itk::MINC2ImageIO Class Reference

#include <itkMINC2ImageIO.h>

Inheritance diagram for itk::MINC2ImageIO:

Collaboration diagram for itk::MINC2ImageIO:

Detailed Description

Class that defines how to read MINC2 file format. Note,like ITK, MINC2 is N dimensional and dimensions can be submitted in any arbitrary order. Here we make sure the dimensions are ordered as xspace, yspace, zspace, time and vector_dimension and so on or xfrequencey, yfrequency, zfrequency, tfrequency and vector_dimension and so on NOTE** This class only reads the regularly sampled dimensions as I am not sure how to deal with "iregularly sampled" dimensions yet!

Author

Leila Baghdadi This code was contributed in the Insight Journal paper: "MINC2.0 IO Support for ITK" by Baghdadi L. http://hdl.handle.net/1926/191 http://www.insight-journal.org/browse/publication/88

Definition at line 61 of file itkMINC2ImageIO.h.

Public Types
typedef Matrix< float, 3, 3 >	MatrixType
typedef SmartPointer< Self >	Pointer
typedef MINC2ImageIO	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 *)
virtual bool	CanWriteFile (const char *)
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
char *	GetDimensionOrder ()
virtual const char *	GetNameOfClass () const
virtual void	Read (void *buffer)
virtual void	ReadImageInformation ()
void	SetDimensionOrder (char *dimorder)
virtual void	Write (const void *buffer)
virtual void	WriteImageInformation ()
void	XYZFromDirectionCosines (midimhandle_t *hdims, int *dim_indices, unsigned int *number_of_components)
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 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 unsigned int	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, std::vector< double > &direction)
virtual void	SetDirection (unsigned int i, vnl_vector< double > &direction)
void	SetFileTypeToBinary ()
void	SetNumberOfDimensions (unsigned int)
virtual void	SetOrigin (unsigned int i, double origin)
template<class 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 ()
virtual void	SetPixelType (const IOPixelType _arg)
virtual IOPixelType	GetPixelType () const
virtual void	SetNumberOfComponents (unsigned int _arg)
virtual const unsigned int &	GetNumberOfComponents ()
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 ()
virtual void	SetAbortGenerateData (bool _arg)
virtual void	UpdateOutputData ()
void	UpdateProgress (float amount)
virtual void	SetProgress (float _arg)
virtual const float &	GetProgress ()
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 (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) 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
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int)
virtual void	UnRegister () 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
int	CheckDimensionOrder (char *userdimorder)
virtual char *	GetDimensionName (unsigned int i)
	MINC2ImageIO ()
void	PrintSelf (std::ostream &os, Indent indent) const
virtual void	SetDimensionName (unsigned int i, char *name)
void	WriteSlice (std::string &fileName, const void *buffer)
	~MINC2ImageIO ()
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 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	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 ()

Protected Attributes
int	m_Complex
int *	m_DimensionIndices
char **	m_DimensionName
char *	m_DimensionOrder
unsigned int *	m_DimensionSize
double *	m_DimensionStart
double *	m_DimensionStep
MatrixType	m_DirectionCosines
unsigned int	m_NDims
double	m_OriginalStart [3]
double	m_Scale
double	m_Shift
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

Private Member Functions
	MINC2ImageIO (const Self &)
void	operator= (const Self &)
void	SetSliceScalingFromGlobalScaling (mihandle_t volume)
void	SetSliceScalingFromLocalScaling (mihandle_t volume)

Additional Inherited Members
Protected Types inherited from itk::LightObject
typedef int	InternalReferenceCountType

Member Typedef Documentation

typedef Matrix< float, 3, 3 > itk::MINC2ImageIO::MatrixType

Definition at line 68 of file itkMINC2ImageIO.h.

typedef SmartPointer< Self > itk::MINC2ImageIO::Pointer

Definition at line 67 of file itkMINC2ImageIO.h.

typedef MINC2ImageIO itk::MINC2ImageIO::Self

Standard class typedefs.

Definition at line 65 of file itkMINC2ImageIO.h.

typedef ImageIOBase itk::MINC2ImageIO::Superclass

Definition at line 66 of file itkMINC2ImageIO.h.

