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import sys | |
import argparse | |
import os | |
from lungtumormask import mask | |
def path(string): | |
if os.path.exists(string): | |
return string | |
else: | |
sys.exit(f'File not found: {string}') | |
def main(): | |
parser = argparse.ArgumentParser() | |
parser.add_argument('input', metavar='input', type=path, help='Path to the input image, should be .nifti') | |
parser.add_argument('output', metavar='output', type=str, help='Filepath for output tumormask') | |
parser.add_argument('--lung-filter', action='store_true', help='whether to apply lungmask postprocessing.') | |
parser.add_argument('--threshold', metavar='threshold', type=float, default=0.5, | |
help='which threshold to use for assigning voxel-wise classes.') | |
parser.add_argument('--radius', metavar='radius', type=int, default=1, | |
help='which radius to use for morphological post-processing segmentation smoothing.') | |
argsin = sys.argv[1:] | |
args = parser.parse_args(argsin) | |
mask.mask(args.input, args.output, args.lung_filter, args.threshold, args.radius) | |