def _toggle_debug(_old_value, _new_value):
# TODO: Toggle dosma logging to debug mode.
if _old_value == _new_value:
return
if _new_value:
preferences.set("nipype", value="stream", prefix="logging")
else:
preferences.set("nipype", value="file_stderr", prefix="logging")
def parse_args(f_input=None):
"""Parse arguments given through command line (argv)
:raises ValueError if dicom path is not provided
:raises NotADirectoryError if dicom path does not exist or is not a directory
"""
parser = argparse.ArgumentParser(
prog='DOSMA',
description='A deep-learning powered open source MRI analysis pipeline',
epilog='Either `--dicom` or `--load` must be specified. '
'If both are given, `--dicom` will be used')
parser.add_argument('--%s' % DEBUG_KEY,
action='store_true',
help='use debug mode')
# Dicom and results paths
parser.add_argument('--d',
'--%s' % DICOM_KEY,
metavar='D',
type=str,
default=None,
nargs='?',
dest=DICOM_KEY,
help='path to directory storing dicom files')
parser.add_argument('--l',
'--%s' % LOAD_KEY,
metavar='L',
type=str,
default=None,
nargs='?',
dest=LOAD_KEY,
help='path to data directory to load from')
parser.add_argument('--s',
'--%s' % SAVE_KEY,
metavar='S',
type=str,
default=None,
nargs='?',
dest=SAVE_KEY,
help='path to data directory to save to. Default: L/D')
parser.add_argument(
'--%s' % IGNORE_EXT_KEY,
action='store_true',
default=False,
dest=IGNORE_EXT_KEY,
help='ignore .dcm extension when loading dicoms. Default: False')
parser.add_argument(
'--%s' % SPLIT_BY_KEY,
metavar='G',
type=str,
default=None,
nargs='?',
dest=SPLIT_BY_KEY,
help='override dicom tag to split volumes by (eg. `EchoNumbers`)')
parser.add_argument('--%s' % GPU_KEY,
metavar='G',
type=str,
default=None,
nargs='?',
dest=GPU_KEY,
help='gpu id. Default: None')
# Add preferences
preferences_flags = preferences.cmd_line_flags()
for flag in preferences_flags.keys():
argparse_kwargs = preferences_flags[flag]
argparse_kwargs['dest'] = flag
aliases = argparse_kwargs.pop('aliases', None)
name = argparse_kwargs.pop('name', None)
parser.add_argument(*aliases, **argparse_kwargs)
subparsers = parser.add_subparsers(help='sub-command help', dest=SCAN_KEY)
add_scans(subparsers)
# MSK knee parser
knee.knee_parser(subparsers)
start_time = time.time()
if f_input:
args = parser.parse_args(f_input)
else:
args = parser.parse_args()
# Only initialize logger if called from command line.
# If UI is using it, the logger should be initialized by the UI.
io_utils.init_logger(fc.LOG_FILE_PATH, args.debug)
vargin = vars(args)
if vargin[DEBUG_KEY]:
fc.set_debug()
gpu = vargin[GPU_KEY]
logging.debug(vargin)
if gpu is not None:
os.environ['CUDA_VISIBLE_DEVICES'] = gpu
if not gpu:
os.environ['CUDA_VISIBLE_DEVICES'] = '-1'
# parse and update preferences
for flag in preferences_flags.keys():
preferences.set(flag, vargin[flag])
dicom_path = vargin[DICOM_KEY]
load_path = vargin[LOAD_KEY]
if not dicom_path and not load_path:
raise ValueError(
'Must provide path to dicoms or path to load data from')
save_path = vargin[SAVE_KEY]
if not save_path:
save_path = load_path if load_path else '%s/data' % dicom_path
vargin[SAVE_KEY] = save_path
if not os.path.isdir(save_path):
os.makedirs(save_path)
tissues = parse_tissues(vargin)
vargin['tissues'] = tissues
vargin[SPLIT_BY_KEY] = parse_dicom_tag_splitby(vargin[SPLIT_BY_KEY])
args.func(vargin)
time_elapsed = (time.time() - start_time)
logging.info("Time Elapsed: {:.2f} seconds".format(time.time() -
start_time))
return time_elapsed
def parse_args(f_input=None):
"""Parse arguments given through command line (argv)
