synthba

#!/bin/bash

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


HELP_MESSAGE="usage: synthba.py [-h] -i I -o O -c C [-b B] [-m M] [-t T]

options:
  -h, --help  show this help message and exit
  -i I        Input folder with nifti files.
  -o O        Output folder where to store the predictions and (optionally)
              intermediate files
  -c C        SynthBA checkpoints directory
  -b B        Batch size
  -m M        SynthBA model (available configurations = [u, g])
  -t T        Template for registration (available templates = [T1w_1mm,
              T1w_2mm, T2w_1mm])"


# 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 "Usage: $0 <input_path> <output_path> [-m <model>] [-b <batchsize>] [-t <template>]"
    exit 1
fi

# Assign arguments to variables
INPUT_PATH=$1
OUTPUT_PATH=$2

# Default values for optional arguments
MODEL="u"
BATCHSIZE="1"
TEMPLATE="T1w_1mm"

# Shift past the first two arguments (input and output)
shift 2

# Parse the optional arguments
while getopts "m:b:t:" opt; do
    case $opt in
        m) MODEL=$OPTARG ;;
        b) BATCHSIZE=$OPTARG ;;
        t) TEMPLATE=$OPTARG ;;
        *) echo "Usage: $0 <input_path> <output_path> [-m <model>] [-b <batchsize>] [-t <template>]"
           exit 1 ;;
    esac
done

echo "$MODEL"

# Run the Docker command with the specified arguments
docker run --rm \
    -v "$INPUT_PATH":/home/inputs \
    -v "$OUTPUT_PATH":/home/outputs \
    lemuelpuglisi/synthba:latest \
    -m "$MODEL" -b "$BATCHSIZE" -t "$TEMPLATE"