#include <itkHDF5ImageIO.h>

Inheritance diagram for itk::HDF5ImageIO:

Collaboration diagram for itk::HDF5ImageIO:

Detailed Description

Class that defines how to read HDF5 file format. HDF5 IMAGE FILE FORMAT - As much information as I can determine from sourceforge.net/projects/HDF5lib.

Author: Kent Williams

HDF5 paths for elements in file

N is dimension of image
\/ITKVersion ITK Library Version string
\/HDFVersion HDF Version String
\/ITKImage Root Image Group
\/ITKImage\/<name> name is arbitrary, but to parallel Transform I/O keep an image in a subgroup. The idea is to parallel transform file structure.
\/ITKImage\/<name>\/Origin N-D point double
\/ITKImage\/<name>\/Directions N N-vectors double
\/ITKImage\/<name>\/Spacing N-vector double
\/ITKImage\/<name>\/Dimensions N-vector itk::SizeValueType
\/ITKImage\/<name>\/VoxelType String representing voxel type. This can be inferred from the VoxelData type info, but it makes the file more user friendly with respect to HDF5 viewers.
\/ITKImage\/<name>\/VoxelData multi-dim array of voxel data in the case of non-scalar voxel type, keep voxel components together, to make loading possible without
\/ITKImage\/<name>\/MetaData Group for storing metadata from MetaDataDictionary
\/ITKImage\/<name>\/MetaData\/<item-name> Dataset containing data for item-name in the MetaDataDictionary re-arrangement.

Definition at line 85 of file itkHDF5ImageIO.h.

Public Types
using	Pointer = SmartPointer< Self >

using	Self = HDF5ImageIO

using	Superclass = StreamingImageIOBase

Public Types inherited from itk::StreamingImageIOBase
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

enum	ByteOrder { BigEndian, LittleEndian, OrderNotApplicable }

using	ConstPointer = SmartPointer< const Self >

enum	FileType { ASCII, Binary, TypeNotApplicable }

using	IndexValueType = ::itk::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 }

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	CanReadFile (const char *FileNameToRead) override

bool	CanWriteFile (const char *FileNameToWrite) override

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

virtual const char *	GetNameOfClass () const

void	Read (void *buffer) override

void	ReadImageInformation () override

void	Write (const void *buffer) override

void	WriteImageInformation () override

Public Member Functions inherited from itk::StreamingImageIOBase
bool	CanStreamRead () override

bool	CanStreamWrite () override

ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const override

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

Public Member Functions inherited from itk::ImageIOBase
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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexceptoverride

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
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 ()

Protected Member Functions
SizeType	GetHeaderSize () const override

	HDF5ImageIO ()

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

	~HDF5ImageIO () override

Protected Member Functions inherited from itk::StreamingImageIOBase
virtual SizeType	GetDataPosition () const

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

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

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

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)

	~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 ()

Private Member Functions
void	CloseDataSet ()

void	CloseH5File ()

std::vector< std::vector < double > >	ReadDirections (const std::string &path)

template<typename TScalar >
TScalar	ReadScalar (const std::string &DataSetName)

std::string	ReadString (const std::string &path)

template<typename TScalar >
std::vector< TScalar >	ReadVector (const std::string &DataSetName)

void	SetupStreaming (H5::DataSpace imageSpace, H5::DataSpace slabSpace)

template<typename TType >
void	StoreMetaData (MetaDataDictionary *metaDict, const std::string &HDFPath, const std::string &name, unsigned long numElements)

void	WriteDirections (const std::string &path, const std::vector< std::vector< double > > &dir)

template<typename TType >
bool	WriteMeta (const std::string &name, MetaDataObjectBase *metaObj)

template<typename TType >
bool	WriteMetaArray (const std::string &name, MetaDataObjectBase *metaObj)

void	WriteScalar (const std::string &path, const bool &value)

void	WriteScalar (const std::string &path, const long &value)

void	WriteScalar (const std::string &path, const unsigned long &value)

void	WriteScalar (const std::string &path, const long long &value)

void	WriteScalar (const std::string &path, const unsigned long long &value)

template<typename TScalar >
void	WriteScalar (const std::string &path, const TScalar &value)

void	WriteString (const std::string &path, const std::string &value)

void	WriteString (const std::string &path, const char *s)

template<typename TScalar >
void	WriteVector (const std::string &path, const std::vector< TScalar > &vec)

Private Attributes
H5::H5File *	m_H5File {nullptr}

bool	m_ImageInformationWritten {false}

H5::DataSet *	m_VoxelDataSet {nullptr}

Additional Inherited Members
Protected Attributes inherited from itk::ImageIOBase
ByteOrder	m_ByteOrder {OrderNotApplicable}

IOComponentType	m_ComponentType {UNKNOWNCOMPONENTTYPE}

std::vector< SizeValueType >	m_Dimensions

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

bool	m_ExpandRGBPalette

std::string	m_FileName

FileType	m_FileType {TypeNotApplicable}

bool	m_Initialized

ImageIORegion	m_IORegion

bool	m_IsReadAsScalarPlusPalette

unsigned int	m_NumberOfComponents

unsigned int	m_NumberOfDimensions {0}

std::vector< double >	m_Origin

IOPixelType	m_PixelType {SCALAR}

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
std::atomic< int >	m_ReferenceCount

Member Typedef Documentation

using itk::HDF5ImageIO::Pointer = SmartPointer< Self >

Definition at line 93 of file itkHDF5ImageIO.h.

using itk::HDF5ImageIO::Self = HDF5ImageIO

Standard class type aliases.

