Convert QuPath's GeoJson annotations to Json for WholeSlideData library

convert_geojson_to_json.py

import os
import glob
import json
import numpy as np

LABELS = {
  'Tissue': 1,
  'Tumor': 2
}
  
def main(folder):
    files = glob.glob(os.path.join(folder, "*.geojson"))
    for src in files:
        with open(src) as f:
            data = json.load(f)
        
        new_data = []
        for ann in data:
            tmp = dict()
            name = ann["properties"]["classification"]["name"]
            tmp["label"] = dict(
                name = name.lower(),
                value = LABELS[name]
            )
            tmp["coordinates"] = ann['geometry']['coordinates']
            new_data.append(tmp)

        with open(src.replace(".geojson", ".json"), "w") as f:
            json.dump(new_data, f)

if __name__ == "__main__":
    folder = "./"
    main(folder)