Spaces:
Runtime error
Runtime error
| import subprocess | |
| import argparse | |
| import os | |
| import shutil | |
| def save_tiles(slide_path): | |
| filename = os.path.basename(slide_path) | |
| FILEID = filename.rsplit('.', maxsplit=1)[0] | |
| PATCHES_DIR = os.environ['PATCHES_DIR'] | |
| SLIDES_DIR = os.environ['SLIDES_DIR'] | |
| os.makedirs(PATCHES_DIR, exist_ok=True) | |
| os.makedirs(SLIDES_DIR, exist_ok=True) | |
| shutil.copy(slide_path, SLIDES_DIR) | |
| INPUT_PATH = os.path.join(SLIDES_DIR, filename) | |
| CMD = ['python3', 'src/tile_WSI.py', '-s', '512', '-e', '0', '-j', '16', '-B', '50', '-M', '20', '-o', PATCHES_DIR, INPUT_PATH] | |
| subprocess.call(CMD) | |
| if __name__ == '__main__': | |
| parser = argparse.ArgumentParser(description='PyTorch Classification') | |
| parser.add_argument('--slide_path', type=str, help='path to the WSI slide') | |
| args = parser.parse_args() | |
| filename = os.path.basename(args.slide_path) | |
| FILEID = filename.rsplit('.', maxsplit=1)[0] | |
| PATCHES_DIR = os.environ['PATCHES_DIR'] | |
| SLIDES_DIR = os.environ['SLIDES_DIR'] | |
| os.makedirs(PATCHES_DIR, exist_ok=True) | |
| os.makedirs(SLIDES_DIR, exist_ok=True) | |
| shutil.move(args.slide_path, SLIDES_DIR) | |
| INPUT_PATH = os.path.join(SLIDES_DIR, filename) | |
| CMD = ['python3', 'src/tile_WSI.py', '-s', '512', '-e', '0', '-j', '16', '-B', '50', '-M', '20', '-o', PATCHES_DIR, INPUT_PATH] | |
| subprocess.call(CMD) | |