Furen Xiao
8c813db209
Update README.md to include detailed project overview, environment requirements, data sources, and a comprehensive directory layout. Add nnU-Net pipeline documentation and directory descriptions. Update .gitignore to exclude nnU-Net specific directories and add new scripts directory for nnU-Net pipeline. Add initial nnU-Net pipeline scripts.
27 lines
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889 B
Python
27 lines
No EOL
889 B
Python
"""Build/rebuild the nnU-Net raw dataset (Dataset210_NTUH_T1C_PL) from rows jsonl.
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rows: {key, pimg, label} where label is an absolute path to a 0/1 nifti mask.
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Rebuilds imagesTr/labelsTr as symlinks and writes dataset.json.
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Usage: python scripts_nnu/01_nnu_prepare_dataset.py --rows <rows.jsonl>
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"""
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import argparse
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import os
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import sys
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sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
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sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
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from src.common import load_jsonl
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from nnu_common import make_raw_dataset, raw_ds
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def main():
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ap = argparse.ArgumentParser()
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ap.add_argument("--rows", required=True, help="jsonl with {key, pimg, label}")
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args = ap.parse_args()
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rows = load_jsonl(args.rows)
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n = make_raw_dataset(rows)
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print(f"[nnu:prepare] {raw_ds()}: {n} cases", flush=True)
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if __name__ == "__main__":
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main() |