Interface for all biological file format writers. More...

#include <ome/bioformats/FormatWriter.h>

Inheritance diagram for ome::bioformats::FormatWriter:

Collaboration diagram for ome::bioformats::FormatWriter:

Public Types
typedef uint16_t	frame_rate_type
	Frame rate type.

Public Member Functions
virtual	~FormatWriter ()
	Destructor.

virtual void	setLookupTable (dimension_size_type plane, const VariantPixelBuffer &buf)=0
	Set the color lookup table associated with the current series. More...

virtual void	saveBytes (dimension_size_type plane, VariantPixelBuffer &buf)=0
	Save an image plane. More...

virtual void	saveBytes (dimension_size_type plane, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h)=0
	Save an image plane. More...

virtual void	setSeries (dimension_size_type series) const =0
	Set the active series. More...

virtual dimension_size_type	getSeries () const =0
	Get the active series. More...

virtual void	setPlane (dimension_size_type plane) const =0
	Set the active plane. More...

virtual dimension_size_type	getPlane () const =0
	Get the active plane. More...

virtual bool	canDoStacks () const =0
	Get whether or not the writer can save multiple images in a single file. More...

virtual void	setMetadataRetrieve (ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > &retrieve)=0
	Set the default metadata store for this writer. More...

virtual const ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > &	getMetadataRetrieve () const =0
	Get the current metadata store for this writer. More...

virtual ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > &	getMetadataRetrieve ()=0
	Get the current metadata store for this writer. More...

virtual void	setFramesPerSecond (frame_rate_type rate)=0
	Set the frame rate to use when writing. More...

virtual frame_rate_type	getFramesPerSecond () const =0
	Get the frame rate to use when writing. More...

virtual const std::set< ome::xml::model::enums::PixelType > &	getPixelTypes () const =0
	Get supported pixel types. More...

virtual const std::set< ome::xml::model::enums::PixelType > &	getPixelTypes (const std::string &codec) const =0
	Get supported pixel types for the given codec. More...

virtual bool	isSupportedType (ome::xml::model::enums::PixelType type) const =0
	Check if the pixel type is supported. More...

virtual bool	isSupportedType (ome::xml::model::enums::PixelType type, const std::string &codec) const =0
	Check if the pixel type is supported by the given codex. More...

virtual const std::set< std::string > &	getCompressionTypes () const =0
	Get supported compression types. More...

virtual void	setCompression (const std::string &compression)=0
	Set the compression type to use when writing. More...

virtual const boost::optional< std::string > &	getCompression () const =0
	Get the compression type to use when writing. More...

virtual void	setInterleaved (bool interleaved)=0
	Set subchannel interleaving. More...

virtual const boost::optional< bool > &	getInterleaved () const =0
	Set subchannel interleaving. More...

virtual void	changeOutputFile (const boost::filesystem::path &id)=0
	Switch the output file for the current dataset. More...

virtual void	setWriteSequentially (bool sequential=true)=0
	Write planes sequentially. More...

virtual bool	getWriteSequentially () const =0
	Check if planes are written sequentially. More...

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

virtual bool	isThisType (const boost::filesystem::path &name, bool open=true) const =0
	Check if the given file is a valid instance of this file format. More...

virtual const std::string &	getFormat () const =0
	Get the name of this file format. More...

virtual const std::string &	getFormatDescription () const =0
	Get the description of this file format. More...

virtual const std::vector< boost::filesystem::path > &	getSuffixes () const =0
	Get the default file suffixes for this file format. More...

virtual const std::vector< boost::filesystem::path > &	getCompressionSuffixes () const =0
	Get the default compression suffixes for this file format. More...

virtual void	setId (const boost::filesystem::path &id)=0
	Set the current file name. More...

virtual void	close (bool fileOnly=false)=0
	Close the currently open file. More...

Protected Member Functions
	FormatWriter ()
	Constructor.

