def main():
"""Main function."""
sct.init_sct()
parser = get_parser()
args = sys.argv[1:]
arguments = parser.parse(args)
fname_image = os.path.abspath(arguments['-i'])
contrast_type = arguments['-c']
ctr_algo = arguments["-centerline"]
if "-brain" not in args:
if contrast_type in ['t2s', 'dwi']:
brain_bool = False
if contrast_type in ['t1', 't2']:
brain_bool = True
else:
brain_bool = bool(int(arguments["-brain"]))
kernel_size = arguments["-kernel"]
if kernel_size == '3d' and contrast_type == 'dwi':
kernel_size = '2d'
sct.printv('3D kernel model for dwi contrast is not available. 2D kernel model is used instead.', type="warning")
if '-ofolder' not in args:
output_folder = os.getcwd()
else:
output_folder = arguments["-ofolder"]
if ctr_algo == 'file' and "-file_centerline" not in args:
sct.log.warning('Please use the flag -file_centerline to indicate the centerline filename.')
sys.exit(1)
if "-file_centerline" in args:
manual_centerline_fname = arguments["-file_centerline"]
ctr_algo = 'file'
else:
manual_centerline_fname = None
remove_temp_files = int(arguments['-r'])
verbose = int(arguments['-v'])
path_qc = arguments.get("-qc", None)
algo_config_stg = '\nMethod:'
algo_config_stg += '\n\tCenterline algorithm: ' + str(ctr_algo)
algo_config_stg += '\n\tAssumes brain section included in the image: ' + str(brain_bool)
algo_config_stg += '\n\tDimension of the segmentation kernel convolutions: ' + kernel_size + '\n'
sct.printv(algo_config_stg)
im_image = Image(fname_image)
# note: below we pass im_image.copy() otherwise the field absolutepath becomes None after execution of this function
im_seg, im_image_RPI_upsamp, im_seg_RPI_upsamp, im_labels_viewer, im_ctr = deep_segmentation_spinalcord(
im_image.copy(), contrast_type, ctr_algo=ctr_algo, ctr_file=manual_centerline_fname,
brain_bool=brain_bool, kernel_size=kernel_size, remove_temp_files=remove_temp_files, verbose=verbose)
# Save segmentation
fname_seg = os.path.abspath(os.path.join(output_folder, sct.extract_fname(fname_image)[1] + '_seg' +
sct.extract_fname(fname_image)[2]))
im_seg.save(fname_seg)
if ctr_algo == 'viewer':
# Save labels
fname_labels = os.path.abspath(os.path.join(output_folder, sct.extract_fname(fname_image)[1] + '_labels-centerline' +
sct.extract_fname(fname_image)[2]))
im_labels_viewer.save(fname_labels)
if verbose == 2:
# Save ctr
fname_ctr = os.path.abspath(os.path.join(output_folder, sct.extract_fname(fname_image)[1] + '_centerline' +
sct.extract_fname(fname_image)[2]))
im_ctr.save(fname_ctr)
if path_qc is not None:
generate_qc(fname_image, fname_seg=fname_seg, args=args, path_qc=os.path.abspath(path_qc),
process='sct_deepseg_sc')
sct.display_viewer_syntax([fname_image, fname_seg], colormaps=['gray', 'red'], opacities=['', '0.7'])
def main():
"""Main function."""
parser = get_parser()
args = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
fname_image = os.path.abspath(args.i)
contrast_type = args.c
ctr_algo = args.centerline
if args.brain is None:
if contrast_type in ['t2s', 'dwi']:
brain_bool = False
if contrast_type in ['t1', 't2']:
brain_bool = True
else:
brain_bool = bool(args.brain)
if bool(args.brain) and ctr_algo == 'svm':
sct.printv(
'Please only use the flag "-brain 1" with "-centerline cnn".', 1,
'warning')
sys.exit(1)
kernel_size = args.kernel
if kernel_size == '3d' and contrast_type == 'dwi':
kernel_size = '2d'
sct.printv(
'3D kernel model for dwi contrast is not available. 2D kernel model is used instead.',
type="warning")
if ctr_algo == 'file' and args.file_centerline is None:
sct.printv(
'Please use the flag -file_centerline to indicate the centerline filename.',
1, 'warning')
sys.exit(1)
if args.file_centerline is not None:
manual_centerline_fname = args.file_centerline
ctr_algo = 'file'
else:
manual_centerline_fname = None
threshold = args.thr
if threshold is not None:
if threshold > 1.0 or (threshold < 0.0 and threshold != -1.0):
raise SyntaxError(
"Threshold should be between 0 and 1, or equal to -1 (no threshold)"
)
remove_temp_files = args.r
verbose = args.v
init_sct(log_level=verbose, update=True) # Update log level
path_qc = args.qc
qc_dataset = args.qc_dataset
qc_subject = args.qc_subject
output_folder = args.ofolder
# check if input image is 2D or 3D
sct.check_dim(fname_image, dim_lst=[2, 3])
# Segment image
from spinalcordtoolbox.image import Image
from spinalcordtoolbox.deepseg_sc.core import deep_segmentation_spinalcord
from spinalcordtoolbox.reports.qc import generate_qc
im_image = Image(fname_image)
# note: below we pass im_image.copy() otherwise the field absolutepath becomes None after execution of this function
im_seg, im_image_RPI_upsamp, im_seg_RPI_upsamp = \
deep_segmentation_spinalcord(im_image.copy(), contrast_type, ctr_algo=ctr_algo,
ctr_file=manual_centerline_fname, brain_bool=brain_bool, kernel_size=kernel_size,
threshold_seg=threshold, remove_temp_files=remove_temp_files, verbose=verbose)
# Save segmentation
fname_seg = os.path.abspath(
os.path.join(
output_folder,
sct.extract_fname(fname_image)[1] + '_seg' +
sct.extract_fname(fname_image)[2]))
im_seg.save(fname_seg)
# Generate QC report
if path_qc is not None:
generate_qc(fname_image,
fname_seg=fname_seg,
args=sys.argv[1:],
path_qc=os.path.abspath(path_qc),
dataset=qc_dataset,
subject=qc_subject,
process='sct_deepseg_sc')
sct.display_viewer_syntax([fname_image, fname_seg],
colormaps=['gray', 'red'],
opacities=['', '0.7'])
def main():
"""Main function."""
parser = get_parser()
args = parser.parse_args(args=None if sys.argv[1:] else ['--help'])
fname_image = os.path.abspath(args.i)
contrast_type = args.c
ctr_algo = args.centerline
if args.brain is None:
if contrast_type in ['t2s', 'dwi']:
brain_bool = False
if contrast_type in ['t1', 't2']:
brain_bool = True
else:
brain_bool = bool(args.brain)
kernel_size = args.kernel
if kernel_size == '3d' and contrast_type == 'dwi':
kernel_size = '2d'
sct.printv('3D kernel model for dwi contrast is not available. 2D kernel model is used instead.',
type="warning")
if ctr_algo == 'file' and args.file_centerline is None:
sct.printv('Please use the flag -file_centerline to indicate the centerline filename.', 1, 'warning')
sys.exit(1)
if args.file_centerline is not None:
manual_centerline_fname = args.file_centerline
ctr_algo = 'file'
else:
manual_centerline_fname = None
remove_temp_files = args.r
verbose = args.v
sct.init_sct(log_level=verbose, update=True) # Update log level
path_qc = args.qc
qc_dataset = args.qc_dataset
qc_subject = args.qc_subject
output_folder = args.ofolder
algo_config_stg = '\nMethod:'
algo_config_stg += '\n\tCenterline algorithm: ' + str(ctr_algo)
algo_config_stg += '\n\tAssumes brain section included in the image: ' + str(brain_bool)
algo_config_stg += '\n\tDimension of the segmentation kernel convolutions: ' + kernel_size + '\n'
sct.printv(algo_config_stg)
# Segment image
from spinalcordtoolbox.image import Image
from spinalcordtoolbox.deepseg_sc.core import deep_segmentation_spinalcord
from spinalcordtoolbox.reports.qc import generate_qc
im_image = Image(fname_image)
# note: below we pass im_image.copy() otherwise the field absolutepath becomes None after execution of this function
im_seg, im_image_RPI_upsamp, im_seg_RPI_upsamp, im_labels_viewer, im_ctr = \
deep_segmentation_spinalcord(im_image.copy(), contrast_type, ctr_algo=ctr_algo,
ctr_file=manual_centerline_fname, brain_bool=brain_bool, kernel_size=kernel_size,
remove_temp_files=remove_temp_files, verbose=verbose)
# Save segmentation
fname_seg = os.path.abspath(os.path.join(output_folder, sct.extract_fname(fname_image)[1] + '_seg' +
sct.extract_fname(fname_image)[2]))
# copy q/sform from input image to output segmentation
im_seg.copy_qform_from_ref(im_image)
im_seg.save(fname_seg)
if ctr_algo == 'viewer':
# Save labels
fname_labels = os.path.abspath(os.path.join(output_folder, sct.extract_fname(fname_image)[1] + '_labels-centerline' +
sct.extract_fname(fname_image)[2]))
im_labels_viewer.save(fname_labels)
if verbose == 2:
# Save ctr
fname_ctr = os.path.abspath(os.path.join(output_folder, sct.extract_fname(fname_image)[1] + '_centerline' +
sct.extract_fname(fname_image)[2]))
im_ctr.save(fname_ctr)
if path_qc is not None:
generate_qc(fname_image, fname_seg=fname_seg, args=sys.argv[1:], path_qc=os.path.abspath(path_qc),
dataset=qc_dataset, subject=qc_subject, process='sct_deepseg_sc')
sct.display_viewer_syntax([fname_image, fname_seg], colormaps=['gray', 'red'], opacities=['', '0.7'])
def main():
"""Main function."""
