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_image_registration():
with TemporaryDirectory() as temp_out_dir:
static, moving, static_g2w, moving_g2w, smask, mmask, M\
= setup_random_transform(transform=regtransforms[('AFFINE', 3)],
rfactor=0.1)
save_nifti(pjoin(temp_out_dir, 'b0.nii.gz'),
data=static,
affine=static_g2w)
save_nifti(pjoin(temp_out_dir, 't1.nii.gz'),
data=moving,
affine=moving_g2w)
static_image_file = pjoin(temp_out_dir, 'b0.nii.gz')
moving_image_file = pjoin(temp_out_dir, 't1.nii.gz')
image_registration_flow = ImageRegistrationFlow()
def read_distance(qual_fname):
temp_val = 0
with open(pjoin(temp_out_dir, qual_fname), 'r') as f:
temp_val = f.readlines()[-1]
return float(temp_val)
def test_com():
out_moved = pjoin(temp_out_dir, "com_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "com_affine.txt")
image_registration_flow._force_overwrite = True
image_registration_flow.run(static_image_file,
moving_image_file,
transform='com',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine)
check_existence(out_moved, out_affine)
def test_translation():
out_moved = pjoin(temp_out_dir, "trans_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "trans_affine.txt")
image_registration_flow._force_overwrite = True
image_registration_flow.run(static_image_file,
moving_image_file,
transform='trans',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
save_metric=True,
level_iters=[100, 10, 1],
out_quality='trans_q.txt')
dist = read_distance('trans_q.txt')
npt.assert_almost_equal(float(dist), -0.3953547764454917, 1)
check_existence(out_moved, out_affine)
def test_rigid():
out_moved = pjoin(temp_out_dir, "rigid_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "rigid_affine.txt")
image_registration_flow._force_overwrite = True
image_registration_flow.run(static_image_file,
moving_image_file,
transform='rigid',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
save_metric=True,
level_iters=[100, 10, 1],
out_quality='rigid_q.txt')
dist = read_distance('rigid_q.txt')
npt.assert_almost_equal(dist, -0.6900534794005155, 1)
check_existence(out_moved, out_affine)
def test_rigid_isoscaling():
out_moved = pjoin(temp_out_dir, "rigid_isoscaling_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "rigid_isoscaling_affine.txt")
image_registration_flow._force_overwrite = True
image_registration_flow.run(static_image_file,
moving_image_file,
transform='rigid_isoscaling',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
save_metric=True,
level_iters=[100, 10, 1],
out_quality='rigid_isoscaling_q.txt')
dist = read_distance('rigid_isoscaling_q.txt')
npt.assert_almost_equal(dist, -0.6960044668271375, 1)
check_existence(out_moved, out_affine)
def test_rigid_scaling():
out_moved = pjoin(temp_out_dir, "rigid_scaling_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "rigid_scaling_affine.txt")
image_registration_flow._force_overwrite = True
image_registration_flow.run(static_image_file,
moving_image_file,
transform='rigid_scaling',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
save_metric=True,
level_iters=[100, 10, 1],
out_quality='rigid_scaling_q.txt')
dist = read_distance('rigid_scaling_q.txt')
npt.assert_almost_equal(dist, -0.698688892993124, 1)
check_existence(out_moved, out_affine)
def test_affine():
out_moved = pjoin(temp_out_dir, "affine_moved.nii.gz")
out_affine = pjoin(temp_out_dir, "affine_affine.txt")
image_registration_flow._force_overwrite = True
image_registration_flow.run(static_image_file,
moving_image_file,
transform='affine',
out_dir=temp_out_dir,
out_moved=out_moved,
out_affine=out_affine,
save_metric=True,
level_iters=[100, 10, 1],
out_quality='affine_q.txt')
dist = read_distance('affine_q.txt')
npt.assert_almost_equal(dist, -0.7670650775914811, 1)
check_existence(out_moved, out_affine)
# Creating the erroneous behavior
def test_err():
image_registration_flow._force_overwrite = True
npt.assert_raises(ValueError,
image_registration_flow.run,
static_image_file,
moving_image_file,
transform='notransform')
image_registration_flow._force_overwrite = True
npt.assert_raises(ValueError,
image_registration_flow.run,
static_image_file,
moving_image_file,
metric='wrong_metric')
def check_existence(movedfile, affine_mat_file):
assert os.path.exists(movedfile)
assert os.path.exists(affine_mat_file)
return True
test_com()
test_translation()
test_rigid()
test_rigid_isoscaling()
test_rigid_scaling()
test_affine()
test_err()
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"))