def set_sub_flows_optionals(self, opts):
""" Sets the self._optionals variable with all sub flow arguments
that were passed in the commandline.
"""
self._optionals = {}
for key, sub_dict in iteritems(opts): #opts.iteritems():
self._optionals[key] = \
dict((k, v) for k, v in iteritems(sub_dict) if v is not None)
def set_sub_flows_optionals(self, opts):
""" Sets the self._optionals variable with all sub flow arguments
that were passed in the commandline.
"""
self._optionals = {}
for key, sub_dict in iteritems(opts): #opts.iteritems():
self._optionals[key] = \
dict((k, v) for k, v in iteritems(sub_dict) if v is not None)
def run_flow(flow):
""" Wraps the process of building an argparser that reflects the workflow
that we want to run along with some generic parameters like logging,
force and output strategies. The resulting parameters are then fed to
the workflow's run method.
"""
parser = IntrospectiveArgumentParser()
sub_flows_dicts = parser.add_workflow(flow)
# Common workflow arguments
parser.add_argument('--force',
dest='force',
action='store_true',
default=False,
help='Force overwriting output files.')
parser.add_argument('--out_strat',
action='store',
dest='out_strat',
metavar='string',
required=False,
default='append',
help='Strategy to manage output creation.')
parser.add_argument('--mix_names',
dest='mix_names',
action='store_true',
default=False,
help='Prepend mixed input names to output names.')
# Add logging parameters common to all workflows
msg = 'Log messsages display level. Accepted options include CRITICAL,'
msg += ' ERROR, WARNING, INFO, DEBUG and NOTSET (default INFO).'
parser.add_argument('--log_level',
action='store',
dest='log_level',
metavar='string',
required=False,
default='INFO',
help=msg)
parser.add_argument('--log_file',
action='store',
dest='log_file',
metavar='string',
required=False,
default='',
help='Log file to be saved.')
args = parser.get_flow_args()
logging.basicConfig(filename=args['log_file'],
format='%(levelname)s:%(message)s',
level=get_level(args['log_level']))
# Output management parameters
flow._force_overwrite = args['force']
flow._output_strategy = args['out_strat']
flow._mix_names = args['mix_names']
# Keep only workflow related parameters
del args['force']
del args['log_level']
del args['log_file']
del args['out_strat']
del args['mix_names']
# Remove subflows related params
for sub_flow, params_dict in iteritems(sub_flows_dicts):
for key, _ in iteritems(params_dict):
if key in args.keys():
params_dict[key] = args.pop(key)
# Rename dictionary key to the original param name
params_dict[key.split('.')[1]] = params_dict.pop(key)
if sub_flows_dicts:
flow.set_sub_flows_optionals(sub_flows_dicts)
return flow.run(**args)
def run_flow(flow):
""" Wraps the process of building an argparser that reflects the workflow
that we want to run along with some generic parameters like logging,
force and output strategies. The resulting parameters are then fed to
the workflow's run method.
"""
parser = IntrospectiveArgumentParser()
sub_flows_dicts = parser.add_workflow(flow)
# Common workflow arguments
parser.add_argument('--force', dest='force',
action='store_true', default=False,
help='Force overwriting output files.')
parser.add_argument('--version', action='version',
version='DIPY {}'.format(dipy_version))
parser.add_argument('--out_strat', action='store', dest='out_strat',
metavar='string', required=False, default='absolute',
help='Strategy to manage output creation.')
parser.add_argument('--mix_names', dest='mix_names',
action='store_true', default=False,
help='Prepend mixed input names to output names.')
# Add logging parameters common to all workflows
msg = 'Log messsages display level. Accepted options include CRITICAL,'
msg += ' ERROR, WARNING, INFO, DEBUG and NOTSET (default INFO).'
parser.add_argument('--log_level', action='store', dest='log_level',
metavar='string', required=False, default='INFO',
help=msg)
parser.add_argument('--log_file', action='store', dest='log_file',
metavar='string', required=False, default='',
help='Log file to be saved.')
args = parser.get_flow_args()
logging.basicConfig(filename=args['log_file'],
format='%(levelname)s:%(message)s',
level=get_level(args['log_level']))
# Output management parameters
flow._force_overwrite = args['force']
flow._output_strategy = args['out_strat']
flow._mix_names = args['mix_names']
# Keep only workflow related parameters
del args['force']
del args['log_level']
del args['log_file']
del args['out_strat']
del args['mix_names']
# Remove subflows related params
for sub_flow, params_dict in iteritems(sub_flows_dicts):
for key, _ in iteritems(params_dict):
if key in args.keys():
params_dict[key] = args.pop(key)
# Rename dictionary key to the original param name
params_dict[key.split('.')[1]] = params_dict.pop(key)
if sub_flows_dicts:
flow.set_sub_flows_optionals(sub_flows_dicts)
return flow.run(**args)