ome::bioformats::tiff::IFD Class Reference

Image File Directory (IFD). More...

#include <ome/bioformats/tiff/IFD.h>

Inheritance diagram for ome::bioformats::tiff::IFD:

Collaboration diagram for ome::bioformats::tiff::IFD:

Classes
class	Impl
	Internal implementation details of OffsetIFD. More...

Public Member Functions
virtual	~IFD ()
	Destructor.
ome::compat::shared_ptr< TIFF > &	getTIFF () const
	Get the source TIFF this descriptor belongs to. More...
void	makeCurrent () const
	Make this IFD the current directory. More...
offset_type	getOffset () const
	Get the directory offset. More...
void	getRawField (tag_type tag,...) const
	Get a field by its tag number. More...
void	setRawField (tag_type tag,...)
	Set a field by its tag number. More...
template<typename TagCategory >
Field< TagCategory >	getField (TagCategory tag)
	Get a Field by its tag enumeration. More...
template<typename TagCategory >
const Field< TagCategory >	getField (TagCategory tag) const
	Get a Field by its tag enumeration. More...
TileType	getTileType () const
	Get the tile type. More...
void	setTileType (TileType type)
	Set the tile type. More...
dimension_size_type	getCurrentTile () const
	Get the current tile being written. More...
void	setCurrentTile (dimension_size_type tile)
	Set the current tile being written. More...
TileInfo	getTileInfo ()
	Get tiling metadata. More...
const TileInfo	getTileInfo () const
	Get tiling metadata. More...
std::vector< TileCoverage > &	getTileCoverage ()
	Get tile coverage cache. More...
const std::vector< TileCoverage > &	getTileCoverage () const
	Get tile coverage cache. More...
uint32_t	getImageWidth () const
	Get the image width. More...
void	setImageWidth (uint32_t width)
	Set the image width. More...
uint32_t	getImageHeight () const
	Get the image height. More...
void	setImageHeight (uint32_t height)
	Set the image height. More...
uint32_t	getTileWidth () const
	Get the tile width. More...
void	setTileWidth (uint32_t width)
	Set the tile width. More...
uint32_t	getTileHeight () const
	Get the tile height. More...
void	setTileHeight (uint32_t height)
	Set the tile height. More...
::ome::xml::model::enums::PixelType	getPixelType () const
	Get the OME data model PixelType. More...
void	setPixelType (::ome::xml::model::enums::PixelType type)
	Set the OME data model PixelType. More...
uint16_t	getSamplesPerPixel () const
	Get samples per pixel. More...
void	setSamplesPerPixel (uint16_t samples)
	Set samples per pixel. More...
PlanarConfiguration	getPlanarConfiguration () const
	Get planar configuration. More...
void	setPlanarConfiguration (PlanarConfiguration planarconfig)
	Set planar configuration. More...
PhotometricInterpretation	getPhotometricInterpretation () const
	Get photometric interpretation. More...
void	setPhotometricInterpretation (PhotometricInterpretation photometric)
	Set photometric interpretation. More...
void	readImage (VariantPixelBuffer &buf) const
	Read a whole image plane into a pixel buffer. More...
void	readImage (VariantPixelBuffer &dest, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h) const
	Read a region of an image plane into a pixel buffer. More...
void	readLookupTable (VariantPixelBuffer &buf) const
	Read a lookup table into a pixel buffer. More...
void	writeImage (const VariantPixelBuffer &buf)
	Write a whole image plane from a pixel buffer. More...
void	writeImage (const VariantPixelBuffer &source, dimension_size_type x, dimension_size_type y, dimension_size_type w, dimension_size_type h)
	Write a whole image plane from a pixel buffer. More...
ome::compat::shared_ptr< IFD >	next () const
	Get next directory. More...
bool	last () const
	Check if this is the last directory. More...

Static Public Member Functions
static ome::compat::shared_ptr< IFD >	openIndex (ome::compat::shared_ptr< TIFF > &tiff, directory_index_type index)
	Open an IFD by index. More...
static ome::compat::shared_ptr< IFD >	openOffset (ome::compat::shared_ptr< TIFF > &tiff, offset_type offset)
	Open an IFD. More...
static ome::compat::shared_ptr< IFD >	current (ome::compat::shared_ptr< TIFF > &tiff)
	Get the current IFD. More...

