makepyramid-scn

#!/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)"
}

scnmeta() {
    tiffcomment "$1" | egrep "<pixels|dimension" | sed  -e 's;.*<dimension.* ifd="\([0-9][0-9]*\)".*;\1;' -e 's;.*<pixels.*;series;'
}

scnifds() {
    scnmeta "$1" | grep -v "series"
}

scnmainifds() {
    scnmeta "$1" | grep -h -A1 series | egrep -v "series|--"
}

scnsubifds() {
    filter="series"
    for ifd in $(scnmainifds "$1"); do
        filter="$filter|$ifd"
    done
    scnmeta "$1" | egrep -v "^$filter\$"
}

scnseriessubifds() {
    scnmeta "$1" | sed -n "/^$2\$/,/series/p" | egrep -v "^($2|series)\$"
}

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

for srcfile in $src; do
    echo "Processing $srcfile"

    base="$(basename $srcfile)"
    dest="new/${base%.scn}-subifds.tiff"

    cp "$srcfile" "$dest"

    if bigtiff "$dest"; then
        echo "Using BigTIFF offsets"
    fi

    nifds=$(scnifds "$srcfile" | wc -l)
    ifds=$(scnifds "$srcfile")
    mainifds=$(scnmainifds "$srcfile")
    subifds=$(scnsubifds "$srcfile")
    nmainifds=$(echo "$mainifds" | wc -l)
    echo "IFD count: $(echo $nifds)"
    echo "IFDs: $(echo $ifds)"
    echo "Main IFDs: $(echo $mainifds)"
    echo "SUBIFDs: $(echo $subifds)"

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

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

    # SubIFDs
    for mainifd in $mainifds; do
        subifds=$(scnseriessubifds "$srcfile" "$mainifd")
        nsubifds=$(echo "$subifds" | wc -l)
        subifds_start=$(echo "$subifds" | head -n1)
        subifds_end=$(echo "$subifds" | tail -n1)
        subifds_diroffs=$(echo $(tiffinfo "$dest" | grep "TIFF Directory at offset" | sed -e 's;.*(\(.*\))$;\1;' | head -n$(($subifds_end+1)) | tail -n$nsubifds))
        echo "SubIFDs for series $mainifd: $subifds_diroffs"
        tiffset -d $mainifd -s 330 $nsubifds $subifds_diroffs "$dest"
        subifds_diroffs=$(echo $(tiffinfo "$dest" | grep "TIFF Directory at offset" | sed -e 's;.*(\(.*\))$;\1;' | head -n$(($subifds_end+1)) | tail -n$nsubifds))
        echo "Updated SubIFDs for series $mainifd: $subifds_diroffs"
    done

    echo "New directories:"
    diroffsets "$dest"

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

    # Relink IFDs to elide SubIFDs.  Run backward to keep the file readable between iterations.
    nextdiroff=0
    for mainifd in $(echo "$mainifds" | tac); do
        subifds=$(scnseriessubifds "$srcfile" "$mainifd")
        nsubifds=$(echo "$subifds" | wc -l)
        subifds_start=$(echo "$subifds" | head -n1)
        subifds_end=$(echo "$subifds" | tail -n1)
        subifds_diroffs=$(echo $(tiffinfo "$dest" | grep "TIFF Directory at offset" | sed -e 's;.*(\(.*\))$;\1;' | head -n$(($subifds_end+1)) | tail -n$nsubifds))

        for offset in $subifds_diroffs; do
            noffset="$(nextoffset $offset "$dest")"
            update_uint64_le 0 "$dest" $noffset
        done

        maindir="$(diroffset $mainifd "$dest")"
        noffset="$(nextoffset $maindir "$dest")"

        update_uint64_le $nextdiroff "$dest" $noffset

        nextdiroff="$(diroffset $mainifd "$dest")"
    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="$(makeuuid)"
    ome_attr="Creator=\"makepyramid-scn\" UUID=\"${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="$(seq 0 $(($nmainifds - 1 )))"
    omexml="$(printf "$omexml_fmt" $ifds)"

    flatifds="$(echo $mainifds)"
    omexml_flat="$(printf "$omexml_fmt" $flatifds)"

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