def __init__(self,
ants_image_fixed=[[0.0]],
ants_image_moving=[[0.0]],
**options):
import ants
self.txfile = ants.affine_initializer(ants_image_fixed,
ants_image_moving, **options)
def performAntsRegistration(param,
mv_path,
target_path,
registration_type='syn',
record_path=None,
ml_path=None,
tl_path=None,
fname=None):
"""
call [AntsPy](https://github.com/ANTsX/ANTsPy),
:param param: ParameterDict, affine related params
:param mv_path: path of moving image
:param target_path: path of target image
:param registration_type: type of registration, support 'affine' and 'syn'(include affine)
:param record_path: path of saving results
:param ml_path: path of label of moving image
:param tl_path: path of label fo target image
:param fname: pair name or saving name of the image pair
:return: warped image, warped label, transformation map (None), jacobian map
"""
loutput = None
phi = None
moving = ants.image_read(mv_path)
target = ants.image_read(target_path)
if ml_path is not None:
ml_sitk = sitk.ReadImage(ml_path)
tl_sitk = sitk.ReadImage(tl_path)
ml_np = sitk.GetArrayFromImage(ml_sitk)
tl_np = sitk.GetArrayFromImage(tl_sitk)
l_moving = ants.from_numpy(np.transpose(ml_np),
spacing=moving.spacing,
direction=moving.direction,
origin=moving.origin)
l_target = ants.from_numpy(np.transpose(tl_np),
spacing=target.spacing,
direction=target.direction,
origin=target.origin)
start = time.time()
if registration_type == 'affine':
affine_file = ants.affine_initializer(target, moving)
af_img = ants.apply_transforms(fixed=target,
moving=moving,
transformlist=affine_file)
if ml_path is not None:
loutput = ants.apply_transforms(fixed=l_target,
moving=l_moving,
transformlist=affine_file,
interpolator='nearestNeighbor')
loutput = loutput.numpy()
output = af_img.numpy()
print('affine registration finished and takes: :', time.time() - start)
#print("param_in_ants:{}".format(param_in_ants))
if registration_type == 'syn':
syn_res = ants.registration(
fixed=target,
moving=moving,
type_of_transform='SyNCC',
grad_step=0.2,
flow_sigma=3, # intra 3
total_sigma=0.1,
aff_metric='mattes',
aff_sampling=8,
syn_metric='mattes',
syn_sampling=32,
reg_iterations=(80, 50, 20))
print(syn_res['fwdtransforms'])
if 'GenericAffine.mat' in syn_res['fwdtransforms'][0]:
tmp1 = syn_res['fwdtransforms'][0]
tmp2 = syn_res['fwdtransforms'][1]
syn_res['fwdtransforms'][0] = tmp2
syn_res['fwdtransforms'][1] = tmp1
if ml_path is not None:
time.sleep(1)
loutput = ants.apply_transforms(
fixed=l_target,
moving=l_moving,
transformlist=syn_res['fwdtransforms'],
interpolator='nearestNeighbor')
loutput = loutput.numpy()
output = syn_res['warpedmovout'].numpy()
print('syn registration finished and takes: :', time.time() - start)
output = np.transpose(output, (2, 1, 0))
loutput = np.transpose(loutput, (2, 1, 0)) if loutput is not None else None
# #disp = nifty_read_phi(syn_res['fwdtransforms'][0])
# #disp = np.transpose(disp, (0,1,4, 3, 2))
# composed_transform = ants.apply_transforms(fixed=target, moving=moving,
# transformlist=syn_res['fwdtransforms'],compose= record_path)
# cmd = 'mv ' + composed_transform + ' ' + os.path.join(record_path,fname+'_disp.nii.gz')
# composed_inv_transform = ants.apply_transforms(fixed=target, moving=moving,
# transformlist=syn_res['invtransforms'],compose= record_path)
# cmd = 'mv ' + composed_inv_transform + ' ' + os.path.join(record_path,fname+'_invdisp.nii.gz')
cmd = 'mv ' + syn_res['fwdtransforms'][0] + ' ' + os.path.join(
record_path, fname + '_disp.nii.gz')
cmd += '\n mv ' + syn_res['fwdtransforms'][1] + ' ' + os.path.join(
record_path, fname + '_affine.mat')
cmd += '\n mv ' + syn_res['invtransforms'][0] + ' ' + os.path.join(
record_path, fname + '_invdisp.nii.gz')
process = subprocess.Popen(cmd, shell=True)
process.wait()
jacobian_np = None
if registration_type == 'syn':
jacobian = ants.create_jacobian_determinant_image(
target, os.path.join(record_path, fname + '_disp.nii.gz'), False)
jacobian_np = jacobian.numpy()
return expand_batch_ch_dim(output), expand_batch_ch_dim(
loutput), phi, jacobian_np
def test_example(self):
# test ANTsPy/ANTsR example
fi = ants.image_read(ants.get_ants_data("r16"))
mi = ants.image_read(ants.get_ants_data("r27"))
txfile = ants.affine_initializer(fi, mi)
tx = ants.read_transform(txfile, dimension=2)