def run():
"""
meta_parser is first used to find out location
of the configuration file. Based on the application_name
or meta_parser.prog name, the section parsers are organised
to find system parameters and application specific
parameters.
:return: system parameters is a group of parameters including
SYSTEM_SECTIONS and app_module.REQUIRED_CONFIG_SECTION
input_data_args is a group of input data sources to be
used by niftynet.io.ImageReader
"""
meta_parser = argparse.ArgumentParser(
description="Launch a NiftyNet application.",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=textwrap.dedent(EPILOG_STRING))
version_string = get_niftynet_version_string()
meta_parser.add_argument("action",
help="train networks, run inferences "
"or evaluate inferences",
metavar='ACTION',
choices=list(ACTIONS))
meta_parser.add_argument("-v",
"--version",
action='version',
version=version_string)
meta_parser.add_argument("-c",
"--conf",
help="specify configurations from a file",
metavar="CONFIG_FILE")
meta_parser.add_argument("-a",
"--application_name",
help="specify an application module name",
metavar='APPLICATION_NAME',
default="")
meta_args, args_from_cmdline = meta_parser.parse_known_args()
print(version_string)
# read configurations, to be parsed by sections
config_file_name = __resolve_config_file_path(meta_args.conf)
config = NiftyNetLaunchConfig()
config.read([config_file_name])
# infer application name from command
app_name = None
try:
parser_prog = meta_parser.prog.replace('.py', '')
app_name = parser_prog if parser_prog in SUPPORTED_APP \
else meta_args.application_name
assert app_name
except (AttributeError, AssertionError):
raise ValueError("\nUnknown application {}, or did you forget '-a' "
"command argument?{}".format(app_name, EPILOG_STRING))
# load application by name
app_module = ApplicationFactory.create(app_name)
try:
assert app_module.REQUIRED_CONFIG_SECTION, \
"\nREQUIRED_CONFIG_SECTION should be static variable " \
"in {}".format(app_module)
has_section_in_config(config, app_module.REQUIRED_CONFIG_SECTION)
except AttributeError:
raise AttributeError(
"Application code doesn't have REQUIRED_CONFIG_SECTION property. "
"{} should be an instance of "
"niftynet.application.base_application".format(app_module))
except ValueError:
raise ValueError(
"\n{} requires [{}] section in the config file.{}".format(
app_name, app_module.REQUIRED_CONFIG_SECTION, EPILOG_STRING))
# check keywords in configuration file
_check_config_file_keywords(config)
# using configuration as default, and parsing all command line arguments
# command line args override the configure file options
all_args = {}
for section in config.sections():
# try to rename user-specified sections for consistency
section = standardise_section_name(config, section)
section_defaults = dict(config.items(section))
section_args, args_from_cmdline = \
_parse_arguments_by_section([],
section,
section_defaults,
args_from_cmdline,
app_module.REQUIRED_CONFIG_SECTION)
all_args[section] = section_args
# check if any args from command line not recognised
_check_cmd_remaining_keywords(list(args_from_cmdline))
# split parsed results in all_args
# into dictionaries of system_args and input_data_args
system_args, input_data_args = {}, {}
for section in all_args:
# copy system default sections to ``system_args``
if section in SYSTEM_SECTIONS:
system_args[section] = all_args[section]
continue
# copy application specific sections to ``system_args``
if section == app_module.REQUIRED_CONFIG_SECTION:
system_args['CUSTOM'] = all_args[section]
vars(system_args['CUSTOM'])['name'] = app_name
continue
# copy non-default sections to ``input_data_args``
input_data_args[section] = all_args[section]
# set the output path of csv list if not exists
try:
csv_path = resolve_file_name(
input_data_args[section].csv_file,
(os.path.dirname(config_file_name), NIFTYNET_HOME))
input_data_args[section].csv_file = csv_path
# don't search files if csv specified in config
try:
delattr(input_data_args[section], 'path_to_search')
except AttributeError:
pass
except (IOError, TypeError):
input_data_args[section].csv_file = ''
# preserve ``config_file`` and ``action parameter`` from the meta_args
system_args['CONFIG_FILE'] = argparse.Namespace(path=config_file_name)
# mapping the captured action argument to a string in ACTIONS
system_args['SYSTEM'].action = \
look_up_operations(meta_args.action, ACTIONS)
if not system_args['SYSTEM'].model_dir:
system_args['SYSTEM'].model_dir = os.path.join(
os.path.dirname(config_file_name), 'model')
return system_args, input_data_args
def run():
"""
meta_parser is first used to find out location
of the configuration file. based on the application_name
or meta_parser.prog name, the section parsers are organised
to find system parameters and application specific
parameters.
