ITK  5.3.0
Insight Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
itk::MRCImageIO Class Reference

#include <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 ConstPointer = SmartPointer< const Self >
using Pointer = SmartPointer< Self >
using Self = ImageIOBase
using Superclass = LightProcessObject
using IndexValueType = ::itk::IndexValueType
using SizeValueType = ::itk::SizeValueType
using IOComponentEnum = itk::IOComponentEnum
using IOFileEnum = itk::IOFileEnum
using IOByteOrderEnum = itk::IOByteOrderEnum
using SizeType = ::itk::intmax_t
using BufferSizeType = ::itk::OffsetValueType
using ArrayOfExtensionsType = std::vector< std::string >
- 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
virtual ::itk::LightObject::Pointer CreateAnother () const
virtual const char * GetNameOfClass () const
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
virtual void SetFileName (const char *_arg)
virtual const char * GetFileName () const
void SetNumberOfDimensions (unsigned int)
virtual unsigned int GetNumberOfDimensions () const
virtual void SetDimensions (unsigned int i, SizeValueType dim)
virtual SizeValueType GetDimensions (unsigned int i) const
virtual void SetOrigin (unsigned int i, double origin)
virtual double GetOrigin (unsigned int i) const
virtual void SetSpacing (unsigned int i, double spacing)
virtual double GetSpacing (unsigned int i) const
virtual void SetDirection (unsigned int i, const std::vector< double > &direction)
virtual void SetDirection (unsigned int i, const vnl_vector< double > &direction)
virtual std::vector< double > GetDirection (unsigned int i) const
virtual std::vector< double > GetDefaultDirection (unsigned int k) const
virtual void SetIORegion (ImageIORegion _arg)
virtual const ImageIORegionGetIORegion () const
virtual void SetPixelType (const ::itk::CommonEnums::IOPixel _arg)
virtual ::itk::CommonEnums::IOPixel GetPixelType () const
virtual void SetComponentType (const IOComponentEnum _arg)
virtual IOComponentEnum GetComponentType () const
virtual const std::type_info & GetComponentTypeInfo () 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 SetCompressionLevel (int _arg)
virtual int GetCompressionLevel () const
virtual void SetCompressor (std::string _c)
virtual const std::string & GetCompressor () const
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 SetWritePalette (bool _arg)
virtual bool GetWritePalette () const
virtual void WritePaletteOn ()
virtual void WritePaletteOff ()
virtual bool GetIsReadAsScalarPlusPalette () const
virtual void SetFileType (const IOFileEnum _arg)
virtual IOFileEnum GetFileType () const
void SetFileTypeToASCII ()
void SetFileTypeToBinary ()
virtual void SetByteOrder (const IOByteOrderEnum _arg)
virtual IOByteOrderEnum GetByteOrder () const
void SetByteOrderToBigEndian ()
void SetByteOrderToLittleEndian ()
std::string GetFileTypeAsString (IOFileEnum) const
std::string GetByteOrderAsString (IOByteOrderEnum) const
virtual SizeType GetPixelStride () const
SizeType GetImageSizeInPixels () const
SizeType GetImageSizeInBytes () const
SizeType GetImageSizeInComponents () const
virtual unsigned int GetComponentSize () const
virtual bool SupportsDimension (unsigned long dim)
virtual ImageIORegion GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
const ArrayOfExtensionsTypeGetSupportedReadExtensions () const
const ArrayOfExtensionsTypeGetSupportedWriteExtensions () const
template<typename TPixel >
void SetTypeInfo (const TPixel *)
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 VLength>
void SetPixelTypeInfo (const Offset< VLength > *)
template<typename TPixel , unsigned VLength>
void SetPixelTypeInfo (const Vector< TPixel, VLength > *)
template<typename TCoordRep , unsigned NPointDimension>
void SetPixelTypeInfo (const Point< TCoordRep, NPointDimension > *)
template<typename TPixel , unsigned VLength>
void SetPixelTypeInfo (const CovariantVector< TPixel, VLength > *)
template<typename TPixel , unsigned 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 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 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 AbortGenerateDataOff ()
virtual void AbortGenerateDataOn ()
virtual const bool & GetAbortGenerateData () const
virtual void SetAbortGenerateData (bool _arg)
virtual void SetProgress (float _arg)
virtual const float & GetProgress () const
void UpdateProgress (float amount)
virtual void UpdateOutputData ()
- Public Member Functions inherited from itk::Object
unsigned long AddObserver (const EventObject &event, Command *)
unsigned long AddObserver (const EventObject &event, Command *) const
unsigned long AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const
virtual void DebugOff () const
virtual void DebugOn () const
CommandGetCommand (unsigned long tag)
bool GetDebug () const
MetaDataDictionaryGetMetaDataDictionary ()
const MetaDataDictionaryGetMetaDataDictionary () const
virtual ModifiedTimeType GetMTime () const
virtual const TimeStampGetTimeStamp () 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)
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
 ImageIOBase ()
 ~ImageIOBase () override
virtual const ImageRegionSplitterBaseGetImageRegionSplitter () const
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
virtual void InternalSetCompressor (const std::string &_compressor)
virtual void Reset (const bool freeDynamic=true)
void Resize (const unsigned int numDimensions, const unsigned int *dimensions)
virtual unsigned int GetPixelSize () const
void ComputeStrides ()
SizeType GetComponentStride () const
SizeType GetRowStride () const
SizeType GetSliceStride () const
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 WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentEnum ctype, SizeType numComp)
virtual void ReadBufferAsASCII (std::istream &is, void *buffer, IOComponentEnum ctype, SizeType numComp)
bool ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)
void AddSupportedReadExtension (const char *extension)
void AddSupportedWriteExtension (const char *extension)
void SetSupportedReadExtensions (const ArrayOfExtensionsType &)
void SetSupportedWriteExtensions (const ArrayOfExtensionsType &)
virtual unsigned int GetActualNumberOfSplitsForWritingCanStreamWrite (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion) const
virtual ImageIORegion GetSplitRegionForWritingCanStreamWrite (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion) const
- Protected Member Functions inherited from itk::LightProcessObject
 LightProcessObject ()
 ~LightProcessObject () override
virtual void GenerateData ()
- Protected Member Functions inherited from itk::Object
 Object ()
 ~Object () override
bool PrintObservers (std::ostream &os, Indent indent) const
virtual void SetTimeStamp (const TimeStamp &timeStamp)
- 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
IOPixelEnum m_PixelType { IOPixelEnum::SCALAR }
IOComponentEnum m_ComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }
IOByteOrderEnum m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }
IOFileEnum m_FileType { IOFileEnum::TypeNotApplicable }
bool m_Initialized
std::string m_FileName
unsigned int m_NumberOfComponents
unsigned int m_NumberOfDimensions { 0 }
bool m_UseCompression { false }
int m_CompressionLevel { 30 }
int m_MaximumCompressionLevel { 100 }
std::string m_Compressor { "uninitialized" }
bool m_UseStreamedReading
bool m_UseStreamedWriting
bool m_ExpandRGBPalette
bool m_IsReadAsScalarPlusPalette
bool m_WritePalette
ImageIORegion m_IORegion
std::vector< SizeValueTypem_Dimensions
std::vector< double > m_Spacing
std::vector< double > m_Origin
std::vector< std::vector< double > > m_Direction
std::vector< SizeTypem_Strides
- Protected Attributes inherited from itk::LightObject
std::atomic< int > m_ReferenceCount

