def create_line(param, fname, coord, nz):
"""
Create vertical line in 3D volume
:param param:
:param fname:
:param coord:
:param nz:
:return:
"""
# duplicate volume (assumes input file is nifti)
copy(fname, 'line.nii', verbose=param.verbose)
# set all voxels to zero
img = Image('line.nii')
data = get_data_or_scalar('0', img.data)
data_concat = concatenate_along_4th_dimension(img.data, data)
img.data = np.prod(data_concat, axis=3)
img.save()
labels = []
if isinstance(coord[0], Coordinate):
for x, y, _, _ in coord:
labels.extend([Coordinate([x, y, iz, 1]) for iz in range(nz)])
else:
# backwards compat
labels.extend(
[Coordinate([coord[0], coord[1], iz, 1]) for iz in range(nz)])
create_labels(img, labels).save()
return 'line.nii'
def create_line(param, fname, coord, nz):
"""
Create vertical line in 3D volume
:param param:
:param fname:
:param coord:
:param nz:
:return:
"""
# duplicate volume (assumes input file is nifti)
copy(fname, 'line.nii', verbose=param.verbose)
# set all voxels to zero
run_proc(['sct_maths', '-i', 'line.nii', '-mul', '0', '-o', 'line.nii'], param.verbose)
labels = []
if isinstance(coord[0], Coordinate):
for x, y, _, _ in coord:
labels.extend([Coordinate([x, y, iz, 1]) for iz in range(nz)])
else:
# backwards compat
labels.extend([Coordinate([coord[0], coord[1], iz, 1]) for iz in range(nz)])
create_labels(Image("line.nii"), labels).save(path="line.nii")
return 'line.nii'
def test_create_labels(test_image):
a = test_image.copy()
labels = [Coordinate(l) for l in [[0, 1, 0, 99], [0, 1, 2, 5]]]
b = sct_labels.create_labels(a, labels)
assert b.data[0, 1, 0] == 99
assert b.data[0, 1, 2] == 5
def main(argv: Sequence[str]):
"""
Main function. When this script is run via CLI, the main function is called using main(sys.argv[1:]).
:param argv: A list of unparsed arguments, which is passed to ArgumentParser.parse_args()
"""
for i, arg in enumerate(argv):
if arg == '-create-seg' and len(argv) > i+1 and '-1,' in argv[i+1]:
raise DeprecationWarning("The use of '-1' for '-create-seg' has been deprecated. Please use "
"'-create-seg-mid' instead.")
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
input_filename = arguments.i
output_fname = arguments.o
img = Image(input_filename)
dtype = None
if arguments.add is not None:
value = arguments.add
out = sct_labels.add(img, value)
elif arguments.create is not None:
labels = arguments.create
out = sct_labels.create_labels_empty(img, labels)
elif arguments.create_add is not None:
labels = arguments.create_add
out = sct_labels.create_labels(img, labels)
elif arguments.create_seg is not None:
labels = arguments.create_seg
out = sct_labels.create_labels_along_segmentation(img, labels)
elif arguments.create_seg_mid is not None:
labels = [(-1, arguments.create_seg_mid)]
out = sct_labels.create_labels_along_segmentation(img, labels)
elif arguments.cubic_to_point:
out = sct_labels.cubic_to_point(img)
elif arguments.display:
display_voxel(img, verbose)
return
elif arguments.increment:
out = sct_labels.increment_z_inverse(img)
elif arguments.disc is not None:
ref = Image(arguments.disc)
out = sct_labels.labelize_from_discs(img, ref)
elif arguments.vert_body is not None:
levels = arguments.vert_body
if len(levels) == 1 and levels[0] == 0:
levels = None # all levels
out = sct_labels.label_vertebrae(img, levels)
elif arguments.vert_continuous:
out = sct_labels.continuous_vertebral_levels(img)
dtype = 'float32'
elif arguments.MSE is not None:
ref = Image(arguments.MSE)
mse = sct_labels.compute_mean_squared_error(img, ref)
printv(f"Computed MSE: {mse}")
return
elif arguments.remove_reference is not None:
ref = Image(arguments.remove_reference)
out = sct_labels.remove_missing_labels(img, ref)
elif arguments.remove_sym is not None:
# first pass use img as source
ref = Image(arguments.remove_reference)
out = sct_labels.remove_missing_labels(img, ref)
# second pass use previous pass result as reference
ref_out = sct_labels.remove_missing_labels(ref, out)
ref_out.save(path=ref.absolutepath)
elif arguments.remove is not None:
labels = arguments.remove
out = sct_labels.remove_labels_from_image(img, labels)
elif arguments.keep is not None:
labels = arguments.keep
out = sct_labels.remove_other_labels_from_image(img, labels)
elif arguments.create_viewer is not None:
msg = "" if arguments.msg is None else f"{arguments.msg}\n"
if arguments.ilabel is not None:
input_labels_img = Image(arguments.ilabel)
out = launch_manual_label_gui(img, input_labels_img, parse_num_list(arguments.create_viewer), msg)
else:
out = launch_sagittal_viewer(img, parse_num_list(arguments.create_viewer), msg)
printv("Generating output files...")
