ThyroidProject/database_crawlers/image_patcher/national_cancer_patcher.py

import concurrent.futures
import os
import pathlib

from tqdm import tqdm

from config import Config
from image_patcher import ImageAndSlidePatcher
from national_cancer_institute.read_xml_file import get_slide_info_from_bcr_xml


def save_national_cancer_institute_patch(database_path):
    def patch_image(image_path):
        try:
            image_path = str(image_path)
            print()
            print("image path: ", image_path)
            file_name = ImageAndSlidePatcher._get_file_name_from_path(image_path)
            slide_id = file_name.split(".")[0]
            slide_patch_dir = os.path.join(patch_dir, slide_id)
            if os.path.isdir(slide_patch_dir):
                print("it has already been patched")
                return
            web_label = slide_infos.get(slide_id, None)
            if web_label is None:
                print("Ignored")
                return
            web_details = {"database_name": "NationalCancerInstitute",
                           "image_id": slide_id,
                           "image_web_label": web_label,
                           "image_class_label": web_label,
                           "report": None,
                           "stain_type": "H&E",
                           "is_wsi": True}
            return ImageAndSlidePatcher.save_image_patches_and_update_csv(web_label, None, csv_writer, web_details,
                                                                          image_path, slide_patch_dir, slide_id)
        except Exception as e:
            print(e)

    data_dir = os.path.join(database_path, "data")
    slide_infos = {}
    for xml_path in pathlib.Path(data_dir).glob("**/*.xml"):
        slide_infos.update(get_slide_info_from_bcr_xml(str(xml_path)))

    data_dir, patch_dir, csv_writer, csv_file = ImageAndSlidePatcher.create_patch_dir_and_initialize_csv(database_path)
    csv_file.flush()

    with concurrent.futures.ThreadPoolExecutor(max_workers=Config.workers) as executor:
        image_paths = pathlib.Path(data_dir).glob("**/*.svs")
        image_paths = [i for i in image_paths]
        print()
        for res in tqdm(executor.map(patch_image, image_paths), total=len(image_paths)):
            if res:
                csv_file.flush()
    csv_file.flush()


if __name__ == '__main__':
    database_directory = "../"
    save_national_cancer_institute_patch(os.path.join(database_directory, "national_cancer_institute"))