| """ |
| validate_dataset.py — ERYON dataset validation gate. |
| |
| Runs mandatory checks before a dataset becomes trainable: |
| 1. Corruption scan — every PNG opens without error |
| 2. Manifest validation — all required fields present, paths exist |
| 3. Checksum verification — stored sha256 matches file on disk |
| 4. Split completeness — every series_id in manifest has a split assignment |
| |
| Exits with code 1 if any check fails. Writes a JSON report to reports/validation/. |
| |
| Usage: |
| python validate_dataset.py \\ |
| --root /mnt/raw/lidc \\ |
| --manifest manifests/lidc/manifest_v1.0.0.jsonl \\ |
| --splits manifests/lidc/splits_v1.0.0.json \\ |
| --out reports/validation/lidc_v1.0.0.json |
| """ |
|
|
| import argparse |
| import hashlib |
| import json |
| import sys |
| from pathlib import Path |
|
|
| from PIL import Image |
|
|
| REQUIRED_FIELDS = { |
| "patient_id", "study_id", "series_id", "image_path", |
| "modality", "split", "label", "dataset_version", |
| "preprocessing_version", "sha256", |
| } |
|
|
|
|
| def sha256_file(path: Path) -> str: |
| h = hashlib.sha256() |
| with open(path, "rb") as f: |
| for chunk in iter(lambda: f.read(65536), b""): |
| h.update(chunk) |
| return h.hexdigest() |
|
|
|
|
| def validate(root: Path, manifest_path: Path, splits_path: Path) -> dict: |
| records = [json.loads(l) for l in manifest_path.read_text().splitlines() if l.strip()] |
| splits_data = json.loads(splits_path.read_text()) if splits_path else {} |
| split_map = splits_data.get("splits", {}) if splits_data else {} |
|
|
| errors: list[str] = [] |
| warnings: list[str] = [] |
|
|
| for i, rec in enumerate(records): |
| missing = REQUIRED_FIELDS - rec.keys() |
| if missing: |
| errors.append(f"record {i}: missing fields {missing}") |
| continue |
|
|
| img_path = root / rec["image_path"] |
| if not img_path.exists(): |
| errors.append(f"record {i}: file not found {img_path}") |
| continue |
|
|
| |
| try: |
| with Image.open(img_path) as img: |
| img.verify() |
| except Exception as exc: |
| errors.append(f"record {i}: corrupt image {img_path}: {exc}") |
| continue |
|
|
| |
| actual = sha256_file(img_path) |
| if actual != rec["sha256"]: |
| errors.append(f"record {i}: sha256 mismatch {rec['image_path']}") |
|
|
| |
| if split_map and rec["series_id"] not in split_map: |
| warnings.append(f"record {i}: series_id {rec['series_id']} has no split assignment") |
|
|
| return { |
| "total_records": len(records), |
| "errors": errors, |
| "warnings": warnings, |
| "passed": len(errors) == 0, |
| } |
|
|
|
|
| def main() -> None: |
| parser = argparse.ArgumentParser() |
| parser.add_argument("--root", required=True) |
| parser.add_argument("--manifest", required=True) |
| parser.add_argument("--splits", default=None) |
| parser.add_argument("--out", required=True) |
| args = parser.parse_args() |
|
|
| result = validate( |
| root=Path(args.root), |
| manifest_path=Path(args.manifest), |
| splits_path=Path(args.splits) if args.splits else None, |
| ) |
|
|
| out_path = Path(args.out) |
| out_path.parent.mkdir(parents=True, exist_ok=True) |
| out_path.write_text(json.dumps(result, indent=2)) |
|
|
| status = "PASSED" if result["passed"] else "FAILED" |
| print(f"Validation {status}: {len(result['errors'])} errors, {len(result['warnings'])} warnings") |
| print(f"Report: {out_path}") |
|
|
| if not result["passed"]: |
| for e in result["errors"]: |
| print(f" ERROR: {e}", file=sys.stderr) |
| sys.exit(1) |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
