#include <itkMRCImageIO.h>

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. https://doi.org/10.54294/olkmog9

See also: ImageFileWriter ImageFileReader ImageIOBase

Definition at line 58 of file itkMRCImageIO.h.

Inheritance diagram for itk::MRCImageIO:

Collaboration diagram for itk::MRCImageIO:

Public Types
using	Pointer = SmartPointer< Self >

using	Self = MRCImageIO

using	Superclass = StreamingImageIOBase

Public Types inherited from itk::StreamingImageIOBase
using	Pointer = SmartPointer< Self >

using	Self = StreamingImageIOBase

using	Superclass = ImageIOBase

Public Types inherited from itk::ImageIOBase
using	ArrayOfExtensionsType = std::vector< std::string >

using	BufferSizeType = itk::OffsetValueType

using	ConstPointer = SmartPointer< const Self >

using	IndexValueType = itk::IndexValueType

using	IOByteOrderEnum = itk::IOByteOrderEnum

using	IOComponentEnum = itk::IOComponentEnum

using	IOFileEnum = itk::IOFileEnum

using	Pointer = SmartPointer< Self >

using	Self = ImageIOBase

using	SizeType = itk::intmax_t

using	SizeValueType = itk::SizeValueType

using	Superclass = LightProcessObject

Public Types inherited from itk::LightProcessObject
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = LightProcessObject

using	Superclass = Object

Public Types inherited from itk::Object
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

Public Types inherited from itk::LightObject
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = LightObject

Public Member Functions
bool	CanReadFile (const char *) override

bool	CanWriteFile (const char *) override

const char *	GetNameOfClass () const override

void	Read (void *buffer) override

void	ReadImageInformation () override

void	Write (const void *buffer) override

void	WriteImageInformation () override

Public Member Functions inherited from itk::StreamingImageIOBase
bool	CanStreamRead () override

bool	CanStreamWrite () override

ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requestedRegion) const override

unsigned int	GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) override

Public Member Functions inherited from itk::ImageIOBase
std::string	GetByteOrderAsString (IOByteOrderEnum) const

virtual unsigned int	GetComponentSize () const

virtual IOComponentEnum	GetComponentType () const

virtual const std::type_info &	GetComponentTypeInfo () const

virtual int	GetCompressionLevel () const

virtual const std::string &	GetCompressor () const

virtual std::vector< double >	GetDefaultDirection (unsigned int k) const

virtual SizeValueType	GetDimensions (unsigned int i) const

virtual std::vector< double >	GetDirection (unsigned int i) const

std::string	GetFileTypeAsString (IOFileEnum) 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 IOComponentEnum _arg)

virtual void	SetCompressionLevel (int _arg)

virtual void	SetCompressor (std::string _c)

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)

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 itk::CommonEnums::IOPixel _arg)

virtual itk::CommonEnums::IOPixel	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	SetUseStreamedReading (bool _arg)

virtual bool	GetUseStreamedReading () const

virtual void	UseStreamedReadingOn ()

virtual void	SetUseStreamedWriting (bool _arg)

virtual bool	GetUseStreamedWriting () const

virtual void	UseStreamedWritingOn ()

virtual void	SetExpandRGBPalette (bool _arg)

virtual bool	GetExpandRGBPalette () const

virtual void	ExpandRGBPaletteOn ()

virtual void	SetWritePalette (bool _arg)

virtual bool	GetWritePalette () const

virtual void	WritePaletteOn ()

virtual void	SetFileType (const IOFileEnum _arg)

virtual IOFileEnum	GetFileType () const

void	SetFileTypeToASCII ()

virtual void	SetByteOrder (const IOByteOrderEnum _arg)

virtual IOByteOrderEnum	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<unsigned int VLength>
void	SetPixelTypeInfo (const Offset< VLength > *)

template<typename TPixel , unsigned int VLength>
void	SetPixelTypeInfo (const Vector< TPixel, VLength > *)

template<typename TCoordRep , unsigned int VPointDimension>
void	SetPixelTypeInfo (const Point< TCoordRep, VPointDimension > *)

template<typename TPixel , unsigned int VLength>
void	SetPixelTypeInfo (const CovariantVector< TPixel, VLength > *)

template<typename TPixel , unsigned int VLength>
void	SetPixelTypeInfo (const SymmetricSecondRankTensor< TPixel, VLength > *)

template<typename TPixel >
void	SetPixelTypeInfo (const DiffusionTensor3D< TPixel > *)

template<typename TPixel >
void	SetPixelTypeInfo (const std::complex< TPixel > *)

template<typename TPixel , unsigned int VLength>
void	SetPixelTypeInfo (const FixedArray< TPixel, VLength > *)

template<typename TPixel >
void	SetPixelTypeInfo (const VariableLengthVector< TPixel > *)

template<typename TValue >
void	SetPixelTypeInfo (const Array< TValue > *)

template<typename TPixel , unsigned int VLength>
void	SetPixelTypeInfo (const Matrix< TPixel, VLength, VLength > *)

template<typename TValue >
void	SetPixelTypeInfo (const VariableSizeMatrix< TValue > *)

Public Member Functions inherited from itk::LightProcessObject
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 *cmd) const

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag) const

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexcept override

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
Pointer	Clone () const

virtual void	Delete ()

virtual int	GetReferenceCount () const

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 (IOComponentEnum)

static IOComponentEnum	GetComponentTypeFromString (const std::string &typeString)

static std::string	GetPixelTypeAsString (IOPixelEnum)

static IOPixelEnum	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 val)

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
SizeType	GetHeaderSize () const override

	MRCImageIO ()

