ScriptOption('-p', 'Particle list.', True, False), ScriptOption('-c', 'Class label file.', True, False), ScriptOption('-o', 'Output particle list.', True, False), ScriptOption('-t', 'True positive class.', True, True), ScriptOption(['-h', '--help'], 'Help.', False, True) ]) if len(sys.argv) == 1: print(helper) sys.exit() try: pl_filename, class_label_filename, output, tp_label, help = parse_script_options( sys.argv[1:], helper) except Exception as e: print(e) sys.exit() if help is True: print(helper) sys.exit() if tp_label is None: tp_label = 1 else: tp_label = int(tp_label) from pytom.basic.structures import ParticleList pl = ParticleList(".") pl.fromXMLFile(pl_filename) pl.setClassFromLocalizationClassList(class_label_filename) new_pl = pl.particlesFromClass(tp_label) new_pl.toXMLFile(output)