run

#!/bin/bash
#
#	template based on:  https://github.com/scitran-apps/fsl-bet/blob/master/run
#
#

CONTAINER="[deepliif-predict]"
echo -e "$(date -u) $CONTAINER  Initiated"

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

###############################################################################
## Configure the ENV
export USER=Flywheel

###############################################################################
## Execute the main processes
function jsonValue() {
KEY=$1
num=$2
awk -F"[,:}]" '{for(i=1;i<=NF;i++){if($i~/'$KEY'\042/){print $(i+1)}}}' | tr -d '"' | sed -n ${num}p
}

## get all user configurations
if [[ -f $CONFIG_FILE ]]; then # if there's a user config file, use it, otherwise use manifest defaults
  echo "$(date -u) $CONTAINER  $CONFIG_FILE found. Loading config..."
  tile_size="$(cat $CONFIG_FILE | jsonValue tile_size)"
  region_size="$(cat $CONFIG_FILE | jsonValue region_size)"
  wsi="$(cat $CONFIG_FILE | jsonValue wsi)"
  output_results_pickle="$(cat $CONFIG_FILE | jsonValue output_results_pickle)"

else
  echo "$(date -u) $CONTAINER  $CONFIG_FILE not found. Loading defaults from $MANIFEST..."
  tile_size="$(cat $MANIFEST | jsonValue tile_size default)"
  region_size="$(cat $MANIFEST | jsonValue region_size default)"
  wsi="$(cat $MANIFEST | jsonValue wsi default)"
  output_results_pickle="$(cat $MANIFEST | jsonValue output_results_pickle default)"

fi

## Find the input files
im_file=$(find $im_DIR/* -maxdepth 0 -type f)

# out_path="output/"
# out_path+=$output_fn
# out_path="$(echo -e "${out_path}" | tr -d '[:space:]')" # strip spaces

## If necessary input files are found, run the thing
if [[ -f $im_file ]] ; then

  if [[ ! -d $OUTPUT_DIR ]] ; then
    mkdir $OUTPUT_DIR
  fi

  if $wsi ; then
    echo "$(date -u) $CONTAINER  Running DeepLIIF inference (tile size: $tile_size; region size $region_size)"
    deepliif test --input-dir $im_DIR --output-dir $OUTPUT_DIR --tile-size ${tile_size} --region-size ${region_size} --model-dir DeepLIIF_Latest_Model
    # restructure output files
    mv $OUTPUT_DIR/*/* $OUTPUT_DIR/
    if ! $output_results_pickle ; then
      rm $OUTPUT_DIR/results.pickle
    fi
  else
    echo "$(date -u) $CONTAINER  Running DeepLIIF inference (tile size: $tile_size)"
    deepliif test --input-dir $im_DIR --output-dir $OUTPUT_DIR --tile-size ${tile_size} --model-dir DeepLIIF_Latest_Model
  fi

################# Finish up #################
  STATUS=$?
else
  echo "$(date -u) $CONTAINER  Input files not found!"
  exit 1
fi

# Check exit status
if [[ $STATUS == 0 ]]
  then
    echo -e "$(date -u) $CONTAINER  Done!"

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

exit 0