def _run(self): ph.print_title("Volume-to-Volume Registration") for i in range(0, len(self._stacks)): txt = "Volume-to-Volume Registration -- " \ "Stack %d/%d" % (i + 1, len(self._stacks)) if self._verbose: ph.print_subtitle(txt) else: ph.print_info(txt) if self._robust: transform_initializer = tinit.TransformInitializer( fixed=self._reference, moving=self._stacks[i], similarity_measure="NCC", refine_pca_initializations=True, ) transform_initializer.run() transform_sitk = transform_initializer.get_transform_sitk() transform_sitk = sitk.AffineTransform( transform_sitk.GetInverse()) else: self._registration_method.set_moving(self._reference) self._registration_method.set_fixed(self._stacks[i]) self._registration_method.run() transform_sitk = self._registration_method.get_registration_transform_sitk() # Update position of stack self._stacks[i].update_motion_correction(transform_sitk)
def main(): time_start = ph.start_timing() np.set_printoptions(precision=3) input_parser = InputArgparser( description="Register an obtained reconstruction (moving) " "to a template image/space (fixed) using rigid registration. " "The resulting registration can optionally be applied to previously " "obtained motion correction slice transforms so that a volumetric " "reconstruction is possible in the (standard anatomical) space " "defined by the fixed.", ) input_parser.add_fixed(required=True) input_parser.add_moving(required=True) input_parser.add_output(help="Path to registration transform (.txt)", required=True) input_parser.add_fixed_mask(required=False) input_parser.add_moving_mask(required=False) input_parser.add_option( option_string="--initial-transform", type=str, help="Path to initial transform. " "If not provided, registration will be initialized based on " "rigid alignment of eigenbasis of the fixed/moving image masks " "using principal component analysis", default=None) input_parser.add_v2v_method( option_string="--method", help="Registration method used for the registration.", default="RegAladin", ) input_parser.add_argument( "--refine-pca", "-refine-pca", action='store_true', help="If given, PCA-based initializations will be refined using " "RegAladin registrations.") input_parser.add_dir_input_mc() input_parser.add_verbose(default=0) input_parser.add_log_config(default=1) args = input_parser.parse_args() input_parser.print_arguments(args) if args.log_config: input_parser.log_config(os.path.abspath(__file__)) if not args.output.endswith(".txt"): raise IOError("output transformation path must end in '.txt'") dir_output = os.path.dirname(args.output) ph.create_directory(dir_output) # --------------------------------Read Data-------------------------------- ph.print_title("Read Data") fixed = st.Stack.from_filename(file_path=args.fixed, file_path_mask=args.fixed_mask, extract_slices=False) moving = st.Stack.from_filename(file_path=args.moving, file_path_mask=args.moving_mask, extract_slices=False) path_to_tmp_output = os.path.join( DIR_TMP, ph.append_to_filename(os.path.basename(args.moving), "_warped")) # ---------------------------- Initialization ---------------------------- if args.initial_transform is None: ph.print_title("Estimate initial transform using PCA") if args.moving_mask is None or args.fixed_mask is None: ph.print_warning("Fixed and moving masks are strongly recommended") transform_initializer = tinit.TransformInitializer( fixed=fixed, moving=moving, similarity_measure="NMI", refine_pca_initializations=args.refine_pca, ) transform_initializer.run() transform_init_sitk = transform_initializer.get_transform_sitk() else: transform_init_sitk = sitkh.read_transform_sitk(args.initial_transform) sitk.WriteTransform(transform_init_sitk, args.output) # -------------------Register Reconstruction to Template------------------- ph.print_title("Registration") if