:return: system parameters is a group of parameters including
SYSTEM_SECTIONS and app_module.REQUIRED_CONFIG_SECTION
input_data_args is a group of input data sources to be
used by niftynet.io.ImageReader
"""
meta_parser = argparse.ArgumentParser(
description="Launch a NiftyNet application.",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=textwrap.dedent(epilog_string))
version_string = get_niftynet_version_string()
meta_parser.add_argument("action",
help="train networks or run inferences",
metavar='ACTION',
choices=['train', 'inference'])
meta_parser.add_argument("-v",
"--version",
action='version',
version=version_string)
meta_parser.add_argument("-c",
"--conf",
help="specify configurations from a file",
metavar="CONFIG_FILE")
meta_parser.add_argument("-a",
"--application_name",
help="specify an application module name",
metavar='APPLICATION_NAME',
default="")
meta_args, args_from_cmdline = meta_parser.parse_known_args()
print(version_string)
# read configurations, to be parsed by sections
if not meta_args.conf:
print("\nNo configuration file has been provided, did you "
"forget '-c' command argument?{}".format(epilog_string))
raise IOError
# Resolve relative configuration file location
config_path = meta_args.conf
if not os.path.isfile(config_path):
relative_conf_file = os.path.join(
NiftyNetGlobalConfig().get_default_examples_folder(), config_path,
config_path + "_config.ini")
if os.path.isfile(relative_conf_file):
config_path = relative_conf_file
os.chdir(os.path.dirname(config_path))
else:
print("\nConfiguration file not found: {}.{}".format(
config_path, epilog_string))
raise IOError
config = configparser.ConfigParser()
config.read([config_path])
app_module = None
module_name = None
try:
if meta_parser.prog[:-3] in SUPPORTED_APP:
module_name = meta_parser.prog[:-3]
elif meta_parser.prog in SUPPORTED_APP:
module_name = meta_parser.prog
else:
module_name = meta_args.application_name
app_module = ApplicationFactory.create(module_name)
assert app_module.REQUIRED_CONFIG_SECTION, \
"\nREQUIRED_CONFIG_SECTION should be static variable " \
"in {}".format(app_module)
has_section_in_config(config, app_module.REQUIRED_CONFIG_SECTION)
except ValueError:
if app_module:
section_name = app_module.REQUIRED_CONFIG_SECTION
print('\n{} requires [{}] section in the config file.{}'.format(
module_name, section_name, epilog_string))
if not module_name:
print("\nUnknown application {}, or did you forget '-a' "
"command argument?{}".format(module_name, epilog_string))
raise
# check keywords in configuration file
check_keywords(config)
# using configuration as default, and parsing all command line arguments
all_args = {}
for section in config.sections():
# try to rename user-specified sections for consistency
section = standardise_section_name(config, section)
section_defaults = dict(config.items(section))
section_args, args_from_cmdline = \
_parse_arguments_by_section([],
section,
section_defaults,
args_from_cmdline,
app_module.REQUIRED_CONFIG_SECTION)
all_args[section] = section_args
# command line parameters should be valid
assert not args_from_cmdline, \
'\nUnknown parameter: {}{}'.format(args_from_cmdline, epilog_string)
# split parsed results in all_args
# into dictionaries of system_args and input_data_args
system_args = {}
input_data_args = {}
# copy system default sections to ``system_args``
for section in all_args:
if section in SYSTEM_SECTIONS:
system_args[section] = all_args[section]
elif section == app_module.REQUIRED_CONFIG_SECTION:
system_args['CUSTOM'] = all_args[section]
vars(system_args['CUSTOM'])['name'] = module_name
if all_args['SYSTEM'].model_dir is None:
all_args['SYSTEM'].model_dir = os.path.join(
os.path.dirname(meta_args.conf), 'model')
# copy non-default sections to ``input_data_args``
for section in all_args:
if section in SYSTEM_SECTIONS:
continue
if section == app_module.REQUIRED_CONFIG_SECTION:
continue
input_data_args[section] = all_args[section]
# set the output path of csv list if not exists
csv_path = input_data_args[section].csv_file
if os.path.isfile(csv_path):
# don't search files if csv specified in config
try:
delattr(input_data_args[section], 'path_to_search')
except AttributeError:
pass
else:
input_data_args[section].csv_file = ''
# preserve ``config_file`` and ``action parameter`` from the meta_args
system_args['CONFIG_FILE'] = argparse.Namespace(path=meta_args.conf)
system_args['SYSTEM'].action = meta_args.action
return system_args, input_data_args
def run():
"""
meta_parser is first used to find out location
of the configuration file. based on the application_name
or meta_parser.prog name, the section parsers are organised
to find system parameters and application specific
parameters
:return: system parameters is a group of parameters including
SYSTEM_SECTIONS and app_module.REQUIRED_CONFIG_SECTION
input_data_args is a group of input data sources to be
used by niftynet.io.ImageReader
"""
meta_parser = argparse.ArgumentParser(
epilog=
'Please visit https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/tree/dev/demos '
'for more info.')
version_string = get_niftynet_version_string()
meta_parser.add_argument("-v",
"--version",
action='version',
version=version_string)
meta_parser.add_argument(
"-c",
"--conf",
help="Specify configurations from a file",
metavar="File",
)
meta_parser.add_argument(
"-a",
"--application_name",
help="Specify application name",
default="",
)
meta_args, args_from_cmdline = meta_parser.parse_known_args()
print(version_string)
# read configurations, to be parsed by sections
if (meta_args.conf is None) or (not os.path.isfile(meta_args.conf)):
raise IOError("Configuration file not found {}".format(meta_args.conf))
config = configparser.ConfigParser()
config.read([meta_args.conf])
try:
if meta_parser.prog[:-3] in SUPPORTED_APP:
module_name = meta_parser.prog[:-3]
elif meta_parser.prog in SUPPORTED_APP:
module_name = meta_parser.prog
else:
module_name = meta_args.application_name
app_module = ApplicationFactory.create(module_name)
assert app_module.REQUIRED_CONFIG_SECTION, \
"REQUIRED_CONFIG_SECTION should be static variable " \
"in {}".format(app_module)
has_section_in_config(config, app_module.REQUIRED_CONFIG_SECTION)
except ValueError:
raise ValueError('{} requires [{}] section in the config file'.format(
module_name, app_module.REQUIRED_CONFIG_SECTION))
# check keywords in configuration file
check_keywords(config)
# using configuration as default, and parsing all command line arguments
all_args = {}
for section in config.sections():
# try to rename user-specified sections for consistency
section = standardise_section_name(config, section)
section_defaults = dict(config.items(section))
section_args, args_from_cmdline = \
_parse_arguments_by_section([],
section,
section_defaults,
args_from_cmdline,
app_module.REQUIRED_CONFIG_SECTION)
all_args[section] = section_args
# command line parameters should be valid
assert not args_from_cmdline, \
'unknown parameter: {}'.format(args_from_cmdline)
# split parsed results in all_args
# into dictionary of system_args and input_data_args
system_args = {}
input_data_args = {}
for section in all_args:
if section in SYSTEM_SECTIONS:
system_args[section] = all_args[section]
elif section == app_module.REQUIRED_CONFIG_SECTION:
system_args['CUSTOM'] = all_args[section]
vars(system_args['CUSTOM'])['name'] = module_name
else:
input_data_args[section] = all_args[section]
# set the output path of csv list if not exists
csv_path = input_data_args[section].csv_file
if not os.path.isfile(csv_path):
csv_filename = os.path.join(all_args['SYSTEM'].model_dir,
'{}.csv'.format(section))
input_data_args[section].csv_file = csv_filename
else:
# don't search files if csv specified in config
try:
delattr(input_data_args[section], 'path_to_search')
except AttributeError:
pass
# update conf path
system_args['CONFIG_FILE'] = argparse.Namespace(path=meta_args.conf)
return system_args, input_data_args
def run():
"""
meta_parser is first used to find out location
of the configuration file. based on the application_name
or meta_parser.prog name, the section parsers are organised
to find system parameters and application specific
parameters.
