#include <itkStreamingImageIOBase.h>

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 from the Insight Journal: https://doi.org/10.54294/olkmog9

See also: itk::ImageFileReader itk::ImageFileWriter

Definition at line 52 of file 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	ArrayOfExtensionsType = std::vector< std::string >

using	BufferSizeType = itk::OffsetValueType

using	ConstPointer = SmartPointer< const Self >

using	IndexValueType = itk::IndexValueType

using	IOByteOrderEnum = itk::IOByteOrderEnum

using	IOComponentEnum = itk::IOComponentEnum

using	IOFileEnum = itk::IOFileEnum

using	Pointer = SmartPointer< Self >

using	Self = ImageIOBase

using	SizeType = itk::intmax_t

using	SizeValueType = itk::SizeValueType

using	Superclass = LightProcessObject

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

const char *	GetNameOfClass () const override

Public Member Functions inherited from itk::ImageIOBase
virtual bool	CanReadFile (const char *)=0

virtual bool	CanStreamRead ()

virtual bool	CanStreamWrite ()

virtual bool	CanWriteFile (const char *)=0

virtual ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const

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

std::string	GetByteOrderAsString (IOByteOrderEnum) const

virtual unsigned int	GetComponentSize () const

virtual IOComponentEnum	GetComponentType () const

virtual const std::type_info &	GetComponentTypeInfo () const

virtual int	GetCompressionLevel () const

virtual const std::string &	GetCompressor () const

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

virtual SizeValueType	GetDimensions (unsigned int i) const

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

std::string	GetFileTypeAsString (IOFileEnum) const

SizeType	GetImageSizeInBytes () const

SizeType	GetImageSizeInComponents () const

SizeType	GetImageSizeInPixels () const

virtual bool	GetIsReadAsScalarPlusPalette () const

const char *	GetNameOfClass () const override

virtual unsigned int	GetNumberOfDimensions () const

virtual double	GetOrigin (unsigned int i) const

virtual SizeType	GetPixelStride () const

virtual double	GetSpacing (unsigned int i) const

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

const ArrayOfExtensionsType &	GetSupportedReadExtensions () const

const ArrayOfExtensionsType &	GetSupportedWriteExtensions () const

virtual void	Read (void *buffer)=0

virtual void	ReadImageInformation ()=0

void	SetByteOrderToLittleEndian ()

virtual void	SetComponentType (const IOComponentEnum _arg)

virtual void	SetCompressionLevel (int _arg)

virtual void	SetCompressor (std::string _c)

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

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

void	SetFileTypeToBinary ()

void	SetNumberOfDimensions (unsigned int)

virtual void	SetOrigin (unsigned int i, double origin)

virtual void	SetSpacing (unsigned int i, double spacing)

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

virtual bool	SupportsDimension (unsigned long dim)

virtual void	Write (const void *buffer)=0

virtual void	WriteImageInformation ()=0

virtual void	SetFileName (const char *_arg)

virtual const char *	GetFileName () const

virtual void	SetDimensions (unsigned int i, SizeValueType dim)

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	SetNumberOfComponents (unsigned int _arg)

virtual const unsigned int &	GetNumberOfComponents () const

virtual void	SetUseCompression (bool _arg)

virtual bool	GetUseCompression () const

virtual void	UseCompressionOn ()

virtual void	SetUseStreamedReading (bool _arg)

virtual bool	GetUseStreamedReading () const

virtual void	UseStreamedReadingOn ()

virtual void	SetUseStreamedWriting (bool _arg)

virtual bool	GetUseStreamedWriting () const

virtual void	UseStreamedWritingOn ()

virtual void	SetExpandRGBPalette (bool _arg)

virtual bool	GetExpandRGBPalette () const

virtual void	ExpandRGBPaletteOn ()

virtual void	SetWritePalette (bool _arg)

virtual bool	GetWritePalette () const

virtual void	WritePaletteOn ()

virtual void	SetFileType (const IOFileEnum _arg)

virtual IOFileEnum	GetFileType () const

void	SetFileTypeToASCII ()

virtual void	SetByteOrder (const IOByteOrderEnum _arg)

virtual IOByteOrderEnum	GetByteOrder () const

void	SetByteOrderToBigEndian ()

