qa_image

#!/usr/bin/env bash
set -euo pipefail
trap 'e=$?; [ $e -ne 0 ] && echo "$0 exited in error"' EXIT

# 20201102WF - extract from preproc_functions/helper_functions
qa_image_usage(){
   cat <<HERE
   generate grid of nii slices w/optional overlay and title

   $0 [-gif] [-small] underlay.nii.gz overlay.nii.gz slice_grid.png ["title"]

   use "" for overlay for none
HERE
  exit 1
}

qa_image() {
    local underlay="$1"; shift
    local overlay="$1"; shift
    local fname="$1"; shift
    [ $# -eq 0 ] && title="" || title="$1"

    # set scale of slicer depending on size of images (since pngs from larger 3d images are larger in pixel size)
    local scale=3
    local fsize=26

    # if the underlay is big, reduce the scale
    local xsize=$(fslval "$underlay" dim1)
    if [ $xsize -gt 100 ]; then
        scale=2
        fsize=36
    fi
    
    # default to current directory if not specified
    local qa_imgdir=""
    ! env|grep -q ^qa_imgdir=. && qa_imgdir="$(pwd)"
    [[ "$fname" =~ ^/ ]] && qa_imgdir=""
    output="${qa_imgdir}/$fname"

    # make overlay optional. only quote if it's not zero
    [ -n "$overlay" ] && overlay=$(printf %q "$overlay")

    slicer "$underlay" $overlay -s $scale \
       -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png \
       -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png \
       -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png

    pngappend sla.png + slb.png + slc.png + sld.png - \
              sle.png + slf.png + slg.png + slh.png - \
              sli.png + slj.png + slk.png + sll.png "$output"

    local label="${title}\nunderlay:$(basename "$underlay")\noverlay:$(basename "$overlay")"
    [ -n "$title" ] && qa_title "$label" "$output" "$fsize"
    rm -f sl?.png #cleanup
    echo "$output"
    return 0
}
qa_title(){
   local label="$1"; shift
   local output="$1"; shift
   local fsize=50
   [ $# -ne 0 ] &&  fsize="$1";
   montage -label "$label" "$output" -pointsize $fsize -geometry +0+0 "$output"
}

crossfade(){
 local frmt="format=rgba,fade=d=1:t=in:alpha=1,setpts=PTS-STARTPTS"
 ffmpeg -y   \
    -framerate 5 -loop 1 -t 2 -i "$1" \
    -framerate 5 -loop 1 -t 4 -i "$2" \
    -framerate 5 -loop 1 -t 2 -i "$1" \
    -filter_complex   \
     "[1]$frmt+2/TB[f0]; \
      [2]$frmt+6/TB[f1]; \
      [0][f0]overlay[bg1];[bg1][f1]overlay,split[v0][v1]; \
      [v0]palettegen[p];[v1][p]paletteuse[v]" \
     -map "[v]" \
     "$3"
}

_qa_image_main(){
   local mksmall=0
   local mkanimate=""
   while [[ $1 =~ ^- ]]; do
      case "$1" in
         -gif) mkanimate=gif; shift;;
         -svg) mkanimate=svg; shift;;
         -small) mksmall=1; shift;;
         -verbose) set -x; shift;;
         *) echo "unknown option '$1'"; qa_image_usage;;
      esac
   done

   [ $# -ne 3 -a $# -ne 4 ] && qa_image_usage
   [ ! -r "$1" ] && echo "ERROR: cannot read underlay '$1'" && exit 1
   [ "x$2" != "x" -a ! -r "$2" ] && echo "ERROR: cannot read overlay '$2'" && exit 1

   
   case $mkanimate in
      gif)
         qa_image "$1" "" tmp_underlay.png >/dev/null
         qa_image "$2" "" tmp_overlay.png >/dev/null

         qa_title "$(basename "$1" .nii.gz)" "tmp_underlay.png"
         qa_title "$(basename "$2" .nii.gz)" "tmp_overlay.png"  

         out="$(echo "$3" | sed 's/.gif$\|.png$//').gif"
         crossfade tmp_{underlay,overlay}.png "$out"
         rm tmp_{underlay,overlay}.png 
         ;;
      svg)
         echo "SVG NOT IMPLEMENTED"; exit 1;;
      *)
         out="$(qa_image "$@")"
         ;;
   esac

   if [ $mksmall -eq 1 ]; then
      local width=500
      [ $mkgif -eq 1 ] &&
       convert "$out" -coalesce -resize ${width}x -deconstruct "$out" ||
       convert "$out" -resize ${width}x "$out"
   fi

   return 0
}

[[ "$(caller)" != "0 "* ]] || _qa_image_main "$@"