:return: system parameters is a group of parameters including
SYSTEM_SECTIONS and app_module.REQUIRED_CONFIG_SECTION
input_data_args is a group of input data sources to be
used by niftynet.io.ImageReader
"""
meta_parser = argparse.ArgumentParser(
description="Launch a NiftyNet application.",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=textwrap.dedent(epilog_string))
version_string = get_niftynet_version_string()
meta_parser.add_argument("action",
help="train networks or run inferences",
metavar='ACTION',
choices=['train', 'inference'])
meta_parser.add_argument("-v", "--version",
action='version',
version=version_string)
meta_parser.add_argument("-c", "--conf",
help="specify configurations from a file",
metavar="CONFIG_FILE")
meta_parser.add_argument("-a", "--application_name",
help="specify an application module name",
metavar='APPLICATION_NAME',
default="")
meta_args, args_from_cmdline = meta_parser.parse_known_args()
print(version_string)
# read configurations, to be parsed by sections
if not meta_args.conf:
print("\nNo configuration file has been provided, did you "
"forget '-c' command argument?{}".format(epilog_string))
raise IOError
# Resolve relative configuration file location
config_path = os.path.expanduser(meta_args.conf)
if not os.path.isfile(config_path):
relative_conf_file = os.path.join(
NiftyNetGlobalConfig().get_default_examples_folder(),
config_path,
config_path + "_config.ini")
if os.path.isfile(relative_conf_file):
config_path = relative_conf_file
os.chdir(os.path.dirname(config_path))
else:
print("\nConfiguration file not found: {}.{}".format(
config_path, epilog_string))
raise IOError
config = configparser.ConfigParser()
config.read([config_path])
app_module = None
module_name = None
try:
if meta_parser.prog[:-3] in SUPPORTED_APP:
module_name = meta_parser.prog[:-3]
elif meta_parser.prog in SUPPORTED_APP:
module_name = meta_parser.prog
else:
module_name = meta_args.application_name
app_module = ApplicationFactory.create(module_name)
assert app_module.REQUIRED_CONFIG_SECTION, \
"\nREQUIRED_CONFIG_SECTION should be static variable " \
"in {}".format(app_module)
has_section_in_config(config, app_module.REQUIRED_CONFIG_SECTION)
except ValueError:
if app_module:
section_name = app_module.REQUIRED_CONFIG_SECTION
print('\n{} requires [{}] section in the config file.{}'.format(
module_name, section_name, epilog_string))
if not module_name:
print("\nUnknown application {}, or did you forget '-a' "
"command argument?{}".format(module_name, epilog_string))
raise
# check keywords in configuration file
check_keywords(config)
# using configuration as default, and parsing all command line arguments
all_args = {}
for section in config.sections():
# try to rename user-specified sections for consistency
section = standardise_section_name(config, section)
section_defaults = dict(config.items(section))
section_args, args_from_cmdline = \
_parse_arguments_by_section([],
section,
section_defaults,
args_from_cmdline,
app_module.REQUIRED_CONFIG_SECTION)
all_args[section] = section_args
# command line parameters should be valid
assert not args_from_cmdline, \
'\nUnknown parameter: {}{}'.format(args_from_cmdline, epilog_string)
# split parsed results in all_args
# into dictionaries of system_args and input_data_args
system_args = {}
input_data_args = {}
# copy system default sections to ``system_args``
for section in all_args:
if section in SYSTEM_SECTIONS:
system_args[section] = all_args[section]
elif section == app_module.REQUIRED_CONFIG_SECTION:
system_args['CUSTOM'] = all_args[section]
vars(system_args['CUSTOM'])['name'] = module_name
if all_args['SYSTEM'].model_dir is None:
all_args['SYSTEM'].model_dir = os.path.join(
os.path.dirname(meta_args.conf), 'model')
# copy non-default sections to ``input_data_args``
for section in all_args:
if section in SYSTEM_SECTIONS:
continue
if section == app_module.REQUIRED_CONFIG_SECTION:
continue
input_data_args[section] = all_args[section]
# set the output path of csv list if not exists
csv_path = input_data_args[section].csv_file
if os.path.isfile(csv_path):
# don't search files if csv specified in config
try:
delattr(input_data_args[section], 'path_to_search')
except AttributeError:
pass
else:
input_data_args[section].csv_file = ''
# preserve ``config_file`` and ``action parameter`` from the meta_args
system_args['CONFIG_FILE'] = argparse.Namespace(path=meta_args.conf)
system_args['SYSTEM'].action = meta_args.action
return system_args, input_data_args
def run():
"""
meta_parser is first used to find out location
of the configuration file. Based on the application_name
or meta_parser.prog name, the section parsers are organised
to find system parameters and application specific
parameters.
:return: system parameters is a group of parameters including
SYSTEM_SECTIONS and app_module.REQUIRED_CONFIG_SECTION
input_data_args is a group of input data sources to be
used by niftynet.io.ImageReader
"""
meta_parser = argparse.ArgumentParser(
description="Launch a NiftyNet application.",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=textwrap.dedent(EPILOG_STRING))
version_string = get_niftynet_version_string()
meta_parser.add_argument("action",
help="train networks, run inferences "
"or evaluate inferences",
metavar='ACTION',
choices=['train', 'inference', 'evaluation'])
meta_parser.add_argument("-v", "--version",
action='version',
version=version_string)
meta_parser.add_argument("-c", "--conf",
help="specify configurations from a file",
metavar="CONFIG_FILE")
meta_parser.add_argument("-a", "--application_name",
help="specify an application module name",
metavar='APPLICATION_NAME',
default="")
meta_args, args_from_cmdline = meta_parser.parse_known_args()
print(version_string)
# read configurations, to be parsed by sections
config_file_name = __resolve_config_file_path(meta_args.conf)
config = configparser.ConfigParser()
config.read([config_file_name])
# infer application name from command
app_name = None
try:
parser_prog = meta_parser.prog.replace('.py', '')
app_name = parser_prog if parser_prog in SUPPORTED_APP \
else meta_args.application_name
assert app_name
except (AttributeError, AssertionError):
raise ValueError(
"\nUnknown application {}, or did you forget '-a' "
"command argument?{}".format(app_name, EPILOG_STRING))
# load application by name
app_module = ApplicationFactory.create(app_name)
try:
assert app_module.REQUIRED_CONFIG_SECTION, \
"\nREQUIRED_CONFIG_SECTION should be static variable " \
"in {}".format(app_module)
has_section_in_config(config, app_module.REQUIRED_CONFIG_SECTION)
except AttributeError:
raise AttributeError(
"Application code doesn't have REQUIRED_CONFIG_SECTION property. "
"{} should be an instance of "
"niftynet.application.base_application".format(app_module))
except ValueError:
raise ValueError(
"\n{} requires [{}] section in the config file.{}".format(
app_name, app_module.REQUIRED_CONFIG_SECTION, EPILOG_STRING))
# check keywords in configuration file
_check_config_file_keywords(config)
# using configuration as default, and parsing all command line arguments
# command line args override the configure file options
all_args = {}
for section in config.sections():
# try to rename user-specified sections for consistency
section = standardise_section_name(config, section)
section_defaults = dict(config.items(section))
section_args, args_from_cmdline = \
_parse_arguments_by_section([],
section,
section_defaults,
args_from_cmdline,
app_module.REQUIRED_CONFIG_SECTION)
all_args[section] = section_args
# check if any args from command line not recognised
_check_cmd_remaining_keywords(list(args_from_cmdline))
# split parsed results in all_args
# into dictionaries of system_args and input_data_args
system_args, input_data_args = {}, {}
for section in all_args:
# copy system default sections to ``system_args``
if section in SYSTEM_SECTIONS:
system_args[section] = all_args[section]
continue
# copy application specific sections to ``system_args``
if section == app_module.REQUIRED_CONFIG_SECTION:
system_args['CUSTOM'] = all_args[section]
vars(system_args['CUSTOM'])['name'] = app_name
continue
# copy non-default sections to ``input_data_args``
input_data_args[section] = all_args[section]
# set the output path of csv list if not exists
try:
csv_path = resolve_file_name(
input_data_args[section].csv_file,
(os.path.dirname(config_file_name), NIFTYNET_HOME))
input_data_args[section].csv_file = csv_path
# don't search files if csv specified in config
try:
delattr(input_data_args[section], 'path_to_search')
except AttributeError:
pass
except (IOError, TypeError):
input_data_args[section].csv_file = ''
# preserve ``config_file`` and ``action parameter`` from the meta_args
system_args['CONFIG_FILE'] = argparse.Namespace(path=config_file_name)
system_args['SYSTEM'].action = meta_args.action
if not system_args['SYSTEM'].model_dir:
system_args['SYSTEM'].model_dir = os.path.join(
os.path.dirname(config_file_name), 'model')
return system_args, input_data_args