ITK  5.0.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
itk::MGHImageIO Class Reference

#include <itkMGHImageIO.h>

+ Inheritance diagram for itk::MGHImageIO:
+ Collaboration diagram for itk::MGHImageIO:

Detailed Description

Class that defines how to read MGH file format. Originally developed as part of the Slicer software package under grants XXXX.

Author
Hans J. Johnson

Definition at line 40 of file itkMGHImageIO.h.

Public Types

using Pointer = SmartPointer< Self >
 
using Self = MGHImageIO
 
using Superclass = ImageIOBase
 
- Public Types inherited from itk::ImageIOBase
using ArrayOfExtensionsType = std::vector< std::string >
 
using BufferSizeType = ::itk::OffsetValueType
 
enum  ByteOrder {
  BigEndian,
  LittleEndian,
  OrderNotApplicable
}
 
using ConstPointer = SmartPointer< const Self >
 
enum  FileType {
  ASCII,
  Binary,
  TypeNotApplicable
}
 
using IndexValueType = ::itk::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
}
 
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 *FileNameToRead) override
 
bool CanWriteFile (const char *FileNameToWrite) 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::ImageIOBase
virtual bool CanStreamRead ()
 
virtual bool CanStreamWrite ()
 
virtual ImageIORegion GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const
 
virtual unsigned int GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
 
std::string GetByteOrderAsString (ByteOrder) 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 ArrayOfExtensionsTypeGetSupportedReadExtensions () const
 
const ArrayOfExtensionsTypeGetSupportedWriteExtensions () 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 ImageIORegionGetIORegion () 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
 
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 noexceptoverride
 
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
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 ()
 

Protected Member Functions

 MGHImageIO ()
 
void PrintSelf (std::ostream &os, Indent indent) const override
 
void ReadVolumeHeader ()
 
 ~MGHImageIO () override
 
- 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
 
virtual bool HasSupportedReadExtension (const char *fileName, bool ignoreCase=true)
 
virtual bool HasSupportedWriteExtension (const char *fileName, bool ignoreCase=true)
 
- 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)
 
 ~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 CloseFile ()
 
unsigned int GetComponentSize () const override
 
std::string GetOrientation (itk::Matrix< double > directions)
 
void OpenFile ()
 
void PermuteFrameValues (const void *buffer, char *tempmemory)
 
template<typename TDiskType , typename TOutType >
int TRead (TOutType &outValue)
 
template<typename TInType , typename TDiskType >
int TWrite (const TInType inValue)
 
int TWrite (const char *buf, const unsigned long count)
 
void WriteData (const void *buffer)
 
void WriteHeader ()
 
bool IsCompressedFilename (const std::string fname)
 
void SwapBytesIfNecessary (void *const buffer, const unsigned long numberOfPixels)
 

Private Attributes

gzFile m_GZFile
 
bool m_IsCompressed
 
std::ofstream m_Output
 

Static Private Attributes

static const unsigned int FS_DIMENSION_HEADER_SIZE = sizeof(int) * 7
 
static const unsigned int FS_RAS_HEADER_SIZE = (sizeof(float) * 15) + sizeof(short)
 
static const unsigned int FS_UNUSED_HEADER_SIZE = 256 - FS_RAS_HEADER_SIZE
 
static const unsigned int FS_WHOLE_HEADER_SIZE
 
static const int MRI_FLOAT = 3
 
static const int MRI_INT = 1
 
static const int MRI_SHORT = 4
 
static const int MRI_TENSOR = 6
 
static const int MRI_UCHAR = 0
 

Additional Inherited Members

- Protected Attributes inherited from itk::ImageIOBase
ByteOrder m_ByteOrder {OrderNotApplicable}
 
IOComponentType m_ComponentType {UNKNOWNCOMPONENTTYPE}
 
std::vector< SizeValueTypem_Dimensions
 
std::vector< std::vector
< double > > 
m_Direction
 
bool m_ExpandRGBPalette
 
std::string m_FileName
 
FileType m_FileType {TypeNotApplicable}
 
bool m_Initialized
 
ImageIORegion m_IORegion
 
bool m_IsReadAsScalarPlusPalette
 
unsigned int m_NumberOfComponents
 
unsigned int m_NumberOfDimensions {0}
 
std::vector< double > m_Origin
 
IOPixelType m_PixelType {SCALAR}
 
std::vector< double > m_Spacing
 
std::vector< SizeTypem_Strides
 
bool m_UseCompression
 
bool m_UseStreamedReading
 
bool m_UseStreamedWriting
 
- Protected Attributes inherited from itk::LightObject
std::atomic< int > m_ReferenceCount
 

Member Typedef Documentation

Definition at line 46 of file itkMGHImageIO.h.

Standard class type alias.

Definition at line 44 of file itkMGHImageIO.h.

