#include <itkStreamingImageIOBase.h>

Inheritance diagram for itk::StreamingImageIOBase:

Collaboration diagram for itk::StreamingImageIOBase:

Public Types
using	Pointer = SmartPointer< Self >

using	Self = StreamingImageIOBase

using	Superclass = ImageIOBase

Public Types inherited from itk::ImageIOBase
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = ImageIOBase

using	Superclass = LightProcessObject

using	IndexValueType = ::itk::IndexValueType

using	SizeValueType = ::itk::SizeValueType

using	IOComponentEnum = itk::IOComponentEnum

using	IOFileEnum = itk::IOFileEnum

using	IOByteOrderEnum = itk::IOByteOrderEnum

using	SizeType = ::itk::intmax_t

using	BufferSizeType = ::itk::OffsetValueType

using	ArrayOfExtensionsType = std::vector< std::string >

Public Types inherited from itk::LightProcessObject
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = LightProcessObject

using	Superclass = Object

Public Types inherited from itk::Object
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

Public Types inherited from itk::LightObject
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = LightObject

Public Member Functions
bool	CanStreamRead () override

bool	CanStreamWrite () override

ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requestedRegion) const override

unsigned int	GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) override

virtual const char *	GetNameOfClass () const

Public Member Functions inherited from itk::ImageIOBase
virtual void	SetFileName (const char *_arg)

virtual const char *	GetFileName () const

void	SetNumberOfDimensions (unsigned int)

virtual unsigned int	GetNumberOfDimensions () const

virtual void	SetDimensions (unsigned int i, SizeValueType dim)

virtual SizeValueType	GetDimensions (unsigned int i) const

virtual void	SetOrigin (unsigned int i, double origin)

virtual double	GetOrigin (unsigned int i) const

virtual void	SetSpacing (unsigned int i, double spacing)

virtual double	GetSpacing (unsigned int i) const

virtual void	SetDirection (unsigned int i, const std::vector< double > &direction)

virtual void	SetDirection (unsigned int i, const vnl_vector< double > &direction)

virtual std::vector< double >	GetDirection (unsigned int i) const

virtual std::vector< double >	GetDefaultDirection (unsigned int k) const

virtual void	SetIORegion (ImageIORegion _arg)

virtual const ImageIORegion &	GetIORegion () const

virtual void	SetPixelType (const ::itk::CommonEnums::IOPixel _arg)

virtual ::itk::CommonEnums::IOPixel	GetPixelType () const

virtual void	SetComponentType (const IOComponentEnum _arg)

virtual IOComponentEnum	GetComponentType () const

virtual const std::type_info &	GetComponentTypeInfo () const

virtual void	SetNumberOfComponents (unsigned int _arg)

virtual const unsigned int &	GetNumberOfComponents () const

virtual void	SetUseCompression (bool _arg)

virtual bool	GetUseCompression () const

virtual void	UseCompressionOn ()

virtual void	UseCompressionOff ()

virtual void	SetCompressionLevel (int _arg)

virtual int	GetCompressionLevel () const

virtual void	SetCompressor (std::string _c)

virtual const std::string &	GetCompressor () const

virtual void	SetUseStreamedReading (bool _arg)

virtual bool	GetUseStreamedReading () const

virtual void	UseStreamedReadingOn ()

virtual void	UseStreamedReadingOff ()

virtual void	SetUseStreamedWriting (bool _arg)

virtual bool	GetUseStreamedWriting () const

virtual void	UseStreamedWritingOn ()

virtual void	UseStreamedWritingOff ()

virtual void	SetExpandRGBPalette (bool _arg)

virtual bool	GetExpandRGBPalette () const

virtual void	ExpandRGBPaletteOn ()

virtual void	ExpandRGBPaletteOff ()

virtual void	SetWritePalette (bool _arg)

virtual bool	GetWritePalette () const

virtual void	WritePaletteOn ()

virtual void	WritePaletteOff ()

virtual bool	GetIsReadAsScalarPlusPalette () const

virtual void	SetFileType (const IOFileEnum _arg)