Protected Member Functions
	IFD (ome::compat::shared_ptr< TIFF > &tiff, offset_type offset)
	Constructor (not public).
	IFD (ome::compat::shared_ptr< TIFF > &tiff)
	Constructor (not public).

Private Member Functions
	IFD (const IFD &)
	Copy constructor (deleted).
IFD &	operator= (const IFD &)
	Assignment operator (deleted).

Private Attributes
ome::compat::shared_ptr< Impl >	impl
	Private implementation details.

Detailed Description

Image File Directory (IFD).

An IFD represents a subfile within a TIFF.

Member Function Documentation

ome::compat::shared_ptr< IFD > ome::bioformats::tiff::IFD::current ( ome::compat::shared_ptr< TIFF > &  tiff )

static

Get the current IFD.

Parameters

tiff	the source TIFF.

Returns

the open IFD.

Referenced by ome::bioformats::tiff::TIFF::getCurrentDirectory().

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dimension_size_type ome::bioformats::tiff::IFD::getCurrentTile

(

)

const

Get the current tile being written.

This is the tile currently being modified pending flush.

Returns

the current tile.

References impl.

template<typename TagCategory >

Field<TagCategory> ome::bioformats::tiff::IFD::getField ( TagCategory  tag )

inline

Get a Field by its tag enumeration.

Parameters

tag	the field identifier.

Returns

the Field corresponding to the tag.

Referenced by getImageHeight(), getImageWidth(), getPhotometricInterpretation(), getPixelType(), getPlanarConfiguration(), getSamplesPerPixel(), getTileHeight(), getTileType(), getTileWidth(), ome::bioformats::tiff::ImageJMetadata::ImageJMetadata(), ome::bioformats::tiff::makeCoreMetadata(), readImage(), readLookupTable(), setImageHeight(), setImageWidth(), setPhotometricInterpretation(), setPixelType(), setPlanarConfiguration(), setSamplesPerPixel(), setTileHeight(), setTileWidth(), and writeImage().

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template<typename TagCategory >

const Field<TagCategory> ome::bioformats::tiff::IFD::getField ( TagCategory  tag ) const

inline

Get a Field by its tag enumeration.

Parameters

tag	the field identifier.

Returns

the Field corresponding to the tag.

uint32_t ome::bioformats::tiff::IFD::getImageHeight

(

)

const

Get the image height.

Returns

the image height.

References getField(), ome::bioformats::tiff::IMAGELENGTH, and impl.

Referenced by ome::bioformats::tiff::makeCoreMetadata(), readImage(), and writeImage().

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uint32_t ome::bioformats::tiff::IFD::getImageWidth

(

)

const

Get the image width.

Returns

the image width.

References getField(), ome::bioformats::tiff::IMAGEWIDTH, and impl.

Referenced by getTileWidth(), ome::bioformats::tiff::makeCoreMetadata(), readImage(), and writeImage().

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offset_type ome::bioformats::tiff::IFD::getOffset

(

)

const

Get the directory offset.

Internally this is simply a call to TIFFCurrentDirOffset.

Returns

the directory offset.

References impl.

PhotometricInterpretation ome::bioformats::tiff::IFD::getPhotometricInterpretation

(

)

const

Get photometric interpretation.

Returns

the photometric interpretation of sample values.

References getField(), impl, and ome::bioformats::tiff::PHOTOMETRIC.

Referenced by ome::bioformats::tiff::makeCoreMetadata().

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ome::xml::model::enums::PixelType ome::bioformats::tiff::IFD::getPixelType

(

)

const

Get the OME data model PixelType.

This is computed based upon the SampleFormat and BitsPerSample tags for this IFD.

Returns

the PixelType.

Exceptions

an	Exception if there is no corresponding PixelType for the SampleFormat and BitsPerSample in use.

References ome::bioformats::tiff::BITSPERSAMPLE, ome::bioformats::tiff::COMPLEX_FLOAT, ome::bioformats::tiff::FLOAT, getField(), impl, ome::bioformats::tiff::SAMPLEFORMAT, ome::bioformats::tiff::SIGNED_INT, and ome::bioformats::tiff::UNSIGNED_INT.

Referenced by ome::bioformats::tiff::makeCoreMetadata(), readImage(), and writeImage().

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PlanarConfiguration ome::bioformats::tiff::IFD::getPlanarConfiguration

(

)

const

Get planar configuration.

Returns

the number of planar configuration.

References getField(), impl, and ome::bioformats::tiff::PLANARCONFIG.

void ome::bioformats::tiff::IFD::getRawField	(	tag_type	tag,
			...
	)		const

Get a field by its tag number.

Note

This should not be used except internally. Use getField(TagCategory) instead which offers a type-safe interface on top of this lower-level TIFFGetField wrapper.

Parameters

tag	the tag number.
...	pointers to variables to store the value(s) in.

References ome::bioformats::tiff::Sentry::error(), getTIFF(), and makeCurrent().

uint16_t ome::bioformats::tiff::IFD::getSamplesPerPixel

(

)

const

Get samples per pixel.

Returns

the number of samples per pixel.

References getField(), impl, and ome::bioformats::tiff::SAMPLESPERPIXEL.

Referenced by ome::bioformats::tiff::makeCoreMetadata().

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ome::compat::shared_ptr< TIFF > & ome::bioformats::tiff::IFD::getTIFF

(

)

const

Get the source TIFF this descriptor belongs to.

Returns

the source TIFF.

References impl.

Referenced by getRawField(), last(), makeCurrent(), next(), and setRawField().

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std::vector< TileCoverage > & ome::bioformats::tiff::IFD::getTileCoverage

(

)

Get tile coverage cache.

Returns

the TileCoverage cache for this IFD.

References impl.

const std::vector< TileCoverage > & ome::bioformats::tiff::IFD::getTileCoverage

(

)

const

Get tile coverage cache.

Returns

the TileCoverage cache for this IFD.

References impl.

uint32_t ome::bioformats::tiff::IFD::getTileHeight

(

)

const

Get the tile height.

Returns

the tile height.

References getField(), getTileType(), impl, ome::bioformats::tiff::ROWSPERSTRIP, ome::bioformats::tiff::TILE, and ome::bioformats::tiff::TILELENGTH.

TileInfo ome::bioformats::tiff::IFD::getTileInfo

(

)

Get tiling metadata.

Returns

the TileInfo metadata for this IFD.

Exceptions

an	Exception if tiles are not supported.

Referenced by readImage(), and writeImage().

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const TileInfo ome::bioformats::tiff::IFD::getTileInfo

(

)

const

Get tiling metadata.

Returns

the TileInfo metadata for this IFD.

Exceptions

an	Exception if tiles are not supported.

TileType ome::bioformats::tiff::IFD::getTileType

(

)

const

Get the tile type.

Returns

the tile type.

References getField(), impl, ome::bioformats::tiff::ROWSPERSTRIP, ome::bioformats::tiff::STRIP, ome::bioformats::tiff::TILE, ome::bioformats::tiff::TILELENGTH, and ome::bioformats::tiff::TILEWIDTH.

Referenced by getTileHeight(), getTileWidth(), setTileHeight(), and setTileWidth().

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uint32_t ome::bioformats::tiff::IFD::getTileWidth

(

)

const

Get the tile width.

Returns

the tile width.

References getField(), getImageWidth(), getTileType(), impl, ome::bioformats::tiff::TILE, and ome::bioformats::tiff::TILEWIDTH.

bool ome::bioformats::tiff::IFD::last

(

)

const

Check if this is the last directory.

Returns

true if last, false otherwise.

References getTIFF(), and makeCurrent().

void ome::bioformats::tiff::IFD::makeCurrent

(

)

const

Make this IFD the current directory.

Internally this is simply a call to TIFFSetDirectory.

References ome::bioformats::tiff::Sentry::error(), getTIFF(), and impl.

Referenced by getRawField(), last(), next(), and setRawField().

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ome::compat::shared_ptr< IFD > ome::bioformats::tiff::IFD::next

(

)

const

Get next directory.

Returns

the next directory, or null if this is the last directory.

References getTIFF(), makeCurrent(), and openOffset().

ome::compat::shared_ptr< IFD > ome::bioformats::tiff::IFD::openIndex ( ome::compat::shared_ptr< TIFF > &  tiff, directory_index_type  index  )

static

Open an IFD by index.

Parameters

tiff	the source TIFF.
index	the directory index.

Returns

the open IFD.

References ome::bioformats::tiff::Sentry::error(), and openOffset().

Referenced by ome::bioformats::tiff::TIFF::getDirectoryByIndex().

