convert_xml_to_json.py

import json
from wsi_annotations_kit import wsi_annotations_kit as wak
from typing import Dict

def xml_to_json(xml_file_path: str, json_file_path: str, annotation_map: Dict[str, int] = None) -> None:
    """
    Convert an XML annotation file to a JSON format and update its annotations.

    Parameters:
    - xml_file_path (str): Path to the input XML annotation file.
    - json_file_path (str): Path to save the output JSON file.
    - annotation_map (Dict[str, int], optional): A dictionary to map annotation types to IDs.
      Default is {'Nuclei': 1}.
    """
    if annotation_map is None:
        annotation_map = {'Nuclei': 1}

    try:
        # Step 1: Convert XML to JSON and save to specified path
        print(f"Converting XML ({xml_file_path}) to JSON ({json_file_path})...")
        converter = wak.Converter(xml_file_path, annotation_map)
        converter.json_save(json_file_path)
        print(f"Initial JSON saved to {json_file_path}.")

        # Step 2: Load the JSON file
        with open(json_file_path, 'r') as file:
            annotations = json.load(file)

        # Step 3: Update the JSON annotations
        print("Updating JSON annotations with line color...")
        for annotation_dict in annotations:
            annotation = annotation_dict.get("annotation")
            if annotation and "elements" in annotation:
                for element in annotation["elements"]:
                    element["lineColor"] = "rgba(255, 0, 0, 255)"

        # Step 4: Save the updated JSON back to the file
        with open(json_file_path, 'w') as file:
            json.dump(annotations, file, indent=4)

        print(f"Updated JSON successfully saved to {json_file_path}.")

    except Exception as e:
        print(f"An error occurred during XML to JSON conversion: {e}")
        raise