Buffer for all pixel types. More...

#include <ome/bioformats/VariantPixelBuffer.h>

Classes
struct	make_buffer
	Convert T into a buffer. More...

Public Types
typedef boost::make_variant_over< pixel_buffer_types >::type	variant_buffer_type
	Buffer type, allowing assignment of all buffer types.

typedef PixelProperties< ::ome::xml::model::enums::PixelType::UINT8 >::std_type	raw_type
	Raw pixel type used in public interfaces.

typedef boost::multi_array_types::size_type	size_type
	Size type.

typedef ome::compat::array< boost::multi_array_types::index, PixelBufferBase::dimensions >	indices_type
	Type used to index all dimensions in public interfaces.

typedef PixelBufferBase::storage_order_type	storage_order_type
	Storage ordering type for controlling pixel memory layout.

typedef PixelBufferBase::range_type	range_type
	Extent range type.

Public Member Functions
	VariantPixelBuffer ()
	Default constructor. More...

template<class ExtentList >
	VariantPixelBuffer (const ExtentList &extents,::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, const storage_order_type &storage=PixelBufferBase::default_storage_order())
	Construct from extents (internal storage). More...

	VariantPixelBuffer (const range_type &range,::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, const storage_order_type &storage=PixelBufferBase::default_storage_order())
	Construct from ranges (internal storage). More...

	VariantPixelBuffer (const VariantPixelBuffer &buffer)
	Copy constructor. More...

template<typename T >
	VariantPixelBuffer (ome::compat::shared_ptr< PixelBuffer< T > > &buffer)
	Construct from existing pixel buffer. More...

virtual	~VariantPixelBuffer ()
	Destructor.

variant_buffer_type &	vbuffer ()
	Get a reference to the variant buffer. More...

const variant_buffer_type &	vbuffer () const
	Get a reference to the variant buffer. More...

template<class ExtentList >
void	setBuffer (const ExtentList &extents,::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, const storage_order_type &storage=PixelBufferBase::default_storage_order())
	Set the buffer from extents (helper). More...

void	setBuffer (const range_type &range,::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, const storage_order_type &storage=PixelBufferBase::default_storage_order())
	Set the buffer from ranges (internal storage). More...

bool	managed () const
	Check if the buffer is internally managed. More...

size_type	num_elements () const
	Get the number of pixel elements in the multi-dimensional array.

size_type	num_dimensions () const
	Get the number of dimensions in the multi-dimensional array.

const size_type *	shape () const
	Get the shape of the multi-dimensional array. More...

const boost::multi_array_types::index *	strides () const
	Get the strides of the multi-dimensional array. More...

const boost::multi_array_types::index *	index_bases () const
	Get the index bases of the multi-dimensional array. More...

template<typename T >
const T *	origin () const
	Get the origin of the array. More...

const storage_order_type &	storage_order () const
	Get the array storage order. More...

::ome::xml::model::enums::PixelType	pixelType () const
	Get the type of pixels stored in the buffer.

EndianType	endianType () const
	Get the endianness of the pixel type stored in the buffer.

template<typename T >
PixelBuffer< T >::array_ref_type &	array ()
	Get the pixel data. More...

template<typename T >
const PixelBuffer< T >::array_ref_type &	array () const
	Get the pixel data. More...

raw_type *	data ()
	Get raw buffered data. More...

const raw_type *	data () const
	Get raw buffered data. More...

template<typename T >
T *	data ()
	Get raw buffered data. More...

template<typename T >
const T *	data () const
	Get raw buffered data. More...

bool	valid () const
	Check the buffer validity. More...

VariantPixelBuffer &	operator= (const VariantPixelBuffer &rhs)
	Assign a pixel buffer. More...

bool	operator== (const VariantPixelBuffer &rhs) const
	Compare a pixel buffer for equality. More...

bool	operator!= (const VariantPixelBuffer &rhs) const
	Compare a pixel buffer for inequality. More...

template<typename InputIterator >
void	assign (InputIterator begin, InputIterator end)
	Assign pixel values. More...

template<class charT , class traits >
void	read (std::basic_istream< charT, traits > &stream)
	Read raw pixel data from a stream in physical storage order. More...

template<class charT , class traits >
void	write (std::basic_ostream< charT, traits > &stream) const
	Write raw pixel data to a stream in physical storage order. More...

template<typename T >
PixelBuffer< T >::array_ref_type &	array ()
	Get the pixel data. More...

template<typename T >
const PixelBuffer< T >::array_ref_type &	array () const
	Get the pixel data. More...

