor_corners=False)
DisplacementField.generate(shape,
approach="control_points",
anchor_corners=True)
def test_illegal_kwarg(self):
"""Test that illegal kwarg not accepted"""
with pytest.raises(ValueError):
shape = (20, 13)
DisplacementField.generate(
shape,
approach="edge_stretching",
edge_mask=np.zeros(shape, dtype=bool),
n_perturbation_points=10,
i_am_illegal=1,
)
def test_displacement_field(self, tmp_path, img_grayscale):
"""Make sure that the displacement extracted can reproduce the registered moving image.
Done by comparing with the image contained in the registration output.
"""
fixed_img = img_grayscale
size = fixed_img.shape
df = DisplacementField.generate(
size, approach="affine_simple", translation_x=20, translation_y=20
)
moving_img = df.warp(img_grayscale)
df_final, meta = antspy_registration(fixed_img, moving_img, path=tmp_path)
img1 = meta["warpedmovout"].numpy()
img2 = df_final.warp(
moving_img, interpolation="linear", border_mode="constant", c=0
)
if img_grayscale.dtype == "uint8":
epsilon = 1
else:
epsilon = 0.005
assert abs(img1 - img2).mean() < epsilon
def test_different_types(
self, tmp_path, monkeypatch, img_grayscale_uint, img_grayscale_float
):
"""Make sure that the registration does not depend on the type of input images.
Notes
-----
Marked as `todo` because we did not find a way how to force ANTsPY to be always reproducible.
"""
monkeypatch.setenv("ANTS_RANDOM_SEED", "4")
monkeypatch.setenv("ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS", "1")
size = img_grayscale_uint.shape
p = img_grayscale_uint / np.sum(img_grayscale_uint)
df = DisplacementField.generate(size, approach="paper", p=p)
moving_img_uint = df.warp(img_grayscale_uint)
moving_img_float = df.warp(img_grayscale_float)
df_final1, meta1 = antspy_registration(
img_grayscale_uint, moving_img_uint, path=tmp_path, verbose=False
)
df_final2, meta2 = antspy_registration(
img_grayscale_float, moving_img_float, path=tmp_path, verbose=False
)
assert np.allclose(df_final1.delta_x, df_final2.delta_x, atol=0.1)
assert np.allclose(df_final1.delta_y, df_final2.delta_y, atol=0.1)
def generate_mov2art(img_mov, verbose=True, radius_max=60, use_normal=True):
"""Generate geometric augmentation and its inverse."""
shape = img_mov.shape
img_mov_float = img_as_float32(img_mov)
edge_mask = canny(img_mov_float)
if use_normal:
c = np.random.normal(0.7, 0.3)
else:
c = np.random.random()
if verbose:
print("Scalar: {}".format(c))
mov2art = c * DisplacementField.generate(
shape,
approach="edge_stretching",
edge_mask=edge_mask,
interpolation_method="rbf",
interpolator_kwargs={"function": "linear"},
n_perturbation_points=6,
radius_max=radius_max,
)
return mov2art
def test_warp_invariance(self, img, h_delta, w_delta):
"""Test that df_resized.warp(img) ~ resized(df.warp(img))."""
shape = img.shape
new_shape = (shape[0] + h_delta, shape[1] + w_delta)
assert (new_shape[0] > 0 and new_shape[1] > 0
) # if not satisfied fixture image too small
# Zoom in
df = DisplacementField.generate(shape,
approach="affine_simple",
scale_x=0.8)
df_resized = df.resize(new_shape)
img_1 = df_resized.warp(img)
img_2 = resize(df.warp(img), new_shape,
preserve_range=True) # preserving dtype
# WARNING MAKE SURE THAT DOES NOT RUN INTO OVERFLOW FOR UINT8
adiff = abs(np.subtract(img_1, img_2, dtype="float"))
if img.dtype == np.uint8:
eps = 25
elif img.dtype == np.float32:
eps = 1e-1
else:
raise ValueError(
"This test is only made for uint8 and float32 images.")
assert np.median(adiff) < eps
def test_small_shift(self, translation_xy, approach, dtype):
"""Test that small shifts do not affect the warp.
Notes
-----
Anything that is withing a diameter of 1 (=radius of 0.5) should be assigned to the same point.
