#!/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 segmentix 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 = {'Segmentix': dict(), 'Preprocessing': dict()}
# Segmentation settings
settings_dict['Sementix'] = dict()
settings_dict['Segmentix']['type'] =\
str(settings['Segmentix']['segtype'])
settings_dict['Segmentix']['mask'] =\
str(settings['Segmentix']['mask'])
settings_dict['Segmentix']['radius'] =\
int(settings['Segmentix']['segradius'])
settings_dict['Segmentix']['N_blobs'] =\
int(settings['Segmentix']['N_blobs'])
settings_dict['Segmentix']['fillholes'] =\
settings['Segmentix'].getboolean('fillholes')
settings_dict['Segmentix']['remove_small_objects'] =\
settings['Segmentix'].getboolean('remove_small_objects')
settings_dict['Segmentix']['min_object_size'] =\
int(settings['Segmentix']['min_object_size'])
settings_dict['Segmentix']['AssumeSameImageAndMaskMetadata'] =\
settings['General'].getboolean('AssumeSameImageAndMaskMetadata')
# Check spacing
settings_dict['Preprocessing']['CheckSpacing'] =\
settings['Preprocessing'].getboolean('CheckSpacing')
# Re-orientation
settings_dict['Preprocessing']['CheckOrientation'] =\
settings['Preprocessing'].getboolean('CheckOrientation')
settings_dict['Preprocessing']['OrientationPrimaryAxis'] =\
str(settings['Preprocessing']['OrientationPrimaryAxis'])
# Resampling
settings_dict['Preprocessing']['Resampling'] =\
settings['Preprocessing'].getboolean('Resampling')
settings_dict['Preprocessing']['Resampling_spacing'] =\
[float(item) for item in
settings['Preprocessing']['Resampling_spacing'].split(',')]
if len(settings_dict['Preprocessing']['Resampling_spacing']) != 3:
s = settings_dict['Preprocessing']['Resampling_spacing']
raise ae.WORCValueError(f'Resampling spacing should be three elements, got {s}')
return settings_dict