run

#! /bin/bash
#
#

CONTAINER="[scitran/fslmerge]"
echo -e "$CONTAINER  Initiated"


###############################################################################
# Built to flywheel-v0 spec.
FLYWHEEL_BASE=/flywheel/v0
OUTPUT_DIR=$FLYWHEEL_BASE/output
INPUT_DIR=$FLYWHEEL_BASE/input
MANIFEST=$FLYWHEEL_BASE/manifest.json
CONFIG_FILE=$FLYWHEEL_BASE/config.json


###############################################################################
# Configure the ENV
chmod +x /etc/fsl/5.0/fsl.sh
source /etc/fsl/5.0/fsl.sh


###############################################################################
# Initialize config parameters
catTime=' '
catX=' '
catY=' '
catX=' '
auto=' '
catTR=' '

###############################################################################
# Generate flags from the manifest

catTime_flag=$(jq -r <$MANIFEST '''.config.catTime.id')
catX_flag=$(jq -r <$MANIFEST '''.config.catX.id')
catY_flag=$(jq -r <$MANIFEST '''.config.catY.id')
catZ_flag=$(jq -r <$MANIFEST '''.config.catZ.id')
auto_flag=$(jq -r <$MANIFEST '''.config.auto.id')
catTR_flag=$(jq -r <$MANIFEST '''.config.catTR.id')


###############################################################################
# Parse config options from CONFIG file or MANIFEST

function parse_config {

  CONFIG_FILE=$FLYWHEEL_BASE/config.json
  MANIFEST_FILE=$FLYWHEEL_BASE/manifest.json

  if [[ -f $CONFIG_FILE ]]; then
    echo -e "$(cat $CONFIG_FILE | jq -r '.config.'$1)"
  else
    CONFIG_FILE=$MANIFEST_FILE
    echo -e "$(cat $MANIFEST_FILE | jq -r '.config.'$1'.default')"
  fi

}

# String parsing
config_catTime="$(parse_config 'catTime')"
config_catX="$(parse_config 'catX')"
config_catY="$(parse_config 'catY')"
config_catZ="$(parse_config 'catZ')"
config_auto="$(parse_config 'auto')"
config_catTR="$(parse_config 'catTR')"
config_base_outname="$(parse_config 'base_outname')"

# Boolean parsing
if [[ $config_catTime == 'true' ]]; then
  catTime=$catTime_flag
fi
if [[ $config_catX == 'true' ]]; then
  catX=$catX_flag
fi
if [[ $config_catY == 'true' ]]; then
  catY=$catY_flag
fi
if [[ $config_catZ == 'true' ]]; then
  catZ=$catZ_flag
fi
if [[ $config_auto == 'true' ]]; then
  auto=$auto_flag
fi
if [[ $config_base_outname != 'none' ]]; then
  output_file_base="$config_base_outname"
fi
if [[ $config_catTR == 0 ]]; then
  TR=' '
else
  catTR=$catTR_flag
  TR=$config_catTR
fi


###############################################################################
# Compile options string

OPTIONS="$catTime $catX $catY $catZ $auto $catTR"


###############################################################################
# Generate paths to input data

NIFTI_1=$(find $INPUT_DIR/NIFTI_1/* -type f -name "*.nii*" | head -1)
NIFTI_2=$(find $INPUT_DIR/NIFTI_2/* -type f -name "*.nii*" | head -1)

if [[ -d $INPUT_DIR/BVAL_1 ]] && [[ -d $INPUT_DIR/BVAL_2 ]]; then
  BVAL_1=$(find $INPUT_DIR/BVAL_1/* -type f -name "*.bval*" | head -1)
  BVAL_2=$(find $INPUT_DIR/BVAL_2/* -type f -name "*.bval*" | head -1)
else
  BVAL_1=''
  BVAL_2=''
fi

if [[ -d $INPUT_DIR/BVEC_1 ]] && [[ -d $INPUT_DIR/BVEC_2 ]]; then
  BVEC_1=$(find $INPUT_DIR/BVEC_1/* -type f -name "*.bvec*" | head -1)
  BVEC_2=$(find $INPUT_DIR/BVEC_2/* -type f -name "*.bvec*" | head -1)
else
  BVEC_1=''
  BVEC_2=''
fi


###############################################################################
# Merge functions for diffusion data

merge_bvec () {
  for L in $(seq 3); do
    linea=$(sed -n "$L"p "$1" | tr -d "\n")
    lineb=$(sed -n "$L"p "$2")
    echo -e "$linea\t$lineb" >> "$3"
  done
}

merge_bval () {
  bvala=$(cat "$1" | tr -d "\n")
  bvalb=$(cat "$2")
  echo -e "$bvala\t$bvalb" >> "$3"
}


###############################################################################
# RUN the MERGE Algorithm

if [[ -n "$NIFTI_1" ]] && [[ -n "$NIFTI_2" ]]; then
  echo "$CONTAINER  Running fslmerge on $NIFTI_1 & $NIFTI_2..."

  # Set the output file basename if not already defined by config
  if [[ -z $output_file_base ]]; then
    output_file_base=$OUTPUT_DIR/`basename "$NIFTI_1" .nii.gz`_`basename "$NIFTI_2" .nii.gz`
    output_file_base=$(echo -e "${output_file_base}" | tr -d '[:space:]')
  fi

  # Merge the images
  fslmerge ${OPTIONS} "$output_file_base".nii.gz "$NIFTI_1" "$NIFTI_2" $TR
  exit_status=$?
  if [[ $exit_status != 0 ]]; then
    echo "$CONTAINER  fslmerge exited with failures ($exit_status)"
    exit 1
  fi
else
  echo "$CONTAINER  $INPUT_DIR has no valid input files!"
  exit 1
fi

if [[ -n "$BVAL_1" ]] && [[ -n "$BVAL_2" ]]; then
  echo "$CONTAINER  Running merge_bval on $BVAL_1 & $BVAL_2..."
  merge_bval "$BVAL_1" "$BVAL_2" "$output_file_base".bval
  merge_bval_exit=$?
else
  merge_bval_exit=0
fi

if [[ -n "$BVEC_1" ]] && [[ -n "$BVEC_2" ]]; then
  echo "$CONTAINER  Running merge_bvec on $BVEC_1 & $BVEC_2..."
  merge_bvec "$BVEC_1" "$BVEC_2" "$output_file_base".bvec
  merge_bvec_exit=$?
else
  merge_bvec_exit=0
fi


###############################################################################
# Check status and exit accordingly

if [[ $exit_status == 0 ]] && [[ $merge_bval_exit == 0 ]] && [[ $merge_bvec_exit == 0 ]]; then
  echo -e "$CONTAINER  Done!"
  exit 0
else
  echo -e "$CONTAINER  Exiting with failures! (fslmerge=$exit_status, merge_bval=$merge_bval_exit, merge_bvec=$merge_bvec_exit)"
  exit 1
fi