| |
| """Download one M4Raw Brain examination from Hugging Face.""" |
|
|
| from __future__ import annotations |
|
|
| import argparse |
| import csv |
| from pathlib import Path |
|
|
| from huggingface_hub import hf_hub_download |
|
|
|
|
| REPO_ID = "mylyu/M4Raw_brain" |
| MANIFESTS = { |
| "T1": "metadata/T1_manifest.tsv", |
| "T2": "metadata/T2_manifest.tsv", |
| "FLAIR": "metadata/FLAIR_manifest.tsv", |
| "GRE": "metadata/GRE_manifest.tsv", |
| } |
| REP_FIELDS = tuple(f"h5_rep{index:02d}" for index in range(1, 7)) |
|
|
|
|
| def parse_args() -> argparse.Namespace: |
| parser = argparse.ArgumentParser(description=__doc__) |
| parser.add_argument("scan_id") |
| parser.add_argument("--sequence", choices=tuple(MANIFESTS), required=True) |
| parser.add_argument("--output", type=Path, default=Path("M4Raw_case")) |
| parser.add_argument("--repo-id", default=REPO_ID) |
| parser.add_argument("--revision", default="v1.6.0") |
| parser.add_argument( |
| "--include-gre", |
| action="store_true", |
| help="Also download GRE for an original-cohort T1/T2/FLAIR examination.", |
| ) |
| return parser.parse_args() |
|
|
|
|
| def download(repo_id: str, revision: str, filename: str, output: Path) -> Path: |
| return Path( |
| hf_hub_download( |
| repo_id=repo_id, |
| repo_type="dataset", |
| revision=revision, |
| filename=filename, |
| local_dir=output, |
| ) |
| ) |
|
|
|
|
| def manifest_row(path: Path, scan_id: str) -> dict[str, str]: |
| with path.open(newline="", encoding="utf-8") as handle: |
| rows = [ |
| row |
| for row in csv.DictReader(handle, delimiter="\t") |
| if row["scan_id"] == scan_id |
| ] |
| if len(rows) != 1: |
| raise RuntimeError( |
| f"Expected one manifest row for {scan_id}, found {len(rows)}" |
| ) |
| return rows[0] |
|
|
|
|
| def paths_for_sequence(args: argparse.Namespace, sequence: str) -> list[str]: |
| manifest_name = MANIFESTS[sequence] |
| local_manifest = download(args.repo_id, args.revision, manifest_name, args.output) |
| row = manifest_row(local_manifest, args.scan_id) |
| return [manifest_name, *(row[field] for field in REP_FIELDS if row.get(field))] |
|
|
|
|
| def main() -> None: |
| args = parse_args() |
| if args.include_gre and args.sequence == "GRE": |
| raise SystemExit("--include-gre is unnecessary with --sequence GRE") |
| args.output.mkdir(parents=True, exist_ok=True) |
| paths = paths_for_sequence(args, args.sequence) |
| if args.include_gre: |
| paths.extend(paths_for_sequence(args, "GRE")) |
| unique_paths = list(dict.fromkeys(paths)) |
| for filename in unique_paths: |
| print(download(args.repo_id, args.revision, filename, args.output)) |
| print(f"Downloaded {len(unique_paths)} files for {args.scan_id}") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
|
|