Static Protected Member Functions
template<class T , class ExtentList >
static variant_buffer_type	makeBuffer (const ExtentList &extents, const storage_order_type &storage,::ome::xml::model::enums::PixelType pixeltype)
	Create buffer from extents (helper). More...

template<class T >
static variant_buffer_type	makeBuffer (const range_type &range, const storage_order_type &storage,::ome::xml::model::enums::PixelType pixeltype)
	Create buffer from ranges (helper). More...

template<class ExtentList >
static variant_buffer_type	createBuffer (const ExtentList &extents,::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, const storage_order_type &storage=PixelBufferBase::default_storage_order())
	Create buffer from extents (internal storage). More...

static variant_buffer_type	createBuffer (const range_type &range,::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, const storage_order_type &storage=PixelBufferBase::default_storage_order())
	Create buffer from ranges (helper). More...

Protected Attributes
variant_buffer_type	buffer
	Pixel storage.

Private Types
typedef boost::mpl::vector< PixelProperties< ::ome::xml::model::enums::PixelType::INT8 >, PixelProperties< ::ome::xml::model::enums::PixelType::INT16 >, PixelProperties< ::ome::xml::model::enums::PixelType::INT32 >, PixelProperties< ::ome::xml::model::enums::PixelType::UINT8 >, PixelProperties< ::ome::xml::model::enums::PixelType::UINT16 >, PixelProperties< ::ome::xml::model::enums::PixelType::UINT32 >, PixelProperties< ::ome::xml::model::enums::PixelType::BIT > >	integer_pixel_types
	Integer pixel types.

typedef boost::mpl::vector< PixelProperties< ::ome::xml::model::enums::PixelType::FLOAT >, PixelProperties< ::ome::xml::model::enums::PixelType::DOUBLE >, PixelProperties< ::ome::xml::model::enums::PixelType::COMPLEX >, PixelProperties< ::ome::xml::model::enums::PixelType::DOUBLECOMPLEX > >	float_pixel_types
	Floating-point pixel types.

typedef boost::mpl::joint_view< integer_pixel_types, float_pixel_types >::type	basic_pixel_types_view
	Aggregate view of all numeric types.

typedef boost::mpl::transform_view< basic_pixel_types_view, make_buffer< boost::mpl::_1 > >::type	pixel_buffer_types_view
	Aggregate view of all buffer types.

typedef boost::mpl::vector	empty_types
	Empty vector placeholder.

typedef boost::mpl::insert_range< empty_types, boost::mpl::end< empty_types >::type, pixel_buffer_types_view >::type	pixel_buffer_types
	List of all pixel buffer types.

Detailed Description

Buffer for all pixel types.

The purpose of this class is to allow transfer of pixel data of any type and of any dimensionality.

This class uses Boost.Variant to support specializations of PixelBuffer for all combinations of pixel type (excluding endian variants).

For high performance access to the pixel data, use of a boost::static_visitor is recommended. This has the benefit of generalising the algorithm to operate on all PixelBuffer types, as well as allowing special casing for particular types (e.g. integer vs. float, signed vs. unsigned, simple vs. complex, or any other distinction which affects the algorithm). This will also allow subsetting of the data if required, again for all pixel types with special casing being possible.

Todo:: Add support for subsetting dimensions.

Constructor & Destructor Documentation

ome::bioformats::VariantPixelBuffer::VariantPixelBuffer ( )

inlineexplicit

Default constructor.

This constructs a pixel buffer of unspecified type, of size 1 in all dimensions. The desired type and size should be set after construction.

template<class ExtentList >

ome::bioformats::VariantPixelBuffer::VariantPixelBuffer	(	const ExtentList &	extents,
		::ome::xml::model::enums::PixelType	pixeltype = `::ome::xml::model::enums::PixelType::UINT8`,
		const storage_order_type &	storage = `PixelBufferBase::default_storage_order()`
	)

inlineexplicit

Construct from extents (internal storage).

Storage for the buffer will be allocated internally.

