def reg_epi(ref, flo_path):
i = 0
resampler2 = Reg.NiftyAladinSym()
resampler2.set_reference_image(ref)
for image in sorted_alphanumeric(os.listdir(flo_path)):
flo_file = flo_path + image
print(flo_file)
flo = Eng_flo.ImageData(flo_file)
resampler2.set_floating_image(flo)
resampler2.process()
tm_epi = resampler2.get_transformation_matrix_forward()
tm_epi.write(path_EPI + 'tm_epi_' + str(i))
i += 1
def reg_nac(ref, flo_path, list_NACs):
i = 0
nac_reg = Reg.NiftyAladinSym()
nac_reg.set_reference_image(ref)
for image in sorted_alphanumeric(list_NACs):
nac_file = flo_path + image
print(nac_file)
flo = Eng_flo.ImageData(nac_file)
nac_reg.set_floating_image(flo)
nac_reg.process()
tm_nac = nac_reg.get_transformation_matrix_forward()
tm_nac.write(path_moco + 'tm_nac_' + str(i))
i += 1
def register_data(static_path, dynamic_path, output_path):
path_new_displacement_fields = "{0}/new_displacement_fields/".format(
output_path)
if not os.path.exists(path_new_displacement_fields):
os.makedirs(path_new_displacement_fields, mode=0o770)
path_new_deformation_fields = "{0}/new_deformation_fields/".format(
output_path)
if not os.path.exists(path_new_deformation_fields):
os.makedirs(path_new_deformation_fields, mode=0o770)
path_new_tm = "{0}/new_tm/".format(output_path)
if not os.path.exists(path_new_tm):
os.makedirs(path_new_tm, mode=0o770)
algo = reg.NiftyAladinSym()
dvf_path = []
for i in range(len(dynamic_path)):
ref = reg.ImageData(dynamic_path[i])
flo = reg.ImageData(static_path)
algo.set_reference_image(ref)
algo.set_floating_image(flo)
algo.process()
displacement_field = algo.get_displacement_field_forward()
displacement_field.write("{0}/new_displacement_field_{1}.nii".format(
path_new_displacement_fields, str(i)))
dvf_path.append("{0}/new_DVF_field_{1}.nii".format(
path_new_deformation_fields, str(i)))
deformation_field = algo.get_deformation_field_forward()
deformation_field.write(dvf_path[i])
tm = algo.get_transformation_matrix_forward()
tm.write("{0}/new_tm_{1}.nii".format(path_new_tm, str(i)))
return dvf_path
os.makedirs(path_recon, mode=0o770)
print('Create Folder: {}'.format(path_recon))
if not os.path.exists(path_NAC):
os.makedirs(path_NAC, mode=0o770)
print('Create Folder: {}'.format(path_NAC))
if not os.path.exists(path_moco_NAC):
os.makedirs(path_moco_NAC, mode=0o770)
print('Create Folder: {}'.format(path_moco_NAC))
#%% register EPI to PET with NiftyReg
ref_file = path_NAC + '/nii/' + 'NAC_0.nii'
flo_file = data_path_EPI_image
ref = Eng_ref.ImageData(ref_file)
flo = Eng_ref.ImageData(flo_file)
register = Reg.NiftyAladinSym()
register.set_reference_image(ref)
register.set_floating_image(flo)
register.process()
tm_fwd = register.get_transformation_matrix_forward()
tm_fwd.write(working_folder + '/tm_fwd.txt')
tm_inv = register.get_transformation_matrix_inverse()
tm_inv.write(working_folder + '/tm_inv.txt')
# idy = tm_inv * tm_fwd
# idy.write(working_folder + '/idy.txt')
matrix = numpy.loadtxt('tm_test_epi.txt')
inverse = numpy.linalg.inv(matrix)
tm_fwd2 = Reg.AffineTransformation(matrix)
tm_inv2 = Reg.AffineTransformation(inverse)