Interface for all biological file format writers (default behaviour). More...

#include <ome/bioformats/detail/FormatWriter.h>

Inheritance diagram for ome::bioformats::detail::FormatWriter:

Collaboration diagram for ome::bioformats::detail::FormatWriter:

Public Member Functions
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...

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

void	saveBytes (dimension_size_type no, VariantPixelBuffer &buf)
	Save an image plane. More...

void	saveBytes (dimension_size_type no, VariantPixelBuffer &buf, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h)=0
	Save an image plane. More...

void	setSeries (dimension_size_type no) const
	Set the active series. More...

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

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

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

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

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

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	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...

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

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

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

Protected Member Functions
	FormatWriter (const WriterProperties &)
	Constructor.

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

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

Protected Attributes
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.

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

dimension_size_type	series
	Current series.

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

bool	sequential
	Planes are written sequentially.

frame_rate_type	framesPerSecond
	The frames per second to use when writing.

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

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

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

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

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 (default behaviour).

Note: The ColorModel isn't stored here; this is Java-specific and not implemented in C++.; The current output stream isn't stored here; this is the responsibility of the individual writer. Having a reference to the base ostream here and keeping this in sync with the derived writer is an unnecessary complication.

Member Function Documentation

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

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.

Implements ome::bioformats::FormatWriter.

References ome::bioformats::detail::WriterProperties::stacks, and writerProperties.

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

virtual

Switch the output file for the current dataset.

Parameters

id	the new file name.

Implements ome::bioformats::FormatWriter.

References ome::bioformats::FormatHandler::assertId(), currentId, and setId().

void ome::bioformats::detail::FormatWriter::close ( bool fileOnly = false )

virtual

Close the currently open file.

Parameters

fileOnly close the open file only if true, or else free all internal state if false.

Implements ome::bioformats::FormatHandler.

References currentId, out, and series.

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

virtual

Get the compression type to use when writing.

Returns: the compression type.

Implements ome::bioformats::FormatWriter.

References compression.

const std::vector< boost::filesystem::path > & ome::bioformats::detail::FormatWriter::getCompressionSuffixes ( ) const

virtual

Get the default compression suffixes for this file format.

Returns: a list of file suffixes.

Implements ome::bioformats::FormatHandler.

References ome::bioformats::detail::WriterProperties::compression_suffixes, and writerProperties.

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

virtual

Get supported compression types.

Returns: the supported compression types.

Implements ome::bioformats::FormatWriter.

References ome::bioformats::detail::WriterProperties::compression_types, and writerProperties.

const std::string & ome::bioformats::detail::FormatWriter::getFormat ( ) const

virtual

Get the name of this file format.

Returns: the file format name.

Implements ome::bioformats::FormatHandler.

References ome::bioformats::detail::WriterProperties::name, and writerProperties.

const std::string & ome::bioformats::detail::FormatWriter::getFormatDescription ( ) const

virtual

Get the description of this file format.

Returns: the file format description.

Implements ome::bioformats::FormatHandler.

References ome::bioformats::detail::WriterProperties::description, and writerProperties.

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

virtual

Get the frame rate to use when writing.

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

Implements ome::bioformats::FormatWriter.

References framesPerSecond.

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

virtual

Get the current metadata store for this writer.

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

Implements ome::bioformats::FormatWriter.

References metadataRetrieve.

Referenced by setId().

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

virtual

Get the current metadata store for this writer.

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

Implements ome::bioformats::FormatWriter.

References metadataRetrieve.

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

virtual

Get supported pixel types.

Returns: the supported pixel types.

Implements ome::bioformats::FormatWriter.

Referenced by isSupportedType().

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

virtual

Get supported pixel types for the given codec.

Parameters

codec the codec to check.

Returns: the supported pixel types.

Implements ome::bioformats::FormatWriter.

References ome::bioformats::detail::WriterProperties::codec_pixel_types, and writerProperties.

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

virtual

Get the active series.

Returns: the active series.

Implements ome::bioformats::FormatWriter.

References series.

Referenced by saveBytes().

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const std::vector< boost::filesystem::path > & ome::bioformats::detail::FormatWriter::getSuffixes ( ) const

virtual

Get the default file suffixes for this file format.

Returns: a list of file suffixes.

Implements ome::bioformats::FormatHandler.

References ome::bioformats::detail::WriterProperties::suffixes, and writerProperties.

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

virtual

Check if planes are written sequentially.

Returns: true if sequential, false if not.

Implements ome::bioformats::FormatWriter.

References sequential.

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

virtual

Check if the pixel type is supported.

Parameters

type	the pixel type to check.

Returns: true if supported, false otherwise.

Implements ome::bioformats::FormatWriter.

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

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.

Implements ome::bioformats::FormatWriter.

References getPixelTypes().

bool ome::bioformats::detail::FormatWriter::isThisType	(	const boost::filesystem::path &	name,
		bool	open = `true`
	)		const

virtual

Check if the given file is a valid instance of this file format.

Parameters

name	the file to open for checking.
open	If `true`, and the file extension is insufficient to determine the file type, the file may be opened for further analysis, or other relatively expensive file system operations (such as file existence tests and directory listings) may be performed. If `false`, file system access is not allowed.

Returns: true if the file is valid, false otherwise.

Todo:: Could this method be static?

Implements ome::bioformats::FormatHandler.

References ome::bioformats::FormatHandler::checkSuffix(), ome::bioformats::detail::WriterProperties::compression_suffixes, ome::bioformats::detail::WriterProperties::suffixes, and writerProperties.

void ome::bioformats::detail::FormatWriter::saveBytes	(	dimension_size_type	no,
		VariantPixelBuffer &	buf
	)

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

no	the image index within the file.
buf	the source pixel buffer.

Exceptions

FormatException if any of the parameters are invalid.

Implements ome::bioformats::FormatWriter.

References ome::bioformats::FormatHandler::assertId(), currentId, getSeries(), and metadataRetrieve.

void ome::bioformats::detail::FormatWriter::saveBytes	(	dimension_size_type	no,
		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

no	the image index within the file.
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::bioformats::FormatWriter.

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

virtual

Set the compression type to use when writing.

Parameters

compression the compression type.

Implements ome::bioformats::FormatWriter.

References compression, ome::bioformats::detail::WriterProperties::compression_types, and writerProperties.

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

virtual

Set the frame rate to use when writing.

Parameters

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

Implements ome::bioformats::FormatWriter.

References framesPerSecond.

void ome::bioformats::detail::FormatWriter::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.

Implements ome::bioformats::FormatHandler.

References currentId, getMetadataRetrieve(), out, and setSeries().

Referenced by changeOutputFile().

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void ome::bioformats::detail::FormatWriter::setLookupTable ( const VariantPixelBuffer & buf )

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

buf	the source pixel buffer.

Implements ome::bioformats::FormatWriter.

References ome::bioformats::FormatHandler::assertId(), and currentId.

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

virtual

Set the default metadata store for this writer.

Parameters

retrieve a metadata retrieve implementation.

Implements ome::bioformats::FormatWriter.

References ome::bioformats::FormatHandler::assertId(), currentId, and metadataRetrieve.

void ome::bioformats::detail::FormatWriter::setSeries ( dimension_size_type no ) const

virtual

Set the active series.

Parameters

no	the series to activate.

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

Implements ome::bioformats::FormatWriter.

References metadataRetrieve, and series.

Referenced by setId().

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

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.

Implements ome::bioformats::FormatWriter.

References sequential.

Member Data Documentation

ome::compat::shared_ptr< ::ome::xml::meta::MetadataRetrieve> ome::bioformats::detail::FormatWriter::metadataRetrieve

protected

Current metadata store.

Should never be accessed directly as the semantics of getMetadataRetrieve() prevent "null" access.

Referenced by getMetadataRetrieve(), saveBytes(), setMetadataRetrieve(), and setSeries().

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

ome/bioformats/detail/FormatWriter.h
ome/bioformats/detail/FormatWriter.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

Member Data Documentation