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 int VLength>
void	SetPixelTypeInfo (const Offset< VLength > *)

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

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

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

template<typename TPixel , unsigned int 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 int 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 int 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	AbortGenerateDataOn ()

virtual const bool &	GetAbortGenerateData () const

const char *	GetNameOfClass () const override

virtual void	SetAbortGenerateData (bool _arg)

virtual void	UpdateOutputData ()

void	UpdateProgress (float amount)

virtual void	SetProgress (float _arg)

virtual const float &	GetProgress () const

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

const char *	GetNameOfClass () const override

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) const

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 Pointer	CreateAnother () const

virtual void	Delete ()

virtual const char *	GetNameOfClass () const

virtual int	GetReferenceCount () const

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

virtual void	Register () const

virtual void	SetReferenceCount (int)

virtual void	UnRegister () const noexcept

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
void	AddSupportedReadExtension (const char *extension)

void	AddSupportedWriteExtension (const char *extension)

void	ComputeStrides ()

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

SizeType	GetComponentStride () const

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

virtual unsigned int	GetPixelSize () const

SizeType	GetRowStride () const

SizeType	GetSliceStride () const

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

	ImageIOBase ()

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

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)

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

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

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

virtual void	Reset (const bool freeDynamic=true)

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

void	SetSupportedReadExtensions (const ArrayOfExtensionsType &)

void	SetSupportedWriteExtensions (const ArrayOfExtensionsType &)

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

	~ImageIOBase () override

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

Protected Member Functions inherited from itk::LightProcessObject
virtual void	GenerateData ()

	LightProcessObject ()

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

	~LightProcessObject () override

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

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

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

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

	~Object () override

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

	LightObject ()

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

virtual void	PrintSelf (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
IOByteOrderEnum	m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }

IOComponentEnum	m_ComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

int	m_CompressionLevel { 30 }

std::string	m_Compressor { "uninitialized" }

std::vector< SizeValueType >	m_Dimensions {}

std::vector< std::vector< double > >	m_Direction {}

bool	m_ExpandRGBPalette {}

std::string	m_FileName {}

IOFileEnum	m_FileType { IOFileEnum::TypeNotApplicable }

bool	m_Initialized {}

ImageIORegion	m_IORegion {}

bool	m_IsReadAsScalarPlusPalette {}

int	m_MaximumCompressionLevel { 100 }

unsigned int	m_NumberOfComponents {}

unsigned int	m_NumberOfDimensions { 0 }

std::vector< double >	m_Origin {}

IOPixelEnum	m_PixelType { IOPixelEnum::SCALAR }

std::vector< double >	m_Spacing {}

std::vector< SizeType >	m_Strides {}

bool	m_UseCompression { false }

bool	m_UseStreamedReading {}

bool	m_UseStreamedWriting {}

bool	m_WritePalette {}

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

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 dimensionally clipped) and greater or equal to the RequestedRegion

the resulting IORegion may be a greater dimensions the requested IORegion, if 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::HDF5ImageIO, itk::JPEG2000ImageIO, itk::MRCImageIO, and itk::VTKImageIO.

◆ GetNameOfClass()

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

overridevirtual

See also: LightObject::GetNameOfClass()

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

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::ImageIOBase.

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

◆ ReadBufferAsBinary()

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

protectedvirtual

Reimplemented from superclass 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 regard 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

file	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 determine where the data is located in the file. It uses ImageIOBase::m_IORegion to determine 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 ImageIOBase::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

file	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 determine where the data is located in the file. It uses ImageIOBase::m_IORegion determine 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

Detailed Description

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

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()