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.

See also
ImageFileWriter ImageFileReader ImageIOBase

Definition at line 58 of file itkMRCImageIO.h.

Member Typedef Documentation

◆ Pointer

Definition at line 66 of file itkMRCImageIO.h.

◆ Self

Standard class type aliases.

Definition at line 64 of file itkMRCImageIO.h.

◆ Superclass

Definition at line 65 of file itkMRCImageIO.h.

Constructor & Destructor Documentation

◆ MRCImageIO()

itk::MRCImageIO::MRCImageIO ( )

Member Function Documentation

◆ CanReadFile()

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

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

Implements itk::ImageIOBase.

◆ CanWriteFile()

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

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.

◆ CreateAnother()

virtual::itk::LightObject::Pointer itk::MRCImageIO::CreateAnother ( ) const

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.

◆ GetHeaderSize()

SizeType itk::MRCImageIO::GetHeaderSize ( ) const

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()

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

Run-time type information (and related methods).

Reimplemented from itk::StreamingImageIOBase.

◆ InternalReadImageInformation()

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

◆ New()

static Pointer itk::MRCImageIO::New ( )

Method for creation through the object factory.

◆ PrintSelf()

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

Types for managing image size and image index components.

Reimplemented from itk::StreamingImageIOBase.

◆ Read()

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

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

◆ ReadImageInformation()

void itk::MRCImageIO::ReadImageInformation ( )

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 ( )

◆ UpdateHeaderWithMinMaxMean() [1/2]

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

◆ UpdateHeaderWithMinMaxMean() [2/2]

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

◆ Write()

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

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 ( )

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)

Member Data Documentation

◆ m_MetaDataHeaderName

const char* itk::MRCImageIO::m_MetaDataHeaderName
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

Definition at line 149 of file itkMRCImageIO.h.

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