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

Private Member Functions
	FormatWriter (const FormatWriter &)
	Copy constructor (deleted).

FormatWriter &	operator= (const FormatWriter &)
	Assignment operator (deleted).

Additional Inherited Members
Static Public Member Functions inherited from ome::bioformats::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

Interface for all biological file format writers.

Note: No IOException in C++.; getColorModel and setColorModel not implemented; it is Java-specific and if needed will require reimplementing in C++.; getCodecOptions and setCodec options not implemented; these rely on the Java-specific ColorModel and its design reflects that of Java c javax.imageio which we can't use here, though bits of it might require reimplementing.

Todo:: Implement saveBytes methods using 2D Region with and/or in terms of Boost.MultiArray index ranges.

Member Function Documentation

virtual bool ome::bioformats::FormatWriter::canDoStacks ( ) const

pure virtual

Get whether or not the writer can save multiple images in a single file.

Returns: true if the writer supports multiple images, false otherwise.

Implemented in ome::bioformats::detail::FormatWriter.

virtual void ome::bioformats::FormatWriter::changeOutputFile ( const boost::filesystem::path & id )

pure virtual

Switch the output file for the current dataset.

Parameters

id	the new file name.

Implemented in ome::bioformats::detail::FormatWriter.

virtual const boost::optional<std::string>& ome::bioformats::FormatWriter::getCompression ( ) const

pure virtual

Get the compression type to use when writing.

Returns: the compression type.

Implemented in ome::bioformats::detail::FormatWriter.

virtual const std::set<std::string>& ome::bioformats::FormatWriter::getCompressionTypes ( ) const

pure virtual

Get supported compression types.

Returns: the supported compression types.

Implemented in ome::bioformats::detail::FormatWriter.

virtual frame_rate_type ome::bioformats::FormatWriter::getFramesPerSecond ( ) const

pure virtual

Get the frame rate to use when writing.

Returns: the frame rate (number of frames per second).

Implemented in ome::bioformats::detail::FormatWriter.

virtual const boost::optional<bool>& ome::bioformats::FormatWriter::getInterleaved ( ) const

pure virtual

Set subchannel interleaving.

Returns: the current interleaving setting; false if unset.

Implemented in ome::bioformats::detail::FormatWriter.

virtual const ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve>& ome::bioformats::FormatWriter::getMetadataRetrieve ( ) const

pure virtual

Get the current metadata store for this writer.

Returns: the metadata store, which will never be null.

Implemented in ome::bioformats::detail::FormatWriter.

virtual ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve>& ome::bioformats::FormatWriter::getMetadataRetrieve ( )

pure virtual

Get the current metadata store for this writer.

Returns: the metadata store, which will never be null.

Implemented in ome::bioformats::detail::FormatWriter.

virtual const std::set<ome::xml::model::enums::PixelType>& ome::bioformats::FormatWriter::getPixelTypes ( ) const

pure virtual

Get supported pixel types.

Returns: the supported pixel types.

Implemented in ome::bioformats::detail::FormatWriter.

virtual const std::set<ome::xml::model::enums::PixelType>& ome::bioformats::FormatWriter::getPixelTypes ( const std::string & codec ) const

pure virtual

Get supported pixel types for the given codec.

Parameters

codec the codec to check.

Returns: the supported pixel types.

Implemented in ome::bioformats::detail::FormatWriter.

virtual dimension_size_type ome::bioformats::FormatWriter::getPlane ( ) const

pure virtual

Get the active plane.

Returns: the active plane.

Implemented in ome::bioformats::detail::FormatWriter.

virtual dimension_size_type ome::bioformats::FormatWriter::getSeries ( ) const

pure virtual

Get the active series.

Returns: the active series.

Implemented in ome::bioformats::detail::FormatWriter.

virtual bool ome::bioformats::FormatWriter::getWriteSequentially ( ) const

pure virtual

Check if planes are written sequentially.

