dimension_size_type
FormatWriter::getPlane() const
{
assertId(currentId, true);
return plane;
}
void
FormatWriter::changeOutputFile(const boost::filesystem::path& id)
{
assertId(currentId, true);
setId(id);
}
dimension_size_type
FormatWriter::getSeries() const
{
assertId(currentId, true);
return series;
}
void
FormatWriter::setLookupTable(dimension_size_type /* plane */,
const VariantPixelBuffer& /* buf */)
{
assertId(currentId, true);
throw std::runtime_error("Writer does not implement lookup tables");
}
void
FormatWriter::setMetadataRetrieve(ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve>& retrieve)
{
assertId(currentId, false);
if (!retrieve)
throw std::logic_error("MetadataStore can not be null");
metadataRetrieve = retrieve;
}
void
FormatWriter::saveBytes(dimension_size_type plane,
VariantPixelBuffer& buf)
{
assertId(currentId, true);
dimension_size_type width = metadataRetrieve->getPixelsSizeX(getSeries());
dimension_size_type height = metadataRetrieve->getPixelsSizeY(getSeries());
saveBytes(plane, buf, 0, 0, width, height);
}
ome::compat::array<dimension_size_type, 3>
FormatWriter::getZCTCoords(dimension_size_type index) const
{
assertId(currentId, true);
return ome::bioformats::getZCTCoords(getDimensionOrder(),
getSizeZ(),
getEffectiveSizeC(),
getSizeT(),
getImageCount(),
index);
}
dimension_size_type
FormatWriter::getIndex(dimension_size_type z,
dimension_size_type c,
dimension_size_type t) const
{
assertId(currentId, true);
return ome::bioformats::getIndex(getDimensionOrder(),
getSizeZ(),
getEffectiveSizeC(),
getSizeT(),
getImageCount(),
z, c, t);
}
void
MinimalTIFFReader::openBytesImpl(dimension_size_type plane,
VariantPixelBuffer& buf,
dimension_size_type x,
dimension_size_type y,
dimension_size_type w,
dimension_size_type h) const
{
assertId(currentId, true);
const ome::compat::shared_ptr<const IFD>& ifd(ifdAtIndex(plane));
ifd->readImage(buf, x, y, w, h);
}
FormatWriter::FormatWriter(const WriterProperties& writerProperties):
writerProperties(writerProperties),
currentId(boost::none),
out(),
series(0),
plane(0),
compression(boost::none),
interleaved(boost::none),
sequential(false),
framesPerSecond(0),
metadataRetrieve(ome::compat::make_shared<DummyMetadata>())
{
assertId(currentId, false);
}
void
MinimalTIFFReader::getLookupTable(dimension_size_type plane,
VariantPixelBuffer& buf) const
{
assertId(currentId, true);
const ome::compat::shared_ptr<const IFD>& ifd(ifdAtIndex(plane));
try
{
ifd->readLookupTable(buf);
}
catch (const std::exception& e)
{
boost::format fmt("Failed to get lookup table:");
fmt % e.what();
throw FormatException(fmt.str());
}
}
void
FormatWriter::setPlane(dimension_size_type plane) const
{
assertId(currentId, true);
if (plane >= getImageCount())
{
boost::format fmt("Invalid plane: %1%");
fmt % plane;
throw std::logic_error(fmt.str());
}
const dimension_size_type currentPlane = getPlane();
if (currentPlane != plane &&
(plane > 0 && currentPlane != plane - 1))
{
boost::format fmt("Plane set out of order: %1% (currently %2%)");
fmt % plane % currentPlane;
throw std::logic_error(fmt.str());
}
this->plane = plane;
}
void
MinimalTIFFWriter::saveBytes(dimension_size_type plane,
VariantPixelBuffer& buf,
dimension_size_type x,
dimension_size_type y,
dimension_size_type w,
dimension_size_type h)
{
assertId(currentId, true);
setPlane(plane);
dimension_size_type expectedIndex =
tiff::ifdIndex(seriesIFDRange, getSeries(), plane);
if (ifdIndex != expectedIndex)
{
boost::format fmt("IFD index mismatch: actual is %1% but %2% expected");
fmt % ifdIndex % expectedIndex;
throw FormatException(fmt.str());
}
ifd->writeImage(buf, x, y, w, h);
}
void
FormatWriter::setSeries(dimension_size_type series) const
{
assertId(currentId, true);
if (series >= getSeriesCount())
{
boost::format fmt("Invalid series: %1%");
fmt % series;
throw std::logic_error(fmt.str());
}
const dimension_size_type currentSeries = getSeries();
if (currentSeries != series &&
(series > 0 && currentSeries != series - 1))
{
boost::format fmt("Series set out of order: %1% (currently %2%)");
fmt % series % currentSeries;
throw std::logic_error(fmt.str());
}
this->series = series;
this->plane = 0U;
}