run

#! /bin/bash
#
#

CONTAINER="[vistalab/dwi-flip-bvec]"
echo -e "$CONTAINER  Initiated"


# Built to flywheel-v0 spec.
FLYWHEEL_BASE=/flywheel/v0
MCR_ROOT=/opt/mcr/v92/
OUTPUT_DIR=$FLYWHEEL_BASE/output


# Make sure that /output directory exists
if [[ ! -d "$OUTPUT_DIR" ]]
    then
        echo "$CONTAINER  $OUTPUT_DIR not found!"
        exit 1
fi


# Set paths to input files
bvecFile=$(find $FLYWHEEL_BASE/input/bvec/ -type f -name "*.bvec*")
CONFIG_FILE=${FLYWHEEL_BASE}/config.json

# Check for required inputs
if [[ -z "$bvecFile" ]]; then
  echo -e "$CONTAINER  Bvec input file not found! Exiting!"
  exit 1
fi


# Parse Config File
if [[ -f $CONFIG_FILE ]]; then
  # Parse config from config.json
  echo -e "$CONTAINER  Loading configuration from ${CONFIG_FILE}"
  xFlip=$(cat $CONFIG_FILE | jq -r '.config.xFlip')
  yFlip=$(cat $CONFIG_FILE | jq -r '.config.yFlip')
  zFlip=$(cat $CONFIG_FILE | jq -r '.config.zFlip')
  echo "$CONTAINER  xFlip has been set to $xFlip"
  echo "$CONTAINER  yFlip has been set to $yFlip"
  echo "$CONTAINER  zFlip has been set to $zFlip"
else
  # Parse defaults from the manifest.json
  CONFIG_FILE=$FLYWHEEL_BASE/manifest.json
  echo -e "$CONTAINER  Loading defaults from ${CONFIG_FILE}"
  xFlip=$(cat $CONFIG_FILE | jq -r '.config.xFlip.default')
  yFlip=$(cat $CONFIG_FILE | jq -r '.config.yFlip.default')
  zFlip=$(cat $CONFIG_FILE | jq -r '.config.zFlip.default')
  echo "$CONTAINER  xFlip has been set to $xFlip"
  echo "$CONTAINER  yFlip has been set to $yFlip"
  echo "$CONTAINER  zFlip has been set to $zFlip"
fi


# Run the Matlab executable
time /msa/run_dwiflipbvec.sh "${MCR_ROOT}" "${bvecFile}" "${xFlip}" "${yFlip}" "${zFlip}"  "${OUTPUT_DIR}"


# Check exit status
exit_status=$?
if [[ $exit_status != 0 ]]; then
  echo -e "$CONTAINER  An error occurred during execution of the Matlab executable. Exiting!"
  exit 1
fi


# Get a list of the files in the output directory
outputs=$(find $OUTPUT_DIR/* -maxdepth 0 -type f)


# If outputs exist, generate metadata, and exit
if [[ -z $outputs ]]; then
  echo "$CONTAINER  No results found in output directory... Exiting"
  exit 1
else
  cd $OUTPUT_DIR
  echo -e "$CONTAINER  Wrote: `ls`"
  echo -e "$CONTAINER  Done!"
fi


# Handle permissions of the outputs
chmod -R 777 $OUTPUT_DIR


# Exit
exit 0