#include <itkStreamingImageIOBase.h>

Inheritance diagram for itk::StreamingImageIOBase:

Collaboration diagram for itk::StreamingImageIOBase:

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, FLOAT, DOUBLE }
enum	IOPixelType { UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR, POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D, COMPLEX, FIXEDARRAY, MATRIX }
typedef ::itk::intmax_t	SizeType
typedef ::itk::SizeValueType	SizeValueType
Public Types inherited from itk::LightProcessObject
typedef SmartPointer< const Self >	ConstPointer
Public Types inherited from itk::Object
Public Types inherited from itk::LightObject

Public Member Functions
virtual bool	CanStreamRead (void)
virtual bool	CanStreamWrite (void)
virtual ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const
virtual unsigned int	GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
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 unsigned int	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 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, std::vector< double > &direction)
virtual void	SetDirection (unsigned int i, vnl_vector< double > &direction)
void	SetFileTypeToBinary ()
void	SetNumberOfDimensions (unsigned int)
virtual void	SetOrigin (unsigned int i, double origin)
template<class 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, unsigned int dim)
virtual void	SetIORegion (ImageIORegion _arg)
virtual const ImageIORegion &	GetIORegion ()
virtual void	SetPixelType (const IOPixelType _arg)
virtual IOPixelType	GetPixelType () const
virtual void	SetNumberOfComponents (unsigned int _arg)
virtual const unsigned int &	GetNumberOfComponents ()
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	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 (void) const
virtual const bool &	GetAbortGenerateData ()
virtual void	SetAbortGenerateData (bool _arg)
virtual void	UpdateOutputData ()
void	UpdateProgress (float amount)
virtual void	SetProgress (float _arg)
virtual const float &	GetProgress ()
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 (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
virtual unsigned long	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
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int)
virtual void	UnRegister () 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	OpenFileForReading (std::ifstream &os, const char *filename)
virtual void	OpenFileForWriting (std::ofstream &os, const char *filename, bool truncate)
virtual void	PrintSelf (std::ostream &os, Indent indent) const
virtual bool	ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)
virtual bool	RequestedToStream (void) 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 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	ReadBufferAsASCII (std::istream &os, void *buffer, IOComponentType ctype, 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 ()
Protected Member Functions inherited from itk::LightProcessObject
	LightProcessObject ()
	~LightProcessObject ()
virtual void	GenerateData ()
Protected Member Functions inherited from itk::Object
	Object ()
bool	PrintObservers (std::ostream &os, Indent indent) const
virtual void	SetTimeStamp (const TimeStamp &time)
virtual	~Object ()
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 ()

Private Member Functions
void	operator= (const Self &)
	StreamingImageIOBase (const Self &)

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 void	SetGlobalWarningDisplay (bool flag)
Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()
Protected Attributes inherited from itk::ImageIOBase
ByteOrder	m_ByteOrder
IOComponentType	m_ComponentType
std::vector< SizeValueType >	m_Dimensions
std::vector< std::vector < double > >	m_Direction
std::string	m_FileName
FileType	m_FileType
bool	m_Initialized
ImageIORegion	m_IORegion
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

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

See also:: itk::ImageFileReader itk::ImageFileWriter

Definition at line 51 of file itkStreamingImageIOBase.h.

Member Typedef Documentation

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

Reimplemented from itk::ImageIOBase.

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

Definition at line 57 of file itkStreamingImageIOBase.h.

typedef StreamingImageIOBase itk::StreamingImageIOBase::Self

Standard class typedefs.

Reimplemented from itk::ImageIOBase.

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

Definition at line 55 of file itkStreamingImageIOBase.h.

typedef ImageIOBase itk::StreamingImageIOBase::Superclass

Reimplemented from itk::ImageIOBase.

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

Definition at line 56 of file itkStreamingImageIOBase.h.

Constructor & Destructor Documentation

itk::StreamingImageIOBase::StreamingImageIOBase ( )

protected

itk::StreamingImageIOBase::StreamingImageIOBase ( const Self & )

private

Member Function Documentation

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

virtual

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 )

virtual

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

virtual

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
	)

virtual

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 152 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::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::MRCImageIO, itk::VTKImageIO, and itk::JPEG2000ImageIO.

virtual void itk::StreamingImageIOBase::OpenFileForReading	(	std::ifstream &	os,
		const char *	filename
	)

protectedvirtual

Opens a file for reading and random access.

The stream is closed if it's already opened. If an error is encountered then an exception will be thrown.

virtual void itk::StreamingImageIOBase::OpenFileForWriting	(	std::ofstream &	os,
		const char *	filename,
		bool	truncate
	)

protectedvirtual

Opens a file for writing and random access.

Parameters:

os	is an ostream presumed to be opened for writing
filename	is the name of the file
truncate	if true then the file is truncated

The stream is closed if it's already opened. If an error is encountered then an exception will be thrown.

void itk::StreamingImageIOBase::operator= ( const Self & )

private

This method causes the filter to generate its output.

Reimplemented from itk::ImageIOBase.

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

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

protectedvirtual

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.

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

Reimplemented from itk::ImageIOBase.

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

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation