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#!/bin/bash
# ============================
# Docker Container Activation
# ============================
echo "Starting Docker container..."
cd "$(dirname "$0")/.." # Go to project root
# Remove existing container if it exists
docker rm -f nodule_seg_pipeline 2>/dev/null || true
# Start container using existing medical imaging image
docker run -d --name nodule_seg_pipeline \
-v "$(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 nodule_seg_pipeline mkdir -p /app/demofolder/output/DLCS24_64Q_CAD_patches
docker exec nodule_seg_pipeline chmod -R 777 /app/demofolder/output/
echo "Installing missing Python packages..."
docker exec nodule_seg_pipeline apt-get update > /dev/null 2>&1
docker exec nodule_seg_pipeline apt-get install -y libgl1 libglib2.0-0 > /dev/null 2>&1
docker exec nodule_seg_pipeline pip install opencv-python-headless torch torchvision monai "numpy<2.0" --quiet
echo "Docker container is running with all dependencies installed"
# ============================
# Configuration Variables
# ============================
# Define paths
PYTHON_SCRIPT="/app/scr/candidate_worldCoord_patchExtarctor_pipeline.py" # Path inside container
DATASET_NAME="DLCSD24"
RAW_DATA_PATH="/app/demofolder/data/DLCS24/"
CSV_SAVE_PATH="/app/demofolder/output/DLCS24_64Q_CAD_patches/"
DATASET_CSV="/app/demofolder/data/DLCSD24_Annotations_N2.csv"
NIFTI_CLM_NAME="ct_nifti_file"
UNIQUE_ANNOTATION_ID="nodule_id" # Leave empty or remove if not in CSV
MALIGNANT_LBL="Malignant_lbl"
COORD_X="coordX"
COORD_Y="coordY"
COORD_Z="coordZ"
W="w"
H="h"
D="d"
SAVE_NIFTI_PATH="/app/demofolder/output/DLCS24_64Q_CAD_patches/nifti/"
PATCH_SIZE="64 64 64"
NORMALIZATION="-1000 500 0 1"
CLIP="True" # Change to "False" if needed
# ============================
# Run the Python script in Docker
# ============================
echo "Running segmentation in Docker container..."
docker exec nodule_seg_pipeline python3 "$PYTHON_SCRIPT" \
--dataset_name "$DATASET_NAME" \
--raw_data_path "$RAW_DATA_PATH" \
--csv_save_path "$CSV_SAVE_PATH" \
--dataset_csv "$DATASET_CSV" \
--nifti_clm_name "$NIFTI_CLM_NAME" \
--unique_Annotation_id "$UNIQUE_ANNOTATION_ID" \
--Malignant_lbl "$MALIGNANT_LBL" \
--coordX "$COORD_X" \
--coordY "$COORD_Y" \
--coordZ "$COORD_Z" \
--patch_size $PATCH_SIZE \
--normalization $NORMALIZATION \
--clip "$CLIP" \
--save_nifti_path "$SAVE_NIFTI_PATH"
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