def main():
system_param, input_data_param = user_parameters_parser.run()
if util.has_bad_inputs(system_param):
return -1
# print all parameters to txt file for future reference
all_param = {}
all_param.update(system_param)
all_param.update(input_data_param)
# Set up path for niftynet model_root
# (rewriting user input with an absolute path)
system_param['SYSTEM'].model_dir = resolve_module_dir(
system_param['SYSTEM'].model_dir,
create_new=system_param['SYSTEM'].action == "train")
# writing all params for future reference
txt_file = 'settings_{}.txt'.format(system_param['SYSTEM'].action)
txt_file = os.path.join(system_param['SYSTEM'].model_dir, txt_file)
util.print_save_input_parameters(all_param, txt_file)
# keep all commandline outputs to model_root
log_file_name = os.path.join(
system_param['SYSTEM'].model_dir,
'{}_{}'.format(all_param['SYSTEM'].action, 'niftynet_log'))
set_logger(file_name=log_file_name)
# set up all model folder related parameters here
# see https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/issues/168
# 1. resolve mapping file:
try:
if system_param['NETWORK'].histogram_ref_file:
system_param['NETWORK'].histogram_ref_file = to_absolute_path(
input_path=system_param['NETWORK'].histogram_ref_file,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# 2. resolve output file:
try:
if system_param['INFERENCE'].save_seg_dir:
system_param['INFERENCE'].save_seg_dir = to_absolute_path(
input_path=system_param['INFERENCE'].save_seg_dir,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# start application
app_driver = ApplicationDriver()
app_driver.initialise_application(system_param, input_data_param)
app_driver.run_application()
return 0
def main():
set_logger()
system_param, input_data_param = user_parameters_parser.run()
if util.has_bad_inputs(system_param):
return -1
# print all parameters to txt file for future reference
all_param = {}
all_param.update(system_param)
all_param.update(input_data_param)
# Set up path for niftynet model_root
# (rewriting user input with an absolute path)
system_param['SYSTEM'].model_dir = resolve_module_dir(
system_param['SYSTEM'].model_dir,
create_new=system_param['SYSTEM'].action == "train")
# writing all params for future reference
txt_file = 'settings_{}.txt'.format(system_param['SYSTEM'].action)
txt_file = os.path.join(system_param['SYSTEM'].model_dir, txt_file)
try:
util.print_save_input_parameters(all_param, txt_file)
except IOError:
tf.logging.fatal(
'Unable to write %s,\nplease check '
'model_dir parameter, current value: %s',
txt_file, system_param['SYSTEM'].model_dir)
raise
# keep all commandline outputs to model_root
log_file_name = os.path.join(
system_param['SYSTEM'].model_dir,
'{}_{}'.format(all_param['SYSTEM'].action, 'niftynet_log'))
set_logger(file_name=log_file_name)
# set up all model folder related parameters here
# see https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/issues/168
# 1. resolve mapping file:
try:
if system_param['NETWORK'].histogram_ref_file:
system_param['NETWORK'].histogram_ref_file = to_absolute_path(
input_path=system_param['NETWORK'].histogram_ref_file,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# 2. resolve output file:
try:
if system_param['INFERENCE'].save_seg_dir:
system_param['INFERENCE'].save_seg_dir = to_absolute_path(
input_path=system_param['INFERENCE'].save_seg_dir,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# 3. resolve dataset splitting file:
try:
if system_param['SYSTEM'].dataset_split_file:
system_param['SYSTEM'].dataset_split_file = to_absolute_path(
input_path=system_param['SYSTEM'].dataset_split_file,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# start application
app_driver = ApplicationDriver()
app_driver.initialise_application(system_param, input_data_param)
app_driver.run_application()
return 0
def main():
set_logger()
print("Hola como vai estoy en el init de niftynet ################")
system_param, input_data_param = user_parameters_parser.run()
if util.has_bad_inputs(system_param):
return -1
# print all parameters to txt file for future reference
all_param = {}
all_param.update(system_param)
all_param.update(input_data_param)
# Set up path for niftynet model_root
# (rewriting user input with an absolute path)
system_param['SYSTEM'].model_dir = resolve_module_dir(
system_param['SYSTEM'].model_dir,
create_new=system_param['SYSTEM'].action == "train")
# writing all params for future reference
txt_file = 'settings_{}.txt'.format(system_param['SYSTEM'].action)
