run

#! /bin/bash
#
#
CONTAINER="[optibet]"
echo -e "$CONTAINER  Initiated"

# Built to flywheel-v0 spec.
FLYWHEEL_BASE=/flywheel/v0


OUTPUT_DIR=$FLYWHEEL_BASE/output
INPUT_DIR=$FLYWHEEL_BASE/input/nifti
MANIFEST=$FLYWHEEL_BASE/manifest.json
CONFIG_FILE=$FLYWHEEL_BASE/config.json

# Initialize config parameters
use_fsl=' '
use_afni=' '
mni152_1mm_t1w_mask=' '
mni152_2mm_t1w_mask=' '
avg152t1_brain_mask=' '
debug=' '


# Generate flags from the manifest
use_fsl_flag=$(jq -r <$MANIFEST '''.config.use_fsl.id')
use_afni_flag=$(jq -r <$MANIFEST '''.config.use_afni.id')
mni152_1mm_t1w_mask_flag=$(jq -r <$MANIFEST '''.config.mni152_1mm_t1w_mask.id')
mni152_2mm_t1w_mask_flag=$(jq -r <$MANIFEST '''.config.mni152_2mm_t1w_mask.id')
avg152t1_brain_mask_flag=$(jq -r <$MANIFEST '''.config.avg152t1_brain_mask.id')
debug_flag=$(jq -r <$MANIFEST '''.config.debug.id')


# Parse config options from CONFIG file or MANIFEST
if [[ -f $CONFIG_FILE ]]; then
  echo "$CONFIG_FILE found. Loading config..."

  if [[ $(jq -r <$CONFIG_FILE '''.config.use_fsl') == 'true' ]]; then
    use_fsl=$use_fsl_flag
  fi

  if [[ $(jq -r <$CONFIG_FILE '''.config.use_afni') == 'true' ]]; then
    use_afni=$use_afni_flag
  fi

  if [[ $(jq -r <$CONFIG_FILE '''.config.mni152_1mm_t1w_mask') == 'true' ]]; then
    mni152_1mm_t1w_mask=$mni152_1mm_t1w_mask_flag
  fi

  if [[ $(jq -r <$CONFIG_FILE '''.config.mni152_2mm_t1w_mask') == 'true' ]]; then
    mni152_2mm_t1w_mask=$mni152_2mm_t1w_mask_flag
  fi

  if [[ $(jq -r <$CONFIG_FILE '''.config.avg152t1_brain_mask') == 'true' ]]; then
    avg152t1_brain_mask=$avg152t1_brain_mask_flag
  fi
  
  if [[ $(jq -r <$CONFIG_FILE '''.config.debug') == 'true' ]]; then
    debug=$debug_flag
  fi

else
  echo "$CONFIG_FILE not found. Loading defaults from $MANIFEST..."

  if [[ $(jq -r <$MANIFEST '''.config.use_fsl.default') == 'true' ]]; then
    use_fsl=$use_fsl_flag
  fi

  if [[ $(jq -r <$MANIFEST '''.config.use_afni.default') == 'true' ]]; then
    use_afni=$use_afni_flag
  fi

  if [[ $(jq -r <$MANIFEST '''.config.mni152_1mm_t1w_mask.default') == 'true' ]]; then
    mni152_1mm_t1w_mask=$mni152_1mm_t1w_mask_flag
  fi

  if [[ $(jq -r <$MANIFEST '''.config.mni152_2mm_t1w_mask.default') == 'true' ]]; then
    mni152_2mm_t1w_mask=$mni152_2mm_t1w_mask_flag
  fi

  if [[ $(jq -r <$MANIFEST '''.config.avg152t1_brain_mask.default') == 'true' ]]; then
    avg152t1_brain_mask=$avg152t1_brain_mask_flag
  fi

  if [[ $(jq -r <$MANIFEST '''.config.debug.default') == 'true' ]]; then
    debug=$debug_flag
  fi

fi

# Compile options string
OPTIONS="$use_fsl $use_afni $mni152_1mm_t1w_mask $mni152_2mm_t1w_mask $avg152t1_brain_mask $debug"
echo -e "optibet options are: ${OPTIONS}"

# Execute the algorithm
input_file=$(find $INPUT_DIR/* -maxdepth 0 -type f -name "*.nii*")
if [[ -f $input_file ]]; then
  
  input_file_despaced=$(echo -e "${input_file}" | tr -d '[:space:]')
  mv "${input_file}" "${input_file_despaced}"
  input_file=$input_file_despaced
  
  echo "$CONTAINER  Running optibet on `basename "$input_file"`"
  output_file_base=$OUTPUT_DIR/$(basename "$input_file" .nii.gz)
  output_file_base=$OUTPUT_DIR/$(basename "$output_file_base" .nii)
  bash /optiBET.sh -i "$input_file" $OPTIONS
  STATUS=$?
else
  echo "$CONTAINER  No inputs were provided and $INPUT_DIR has no valid input files!"
  exit 1
fi

# Check exit status
if [[ $STATUS == 0 ]]
  then
    echo -e "$CONTAINER  Wrote: `ls $OUTPUT_DIR`"
    echo -e "$CONTAINER  Done!"

  else
    echo "$CONTAINER  command returned a non-zero exit code = [$STATUS]."
    exit 1
fi

exit 0