ImageJMetadata::ImageJMetadata(const IFD& ifd)
{
ifd.getField(IMAGEJ_META_DATA_BYTE_COUNTS).get(counts);
ifd.getField(IMAGEJ_META_DATA).get(data);
std::string desc;
ifd.getField(IMAGEDESCRIPTION).get(desc);
map = parse_imagedescription(desc);
parse_value("images", images);
parse_value("channels", channels);
parse_value("slices", slices);
parse_value("frames", frames);
parse_value("unit", unit);
parse_value("spacing", spacing);
parse_value("finterval", finterval);
parse_value("xorigin", xorigin);
parse_value("yorigin", yorigin);
parse_value("mode", mode);
parse_value("loop", loop);
}
void
getCoreMetadata(const IFD& ifd,
CoreMetadata& core)
{
core.dimensionOrder = ome::xml::model::enums::DimensionOrder::XYCZT;
core.sizeX = ifd.getImageWidth();
core.sizeY = ifd.getImageHeight();
core.pixelType = ifd.getPixelType();
core.bitsPerPixel = significantBitsPerPixel(core.pixelType);
pixel_size_type psize = ifd.getBitsPerSample();
if (psize < core.bitsPerPixel)
core.bitsPerPixel = psize;
uint16_t samples = ifd.getSamplesPerPixel();
tiff::PhotometricInterpretation photometric = ifd.getPhotometricInterpretation();
core.sizeC.clear();
core.sizeC.push_back(samples);
core.sizeZ = core.sizeT = core.imageCount = 1U;
// libtiff does any needed endian conversion
// automatically, so the data is always in the native
// byte order.
#ifdef BOOST_BIG_ENDIAN
core.littleEndian = false;
#else // ! BOOST_BIG_ENDIAN
core.littleEndian = true;
#endif // BOOST_BIG_ENDIAN
// This doesn't match the reality, but since subchannels are
// addressed as planes this is needed.
core.interleaved = (ifd.getPlanarConfiguration() == tiff::CONTIG);
// Indexed samples.
if (samples == 1 && photometric == tiff::PALETTE)
{
try
{
ome::compat::array<std::vector<uint16_t>, 3> cmap;
ifd.getField(tiff::COLORMAP).get(cmap);
core.indexed = true;
}
catch (...)
{
}
}
// Indexed samples for different photometric interpretations;
// not currently supported fully.
else
{
try
{
uint16_t indexed;
ifd.getField(tiff::INDEXED).get(indexed);
if (indexed)
{
core.indexed = true;
}
}
catch (...)
{
}
}
// Add series metadata from tags.
setMetadata(ifd, core, "PageName #", PAGENAME);
setMetadata(ifd, core, "ImageWidth", IMAGEWIDTH);
setMetadata(ifd, core, "ImageLength", IMAGELENGTH);
setMetadata(ifd, core, "BitsPerSample", BITSPERSAMPLE);
/// @todo EXIF IFDs
setMetadata(ifd, core, "PhotometricInterpretation", PHOTOMETRIC);
/// @todo Text stream output for Tag enums.
/// @todo Metadata type for PhotometricInterpretation.
try
{
setMetadata(ifd, core, "Artist", ARTIST);
Threshholding th;
ifd.getField(THRESHHOLDING).get(th);
core.seriesMetadata.set("Threshholding", th);
if (th == HALFTONE)
{
setMetadata(ifd, core, "CellWidth", CELLWIDTH);
setMetadata(ifd, core, "CellLength", CELLLENGTH);
}
}
catch (...)
{
}
setMetadata(ifd, core, "Orientation", ORIENTATION);
/// @todo Image orientation (storage order and direction) from
/// ORIENTATION; fix up width and length from orientation.
setMetadata(ifd, core, "SamplesPerPixel", SAMPLESPERPIXEL);
setMetadata(ifd, core, "Software", SOFTWARE);
setMetadata(ifd, core, "Instrument Make", MAKE);
setMetadata(ifd, core, "Instrument Model", MODEL);
setMetadata(ifd, core, "Make", MAKE);
setMetadata(ifd, core, "Model", MODEL);
setMetadata(ifd, core, "Document Name", DOCUMENTNAME);
setMetadata(ifd, core, "Date Time", DATETIME);
setMetadata(ifd, core, "Artist", ARTIST);
setMetadata(ifd, core, "Host Computer", HOSTCOMPUTER);
setMetadata(ifd, core, "Copyright", COPYRIGHT);
setMetadata(ifd, core, "Subfile Type", SUBFILETYPE);
setMetadata(ifd, core, "Fill Order", FILLORDER);
setMetadata(ifd, core, "Min Sample Value", MINSAMPLEVALUE);
setMetadata(ifd, core, "Max Sample Value", MAXSAMPLEVALUE);
setMetadata(ifd, core, "XResolution", XRESOLUTION);
setMetadata(ifd, core, "YResolution", YRESOLUTION);
setMetadata(ifd, core, "Planar Configuration", PLANARCONFIG);
setMetadata(ifd, core, "XPosition", XPOSITION);
setMetadata(ifd, core, "YPosition", YPOSITION);
/// @todo Only set if debugging/verbose.
