Export DICOM medical images (MR, CT, X-Ray, etc.) to PNG files

dicom2png.py

import os
import pydicom
from PIL import Image
import sys

def save_image(pixel_array, output_path):
    if pixel_array.dtype != 'uint8':
        pixel_array = ((pixel_array - pixel_array.min()) / (pixel_array.max() - pixel_array.min()) * 255).astype('uint8')

    img = Image.fromarray(pixel_array)
    img.save(output_path)
    print(f"Saved image to {output_path}")

def process_dicom_directory(dicomdir_path, save_directory):
    if not os.path.exists(save_directory):
        os.makedirs(save_directory)

    dicomdir = pydicom.dcmread(dicomdir_path)

    for patient_record in dicomdir.patient_records:
        if 'PatientName' in patient_record:
            print(f"Patient: {patient_record.PatientName}")

        for study_record in patient_record.children:
            if 'StudyDate' in study_record:
                print(f"Study: {study_record.StudyDate}")

            for series_record in study_record.children:
                for image_record in series_record.children:
                    if 'ReferencedFileID' in image_record:
                        file_id = list(map(str, image_record.ReferencedFileID))
                        file_id_path = os.path.join(*file_id)
                        print(f"Image: {file_id_path}")

                        image_path = os.path.join(os.path.dirname(dicomdir_path), file_id_path)
                        
                        modified_filename = '_'.join(file_id) + '.png'
                        image_save_path = os.path.join(save_directory, modified_filename)

                        try:
                            img_data = pydicom.dcmread(image_path)
                            print("DICOM image loaded successfully.")
                            save_image(img_data.pixel_array, image_save_path)
                        except FileNotFoundError as e:
                            print(f"Failed to read DICOM file at {image_path}: {e}")
                        except Exception as e:
                            print(f"An error occurred: {e}")

if __name__ == "__main__":
    if len(sys.argv) < 3:
        print("Usage: python dicom2png.py <path_to_DICOMDIR> <path_to_save_images>")
        sys.exit(1)
    
    dicomdir_path = sys.argv[1]
    save_directory = sys.argv[2]
    process_dicom_directory(dicomdir_path, save_directory)