def main():
# initialization
param = ParamMoco(is_diffusion=True, group_size=3, metric='MI', smooth='1')
# Fetch user arguments
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
param.fname_data = arguments['-i']
param.fname_bvecs = os.path.abspath(arguments['-bvec'])
if '-bval' in arguments:
param.fname_bvals = os.path.abspath(arguments['-bval'])
if '-bvalmin' in arguments:
param.bval_min = arguments['-bvalmin']
if '-g' in arguments:
param.group_size = arguments['-g']
if '-m' in arguments:
param.fname_mask = arguments['-m']
if '-param' in arguments:
param.update(arguments['-param'])
if '-x' in arguments:
param.interp = arguments['-x']
if '-ofolder' in arguments:
param.path_out = arguments['-ofolder']
if '-r' in arguments:
param.remove_temp_files = int(arguments['-r'])
param.verbose = int(arguments.get('-v'))
# Update log level
sct.init_sct(log_level=param.verbose, update=True)
# run moco
moco_wrapper(param)
def main():
# initialization
param = ParamMoco(is_diffusion=True, group_size=3, metric='MI', smooth='1')
# Fetch user arguments
parser = get_parser()
arguments = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
param.fname_data = arguments.i
param.fname_bvecs = os.path.abspath(arguments.bvec)
param.fname_bvals = arguments.bval
param.bval_min = arguments.bvalmin
param.group_size = arguments.g
param.fname_mask = arguments.m
param.interp = arguments.x
param.path_out = arguments.ofolder
param.remove_temp_files = arguments.r
if arguments.param is not None:
param.update(arguments.param)
param.verbose = int(arguments.v)
# Update log level
init_sct(log_level=param.verbose, update=True)
# run moco
moco_wrapper(param)
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
# initialization
param = ParamMoco(is_diffusion=True, group_size=3, metric='MI', smooth='1')
# Fetch user arguments
param.fname_data = arguments.i
param.fname_bvecs = arguments.bvec
param.fname_bvals = arguments.bval
param.bval_min = arguments.bvalmin
param.group_size = arguments.g
param.fname_mask = arguments.m
param.interp = arguments.x
param.path_out = arguments.ofolder
param.remove_temp_files = arguments.r
if arguments.param is not None:
param.update(arguments.param)
path_qc = arguments.qc
qc_fps = arguments.qc_fps
qc_dataset = arguments.qc_dataset
qc_subject = arguments.qc_subject
qc_seg = arguments.qc_seg
mutually_inclusive_args = (path_qc, qc_seg)
is_qc_none, is_seg_none = [arg is None for arg in mutually_inclusive_args]
if not (is_qc_none == is_seg_none):
raise parser.error(
"Both '-qc' and '-qc-seg' are required in order to generate a QC report."
)
# run moco
fname_output_image = moco_wrapper(param)
set_global_loglevel(
verbose) # moco_wrapper changes verbose to 0, see issue #3341
# QC report
if path_qc is not None:
generate_qc(fname_in1=fname_output_image,
fname_in2=param.fname_data,
fname_seg=qc_seg,
args=sys.argv[1:],
path_qc=os.path.abspath(path_qc),
fps=qc_fps,
dataset=qc_dataset,
subject=qc_subject,
process='sct_dmri_moco')
display_viewer_syntax([fname_output_image, param.fname_data],
mode='ortho,ortho')
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
# initialization
param = ParamMoco(is_diffusion=True, group_size=3, metric='MI', smooth='1')
# Fetch user arguments
param.fname_data = arguments.i
param.fname_bvecs = os.path.abspath(arguments.bvec)
param.fname_bvals = arguments.bval
param.bval_min = arguments.bvalmin
param.group_size = arguments.g
param.fname_mask = arguments.m
param.interp = arguments.x
param.path_out = arguments.ofolder
param.remove_temp_files = arguments.r
if arguments.param is not None:
param.update(arguments.param)
# run moco
moco_wrapper(param)