#include <itkVoxBoCUBImageIO.h>

Inheritance diagram for itk::VoxBoCUBImageIO:

Collaboration diagram for itk::VoxBoCUBImageIO:

Detailed Description

Read VoxBoCUBImage file format.

A generic reader and writer object for VoxBo files. Basically it provides uniform access to gzip and normal files

Author: Burstein, Pablo D.; Yushkevich, Paul; Gee, James C.

This implementation was contributed as a paper to the Insight Journal https://hdl.handle.net/1926/303

Definition at line 50 of file itkVoxBoCUBImageIO.h.

Public Types
typedef SmartPointer< Self >	Pointer

typedef VoxBoCUBImageIO	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	CanReadFile (const char *) override

virtual bool	CanWriteFile (const char *) override

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

virtual const char *	GetNameOfClass () const

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

virtual void	Read (void *buffer) override

virtual void	ReadImageInformation () override

	VoxBoCUBImageIO ()

virtual void	Write (const void *buffer) override

virtual void	WriteImageInformation () override

	~VoxBoCUBImageIO ()

Public Member Functions inherited from itk::ImageIOBase
virtual bool	CanStreamRead ()

virtual bool	CanStreamWrite ()

virtual ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const

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

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

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	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 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

Static Public Member Functions
static Pointer	New ()

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 ()

Private Types
typedef std::map < OrientationFlags, std::string >	InverseOrientationMap

typedef SpatialOrientation::ValidCoordinateOrientationFlags	OrientationFlags

typedef std::map< std::string, OrientationFlags >	OrientationMap

Private Member Functions
bool	CheckExtension (const char *, bool &isCompressed)

GenericCUBFileAdaptor *	CreateReader (const char *filename)

GenericCUBFileAdaptor *	CreateWriter (const char *filename)

void	InitializeOrientationMap ()

void	SwapBytesIfNecessary (void *buffer, BufferSizeType numberOfBytes)

Private Attributes
InverseOrientationMap	m_InverseOrientationMap

OrientationMap	m_OrientationMap

GenericCUBFileAdaptor *	m_Reader

GenericCUBFileAdaptor *	m_Writer

Static Private Attributes
static const char *	m_VB_BYTEORDER

static const char *	m_VB_BYTEORDER_LSB

static const char *	m_VB_BYTEORDER_MSB

static const char *	m_VB_DATATYPE

static const char *	m_VB_DATATYPE_BYTE

static const char *	m_VB_DATATYPE_DOUBLE

static const char *	m_VB_DATATYPE_FLOAT

static const char *	m_VB_DATATYPE_INT

static const char *	m_VB_DIMENSIONS

static const char *	m_VB_IDENTIFIER_FILETYPE

static const char *	m_VB_IDENTIFIER_SYSTEM

static const char *	m_VB_ORIENTATION

static const char *	m_VB_ORIGIN

static const char *	m_VB_SPACING

Additional Inherited Members
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 ()

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 std::map< OrientationFlags, std::string > itk::VoxBoCUBImageIO::InverseOrientationMap

private

Definition at line 110 of file itkVoxBoCUBImageIO.h.

typedef SpatialOrientation::ValidCoordinateOrientationFlags itk::VoxBoCUBImageIO::OrientationFlags

private

Definition at line 108 of file itkVoxBoCUBImageIO.h.

typedef std::map< std::string, OrientationFlags > itk::VoxBoCUBImageIO::OrientationMap

private

Definition at line 109 of file itkVoxBoCUBImageIO.h.

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

Definition at line 56 of file itkVoxBoCUBImageIO.h.

typedef VoxBoCUBImageIO itk::VoxBoCUBImageIO::Self

Standard class typedefs.

Definition at line 54 of file itkVoxBoCUBImageIO.h.

typedef ImageIOBase itk::VoxBoCUBImageIO::Superclass

Definition at line 55 of file itkVoxBoCUBImageIO.h.

Constructor & Destructor Documentation

itk::VoxBoCUBImageIO::VoxBoCUBImageIO ( )

itk::VoxBoCUBImageIO::~VoxBoCUBImageIO ( )

Member Function Documentation

virtual bool itk::VoxBoCUBImageIO::CanReadFile ( const char * )

overridevirtual

Determine the file type. Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

virtual bool itk::VoxBoCUBImageIO::CanWriteFile ( const char * )

overridevirtual

Determine the file type. Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

bool itk::VoxBoCUBImageIO::CheckExtension	(	const char *	,
		bool &	isCompressed
	)

private

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

virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::LightProcessObject.

GenericCUBFileAdaptor* itk::VoxBoCUBImageIO::CreateReader ( const char * filename )

private

GenericCUBFileAdaptor* itk::VoxBoCUBImageIO::CreateWriter ( const char * filename )

private

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

void itk::VoxBoCUBImageIO::InitializeOrientationMap ( )

private

static Pointer itk::VoxBoCUBImageIO::New ( )

static

Method for creation through the object factory.

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

overridevirtual

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.

virtual void itk::VoxBoCUBImageIO::Read ( void * buffer )

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::VoxBoCUBImageIO::ReadImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

void itk::VoxBoCUBImageIO::SwapBytesIfNecessary	(	void *	buffer,
		BufferSizeType	numberOfBytes
	)

private

virtual void itk::VoxBoCUBImageIO::Write ( const void * buffer )

overridevirtual

Writes the data to disk from the memory buffer provided. Make sure that the IORegions has been set properly.

Implements itk::ImageIOBase.

virtual void itk::VoxBoCUBImageIO::WriteImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

Member Data Documentation

InverseOrientationMap itk::VoxBoCUBImageIO::m_InverseOrientationMap

private

Definition at line 113 of file itkVoxBoCUBImageIO.h.

OrientationMap itk::VoxBoCUBImageIO::m_OrientationMap

private

Definition at line 112 of file itkVoxBoCUBImageIO.h.

GenericCUBFileAdaptor* itk::VoxBoCUBImageIO::m_Reader

private

Definition at line 102 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_BYTEORDER

staticprivate

Definition at line 125 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_BYTEORDER_LSB

staticprivate

Definition at line 128 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_BYTEORDER_MSB

staticprivate

Definition at line 127 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE

staticprivate

Definition at line 124 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE_BYTE

staticprivate

Definition at line 129 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE_DOUBLE

staticprivate

Definition at line 132 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE_FLOAT

staticprivate

Definition at line 131 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE_INT

staticprivate

Definition at line 130 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DIMENSIONS

staticprivate

Definition at line 121 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_IDENTIFIER_FILETYPE

staticprivate

Definition at line 120 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_IDENTIFIER_SYSTEM

staticprivate

Definition at line 119 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_ORIENTATION

staticprivate

Definition at line 126 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_ORIGIN

staticprivate

Definition at line 123 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_SPACING

staticprivate

Definition at line 122 of file itkVoxBoCUBImageIO.h.

GenericCUBFileAdaptor * itk::VoxBoCUBImageIO::m_Writer

private

Definition at line 102 of file itkVoxBoCUBImageIO.h.

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

itkVoxBoCUBImageIO.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation