itk::MRCImageIO Class Reference

#include <itkMRCImageIO.h>

Inheritance diagram for itk::MRCImageIO:

Collaboration diagram for itk::MRCImageIO:

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 https://hdl.handle.net/10380/3171

See Also

ImageFileWriter ImageFileReader ImageIOBase

Definition at line 58 of file itkMRCImageIO.h.

Public Types
typedef SmartPointer< Self >	Pointer
typedef MRCImageIO	Self
typedef StreamingImageIOBase	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,   ULONGLONG,   LONGLONG,   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 *) override
virtual bool	CanWriteFile (const char *) 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 (void) 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 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
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 ()

Static Public Attributes
static const char *	m_MetaDataHeaderName

Protected Member Functions
virtual SizeType	GetHeaderSize (void) const override
	MRCImageIO ()
virtual void	PrintSelf (std::ostream &os, Indent indent) const override
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 () override
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)
virtual	~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	InternalReadImageInformation (std::ifstream &is)
void	UpdateHeaderFromImageIO ()
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

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
bool	m_ExpandRGBPalette
std::string	m_FileName
FileType	m_FileType
bool	m_Initialized
ImageIORegion	m_IORegion
bool	m_IsReadAsScalarPlusPalette
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::MRCImageIO::Pointer

Definition at line 65 of file itkMRCImageIO.h.

typedef MRCImageIO itk::MRCImageIO::Self

Standard class typedefs.

Definition at line 63 of file itkMRCImageIO.h.

typedef StreamingImageIOBase itk::MRCImageIO::Superclass

Definition at line 64 of file itkMRCImageIO.h.

Constructor & Destructor Documentation

itk::MRCImageIO::MRCImageIO ( )

protected

Member Function Documentation

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

overridevirtual

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

Implements itk::ImageIOBase.

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

overridevirtual

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 ( ) 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

overrideprotectedvirtual

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.

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

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::MRCImageIO::ReadImageInformation ( )

overridevirtual

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 ( )

private

template<typename TPixelType >

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

private

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

private

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

overridevirtual

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  )

inlineoverridevirtual

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

Implements itk::ImageIOBase.

Definition at line 74 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 104 of file itkMRCImageIO.h.

MRCHeaderObject::Pointer itk::MRCImageIO::m_MRCHeader

private

Definition at line 137 of file itkMRCImageIO.h.

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

• itkMRCImageIO.h