Constructor & Destructor Documentation

itk::MINC2ImageIO::MINC2ImageIO ( )

protected

itk::MINC2ImageIO::~MINC2ImageIO ( )

protected

itk::MINC2ImageIO::MINC2ImageIO ( const Self &  )

private

Member Function Documentation

virtual bool itk::MINC2ImageIO::CanReadFile ( const char *  )

virtual

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

Implements itk::ImageIOBase.

virtual bool itk::MINC2ImageIO::CanWriteFile ( const char *  )

virtual

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

Implements itk::ImageIOBase.

int itk::MINC2ImageIO::CheckDimensionOrder ( char *  userdimorder )

protected

virtual::itk::LightObject::Pointer itk::MINC2ImageIO::CreateAnother ( void  ) 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 char* itk::MINC2ImageIO::GetDimensionName ( unsigned int  i )

inlineprotectedvirtual

Definition at line 121 of file itkMINC2ImageIO.h.

char* itk::MINC2ImageIO::GetDimensionOrder ( )

inline

Definition at line 102 of file itkMINC2ImageIO.h.

virtual const char* itk::MINC2ImageIO::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

static Pointer itk::MINC2ImageIO::New ( )

static

Method for creation through the object factory.

void itk::MINC2ImageIO::operator= ( const Self &  )

private

void itk::MINC2ImageIO::PrintSelf ( std::ostream &  os, Indent  indent  ) const

protectedvirtual

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.

virtual void itk::MINC2ImageIO::Read ( void *  buffer )

virtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::MINC2ImageIO::ReadImageInformation ( )

virtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

virtual void itk::MINC2ImageIO::SetDimensionName ( unsigned int  i, char *  name  )

protectedvirtual

void itk::MINC2ImageIO::SetDimensionOrder ( char *  dimorder )

inline

Definition at line 103 of file itkMINC2ImageIO.h.

void itk::MINC2ImageIO::SetSliceScalingFromGlobalScaling ( mihandle_t  volume )

private

void itk::MINC2ImageIO::SetSliceScalingFromLocalScaling ( mihandle_t  volume )

private

virtual void itk::MINC2ImageIO::Write ( const void *  buffer )

virtual

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

Implements itk::ImageIOBase.

virtual void itk::MINC2ImageIO::WriteImageInformation ( )

virtual

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

Implements itk::ImageIOBase.

void itk::MINC2ImageIO::WriteSlice ( std::string &  fileName, const void *  buffer  )

protected

void itk::MINC2ImageIO::XYZFromDirectionCosines	(	midimhandle_t *	hdims,
		int *	dim_indices,
		unsigned int *	number_of_components
	)

Member Data Documentation

int itk::MINC2ImageIO::m_Complex

protected

Definition at line 146 of file itkMINC2ImageIO.h.

int* itk::MINC2ImageIO::m_DimensionIndices

protected

Definition at line 136 of file itkMINC2ImageIO.h.

char** itk::MINC2ImageIO::m_DimensionName

protected

Definition at line 118 of file itkMINC2ImageIO.h.

char* itk::MINC2ImageIO::m_DimensionOrder

protected

Definition at line 123 of file itkMINC2ImageIO.h.

unsigned int* itk::MINC2ImageIO::m_DimensionSize

protected

Definition at line 130 of file itkMINC2ImageIO.h.

double* itk::MINC2ImageIO::m_DimensionStart

protected

Definition at line 131 of file itkMINC2ImageIO.h.

double* itk::MINC2ImageIO::m_DimensionStep

protected

Definition at line 132 of file itkMINC2ImageIO.h.

MatrixType itk::MINC2ImageIO::m_DirectionCosines

protected

Definition at line 134 of file itkMINC2ImageIO.h.

unsigned int itk::MINC2ImageIO::m_NDims

protected

Definition at line 116 of file itkMINC2ImageIO.h.

double itk::MINC2ImageIO::m_OriginalStart[3]

protected

Definition at line 144 of file itkMINC2ImageIO.h.

double itk::MINC2ImageIO::m_Scale

protected

Definition at line 127 of file itkMINC2ImageIO.h.

double itk::MINC2ImageIO::m_Shift

protected

Definition at line 126 of file itkMINC2ImageIO.h.

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

• itkMINC2ImageIO.h