virtual IOFileEnum	GetFileType () const

void	SetFileTypeToASCII ()

void	SetFileTypeToBinary ()

virtual void	SetByteOrder (const IOByteOrderEnum _arg)

virtual IOByteOrderEnum	GetByteOrder () const

void	SetByteOrderToBigEndian ()

void	SetByteOrderToLittleEndian ()

std::string	GetFileTypeAsString (IOFileEnum) const

std::string	GetByteOrderAsString (IOByteOrderEnum) const

virtual SizeType	GetPixelStride () const

SizeType	GetImageSizeInPixels () const

SizeType	GetImageSizeInBytes () const

SizeType	GetImageSizeInComponents () const

virtual unsigned int	GetComponentSize () const

virtual bool	CanReadFile (const char *)=0

virtual void	ReadImageInformation ()=0

virtual void	Read (void *buffer)=0

virtual bool	CanWriteFile (const char *)=0

virtual void	WriteImageInformation ()=0

virtual void	Write (const void *buffer)=0

virtual bool	SupportsDimension (unsigned long dim)

virtual ImageIORegion	GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)

const ArrayOfExtensionsType &	GetSupportedReadExtensions () const

const ArrayOfExtensionsType &	GetSupportedWriteExtensions () const

template<typename TPixel >
void	SetTypeInfo (const TPixel *)

template<typename TPixel >
void	SetPixelTypeInfo (const TPixel *)

template<typename TPixel >
void	SetPixelTypeInfo (const RGBPixel< TPixel > *)

template<typename TPixel >
void	SetPixelTypeInfo (const RGBAPixel< TPixel > *)

template<unsigned VLength>
void	SetPixelTypeInfo (const Offset< VLength > *)

template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const Vector< TPixel, VLength > *)

template<typename TCoordRep , unsigned NPointDimension>
void	SetPixelTypeInfo (const Point< TCoordRep, NPointDimension > *)

template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const CovariantVector< TPixel, VLength > *)

template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const SymmetricSecondRankTensor< TPixel, VLength > *)

template<typename TPixel >
void	SetPixelTypeInfo (const DiffusionTensor3D< TPixel > *)

template<typename TPixel >
void	SetPixelTypeInfo (const std::complex< TPixel > *)

template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const FixedArray< TPixel, VLength > *)

template<typename TPixel >
void	SetPixelTypeInfo (const VariableLengthVector< TPixel > *)

template<typename TValue >
void	SetPixelTypeInfo (const Array< TValue > *)

template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const Matrix< TPixel, VLength, VLength > *)

template<typename TValue >
void	SetPixelTypeInfo (const VariableSizeMatrix< TValue > *)

Public Member Functions inherited from itk::LightProcessObject
virtual void	AbortGenerateDataOff ()

virtual void	AbortGenerateDataOn ()

virtual ::itk::LightObject::Pointer	CreateAnother () const

virtual const bool &	GetAbortGenerateData () const

virtual void	SetAbortGenerateData (bool _arg)

virtual void	SetProgress (float _arg)

virtual const float &	GetProgress () const

void	UpdateProgress (float amount)

virtual void	UpdateOutputData ()

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)

unsigned long	AddObserver (const EventObject &event, Command *) const

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

virtual void	DebugOff () const

virtual void	DebugOn () const

Command *	GetCommand (unsigned long tag)

bool	GetDebug () const

MetaDataDictionary &	GetMetaDataDictionary ()

const MetaDataDictionary &	GetMetaDataDictionary () const

virtual ModifiedTimeType	GetMTime () const

virtual const TimeStamp &	GetTimeStamp () const

bool	HasObserver (const EventObject &event) const

void	InvokeEvent (const EventObject &)

void	InvokeEvent (const EventObject &) const

virtual void	Modified () const

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexcept override

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
Pointer	Clone () const

virtual void	Delete ()

virtual int	GetReferenceCount () const

void	Print (std::ostream &os, Indent indent=0) const

Protected Member Functions
virtual SizeType	GetDataPosition () const

virtual SizeType	GetHeaderSize () const =0

void	PrintSelf (std::ostream &os, Indent indent) const override

virtual bool	ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)

virtual bool	RequestedToStream () const

	StreamingImageIOBase ()

virtual bool	StreamReadBufferAsBinary (std::istream &file, void *_buffer)

virtual bool	StreamWriteBufferAsBinary (std::ostream &file, const void *_buffer)

virtual bool	WriteBufferAsBinary (std::ostream &os, const void *buffer, SizeType num)

