Source code for WORC.IOparser.config_preprocessing

#!/usr/bin/env python

# Copyright 2016-2020 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.


import configparser
import os
import WORC.addexceptions as ae


[docs]def load_config(config_file_path): """ Parse a WORC configuration file. Arguments: config_file_path: path to the configuration file to be parsed. Returns: settings_dict: dictionary containing all parsed settings. """ if not os.path.exists(config_file_path): e = f'File {config_file_path} does not exist!' raise ae.WORCKeyError(e) settings = configparser.ConfigParser() settings.read(config_file_path) settings_dict = {'Preprocessing': dict(), 'ImageFeatures': dict(), 'General': dict()} settings_dict['Preprocessing']['Normalize'] =\ settings['Preprocessing'].getboolean('Normalize') settings_dict['Preprocessing']['Normalize_ROI'] =\ str(settings['Preprocessing']['Normalize_ROI']) settings_dict['Preprocessing']['ROIdilate'] =\ str(settings['Preprocessing']['ROIdilate']) settings_dict['Preprocessing']['ROIDetermine'] =\ str(settings['Preprocessing']['ROIDetermine']) settings_dict['Preprocessing']['ROIdilateradius'] =\ int(settings['Preprocessing']['ROIdilateradius']) settings_dict['Preprocessing']['Method'] =\ str(settings['Preprocessing']['Method']) settings_dict['ImageFeatures']['image_type'] =\ [str(item).strip() for item in settings['ImageFeatures']['image_type'].split(',')] settings_dict['General']['AssumeSameImageAndMaskMetadata'] =\ settings['General'].getboolean('AssumeSameImageAndMaskMetadata') return settings_dict