args.method == "RegAladin": path_to_transform_regaladin = os.path.join(DIR_TMP, "transform_regaladin.txt") # Convert SimpleITK to RegAladin transform cmd = "simplereg_transform -sitk2nreg %s %s" % ( args.output, path_to_transform_regaladin) ph.execute_command(cmd, verbose=False) # Run NiftyReg cmd_args = ["reg_aladin"] cmd_args.append("-ref '%s'" % args.fixed) cmd_args.append("-flo '%s'" % args.moving) cmd_args.append("-res '%s'" % path_to_tmp_output) cmd_args.append("-inaff '%s'" % path_to_transform_regaladin) cmd_args.append("-aff '%s'" % path_to_transform_regaladin) cmd_args.append("-rigOnly") cmd_args.append("-ln 2") # seems to perform better for spina bifida cmd_args.append("-voff") if args.fixed_mask is not None: cmd_args.append("-rmask '%s'" % args.fixed_mask) # To avoid error "0 correspondences between blocks were found" that can # occur for some cases. Also, disable moving mask, as this would be ignored # anyway cmd_args.append("-noSym") # if args.moving_mask is not None: # cmd_args.append("-fmask '%s'" % args.moving_mask) ph.print_info("Run Registration (RegAladin) ... ", newline=False) ph.execute_command(" ".join(cmd_args), verbose=False) print("done") # Convert RegAladin to SimpleITK transform cmd = "simplereg_transform -nreg2sitk '%s' '%s'" % ( path_to_transform_regaladin, args.output) ph.execute_command(cmd, verbose=False) else: path_to_transform_flirt = os.path.join(DIR_TMP, "transform_flirt.txt") # Convert SimpleITK into FLIRT transform cmd = "simplereg_transform -sitk2flirt '%s' '%s' '%s' '%s'" % ( args.output, args.fixed, args.moving, path_to_transform_flirt) ph.execute_command(cmd, verbose=False) # Define search angle ranges for FLIRT in all three dimensions search_angles = [ "-searchr%s -%d %d" % (x, 180, 180) for x in ["x", "y", "z"] ] cmd_args = ["flirt"] cmd_args.append("-in '%s'" % args.moving) cmd_args.append("-ref '%s'" % args.fixed) if args.initial_transform is not None: cmd_args.append("-init '%s'" % path_to_transform_flirt) cmd_args.append("-omat '%s'" % path_to_transform_flirt) cmd_args.append("-out '%s'" % path_to_tmp_output) cmd_args.append("-dof 6") cmd_args.append((" ").join(search_angles)) if args.moving_mask is not None: cmd_args.append("-inweight '%s'" % args.moving_mask) if args.fixed_mask is not None: cmd_args.append("-refweight '%s'" % args.fixed_mask) ph.print_info("Run Registration (FLIRT) ... ", newline=False) ph.execute_command(" ".join(cmd_args), verbose=False) print("done") # Convert FLIRT to SimpleITK transform cmd = "simplereg_transform -flirt2sitk '%s' '%s' '%s' '%s'" % ( path_to_transform_flirt, args.fixed, args.moving, args.output) ph.execute_command(cmd, verbose=False) if args.dir_input_mc is not None: ph.print_title("Update Motion-Correction Transformations") transform_sitk = sitkh.read_transform_sitk(args.output, inverse=1) if args.dir_input_mc.endswith("/"): subdir_mc = args.dir_input_mc.split("/")[-2] else: subdir_mc = args.dir_input_mc.split("/")[-1] dir_output_mc = os.path.join(dir_output, subdir_mc) ph.create_directory(dir_output_mc, delete_files=True) pattern = REGEX_FILENAMES + "[.]tfm" p = re.compile(pattern) trafos = [t for t in os.listdir(args.dir_input_mc) if p.match(t)] for t in trafos: path_to_input_transform = os.path.join(args.dir_input_mc, t) path_to_output_transform = os.path.join(dir_output_mc, t) t_sitk = sitkh.read_transform_sitk(path_to_input_transform) t_sitk = sitkh.get_composite_sitk_affine_transform( transform_sitk, t_sitk) sitk.WriteTransform(t_sitk, path_to_output_transform) ph.print_info("%d transformations written to '%s'" % (len(trafos), dir_output_mc)) if args.verbose: ph.show_niftis([args.fixed, path_to_tmp_output]) elapsed_time_total = ph.stop_timing(time_start) # Summary ph.print_title("Summary") print("Computational Time: %s" % (elapsed_time_total)) return 0