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. More...

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

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.

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.

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 ) [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 [protected, virtual]

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 `[protected, virtual]`

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 unsigned long &	value
	)		`[private]`

template<typename TScalar >

void itk::HDF5ImageIO::WriteScalar	(	const std::string &	path,
		const TScalar &	value
	)		`[private]`

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

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

itkHDF5ImageIO.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation