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

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

Inheritance diagram for ome::files::detail::FormatWriter:

Collaboration diagram for ome::files::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...

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...

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

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

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

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...

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

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

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

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

Public Member Functions inherited from ome::files::FormatWriter
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...

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

Protected Member Functions
	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
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...

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

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

◆ canDoStacks()

bool ome::files::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::files::FormatWriter.

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

◆ changeOutputFile()

void ome::files::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::files::FormatWriter.

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

◆ close()

void ome::files::detail::FormatWriter::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.

Implements ome::files::FormatHandler.

Reimplemented in ome::files::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References compression, currentId, framesPerSecond, metadataRetrieve, out, plane, sequential, and series.

Referenced by ome::files::out::MinimalTIFFWriter::close(), ome::files::out::OMETIFFWriter::close(), and ~FormatWriter().

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◆ getBitsPerPixel()

pixel_size_type ome::files::detail::FormatWriter::getBitsPerPixel ( ) const

virtual

Get the number of valid bits per pixel.

The number of valid bits per pixel is always less than or equal to the number of bits per pixel that correspond to getPixelType().

Returns: the number of valid bits per pixel.

References getSeries(), metadataRetrieve, and series.

◆ getCompression()

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

virtual

Get the compression type to use when writing.

Returns: the compression type.

Implements ome::files::FormatWriter.

References compression.

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ getCompressionSuffixes()

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

virtual

Get the default compression suffixes for this file format.

Returns: a list of file suffixes.

Implements ome::files::FormatHandler.

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

◆ getCompressionTypes() [1/2]

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

virtual

Get supported compression types.

Returns: the supported compression types.

Implements ome::files::FormatWriter.

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

◆ getCompressionTypes() [2/2]

const std::set< std::string > & ome::files::detail::FormatWriter::getCompressionTypes ( ome::xml::model::enums::PixelType type ) const

virtual

Get supported compression types for a given pixel type.

Parameters

type	the pixel type to use.

Returns: the supported compression types.

Implements ome::files::FormatWriter.

References ome::files::detail::WriterProperties::pixel_compression_types, and writerProperties.

◆ getDimensionOrder()

const std::string & ome::files::detail::FormatWriter::getDimensionOrder ( ) const

virtual

Get the dimension order.

The dimension order is a five-character string representing the order in which planes will be returned. Valid orders are:

XYCTZ
XYCZT
XYTCZ
XYTZC
XYZCT
XYZTC

In cases where the channels are interleaved (e.g. CXYTZ), C will be the first dimension after X and Y (e.g. XYCTZ) and the isInterleaved() method will return true.

Returns: the dimension order.

References getSeries(), metadataRetrieve, and series.

Referenced by getIndex(), and getZCTCoords().

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◆ getEffectiveSizeC()

dimension_size_type ome::files::detail::FormatWriter::getEffectiveSizeC ( ) const

virtual

Get the effective size of the C dimension.

This guarantees that

getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount()

regardless of the result of isRGB().

Returns: the effective C dimension size.

References getSeries(), metadataRetrieve, and series.

Referenced by getImageCount(), getIndex(), and getZCTCoords().

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◆ getFormat()

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

virtual

Get the name of this file format.

Returns: the file format name.

Implements ome::files::FormatHandler.

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

◆ getFormatDescription()

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

virtual

Get the description of this file format.

Returns: the file format description.

Implements ome::files::FormatHandler.

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

◆ getFramesPerSecond()

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

virtual

Get the frame rate to use when writing.

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

Implements ome::files::FormatWriter.

References framesPerSecond.

◆ getImageCount()

dimension_size_type ome::files::detail::FormatWriter::getImageCount ( ) const

virtual

Determine the number of image planes in the current series.

Returns: the number of image planes.

References getEffectiveSizeC(), getSizeT(), and getSizeZ().

Referenced by getIndex(), getZCTCoords(), ome::files::out::MinimalTIFFWriter::setId(), and setPlane().

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◆ getIndex()

dimension_size_type ome::files::detail::FormatWriter::getIndex	(	dimension_size_type	z,
		dimension_size_type	c,
		dimension_size_type	t
	)		const

virtual

Get the linear index of a Z, C and T coordinate.

The index is computed using the DimensionOrder.

Parameters

z	the `Z` coordinate (real size).
c	the `C` coordinate (real size).
t	the `T` coordinate (real size).

Returns: the linear index.

Todo:

unify with the pixel buffer dimension indexes.

Don't use separate values to match the return of getZCTCoords.

References ome::files::FormatHandler::assertId(), currentId, getDimensionOrder(), getEffectiveSizeC(), getImageCount(), ome::files::getIndex(), getSizeT(), and getSizeZ().

◆ getInterleaved()

const boost::optional< bool > & ome::files::detail::FormatWriter::getInterleaved ( ) const

virtual

Set subchannel interleaving.

Returns: the current interleaving setting; false if unset.

Implements ome::files::FormatWriter.

References interleaved.

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ getMetadataRetrieve() [1/2]

const std::shared_ptr<::ome::xml::meta::MetadataRetrieve > & ome::files::detail::FormatWriter::getMetadataRetrieve ( ) const

virtual

Get the current metadata store for this writer.

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

Implements ome::files::FormatWriter.

References metadataRetrieve.

Referenced by ome::files::out::MinimalTIFFWriter::setId(), and ome::files::out::OMETIFFWriter::setId().

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◆ getMetadataRetrieve() [2/2]

std::shared_ptr<::ome::xml::meta::MetadataRetrieve > & ome::files::detail::FormatWriter::getMetadataRetrieve ( )

virtual

Get the current metadata store for this writer.

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

Implements ome::files::FormatWriter.

References metadataRetrieve.

◆ getPixelType()

ome::xml::model::enums::PixelType ome::files::detail::FormatWriter::getPixelType ( ) const

virtual

Get the pixel type.

Returns: the pixel type.

References getSeries(), metadataRetrieve, and series.

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ getPixelTypes() [1/2]

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

virtual

Get supported pixel types.

Returns: the supported pixel types.

Implements ome::files::FormatWriter.

◆ getPixelTypes() [2/2]

const std::set< ome::xml::model::enums::PixelType > ome::files::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::files::FormatWriter.

References ome::files::detail::WriterProperties::pixel_compression_types, and writerProperties.

◆ getPlane()

dimension_size_type ome::files::detail::FormatWriter::getPlane ( ) const

virtual

Get the active plane.

Returns: the active plane.

Implements ome::files::FormatWriter.

References ome::files::FormatHandler::assertId(), currentId, and plane.

Referenced by ome::files::out::MinimalTIFFWriter::setPlane(), ome::files::out::OMETIFFWriter::setPlane(), setPlane(), ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ getRGBChannelCount()

dimension_size_type ome::files::detail::FormatWriter::getRGBChannelCount ( dimension_size_type channel ) const

virtual

Get the number of channels required for a call to saveBytes().

The most common case where this value is greater than 1 is for interleaved RGB data, such as a 24-bit color image plane. However, it is possible for this value to be greater than 1 for non-interleaved data, such as an RGB TIFF with Planar rather than Chunky configuration.

Parameters

channel the channel to use, range [0, EffectiveSizeC).

Returns: the number of channels.

References getSeries(), metadataRetrieve, and series.

Referenced by isRGB(), ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ getSeries()

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

virtual

Get the active series.

Returns: the active series.

Implements ome::files::FormatWriter.

References ome::files::FormatHandler::assertId(), currentId, and series.

Referenced by getBitsPerPixel(), getDimensionOrder(), getEffectiveSizeC(), getPixelType(), getRGBChannelCount(), getSizeC(), getSizeT(), getSizeX(), getSizeY(), getSizeZ(), getTileSizeX(), getTileSizeY(), ome::files::out::MinimalTIFFWriter::saveBytes(), saveBytes(), ome::files::out::OMETIFFWriter::saveBytes(), ome::files::out::MinimalTIFFWriter::setSeries(), ome::files::out::OMETIFFWriter::setSeries(), and setSeries().

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◆ getSeriesCount()

dimension_size_type ome::files::detail::FormatWriter::getSeriesCount ( ) const

virtual

Get the number of image series in this file.

Returns: the number of image series.

Exceptions

std::logic_error if the sub-resolution metadata (if any) is invalid; this will only occur if the reader sets invalid metadata.

References metadataRetrieve.

Referenced by ome::files::out::OMETIFFWriter::fillMetadata(), and setSeries().

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◆ getSizeC()

dimension_size_type ome::files::detail::FormatWriter::getSizeC ( ) const

virtual

Get the size of the C dimension.

Returns: the C dimension size.

References getSeries(), metadataRetrieve, and series.

◆ getSizeT()

dimension_size_type ome::files::detail::FormatWriter::getSizeT ( ) const

virtual

Get the size of the T dimension.

Returns: the T dimension size.

References getSeries(), metadataRetrieve, and series.

Referenced by getImageCount(), getIndex(), and getZCTCoords().

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◆ getSizeX()

dimension_size_type ome::files::detail::FormatWriter::getSizeX ( ) const

virtual

Get the size of the X dimension.

Returns: the X dimension size.

References getSeries(), metadataRetrieve, and series.