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

Protected Member Functions inherited from itk::StreamingImageIOBase
virtual SizeType	GetDataPosition () const

virtual bool	ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)

virtual bool	RequestedToStream () const

	StreamingImageIOBase ()

virtual bool	StreamReadBufferAsBinary (std::istream &file, void *_buffer)

virtual bool	StreamWriteBufferAsBinary (std::ostream &file, const void *_buffer)

virtual bool	WriteBufferAsBinary (std::ostream &os, 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	InternalSetCompressor (const std::string &_compressor)

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 &is, void *buffer, IOComponentEnum ctype, SizeType numComp)

bool	ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)

virtual void	Reset (const bool freeDynamic=true)

void	Resize (const unsigned int numDimensions, const unsigned int *dimensions)

void	SetSupportedReadExtensions (const ArrayOfExtensionsType &)

void	SetSupportedWriteExtensions (const ArrayOfExtensionsType &)

virtual void	WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentEnum ctype, SizeType numComp)

	~ImageIOBase () override

virtual bool	HasSupportedReadExtension (const char *fileName, bool ignoreCase=true)

virtual bool	HasSupportedWriteExtension (const char *fileName, bool ignoreCase=true)

virtual void	SetMaximumCompressionLevel (int)

virtual int	GetMaximumCompressionLevel () const

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 &timeStamp)

	~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 &file)

void	UpdateHeaderFromImageIO ()

template<typename TPixelType >
void	UpdateHeaderWithMinMaxMean (const TPixelType *bufferBegin)

void	UpdateHeaderWithMinMaxMean (const void *bufferBegin)

virtual void	WriteImageInformation (const void *buffer)

Private Attributes
MRCHeaderObject::Pointer	m_MRCHeader {}

Additional Inherited Members
Protected Attributes inherited from itk::ImageIOBase
IOByteOrderEnum	m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }

IOComponentEnum	m_ComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

int	m_CompressionLevel { 30 }

std::string	m_Compressor { "uninitialized" }

std::vector< SizeValueType >	m_Dimensions {}

std::vector< std::vector< double > >	m_Direction {}

bool	m_ExpandRGBPalette {}

std::string	m_FileName {}

IOFileEnum	m_FileType { IOFileEnum::TypeNotApplicable }

bool	m_Initialized {}

ImageIORegion	m_IORegion {}

bool	m_IsReadAsScalarPlusPalette {}

int	m_MaximumCompressionLevel { 100 }

unsigned int	m_NumberOfComponents {}

unsigned int	m_NumberOfDimensions { 0 }

std::vector< double >	m_Origin {}

IOPixelEnum	m_PixelType { IOPixelEnum::SCALAR }

std::vector< double >	m_Spacing {}

std::vector< SizeType >	m_Strides {}

bool	m_UseCompression { false }

bool	m_UseStreamedReading {}

bool	m_UseStreamedWriting {}

bool	m_WritePalette {}

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}

Member Typedef Documentation

◆ Pointer

using itk::MRCImageIO::Pointer = SmartPointer<Self>

Definition at line 66 of file itkMRCImageIO.h.

◆ Self

using itk::MRCImageIO::Self = MRCImageIO

Standard class type aliases.

Definition at line 64 of file itkMRCImageIO.h.

◆ Superclass

using itk::MRCImageIO::Superclass = StreamingImageIOBase

Definition at line 65 of file itkMRCImageIO.h.

Constructor & Destructor Documentation

◆ MRCImageIO()

itk::MRCImageIO::MRCImageIO ( )

protected

Member Function Documentation

◆ CanReadFile()

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

overridevirtual

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

Implements itk::ImageIOBase.

◆ CanWriteFile()

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.

◆ GetHeaderSize()

SizeType itk::MRCImageIO::GetHeaderSize ( ) 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.

◆ GetNameOfClass()

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

overridevirtual

See also: LightObject::GetNameOfClass()

Reimplemented from itk::StreamingImageIOBase.

◆ InternalReadImageInformation()

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

private

◆ New()

static Pointer itk::MRCImageIO::New ( )

static

Method for creation through the object factory.

◆ PrintSelf()

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.

◆ Read()

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

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

◆ ReadImageInformation()

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.

◆ UpdateHeaderFromImageIO()

void itk::MRCImageIO::UpdateHeaderFromImageIO ( )

private

◆ UpdateHeaderWithMinMaxMean() [1/2]

template<typename TPixelType >

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

private

◆ UpdateHeaderWithMinMaxMean() [2/2]

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

private

◆ Write()

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.

◆ WriteImageInformation() [1/2]

void itk::MRCImageIO::WriteImageInformation ( )

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 76 of file itkMRCImageIO.h.

◆ WriteImageInformation() [2/2]

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

privatevirtual

Member Data Documentation

◆ m_MetaDataHeaderName

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 112 of file itkMRCImageIO.h.

◆ m_MRCHeader

MRCHeaderObject::Pointer itk::MRCImageIO::m_MRCHeader {}

private

Definition at line 149 of file itkMRCImageIO.h.

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

itkMRCImageIO.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ Pointer

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ MRCImageIO()

Member Function Documentation

◆ CanReadFile()

◆ CanWriteFile()

◆ GetHeaderSize()

◆ GetNameOfClass()

◆ InternalReadImageInformation()

◆ New()

◆ PrintSelf()

◆ Read()

◆ ReadImageInformation()

◆ UpdateHeaderFromImageIO()

◆ UpdateHeaderWithMinMaxMean() [1/2]

◆ UpdateHeaderWithMinMaxMean() [2/2]

◆ Write()

◆ WriteImageInformation() [1/2]

◆ WriteImageInformation() [2/2]

Member Data Documentation

◆ m_MetaDataHeaderName

◆ m_MRCHeader