:raises ValueError if dicom path is not provided
:raises NotADirectoryError if dicom path does not exist or is not a directory
"""
parser = argparse.ArgumentParser(
prog="DOSMA",
description="A deep-learning powered open source MRI analysis pipeline",
epilog="Either `--dicom` or `--load` must be specified. "
"If both are given, `--dicom` will be used",
)
parser.add_argument("--%s" % DEBUG_KEY, action="store_true", help="use debug mode")
# Dicom and results paths
parser.add_argument(
"--d",
"--%s" % DICOM_KEY,
metavar="D",
type=str,
default=None,
nargs="?",
dest=DICOM_KEY,
help="path to directory storing dicom files",
)
parser.add_argument(
"--l",
"--%s" % LOAD_KEY,
metavar="L",
type=str,
default=None,
nargs="?",
dest=LOAD_KEY,
help="path to data directory to load from",
)
parser.add_argument(
"--s",
"--%s" % SAVE_KEY,
metavar="S",
type=str,
default=None,
nargs="?",
dest=SAVE_KEY,
help="path to data directory to save to. Default: L/D",
)
parser.add_argument(
"--%s" % IGNORE_EXT_KEY,
action="store_true",
default=False,
dest=IGNORE_EXT_KEY,
help="ignore .dcm extension when loading dicoms. Default: False",
)
parser.add_argument(
"--%s" % SPLIT_BY_KEY,
metavar="G",
type=str,
default=None,
nargs="?",
dest=SPLIT_BY_KEY,
help="override dicom tag to split volumes by (eg. `EchoNumbers`)",
)
parser.add_argument(
"--%s" % GPU_KEY,
metavar="G",
type=str,
default=None,
nargs="?",
dest=GPU_KEY,
help="gpu id. Default: None",
)
parser.add_argument(
"--%s" % NUM_WORKERS_KEY,
metavar="G",
type=int,
default=0,
dest=NUM_WORKERS_KEY,
help="num cpu workers. Default: 0",
)
# Add preferences
preferences_flags = preferences.cmd_line_flags()
for flag in preferences_flags.keys():
argparse_kwargs = preferences_flags[flag]
argparse_kwargs["dest"] = flag
aliases = argparse_kwargs.pop("aliases", None)
name = argparse_kwargs.pop("name", None) # noqa: F841
parser.add_argument(*aliases, **argparse_kwargs)
subparsers = parser.add_subparsers(help="sub-command help", dest=SCAN_KEY)
add_scans(subparsers)
# MSK knee parser
knee.knee_parser(subparsers)
start_time = time.time()
if f_input:
args = parser.parse_args(f_input)
else:
args = parser.parse_args()
# Only initialize logger if called from command line.
# If UI is using it, the logger should be initialized by the UI.
io_utils.init_logger(env.log_file_path(), args.debug)
vargin = vars(args)
if vargin[DEBUG_KEY]:
env.debug(True)
gpu = vargin[GPU_KEY]
logging.debug(vargin)
if gpu is not None:
os.environ["CUDA_VISIBLE_DEVICES"] = gpu
elif "CUDA_VISIBLE_DEVICES" not in os.environ:
os.environ["CUDA_VISIBLE_DEVICES"] = "-1"
# parse and update preferences
for flag in preferences_flags.keys():
preferences.set(flag, vargin[flag])
dicom_path = vargin[DICOM_KEY]
load_path = vargin[LOAD_KEY]
if not dicom_path and not load_path:
raise ValueError("Must provide path to dicoms or path to load data from")
save_path = vargin[SAVE_KEY]
if not save_path:
save_path = load_path if load_path else "%s/data" % dicom_path
vargin[SAVE_KEY] = save_path
if not os.path.isdir(save_path):
os.makedirs(save_path)
tissues = parse_tissues(vargin)
vargin["tissues"] = tissues
vargin[SPLIT_BY_KEY] = parse_dicom_tag_splitby(vargin[SPLIT_BY_KEY])
args.func(vargin)
time_elapsed = time.time() - start_time
logging.info("Time Elapsed: {:.2f} seconds".format(time.time() - start_time))
return time_elapsed
def _apply_settings(self):
for preference in self._preference_elements.keys():
new_val = self._preference_elements[preference].tk_var.get()
preferences.set(preference, new_val)