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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_KNN_2mm_Extend_Seg
docker exec nodule_seg_pipeline chmod -R 777 /app/demofolder/output/
echo "Installing missing Python packages if needed..."
docker exec nodule_seg_pipeline pip install opencv-python-headless --quiet > /dev/null 2>&1 || true
echo "Docker container is running with write permissions set"
# ============================
# Configuration Variables
# ============================
# Define paths
PYTHON_SCRIPT="/app/scr/candidateSeg_pipiline.py" # Path inside container
PARAMS_JSON="/app/scr/Pyradiomics_feature_extarctor_pram.json" # Path inside container
DATASET_NAME="DLCSD24"
RAW_DATA_PATH="/app/demofolder/data/DLCS24/"
CSV_SAVE_PATH="/app/demofolder/output/"
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"
SEG_ALG="knn" # Choose from: gmm, knn, fcm, otsu
EXPANSION_MM=2.0 # Set the expansion in millimeters
SAVE_NIFTI_PATH="/app/demofolder/output/DLCS24_KNN_2mm_Extend_Seg/"
SAVE_MASK_FLAG="--save_the_generated_mask" # Remove if you don't want to save masks
USE_EXPAND_FLAG="--use_expand" # Include if you want to use expansion
EXTRACT_RADIOMICS_FLAG="" # Include if you want to extract radiomics "--extract_radiomics"
# ============================
# 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 "$COORD_Z" \
--w "$W" \
--h "$H" \
--d "$D" \
--seg_alg "$SEG_ALG" \
--expansion_mm "$EXPANSION_MM" \
--params_json "$PARAMS_JSON" \
--save_nifti_path "$SAVE_NIFTI_PATH" \
$USE_EXPAND_FLAG \
$EXTRACT_RADIOMICS_FLAG \
$SAVE_MASK_FLAG
echo "✅ Segmentation completed! Check demofolder/output/ directory for results." |