itk::HDF5ImageIO Class Reference

#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 86 of file itkHDF5ImageIO.h.

Public Types
typedef SmartPointer< Self >	Pointer
typedef HDF5ImageIO	Self
typedef ImageIOBase	Superclass
Public Types inherited from itk::StreamingImageIOBase
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 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 *FileNameToRead) override
virtual bool	CanWriteFile (const char *FileNameToWrite) override
virtual ::itk::LightObject::Pointer	CreateAnother () const
virtual const char *	GetNameOfClass () const
virtual void	Read (void *buffer) override
virtual void	ReadImageInformation () override
virtual void	Write (const void *buffer) override
virtual void	WriteImageInformation () override
Public Member Functions inherited from itk::StreamingImageIOBase
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
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 itk::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 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, unsigned int 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	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 ()

Protected Member Functions
virtual SizeType	GetHeaderSize (void) const override
	HDF5ImageIO ()
virtual void	PrintSelf (std::ostream &os, Indent indent) const override
	~HDF5ImageIO ()
Protected Member Functions inherited from itk::StreamingImageIOBase
virtual SizeType	GetDataPosition (void) 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 ()
Protected Member Functions inherited from itk::LightProcessObject
virtual void	GenerateData ()
	LightProcessObject ()
	~LightProcessObject ()
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
	HDF5ImageIO (const Self &) ITK_DELETE_FUNCTION
void	operator= (const Self &) ITK_DELETE_FUNCTION
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)
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
bool	m_ImageInformationWritten
H5::DataSet *	m_VoxelDataSet

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

Member Typedef Documentation

typedef SmartPointer< Self > itk::HDF5ImageIO::Pointer

Definition at line 92 of file itkHDF5ImageIO.h.

typedef HDF5ImageIO itk::HDF5ImageIO::Self

Standard class typedefs.

Definition at line 90 of file itkHDF5ImageIO.h.

typedef ImageIOBase itk::HDF5ImageIO::Superclass

Definition at line 91 of file itkHDF5ImageIO.h.

Constructor & Destructor Documentation

itk::HDF5ImageIO::HDF5ImageIO ( )

protected

itk::HDF5ImageIO::~HDF5ImageIO ( )

protected

itk::HDF5ImageIO::HDF5ImageIO ( const Self &  )

private

Member Function Documentation

virtual 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.

virtual 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.

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.

virtual SizeType itk::HDF5ImageIO::GetHeaderSize ( void  ) 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::operator= ( const Self &  )

private

virtual 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.

virtual 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

virtual 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

virtual 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

virtual 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

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

private

Definition at line 190 of file itkHDF5ImageIO.h.

bool itk::HDF5ImageIO::m_ImageInformationWritten

private

Definition at line 192 of file itkHDF5ImageIO.h.

H5::DataSet* itk::HDF5ImageIO::m_VoxelDataSet

private

Definition at line 191 of file itkHDF5ImageIO.h.

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

• itkHDF5ImageIO.h