turboprep-docker

#!/bin/bash

# Check if the Docker image exists locally
IMAGE="lemuelpuglisi/turboprep:latest"
if ! docker image inspect "$IMAGE" > /dev/null 2>&1; then
    echo "Installing turboprep Docker container..."
    docker pull "$IMAGE"
fi


HELP_MESSAGE="Usage: turboprep-docker <image_path> <output_folder> <template_path> [OPTIONS]

Options:
  -t, --threads <threads>               Threads (default: number of cores)
  -s, --shrink-factor                   Bias field correction shrink factor (default: 3), see N4BiasFieldCorrection
  -m, --modality <modality>             Modality {t2,other,md,t1,pd,flair} (default is t1)
  -r, --registration-type <type>        Registration type {t,r,a} (default is 'a' (affine), see antsRegistrationSyNQuick.sh)
  --no-bfc                              Skip bias field correction step
  --keep                                Keep intermediate files"


# Check if the first argument is --help, then show help and exit
if [ "$1" == "--help" ]; then
    echo "$HELP_MESSAGE"
    exit 0
fi

# Check if the number of arguments is correct
if [ "$#" -lt 2 ]; then
    echo "$HELP_MESSAGE"
    exit 1
fi

# Assign arguments to variables
INPUT_PATH=$1
OUTPUT_DIR=$2
TEMPLATE_PATH=$3

# Ensure INPUT_PATH, OUTPUT_DIR, and TEMPLATE_PATH are absolute paths
if [[ "$INPUT_PATH" != /* ]]; then
    INPUT_PATH="$(realpath "$INPUT_PATH")"
fi

if [[ "$OUTPUT_DIR" != /* ]]; then
    OUTPUT_DIR="$(realpath "$OUTPUT_DIR")"
fi

if [[ "$TEMPLATE_PATH" != /* ]]; then
    TEMPLATE_PATH="$(realpath "$TEMPLATE_PATH")"
fi

shift 3  # Shift positional arguments so options can be processed

# Default values for options
THREADS=$(nproc)  # Default to number of cores
SHRINK_FACTOR=3
MODALITY="t1"
REGISTRATION_TYPE="a"
NO_BFC=false
KEEP=false

# Parse options
while [[ $# -gt 0 ]]; do
    case "$1" in
        -t|--threads)
            THREADS=$2
            shift 2
            ;;
        -s|--shrink-factor)
            SHRINK_FACTOR=$2
            shift 2
            ;;
        -m|--modality)
            MODALITY=$2
            shift 2
            ;;
        -r|--registration-type)
            REGISTRATION_TYPE=$2
            shift 2
            ;;
        --no-bfc)
            NO_BFC=true
            shift
            ;;
        --keep)
            KEEP=true
            shift
            ;;
        *)
            echo "Unknown option: $1"
            echo "$HELP_MESSAGE"
            exit 1
            ;;
    esac
done

# Extract the directory where INPUT_PATH, OUTPUT_DIR, and TEMPLATE_PATH are stored
INPUT_DIR=$(dirname "$INPUT_PATH")
TEMPLATE_DIR=$(dirname "$TEMPLATE_PATH")

# Set the container paths
CONTAINER_INPUT_DIR="/app/input"
CONTAINER_OUTPUT_DIR="/app/output"
CONTAINER_TEMPLATE_DIR="/app/template"

# Set the container file paths
CONTAINER_INPUT_PATH="$CONTAINER_INPUT_DIR/$(basename "$INPUT_PATH")"
CONTAINER_TEMPLATE_PATH="$CONTAINER_TEMPLATE_DIR/$(basename "$TEMPLATE_PATH")"

# Construct the docker command
DOCKER_CMD="docker run --rm \
    -v $INPUT_DIR:$CONTAINER_INPUT_DIR \
    -v $OUTPUT_DIR:$CONTAINER_OUTPUT_DIR \
    -v $TEMPLATE_DIR:$CONTAINER_TEMPLATE_DIR \
    $IMAGE \
    $CONTAINER_INPUT_PATH $CONTAINER_OUTPUT_DIR $CONTAINER_TEMPLATE_PATH \
    -t $THREADS \
    -s $SHRINK_FACTOR \
    -m $MODALITY \
    -r $REGISTRATION_TYPE"

# Add optional flags
if [ "$NO_BFC" = true ]; then
    DOCKER_CMD="$DOCKER_CMD --no-bfc"
fi
if [ "$KEEP" = true ]; then
    DOCKER_CMD="$DOCKER_CMD --keep"
fi

# # Run the docker command
eval "$DOCKER_CMD"