TIFF writer with support for OME-XML metadata. More...

#include <ome/files/out/OMETIFFWriter.h>

Inheritance diagram for ome::files::out::OMETIFFWriter:

Collaboration diagram for ome::files::out::OMETIFFWriter:

Classes
struct	SeriesState
	Current state of an image series. More...

struct	TIFFState
	State of TIFF file. More...

Public Member Functions
	OMETIFFWriter ()
	Constructor.

virtual	~OMETIFFWriter ()
	Destructor.

void	setId (const boost::filesystem::path &id)
	Set the current file name. More...

void	close (bool fileOnly=false)
	Close the currently open file. More...

void	setSeries (dimension_size_type series) const
	Set the active series. More...

void	setPlane (dimension_size_type plane) const
	Set the active plane. More...

dimension_size_type	getTileSizeX () const
	Get the effective tile width. More...

dimension_size_type	getTileSizeY () const
	Get the effective tile height. More...

void	saveBytes (dimension_size_type plane, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h)
	Save an image plane. More...

void	setBigTIFF (boost::optional< bool > big=true)
	Set use of BigTIFF support. More...

boost::optional< bool >	getBigTIFF () const
	Query use of BigTIFF support. More...

Public Member Functions inherited from ome::files::detail::FormatWriter
virtual	~FormatWriter ()
	Destructor.

bool	isThisType (const boost::filesystem::path &name, bool open=true) const
	Check if the given file is a valid instance of this file format. More...

virtual dimension_size_type	getSeriesCount () const
	Get the number of image series in this file. More...

void	setLookupTable (dimension_size_type plane, const VariantPixelBuffer &buf)
	Set the color lookup table associated with the current series. More...

void	saveBytes (dimension_size_type plane, VariantPixelBuffer &buf)
	Save an image plane. More...

dimension_size_type	getSeries () const
	Get the active series. More...

dimension_size_type	getPlane () const
	Get the active plane. More...

bool	canDoStacks () const
	Get whether or not the writer can save multiple images in a single file. More...

void	setMetadataRetrieve (std::shared_ptr<::ome::xml::meta::MetadataRetrieve > &retrieve)
	Set the default metadata store for this writer. More...

const std::shared_ptr<::ome::xml::meta::MetadataRetrieve > &	getMetadataRetrieve () const
	Get the current metadata store for this writer. More...

std::shared_ptr<::ome::xml::meta::MetadataRetrieve > &	getMetadataRetrieve ()
	Get the current metadata store for this writer. More...

virtual dimension_size_type	getImageCount () const
	Determine the number of image planes in the current series. More...

virtual bool	isRGB (dimension_size_type channel) const
	Does a channel contain subchannels? More...

virtual dimension_size_type	getSizeX () const
	Get the size of the X dimension. More...

virtual dimension_size_type	getSizeY () const
	Get the size of the Y dimension. More...

virtual dimension_size_type	getSizeZ () const
	Get the size of the Z dimension. More...

virtual dimension_size_type	getSizeT () const
	Get the size of the T dimension. More...

virtual dimension_size_type	getSizeC () const
	Get the size of the C dimension. More...

virtual ome::xml::model::enums::PixelType	getPixelType () const
	Get the pixel type. More...

virtual pixel_size_type	getBitsPerPixel () const
	Get the number of valid bits per pixel. More...

virtual dimension_size_type	getEffectiveSizeC () const
	Get the effective size of the C dimension. More...

virtual dimension_size_type	getRGBChannelCount (dimension_size_type channel) const
	Get the number of channels required for a call to saveBytes(). More...

virtual const std::string &	getDimensionOrder () const
	Get the dimension order. More...

virtual dimension_size_type	getIndex (dimension_size_type z, dimension_size_type c, dimension_size_type t) const
	Get the linear index of a `Z`, `C` and `T` coordinate. More...

virtual std::array< dimension_size_type, 3 >	getZCTCoords (dimension_size_type index) const
	Get the `Z`, `C` and `T` coordinate of a linear index. More...

void	setFramesPerSecond (frame_rate_type rate)
	Set the frame rate to use when writing. More...

frame_rate_type	getFramesPerSecond () const
	Get the frame rate to use when writing. More...

const std::set< ome::xml::model::enums::PixelType >	getPixelTypes () const
	Get supported pixel types. More...

const std::set< ome::xml::model::enums::PixelType >	getPixelTypes (const std::string &codec) const
	Get supported pixel types for the given codec. More...

bool	isSupportedType (ome::xml::model::enums::PixelType type) const
	Check if the pixel type is supported. More...

bool	isSupportedType (ome::xml::model::enums::PixelType type, const std::string &codec) const
	Check if the pixel type is supported by the given codex. More...

