run

#! /bin/bash
#
#

CONTAINER="[scitran/dwi-split-shells]"
echo -e "$CONTAINER  Initiated"


# Built to flywheel-v0 spec.
FLYWHEEL_BASE=/flywheel/v0
MCR_ROOT=/opt/mcr/v93/
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 $FLYWHEEL_BASE/input/bvec/ -type f -name "*.bvec*")
bvalFile=$(find $FLYWHEEL_BASE/input/bval/ -type f -name "*.bval*")
dwiFile=$(find $FLYWHEEL_BASE/input/dwi/ -type f -name "*.nii*")
CONFIG_FILE=${FLYWHEEL_BASE}/input/config.json

# Check for required inputs
if [[ -z "$bvecFile" ]] ||  [[ -z "$bvalFile" ]] || [[ -z "$dwiFile" ]]; then
  echo -e "$CONTAINER  One or more input files were 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 ${CONFIG_FILE}"
  doNorm=$(cat $CONFIG_FILE | jq -r '.config.doNorm')
  echo "$CONTAINER  BVALUE normalization has been set to $doNorm"
else
  # Parse defaults from the manifest.json
  CONFIG_FILE=$FLYWHEEL_BASE/manifest.json
  echo -e "$CONTAINER  Loading defaults from ${CONFIG_FILE}"
  doNorm=$(cat $CONFIG_FILE | jq -r '.config.doNorm.default')
  echo "$CONTAINER  BVALUE normalization has been set to $doNorm"
fi


# Run the Matlab executable
time /msa/run_dwisplitshells.sh "${MCR_ROOT}" "${bvecFile}" "${bvalFile}" "${dwiFile}" "${doNorm}"  "${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