Parameters

extents	the extent of each dimension.
storage	the storage ordering, defaulting to C array storage ordering.
pixeltype	the pixel type to store.

ome::bioformats::VariantPixelBuffer::VariantPixelBuffer	(	const range_type &	range,
		::ome::xml::model::enums::PixelType	pixeltype = `::ome::xml::model::enums::PixelType::UINT8`,
		const storage_order_type &	storage = `PixelBufferBase::default_storage_order()`
	)

inlineexplicit

Construct from ranges (internal storage).

Storage for the buffer will be allocated internally.

Parameters

range	the range of each dimension.
storage	the storage ordering, defaulting to C array storage ordering.
pixeltype	the pixel type to store.

ome::bioformats::VariantPixelBuffer::VariantPixelBuffer ( const VariantPixelBuffer & buffer )

explicit

Copy constructor.

Note that due to the use of shared pointers this only performs a shallow copy.

Parameters

buffer the buffer to copy.

References buffer.

template<typename T >

ome::bioformats::VariantPixelBuffer::VariantPixelBuffer ( ome::compat::shared_ptr< PixelBuffer< T > > & buffer )

inlineexplicit

Construct from existing pixel buffer.

Use for referencing external data.

Parameters

buffer the buffer to contain.

Member Function Documentation

template<typename T >

PixelBuffer<T>::array_ref_type& ome::bioformats::VariantPixelBuffer::array ( )

Get the pixel data.

Returns: the multidimensional pixel data array; this value will never be null.

Exceptions

if	the contained PixelBuffer is not of the specified type.

template<typename T >

const PixelBuffer<T>::array_ref_type& ome::bioformats::VariantPixelBuffer::array ( ) const

Get the pixel data.

Returns: the multidimensional pixel data array; this value will never be null.

Exceptions

if	the contained PixelBuffer is not of the specified type.

template<typename T >

PixelBuffer<T>::array_ref_type& ome::bioformats::VariantPixelBuffer::array ( )

inline

Get the pixel data.

Returns: the multidimensional pixel data array; this value will never be null.

Exceptions

if	the contained PixelBuffer is not of the specified type.

References buffer.

template<typename T >

const PixelBuffer<T>::array_ref_type& ome::bioformats::VariantPixelBuffer::array ( ) const

inline

Get the pixel data.

Returns: the multidimensional pixel data array; this value will never be null.

Exceptions

if	the contained PixelBuffer is not of the specified type.

References buffer.

template<typename InputIterator >

void ome::bioformats::VariantPixelBuffer::assign	(	InputIterator	begin,
		InputIterator	end
	)

inline

Assign pixel values.

Assign all pixel values from an input iterator.

Note that the range to assign must be equal to num_elements().

Parameters

begin	the start of the range to assign.
end	the end of the range to assign.
begin	the start of input.
end	the end of input.

Exceptions

if	the PixelBuffer is null or the PixelBuffer's data array is null.

References buffer.

template<class ExtentList >

static variant_buffer_type ome::bioformats::VariantPixelBuffer::createBuffer	(	const ExtentList &	extents,
		::ome::xml::model::enums::PixelType	pixeltype = `::ome::xml::model::enums::PixelType::UINT8`,
		const storage_order_type &	storage = `PixelBufferBase::default_storage_order()`
	)

inlinestaticprotected

Create buffer from extents (internal storage).

Storage for the buffer will be allocated internally.

Parameters

extents	the extent of each dimension.
pixeltype	the pixel type to store.
storage	the storage ordering, defaulting to C array storage ordering.

Returns: the new buffer contained in a variant.

Referenced by setBuffer().

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static variant_buffer_type ome::bioformats::VariantPixelBuffer::createBuffer	(	const range_type &	range,
		::ome::xml::model::enums::PixelType	pixeltype = `::ome::xml::model::enums::PixelType::UINT8`,
		const storage_order_type &	storage = `PixelBufferBase::default_storage_order()`
	)

inlinestaticprotected

Create buffer from ranges (helper).

Storage for the buffer will be allocated internally.

Parameters

range	the range of each dimension.
pixeltype	the pixel type to store.
storage	the storage ordering, defaulting to C array storage ordering.

Returns: the new buffer contained in a variant.

VariantPixelBuffer::raw_type * ome::bioformats::VariantPixelBuffer::data ( )

Get raw buffered data.

Returns: a pointer to the buffer start address.

References buffer.

const VariantPixelBuffer::raw_type * ome::bioformats::VariantPixelBuffer::data ( ) const

Get raw buffered data.

Returns: a pointer to the buffer start address.

References buffer.

template<typename T >

T * ome::bioformats::VariantPixelBuffer::data ( )

inline

Get raw buffered data.

Returns: a pointer to the buffer start address.

Exceptions

if	the contained PixelBuffer is not of the specified type.

References buffer.

template<typename T >

const T * ome::bioformats::VariantPixelBuffer::data ( ) const

inline

Get raw buffered data.

Returns: a pointer to the buffer start address.

Exceptions

if	the contained PixelBuffer is not of the specified type.

References buffer.

const boost::multi_array_types::index * ome::bioformats::VariantPixelBuffer::index_bases ( ) const

Get the index bases of the multi-dimensional array.

The index bases are the numeric index of the first element for each array dimension of the multi-dimensional array.

Returns: an array of index bases (size is the dimension size).

References buffer.

template<class T , class ExtentList >

static variant_buffer_type ome::bioformats::VariantPixelBuffer::makeBuffer	(	const ExtentList &	extents,
		const storage_order_type &	storage,
		::ome::xml::model::enums::PixelType	pixeltype
	)

inlinestaticprotected

Create buffer from extents (helper).

Storage for the buffer will be allocated internally.

Parameters

extents	the extent of each dimension.
storage	the storage ordering, defaulting to C array storage ordering.
pixeltype	the pixel type to store.

Returns: the new buffer contained in a variant.

References ome::bioformats::ENDIAN_NATIVE.

template<class T >

static variant_buffer_type ome::bioformats::VariantPixelBuffer::makeBuffer	(	const range_type &	range,
		const storage_order_type &	storage,
		::ome::xml::model::enums::PixelType	pixeltype
	)

inlinestaticprotected

Create buffer from ranges (helper).

Storage for the buffer will be allocated internally.

Parameters

range	the range of each dimension.
storage	the storage ordering, defaulting to C array storage ordering.
pixeltype	the pixel type to store.

Returns: the new buffer contained in a variant.

References ome::bioformats::ENDIAN_NATIVE.

bool ome::bioformats::VariantPixelBuffer::managed ( ) const

Check if the buffer is internally managed.

Returns: true if the MultiArray data is managed internally (i.e. is a multi_array) or false if not managed (i.e. is a multi_array_ref).

References buffer.

bool ome::bioformats::VariantPixelBuffer::operator!= ( const VariantPixelBuffer & rhs ) const

Compare a pixel buffer for inequality.

Parameters

rhs	the pixel buffer to compare with.

Returns: true if not equal, false if equal.

VariantPixelBuffer & ome::bioformats::VariantPixelBuffer::operator= ( const VariantPixelBuffer & rhs )

Assign a pixel buffer.

The dimension extents must be compatible, but the storage ordering does not. The buffer contents will be assigned in the logical order rather than the storage order.

Parameters

rhs	the pixel buffer to assign.

Returns: the assigned buffer.

References buffer.

bool ome::bioformats::VariantPixelBuffer::operator== ( const VariantPixelBuffer & rhs ) const

Compare a pixel buffer for equality.

Parameters

rhs	the pixel buffer to compare with.

Returns: true if equal, false if not equal.

References buffer.

template<typename T >

const T * ome::bioformats::VariantPixelBuffer::origin ( ) const

inline

Get the origin of the array.

This is the address of the element at [0][0][0][0][0][0][0][0][0]. Note that this is not always the buffer start address, depending upon the dimension ordering.

Returns: the address of the array origin.

References buffer.

template<class charT , class traits >

void ome::bioformats::VariantPixelBuffer::read ( std::basic_istream< charT, traits > & stream )

inline

Read raw pixel data from a stream in physical storage order.

Note that the pixels will be read in the physical storage order. This will typically be a contiguous read, but this is not guaranteed. The current implementation iterates over each pixel and so may be slower than strictly necessary.

Parameters

stream the stream to read from.

