import logging
import argparse
import sys
import traceback
from pathlib import Path
from cellmil.interfaces import GraphCreatorConfig
from cellmil.graph import GraphCreator
from cellmil.interfaces.GraphCreatorConfig import GraphCreatorType
from cellmil.interfaces.CellSegmenterConfig import ModelType
# 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 graph_creation(args: argparse.Namespace) -> None:
"""Create graph from whole slide images with specified configuration."""
try:
# Create configuration
config = GraphCreatorConfig(
method=args.method,
patched_slide_path=args.patched_slide_path,
segmentation_model=args.segmentation_model,
gpu=args.gpu,
plot=True,
debug=args.debug
)
# Process slide
slide_processor = GraphCreator(config)
slide_processor.create_graph()
if not args.debug:
logger.info("Finished Graph Creation.")
else:
logger.info("Debug visualizer closed.")
except Exception as e:
# Get traceback information
tb = traceback.format_exc()
logger.error(f"Error during graph 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 preparing data from whole slide images"
)
# Graph creation arguments
parser.add_argument(
"--method",
type=str,
required=True,
choices=GraphCreatorType.values(),
help="Graph creation method to use, options are: " + ", ".join(GraphCreatorType.values()),
)
parser.add_argument(
"--patched_slide_path",
type=Path,
required=True,
help="Path to the patched slide image folder",
)
parser.add_argument(
"--segmentation_model",
type=str,
required=True,
choices=ModelType.values(),
help="Segmentation model used to extract cells",
)
parser.add_argument(
"--gpu",
type=int,
default=0,
help="GPU device ID to use for processing",
)
parser.add_argument(
"--debug",
action="store_true",
help="Enable debug mode with interactive visualization for hyperparameter tuning",
)
return parser
[docs]def main():
"""Entry point for the CLI tool."""
parser = setup_parser()
args = parser.parse_args()
# Call graph creation directly
graph_creation(args)
if __name__ == "__main__":
main()