out.save(path=output_fname, dtype=dtype)
display_viewer_syntax([input_filename, output_fname])
if arguments.qc is not None:
generate_qc(fname_in1=input_filename, fname_seg=output_fname, args=argv,
path_qc=os.path.abspath(arguments.qc), dataset=arguments.qc_dataset,
subject=arguments.qc_subject, process='sct_label_utils')
def main(args=None):
parser = get_parser()
if args:
arguments = parser.parse_args(args)
else:
arguments = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
verbosity = arguments.v
init_sct(log_level=verbosity, update=True) # Update log level
input_filename = arguments.i
output_fname = arguments.o
img = Image(input_filename)
dtype = None
if arguments.add is not None:
value = arguments.add
out = sct_labels.add(img, value)
elif arguments.create is not None:
labels = arguments.create
out = sct_labels.create_labels_empty(img, labels)
elif arguments.create_add is not None:
labels = arguments.create_add
out = sct_labels.create_labels(img, labels)
elif arguments.create_seg is not None:
labels = arguments.create_seg
out = sct_labels.create_labels_along_segmentation(img, labels)
elif arguments.cubic_to_point:
out = sct_labels.cubic_to_point(img)
elif arguments.display:
display_voxel(img, verbosity)
return
elif arguments.increment:
out = sct_labels.increment_z_inverse(img)
elif arguments.disc is not None:
ref = Image(arguments.disc)
out = sct_labels.labelize_from_discs(img, ref)
elif arguments.vert_body is not None:
levels = arguments.vert_body
if len(levels) == 1 and levels[0] == 0:
levels = None # all levels
out = sct_labels.label_vertebrae(img, levels)
elif arguments.vert_continuous:
out = sct_labels.continuous_vertebral_levels(img)
dtype = 'float32'
elif arguments.MSE is not None:
ref = Image(arguments.MSE)
mse = sct_labels.compute_mean_squared_error(img, ref)
printv(f"Computed MSE: {mse}")
return
elif arguments.remove_reference is not None:
ref = Image(arguments.remove_reference)
out = sct_labels.remove_missing_labels(img, ref)
elif arguments.remove_sym is not None:
# first pass use img as source
ref = Image(arguments.remove_reference)
out = sct_labels.remove_missing_labels(img, ref)
# second pass use previous pass result as reference
ref_out = sct_labels.remove_missing_labels(ref, out)
ref_out.save(path=ref.absolutepath)
elif arguments.remove is not None:
labels = arguments.remove
out = sct_labels.remove_labels_from_image(img, labels)
elif arguments.keep is not None:
labels = arguments.keep
out = sct_labels.remove_other_labels_from_image(img, labels)
elif arguments.create_viewer is not None:
msg = "" if arguments.msg is None else f"{arguments.msg}\n"
if arguments.ilabel is not None:
input_labels_img = Image(arguments.ilabel)
out = launch_manual_label_gui(img, input_labels_img, parse_num_list(arguments.create_viewer), msg)
else:
out = launch_sagittal_viewer(img, parse_num_list(arguments.create_viewer), msg)
printv("Generating output files...")
out.save(path=output_fname, dtype=dtype)
display_viewer_syntax([input_filename, output_fname])
if arguments.qc is not None:
generate_qc(fname_in1=input_filename, fname_seg=output_fname, args=args,
path_qc=os.path.abspath(arguments.qc), dataset=arguments.qc_dataset,
subject=arguments.qc_subject, process='sct_label_utils')