return name
def fmt_slc(slc):
return ','.join(map(str, slc))
p = Parser(
'roi-edit', description,
Arg('--dim',
'dimension to flatten',
DimEditType(),
default=[],
action='append'),
Arg('--ndim', 'final number of dimensions', types.Int.positive,
default=-1),
Arg('--pretend',
'do not commit any actions to disk, just pretend',
action='store_true'),
Arg('--rename',
'old,new name mapping, multiple --rename args can be specified',
RenameType(),
default=[],
action='append'), Arg('files', 'roi files to flatten', nargs='+'))
def main():
_, args = p.parse_args()
if args.ns.pretend:
print('Pretending, file saving is disabled')
def inc_uid(uid):
"""Increment the UID"""
ints = map(int, uid.split('.'))
ints[-1] += 1
return '.'.join(map(str, ints))
series_num_type = types.Int.positive | 'smart-pick' | 'pick'
output_series_num_type = types.Int.positive | 'auto' | 'add-100' | 'pick'
p = Parser('asl-rbf-to-dicom', description,
Arg('--disable-cache-update', 'Disable updating of the dicom cache', action='store_true'),
Arg('--verbose', 'Enable verbose printing', action='store_true'),
Arg('--asl-series', 'ASL series number', series_num_type, default='smart-pick'),
Arg('--output-series', 'Series number to save output as', output_series_num_type, default='pick'),
Arg('--pretend', 'Disable writing', action='store_true'),
Arg('--overwrite', 'Overwrite an existing file', action='store_true'),
Arg('rbf', 'ASL rbf.mat file', RBFMatType.r),
Arg('dicom-dir', 'A directory of dicom files from the series that the rbf.mat was derived from', types.Dir.rw))
def main():
parser, args = p.parse_args()
dcms = jtmri.dcm.read(args.ns.dicom_dir, disp=False)
last_dcm = dcms[-1]
if len(dcms) == 0:
parser.error('No dicoms found in %s' % args.ns.dicom_dir)
asl_series = get_asl_series(args.ns.asl_series, dcms)
if asl_series is None:
