brainage/get_brainage.sh

#!/bin/bash

DEBUG=1
EXTENSIONS=('nii.gz' 'nii' 'mgz')

# Initialize variables with default values
INPUT_DIR=""
OUTPUT_DIR=""
BIDS="yes"
CONDOR="yes"
RAW="yes"
RUN_SINGULARITY_FILE=""
SAVE="no"

# Condor specific arguments
CPUS='1'
RAM='8G'
DISK='1G'

# Parse command-line arguments
while [[ "$#" -gt 0 ]]; do
    case $1 in
        -input) INPUT_DIR="$2"; shift ;;
        -output) OUTPUT_DIR="$2"; shift ;;
        -BIDS) BIDS="$2"; shift ;;
        -CONDOR) CONDOR="$2"; shift ;;
        -RAW) RAW="$2"; shift ;;
        -RUN_FILE) RUN_SINGULARITY_FILE="$2"; shift ;;
        -SAVE_FILE) SAVE="$2"; shift ;;
        -CONTAINER_PATH) CONTAINER_PATH="$2"; shift ;;
        -help)
            echo "Usage: $0 -input <input_dir> -output <output_dir> -BIDS <yes/no> -CONDOR <yes/no> -RAW <yes/no> -RUN_FILE <path> -SAVE_FILE <yes/no> -CONTAINER_PATH <path>"
            exit 0
            ;;
        *) echo "Unknown parameter passed: $1"; exit 1 ;;
    esac
    shift
done

# Debugging or verbose mode can be added here if needed.
if [ "$DEBUG" -eq 1 ]; then
  echo "Input directory: $INPUT_DIR" >&2
  echo "Output directory: $OUTPUT_DIR" >&2
  echo "BIDS: $BIDS" >&2
  echo "CONDOR: $CONDOR" >&2
  echo "RAW: $RAW" >&2
  echo "RUN_FILE: $RUN_SINGULARITY_FILE" >&2
  echo "SAVE_ALL: $SAVE" >&2
  echo "CONTAINER_PATH: $CONTAINER_PATH" >&2
fi

# Check if INPUT_DIR exists and is a directory (even if one file)
if [ ! -d "$INPUT_DIR" ]; then
  echo "Error: $INPUT_DIR is not a directory or does not exist." >&2
  exit 1
fi

if [ -z "$( ls -A $INPUT_DIR )" ]; then
   echo "$INPUT_DIR Empty" >&2
   exit 1
fi

# Check if OUTPUT_DIR exists; if not, create it
if [ ! -d "$OUTPUT_DIR" ]; then
  echo "Warning: $OUTPUT_DIR does not exist. Creating it now." >&2
  mkdir -p "$OUTPUT_DIR"
fi

if [ ! -z "$( ls -A $OUTPUT_DIR )" ]; then
   echo "Warning $OUTPUT_DIR is not Empty, files might be overwritten" >&2
fi

LOGS_DIR=${OUTPUT_DIR}/logs

# create the logs dir if it doesn't exist
if [ ! -d "${LOGS_DIR}" ]; then 
  echo "Creating logs diretory ${LOGS_DIR}" >&2
  mkdir -p "${LOGS_DIR}"
fi 

# # print the .submit header

if [ "$CONDOR" == "yes" ]; then

  printf "# The environmentls

  universe       = vanilla
  getenv         = True
  request_cpus   = ${CPUS}
  request_memory = ${RAM}
  request_disk   = ${DISK}

  Requirements = HasSingularity

  # Execution
  executable     = ${RUN_SINGULARITY_FILE}
  notification   = Error
  \n"

fi

# Loop over subjects in INPUT_DIR no BIDS
for type in "${EXTENSIONS[@]}"; do
  if [ "$BIDS" == "no" ]; then
    # no bids
    subj_list=($( find "$INPUT_DIR" -maxdepth 1 -name "*.${type}" \( -type f -o -type l \) ))
  else
    # bids
    subj_list=($( find "${INPUT_DIR}"/sub-*/ses-*/anat -maxdepth 1 -name "*T1*.${type}" \( -type f -o -type l \) ))
  fi
  for subj in "${subj_list[@]}"; do
    #printf "Processing subject: $subj \n" >&2 
    if [ "$CONDOR" == "yes" ]; then
      sub=$(basename $subj)
      printf "arguments = $subj \ \n $OUTPUT_DIR \ \n $CONTAINER_PATH \ \n $SAVE $RAW \ \n"
      printf "log       = ${LOGS_DIR}/\$(Cluster).\$(Process).${sub::-11}.log\n"
      printf "output    = ${LOGS_DIR}/\$(Cluster).\$(Process).${sub::-11}.out\n"
      printf "error     = ${LOGS_DIR}/\$(Cluster).\$(Process).${sub::-11}.err\n"
      printf "Queue\n\n"
    else
      printf "${RUN_SINGULARITY_FILE} $subj $OUTPUT_DIR $CONTAINER_PATH $SAVE $RAW  \n"
    fi
  done

done