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wsi_extraction.py
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wsi_extraction.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Main entry point for patch-preprocessing
#
# @ Fabian Hörst, [email protected]
# Institute for Artifical Intelligence in Medicine,
# University Medicine Essen
import sys
import os
project_root = os.path.dirname(os.path.abspath(__file__))
sys.path.append(project_root)
project_root = os.path.dirname(os.path.abspath(project_root))
sys.path.append(project_root)
import logging
logger = logging.getLogger()
logger.addHandler(logging.NullHandler())
from pathopatch.cli import PreProcessingParser
from pathopatch.patch_extraction.patch_extraction import PreProcessor
from pathopatch.utils.tools import close_logger
def main():
configuration_parser = PreProcessingParser()
configuration, logger = configuration_parser.get_config()
configuration_parser.store_config()
slide_processor = PreProcessor(slide_processor_config=configuration)
slide_processor.sample_patches_dataset()
logger.info("Finished Preprocessing.")
close_logger(logger)
if __name__ == "__main__":
main()