def register_target(self):
# create dir to store warping fields
path_warping_fields = 'warp_target'
if not os.path.exists(path_warping_fields):
os.mkdir(path_warping_fields)
# get 3D images from list of slices
im_dest = self.get_im_from_list(
np.array(
[self.model.mean_image for target_slice in self.target_im]))
im_src = self.get_im_from_list(
np.array([target_slice.im for target_slice in self.target_im]))
# register list of target slices on list of model mean image
im_src_reg, fname_src2dest, fname_dest2src = register_data(
im_src,
im_dest,
param_reg=self.param_data.register_param,
path_copy_warp=path_warping_fields,
rm_tmp=self.param.rm_tmp)
# rename warping fields
fname_src2dest_save = 'warp_target2dic.nii.gz'
fname_dest2src_save = 'warp_dic2target.nii.gz'
shutil.move(os.path.join(path_warping_fields, fname_src2dest),
os.path.join(path_warping_fields, fname_src2dest_save))
shutil.move(os.path.join(path_warping_fields, fname_dest2src),
os.path.join(path_warping_fields, fname_dest2src_save))
#
for i, target_slice in enumerate(self.target_im):
# set moved image for each slice
target_slice.set(im_m=im_src_reg.data[i])
return path_warping_fields
def coregister_model_data(self):
# get mean image
im_mean = Image(param=self.mean_image)
# register all slices WM on mean WM
for dic_slice in self.slices:
# create a directory to get the warping fields
warp_dir = 'wf_slice' + str(dic_slice.id)
if not os.path.exists(warp_dir):
os.mkdir(warp_dir)
# get slice mean WM image
im_slice = Image(param=dic_slice.im)
# register slice image on mean dic image
im_slice_reg, fname_src2dest, fname_dest2src = register_data(
im_src=im_slice,
im_dest=im_mean,
param_reg=self.param_data.register_param,
path_copy_warp=warp_dir)
shape = im_slice_reg.data.shape
# use forward warping field to register all slice wm
list_wmseg_reg = []
for wm_seg in dic_slice.wm_seg:
im_wmseg = Image(param=wm_seg)
im_wmseg_reg = apply_transfo(im_src=im_wmseg,
im_dest=im_mean,
warp=warp_dir + '/' +
fname_src2dest,
interp='nn')
list_wmseg_reg.append(im_wmseg_reg.data.reshape(shape))
# use forward warping field to register gm seg
list_gmseg_reg = []
for gm_seg in dic_slice.gm_seg:
im_gmseg = Image(param=gm_seg)
im_gmseg_reg = apply_transfo(im_src=im_gmseg,
im_dest=im_mean,
warp=warp_dir + '/' +
fname_src2dest,
interp='nn')
list_gmseg_reg.append(im_gmseg_reg.data.reshape(shape))
# set slice attributes with data registered into the model space
dic_slice.set(im_m=im_slice_reg.data)
dic_slice.set(wm_seg_m=list_wmseg_reg)
dic_slice.set(gm_seg_m=list_gmseg_reg)
# remove warping fields directory
if self.param.rm_tmp:
shutil.rmtree(warp_dir)
def register_target(self):
# create dir to store warping fields
path_warping_fields = 'warp_target'
if not os.path.exists(path_warping_fields):
os.mkdir(path_warping_fields)
# get 3D images from list of slices
im_dest = self.get_im_from_list(np.array([self.model.mean_image for target_slice in self.target_im]))
im_src = self.get_im_from_list(np.array([target_slice.im for target_slice in self.target_im]))
# register list of target slices on list of model mean image
im_src_reg, fname_src2dest, fname_dest2src = register_data(im_src, im_dest, param_reg=self.param_data.register_param, path_copy_warp=path_warping_fields, rm_tmp=self.param.rm_tmp)
# rename warping fields
fname_src2dest_save = 'warp_target2dic.nii.gz'
fname_dest2src_save = 'warp_dic2target.nii.gz'
shutil.move(os.path.join(path_warping_fields, fname_src2dest), os.path.join(path_warping_fields, fname_src2dest_save))
shutil.move(os.path.join(path_warping_fields, fname_dest2src), os.path.join(path_warping_fields, fname_dest2src_save))
#
for i, target_slice in enumerate(self.target_im):
# set moved image for each slice
target_slice.set(im_m=im_src_reg.data[i])
return path_warping_fields
def coregister_model_data(self):
# get mean image
im_mean = Image(param=self.mean_image)
# register all slices WM on mean WM
for dic_slice in self.slices:
# create a directory to get the warping fields
warp_dir = 'wf_slice'+str(dic_slice.id)
if not os.path.exists(warp_dir):
os.mkdir(warp_dir)
# get slice mean WM image
im_slice = Image(param=dic_slice.im)
# register slice image on mean dic image
im_slice_reg, fname_src2dest, fname_dest2src = register_data(im_src=im_slice, im_dest=im_mean, param_reg=self.param_data.register_param, path_copy_warp=warp_dir)
shape = im_slice_reg.data.shape
# use forward warping field to register all slice wm
list_wmseg_reg = []
for wm_seg in dic_slice.wm_seg:
im_wmseg = Image(param=wm_seg)
im_wmseg_reg = apply_transfo(im_src=im_wmseg, im_dest=im_mean, warp=warp_dir+'/'+fname_src2dest, interp='nn')
list_wmseg_reg.append(im_wmseg_reg.data.reshape(shape))
# use forward warping field to register gm seg
list_gmseg_reg = []
for gm_seg in dic_slice.gm_seg:
im_gmseg = Image(param=gm_seg)
im_gmseg_reg = apply_transfo(im_src=im_gmseg, im_dest=im_mean, warp=warp_dir+'/'+fname_src2dest, interp='nn')
list_gmseg_reg.append(im_gmseg_reg.data.reshape(shape))
# set slice attributes with data registered into the model space
dic_slice.set(im_m=im_slice_reg.data)
dic_slice.set(wm_seg_m=list_wmseg_reg)
dic_slice.set(gm_seg_m=list_gmseg_reg)
# remove warping fields directory
if self.param.rm_tmp:
shutil.rmtree(warp_dir)
