#include <itkMINCImageIO.h>

Inheritance diagram for itk::MINCImageIO:

Collaboration diagram for itk::MINCImageIO:

Detailed Description

Class that defines how to read MINC file format.

Author: Leila Baghdadi

Note, like ITK, MINC 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!

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

Definition at line 64 of file itkMINCImageIO.h.

Public Types
typedef Matrix< float, 3, 3 >	MatrixType

typedef SmartPointer< Self >	Pointer

typedef MINCImageIO	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 bool	SupportsDimension (unsigned long dim) override

virtual void	Write (const void *buffer) override

virtual void	WriteImageInformation () override


virtual void	SetCompressionLevel (int _arg)

virtual int	GetCompressionLevel () const

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 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 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 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 noexcept override

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
void	AllocateDimensions (int nDims)

void	CleanupDimensions ()

void	CloseVolume ()

	MINCImageIO ()

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

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

	~MINCImageIO ()

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 ()

Protected Attributes
int	m_CompressionLevel

int	m_DimensionIndices [5]

char **	m_DimensionName

misize_t *	m_DimensionSize

double *	m_DimensionStart

double *	m_DimensionStep

MatrixType	m_DirectionCosines

midimhandle_t *	m_MincApparentDims

midimhandle_t *	m_MincFileDims

int	m_NDims

mihandle_t	m_Volume

miclass_t	m_Volume_class

mitype_t	m_Volume_type

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

Private Member Functions
	MINCImageIO (const Self &) ITK_DELETE_FUNCTION

void	operator= (const Self &) ITK_DELETE_FUNCTION

Member Typedef Documentation

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

Definition at line 71 of file itkMINCImageIO.h.

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

Definition at line 70 of file itkMINCImageIO.h.

typedef MINCImageIO itk::MINCImageIO::Self

Standard class typedefs.

Definition at line 68 of file itkMINCImageIO.h.

typedef ImageIOBase itk::MINCImageIO::Superclass

Definition at line 69 of file itkMINCImageIO.h.

Constructor & Destructor Documentation

itk::MINCImageIO::MINCImageIO ( )

protected

itk::MINCImageIO::~MINCImageIO ( )

protected

itk::MINCImageIO::MINCImageIO ( const Self & )

private

Member Function Documentation

void itk::MINCImageIO::AllocateDimensions ( int nDims )

protected

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

overridevirtual

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

Implements itk::ImageIOBase.

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

overridevirtual

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

Implements itk::ImageIOBase.

void itk::MINCImageIO::CleanupDimensions ( )

protected

void itk::MINCImageIO::CloseVolume ( )

protected

virtual::itk::LightObject::Pointer itk::MINCImageIO::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 int itk::MINCImageIO::GetCompressionLevel ( ) const

virtual

Set/Get the level of compression for the output images. 0-9; 0 = none, 9 = maximum.

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

static Pointer itk::MINCImageIO::New ( )

static

Method for creation through the object factory.

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

private

void itk::MINCImageIO::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.

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

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::MINCImageIO::ReadImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

virtual void itk::MINCImageIO::SetCompressionLevel ( int _arg )

virtual

Set/Get the level of compression for the output images. 0-9; 0 = none, 9 = maximum.

virtual bool itk::MINCImageIO::SupportsDimension ( unsigned long dim )

inlineoverridevirtual

Right now MINC supports up to 3D with multiple components

Reimplemented from itk::ImageIOBase.

Definition at line 80 of file itkMINCImageIO.h.

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

overridevirtual

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::MINCImageIO::WriteImageInformation ( )

overridevirtual

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

Implements itk::ImageIOBase.

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

protected

Member Data Documentation

int itk::MINCImageIO::m_CompressionLevel

protected

Definition at line 137 of file itkMINCImageIO.h.

int itk::MINCImageIO::m_DimensionIndices[5]

protected

Definition at line 132 of file itkMINCImageIO.h.

char** itk::MINCImageIO::m_DimensionName

protected

Definition at line 128 of file itkMINCImageIO.h.

misize_t* itk::MINCImageIO::m_DimensionSize

protected

Definition at line 129 of file itkMINCImageIO.h.

double* itk::MINCImageIO::m_DimensionStart

protected

Definition at line 130 of file itkMINCImageIO.h.

double* itk::MINCImageIO::m_DimensionStep

protected

Definition at line 131 of file itkMINCImageIO.h.

MatrixType itk::MINCImageIO::m_DirectionCosines

protected

Definition at line 142 of file itkMINCImageIO.h.

midimhandle_t* itk::MINCImageIO::m_MincApparentDims

protected

Definition at line 134 of file itkMINCImageIO.h.

midimhandle_t* itk::MINCImageIO::m_MincFileDims

protected

Definition at line 133 of file itkMINCImageIO.h.

int itk::MINCImageIO::m_NDims

protected

Definition at line 124 of file itkMINCImageIO.h.

mihandle_t itk::MINCImageIO::m_Volume

protected

Definition at line 140 of file itkMINCImageIO.h.

miclass_t itk::MINCImageIO::m_Volume_class

protected

Definition at line 136 of file itkMINCImageIO.h.

mitype_t itk::MINCImageIO::m_Volume_type

protected

Definition at line 135 of file itkMINCImageIO.h.

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

itkMINCImageIO.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation