run

#! /bin/bash
#
# Run script for flywheel/mri-deface Gear.
#
# Authorship: Jennifer Reiter, Michael Perry
#

##############################################################################
# Define directory names and containers

FLYWHEEL_BASE=/flywheel/v0
INPUT_DIR=$FLYWHEEL_BASE/input/anatomical
OUTPUT_DIR=$FLYWHEEL_BASE/output
CONFIG_FILE=$FLYWHEEL_BASE/config.json
CONTAINER='[flywheel/mri-deface]'


##############################################################################
# Parse configuration

function parse_config {

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

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

config_output_nifti="$(parse_config 'output_nifti')"
config_output_mgh="$(parse_config 'output_mgh')"


##############################################################################
# Define brain and face templates

brain_template=$FLYWHEEL_BASE/talairach_mixed_with_skull.gca
face_template=$FLYWHEEL_BASE/face.gca


##############################################################################
# Handle INPUT file

# Find input file In input directory with the extension
# .nii, .nii.gz, .mgz or .mgh.gz or a .zip DICOM file
input_file=`find $INPUT_DIR -iname '*.nii' -o -iname '*.nii.gz' -o -iname '*.mgz' -o -iname '*.mgh.gz' -o -iname '*.zip'`

# Check that input file exists
if [[ -e $input_file ]]; then
  echo "${CONTAINER}  Input file found: ${input_file}"

  # Determine the type of the input file
  if [[ "$input_file" == *.zip ]]; then
    type=".zip"
  elif [[ "$input_file" == *.nii ]]; then
    type=".nii"
  elif [[ "$input_file" == *.nii.gz ]]; then
    type=".nii.gz"
  elif [[ "$input_file" == *.mgz ]]; then
    type=".mgz"
  elif [[ "$input_file" == *.mgz.gz ]]; then
    type=".mgz.gz"
  fi

  # Get the base filename
  base_filename=`basename "$input_file" $type`
else
  echo "${CONTAINER} No Nifti, DICOM or MGZ inputs were found within input directory $INPUT_DIR"
  exit 1
fi

# If input extension is .zip, then unzip the files (assuming they are DICOM files)
if [[ "$type" == *.zip  ]]; then
  echo "${CONTAINER} Unzipping DICOM files..."
  unzip_dir=/tmp/unzipped
  unzip $input_file -d $unzip_dir

  # Now that the DICOM files are unzipped, need to find the full path to the
  # first file to pass mri_deface
  input_file=`find $unzip_dir/* -type f | head -n 1`
  if [[ -e $input_file ]]; then
    echo "$CONTAINER  Input file set to: $input_file"
    base_filename=`basename "$base_filename" .dicom`
  else
    echo "${CONTAINER}  No input file found in: ${input_file}"
    exit 1
  fi
fi


##############################################################################
# Run MRI_DEFACE algorithm

# Set initial exit status
mri_deface_exit_status_nifti=0
mri_deface_exit_status_mgz=0

# Set base output_file name
output_file=$OUTPUT_DIR/"$base_filename"'_deface'

# Check if user wanted NIfTI output
if [[ $config_output_nifti == 'true' ]]; then
  /flywheel/v0/mri_deface "$input_file" "$brain_template" "$face_template" "$output_file"'.nii.gz'
  mri_deface_exit_status_nifti=$?
fi

# Check if user wanted MGH output
if [[ $config_output_mgh == 'true' ]]; then
  /flywheel/v0/mri_deface "$input_file" "$brain_template" "$face_template" "$output_file"'.mgz'
  mri_deface_exit_status_mgz=$?
fi


##############################################################################
# Handle Exit status

if [[ $mri_deface_exit_status_nifti == 0 ]] && [[ $mri_deface_exit_status_mgz == 0 ]]; then
  echo -e "${CONTAINER} Success!"
  exit 0
else
  echo "${CONTAINER}  Something went wrong! mri_deface exited non-zero!"
  exit 1
fi