Returns: true if sequential, false if not.

Implemented in ome::bioformats::detail::FormatWriter.

virtual bool ome::bioformats::FormatWriter::isSupportedType ( ome::xml::model::enums::PixelType type ) const

pure virtual

Check if the pixel type is supported.

Parameters

type	the pixel type to check.

Returns: true if supported, false otherwise.

Implemented in ome::bioformats::detail::FormatWriter.

virtual bool ome::bioformats::FormatWriter::isSupportedType	(	ome::xml::model::enums::PixelType	type,
		const std::string &	codec
	)		const

pure virtual

Check if the pixel type is supported by the given codex.

Parameters

type	the pixel type to check.
codec	the codec to check.

Returns: true if supported, false otherwise.

Implemented in ome::bioformats::detail::FormatWriter.

virtual void ome::bioformats::FormatWriter::saveBytes	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf
	)

pure 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.

Exceptions

FormatException if any of the parameters are invalid.

Implemented in ome::bioformats::detail::FormatWriter.

virtual void ome::bioformats::FormatWriter::saveBytes	(	dimension_size_type	plane,
		VariantPixelBuffer &	buf,
		dimension_size_type	x,
		dimension_size_type	y,
		dimension_size_type	w,
		dimension_size_type	h
	)

pure 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.

Implemented in ome::bioformats::out::OMETIFFWriter, and ome::bioformats::out::MinimalTIFFWriter.

virtual void ome::bioformats::FormatWriter::setCompression ( const std::string & compression )

pure virtual

Set the compression type to use when writing.

Parameters

compression the compression type.

Implemented in ome::bioformats::detail::FormatWriter.

virtual void ome::bioformats::FormatWriter::setFramesPerSecond ( frame_rate_type rate )

pure virtual

Set the frame rate to use when writing.

Parameters

rate	the frame rate (number of frames per second).

Implemented in ome::bioformats::detail::FormatWriter.

virtual void ome::bioformats::FormatWriter::setInterleaved ( bool interleaved )

pure virtual

Set subchannel interleaving.

Parameters

interleaved true to enable interleaving (chunky) or false to disable interleaving (planar).

Implemented in ome::bioformats::detail::FormatWriter.

virtual void ome::bioformats::FormatWriter::setLookupTable	(	dimension_size_type	plane,
		const VariantPixelBuffer &	buf
	)

pure virtual

Set the color lookup table associated with the current series.

If the pixel type of the lookup table is unsupported by the file format, this method will throw an exception.

Parameters

plane	the plane index within the series.
buf	the source pixel buffer.

Implemented in ome::bioformats::detail::FormatWriter.

virtual void ome::bioformats::FormatWriter::setMetadataRetrieve ( ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve > & retrieve )

pure virtual

Set the default metadata store for this writer.

Parameters

retrieve a metadata retrieve implementation.

Implemented in ome::bioformats::detail::FormatWriter.

virtual void ome::bioformats::FormatWriter::setPlane ( dimension_size_type plane ) const

pure 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.

Implemented in ome::bioformats::detail::FormatWriter, ome::bioformats::out::OMETIFFWriter, and ome::bioformats::out::MinimalTIFFWriter.

virtual void ome::bioformats::FormatWriter::setSeries ( dimension_size_type series ) const

pure 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.

Implemented in ome::bioformats::detail::FormatWriter, ome::bioformats::out::OMETIFFWriter, and ome::bioformats::out::MinimalTIFFWriter.

virtual void ome::bioformats::FormatWriter::setWriteSequentially ( bool sequential = true )

pure virtual

Write planes sequentially.

Set if planes will be written sequentially. If planes are written sequentially and this flag is set, then performance will be slightly improved.

Parameters

sequential true if sequential, false if not.

Implemented in ome::bioformats::detail::FormatWriter.

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

ome/bioformats/FormatWriter.h

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation