makepyramid-ndpi

#!/bin/bash

set -e
set -x

# Check if file is BigTIFF
# $1 file
bigtiff() {
    if [ "0000000 4949 002b" != "$(dd if="$1" iflag=count_bytes count=4 | od -x | head -n1)" ]; then
        return 1
    fi
    return 0
}

# Get fieldoffset for TIFF
# $1 file
fieldoffset() {
    if bigtiff "$1"; then
        echo 8
    else
        echo 2
    fi
}

# Get fieldsize for TIFF
# $1 file
fieldsize() {
    if bigtiff "$1"; then
        echo 20
    else
        echo 12
    fi
}

# Get IFD offsets
# $1=IFD number
# $2=file
diroffsets() {
    tiffinfo "$dest" | grep "TIFF Directory at offset" | sed -e 's;.*(\(.*\))$;\1;'
}

# Get offset for IFD
# $1=IFD number
# $2=file
diroffset() {
    diroffsets "$2" | head -n$(($1 + 1)) | tail -n1
}

# Get number of tags in directory
# $1=IFD offset
# $2=file
ntags() {
    echo "od -j $1 -N 2 -d \"$2\"" >&2
  od -j $1 -N 2 -d "$2" | head -n1 | sed -e 's;^[0-9]* *\(.*\);\1;'
}

# Offset of next pointer in IFD
# $1=IFD offset
# $2=file
nextoffset() {
    echo "$(($1 + $(fieldoffset "$2") + ($(ntags $1 "$2") * $(fieldsize "$2"))))"
}

# Write uint64 little endian value to binary file
# $1=value
# $2=destination file
# $3=offset in file
update_uint64_le() {
    if bigtiff "$2"; then
        printf "$(printf %.16x $1 | sed -e 's;\(..\)\(..\)\(..\)\(..\)\(..\)\(..\)\(..\)\(..\);\8\7\6\5\4\3\2\1;' | sed -e 's;\(..\);\\x\1;g')" | dd of="$2" conv=notrunc,nocreat oflag=seek_bytes seek=$3
    else
        printf "$(printf %.8x $1 | sed -e 's;\(..\)\(..\)\(..\)\(..\);\4\3\2\1;' | sed -e 's;\(..\);\\x\1;g')" | dd of="$2" conv=notrunc,nocreat oflag=seek_bytes seek=$3
    fi
}

makeuuid() {
    echo "urn:uuid:$(uuidgen)"
}

src="$(ls -1 orig/*.ndpi)"
mkdir -p new

for srcfile in $src; do
    base="$(basename $srcfile)"
    dest="new/${base%.ndpi}-subifds.tiff"

    cp "$srcfile" "$dest"

    nifds=$(tiffinfo "$dest" | grep "TIFF Directory at offset" | wc -l)
    echo "IFD count: $nifds"

    ifds=$(seq 0 $(($nifds - 1)))
    mainifd=$(echo "$ifds" | head -n1)
    otherifds=$(echo "$ifds" | tail -n1)
    subifds=$(echo "$ifds" | head -n$((nifds-1)) | tail -n$((nifds-2)))
    nsubifds=$(echo "$subifds" | wc -l)
    echo "IFDs: $ifds"
    echo "Main IFDs: $mainifd"
    echo "Other IFDs: $otherifds"
    echo "SUBIFDs: $subifds"

    # Drop private tags, where present
    private_tags="65420 65421 65422 65423 65424 65425 65426 65427 65428"
    for ifd in $ifds; do
        for tag in $private_tags; do
            tiffset -d $ifd -u $tag "$dest" || true
        done
    done

    # Main header
    tiffset -d 0 -s 270 "OME Pyramid TIFF test (from $base)" "$dest"
    tiffset -d 0 -s 305 "A gnarly shell script (makepyramid-ndpi)" "$dest"
    tiffset -d 0 -s 315 "Roger Leigh <rleigh@dundee.ac.uk>" "$dest"

    # NewSubFileType
    for ifd in $mainifd $otherifds; do
        tiffset -d $ifd -s 254 0 "$dest"
    done
    for ifd in $subifds; do
        tiffset -d $ifd -s 254 1 "$dest"
    done

    # SubIFDs
    subifds_diroffs=$(echo $(tiffinfo "$dest" | grep "TIFF Directory at offset" | sed -e 's;.*(\(.*\))$;\1;' | head -n$((nifds-2)) | tail -n$((nifds-3))))
    echo "SubIFDs for series 0: $subifds_diroffs"
    tiffset -d 0 -s 330 $nsubifds $subifds_diroffs "$dest"
    subifds_diroffs=$(echo $(tiffinfo "$dest" | grep "TIFF Directory at offset" | sed -e 's;.*(\(.*\))$;\1;' | head -n$((nifds-2)) | tail -n$((nifds-3))))
    echo "Updated SubIFDs for series 0: $subifds_diroffs"

    echo "New directories:"
    diroffsets "$dest"

    dest2="${dest%.tiff}-flat.tiff"
    cp "$dest" "$dest2"

    # Relink IFDs to elide SubIFDs
    series0dir="$(diroffset 0 "$dest")"
    echo "s0dir $series0dir"
    seriesndir="$(diroffset $(echo "$otherifds" | head -n1) "$dest")"
    echo "sndir $seriesndir"

    noffset="$(nextoffset $series0dir "$dest")"
    echo "UPDATE: $series0dir $noffset -> [$seriesndir]"
    update_uint64_le $seriesndir "$dest" $noffset

    for offset in $subifds_diroffs; do
        c="$(ntags $offset "$dest")"
        echo "NTAGS: $c"
        noffset="$(nextoffset $offset "$dest")"
        echo "UPDATE: $offset $noffset -> 0"
        update_uint64_le 0 "$dest" $noffset
    done

    tiffinfo "$dest"

    # Create OME-XML metadata for the files.
    dest_ometiff="${dest%.tiff}.ome.tiff"
    dest2_ometiff="${dest2%.tiff}.ome.tiff"
    cp "$dest" "$dest_ometiff"
    cp "$dest2" "$dest2_ometiff"

    bfomexml="$(showinf -nopix -noflat -omexml -omexml-only "$srcfile")"

    # Add TiffData elements.
    uuid="$(makeuuid)"
    ome_attr="Creator=\"makepyramid-ndpi\" UUID=\"${uuid}\""
    tiffdata_fmt="<TiffData FirstC=\"0\" FirstT=\"0\" FirstZ=\"0\" IFD=\"%d\" PlaneCount=\"1\"><UUID FileName=\"$(basename "${dest_ometiff}")\">${uuid}</UUID></TiffData>"
    tiffdata_fmt_flat="<TiffData FirstC=\"0\" FirstT=\"0\" FirstZ=\"0\" IFD=\"%d\" PlaneCount=\"1\"><UUID FileName=\"$(basename "${dest2_ometiff}")\">${uuid}</UUID></TiffData>"

    omexml_fmt="$(echo "$bfomexml" | sed -e "s;\(<OME.*\)\(\">\);\1\" ${ome_attr}>;" -e "s;<MetadataOnly\/>;${tiffdata_fmt};")"
    omexml_fmt_flat="$(echo "$bfomexml" | sed -e "s;\(<OME.*\)\(\">\);\1\" ${ome_attr}>;" -e "s;<MetadataOnly\/>;${tiffdata_fmt_flat};")"

    ifds="0 1"
    omexml="$(printf "$omexml_fmt" $ifds)"

    flatifds="$(echo $mainifd $otherifds)"
    omexml_flat="$(printf "$omexml_fmt" $flatifds)"

    tiffset -d 0 -s 270 "$omexml" "$dest_ometiff"
    tiffset -d 0 -s 270 "$omexml_flat" "$dest2_ometiff"
done