"""
translation_x, translation_y = translation_xy
shape = (9, 10)
random_state = 1
df = DisplacementField.generate(
shape,
approach="affine_simple",
translation_x=translation_x,
translation_y=translation_y,
)
np.random.seed(random_state)
img = np.random.randint(256, size=shape).astype(dtype)
img_warped = df.warp_annotation(img, approach=approach)
assert np.all(img_warped == img)
def test_wrong_inputs_1(self):
"""Test that inconsistent input lengths lead to an error."""
shape = (40, 50)
points = np.array([[0, 1], [10, 10]]) # len(points) = 2
values_delta_x = np.array([0, 10, 0]) # len(values_delta_x) = 3
values_delta_y = np.array([0, 10]) # len(values_delta_y) = 2
with pytest.raises(ValueError):
DisplacementField.generate(
shape,
approach="control_points",
points=points,
values_delta_x=values_delta_x,
values_delta_y=values_delta_y,
)
def test_construction(approach):
"""Just check default factory methods are able to construct the class with no additional parameters."""
shape = (500, 500)
inst = DisplacementField.generate(shape, approach=approach)
assert isinstance(inst, DisplacementField)
def test_basic(self, batch_size, a):
"""Basic functionality"""
(h, w) = 356 // 2, 420 // 2
a_tensor = Input((2, 3))
layer = Affine2DVF((h, w))
x = layer(a_tensor)
assert isinstance(x, tf.Tensor)
assert x.shape.ndims == 4
assert K.int_shape(x) == (None, h, w, 2)
model = Model(inputs=a_tensor, outputs=x)
# Initialize
a_input = np.zeros((batch_size, 2, 3))
dvfs_true = np.zeros((batch_size, h, w, 2))
for i in range(batch_size):
# add random translation for each sample
a_input[i] = a + np.hstack((np.zeros(
(2, 2)), np.random.uniform(-10, 10, size=(2, 1))))
df = DisplacementField.generate((h, w),
approach="affine",
matrix=a_input[i])
dvfs_true[i, :, :, 0] = df.delta_x
dvfs_true[i, :, :, 1] = df.delta_y
# run
dvfs_pred = model.predict(a_input)
assert dvfs_pred.shape == (batch_size, h, w, 2)
assert np.allclose(dvfs_true, dvfs_pred, atol=0.01)
def test_float_values(self, img_grayscale_float, metric):
"""Test that every image similarity metrics output a float."""
size = img_grayscale_float.shape
img_true = img_grayscale_float
df = DisplacementField.generate(size,
approach="affine_simple",
rotation=1)
img_pred = df.warp(img_grayscale_float)
metric_callable = ALL_IMG_METRICS[metric]
# UNMASKED
assert isinstance(metric_callable(img_true, img_pred), float)
# MASKED
mask = np.zeros(size, dtype=bool)
mask[size[0] // 3:2 * (size[1] // 3),
size[0] // 3:2 * (size[1] // 3)] = True
try:
assert isinstance(metric_callable(img_true, img_pred, mask=mask),
float)
except TypeError:
# mask keyword argument not present
pass
def test_reproducible(random_state, approach):
"""Test that the same random seeds lead to identical result whereas different ones do not."""
shape = (100, 120)
df_1 = DisplacementField.generate(shape,
approach=approach,
random_state=random_state)
df_2 = DisplacementField.generate(shape,
approach=approach,
random_state=random_state)
df_3 = DisplacementField.generate(shape,
approach=approach,
random_state=random_state + 1)
assert df_1 == df_2
assert df_1 != df_3
def test_wrong_inputs_0(self):
""" Test that other types then np.ndarray lead to an error"""
shape = (40, 50)
points = "fake"
values_delta_x = (1, 2, 3)
values_delta_y = [1, 1312, "aaa"]
with pytest.raises(TypeError):
DisplacementField.generate(
shape,
approach="control_points",
points=points,
values_delta_x=values_delta_x,
values_delta_y=values_delta_y,
)
def test_wrong_inputs_3(self):
"""Test that other dimensions are also correct."""
shape = (40, 50)
points = np.zeros([1, 2, 3, 4, 5]) # Wrong - needs to be a 2d array
values_delta_x = np.array([1, 2, 3, 4, 5])
values_delta_y = np.array([1, 2, 3, 4, 5])
with pytest.raises(ValueError):
DisplacementField.generate(
shape,
approach="control_points",
points=points,
values_delta_x=values_delta_x,
values_delta_y=values_delta_y,
)
def test_identity(self):
shape = (10, 11)
df = DisplacementField.generate(shape, approach="identity")
df_anchored = df.anchor(ds_f=1)
assert df == df_anchored
def test_wrong_inputs_4(self):
"""Test that out of range control points lead to an error."""
shape = (40, 50)
points = np.array([[100, 10], [12,
12]]) # Wrong - needs to be a 2d array
values_delta_x = np.array([1, 2])
values_delta_y = np.array([0, 13])
with pytest.raises(IndexError):
DisplacementField.generate(
shape,
approach="control_points",
points=points,
values_delta_x=values_delta_x,
values_delta_y=values_delta_y,
)
def minimal_vol(monkeypatch):
sn = [1, 13]
mov_imgs = 2 * [np.zeros((12, 13))]
dvfs = 2 * [DisplacementField.generate((12, 13), approach="identity")]
nvol_mock = MagicMock()
nvol_mock.__getitem__.return_value = np.zeros((len(mov_imgs), 12, 13, 1))
monkeypatch.setattr("atlalign.volume.nissl_volume", lambda: nvol_mock)
return Volume(sn, mov_imgs, dvfs)
def test_wrong_inputs_5(self, metric_name):
"""Wrong input type"""
y_true = np.zeros((2, 20, 12, 2))
y_pred = [
DisplacementField.generate((20, 12), approach="identity"), "faaake"
]
with pytest.raises(TypeError):
ALL_DVF_METRICS[metric_name](y_true, y_pred)
def test_dtype_conversions(self, img, interpolation, border_mode):
"""Test that dtype is conserved (at least for uint8 and float32)"""
df = DisplacementField.generate(img.shape, approach="identity")
warped_img = df.warp(img,
interpolation=interpolation,
border_mode=border_mode)
assert warped_img.dtype == img.dtype
def test_animation(self, img):
"""Possible to generate animations."""
