run

#! /bin/bash
#
#

CONTAINER="[flywheel/fsl-feat]"
echo -e "$CONTAINER  Initiated"


###############################################################################
# Built to flywheel-v0 spec.

FLYWHEEL_BASE=/flywheel/v0
OUTPUT_DIR=$FLYWHEEL_BASE/output
INPUT_DIR=$FLYWHEEL_BASE/input/NIFTI
SLICE_FILE_DIR=$FLYWHEEL_BASE/input/SCLICE_FILE
MANIFEST=$FLYWHEEL_BASE/manifest.json
CONFIG_FILE=$FLYWHEEL_BASE/config.json
TEMPLATE=$FLYWHEEL_BASE/template.fsf

###############################################################################
# Configure the ENV

chmod +x /etc/fsl/5.0/fsl.sh
source /etc/fsl/5.0/fsl.sh
export USER=Flywheel


##############################################################################
# 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
}

FW_CONFIG_BB_THRESH="$(parse_config 'BB_THRESH')"
FW_CONFIG_Z_THRESH="$(parse_config 'Z_THRESH')"
FW_CONFIG_NOISE_LVL="$(parse_config 'NOISE_LVL')"
FW_CONFIG_T_SMOOTH="$(parse_config 'T_SMOOTH')"
FW_CONFIG_MC="$(parse_config 'MC')"
FW_CONFIG_STC="$(parse_config 'STC')"
FW_CONFIG_BET="$(parse_config 'BET')"
FW_CONFIG_FWHM="$(parse_config 'FW_CONFIG_FWHM')"
FW_CONFIG_INT_NORM="$(parse_config 'INT_NORM')"
FW_CONFIG_HPF_CUTOF="$(parse_config 'HPF_CUTOF')"
FW_CONFIG_HPF="$(parse_config 'HPF')"
FW_CONFIG_REG_STANDARD_IMAGE="$(parse_config 'REG_STANDARD_IMAGE')"
FW_CONFIG_LPF="$(parse_config 'LPF')"

###############################################################################
# INPUT File

input_file=`find $INPUT_DIR/* -maxdepth 0 -not -path '*/\.*' -type f -name "*.nii*" | head -1`
if [[ -z $input_file ]]; then
  echo "$CONTAINER  INPUT_DIR has no valid input files!"
  exit 1
fi


####################################################################
# FillTemplate
# Credit goes to David Parker @UPENN

# VOLUME INFO
####################################################################

# THE INPUT FMRI VOLUME TO USE (CAN BE .NII OR .NII.GZ)
INPUT_DATA="${input_file}"

# USE 'FSLHD' TO FIND AND SET THE TR
#TR=` fslhd ${INPUT_DATA} | grep pixdim3 | tr -s ' ' | cut -d' ' -f2 `
TR=` fslhd ${INPUT_DATA} | grep pixdim4 | awk '{print $2}' `

# FOR SOME REASON IT LIKES TO KNOW THE NUMBER OF VOXELS.  WE'LL
# use 'fslhd' again to do this
DXYZ=(` fslhd ${INPUT_DATA} | grep ^dim[1-4] `)
NX=${DXYZ[1]}
NY=${DXYZ[3]}
NZ=${DXYZ[5]}
NUM_VOL=${DXYZ[7]}

# As long as NX NY NZ and NUM_VOL are int, this works fine.
# Decimals will mess it up
NUM_VOX=$(( NX*NY*NZ*NUM_VOL ))

# SET THE NUMBER OF VOLUMES TO DELETE
DEL_VOL=0

# SET THE OUTPUT DIRECTORY
FEAT_OUTPUT_DIR="${OUTPUT_DIR}"/fsl_preproc
if [ ! -e ${FEAT_OUTPUT_DIR} ]; then
    mkdir ${FEAT_OUTPUT_DIR}
fi


####################################################################
# STATISTICS
# Strictly speaking, these aren't important for the preprocessing
# and COULD be ignored
####################################################################

# SET THE BRAIN BACKGROUND THRESHOLD
# It is used in intensity normalization, brain mask
# generation and various other places in the analysis.
BB_THRESH=$FW_CONFIG_BB_THRESH

# SET THE Z THRESHOLD FOR DESIGN EFFICIENCY CALCULATION
# used to determine what level of activation would
# be statistically significant, to be used only in the design
# efficiency calculation. Increasing this will result in higher
# estimates of required effect.
Z_THRESH=$FW_CONFIG_Z_THRESH

# SET THE FMRI NOISE LEVEL
# the standard deviation (over time) for a
# typical voxel, expressed as a percentage of the baseline signal level.
NOISE_LVL=$FW_CONFIG_NOISE_LVL

# SET TNE TEMPORAL SMOOTHNESS
# is the smoothness coefficient in a simple
# AR(1) autocorrelation model (much simpler than that actually used in
# the FILM timeseries analysis but good enough for the efficiency
# calculation here).
T_SMOOTH=$FW_CONFIG_T_SMOOTH

