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 warp_back_seg(self, path_warp):
# get 3D images from list of slices
im_dest = self.get_im_from_list(np.array([target_slice.im for target_slice in self.target_im]))
im_src_gm = self.get_im_from_list(np.array([target_slice.gm_seg_M for target_slice in self.target_im]))
im_src_wm = self.get_im_from_list(np.array([target_slice.wm_seg_M for target_slice in self.target_im]))
#
fname_dic_space2slice_space = slash_at_the_end(path_warp, slash=1)+'warp_dic2target.nii.gz'
interpolation = 'nn' if self.param_seg.type_seg == 'bin' else 'linear'
# warp GM
im_src_gm_reg = apply_transfo(im_src_gm, im_dest, fname_dic_space2slice_space, interp=interpolation, rm_tmp=self.param.rm_tmp)
# warp WM
im_src_wm_reg = apply_transfo(im_src_wm, im_dest, fname_dic_space2slice_space, interp=interpolation, rm_tmp=self.param.rm_tmp)
for i, target_slice in enumerate(self.target_im):
# set GM and WM for each slice
target_slice.set(gm_seg=im_src_gm_reg.data[i], wm_seg=im_src_wm_reg.data[i])
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 warp_back_seg(self, path_warp):
# get 3D images from list of slices
im_dest = self.get_im_from_list(np.array([target_slice.im for target_slice in self.target_im]))
im_src_gm = self.get_im_from_list(np.array([target_slice.gm_seg_M for target_slice in self.target_im]))
#
fname_dic_space2slice_space = slash_at_the_end(path_warp, slash=1) + 'warp_dic2target.nii.gz'
interpolation = 'linear'
# warp GM
im_src_gm_reg = apply_transfo(im_src_gm, im_dest, fname_dic_space2slice_space, interp=interpolation, rm_tmp=self.param.rm_tmp)
for i, target_slice in enumerate(self.target_im):
# set GM for each slice
target_slice.set(gm_seg=im_src_gm_reg.data[i])
def warp_back_seg(self, path_warp):
# get 3D images from list of slices
im_dest = self.get_im_from_list(np.array([target_slice.im for target_slice in self.target_im]))
im_src_gm = self.get_im_from_list(np.array([target_slice.gm_seg_M for target_slice in self.target_im]))
#
fname_dic_space2slice_space = os.path.join(path_warp, 'warp_dic2target.nii.gz')
interpolation = 'linear'
# warp GM
im_src_gm_reg = apply_transfo(im_src_gm, im_dest, fname_dic_space2slice_space, interp=interpolation, rm_tmp=self.param.rm_tmp)
for i, target_slice in enumerate(self.target_im):
# set GM for each slice
target_slice.set(gm_seg=im_src_gm_reg.data[i])