Definition at line 45 of file itkMGHImageIO.h.

Constructor & Destructor Documentation

itk::MGHImageIO::MGHImageIO ( )
protected
itk::MGHImageIO::~MGHImageIO ( )
overrideprotected

Member Function Documentation

bool itk::MGHImageIO::CanReadFile ( const char *  FileNameToRead)
overridevirtual

Determine if the file can be read with this ImageIO implementation.

Parameters
FileNameToReadThe name of the file to test for reading.
Postcondition
Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
Returns
Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

bool itk::MGHImageIO::CanWriteFile ( const char *  FileNameToWrite)
overridevirtual

Determine if the file can be written with this ImageIO implementation.

Parameters
FileNameToWriteThe name of the file to test for writing.
Postcondition
Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
Returns
Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

void itk::MGHImageIO::CloseFile ( )
private
virtual::itk::LightObject::Pointer itk::MGHImageIO::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.

unsigned int itk::MGHImageIO::GetComponentSize ( ) const
overrideprivatevirtual

Compute the size (in bytes) of the components of a pixel. For example, and RGB pixel of unsigned char would have a component size of 1 byte. This method can be invoked only after the component type is set.

Reimplemented from itk::ImageIOBase.

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

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

std::string itk::MGHImageIO::GetOrientation ( itk::Matrix< double >  directions)
private
bool itk::MGHImageIO::IsCompressedFilename ( const std::string  fname)
private

check if a filename is for a compressed file

static Pointer itk::MGHImageIO::New ( )
static

Method for creation through the object factory.

void itk::MGHImageIO::OpenFile ( )
private
void itk::MGHImageIO::PermuteFrameValues ( const void *  buffer,
char *  tempmemory 
)
private
void itk::MGHImageIO::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::ImageIOBase.

void itk::MGHImageIO::Read ( void *  buffer)
overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

void itk::MGHImageIO::ReadImageInformation ( )
overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

void itk::MGHImageIO::ReadVolumeHeader ( )
protected
void itk::MGHImageIO::SwapBytesIfNecessary ( void *const  buffer,
const unsigned long  numberOfPixels 
)
private

processes the actual data buffer

template<typename TDiskType , typename TOutType >
int itk::MGHImageIO::TRead ( TOutType &  outValue)
private
template<typename TInType , typename TDiskType >
int itk::MGHImageIO::TWrite ( const TInType  inValue)
private
int itk::MGHImageIO::TWrite ( const char *  buf,
const unsigned long  count 
)
private
void itk::MGHImageIO::Write ( const void *  buffer)
overridevirtual

Writes the data to disk from the memory buffer provided. Make sure that the IORegions has been set properly.

Implements itk::ImageIOBase.

void itk::MGHImageIO::WriteData ( const void *  buffer)
private
void itk::MGHImageIO::WriteHeader ( )
private

examines the direction cosines and creates encapsulation data

void itk::MGHImageIO::WriteImageInformation ( )
overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

Member Data Documentation

const unsigned int itk::MGHImageIO::FS_DIMENSION_HEADER_SIZE = sizeof(int) * 7
staticprivate

Definition at line 98 of file itkMGHImageIO.h.

const unsigned int itk::MGHImageIO::FS_RAS_HEADER_SIZE = (sizeof(float) * 15) + sizeof(short)
staticprivate

Definition at line 99 of file itkMGHImageIO.h.

const unsigned int itk::MGHImageIO::FS_UNUSED_HEADER_SIZE = 256 - FS_RAS_HEADER_SIZE
staticprivate

Definition at line 100 of file itkMGHImageIO.h.

const unsigned int itk::MGHImageIO::FS_WHOLE_HEADER_SIZE
staticprivate
Initial value:

Definition at line 101 of file itkMGHImageIO.h.

gzFile itk::MGHImageIO::m_GZFile
private

Definition at line 124 of file itkMGHImageIO.h.

bool itk::MGHImageIO::m_IsCompressed
private

Definition at line 123 of file itkMGHImageIO.h.

std::ofstream itk::MGHImageIO::m_Output
private

Definition at line 125 of file itkMGHImageIO.h.

const int itk::MGHImageIO::MRI_FLOAT = 3
staticprivate

Definition at line 95 of file itkMGHImageIO.h.

const int itk::MGHImageIO::MRI_INT = 1
staticprivate

Definition at line 94 of file itkMGHImageIO.h.

const int itk::MGHImageIO::MRI_SHORT = 4
staticprivate

Definition at line 96 of file itkMGHImageIO.h.

const int itk::MGHImageIO::MRI_TENSOR = 6
staticprivate

Definition at line 97 of file itkMGHImageIO.h.

const int itk::MGHImageIO::MRI_UCHAR = 0
staticprivate

Definition at line 93 of file itkMGHImageIO.h.


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