####################################################################
# PREPROCESSING OPTIONS
####################################################################

# RUN MOTION CORRECTION
MC=$FW_CONFIG_MC

# RUN SLICE TIMING CORRECTION
# 0 : None
# 1 : Regular up (0, 1, 2, 3, ...)
# 2 : Regular down
# 3 : Use slice order file
# 4 : Use slice timings file
# 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )
STC=$FW_CONFIG_STC

# SLICE ORDER/TIMING FILE
# If at slice order or timing file is chosen,
# This must also be set
if [[ $STC == 2 ]]; then
  SLICE_FILE=$(find ${SLICE_FILE_DIR}/* -type f)
else
  SLICE_FILE=''
fi
# RUN BRAIN EXTRACTION USING FSL's BET
BET=$FW_CONFIG_BET

# SET THE FWHM FOR SPATIAL SMOOTHING (mm)
FWHM=$FW_CONFIG_FWHM

# RUN INTENSITY NORMALIZATION
INT_NORM=$FW_CONFIG_INT_NORM

# HIGHPASS FILTER CUTOFF (seconds)
HPF_CUTOFF=$FW_CONFIG_HPF_CUTOFF

# RUN HIGHPASS FILTERING
HPF=$FW_CONFIG_HPF

# RUN LOWPASS FILTERING
LPF=$FW_CONFIG_LPF

REG_STANDARD_IMAGE=$FW_CONFIG_REG_STANDARD_IMAGE

####################################################################
# CREATE TEMPLATE
####################################################################

# Create a lost of all the variable names
# which match the place-holding text in the template
VAR_STRINGS=( INPUT_DATA TR NUM_VOL NUM_VOX DEL_VOL FEAT_OUTPUT_DIR BB_THRESH Z_THRESH NOISE_LVL T_SMOOTH MC STC SLICE_FILE BET FWHM INT_NORM HPF_CUTOFF HPF LPF REG_STANDARD_IMAGE )

DESIGN_FILE=${OUTPUT_DIR}/Design.fsf
cp ${TEMPLATE} ${DESIGN_FILE}

# loop through and preform substitution
for var_name in ${VAR_STRINGS[@]}; do

  var_val=` eval 'echo $'$var_name `
  #We need to replace and backslashes with "\/"
  var_val=` echo ${var_val////"\/"} `

  sed -i -e "s/\^${var_name}\^/${var_val}/g" ${DESIGN_FILE}

done


####################################################################
# RUN THE Algorithm with the .FSF FILE
####################################################################

echo -e "${CONTAINER}  Running FEAT..."
time feat ${DESIGN_FILE}
FEAT_EXIT_STATUS=$?

if [[ $FEAT_EXIT_STATUS == 0 ]]; then
  echo -e "${CONTAINER}  FEAT completed successfully!"
fi
####################################################################
# Upon success, convert index to a webpage
####################################################################

if [[ $FEAT_EXIT_STATUS == 0 ]]; then
  # Convert index to standalone index
  echo "$CONTAINER  generating output html..."
  output_html_files=$(find ${OUTPUT_DIR} -type f -name "*.html")
  for f in $output_html_files; do
    web2htmloutput=${OUTPUT_DIR}/`basename $f`
    python /opt/webpage2html/webpage2html.py -q -s "$f" > "$web2htmloutput"
    rm -f $f # Don't keep the html around once the new file is generated.
  done
fi


####################################################################
# CLEANUP THE OUTPUT DIRECTORIES
####################################################################

if [[ $FEAT_EXIT_STATUS == 0 ]]; then

  echo -e "${CONTAINER}  Compressing outputs..."
  # FEAT will create an ${FEAT_OUTPUT_DIR}.feat directory anyways, so we can
  # delete the old one and set the var to the actual output directory
  rm -rf ${FEAT_OUTPUT_DIR}
  FEAT_OUTPUT_DIR=${FEAT_OUTPUT_DIR}.feat

  # Zip and move the relevant files to the output directory
  pushd ${FEAT_OUTPUT_DIR} > /dev/null
  zip -rq ${OUTPUT_DIR}/logs.zip logs && rm -rf logs

  if [[ ${FW_CONFIG_MC} == 1 ]]; then
    zip -rq ${OUTPUT_DIR}/mc.zip mc && rm -rf mc
  fi

  if [[ ${FW_CONFIG_REG_STANDARD_IMAGE} == 1 ]]; then
    zip -rq ${OUTPUT_DIR}/reg.zip reg && rm -rf reg
  fi
  popd > /dev/null
  mv ${FEAT_OUTPUT_DIR}/* ${OUTPUT_DIR} && rm -rf ${FEAT_OUTPUT_DIR}
fi


###############################################################################
# EXIT
###############################################################################

if [[ $FEAT_EXIT_STATUS == 0 ]]; then
  echo -e "$CONTAINER  Done!"
  exit 0
else
  echo "$CONTAINER  Error while running FEAT... Exiting($FEAT_EXIT_STATUS)"
  exit $FEAT_EXIT_STATUS
fi