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ome::compat::shared_ptr< IFD > ome::bioformats::tiff::IFD::openOffset ( ome::compat::shared_ptr< TIFF > &  tiff, offset_type  offset  )

static

Open an IFD.

Parameters

tiff	the source TIFF.
offset	the directory offset.

Returns

the open IFD.

Referenced by ome::bioformats::tiff::TIFF::getDirectoryByOffset(), next(), and openIndex().

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void ome::bioformats::tiff::IFD::readImage

(

VariantPixelBuffer &

buf

)

const

Read a whole image plane into a pixel buffer.

Parameters

buf	the destination pixel buffer.

References getImageHeight(), and getImageWidth().

void ome::bioformats::tiff::IFD::readImage	(	VariantPixelBuffer &	dest,
		dimension_size_type	x,
		dimension_size_type	y,
		dimension_size_type	w,
		dimension_size_type	h
	)		const

Read a region of an image plane into a pixel buffer.

If the destination pixel buffer is of a different size to the region being read, or is of the incorrect pixel type, or has a different storage order, it will be resized using the correct pixel type and storage order.

Parameters

dest	the destination 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.

References ome::bioformats::DIM_CHANNEL, ome::bioformats::DIM_MODULO_C, ome::bioformats::DIM_MODULO_T, ome::bioformats::DIM_MODULO_Z, ome::bioformats::DIM_SPATIAL_X, ome::bioformats::DIM_SPATIAL_Y, ome::bioformats::DIM_SPATIAL_Z, ome::bioformats::DIM_SUBCHANNEL, ome::bioformats::DIM_TEMPORAL_T, ome::bioformats::PixelBufferBase::dimensions, getField(), getPixelType(), getTileInfo(), ome::bioformats::PixelBufferBase::make_storage_order(), ome::bioformats::VariantPixelBuffer::pixelType(), ome::bioformats::tiff::PLANARCONFIG, ome::bioformats::tiff::SAMPLESPERPIXEL, ome::bioformats::tiff::SEPARATE, ome::bioformats::VariantPixelBuffer::setBuffer(), ome::bioformats::VariantPixelBuffer::shape(), ome::bioformats::VariantPixelBuffer::storage_order(), ome::bioformats::tiff::TileInfo::tileCoverage(), ome::bioformats::VariantPixelBuffer::vbuffer(), and ome::xml::model::enums::DimensionOrder::XYZTC.

void ome::bioformats::tiff::IFD::readLookupTable

(

VariantPixelBuffer &

buf

)

const

Read a lookup table into a pixel buffer.

Parameters

buf	the destination pixel buffer.

References ome::bioformats::tiff::COLORMAP, ome::bioformats::DIM_CHANNEL, ome::bioformats::DIM_MODULO_C, ome::bioformats::DIM_MODULO_T, ome::bioformats::DIM_MODULO_Z, ome::bioformats::DIM_SPATIAL_X, ome::bioformats::DIM_SPATIAL_Y, ome::bioformats::DIM_SPATIAL_Z, ome::bioformats::DIM_SUBCHANNEL, ome::bioformats::DIM_TEMPORAL_T, getField(), ome::bioformats::PixelBufferBase::make_storage_order(), ome::bioformats::VariantPixelBuffer::setBuffer(), ome::bioformats::VariantPixelBuffer::vbuffer(), and ome::xml::model::enums::DimensionOrder::XYZTC.

void ome::bioformats::tiff::IFD::setCurrentTile

(

dimension_size_type

tile

)

Set the current tile being written.

This is the tile currently being modified pending flush.

Note

This should not be set by hand; it will be updated by the code writing out tile data called internally by writeImage().

Parameters

tile	the current tile.

References impl.

void ome::bioformats::tiff::IFD::setImageHeight

(

uint32_t

height

)

Set the image height.

Parameters

height

the image height.

References getField(), ome::bioformats::tiff::IMAGELENGTH, and impl.

void ome::bioformats::tiff::IFD::setImageWidth

(

uint32_t

width

)

Set the image width.

Parameters

width

the image width.

References getField(), ome::bioformats::tiff::IMAGEWIDTH, and impl.

void ome::bioformats::tiff::IFD::setPhotometricInterpretation

(

PhotometricInterpretation

photometric

)

Set photometric interpretation.

Parameters

photometric

the photometric interpretation of sample values.

