ITK  4.8.0
Insight Segmentation and Registration 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
Module ITKIOMRC

#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 http://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,
  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 itk::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 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, unsigned int 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 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 ()
 
- Protected Member Functions inherited from itk::LightProcessObject
virtual void GenerateData ()
 
 LightProcessObject ()
 
 ~LightProcessObject ()
 
- 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 ()
 
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
 
std::string m_FileName
 
FileType m_FileType
 
bool m_Initialized
 
ImageIORegion m_IORegion
 
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
itk::MRCImageIO::MRCImageIO ( const Self &  )
private

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.

void itk::MRCImageIO::operator= ( const Self &  )
private
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 138 of file itkMRCImageIO.h.

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