def test_apply_transform_error():
flow = ApplyTransformFlow()
npt.assert_raises(ValueError,
flow.run,
'my_fake_static.nii.gz',
'my_fake_moving.nii.gz',
'my_fake_map.nii.gz',
transform_type='wrong_type')
def test_apply_affine_transform():
with TemporaryDirectory() as temp_out_dir:
factors = {
('TRANSLATION', 3): (2.0, None, np.array([2.3, 4.5, 1.7])),
('RIGID', 3):
(0.1, None, np.array([0.1, 0.15, -0.11, 2.3, 4.5, 1.7])),
('RIGIDISOSCALING', 3):
(0.1, None, np.array([0.1, 0.15, -0.11, 2.3, 4.5, 1.7, 0.8])),
('RIGIDSCALING', 3):
(0.1, None,
np.array([0.1, 0.15, -0.11, 2.3, 4.5, 1.7, 0.8, 0.9, 1.1])),
('AFFINE', 3): (0.1, None,
np.array([
0.99, -0.05, 0.03, 1.3, 0.05, 0.99, -0.10, 2.5,
-0.07, 0.10, 0.99, -1.4
]))
}
image_registration_flow = ImageRegistrationFlow()
apply_trans = ApplyTransformFlow()
for i in factors.keys():
static, moving, static_g2w, moving_g2w, smask, mmask, M = \
setup_random_transform(transform=regtransforms[i],
rfactor=factors[i][0])
stat_file = str(i[0]) + '_static.nii.gz'
mov_file = str(i[0]) + '_moving.nii.gz'
save_nifti(pjoin(temp_out_dir, stat_file),
data=static,
affine=static_g2w)
save_nifti(pjoin(temp_out_dir, mov_file),
data=moving,
affine=moving_g2w)
static_image_file = pjoin(temp_out_dir,
str(i[0]) + '_static.nii.gz')
moving_image_file = pjoin(temp_out_dir,
str(i[0]) + '_moving.nii.gz')
out_moved = pjoin(temp_out_dir, str(i[0]) + "_moved.nii.gz")
out_affine = pjoin(temp_out_dir, str(i[0]) + "_affine.txt")
if str(i[0]) == "TRANSLATION":
transform_type = "trans"
elif str(i[0]) == "RIGIDISOSCALING":
transform_type = "rigid_isoscaling"
elif str(i[0]) == "RIGIDSCALING":
transform_type = "rigid_scaling"
else:
transform_type = str(i[0]).lower()
image_registration_flow.run(static_image_file,
moving_image_file,
transform=transform_type,
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
level_iters=[1, 1, 1],
save_metric=False)
# Checking for the created moved file.
assert os.path.exists(out_moved)
assert os.path.exists(out_affine)
images = pjoin(temp_out_dir, '*moving*')
apply_trans.run(static_image_file,
images,
out_dir=temp_out_dir,
transform_map_file=out_affine)
# Checking for the transformed file.
assert os.path.exists(pjoin(temp_out_dir, "transformed.nii.gz"))
def test_apply_affine_transform():
with TemporaryDirectory() as temp_out_dir:
factors = {
('TRANSLATION', 3): (2.0, None, np.array([2.3, 4.5, 1.7])),
('RIGID', 3): (0.1, None, np.array([0.1, 0.15, -0.11, 2.3, 4.5,
1.7])),
('AFFINE', 3): (0.1, None, np.array([0.99, -0.05, 0.03, 1.3,
0.05, 0.99, -0.10, 2.5,
-0.07, 0.10, 0.99, -1.4]))}
image_registeration_flow = ImageRegistrationFlow()
apply_trans = ApplyTransformFlow()
for i in factors.keys():
static, moving, static_g2w, moving_g2w, smask, mmask, M = \
setup_random_transform(transform=regtransforms[i],
rfactor=factors[i][0])
stat_file = str(i[0]) + '_static.nii.gz'
mov_file = str(i[0]) + '_moving.nii.gz'
save_nifti(pjoin(temp_out_dir, stat_file), data=static,
affine=static_g2w)
save_nifti(pjoin(temp_out_dir, mov_file), data=moving,
affine=moving_g2w)
static_image_file = pjoin(temp_out_dir,
str(i[0]) + '_static.nii.gz')
moving_image_file = pjoin(temp_out_dir,
str(i[0]) + '_moving.nii.gz')
out_moved = pjoin(temp_out_dir,
str(i[0]) + "_moved.nii.gz")
out_affine = pjoin(temp_out_dir,
str(i[0]) + "_affine.txt")
if str(i[0]) == "TRANSLATION":
transform_type = "trans"
else:
transform_type = str(i[0]).lower()
image_registeration_flow.run(static_image_file, moving_image_file,
transform=transform_type,
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
level_iters=[1, 1, 1],
save_metric=False)
# Checking for the created moved file.
assert os.path.exists(out_moved)
assert os.path.exists(out_affine)
images = pjoin(temp_out_dir, '*moving*')
apply_trans.run(static_image_file, images,
out_dir=temp_out_dir,
transform_map_file=out_affine)
# Checking for the transformed file.
assert os.path.exists(pjoin(temp_out_dir, "transformed.nii.gz"))