| | """ |
| | Download MIMIC-CXR images required by qa.json from PhysioNet. |
| | |
| | Prerequisites: |
| | 1. Create a PhysioNet account at https://physionet.org/ |
| | 2. Complete the required CITI training course |
| | 3. Sign the data use agreement for MIMIC-CXR-JPG v2.1.0 |
| | https://physionet.org/content/mimic-cxr-jpg/2.1.0/ |
| | |
| | Usage: |
| | python download_mimic.py --user <username> --password <password> |
| | """ |
| |
|
| | import argparse |
| | import json |
| | import os |
| | import subprocess |
| | import sys |
| |
|
| |
|
| | BASE_URL = "https://physionet.org/files/mimic-cxr-jpg/2.1.0/files" |
| |
|
| |
|
| | def get_required_images(qa_path: str) -> list[str]: |
| | """Extract unique MIMIC image paths from qa.json.""" |
| | with open(qa_path) as f: |
| | data = json.load(f) |
| |
|
| | images = set() |
| | for entry in data: |
| | for key in ("image_1", "image_2"): |
| | path = entry.get(key, "") |
| | if path.startswith("images/mimic/"): |
| | images.add(path) |
| | return sorted(images) |
| |
|
| |
|
| | def download_images(images: list[str], user: str, password: str, root_dir: str): |
| | """Download images from PhysioNet and place them at the expected paths.""" |
| | total = len(images) |
| | print(f"Found {total} MIMIC-CXR images to download.\n") |
| |
|
| | skipped = 0 |
| | downloaded = 0 |
| | failed = 0 |
| |
|
| | for i, image_path in enumerate(images, 1): |
| | dest = os.path.join(root_dir, image_path) |
| |
|
| | if os.path.exists(dest): |
| | skipped += 1 |
| | continue |
| |
|
| | |
| | physionet_path = image_path.removeprefix("images/mimic/") |
| | url = f"{BASE_URL}/{physionet_path}" |
| |
|
| | os.makedirs(os.path.dirname(dest), exist_ok=True) |
| |
|
| | print(f"[{i}/{total}] Downloading {physionet_path} ...") |
| | result = subprocess.run( |
| | [ |
| | "wget", "-q", "-O", dest, |
| | "--user", user, |
| | "--password", password, |
| | url, |
| | ], |
| | capture_output=True, |
| | text=True, |
| | ) |
| |
|
| | if result.returncode != 0: |
| | failed += 1 |
| | print(f" FAILED: {result.stderr.strip()}") |
| | |
| | if os.path.exists(dest) and os.path.getsize(dest) == 0: |
| | os.remove(dest) |
| | else: |
| | downloaded += 1 |
| |
|
| | print(f"\nDone: {downloaded} downloaded, {skipped} skipped (already exist), {failed} failed.") |
| | if failed > 0: |
| | print("Re-run the script to retry failed downloads.") |
| |
|
| |
|
| | def main(): |
| | parser = argparse.ArgumentParser(description="Download MIMIC-CXR images for VLM-SubtleBench.") |
| | parser.add_argument("--user", required=True, help="PhysioNet username") |
| | parser.add_argument("--password", required=True, help="PhysioNet password") |
| | parser.add_argument("--qa-path", default=None, help="Path to qa.json (default: qa.json in the same directory as this script)") |
| | args = parser.parse_args() |
| |
|
| | root_dir = os.path.dirname(os.path.abspath(__file__)) |
| | qa_path = args.qa_path or os.path.join(root_dir, "qa.json") |
| |
|
| | if not os.path.exists(qa_path): |
| | print(f"Error: qa.json not found at {qa_path}", file=sys.stderr) |
| | sys.exit(1) |
| |
|
| | images = get_required_images(qa_path) |
| | if not images: |
| | print("No MIMIC-CXR images found in qa.json.") |
| | sys.exit(0) |
| |
|
| | download_images(images, args.user, args.password, root_dir) |
| |
|
| |
|
| | if __name__ == "__main__": |
| | main() |
| |
|