Protected Member Functions inherited from itk::ImageIOBase
	ImageIOBase ()

	~ImageIOBase () override

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

virtual bool	HasSupportedReadExtension (const char *fileName, bool ignoreCase=true)

virtual bool	HasSupportedWriteExtension (const char *fileName, bool ignoreCase=true)

virtual void	SetMaximumCompressionLevel (int)

virtual int	GetMaximumCompressionLevel () const

virtual void	InternalSetCompressor (const std::string &_compressor)

virtual void	Reset (const bool freeDynamic=true)

void	Resize (const unsigned int numDimensions, const unsigned int *dimensions)

virtual unsigned int	GetPixelSize () const

void	ComputeStrides ()

SizeType	GetComponentStride () const

SizeType	GetRowStride () const

SizeType	GetSliceStride () const

virtual void	OpenFileForReading (std::ifstream &inputStream, const std::string &filename, bool ascii=false)

virtual void	OpenFileForWriting (std::ofstream &outputStream, const std::string &filename, bool truncate=true, bool ascii=false)

virtual void	WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentEnum ctype, SizeType numComp)

virtual void	ReadBufferAsASCII (std::istream &is, void *buffer, IOComponentEnum ctype, SizeType numComp)

bool	ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)

void	AddSupportedReadExtension (const char *extension)

void	AddSupportedWriteExtension (const char *extension)

void	SetSupportedReadExtensions (const ArrayOfExtensionsType &)

void	SetSupportedWriteExtensions (const ArrayOfExtensionsType &)

virtual unsigned int	GetActualNumberOfSplitsForWritingCanStreamWrite (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion) const

virtual ImageIORegion	GetSplitRegionForWritingCanStreamWrite (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion) const

Protected Member Functions inherited from itk::LightProcessObject
	LightProcessObject ()

	~LightProcessObject () override

virtual void	GenerateData ()

Protected Member Functions inherited from itk::Object
	Object ()

	~Object () override

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const

	LightObject ()

virtual void	PrintHeader (std::ostream &os, Indent indent) const

virtual void	PrintTrailer (std::ostream &os, Indent indent) const

virtual	~LightObject ()

Additional Inherited Members
Static Public Member Functions inherited from itk::ImageIOBase
static std::string	GetComponentTypeAsString (IOComponentEnum)

static IOComponentEnum	GetComponentTypeFromString (const std::string &typeString)

static std::string	GetPixelTypeAsString (IOPixelEnum)

static IOPixelEnum	GetPixelTypeFromString (const std::string &pixelString)

Static Public Member Functions inherited from itk::LightProcessObject
static Pointer	New ()

Static Public Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()

static void	GlobalWarningDisplayOff ()

static void	GlobalWarningDisplayOn ()

static Pointer	New ()

static void	SetGlobalWarningDisplay (bool val)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Protected Attributes inherited from itk::ImageIOBase
IOPixelEnum	m_PixelType { IOPixelEnum::SCALAR }

IOComponentEnum	m_ComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

IOByteOrderEnum	m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }

IOFileEnum	m_FileType { IOFileEnum::TypeNotApplicable }

bool	m_Initialized

std::string	m_FileName

unsigned int	m_NumberOfComponents

unsigned int	m_NumberOfDimensions { 0 }

bool	m_UseCompression { false }

int	m_CompressionLevel { 30 }

int	m_MaximumCompressionLevel { 100 }

std::string	m_Compressor { "uninitialized" }

bool	m_UseStreamedReading

bool	m_UseStreamedWriting

bool	m_ExpandRGBPalette

bool	m_IsReadAsScalarPlusPalette

bool	m_WritePalette

ImageIORegion	m_IORegion

std::vector< SizeValueType >	m_Dimensions

std::vector< double >	m_Spacing

std::vector< double >	m_Origin

std::vector< std::vector< double > >	m_Direction

std::vector< SizeType >	m_Strides

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount

Detailed Description

A base class for specific ImageIO file formats which support streaming.

This class overloads the methods needed to enable streaming. These methods are utilized by the ImageFileReader and ImageFileWriter. The implementation supports streaming of an arbitrary sized region as well as pasting to new or existing file ( of the same name, size, and pixel type ).

See also: CanStreamWrite CanStreamRead GenerateStreamableReadRegionFromRequestedRegion GetActualNumberOfSplitsForWriting

Additionally low level IO methods are provided to read and write an IORegion from a file.

See also: StreamReadBufferAsBinary StreamWriteBufferAsBinary

This implementation was taken fron the Insight Joural: https://www.insight-journal.org/browse/publication/729

See also: itk::ImageFileReader itk::ImageFileWriter

Definition at line 52 of file itkStreamingImageIOBase.h.

Member Typedef Documentation

◆ Pointer

using itk::StreamingImageIOBase::Pointer = SmartPointer<Self>

Definition at line 60 of file itkStreamingImageIOBase.h.

◆ Self

using itk::StreamingImageIOBase::Self = StreamingImageIOBase

Standard class type aliases.

Definition at line 58 of file itkStreamingImageIOBase.h.

◆ Superclass

using itk::StreamingImageIOBase::Superclass = ImageIOBase

Definition at line 59 of file itkStreamingImageIOBase.h.

Constructor & Destructor Documentation

◆ StreamingImageIOBase()

itk::StreamingImageIOBase::StreamingImageIOBase ( )

protected

Member Function Documentation

◆ CanStreamRead()

bool itk::StreamingImageIOBase::CanStreamRead ( )

overridevirtual

Determine if the ImageIO can stream reading from the current settings. Default is false. If this is queried after the header of the file has been read then it will indicate if that file can be streamed

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::VTKImageIO.

◆ CanStreamWrite()

bool itk::StreamingImageIOBase::CanStreamWrite ( )

overridevirtual

Determine if the ImageIO can stream write from the current settings.

There are two types of non exclusive streaming: pasting subregions, and iterative

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::JPEG2000ImageIO, and itk::VTKImageIO.

◆ GenerateStreamableReadRegionFromRequestedRegion()

ImageIORegion itk::StreamingImageIOBase::GenerateStreamableReadRegionFromRequestedRegion ( const ImageIORegion & requested ) const

overridevirtual

Method for supporting streaming. Given a requested region, determine what could be the region that we can read from the file. This is called the streamable region, which will be equal or smaller than the LargestPossibleRegion (unless it was dimensionaly clipped) and greater or equal to the RequestedRegion

the resulting IORegion may be a greater dimensions the the requested IORegion, if the the derived class is unable to read the requested region. For example if the file has a size of [ 10, 10, 10] but the requested region is [10, 10] the return may be 3 dimensions.

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::JPEG2000ImageIO.

◆ GetActualNumberOfSplitsForWriting()

unsigned int itk::StreamingImageIOBase::GetActualNumberOfSplitsForWriting	(	unsigned int	numberOfRequestedSplits,
		const ImageIORegion &	pasteRegion,
		const ImageIORegion &	largestPossibleRegion
	)

overridevirtual

Before this method is called all the configuration will be done, that is Streaming/PasteRegion/Compression/Filename etc If pasting is being used the number of requested splits is for that region not the largest. The derived ImageIO class should verify that the file is capable of being written with this configuration. If pasted is enabled and is not support or does not work with the file, then an exception should be thrown.

The default implementation depends on CanStreamWrite. If false then 1 is returned (unless pasting is indicated), so that the whole file will be updated in one region. If true then its assumed that any arbitrary region can be written to any file. So the users request will be respected. If a derived class has more restrictive conditions then they should be checked

Reimplemented from itk::ImageIOBase.