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ getSizeY()

dimension_size_type ome::files::detail::FormatWriter::getSizeY ( ) const

virtual

Get the size of the Y dimension.

Returns: the Y dimension size.

References getSeries(), metadataRetrieve, and series.

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ getSizeZ()

dimension_size_type ome::files::detail::FormatWriter::getSizeZ ( ) const

virtual

Get the size of the Z dimension.

Returns: the Z dimension size.

References getSeries(), metadataRetrieve, and series.

Referenced by getImageCount(), getIndex(), and getZCTCoords().

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◆ getSuffixes()

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

virtual

Get the default file suffixes for this file format.

Returns: a list of file suffixes.

Implements ome::files::FormatHandler.

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

◆ getTileSizeX()

dimension_size_type ome::files::detail::FormatWriter::getTileSizeX ( ) const

virtual

Get the effective tile width.

This is intended for use with saveBytes().

Returns: the effective tile width.

Implements ome::files::FormatWriter.

Reimplemented in ome::files::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References currentId, getSeries(), metadataRetrieve, and tile_size_x.

Referenced by ome::files::out::MinimalTIFFWriter::getTileSizeX(), ome::files::out::OMETIFFWriter::getTileSizeX(), and setTileSizeX().

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◆ getTileSizeY()

dimension_size_type ome::files::detail::FormatWriter::getTileSizeY ( ) const

virtual

Get the effective tile height.

This is intended for use with saveBytes().

Returns: the effective tile height.

Implements ome::files::FormatWriter.

Reimplemented in ome::files::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References currentId, getSeries(), metadataRetrieve, and tile_size_y.

Referenced by ome::files::out::MinimalTIFFWriter::getTileSizeY(), ome::files::out::OMETIFFWriter::getTileSizeY(), and setTileSizeY().

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◆ getWriteSequentially()

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

virtual

Check if planes are written sequentially.

Returns: true if sequential, false if not.

Implements ome::files::FormatWriter.

References sequential.

◆ getZCTCoords()

std::array< dimension_size_type, 3 > ome::files::detail::FormatWriter::getZCTCoords ( dimension_size_type index ) const

virtual

Get the Z, C and T coordinate of a linear index.

Parameters

index the linear index.

Returns: an array containing Z, C and T values (real sizes).

Todo:: unify with the pixel buffer dimension indexes.

References ome::files::FormatHandler::assertId(), currentId, getDimensionOrder(), getEffectiveSizeC(), getImageCount(), getSizeT(), getSizeZ(), and ome::files::getZCTCoords().

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ isRGB()

bool ome::files::detail::FormatWriter::isRGB ( dimension_size_type channel ) const

virtual

Does a channel contain subchannels?

Check if the image planes in the file have more than one subchannel per openBytes() call for the specified channel.

Parameters

channel the channel to use, range [0, EffectiveSizeC).

Returns: true if and only if getRGBChannelCount(channel) returns a value greater than 1, false otherwise.

References getRGBChannelCount().

Referenced by ome::files::out::MinimalTIFFWriter::setupIFD(), and ome::files::out::OMETIFFWriter::setupIFD().

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◆ isSupportedType() [1/2]

bool ome::files::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::files::FormatWriter.

◆ isSupportedType() [2/2]

bool ome::files::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::files::FormatWriter.

References ome::files::detail::WriterProperties::pixel_compression_types, and writerProperties.

◆ isThisType()

bool ome::files::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::files::FormatHandler.

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

◆ saveBytes()

void ome::files::detail::FormatWriter::saveBytes	(	dimension_size_type	plane,
		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

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

Exceptions

FormatException if any of the parameters are invalid.

Implements ome::files::FormatWriter.

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

◆ setCompression()

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

virtual

Set the compression type to use when writing.

Parameters

compression the compression type.

Implements ome::files::FormatWriter.

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

◆ setFramesPerSecond()

void ome::files::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::files::FormatWriter.

References framesPerSecond.

◆ setId()

void ome::files::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::files::FormatHandler.

Reimplemented in ome::files::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References ome::common::canonical(), currentId, and out.

Referenced by changeOutputFile(), and ome::files::out::OMETIFFWriter::setId().

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◆ setInterleaved()

void ome::files::detail::FormatWriter::setInterleaved ( bool interleaved )

virtual

Set subchannel interleaving.

Parameters

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

Implements ome::files::FormatWriter.

References interleaved.

◆ setLookupTable()

void ome::files::detail::FormatWriter::setLookupTable	(	dimension_size_type	plane,
		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

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

Implements ome::files::FormatWriter.

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

◆ setMetadataRetrieve()

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

virtual

Set the default metadata store for this writer.