Definition at line 91 of file itkHDF5ImageIO.h.

using itk::HDF5ImageIO::Superclass = StreamingImageIOBase

Definition at line 92 of file itkHDF5ImageIO.h.

Constructor & Destructor Documentation

itk::HDF5ImageIO::HDF5ImageIO ( )

protected

itk::HDF5ImageIO::~HDF5ImageIO ( )

overrideprotected

Member Function Documentation

bool itk::HDF5ImageIO::CanReadFile ( const char * FileNameToRead )

overridevirtual

Determine if the file can be read with this ImageIO implementation.

Author: Hans J Johnson

Parameters

FileNameToRead The name of the file to test for reading.

Postcondition: Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite

Returns: Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

bool itk::HDF5ImageIO::CanWriteFile ( const char * FileNameToWrite )

overridevirtual

Determine if the file can be written with this ImageIO implementation.

Parameters

FileNameToWrite The name of the file to test for writing.

Author: Hans J. Johnson

Postcondition: Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite

Returns: Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

void itk::HDF5ImageIO::CloseDataSet ( )

private

void itk::HDF5ImageIO::CloseH5File ( )

private

virtual::itk::LightObject::Pointer itk::HDF5ImageIO::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.

SizeType itk::HDF5ImageIO::GetHeaderSize ( ) const

overrideprotectedvirtual

Returns the size of the header in the file.

Implements itk::StreamingImageIOBase.

virtual const char* itk::HDF5ImageIO::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from itk::StreamingImageIOBase.

static Pointer itk::HDF5ImageIO::New ( )

static

Method for creation through the object factory.

void itk::HDF5ImageIO::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::StreamingImageIOBase.

void itk::HDF5ImageIO::Read ( void * buffer )

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

std::vector<std::vector<double> > itk::HDF5ImageIO::ReadDirections ( const std::string & path )

private

void itk::HDF5ImageIO::ReadImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

template<typename TScalar >

TScalar itk::HDF5ImageIO::ReadScalar ( const std::string & DataSetName )

private

std::string itk::HDF5ImageIO::ReadString ( const std::string & path )

private

template<typename TScalar >

std::vector<TScalar> itk::HDF5ImageIO::ReadVector ( const std::string & DataSetName )

private

void itk::HDF5ImageIO::SetupStreaming	(	H5::DataSpace *	imageSpace,
		H5::DataSpace *	slabSpace
	)

private

template<typename TType >

void itk::HDF5ImageIO::StoreMetaData	(	MetaDataDictionary *	metaDict,
		const std::string &	HDFPath,
		const std::string &	name,
		unsigned long	numElements
	)

private

void itk::HDF5ImageIO::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.

void itk::HDF5ImageIO::WriteDirections	(	const std::string &	path,
		const std::vector< std::vector< double > > &	dir
	)

private

void itk::HDF5ImageIO::WriteImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

template<typename TType >

bool itk::HDF5ImageIO::WriteMeta	(	const std::string &	name,
		MetaDataObjectBase *	metaObj
	)

private

template<typename TType >

bool itk::HDF5ImageIO::WriteMetaArray	(	const std::string &	name,
		MetaDataObjectBase *	metaObj
	)

private

void itk::HDF5ImageIO::WriteScalar	(	const std::string &	path,
		const bool &	value
	)

private

void itk::HDF5ImageIO::WriteScalar	(	const std::string &	path,
		const long &	value
	)

private

void itk::HDF5ImageIO::WriteScalar	(	const std::string &	path,
		const unsigned long &	value
	)

private

void itk::HDF5ImageIO::WriteScalar	(	const std::string &	path,
		const long long &	value
	)

private

void itk::HDF5ImageIO::WriteScalar	(	const std::string &	path,
		const unsigned long long &	value
	)

private

template<typename TScalar >

void itk::HDF5ImageIO::WriteScalar	(	const std::string &	path,
		const TScalar &	value
	)

private

void itk::HDF5ImageIO::WriteString	(	const std::string &	path,
		const std::string &	value
	)

private

void itk::HDF5ImageIO::WriteString	(	const std::string &	path,
		const char *	s
	)

private

template<typename TScalar >

void itk::HDF5ImageIO::WriteVector	(	const std::string &	path,
		const std::vector< TScalar > &	vec
	)

private

Member Data Documentation

H5::H5File* itk::HDF5ImageIO::m_H5File {nullptr}

private

Definition at line 196 of file itkHDF5ImageIO.h.

bool itk::HDF5ImageIO::m_ImageInformationWritten {false}

private

Definition at line 198 of file itkHDF5ImageIO.h.

H5::DataSet* itk::HDF5ImageIO::m_VoxelDataSet {nullptr}

private

Definition at line 197 of file itkHDF5ImageIO.h.

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

itkHDF5ImageIO.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation