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Set the default value for -path-label to match -path-img #106

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merged 3 commits into from
Dec 16, 2024
Merged

Set the default value for -path-label to match -path-img #106

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2e44ab9
Set the default value for -path-label to match -path-img
valosekj Dec 12, 2024
34be426
fix indentation
valosekj Dec 12, 2024
a43955f
clarify description
valosekj Dec 12, 2024
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31 changes: 14 additions & 17 deletions manual_correction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,8 @@ def get_parser():
description='Manual correction of spinal cord segmentation, gray matter segmentation, MS and SCI lesion '
'segmentation, disc labels, compression labels, ponto-medullary junction (PMJ) label, and '
'centerline. '
'Manually corrected files will be saved under derivatives/ folder (according to BIDS standard).',
'Manually corrected files will be saved under derivatives/labels folder (according to BIDS '
'standard) if not specified otherwise.',
formatter_class=utils.SmartFormatter,
prog=os.path.basename(__file__).strip('.py')
)
Expand Down Expand Up @@ -107,9 +108,8 @@ def get_parser():
metavar="<folder>",
help=
"R|Full path to the folder with labels (BIDS-compliant). "
"\nIf labels are located in the same folder as the images, provide the same path as '-path-img', for example "
"'output/data_processed'."
"\nIf not provided, '-path-img' + 'derivatives/labels' will be used. ",
"\nIf not provided, '-path-img' will be used (assuming that the labels are in the same folder as images). "
"\nIf your labels are already under 'derivatives/labels', provide the full path to this folder. ",
default=''
)
parser.add_argument(
Expand Down Expand Up @@ -758,23 +758,20 @@ def main():
'FILES_CENTERLINE': args.suffix_files_centerline # e.g., _centerline or _label-centerline
}
path_img = utils.get_full_path(args.path_img)

if args.path_label == '':
path_label = os.path.join(path_img, "derivatives/labels")
else:
path_label = utils.get_full_path(args.path_label)

if args.path_out == '':
path_out = os.path.join(path_img, "derivatives/labels")
else:
path_out = utils.get_full_path(args.path_out)

# If labels are in the same folder as the images, set path_label to path_img
path_label = path_img if args.path_label == '' else utils.get_full_path(args.path_label)

# If not specified, output folder for corrected labels is derivatives/labels in the input folder
path_out = os.path.join(path_img, "derivatives/labels") if args.path_out == '' else utils.get_full_path(
args.path_out)

# Print parsed arguments
logging.info("-" * 100)
logging.info("Parsing of arguments:")
logging.info(" Input folder ('-path-img') .............. " + path_img)
logging.info(" Label folder ('-path-label') .............. " + path_label)
logging.info(" Output folder ('-path-out') ............. " + path_out)
logging.info(" Input folder ('-path-img'): " + path_img)
logging.info(" Label folder ('-path-label'): " + path_label)
logging.info(" Output folder ('-path-out'): " + path_out)
logging.info("-" * 100)

# check that output folder exists or create it
Expand Down
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