#!/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):
"""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(),
'SVMFeatures': dict(), 'Ensemble': dict(),
'Labels': dict()}
settings_dict['ImageFeatures']['image_type'] =\
str(settings['ImageFeatures']['image_type'])
settings_dict['General']['FeatureCalculators'] =\
[str(item).strip('[]') for item in
settings['General']['FeatureCalculators'].split(',')]
settings_dict['General']['Preprocessing'] =\
str(settings['General']['Preprocessing'])
settings_dict['General']['PCE'] =\
settings['General'].getboolean('PCE')
settings_dict['General']['Segmentix'] =\
settings['General'].getboolean('Segmentix')
# Settings for ensembling
settings_dict['Ensemble']['Method'] =\
str(settings['Ensemble']['Method'])
settings_dict['Ensemble']['Size'] =\
int(settings['Ensemble']['Size'])
# Label settings
settings_dict['Labels']['label_names'] =\
[str(item).strip() for item in
settings['Labels']['label_names'].split(',')]
settings_dict['Labels']['modus'] =\
str(settings['Labels']['modus'])
# Whether to use some methods or not
settings_dict['General']['ComBat'] =\
str(settings['General']['ComBat'])
settings_dict['General']['Fingerprint'] =\
str(settings['General']['Fingerprint'])
settings_dict['Preprocessing']['Resampling'] =\
settings['Preprocessing'].getboolean('Resampling')
return settings_dict