#include <itkMRCImageIO.h>

Inheritance diagram for itk::MRCImageIO:

Collaboration diagram for itk::MRCImageIO:

Public Types
typedef SmartPointer< Self >	Pointer
typedef MRCImageIO	Self
typedef StreamingImageIOBase	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 *)
virtual bool	CanWriteFile (const char *)
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 (void)
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
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
void	InternalReadImageInformation (std::ifstream &is)
	MRCImageIO (const Self &)
void	operator= (const Self &)
void	UpdateHeaderFromImageIO (void)
template<typename TPixelType >
void	UpdateHeaderWithMinMaxMean (const TPixelType *bufferBegin)
void	UpdateHeaderWithMinMaxMean (const void *bufferBegin)
virtual void	WriteImageInformation (const void *bufferBegin)

Private Attributes
MRCHeaderObject::Pointer	m_MRCHeader
static const char *	m_MetaDataHeaderName
	MRCImageIO ()
void	PrintSelf (std::ostream &os, Indent indent) const

Additional Inherited Members

Detailed Description

An ImageIO class to read the MRC file format. The MRC file format frequently has the extension ".mrc" or ".rec". It is used frequently for electron microscopy and is an emerging standard for cryo-electron tomography and molecular imaging. The format is used to represent 2D, 3D images along with 2D tilt series for tomography.

The header of the file can contain important information which can not be represented in an Image. Therefor the header is placed into the MetaDataDictionary of "this". The key to access this is MetaDataHeaderName ( fix me when renamed ).

See also:: MRCHeaderObject MetaDataDictionary

This implementation is designed to support IO Streaming of arbitrary regions.

As with all ImageIOs this class is designed to work with ImageFileReader and ImageFileWriter, so its direct use is discouraged.

This code was contributed in the Insight Journal paper: "A Streaming IO Base Class and Support for Streaming the MRC and VTK File Format" by Lowekamp B., Chen D. http://www.insight-journal.org/browse/publication/729 http://hdl.handle.net/10380/3171

See also:: ImageFileWriter ImageFileReader ImageIOBase

Definition at line 59 of file itkMRCImageIO.h.

Member Typedef Documentation

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

Reimplemented from itk::StreamingImageIOBase.

Definition at line 66 of file itkMRCImageIO.h.

typedef MRCImageIO itk::MRCImageIO::Self

Standard class typedefs.

Reimplemented from itk::StreamingImageIOBase.

Definition at line 64 of file itkMRCImageIO.h.

typedef StreamingImageIOBase itk::MRCImageIO::Superclass

Reimplemented from itk::StreamingImageIOBase.

Definition at line 65 of file itkMRCImageIO.h.

Constructor & Destructor Documentation

itk::MRCImageIO::MRCImageIO ( )

protected

Todo:: Move to itkIOCommon with the other MetaDataDictionary keys, likely rename the symbol to something like ITK_MRCHHeader. (remember to fix class doc too)

itk::MRCImageIO::MRCImageIO ( const Self & )

private

Member Function Documentation

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

virtual

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

Implements itk::ImageIOBase.

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

virtual

Returns true if this ImageIO can write the specified file.

The methods verifies that the file extension is known to be supported by this class.

Implements itk::ImageIOBase.

virtual::itk::LightObject::Pointer itk::MRCImageIO::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::MRCImageIO::GetHeaderSize ( void ) const

protectedvirtual

Overloaded to return the actually header size of the file specified. The header must be read before this methods is called.

Implements itk::StreamingImageIOBase.

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::StreamingImageIOBase.

void itk::MRCImageIO::InternalReadImageInformation ( std::ifstream & is )

private

static Pointer itk::MRCImageIO::New ( )

static

Method for creation through the object factory.

Reimplemented from itk::LightProcessObject.

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

private

This method causes the filter to generate its output.

Reimplemented from itk::StreamingImageIOBase.

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

protectedvirtual

Todo:: Move to itkIOCommon with the other MetaDataDictionary keys, likely rename the symbol to something like ITK_MRCHHeader. (remember to fix class doc too)

Reimplemented from itk::StreamingImageIOBase.

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

virtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::MRCImageIO::ReadImageInformation ( )

virtual

Read the spacing and dimensions of the image. Assumes SetFileName has been called with a valid file name.

Implements itk::ImageIOBase.

void itk::MRCImageIO::UpdateHeaderFromImageIO ( void )

private

template<typename TPixelType >

void itk::MRCImageIO::UpdateHeaderWithMinMaxMean ( const TPixelType * bufferBegin )

inlineprivate

Definition at line 126 of file itkMRCImageIO.h.

References itk::min_max_element().

void itk::MRCImageIO::UpdateHeaderWithMinMaxMean ( const void * bufferBegin )

private

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

virtual

Writes the data to disk from the memory buffer provided. Make sure that the IORegions has been set properly. The buffer is cast to a pointer to the beginning of the image data.

Implements itk::ImageIOBase.

virtual void itk::MRCImageIO::WriteImageInformation ( void )

inlinevirtual

Writes the spacing and dimensions of the image. Assumes SetFileName has been called with a valid file name.

Implements itk::ImageIOBase.

Definition at line 75 of file itkMRCImageIO.h.

virtual void itk::MRCImageIO::WriteImageInformation ( const void * bufferBegin )

privatevirtual

Member Data Documentation

const char* itk::MRCImageIO::m_MetaDataHeaderName

static

Todo:: Move to itkIOCommon with the other MetaDataDictionary keys, likely rename the symbol to something like ITK_MRCHHeader. (remember to fix class doc too)

Definition at line 105 of file itkMRCImageIO.h.

MRCHeaderObject::Pointer itk::MRCImageIO::m_MRCHeader

private

Definition at line 156 of file itkMRCImageIO.h.

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

itkMRCImageIO.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation