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Sleeping
import sys | |
import argparse | |
import os | |
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.') | |
parser.add_argument('--batch-size', metavar='batch-size', type=int, default=5, | |
help='which batch size to use for lungmask inference.') | |
parser.add_argument('--cpu', action='store_true', help='whether to force computation to happen on CPU only.') | |
args = parser.parse_args(sys.argv[1:]) | |
# whether to force CPU computation | |
if args.cpu: | |
os.environ["CUDA_VISIBLE_DEVICES"] = "-1" | |
# import method here to enable faster testing | |
from lungtumormask import mask | |
mask.mask(args.input, args.output, args.lung_filter, args.threshold, args.radius, args.batch_size) | |