const std::set< std::string > &	getCompressionTypes () const
	Get supported compression types. More...

const std::set< std::string > &	getCompressionTypes (ome::xml::model::enums::PixelType type) const
	Get supported compression types for a given pixel type. More...

void	setCompression (const std::string &compression)
	Set the compression type to use when writing. More...

const boost::optional< std::string > &	getCompression () const
	Get the compression type to use when writing. More...

void	setInterleaved (bool interleaved)
	Set subchannel interleaving. More...

const boost::optional< bool > &	getInterleaved () const
	Set subchannel interleaving. More...

void	changeOutputFile (const boost::filesystem::path &id)
	Switch the output file for the current dataset. More...

void	setWriteSequentially (bool sequential=true)
	Write planes sequentially. More...

bool	getWriteSequentially () const
	Check if planes are written sequentially. More...

const std::string &	getFormat () const
	Get the name of this file format. More...

const std::string &	getFormatDescription () const
	Get the description of this file format. More...

const std::vector< boost::filesystem::path > &	getSuffixes () const
	Get the default file suffixes for this file format. More...

const std::vector< boost::filesystem::path > &	getCompressionSuffixes () const
	Get the default compression suffixes for this file format. More...

dimension_size_type	setTileSizeX (boost::optional< dimension_size_type > size)
	Set the requested tile width. More...

dimension_size_type	setTileSizeY (boost::optional< dimension_size_type > size)
	Set the requested tile height. More...

Public Member Functions inherited from ome::files::FormatHandler
virtual	~FormatHandler ()
	Destructor.

Protected Types
typedef std::map< boost::filesystem::path, std::string >	file_uuid_map
	Map filename to UUID.

typedef std::map< boost::filesystem::path, TIFFState >	tiff_map
	Map filename to TIFF state.

typedef std::vector< SeriesState >	series_list
	Vector of SeriesState objects.

Protected Member Functions
void	nextIFD () const
	Flush current IFD and create new IFD.

void	setupIFD () const
	Set IFD parameters for the current series.

Protected Member Functions inherited from ome::files::detail::FormatWriter
	FormatWriter (const WriterProperties &)
	Constructor.

Protected Member Functions inherited from ome::files::FormatWriter
	FormatWriter ()
	Constructor.

Protected Member Functions inherited from ome::files::FormatHandler
	FormatHandler ()
	Constructor.

Protected Attributes
ome::common::Logger	logger
	Message logger.

boost::filesystem::path	baseDir
	Base path for computing relative paths in the OME-XML.

file_uuid_map	files
	UUID to filename mapping.

tiff_map	tiffs
	Open TIFF files.

tiff_map::iterator	currentTIFF
	Current TIFF file.

std::string	flags
	TIFF flags.

series_list	seriesState
	State of each series.

std::shared_ptr<::ome::xml::meta::MetadataRetrieve >	originalMetadataRetrieve
	Original MetadataRetrieve. More...

std::shared_ptr< ome::xml::meta::OMEXMLMetadata >	omeMeta
	OME-XML metadata for embedding in the TIFF.

Protected Attributes inherited from ome::files::detail::FormatWriter
const WriterProperties &	writerProperties
	Writer properties specific to the derived file format.

boost::optional< boost::filesystem::path >	currentId
	The identifier (path) of the currently open file.

std::shared_ptr< std::ostream >	out
	Current output.

dimension_size_type	series
	Current series.

dimension_size_type	plane
	Current plane.

boost::optional< std::string >	compression
	The compression type to use.

boost::optional< bool >	interleaved
	Subchannel interleaving enabled.

bool	sequential
	Planes are written sequentially.

frame_rate_type	framesPerSecond
	The frames per second to use when writing.

boost::optional< dimension_size_type >	tile_size_x
	Tile size X.

boost::optional< dimension_size_type >	tile_size_y
	Tile size Y.

std::shared_ptr<::ome::xml::meta::MetadataRetrieve >	metadataRetrieve
	Current metadata store. More...

Private Member Functions
void	fillMetadata ()
	Fill MetadataStore with cached metadata. More...

std::string	getOMEXML (const boost::filesystem::path &id)
	Get OME-XML for embedding into the specified TIFF file. More...

void	saveComment (const boost::filesystem::path &id, const std::string &xml)
	Save OME-XML text in the first IFD of the specified TIFF file. More...

Private Attributes
boost::optional< bool >	bigTIFF
	Write a Big TIFF.

Additional Inherited Members
Public Types inherited from ome::files::FormatWriter
typedef uint16_t	frame_rate_type
	Frame rate type.

