def get_parser():
parser = SCTArgumentParser(
description='Generate Quality Control (QC) report following SCT processing.',
epilog='Examples:\n'
'sct_qc -i t2.nii.gz -s t2_seg.nii.gz -p sct_deepseg_sc\n'
'sct_qc -i t2.nii.gz -s t2_seg_labeled.nii.gz -p sct_label_vertebrae\n'
'sct_qc -i t2.nii.gz -s t2_seg.nii.gz -p sct_deepseg_sc -qc-dataset mydata -qc-subject sub-45'
)
parser.add_argument('-i',
metavar='IMAGE',
help='Input image #1 (mandatory)',
required=True)
parser.add_argument('-p',
help='SCT function associated with the QC report to generate',
choices=('sct_propseg', 'sct_deepseg_sc', 'sct_deepseg_gm', 'sct_register_multimodal',
'sct_register_to_template', 'sct_warp_template', 'sct_label_vertebrae',
'sct_detect_pmj', 'sct_label_utils', 'sct_get_centerline', 'sct_fmri_moco',
'sct_dmri_moco'),
required=True)
parser.add_argument('-s',
metavar='SEG',
help='Input segmentation or label',
required=False)
parser.add_argument('-d',
metavar='DEST',
help='Input image #2 to overlay on image #1 (requires a segmentation), or output of another '
'process (e.g., sct_straighten_spinalcord)',
required=False)
parser.add_argument('-qc',
metavar='QC',
help='Path to save QC report. Default: ./qc',
required=False,
default=os.path.join('.', 'qc'))
parser.add_argument('-qc-dataset',
metavar='DATASET',
help='If provided, this string will be mentioned in the QC report as the dataset the process '
'was run on',
required=False)
parser.add_argument('-qc-subject',
metavar='SUBJECT',
help='If provided, this string will be mentioned in the QC report as the subject the process '
'was run on',
required=False)
parser.add_argument('-fps',
metavar='float',
type=float,
help='The number of frames per second for output gif images. Only useful for sct_fmri_moco and '
'sct_dmri_moco.',
required=False)
parser.add_argument('-v',
action='store_true',
help="Verbose")
parser.add_argument('-h',
'--help',
action="help",
help="show this message and exit")
return parser
def get_parser():
param_default = Param()
parser = SCTArgumentParser(
description=
"Crash and integrity testing for functions of the Spinal Cord Toolbox. Internet connection is required for downloading testing data.",
)
parser.add_argument(
"--function",
"-f",
help="Test this specific script (eg. 'sct_propseg').",
nargs="+",
)
def arg_jobs(s):
jobs = int(s)
if jobs > 0:
pass
elif jobs == 0:
jobs = multiprocessing.cpu_count()
else:
raise ValueError()
return jobs
parser.add_argument(
"--download",
"-d",
action="store_true",
default=param_default.download,
)
parser.add_argument(
"--path",
"-p",
help='Path to testing data. NB: no need to set if using "-d 1"',
default=param_default.path_data,
)
parser.add_argument(
"--remove-temps",
"-r",
help='Remove temporary files.',
action="store_true",
default=param_default.remove_tmp_file,
)
parser.add_argument(
"--jobs",
"-j",
type=arg_jobs,
help=
"# of simultaneous tests to run (jobs). 0 or unspecified means # of available CPU threads ({})"
.format(multiprocessing.cpu_count()),
default=arg_jobs(0),
)
parser.add_argument(
"--verbose",
"-v",
action="store_true",
default=param_default.verbose,
)
parser.add_argument(
"--abort-on-failure",
help=
"Instead of iterating through all tests, abort at the first one that would fail.",
action="store_true",
)
parser.add_argument(
"--continue-from",
help=
"Instead of running all tests (or those specified by --function, start from this one",
)
parser.add_argument(
"--check-filesystem",
help="Check filesystem for unwanted modifications",
action="store_true",
)
parser.add_argument(
"--execution-folder",
help="Folder where to run tests from (default. temporary)",
)
parser.add_argument('-h',
"--help",
help="show this message and exit",
action="help")
return parser