References getField(), impl, and ome::bioformats::tiff::PHOTOMETRIC.

void ome::bioformats::tiff::IFD::setPixelType

(

::ome::xml::model::enums::PixelType

type

)

Set the OME data model PixelType.

This sets the SampleFormat and BitsPerSample tags for this IFD which correspond to the PixelType in use.

Parameters

type	the PixelType to set.

Exceptions

an	Exception if the PixelType is invalid.

References ome::bioformats::tiff::BITSPERSAMPLE, ome::bioformats::tiff::COMPLEX_FLOAT, ome::bioformats::tiff::FLOAT, getField(), impl, ome::bioformats::tiff::SAMPLEFORMAT, ome::bioformats::tiff::SIGNED_INT, and ome::bioformats::tiff::UNSIGNED_INT.

void ome::bioformats::tiff::IFD::setPlanarConfiguration

(

PlanarConfiguration

planarconfig

)

Set planar configuration.

Parameters

planarconfig

the number of planar configuration.

References getField(), impl, and ome::bioformats::tiff::PLANARCONFIG.

void ome::bioformats::tiff::IFD::setRawField	(	tag_type	tag,
			...
	)

Set a field by its tag number.

Note

This should not be used except internally. Use getField(TagCategory) instead which offers a type-safe interface on top of this lower-level TIFFSetField wrapper.

Parameters

tag	the tag number.
...	variables containing the value(s) to set.

References ome::bioformats::tiff::Sentry::error(), getTIFF(), and makeCurrent().

void ome::bioformats::tiff::IFD::setSamplesPerPixel

(

uint16_t

samples

)

Set samples per pixel.

Parameters

samples

the number of samples per pixel.

References getField(), impl, and ome::bioformats::tiff::SAMPLESPERPIXEL.

void ome::bioformats::tiff::IFD::setTileHeight

(

uint32_t

height

)

Set the tile height.

Parameters

height

the tile height.

References getField(), getTileType(), impl, ome::bioformats::tiff::ROWSPERSTRIP, ome::bioformats::tiff::TILE, and ome::bioformats::tiff::TILELENGTH.

void ome::bioformats::tiff::IFD::setTileType

(

TileType

type

)

Set the tile type.

Parameters

type	the tile type.

References impl.

void ome::bioformats::tiff::IFD::setTileWidth

(

uint32_t

width

)

Set the tile width.

Parameters

width

the tile width.

References getField(), getTileType(), impl, ome::bioformats::tiff::TILE, and ome::bioformats::tiff::TILEWIDTH.

void ome::bioformats::tiff::IFD::writeImage

(

const VariantPixelBuffer &

buf

)

Write a whole image plane from a pixel buffer.

Parameters

buf	the source pixel buffer.

References getImageHeight(), and getImageWidth().

void ome::bioformats::tiff::IFD::writeImage	(	const VariantPixelBuffer &	source,
		dimension_size_type	x,
		dimension_size_type	y,
		dimension_size_type	w,
		dimension_size_type	h
	)

Write a whole image plane from a pixel buffer.

The source pixel buffer must match the size of the region being written, and must also the same pixel type and storage ordering as the TIFF image.

Parameters

source	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.

References ome::bioformats::DIM_CHANNEL, ome::bioformats::DIM_MODULO_C, ome::bioformats::DIM_MODULO_T, ome::bioformats::DIM_MODULO_Z, ome::bioformats::DIM_SPATIAL_X, ome::bioformats::DIM_SPATIAL_Y, ome::bioformats::DIM_SPATIAL_Z, ome::bioformats::DIM_SUBCHANNEL, ome::bioformats::DIM_TEMPORAL_T, ome::bioformats::PixelBufferBase::dimensions, getField(), getPixelType(), getTileInfo(), impl, ome::bioformats::PixelBufferBase::make_storage_order(), ome::bioformats::VariantPixelBuffer::pixelType(), ome::bioformats::tiff::PLANARCONFIG, ome::bioformats::tiff::SAMPLESPERPIXEL, ome::bioformats::tiff::SEPARATE, ome::bioformats::VariantPixelBuffer::shape(), ome::bioformats::VariantPixelBuffer::storage_order(), ome::bioformats::tiff::TileInfo::tileCoverage(), ome::bioformats::VariantPixelBuffer::vbuffer(), and ome::xml::model::enums::DimensionOrder::XYZTC.

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

• ome/bioformats/tiff/IFD.h
• ome/bioformats/tiff/IFD.cpp