Commit e7d0d0ec authored by mibaumgartner's avatar mibaumgartner
Browse files

fix seg2det script

parent b5df69f9
...@@ -35,6 +35,7 @@ from nndet.io import get_case_ids_from_dir, load_json, save_json ...@@ -35,6 +35,7 @@ from nndet.io import get_case_ids_from_dir, load_json, save_json
from nndet.io.transforms.instances import get_bbox_np from nndet.io.transforms.instances import get_bbox_np
from nndet.io.itk import copy_meta_data_itk, load_sitk, load_sitk_as_array from nndet.io.itk import copy_meta_data_itk, load_sitk, load_sitk_as_array
from nndet.utils.config import compose from nndet.utils.config import compose
from nndet.utils.check import env_guard
def prepare_detection_label(case_id: str, def prepare_detection_label(case_id: str,
...@@ -103,7 +104,8 @@ def prepare_detection_label(case_id: str, ...@@ -103,7 +104,8 @@ def prepare_detection_label(case_id: str,
sitk.WriteImage(seg_itk, str(label_dir / f"{case_id}_orig.nii.gz")) sitk.WriteImage(seg_itk, str(label_dir / f"{case_id}_orig.nii.gz"))
if __name__ == '__main__': @env_guard
def main():
""" """
This script converts a semantic segmentation dataset into an instance This script converts a semantic segmentation dataset into an instance
segmentation dataset by using connected components on the labels. segmentation dataset by using connected components on the labels.
...@@ -148,7 +150,7 @@ if __name__ == '__main__': ...@@ -148,7 +150,7 @@ if __name__ == '__main__':
action='store_true', action='store_true',
) )
parser.add_argument('--num_processes', type=int, default=4, required=False, parser.add_argument('--num_processes', type=int, default=4, required=False,
help="Number of processes to use for conversion.") help="Number of processes to use for conversion. Default 4.")
args = parser.parse_args() args = parser.parse_args()
tasks = args.tasks tasks = args.tasks
...@@ -212,3 +214,7 @@ if __name__ == '__main__': ...@@ -212,3 +214,7 @@ if __name__ == '__main__':
save_json(ranking, splitted_dir / f"volume_ranking_{postfix}.json") save_json(ranking, splitted_dir / f"volume_ranking_{postfix}.json")
else: else:
logger.info(f"Did not find dir {label_dir} for volume ranking") logger.info(f"Did not find dir {label_dir} for volume ranking")
if __name__ == '__main__':
main()
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