df = DisplacementField.generate(img.shape, approach="identity")
ani = create_animation(df, img)
ani_many = create_animation([df, df], img)
assert isinstance(ani, animation.Animation)
assert isinstance(ani_many, animation.Animation)
def test_invalid_names(self):
shape = (10, 11)
img = np.zeros(shape)
df = DisplacementField.generate(shape, approach="identity")
with pytest.raises(KeyError):
df.warp(img, interpolation="fake_interpolation")
with pytest.raises(KeyError):
df.warp(img, border_mode="fake_border_mode")
def test_conversion_possible(self, df_is, metric_name):
"""List of DisplacementField instances to ndarray."""
custom_list = [
DisplacementField.generate((20, 12), approach="identity")
for _ in range(2)
]
y_true = np.zeros((2, 20, 12, 2)) if df_is == "pred" else custom_list
y_pred = np.zeros((2, 20, 12, 2)) if df_is == "true" else custom_list
_, _ = ALL_DVF_METRICS[metric_name](y_true, y_pred)
def df_id(request):
"""Generate an identity transformation.
In order to specify a shape one decorates the test function in the following way:
`@pytest.mark.parametrize('df_id', [(320, 456)], indirect=True)`
"""
if hasattr(request, "param"):
shape = request.param
else:
shape = (10, 11)
return DisplacementField.generate(shape, approach="identity")
def test_returns_new_array(self, img, interpolation, border_mode):
"""Test that new image is saved in a new array."""
shape = img.shape[:2]
df = DisplacementField.generate(shape, approach="identity")
img_warped = df.warp(img,
interpolation=interpolation,
border_mode=border_mode)
assert not np.may_share_memory(img, img_warped)
assert not np.shares_memory(img, img_warped)
def test_wrong_inputs_2(self):
"""Test that no control points are not allowed.
Notes
-----
Note that if all 3 inputs are None and anchor_corners is True,
then automatically generates 4 control points in the background.
"""
shape = (40, 50)
points = np.zeros((0, 2))
values_delta_x = np.array([])
values_delta_y = np.array([])
with pytest.raises(ValueError):
DisplacementField.generate(
shape,
approach="control_points",
points=points,
values_delta_x=values_delta_x,
values_delta_y=values_delta_y,
)
def test_basic(self, monkeypatch):
shape = (10, 11)
df = DisplacementField.generate(shape, approach="identity")
fake_ax = Mock()
fake_plt = Mock()
fake_plt.subplots = lambda *args, **kwargs: (None, fake_ax)
monkeypatch.setattr("atlalign.base.plt", fake_plt)
df.plot_ranges()
assert fake_ax.scatter.call_count > 0
assert fake_ax.legend.call_count > 0
def test_no_edges(self):
"""Test that no edges lead to identity mapping."""
shape = (20, 13)
# No edges
df_1 = DisplacementField.generate(
shape,
approach="edge_stretching",
edge_mask=np.zeros(shape, dtype=bool),
n_perturbation_points=10,
)
# No perturbation points
df_2 = DisplacementField.generate(
shape,
approach="edge_stretching",
edge_mask=np.ones(shape, dtype=bool),
n_perturbation_points=0,
)
df_id = DisplacementField(np.zeros(shape), np.zeros(shape))
assert df_id == df_1
assert df_id == df_2
def test_scale(self, scale):
"""Make sure that one can scale."""
shape = (40, 50)
matrix = scale * np.array([[1, 0, 0], [0, 1, 0]])
x, y = np.meshgrid(list(range(shape[1])), list(range(shape[0])))
delta_x = scale * x - x
delta_y = scale * y - y
df = DisplacementField.generate(shape=shape,
approach="affine",
matrix=matrix)
df_true = DisplacementField(delta_x, delta_y)
assert df == df_true
def test_approaches_equivalent(self, dtype):
"""Make sure approaches equivalent"""
shape = (10, 11)
img = np.random.randint(1, 256, size=shape).astype(dtype)
df = DisplacementField.generate(shape,
approach="affine_simple",
rotation=np.pi / 10)
all_results = [
df.warp_annotation(img, approach=x)
for x in SUPPORTED_APPROACHES_ANNOTATIONS
]
for i in range(len(all_results) - 1):
assert np.array_equal(all_results[i], all_results[i + 1])