def get_config():
"""
Get the CNN configuration from file
"""
default_config = ConfigParser.SafeConfigParser()
default_config.read(os.path.join(CURRENT_PATH, 'config', 'default.cfg'))
user_config = ConfigParser.RawConfigParser()
user_config.read(os.path.join(CURRENT_PATH, 'config', 'configuration.cfg'))
# read user's configuration file
options = load_options(default_config, user_config)
options['tmp_folder'] = CURRENT_PATH + '/tmp'
# set paths taking into account the host OS
host_os = platform.system()
if host_os == 'Linux':
options['niftyreg_path'] = CURRENT_PATH + '/libs/linux/niftyreg'
options['robex_path'] = CURRENT_PATH + '/libs/linux/ROBEX/runROBEX.sh'
options['test_slices'] = 256
elif host_os == 'Windows':
options['niftyreg_path'] = os.path.normpath(
os.path.join(CURRENT_PATH, 'libs', 'win', 'niftyreg'))
options['robex_path'] = os.path.normpath(
os.path.join(CURRENT_PATH, 'libs', 'win', 'ROBEX', 'runROBEX.bat'))
options['test_slices'] = 256
else:
print "The OS system", host_os, "is not currently supported."
exit()
# print options when debugging
if options['debug']:
print_options(options)
return options
container = args.docker
# --------------------------------------------------
# load default options and update them with user information
# from utils.load_options import *
# --------------------------------------------------
default_config = ConfigParser.SafeConfigParser()
default_config.read(os.path.join(CURRENT_PATH, 'config', 'default.cfg'))
user_config = ConfigParser.RawConfigParser()
user_config.read(os.path.join(CURRENT_PATH, 'config', 'configuration.cfg'))
# read user's configuration file
options = load_options(default_config, user_config)
if options['debug']:
print_options(options)
# tensorflow backend
device = str(options['gpu_number'])
print "DEBUG: ", device
os.environ['KERAS_BACKEND'] = 'tensorflow'
os.environ["CUDA_VISIBLE_DEVICES"] = device
# set paths taking into account the host OS
host_os = platform.system()
if host_os == 'Linux':
options['niftyreg_path'] = CURRENT_PATH + '/libs/linux/niftyreg'
options['robex_path'] = CURRENT_PATH + '/libs/linux/ROBEX/runROBEX.sh'
options['test_slices'] = 256
elif host_os == 'Windows':
options['niftyreg_path'] = os.path.normpath(