◆ GetDataPosition()

virtual SizeType itk::StreamingImageIOBase::GetDataPosition ( ) const

inlineprotectedvirtual

Returns the byte offset into the file where the data is located.

The default implementation is to return the header size.

Definition at line 167 of file itkStreamingImageIOBase.h.

◆ GetHeaderSize()

virtual SizeType itk::StreamingImageIOBase::GetHeaderSize ( ) const

protectedpure virtual

Returns the size of the header in the file.

Implemented in itk::JPEG2000ImageIO, itk::HDF5ImageIO, itk::MRCImageIO, and itk::VTKImageIO.

◆ GetNameOfClass()

virtual const char* itk::StreamingImageIOBase::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::HDF5ImageIO, itk::MRCImageIO, and itk::VTKImageIO.

◆ PrintSelf()

void itk::StreamingImageIOBase::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const

overrideprotectedvirtual

Types for managing image size and image index components.

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::JPEG2000ImageIO, itk::HDF5ImageIO, itk::VTKImageIO, and itk::MRCImageIO.

◆ ReadBufferAsBinary()

virtual bool itk::StreamingImageIOBase::ReadBufferAsBinary	(	std::istream &	is,
		void *	buffer,
		SizeType	num
	)

protectedvirtual

Reimplemented from super class to get around 2GB read/write limitation.

Todo:: Move this method to itk::ImageIOBase

◆ RequestedToStream()

virtual bool itk::StreamingImageIOBase::RequestedToStream ( ) const

protectedvirtual

Returns true if GetIORegion is not the same size as the largest region give by GetNumberOfDimensions.

This compares the IORegion to the size of the image in the file. With out regaurd to the dimensions of either, if the images represent the same region then false is returned.

◆ StreamReadBufferAsBinary()

virtual bool itk::StreamingImageIOBase::StreamReadBufferAsBinary	(	std::istream &	file,
		void *	_buffer
	)

protectedvirtual

Reads the set IORegion from os into buffer.

Parameters

os	is an istream presumed to be opened for reading in binary mode
buffer	is pointer to an allocated block of memory suitable to hold the IORegion of the pixel type

This methods relies on GetDataPosition to determin where the data is located in the file. It uses m_IORegion to determin the requested region to read.

The files data is assumed to be unpadded and continuous in the file for the size of the image in the dimensions of the m_IORegion. This means that the image file could be broken into slices, but not blocks for this methods to be used.

◆ StreamWriteBufferAsBinary()

virtual bool itk::StreamingImageIOBase::StreamWriteBufferAsBinary	(	std::ostream &	file,
		const void *	_buffer
	)

protectedvirtual

Writes the set IORegion from buffer into os.

Parameters

os	is an ostream presumed to be opened for writing and reading
buffer	is a pointer to the data in a continuous block for the region

This methods relies on GetDataPosition to determin where the data is located in the file. It usesy m_IORegion determin the requested region to written.

◆ WriteBufferAsBinary()

virtual bool itk::StreamingImageIOBase::WriteBufferAsBinary	(	std::ostream &	os,
		const void *	buffer,
		SizeType	num
	)

protectedvirtual

Reimplemented from super class to get around 2GB read/write limitation.

Todo:: Move this methods to itk::ImageIOBase

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

itkStreamingImageIOBase.h

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Pointer

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ StreamingImageIOBase()

Member Function Documentation

◆ CanStreamRead()

◆ CanStreamWrite()

◆ GenerateStreamableReadRegionFromRequestedRegion()

◆ GetActualNumberOfSplitsForWriting()

◆ GetDataPosition()

◆ GetHeaderSize()

◆ GetNameOfClass()

◆ PrintSelf()

◆ ReadBufferAsBinary()

◆ RequestedToStream()

◆ StreamReadBufferAsBinary()

◆ StreamWriteBufferAsBinary()

◆ WriteBufferAsBinary()