run

#! /bin/bash

#
CONTAINER="[vistalab/acpc-anat]"
echo -e "$CONTAINER  Initiated"


# Built to flywheel-v0 spec.
FLYWHEEL_BASE=/flywheel/v0
MCR_ROOT=/opt/mcr/v92/
INPUT_DIR=$FLYWHEEL_BASE/input
OUTPUT_DIR=$FLYWHEEL_BASE/output
# Set paths to input files
anatomical=$(find $FLYWHEEL_BASE/input/anatomical/ -type f -name "*.nii*")
CONFIG_FILE=${FLYWHEEL_BASE}/config.json


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



# Check for required inputs
if [[ -z "$anatomical" ]]; then
  echo -e "$CONTAINER  Anatomical 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 ${CONFIG_FILE}"
  userProvidedAcpc=$(cat $CONFIG_FILE | jq -r '.config.userProvidedAcpc')
  AC=$(cat $CONFIG_FILE | jq -r '.config.AC')
  PC=$(cat $CONFIG_FILE | jq -r '.config.PC')
  MS=$(cat $CONFIG_FILE | jq -r '.config.MS')
  echo "$CONTAINER  userProvidedAcpc has been set to $userProvidedAcpc"
  echo "$CONTAINER  AC has been set to $AC"
  echo "$CONTAINER  PC has been set to $PC"
  echo "$CONTAINER  MS has been set to $MS"
else
  # Parse defaults from the manifest.json
  CONFIG_FILE=$FLYWHEEL_BASE/manifest.json
  echo -e "$CONTAINER  Loading defaults from ${CONFIG_FILE}"
  userProvidedAcpc=$(cat $CONFIG_FILE | jq -r '.config.userProvidedAcpc.default')
  AC=$(cat $CONFIG_FILE | jq -r '.config.AC.default')
  PC=$(cat $CONFIG_FILE | jq -r '.config.PC.default')
  MS=$(cat $CONFIG_FILE | jq -r '.config.MS.default')
  echo "$CONTAINER  userProvidedAcpc has been set to $userProvidedAcpc"
  echo "$CONTAINER  AC has been set to $AC"
  echo "$CONTAINER  PC has been set to $PC"
  echo "$CONTAINER  MS has been set to $MS"
fi


# Run the Matlab executable
time /msa/run_acpcAnat.sh "${MCR_ROOT}" "${anatomical}" "${userProvidedAcpc}" "${AC}" "${PC}" "${MS}"


# 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