import logging
import argparse
import sys
import traceback
from pathlib import Path
from cellmil.interfaces import DatasetCreatorConfig
from cellmil.dataset import DatasetCreator
# Setup logging with enhanced format
logging.basicConfig(
level=logging.INFO,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
handlers=[logging.StreamHandler()],
)
logger = logging.getLogger(__name__)
[docs]def create_dataset(args: argparse.Namespace) -> None:
"""Create a dataset for MIL training based on the provided configuration."""
try:
# Create configuration for patch extraction
config = DatasetCreatorConfig(
excel_path=args.excel_path,
output_path=args.output_path,
gpu=args.gpu,
segmentation_models=args.segmentation_models,
extractors=args.extractors,
graph_methods=args.graph_methods
)
dataset_creator = DatasetCreator(config)
dataset_creator.create()
logger.info("Finished creating dataset.")
except Exception as e:
# Get traceback information
tb = traceback.format_exc()
logger.error(f"Error during dataset creation: {e}\n{tb}")
sys.exit(1)
[docs]def setup_parser() -> argparse.ArgumentParser:
"""Set up command line argument parser"""
parser = argparse.ArgumentParser(
description="CLI tool for creating a dataset for MIL training"
)
# Create dataset arguments
parser.add_argument(
"--excel_path",
type=Path,
required=True,
help="Path to the Excel file containing metadata information",
)
parser.add_argument(
"--output_path",
type=Path,
required=True,
help="Path where the dataset will be saved",
)
parser.add_argument(
"--gpu", type=int, default=0, help="GPU index to use for processing (default: 0)"
)
parser.add_argument(
"--segmentation_models",
nargs='+',
required=False,
help="List of segmentation models to use for cell segmentation",
)
parser.add_argument(
"--extractors",
nargs='+',
required=True,
help="List of feature extractors to use for feature extraction",
)
parser.add_argument(
"--graph_methods",
nargs='+',
required=False,
help="List of graph creation methods to use",
)
return parser
[docs]def main() -> None:
"""Main function to run the CLI tool"""
parser = setup_parser()
args = parser.parse_args()
create_dataset(args)
if __name__ == "__main__":
main()