References buffer.

template<class ExtentList >

void ome::bioformats::VariantPixelBuffer::setBuffer	(	const ExtentList &	extents,
		::ome::xml::model::enums::PixelType	pixeltype = `::ome::xml::model::enums::PixelType::UINT8`,
		const storage_order_type &	storage = `PixelBufferBase::default_storage_order()`
	)

inline

Set the buffer from extents (helper).

Storage for the buffer will be allocated internally.

Parameters

extents	the extent of each dimension.
pixeltype	the pixel type to store.
storage	the storage ordering, defaulting to C array storage ordering.

References buffer, and createBuffer().

Referenced by ome::bioformats::detail::CopySubchannelVisitor::operator()(), ome::bioformats::tiff::IFD::readImage(), ome::bioformats::tiff::IFD::readLookupTable(), and ome::bioformats::detail::FormatReader::readPlane().

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void ome::bioformats::VariantPixelBuffer::setBuffer	(	const range_type &	range,
		::ome::xml::model::enums::PixelType	pixeltype = `::ome::xml::model::enums::PixelType::UINT8`,
		const storage_order_type &	storage = `PixelBufferBase::default_storage_order()`
	)

inline

Set the buffer from ranges (internal storage).

Storage for the buffer will be allocated internally.

Parameters

range	the range of each dimension.
pixeltype	the pixel type to store.
storage	the storage ordering, defaulting to C array storage ordering.

References buffer, and createBuffer().

const boost::multi_array_types::size_type * ome::bioformats::VariantPixelBuffer::shape ( ) const

Get the shape of the multi-dimensional array.

The shape is the extent of each array dimension.

Returns: an array of extents (size is the dimension size).

References buffer.

Referenced by ome::bioformats::tiff::IFD::readImage(), ome::bioformats::detail::FormatReader::readPlane(), and ome::bioformats::tiff::IFD::writeImage().

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const VariantPixelBuffer::storage_order_type & ome::bioformats::VariantPixelBuffer::storage_order ( ) const

Get the array storage order.

Returns: the storage order.

References buffer.

Referenced by ome::bioformats::tiff::IFD::readImage(), ome::bioformats::detail::FormatReader::readPlane(), and ome::bioformats::tiff::IFD::writeImage().

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const boost::multi_array_types::index * ome::bioformats::VariantPixelBuffer::strides ( ) const

Get the strides of the multi-dimensional array.

The strides are the stride associated with each array dimension.

Returns: an array of strides (size is the dimension size).

References buffer.

bool ome::bioformats::VariantPixelBuffer::valid ( ) const

Check the buffer validity.

This tests if the MultiArray is not null, and hence safe to use. Note that this is not a guarantee of safety in the case of using an externally managed data buffer, in which case the external buffer must still be valid in addition.

Returns: true if not null, false if null.

References buffer.

variant_buffer_type& ome::bioformats::VariantPixelBuffer::vbuffer ( )

inline

Get a reference to the variant buffer.

Returns: a reference to the buffer.

References buffer.

Referenced by ome::bioformats::in::MinimalTIFFReader::openBytesImpl(), ome::bioformats::in::OMETIFFReader::openBytesImpl(), ome::bioformats::detail::CopySubchannelVisitor::operator()(), ome::bioformats::tiff::IFD::readImage(), ome::bioformats::tiff::IFD::readLookupTable(), ome::bioformats::detail::FormatReader::readPlane(), ome::qtwidgets::gl::Image2D::setPlane(), and ome::bioformats::tiff::IFD::writeImage().

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const variant_buffer_type& ome::bioformats::VariantPixelBuffer::vbuffer ( ) const

inline

Get a reference to the variant buffer.

Returns: a reference to the buffer.

References buffer.

template<class charT , class traits >

void ome::bioformats::VariantPixelBuffer::write ( std::basic_ostream< charT, traits > & stream ) const

inline

Write raw pixel data to a stream in physical storage order.

Note that the pixels will be written in the physical storage order. This will typically be a contiguous read, but this is not guaranteed. The current implementation iterates over each pixel and so may be slower than strictly necessary.

Parameters

stream the stream to write to.

References buffer.

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

ome/bioformats/VariantPixelBuffer.h
ome/bioformats/VariantPixelBuffer.cpp

Classes

Public Types

Public Member Functions

Static Protected Member Functions

Protected Attributes

Private Types

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation