bet-some

#!/usr/bin/env bash
set -euo pipefail
tmpdir=""
trap '[ -n "$tmpdir" -a -d "$tmpdir" ] && rm -r $tmpdir' EXIT SIGINT
[ -v "SCALE" ] || SCALE=200%

imageviewer=${IMAGEVIEWER:-feh}

usage(){
  local exit=0
  [ $# -gt 0 ] && echo "ERROR: $*" && exit=1
  cat<<HD
  $0 niftifile [frac1 frac2 ....]
  $0  -help = this help

run a bunch of bets and show the results in $imageviewer (\$IMAGEVIEWER)
defaults to frac .1 to .9 by 1

SCALE=100% $0 nifile .5 # undo default 200% scaling

IMAGEVIEWER=: $0 nifile .5 # dont open an imageviewer after bets
HD
  exit $exit
}

[ $# -eq 0 ] && usage "need at least a nifti image"
[[ "$1" =~ ^-h*|^-useage ]] && usage
! command -v bet >/dev/null && warn "no 'bet' command! install fsl" && exit 1
! command -v $imageviewer >/dev/null && warn "no image viewer '$imageviewer'. set IMAGEVIEWER. IMAGEVIEWER=':' to ignore" && exit 1

img="$1"; shift
[ $# -eq 0 ] && frac=($(seq .1 .1 .9)) || frac=("$@")

tmpdir=$(mktemp -d /tmp/bet-some-XXX)
echo "# writing to '$tmpdir' (removed when '$imageviewer' closes)"
for frac in ${frac[@]}; do
  echo -n "$frac ... "
  out=$tmpdir/bet-$frac.nii.gz
  sliceout=${out/nii.gz/png}
  bet $img $out -f $frac
  # with the unnamed pipe, we dont wait for convert to finish.
  # 'all.png' will miss last one.  easiest if in two steps
  # slicer -a >(convert -scale $SCALE - -background white label:$frac -gravity center -append $sliceout) $out $img
  slicer -a $sliceout $out $img
  convert -scale $SCALE $sliceout -background white label:$frac -gravity center -append $sliceout
done
echo
convert -append $tmpdir/*.png $tmpdir/all.png
$imageviewer $tmpdir/all.png