changes

.gitignore

@@ -178,3 +178,5 @@ medrax-pdfs/
 model-weights/
 
 .DS_Store
+
+benchmarking/data/

benchmarking/data/rexvqa/download_rexgradient_images.py

@@ -1,172 +0,0 @@
-#!/usr/bin/env python3
-"""
-Utility script to download and extract ReXGradient-160K images.
-
-This script helps users download the actual PNG images from the ReXGradient-160K dataset,
-which are stored as part files on HuggingFace and need to be concatenated and extracted.
-
-Usage:
-    python download_rexgradient_images.py --output_dir /path/to/images
-"""
-
-import argparse
-import subprocess
-from pathlib import Path
-from huggingface_hub import hf_hub_download, list_repo_files
-import requests
-from tqdm import tqdm
-
-
-def download_file(url, output_path, chunk_size=8192):
-    """Download a file with progress bar."""
-    response = requests.get(url, stream=True)
-    total_size = int(response.headers.get('content-length', 0))
-    
-    with open(output_path, 'wb') as f:
-        with tqdm(total=total_size, unit='B', unit_scale=True, desc=output_path.name) as pbar:
-            for chunk in response.iter_content(chunk_size=chunk_size):
-                if chunk:
-                    f.write(chunk)
-                    pbar.update(len(chunk))
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Download ReXGradient-160K images")
-    parser.add_argument(
-        "--output_dir", 
-        type=str, 
-        required=True,
-        help="Directory to save extracted images"
-    )
-    parser.add_argument(
-        "--repo_id",
-        type=str,
-        default="rajpurkarlab/ReXGradient-160K",
-        help="HuggingFace repository ID"
-    )
-    parser.add_argument(
-        "--skip_download",
-        action="store_true",
-        help="Skip downloading and only extract if files exist"
-    )
-    
-    args = parser.parse_args()
-    
-    output_dir = Path(args.output_dir)
-    output_dir.mkdir(parents=True, exist_ok=True)
-    
-    print(f"Output directory: {output_dir}")
-    
-    # Check if we need to accept the license first
-    print("Note: You may need to accept the dataset license on HuggingFace first:")
-    print(f"Visit: https://huggingface.co/datasets/{args.repo_id}")
-    print("Click 'Access repository' and accept the license agreement.")
-    print()
-    
-    try:
-        # List files in the repository
-        print("Listing files in repository...")
-        files = list_repo_files(args.repo_id, repo_type='dataset')
-        part_files = [f for f in files if f.startswith("deid_png.part")]
-        
-        if not part_files:
-            print("No part files found. The images might be in a different format.")
-            print("Available files:")
-            for f in files:
-                print(f"  - {f}")
-            return
-        
-        print(f"Found {len(part_files)} part files:")
-        for f in part_files:
-            print(f"  - {f}")
-        
-        # Download part files
-        if not args.skip_download:
-            print("\nDownloading part files...")
-            for part_file in part_files:
-                output_path = output_dir / part_file
-                if output_path.exists():
-                    print(f"Skipping {part_file} (already exists)")
-                    continue
-                
-                print(f"Downloading {part_file}...")
-                try:
-                    hf_hub_download(
-                        repo_id=args.repo_id,
-                        filename=part_file,
-                        local_dir=output_dir,
-                        local_dir_use_symlinks=False,
-                        repo_type='dataset'
-                    )
-                except Exception as e:
-                    print(f"Error downloading {part_file}: {e}")
-                    print("You may need to accept the license agreement on HuggingFace.")
-                    return
-        
-        # Concatenate part files
-        tar_path = output_dir / "deid_png.tar"
-        if not tar_path.exists():
-            print("\nConcatenating part files...")
-            with open(tar_path, 'wb') as tar_file:
-                for part_file in sorted(part_files):
-                    part_path = output_dir / part_file
-                    if part_path.exists():
-                        print(f"Adding {part_file}...")
-                        with open(part_path, 'rb') as f:
-                            tar_file.write(f.read())
-                    else:
-                        print(f"Warning: {part_file} not found, skipping...")
-        else:
-            print(f"Tar file already exists: {tar_path}")
-        
-        # Extract tar file
-        if tar_path.exists():
-            print("\nExtracting images...")
-            images_dir = output_dir / "images"
-            images_dir.mkdir(exist_ok=True)
-            
-            # Check if already extracted
-            if any(images_dir.glob("*.png")):
-                print("Images already extracted.")
-            else:
-                try:
-                    subprocess.run([
-                        "tar", "-xf", str(tar_path), 
-                        "-C", str(images_dir)
-                    ], check=True)
-                    print("Extraction completed!")
-                except subprocess.CalledProcessError as e:
-                    print(f"Error extracting tar file: {e}")
-                    return
-                except FileNotFoundError:
-                    print("Error: 'tar' command not found. Please install tar or extract manually.")
-                    return
-            
-            # Count extracted images
-            png_files = list(images_dir.glob("*.png"))
-            print(f"Extracted {len(png_files)} PNG images to {images_dir}")
-            
-            # Show some example filenames
-            if png_files:
-                print("\nExample image filenames:")
-                for f in png_files[:5]:
-                    print(f"  - {f.name}")
-                if len(png_files) > 5:
-                    print(f"  ... and {len(png_files) - 5} more")
-        
-        print(f"\nSetup complete! Use this directory as images_dir in ReXVQABenchmark:")
-        print(f"images_dir='{images_dir}'")
-        
-    except Exception as e:
-        print(f"Error: {e}")
-        print("\nManual setup instructions:")
-        print("1. Visit https://huggingface.co/datasets/rajpurkarlab/ReXGradient-160K")
-        print("2. Accept the license agreement")
-        print("3. Download the deid_png.part* files")
-        print("4. Concatenate: cat deid_png.part* > deid_png.tar")
-        print("5. Extract: tar -xf deid_png.tar")
-        print("6. Use the extracted directory as images_dir")
-
-
-if __name__ == "__main__":
-    main() 

medrax/agent/__init__.py

@@ -1 +1 @@
-from .agent import State, Agent
+from .agent import AgentState, Agent