data_download.py

"""
Script to download medical images from The Cancer Imaging Archive (TCIA)
"""
import os
import argparse
from tqdm import tqdm
from tcia_rest_client import TCIA_REST_Client

def download_tcia_collection(collection_name, output_dir, api_key=None):
    """
    Download a specific collection from TCIA
    
    Args:
        collection_name (str): Name of the TCIA collection
        output_dir (str): Directory to save downloaded files
        api_key (str, optional): TCIA API key for private collections
    """
    print(f"Downloading {collection_name} collection...")
    
    # Initialize TCIA client
    client = TCIA_REST_Client(api_key=api_key)
    
    # Create output directory
    os.makedirs(output_dir, exist_ok=True)
    
    # Get patients in the collection
    patients = client.get_patient(collection=collection_name)
    
    for patient in tqdm(patients, desc="Downloading patients"):
        patient_id = patient['PatientID']
        
        # Create patient directory
        patient_dir = os.path.join(output_dir, patient_id)
        os.makedirs(patient_dir, exist_ok=True)
        
        # Get studies for patient
        studies = client.get_patient_study(PatientID=patient_id)
        
        for study in studies:
            study_uid = study['StudyInstanceUID']
            
            # Get series for study
            series = client.get_series(StudyInstanceUID=study_uid)
            
            for s in series:
                series_uid = s['SeriesInstanceUID']
                
                # Download series
                client.get_series_DICOM(
                    SeriesInstanceUID=series_uid,
                    downloadPath=patient_dir
                )
    
    print(f"Download complete. Files saved to {output_dir}")

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='Download TCIA collections')
    parser.add_argument('--collection', type=str, required=True, help='TCIA collection name')
    parser.add_argument('--output', type=str, default='./tcia_data', help='Output directory')
    parser.add_argument('--api_key', type=str, help='TCIA API key (if needed)')
    
    args = parser.parse_args()
    
    download_tcia_collection(args.collection, args.output, args.api_key)