#!/usr/bin/env python
# Copyright 2016-2023 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):
"""
Load the config ini, parse settings to WORC
Args:
config_file_path (String): path of the .ini config file
Returns:
settings_dict (dict): dict with the loaded 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 = {'ComBat': dict()}
# Convert settings
settings_dict['ComBat']['batch'] =\
[str(item).strip() for item in
settings['ComBat']['batch'].split(',')]
settings_dict['ComBat']['mod'] =\
[str(item).strip() for item in
settings['ComBat']['mod'].split(',')]
settings_dict['ComBat']['par'] =\
settings['ComBat'].getint('par')
settings_dict['ComBat']['eb'] =\
settings['ComBat'].getint('eb')
settings_dict['ComBat']['language'] =\
str(settings['ComBat']['language'])
settings_dict['ComBat']['matlab'] =\
str(settings['ComBat']['matlab'])
settings_dict['ComBat']['per_feature'] =\
int(settings['ComBat']['per_feature'])
settings_dict['ComBat']['excluded_features'] =\
[str(item).strip() for item in
settings['ComBat']['excluded_features'].split(',')]
return settings_dict