Static Public Member Functions inherited from ome::files::FormatHandler
static bool	checkSuffix (const boost::filesystem::path &name, const boost::filesystem::path &suffix)
	Perform suffix matching for the given filename. More...

static bool	checkSuffix (const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes)
	Perform suffix matching for the given filename. More...

static bool	checkSuffix (const boost::filesystem::path &name, const std::vector< boost::filesystem::path > &suffixes, const std::vector< boost::filesystem::path > &compression_suffixes)
	Perform suffix matching for the given filename. More...

static void	assertId (const boost::optional< boost::filesystem::path > &id, bool notNull=true)
	Assert that the current file is valid. More...

Detailed Description

TIFF writer with support for OME-XML metadata.

Member Function Documentation

◆ close()

void ome::files::out::OMETIFFWriter::close ( bool fileOnly = false )

virtual

Close the currently open file.

An exception may be thrown when closing the file, for example if there are problems flushing any pending writes, or if there are any inconsistencies in the metadata which prevent completing any final writes. The causes are reader- or writer-dependent, and the exception type is dependent upon the implementation details of the reader or writer in use. It is advised to always explicitly close writers, since if this is automatically called at destruction time, any errors will be lost. If an exception is thrown, the object may be left in an inconsistent state and should not be reused.

Parameters

fileOnly close the open file only if true, or else free all internal state if false; only meaningful for readers, since writers will always free all internal state.

Exceptions

On	error; exception type may vary.

Reimplemented from ome::files::detail::FormatWriter.

References bigTIFF, ome::files::detail::FormatWriter::close(), ome::files::detail::FormatWriter::currentId, currentTIFF, files, fillMetadata(), flags, getOMEXML(), nextIFD(), omeMeta, originalMetadataRetrieve, ome::files::removeBinData(), ome::files::removeTiffData(), saveComment(), seriesState, and tiffs.

Referenced by ~OMETIFFWriter().

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◆ fillMetadata()

void ome::files::out::OMETIFFWriter::fillMetadata ( )

private

Fill MetadataStore with cached metadata.

Set Image, Channel and TiffData elements.

References baseDir, ome::files::detail::FormatWriter::getSeriesCount(), ome::files::getZCTCoords(), make_relative(), ome::files::detail::FormatWriter::metadataRetrieve, omeMeta, ome::files::detail::FormatWriter::plane, ome::files::detail::OMETIFFPlane::PRESENT, ome::files::detail::FormatWriter::series, seriesState, and tiffs.

Referenced by close().

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◆ getBigTIFF()

boost::optional< bool > ome::files::out::OMETIFFWriter::getBigTIFF ( ) const

Query use of BigTIFF support.

If setBigTIFF has not been used to enable or disable BigTIFF explicitly, BigTIFF support will be disabled by default for data less than 4GiB, unless the data would be larger than 4GiB, in which case it will be enabled by default.

Returns: true if BigTIFF support are enabled, or false if disabled.

References bigTIFF.

◆ getOMEXML()

std::string ome::files::out::OMETIFFWriter::getOMEXML ( const boost::filesystem::path & id )

private

Get OME-XML for embedding into the specified TIFF file.

Parameters

id	the TIFF in which to embed the OME-XML.

Returns: the OME-XML text for embedding.

References baseDir, ome::files::getOMEXML(), make_relative(), omeMeta, and tiffs.

Referenced by close().

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◆ getTileSizeX()

dimension_size_type ome::files::out::OMETIFFWriter::getTileSizeX ( ) const

virtual

Get the effective tile width.

This is intended for use with saveBytes().

Returns: the effective tile width.

Reimplemented from ome::files::detail::FormatWriter.

References ome::files::detail::FormatWriter::currentId, currentTIFF, ome::files::detail::FormatWriter::getTileSizeX(), and ome::files::detail::FormatWriter::tile_size_x.

◆ getTileSizeY()

dimension_size_type ome::files::out::OMETIFFWriter::getTileSizeY ( ) const

virtual

Get the effective tile height.

This is intended for use with saveBytes().

Returns: the effective tile height.

Reimplemented from ome::files::detail::FormatWriter.

References ome::files::detail::FormatWriter::currentId, currentTIFF, ome::files::detail::FormatWriter::getTileSizeY(), and ome::files::detail::FormatWriter::tile_size_y.

◆ saveBytes()

void ome::files::out::OMETIFFWriter::saveBytes	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf,
		dimension_size_type	x,
		dimension_size_type	y,
		dimension_size_type	w,
		dimension_size_type	h
	)

virtual

Save an image plane.

Write an image plane from a VariantPixelBuffer of size

getSizeX * getSizeY * bytesPerPixel * getRGBChannelCount()

to the current series in the current file.

Parameters

plane	the plane index within the series.
buf	the source pixel buffer.
x	the `X` coordinate of the upper-left corner of the sub-image.
y	the `Y` coordinate of the upper-left corner of the sub-image.
w	the width of the sub-image.
h	the height of the sub-image.

Exceptions

FormatException if any of the parameters are invalid.

Implements ome::files::FormatWriter.

References ome::files::FormatHandler::assertId(), ome::files::detail::FormatWriter::currentId, currentTIFF, ome::files::detail::FormatWriter::getSeries(), ome::files::detail::OMETIFFPlane::id, ome::files::detail::OMETIFFPlane::PRESENT, seriesState, and setPlane().

◆ saveComment()

void ome::files::out::OMETIFFWriter::saveComment	(	const boost::filesystem::path &	id,
		const std::string &	xml
	)

private

Save OME-XML text in the first IFD of the specified TIFF file.

Parameters

id	the TIFF in which to embed the OME-XML.
xml	the OME-XML text to embed.

References ome::files::ENDIAN_BIG, ome::files::ENDIAN_LITTLE, and ome::files::ENDIAN_NATIVE.

Referenced by close().

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◆ setBigTIFF()

void ome::files::out::OMETIFFWriter::setBigTIFF ( boost::optional< bool > big = true )

Set use of BigTIFF support.

Enable or disable use of BigTIFF support for writing files larger than 4GiB.

Note: libtiff must be compiled with BigTIFF support enabled for this option to have any effect.

Parameters

big	`true` to enable or `false` to disable BigTIFF support.

References bigTIFF.

◆ setId()

void ome::files::out::OMETIFFWriter::setId ( const boost::filesystem::path & id )

virtual

Set the current file name.

Note this will throw FormatException if there are problems opening the file.

Parameters

id	the filename to open.

Reimplemented from ome::files::detail::FormatWriter.

References ome::files::detail::OMETIFFPlane::ABSENT, baseDir, bigTIFF, ome::common::canonical(), ome::files::detail::OMETIFFPlane::certain, ome::files::detail::FormatWriter::currentId, currentTIFF, flags, ome::files::detail::FormatWriter::getMetadataRetrieve(), logger, ome::files::detail::FormatWriter::metadataRetrieve, omeMeta, ome::files::tiff::TIFF::open(), originalMetadataRetrieve, ome::files::pixelSize(), ome::files::detail::FormatWriter::plane, ome::files::out::OMETIFFWriter::SeriesState::planes, ome::files::detail::FormatWriter::series, seriesState, ome::files::detail::FormatWriter::setId(), setupIFD(), ome::files::significantPixelSize(), tiffs, and ome::files::validateModel().

◆ setPlane()

void ome::files::out::OMETIFFWriter::setPlane ( dimension_size_type plane ) const

virtual

Set the active plane.

Parameters

plane the plane to activate.

Todo:: Remove use of stateful API which requires use of plane switching in const methods.

Reimplemented from ome::files::detail::FormatWriter.

References ome::files::detail::FormatWriter::getPlane(), nextIFD(), ome::files::detail::FormatWriter::setPlane(), and setupIFD().

Referenced by saveBytes().

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◆ setSeries()

void ome::files::out::OMETIFFWriter::setSeries ( dimension_size_type series ) const

virtual

Set the active series.

Parameters

series the series to activate.

Todo:: Remove use of stateful API which requires use of series switching in const methods.

Reimplemented from ome::files::detail::FormatWriter.

References ome::files::detail::FormatWriter::getSeries(), nextIFD(), ome::files::detail::FormatWriter::setSeries(), and setupIFD().

Member Data Documentation

◆ originalMetadataRetrieve

std::shared_ptr<::ome::xml::meta::MetadataRetrieve> ome::files::out::OMETIFFWriter::originalMetadataRetrieve

protected

Original MetadataRetrieve.

We replace it with the generated OME-XML metadata store.

Todo:: Overriding getMetadataRetrieve will be a cleaner solution, but need to eliminate all direct use of metadataRetrieve in all writers first.

Referenced by close(), and setId().

The documentation for this class was generated from the following files:

ome/files/out/OMETIFFWriter.h
ome/files/out/OMETIFFWriter.cpp

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ close()

◆ fillMetadata()

◆ getBigTIFF()

◆ getOMEXML()

◆ getTileSizeX()

◆ getTileSizeY()

◆ saveBytes()

◆ saveComment()

◆ setBigTIFF()

◆ setId()

◆ setPlane()

◆ setSeries()

Member Data Documentation

◆ originalMetadataRetrieve