#!/bin/bash
#   Copyright (C) 2016 University of Oxford
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#   fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
export LC_ALL=C
set -e

if [ $# -lt 1 ] ; then
    echo "   "
    echo "Usage:  `basename $0` <bianca_output_map> <threshold> <min_cluster_size> [ <mask> ]"
    echo "   "
    echo "If only 3 inputs provided it will output the total number of clusters and the total WMH volume after applying <threshold>"
    echo "and including clusters bigger than <min_cluster_size>, where the size is expressed in number of voxels"
    echo "   "
    echo "Optional: number of clusters and  WMH volume within a mask"
    echo "<mask> = mask file (in the same space as <bianca_output_map> )"
    echo "   "
    exit 0
fi

bianca_output_map=$1
threshold=$2
min_cluster_size=$3
if [ $# -gt 3 ] ; then
    mask=$4
else
    mask=""
fi

mapname=$(remove_ext $(basename ${bianca_output_map}))
logID=`echo $(date | awk '{print $2 $3 $4}' |  sed 's/://g')`
TMPVISDIR=`mktemp -d ./${mapname}_${logID}_XXXXXX`

# Apply threshold and binarise image
$FSLDIR/bin/fslmaths $bianca_output_map -thr $threshold -bin ${TMPVISDIR}/bianca_thr_bin

# Apply cluster size threshold
$FSLDIR/bin/fsl-cluster -t 0.5 -i ${TMPVISDIR}/bianca_thr_bin --connectivity=26 --oindex=${TMPVISDIR}/bianca_thr_bin_idx --no_table --minextent=$min_cluster_size
$FSLDIR/bin/fslmaths ${TMPVISDIR}/bianca_thr_bin_idx -bin ${TMPVISDIR}/bianca_thr_bin_minsize_bin

# Calculate the total volume/number of clusters
total_clusters_num=`$FSLDIR/bin/fsl-cluster -t 0.5 -i ${TMPVISDIR}/bianca_thr_bin --connectivity=26 --minextent=$min_cluster_size | head -n 2 | tail -n 1 |  awk '{print $1}'`
echo " total WMH number for $bianca_output_map with threshold $threshold and minimum cluster size $min_cluster_size is $total_clusters_num"
total_volume=`$FSLDIR/bin/fslstats ${TMPVISDIR}/bianca_thr_bin_minsize_bin -V | awk '{print $2}'`
echo " total volume for $bianca_output_map with threshold $threshold and minimum cluster size $min_cluster_size is $total_volume"

# Optional: volume/number of clusters within the specified mask
if [ "${mask}" != "" ] ; then
    $FSLDIR/bin/fslmaths ${TMPVISDIR}/bianca_thr_bin_minsize_bin -mas $mask ${TMPVISDIR}/bianca_thr_bin_minsize_bin_masked
    # Calculate number of clusters and volume within mask
    clusters_num_in_mask=`$FSLDIR/bin/fsl-cluster  -t 0.5 -i ${TMPVISDIR}/bianca_thr_bin_minsize_bin_masked --connectivity=26 | head -n 2 | tail -n 1 |  awk '{print $1}'`
    echo " WMH number in $mask for $bianca_output_map with threshold $threshold and minimum cluster size $min_cluster_size is $clusters_num_in_mask"
    volume_in_mask=`$FSLDIR/bin/fslstats ${TMPVISDIR}/bianca_thr_bin_minsize_bin -k $mask -V | awk '{print $2}'`
    echo " WMH volume in $mask for $bianca_output_map with threshold $threshold and minimum cluster size $min_cluster_size is $volume_in_mask"
fi

rm -r ${TMPVISDIR}
