CaNA_expanded_p150_DLCS24.sh

#!/bin/bash

# =====# Create output directory and set proper permissions
echo "📁 Setting up output directories and permissions..."
docker exec cana_pipeline mkdir -p /app/demofolder/output
docker exec cana_pipeline mkdir -p /app/demofolder/output/CaNA_expanded_150_output
docker exec cana_pipeline chmod 777 /app/demofolder/output/CaNA_expanded_150_output
# CaNA Expanded Processing Pipeline
# Docker Container Activation
# ============================
echo "Starting CaNA (Cancer Analysis) Docker container..."
cd "$(dirname "$0")"  # Go to script directory

# Remove existing container if it exists
docker rm -f cana_pipeline 2>/dev/null || true

# Start container using the PiNS medical imaging image
echo "Launching ft42/pins:latest container..."
docker run -d --name cana_pipeline \
  -v "$(pwd):/app" \
  -w /app \
  ft42/pins:latest \
  tail -f /dev/null

# Create output directory and set proper permissions
echo "Setting up output directories and permissions..."
docker exec cana_pipeline mkdir -p /app/demofolder/output/CaNA_expanded_150_output
docker exec cana_pipeline mkdir -p /app/demofolder/output/
docker exec cana_pipeline chmod 777 /app/demofolder/output/CaNA_expanded_150_output
docker exec cana_pipeline chmod 777 /app/demofolder/output/

# Install additional dependencies if needed
echo "Installing missing Python packages if needed..."
docker exec cana_pipeline pip install nibabel scikit-image > /dev/null 2>&1 || echo "⚠️  Some packages may already be installed"

echo "Docker container is running with all dependencies"

# ============================
# Run CaNA Processing Pipeline
# ============================
echo "🧠 Running CaNA (Cancer Analysis) lung nodule expansion processing..."

docker exec cana_pipeline python CaNA_LungNoduleSize_expanded.py \
  --json_path ./demofolder/data/Experiments_DLCSD24_512xy_256z_771p25m_dataset.json \
  --dict_to_read "training" \
  --data_root ./demofolder/data/ \
  --lunglesion_lbl 23 \
  --scale_percent 50 \
  --mode grow \
  --save_dir /app/demofolder/output/CaNA_expanded_150_output \
  --random_seed 42 \
  --prefix Aug23e150_ \
  --log_file /app/demofolder/output/CaNA_expansion_150.log

# ============================
# Cleanup and Results
# ============================
if [ $? -eq 0 ]; then
    echo "✅ CaNA processing completed successfully!"
    echo "📊 Check ./demofolder/output/ directory for results:"
    echo "   - Processing log: CaNA_expansion_150.log"
    echo "   - Expanded masks: CaNA_expanded_150_output/"
    echo "   - File prefix: Aug23e150_"
else
    echo "❌ CaNA processing failed. Check the logs above for errors."
fi

# Stop and remove container
echo " Cleaning up Docker container..."
docker stop cana_pipeline > /dev/null 2>&1
docker rm cana_pipeline > /dev/null 2>&1

echo "CaNA pipeline execution complete!"