run

#! /bin/bash
#
# Run afq Gear
# Built to flywheel-v0 spec.
#

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

# Configure the ENV
export FSLOUTPUTTYPE=NIFTI_GZ
export LD_LIBRARY_PATH=/opt/mcr/v82/runtime/glnxa64:/opt/mcr/v82/bin/glnxa64:/opt/mcr/v82/sys/os/glnxa64:/opt/mcr/v82/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/mcr/v82/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/mcr/v82/sys/java/jre/glnxa64/jre/lib/amd64:$LD_LIBRARY_PATH
export XAPPLRESDIR=/opt/mcr/v82/X11/app-defaults

# Add mrtrix and ants to the path
export PATH=/usr/lib/ants:/usr/lib/mrtrix/bin:$PATH

# Set DISPLAY for xvfb
export DISPLAY=:1.0

# Define the start Xvfb function
start_xvfb() {
  Xvfb :1 -screen 0 1920x1200x24+32 &> /dev/null &
}

# Configure paths
FLYWHEEL_BASE=/flywheel/v0
OUTPUT_DIR=$FLYWHEEL_BASE/output
INPUT_DIR=$FLYWHEEL_BASE/input
ZIP_DIR=$INPUT_DIR/dtiInit_Archive # Must match input from the manifest
WORK_DIR=$INPUT_DIR/work
CONFIG_FILE=${FLYWHEEL_BASE}/config.json
PARAMS_FILE=${WORK_DIR}/AFQ_params.json
LOG_FILE=$OUTPUT_DIR/AFQ_log.txt

# Ensure there is an output directory
if [[ ! -d "$OUTPUT_DIR" ]]
then
  echo "$CONTAINER  $OUTPUT_DIR not found!"
  exit 1
fi

# Make the directories
mkdir $WORK_DIR

# Move files into work directory and do the work
ZIP_FILE=$(find ${ZIP_DIR} -type f -name "*.zip" | head -1)
unzip $ZIP_FILE -d $WORK_DIR

# Find the dt6.mat file and use that as the input to AFQ
DT6_FILE=$(find ${WORK_DIR} -type f -name "dt6.mat" | head -1)
AFQ_INPUT_DIR=$(dirname $DT6_FILE)

# Convert the config json to a dtiinit_params json file
$FLYWHEEL_BASE/parse_config.py --input_file ${CONFIG_FILE} --output_file ${PARAMS_FILE} --input_dir ${AFQ_INPUT_DIR} --output_dir ${OUTPUT_DIR}

# Make sure the params file is saved with the output
cp ${PARAMS_FILE} ${OUTPUT_DIR}

# Start Xvfb and pass the input arguments to AFQ execute the algorithm
start_xvfb && time /usr/local/bin/AFQ "$PARAMS_FILE" 2>&1 | tee $LOG_FILE

# Xvfb occasionally hangs -- make sure that Xvfb dies
kill -9 %1

# If sucessful, the main outputs will be here
AFQ_DIR=$OUTPUT_DIR/AFQ

# Get a list of the files in the output directory
outputs=$(find $AFQ_DIR/* -maxdepth 0 -type f)

# If outputs exist, generate metadata, and exit
if [[ -z $outputs ]]
then
  echo "$CONTAINER  FAILED: No results found in output directory... Exiting"
  exit 1
else
  # Process figures
  FIGURES_DIR=$AFQ_DIR/figures
  PDF_DIR=$AFQ_DIR/pdfs
  mkdir $PDF_DIR

  # Summary pdf
  convert "$FIGURES_DIR/*.{png}" $PDF_DIR/AFQ_Summary.pdf
  convert "$FIGURES_DIR/*.{gif}" $PDF_DIR/AFQ_Fiber_Rendering.pdf

  # Pdf for each measure
  convert "$FIGURES_DIR/md/*.{png}" $PDF_DIR/AFQ_Figures_Mean_Diffusivity.pdf
  convert "$FIGURES_DIR/ad/*.{png}" $PDF_DIR/AFQ_Figures_Axial_Diffusivity.pdf
  convert "$FIGURES_DIR/rd/*.{png}" $PDF_DIR/AFQ_Figures_Radial_Diffusivity.pdf
  convert "$FIGURES_DIR/fa/*.{png}" $PDF_DIR/AFQ_Figures_Fractional_Anisotropy.pdf

  # Copy pdf, csv, mat, gif, and json files to output
  cp $PDF_DIR/*.pdf $OUTPUT_DIR
  cp $AFQ_DIR/csv_files/*.csv $OUTPUT_DIR
  cp $AFQ_DIR/*.mat $AFQ_DIR/*.json $OUTPUT_DIR
  cp $FIGURES_DIR/000_RotatingFibers.gif $OUTPUT_DIR/AFQ_Fiber_Rendering.gif

  # Copy DTIINIT input/ouputs to AFQ
  cp -a $AFQ_INPUT_DIR $AFQ_DIR

  # Get basename for AFQ ouput zip
  AFQ_NAME=$(basename `find $AFQ_DIR/ -type f -name "afq*.mat"` .mat)

  # Rename and Compress AFQ_DIR
  cd $OUTPUT_DIR
  mv AFQ $AFQ_NAME
  chmod -R 777 $OUTPUT_DIR
  zip -r AFQ_Output_$AFQ_NAME.zip $AFQ_NAME && rm -rf $AFQ_NAME

  # Create metadata json file ($OUTPUT_DIR/.metadata.json)
  $FLYWHEEL_BASE/metadata_create.py $OUTPUT_DIR $CONTAINER

  # Set permissions for outputs (prevent root only r/w)
  chmod -R 777 $OUTPUT_DIR

  # End
  echo -e "$CONTAINER  Wrote: `ls`"
  echo -e "$CONTAINER  Done!"
fi

exit 0