import logging
import argparse
import sys
import traceback
from pathlib import Path
from cellmil.interfaces import FeatureVisualizerConfig
from cellmil.visualization import FeatureVisualizer
# 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 visualize_features(args: argparse.Namespace) -> None:
"""Visualize features from a patched slide."""
try:
# Create configuration
config = FeatureVisualizerConfig(
dataset=args.dataset,
)
# Initialize feature visualizer
feature_visualizer = FeatureVisualizer(config)
# Perform visualization
feature_visualizer.visualize()
logger.info("Finished feature visualization.")
except Exception as e:
# Get traceback information
tb = traceback.format_exc()
logger.error(f"Error during feature visualization: {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 visualizing features from a dataset folder with extracted features"
)
# Path to patched slide
parser.add_argument(
"--dataset", type=Path, required=True, help="Path to the folder with "
)
return parser
[docs]def main():
"""Entry point for the CLI tool."""
parser = setup_parser()
args = parser.parse_args()
# Run MIL prediction
visualize_features(args)
