def registraion_to_common_space(self, ref_img, ref_lab, structure=205):
self.structure = structure
for i in range(self.mv_imgs.num_data):
print("processing %d" % (i))
mv_img = self.mv_imgs.get_file_obj(i)
mv_lab = self.mv_labels.get_file_obj(i)
ref_lab = recast_pixel_val(mv_lab, ref_lab)
ref_img = recast_pixel_val(mv_img, ref_img)
initial_transform = sitk.CenteredTransformInitializer(
ref_lab, mv_lab, sitk.Euler3DTransform(),
sitk.CenteredTransformInitializerFilter.GEOMETRY)
# mv_label_resampled=mv_lab
# mv_img_resampled=mv_img
# uncomment the code below if u wanna preregistration
mv_label_resampled = sitk.Resample(mv_lab, ref_lab,
initial_transform,
sitk.sitkNearestNeighbor, 0,
mv_lab.GetPixelID())
initial_transform = sitk.CenteredTransformInitializer(
ref_img, mv_img, sitk.Euler3DTransform(),
sitk.CenteredTransformInitializerFilter.GEOMETRY)
mv_img_resampled = sitk.Resample(mv_img, ref_img,
initial_transform,
sitk.sitkLinear, 0,
mv_img.GetPixelID())
self.__itksave(mv_img, mv_lab, mv_img_resampled,
mv_label_resampled, i)
def registration_back_to_individual_space(self):
for i in range(self.mv_imgs.num_data):
print("processing %d" % (i))
mv_img = self.mv_imgs.get_file_obj(i)
mv_lab = self.mv_labels.get_file_obj(i)
ref_img = self.ref_img.get_file_obj(i)
ref_img = recast_pixel_val(mv_img, ref_img)
initial_transform = sitk.CenteredTransformInitializer(
ref_img, mv_img, sitk.Euler3DTransform(),
sitk.CenteredTransformInitializerFilter.GEOMETRY)
# mv_label_resampled=mv_lab
# mv_img_resampled=mv_img
# uncomment the code below if u wanna preregistration
mv_label_resampled = sitk.Resample(mv_lab, ref_img,
initial_transform,
sitk.sitkNearestNeighbor, 0.0,
mv_lab.GetPixelID())
mv_img_resampled = sitk.Resample(mv_img, ref_img,
initial_transform,
sitk.sitkLinear, 0.0,
mv_img.GetPixelID())
self.__itksave(mv_img,
mv_lab,
mv_img_resampled,
mv_label_resampled,
i,
tag="_reg_back",
need_write_image=False)
def de_rotate(refs, tgts, output_dir):
for r, t in zip(refs, tgts):
ref = sitk.ReadImage(r)
lab = sitk.ReadImage(t)
ref = recast_pixel_val(lab, ref)
initial_transform = sitk.CenteredTransformInitializer(
ref, lab, sitk.Euler3DTransform(),
sitk.CenteredTransformInitializerFilter.GEOMETRY)
lab_resampled = sitk.Resample(lab, ref, initial_transform,
sitk.sitkNearestNeighbor, 0,
lab.GetPixelID())
sitk_write_image(lab_resampled,
dir=output_dir,
name=os.path.basename(t))
def de_rotate(self, structure):
save_dir = self.target_labels.dir_name + "_deRotate"
self.structure = structure
for i in range(self.target_labels.num_data):
print("processing %d" % (i))
ref = self.references.get_file_obj(i)
lab = self.target_labels.get_file_obj(i)
ref = recast_pixel_val(lab, ref)
initial_transform = sitk.CenteredTransformInitializer(
ref, lab, sitk.Euler3DTransform(),
sitk.CenteredTransformInitializerFilter.GEOMETRY)
lab_resampled = sitk.Resample(lab, ref, initial_transform,
sitk.sitkNearestNeighbor, 0,
lab.GetPixelID())
self.__itksave_label(lab_resampled, i, save_dir)
return save_dir