txt_file = os.path.join(system_param['SYSTEM'].model_dir, txt_file)
try:
util.print_save_input_parameters(all_param, txt_file)
except IOError:
tf.logging.fatal(
'Unable to write %s,\nplease check '
'model_dir parameter, current value: %s',
txt_file, system_param['SYSTEM'].model_dir)
raise
# keep all commandline outputs to model_root
log_file_name = os.path.join(
system_param['SYSTEM'].model_dir,
'{}_{}'.format(all_param['SYSTEM'].action, 'niftynet_log'))
set_logger(file_name=log_file_name)
# set up all model folder related parameters here
# see https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/issues/168
# 1. resolve mapping file:
try:
if system_param['NETWORK'].histogram_ref_file:
system_param['NETWORK'].histogram_ref_file = to_absolute_path(
input_path=system_param['NETWORK'].histogram_ref_file,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# 2. resolve output file:
try:
if system_param['INFERENCE'].save_seg_dir:
system_param['INFERENCE'].save_seg_dir = to_absolute_path(
input_path=system_param['INFERENCE'].save_seg_dir,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# 3. resolve dataset splitting file:
try:
if system_param['SYSTEM'].dataset_split_file:
system_param['SYSTEM'].dataset_split_file = to_absolute_path(
input_path=system_param['SYSTEM'].dataset_split_file,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# start application
app_driver = ApplicationDriver()
print("Initializing application$$$$$$$$$$$$$$$$$$$$$BEGIN")
app_driver.initialise_application(system_param, input_data_param)
print("Initializing application$$$$$$$$$$$$$$$$$$$$$END")
print("Initializing RUN application$$$$$$$$$$$$$$$$$$$$$BEGIN")
app_driver.run_application()
print("Initializing RUN application$$$$$$$$$$$$$$$$$$$$$END")
return 0
def main():
system_param, input_data_param = user_parameters_parser.run()
if util.has_bad_inputs(system_param):
return -1
# print all parameters to txt file for future reference
all_param = {}
all_param.update(system_param)
all_param.update(input_data_param)
# Set up path for niftynet model_root
# (rewriting user input with an absolute path)
system_param['SYSTEM'].model_dir = resolve_module_dir(
system_param['SYSTEM'].model_dir,
create_new=system_param['SYSTEM'].action == TRAIN)
# writing all params for future reference
txt_file = 'settings_{}.txt'.format(system_param['SYSTEM'].action)
txt_file = os.path.join(system_param['SYSTEM'].model_dir, txt_file)
try:
util.print_save_input_parameters(all_param, txt_file)
except IOError:
tf.logging.fatal(
'Unable to write %s,\nplease check '
'model_dir parameter, current value: %s',
txt_file, system_param['SYSTEM'].model_dir)
raise
# keep all commandline outputs to model_root
log_file_name = os.path.join(
system_param['SYSTEM'].model_dir,
'{}_{}'.format(all_param['SYSTEM'].action, 'niftynet_log'))
set_logger(file_name=log_file_name)
# set up all model folder related parameters here
# see https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/issues/168
# 1. resolve mapping file:
try:
if system_param['NETWORK'].histogram_ref_file:
system_param['NETWORK'].histogram_ref_file = to_absolute_path(
input_path=system_param['NETWORK'].histogram_ref_file,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# 2. resolve output file:
try:
if system_param['INFERENCE'].save_seg_dir:
system_param['INFERENCE'].save_seg_dir = to_absolute_path(
input_path=system_param['INFERENCE'].save_seg_dir,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# 3. resolve dataset splitting file:
try:
if system_param['SYSTEM'].dataset_split_file:
system_param['SYSTEM'].dataset_split_file = to_absolute_path(
input_path=system_param['SYSTEM'].dataset_split_file,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# 4. resolve evaluation dir:
try:
if system_param['EVALUATION'].save_csv_dir:
system_param['EVALUATION'].save_csv_dir = to_absolute_path(
input_path=system_param['EVALUATION'].save_csv_dir,
model_root=system_param['SYSTEM'].model_dir)
except (AttributeError, KeyError):
pass
# start application
driver_table = {
TRAIN: ApplicationDriver,
INFER: ApplicationDriver,
EVAL: EvaluationApplicationDriver,
EXPORT: ApplicationDriver}
app_driver = driver_table[system_param['SYSTEM'].action]()
app_driver.initialise_application(system_param, input_data_param)
app_driver.run(app_driver.app)
if tf.get_default_session() is not None:
tf.get_default_session().close()
tf.reset_default_graph()
close_logger()
return 0
