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split_dataset.py — ERYON reproducible train/val/test splitter.
Splits at the PATIENT level (not slice level) to prevent leakage.
Writes a splits.json: {series_id: "train" | "val" | "test"}.
Ratios default to 70/15/15. Seed is fixed and written into the output
so splits can be reproduced exactly from the JSON alone.
Usage:
python split_dataset.py \\
--manifest manifests/lidc/manifest_v1.0.0.jsonl \\
--train 0.70 --val 0.15 --test 0.15 \\
--seed 42 \\
--out manifests/lidc/splits_v1.0.0.json
"""
import argparse
import json
import random
from collections import defaultdict
from pathlib import Path
def load_manifest(path: Path) -> list[dict]:
return [json.loads(line) for line in path.read_text().splitlines() if line.strip()]
def split_patients(
records: list[dict],
train_ratio: float,
val_ratio: float,
seed: int,
) -> dict[str, str]:
patient_to_series: dict[str, set] = defaultdict(set)
for r in records:
patient_to_series[r["patient_id"]].add(r["series_id"])
patients = sorted(patient_to_series.keys())
rng = random.Random(seed)
rng.shuffle(patients)
n = len(patients)
n_train = int(n * train_ratio)
n_val = int(n * val_ratio)
train_patients = set(patients[:n_train])
val_patients = set(patients[n_train : n_train + n_val])
test_patients = set(patients[n_train + n_val :])
series_split: dict[str, str] = {}
for pid, series_set in patient_to_series.items():
if pid in train_patients:
split = "train"
elif pid in val_patients:
split = "val"
else:
split = "test"
for sid in series_set:
series_split[sid] = split
return series_split
def main() -> None:
parser = argparse.ArgumentParser()
parser.add_argument("--manifest", required=True)
parser.add_argument("--train", type=float, default=0.70)
parser.add_argument("--val", type=float, default=0.15)
parser.add_argument("--test", type=float, default=0.15)
parser.add_argument("--seed", type=int, default=42)
parser.add_argument("--out", required=True)
args = parser.parse_args()
assert abs(args.train + args.val + args.test - 1.0) < 1e-6, "Ratios must sum to 1.0"
records = load_manifest(Path(args.manifest))
splits = split_patients(records, args.train, args.val, args.seed)
out = {
"seed": args.seed,
"ratios": {"train": args.train, "val": args.val, "test": args.test},
"splits": splits,
}
out_path = Path(args.out)
out_path.parent.mkdir(parents=True, exist_ok=True)
out_path.write_text(json.dumps(out, indent=2))
counts = {"train": 0, "val": 0, "test": 0}
for s in splits.values():
counts[s] += 1
print(f"Split complete: {counts} → {out_path}")
if __name__ == "__main__":
main()
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