itk::HDF5ImageIO Class Reference

#include <itkHDF5ImageIO.h>

Inheritance diagram for itk::HDF5ImageIO:

Collaboration diagram for itk::HDF5ImageIO:

List of all members.

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

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
virtual SizeType	GetHeaderSize (void) const
	HDF5ImageIO ()
void	PrintSelf (std::ostream &os, Indent indent) const
	~HDF5ImageIO ()
Protected Member Functions inherited from itk::StreamingImageIOBase
virtual SizeType	GetDataPosition (void) const
virtual void	OpenFileForReading (std::ifstream &os, const char *filename)
virtual void	OpenFileForWriting (std::ofstream &os, const char *filename, bool truncate)
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
	HDF5ImageIO (const Self &)
void	operator= (const Self &)
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

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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.

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Member Typedef Documentation

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

Reimplemented from itk::StreamingImageIOBase.

Definition at line 91 of file itkHDF5ImageIO.h.

typedef HDF5ImageIO itk::HDF5ImageIO::Self

Standard class typedefs.

Reimplemented from itk::StreamingImageIOBase.

Definition at line 89 of file itkHDF5ImageIO.h.

typedef ImageIOBase itk::HDF5ImageIO::Superclass

Reimplemented from itk::StreamingImageIOBase.

Definition at line 90 of file itkHDF5ImageIO.h.

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Constructor & Destructor Documentation

itk::HDF5ImageIO::HDF5ImageIO ( )

protected

itk::HDF5ImageIO::~HDF5ImageIO ( )

protected

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

private

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Member Function Documentation

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

virtual

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 )

virtual

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 ( void  ) 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

protectedvirtual

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.

Reimplemented from itk::LightProcessObject.

void itk::HDF5ImageIO::operator= ( const Self &  )

private

This method causes the filter to generate its output.

Reimplemented from itk::StreamingImageIOBase.

void itk::HDF5ImageIO::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::StreamingImageIOBase.

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

virtual

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 ( )

virtual

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 )

virtual

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 ( )

virtual

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

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Member Data Documentation

H5::H5File* itk::HDF5ImageIO::m_H5File

private

Definition at line 189 of file itkHDF5ImageIO.h.

bool itk::HDF5ImageIO::m_ImageInformationWritten

private

Definition at line 191 of file itkHDF5ImageIO.h.

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

private

Definition at line 190 of file itkHDF5ImageIO.h.

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

• itkHDF5ImageIO.h