Parameters

retrieve a metadata retrieve implementation.

Implements ome::files::FormatWriter.

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

◆ setPlane()

void ome::files::detail::FormatWriter::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.

Implements ome::files::FormatWriter.

Reimplemented in ome::files::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References ome::files::FormatHandler::assertId(), currentId, getImageCount(), getPlane(), and plane.

Referenced by ome::files::out::MinimalTIFFWriter::setPlane(), and ome::files::out::OMETIFFWriter::setPlane().

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◆ setSeries()

void ome::files::detail::FormatWriter::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.

Implements ome::files::FormatWriter.

Reimplemented in ome::files::out::OMETIFFWriter, and ome::files::out::MinimalTIFFWriter.

References ome::files::FormatHandler::assertId(), currentId, getSeries(), getSeriesCount(), plane, and series.

Referenced by ome::files::out::MinimalTIFFWriter::setSeries(), and ome::files::out::OMETIFFWriter::setSeries().

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◆ setTileSizeX()

dimension_size_type ome::files::detail::FormatWriter::setTileSizeX ( boost::optional< dimension_size_type > size )

virtual

Set the requested tile width.

The requested tile width may not be supported by the underlying file format. If the width requested is unsupported, the writer may set the nearest supported size, or the full image width or greater if no smaller tile sizes are supported. Call getTileSizeX() to get the effective size in use by the writer, or use the return value.

Parameters

size	the requested tile width.

Returns: the effective tile width.

Implements ome::files::FormatWriter.

References getTileSizeX(), and tile_size_x.

◆ setTileSizeY()

dimension_size_type ome::files::detail::FormatWriter::setTileSizeY ( boost::optional< dimension_size_type > size )

virtual

Set the requested tile height.

The requested tile height may not be supported by the underlying file format. If the height requested is unsupported, the writer may set the nearest supported size, or the full image height or greater if no smaller tile sizes are supported. Call getTileSizeY() to get the effective size in use by the writer, or use the return value.

Parameters

size	the requested tile height.

Returns: the effective tile height.

Implements ome::files::FormatWriter.

References getTileSizeY(), and tile_size_y.

◆ setWriteSequentially()

void ome::files::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::files::FormatWriter.

References sequential.

Member Data Documentation

◆ metadataRetrieve

std::shared_ptr<::ome::xml::meta::MetadataRetrieve> ome::files::detail::FormatWriter::metadataRetrieve

protected

Current metadata store.

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

Referenced by close(), ome::files::out::OMETIFFWriter::fillMetadata(), getBitsPerPixel(), getDimensionOrder(), getEffectiveSizeC(), getMetadataRetrieve(), getPixelType(), getRGBChannelCount(), getSeriesCount(), getSizeC(), getSizeT(), getSizeX(), getSizeY(), getSizeZ(), getTileSizeX(), getTileSizeY(), saveBytes(), ome::files::out::MinimalTIFFWriter::setId(), ome::files::out::OMETIFFWriter::setId(), and setMetadataRetrieve().

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

ome/files/detail/FormatWriter.h
ome/files/detail/FormatWriter.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ canDoStacks()

◆ changeOutputFile()

◆ close()

◆ getBitsPerPixel()

◆ getCompression()

◆ getCompressionSuffixes()

◆ getCompressionTypes() [1/2]

◆ getCompressionTypes() [2/2]

◆ getDimensionOrder()

◆ getEffectiveSizeC()

◆ getFormat()

◆ getFormatDescription()

◆ getFramesPerSecond()

◆ getImageCount()

◆ getIndex()

◆ getInterleaved()

◆ getMetadataRetrieve() [1/2]

◆ getMetadataRetrieve() [2/2]

◆ getPixelType()

◆ getPixelTypes() [1/2]

◆ getPixelTypes() [2/2]

◆ getPlane()

◆ getRGBChannelCount()

◆ getSeries()

◆ getSeriesCount()

◆ getSizeC()

◆ getSizeT()

◆ getSizeX()

◆ getSizeY()

◆ getSizeZ()

◆ getSuffixes()

◆ getTileSizeX()

◆ getTileSizeY()

◆ getWriteSequentially()

◆ getZCTCoords()

◆ isRGB()

◆ isSupportedType() [1/2]

◆ isSupportedType() [2/2]

◆ isThisType()

◆ saveBytes()

◆ setCompression()

◆ setFramesPerSecond()

◆ setId()

◆ setInterleaved()

◆ setLookupTable()

◆ setMetadataRetrieve()

◆ setPlane()

◆ setSeries()

◆ setTileSizeX()

◆ setTileSizeY()

◆ setWriteSequentially()

Member Data Documentation

◆ metadataRetrieve