#include <itkStreamingImageIOBase.h>

Inheritance diagram for itk::StreamingImageIOBase:

Collaboration diagram for itk::StreamingImageIOBase:

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://hdl.handle.net/10380/3171

See Also: itk::ImageFileReader itk::ImageFileWriter

Definition at line 52 of file itkStreamingImageIOBase.h.

Public Types
typedef SmartPointer< Self >	Pointer

typedef StreamingImageIOBase	Self

typedef ImageIOBase	Superclass

Public Types inherited from itk::ImageIOBase
typedef std::vector< std::string >	ArrayOfExtensionsType

typedef ::itk::OffsetValueType	BufferSizeType

enum	ByteOrder { BigEndian, LittleEndian, OrderNotApplicable }

enum	FileType { ASCII, Binary, TypeNotApplicable }

typedef ::itk::IndexValueType	IndexValueType

enum	IOComponentType { UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT, INT, ULONG, LONG, ULONGLONG, LONGLONG, FLOAT, DOUBLE }

enum	IOPixelType { UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR, POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D, COMPLEX, FIXEDARRAY, MATRIX }

typedef SmartPointer< Self >	Pointer

typedef ImageIOBase	Self

typedef ::itk::intmax_t	SizeType

typedef ::itk::SizeValueType	SizeValueType

typedef LightProcessObject	Superclass

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

typedef SmartPointer< Self >	Pointer

typedef LightProcessObject	Self

typedef Object	Superclass

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

typedef SmartPointer< Self >	Pointer

typedef Object	Self

typedef LightObject	Superclass

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

typedef SmartPointer< Self >	Pointer

typedef LightObject	Self

Public Member Functions
virtual bool	CanStreamRead (void) override

virtual bool	CanStreamWrite (void) override

virtual ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const override

virtual 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 bool	CanReadFile (const char *)=0

virtual bool	CanWriteFile (const char *)=0

std::string	GetByteOrderAsString (ByteOrder) const

virtual unsigned int	GetComponentSize () const

virtual IOComponentType	GetComponentType () const

virtual const std::type_info &	GetComponentTypeInfo () const

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

virtual SizeValueType	GetDimensions (unsigned int i) const

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

std::string	GetFileTypeAsString (FileType) const

SizeType	GetImageSizeInBytes () const

SizeType	GetImageSizeInComponents () const

SizeType	GetImageSizeInPixels () const

virtual bool	GetIsReadAsScalarPlusPalette () const

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 IOComponentType _arg)

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)

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

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

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

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

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

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 IOPixelType _arg)

virtual IOPixelType	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	UseCompressionOff ()

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	SetFileType (const FileType _arg)

virtual FileType	GetFileType () const

void	SetFileTypeToASCII ()

virtual void	SetByteOrder (const ByteOrder _arg)

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

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

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

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

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	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 *)

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

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

virtual void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int) override

virtual void	UnRegister () const noexceptoverride

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
virtual void	Delete ()

virtual int	GetReferenceCount () const

	itkCloneMacro (Self)

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

Protected Member Functions
virtual SizeType	GetDataPosition (void) const

virtual SizeType	GetHeaderSize (void) const =0

virtual 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 &os, void *buffer)

virtual bool	StreamWriteBufferAsBinary (std::ostream &os, const void *buffer)

virtual bool	WriteBufferAsBinary (std::ostream &is, 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	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	ReadBufferAsASCII (std::istream &os, void *buffer, IOComponentType ctype, SizeType numberOfBytesToBeRead)

bool	ReadBufferAsBinary (std::istream &os, void *buffer, SizeType numberOfBytesToBeRead)

virtual void	Reset (const bool freeDynamic=true)

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

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

	~ImageIOBase () override

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

	LightProcessObject ()

	~LightProcessObject () override

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

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

virtual void	SetTimeStamp (const TimeStamp &time)

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

virtual	~LightObject ()

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

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

static std::string	GetPixelTypeAsString (IOPixelType)

static IOPixelType	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 flag)

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

static Pointer	New ()

Protected Attributes inherited from itk::ImageIOBase
ByteOrder	m_ByteOrder

IOComponentType	m_ComponentType

std::vector< SizeValueType >	m_Dimensions

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

bool	m_ExpandRGBPalette

std::string	m_FileName

FileType	m_FileType

bool	m_Initialized

ImageIORegion	m_IORegion

bool	m_IsReadAsScalarPlusPalette

unsigned int	m_NumberOfComponents

unsigned int	m_NumberOfDimensions

std::vector< double >	m_Origin

IOPixelType	m_PixelType

std::vector< double >	m_Spacing

std::vector< SizeType >	m_Strides

bool	m_UseCompression

bool	m_UseStreamedReading

bool	m_UseStreamedWriting

Protected Attributes inherited from itk::LightObject
AtomicInt< int >	m_ReferenceCount

Member Typedef Documentation

typedef SmartPointer< Self > itk::StreamingImageIOBase::Pointer

Definition at line 58 of file itkStreamingImageIOBase.h.

typedef StreamingImageIOBase itk::StreamingImageIOBase::Self

Standard class typedefs.

Definition at line 56 of file itkStreamingImageIOBase.h.

typedef ImageIOBase itk::StreamingImageIOBase::Superclass

Definition at line 57 of file itkStreamingImageIOBase.h.

Constructor & Destructor Documentation

itk::StreamingImageIOBase::StreamingImageIOBase ( )

protected

Member Function Documentation

virtual bool itk::StreamingImageIOBase::CanStreamRead ( void )

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.

virtual bool itk::StreamingImageIOBase::CanStreamWrite ( void )

overridevirtual

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

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

Reimplemented from itk::ImageIOBase.

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

virtual 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.

virtual 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 excepetion 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 restictive conditions then they should be checked

Reimplemented from itk::ImageIOBase.

virtual SizeType itk::StreamingImageIOBase::GetDataPosition ( void ) 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 153 of file itkStreamingImageIOBase.h.

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

protectedpure virtual

Returns the size of the header in the file.

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

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

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

virtual 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::VTKImageIO, and itk::MRCImageIO.

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

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.

virtual bool itk::StreamingImageIOBase::StreamReadBufferAsBinary	(	std::istream &	os,
		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.

virtual bool itk::StreamingImageIOBase::StreamWriteBufferAsBinary	(	std::ostream &	os,
		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.

virtual bool itk::StreamingImageIOBase::WriteBufferAsBinary	(	std::ostream &	is,
		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

Constructor & Destructor Documentation

Member Function Documentation