// setMetadata(ifd, core, "FreeOffsets", FREEOFFSETS);
// setMetadata(ifd, core, "FreeByteCounts", FREEBYTECOUNTS);
setMetadata(ifd, core, "GrayResponseUnit", GRAYRESPONSEUNIT);
setMetadata(ifd, core, "GrayResponseCurve", GRAYRESPONSECURVE);
try
{
Compression cmpr;
ifd.getField(COMPRESSION).get(cmpr);
core.seriesMetadata.set("Compression", cmpr);
if (cmpr == COMPRESSION_CCITT_T4)
setMetadata(ifd, core, "T4Options", T4OPTIONS);
else if (cmpr == COMPRESSION_CCITT_T6)
setMetadata(ifd, core, "T6Options", T6OPTIONS);
else if (cmpr == COMPRESSION_LZW)
setMetadata(ifd, core, "Predictor", PREDICTOR);
}
catch (...)
{
}
setMetadata(ifd, core, "ResolutionUnit", RESOLUTIONUNIT);
setMetadata(ifd, core, "PageNumber", PAGENUMBER);
// TransferRange only valid if TransferFunction set.
if (setMetadata(ifd, core, "TransferFunction", TRANSFERFUNCTION))
setMetadata(ifd, core, "TransferRange", TRANSFERRANGE);
setMetadata(ifd, core, "WhitePoint", WHITEPOINT);
setMetadata(ifd, core, "PrimaryChromacities", PRIMARYCHROMATICITIES);
setMetadata(ifd, core, "HalftoneHints", HALFTONEHINTS);
setMetadata(ifd, core, "TileWidth", TILEWIDTH);
setMetadata(ifd, core, "TileLength", TILELENGTH);
/// @todo Only set if debugging/verbose.
// setMetadata(ifd, core, "TileOffsets", TILEOFFSETS);
// setMetadata(ifd, core, "TileByteCounts", TILEBYTECOUNTS);
setMetadata(ifd, core, "InkSet", INKSET);
setMetadata(ifd, core, "InkNames", INKNAMES);
setMetadata(ifd, core, "NumberOfInks", NUMBEROFINKS);
setMetadata(ifd, core, "DotRange", DOTRANGE);
setMetadata(ifd, core, "TargetPrinter", TARGETPRINTER);
setMetadata(ifd, core, "ExtraSamples", EXTRASAMPLES);
setMetadata(ifd, core, "SampleFormat", SAMPLEFORMAT);
/// @todo sminsamplevalue
/// @todo smaxsamplevalue
/// @todo Only set if debugging/verbose.
// setMetadata(ifd, core, "StripOffsets", STRIPOFFSETS);
// setMetadata(ifd, core, "StripByteCounts", STRIPBYTECOUNTS);
/// @todo JPEG tags
setMetadata(ifd, core, "YCbCrCoefficients", YCBCRCOEFFICIENTS);
setMetadata(ifd, core, "YCbCrSubSampling", YCBCRSUBSAMPLING);
setMetadata(ifd, core, "YCbCrPositioning", YCBCRPOSITIONING);
setMetadata(ifd, core, "ReferenceBlackWhite", REFERENCEBLACKWHITE);
try
{
uint16_t samples;
ifd.getField(SAMPLESPERPIXEL).get(samples);
PhotometricInterpretation photometric;
ifd.getField(PHOTOMETRIC).get(photometric);
if (photometric == RGB ||
photometric == CFA_ARRAY)
samples = 3;
try
{
std::vector<ExtraSamples> extra;
ifd.getField(EXTRASAMPLES).get(extra);
samples += static_cast<uint16_t>(extra.size());
}
catch (...)
{
}
core.seriesMetadata.set("NumberOfChannels", samples);
}
catch (...)
{
}
core.seriesMetadata.set("BitsPerSample", bitsPerPixel(ifd.getPixelType()));
}