sct.init_sct()
parser = get_parser()
args = sys.argv[1:]
arguments = parser.parse(args)
fname_image = os.path.abspath(arguments['-i'])
contrast_type = arguments['-c']
ctr_algo = arguments["-centerline"]
if "-brain" not in args:
if contrast_type in ['t2s', 'dwi']:
brain_bool = False
if contrast_type in ['t1', 't2']:
brain_bool = True
else:
brain_bool = bool(int(arguments["-brain"]))
kernel_size = arguments["-kernel"]
if kernel_size == '3d' and contrast_type == 'dwi':
kernel_size = '2d'
sct.printv('3D kernel model for dwi contrast is not available. 2D kernel model is used instead.', type="warning")
if '-ofolder' not in args:
output_folder = os.getcwd()
else:
output_folder = arguments["-ofolder"]
if ctr_algo == 'file' and "-file_centerline" not in args:
logger.warning('Please use the flag -file_centerline to indicate the centerline filename.')
sys.exit(1)
if "-file_centerline" in args:
manual_centerline_fname = arguments["-file_centerline"]
ctr_algo = 'file'
else:
manual_centerline_fname = None
remove_temp_files = int(arguments['-r'])
verbose = int(arguments.get('-v'))
sct.init_sct(log_level=verbose, update=True) # Update log level
path_qc = arguments.get("-qc", None)
qc_dataset = arguments.get("-qc-dataset", None)
qc_subject = arguments.get("-qc-subject", None)
algo_config_stg = '\nMethod:'
algo_config_stg += '\n\tCenterline algorithm: ' + str(ctr_algo)
algo_config_stg += '\n\tAssumes brain section included in the image: ' + str(brain_bool)
algo_config_stg += '\n\tDimension of the segmentation kernel convolutions: ' + kernel_size + '\n'
sct.printv(algo_config_stg)
im_image = Image(fname_image)
# note: below we pass im_image.copy() otherwise the field absolutepath becomes None after execution of this function
im_seg, im_image_RPI_upsamp, im_seg_RPI_upsamp, im_labels_viewer, im_ctr = deep_segmentation_spinalcord(
im_image.copy(), contrast_type, ctr_algo=ctr_algo, ctr_file=manual_centerline_fname,
brain_bool=brain_bool, kernel_size=kernel_size, remove_temp_files=remove_temp_files, verbose=verbose)
# Save segmentation
fname_seg = os.path.abspath(os.path.join(output_folder, sct.extract_fname(fname_image)[1] + '_seg' +
sct.extract_fname(fname_image)[2]))
im_seg.save(fname_seg)
if ctr_algo == 'viewer':
# Save labels
fname_labels = os.path.abspath(os.path.join(output_folder, sct.extract_fname(fname_image)[1] + '_labels-centerline' +
sct.extract_fname(fname_image)[2]))
im_labels_viewer.save(fname_labels)
if verbose == 2:
# Save ctr
fname_ctr = os.path.abspath(os.path.join(output_folder, sct.extract_fname(fname_image)[1] + '_centerline' +
sct.extract_fname(fname_image)[2]))
im_ctr.save(fname_ctr)
if path_qc is not None:
generate_qc(fname_image, fname_seg=fname_seg, args=args, path_qc=os.path.abspath(path_qc),
dataset=qc_dataset, subject=qc_subject, process='sct_deepseg_sc')
sct.display_viewer_syntax([fname_image, fname_seg], colormaps=['gray', 'red'], opacities=['', '0.7'])
