| """ |
| 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() |
|
|
