Furen Xiao
b6fa62a763
Add .gitignore, AGENTS.md, scripts directory, and src directory to initialize the repository.
54 lines
No EOL
1.8 KiB
Python
54 lines
No EOL
1.8 KiB
Python
"""Build NTUH2022G4 labeled manifest: native T1c + tumor seg pairs from register_inv.
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Fast listing-only pass (no volume decoding); content validated during preprocessing.
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"""
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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.dirname(os.path.abspath(__file__))))
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import re
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import json
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from src.common import ROOT, save_jsonl
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T1C_RE = re.compile(r"T1.*\+C")
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EXCL_RE = re.compile(r"MRA|FLAIR|TOF|T2|SWI|DWI", re.I)
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def main(limit=None):
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out = os.path.join(ROOT, "data", "manifests", "ntuh.jsonl")
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reg_inv = "/mnt/pve/SRS/NTUH2022G4/register_inv"
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rows = []
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n_subj = 0
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for s in sorted(os.listdir(reg_inv)):
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fp = os.path.join(reg_inv, s)
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if not os.path.isdir(fp):
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continue
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n_subj += 1
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for c in os.listdir(fp):
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cp = os.path.join(fp, c)
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if not os.path.isdir(cp):
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continue
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fl = set(os.listdir(cp))
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for f in sorted(fl):
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if not f.endswith(".nii.gz") or f.endswith((".seg.nii.gz", ".label.nii.gz")):
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continue
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if not T1C_RE.search(f) or EXCL_RE.search(f):
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continue
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seg = f[: -len(".nii.gz")] + ".seg.nii.gz"
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if seg not in fl:
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continue
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rows.append({"key": f"ntuh_{s}_{c}", "subject": s, "case": c,
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"date": c2date(c), "img": os.path.join(cp, f),
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"label": os.path.join(cp, seg), "source": "ntuh"})
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if limit and n_subj >= limit:
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break
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save_jsonl(rows, out)
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print(f"subjects={n_subj} rows={len(rows)}")
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def c2date(c):
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m = re.match(r"case?(\d{4})\.(\d{2})\.(\d{2})\.", c)
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return f"{m.group(1)}-{m.group(2)}-{m.group(3)}" if m else c
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if __name__ == "__main__":
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main() |