#include <itkFreeSurferAsciiMeshIO.h>

Inheritance diagram for itk::FreeSurferAsciiMeshIO:

Collaboration diagram for itk::FreeSurferAsciiMeshIO:

Detailed Description

This class defines how to read and write freesurfer ASCII surface format. To use IO factory, define the suffix as *.fsa.

Definition at line 36 of file itkFreeSurferAsciiMeshIO.h.

Public Types
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef FreeSurferAsciiMeshIO	Self

typedef Superclass::SizeValueType	SizeValueType

typedef MeshIOBase	Superclass

Public Types inherited from itk::MeshIOBase
typedef std::vector< std::string >	ArrayOfExtensionsType

enum	ByteOrder { BigEndian, LittleEndian, OrderNotApplicable }

enum	CellGeometryType { VERTEX_CELL = 0, LINE_CELL, TRIANGLE_CELL, QUADRILATERAL_CELL, POLYGON_CELL, TETRAHEDRON_CELL, HEXAHEDRON_CELL, QUADRATIC_EDGE_CELL, QUADRATIC_TRIANGLE_CELL, LAST_ITK_CELL, MAX_ITK_CELLS = 255 }

typedef SmartPointer< const Self >	ConstPointer

enum	FileType { ASCII, BINARY, TYPENOTAPPLICABLE }

enum	IOComponentType { UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT, INT, ULONG, LONG, LONGLONG, ULONGLONG, FLOAT, DOUBLE, LDOUBLE }

enum	IOPixelType { UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR, POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D, COMPLEX, FIXEDARRAY, ARRAY, MATRIX, VARIABLELENGTHVECTOR, VARIABLESIZEMATRIX }

typedef SmartPointer< Self >	Pointer

typedef MeshIOBase	Self

typedef IdentifierType	SizeValueType

typedef std::streamoff	StreamOffsetType

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 *FileNameToRead) override

virtual bool	CanWriteFile (const char *FileNameToWrite) override

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

virtual const char *	GetNameOfClass () const

virtual void	ReadCellData (void *buffer) override

virtual void	ReadCells (void *buffer) override

virtual void	ReadMeshInformation () override

virtual void	ReadPointData (void *buffer) override

virtual void	ReadPoints (void *buffer) override

virtual void	Write () override

virtual void	WriteCellData (void *buffer) override

virtual void	WriteCells (void *buffer) override

virtual void	WriteMeshInformation () override

virtual void	WritePointData (void *buffer) override

virtual void	WritePoints (void *buffer) override

Public Member Functions inherited from itk::MeshIOBase
std::string	GetByteOrderAsString (ByteOrder) const

unsigned int	GetComponentSize (IOComponentType componentType) const

std::string	GetComponentTypeAsString (IOComponentType) const

std::string	GetFileTypeAsString (FileType) const

std::string	GetPixelTypeAsString (IOPixelType) const

const ArrayOfExtensionsType &	GetSupportedReadExtensions () const

const ArrayOfExtensionsType &	GetSupportedWriteExtensions () const

void	SetByteOrderToBigEndian ()

void	SetByteOrderToLittleEndian ()

void	SetFileTypeToASCII ()

void	SetFileTypeToBinary ()

template<typename T >
void	SetPixelType (const T &, bool UsePointPixel=true)

template<typename T >
void	SetPixelType (const RGBPixel< T > &, bool UsePointPixel=true)

template<typename T >
void	SetPixelType (const RGBAPixel< T > &, bool UsePointPixel=true)

template<typename T , unsigned int VLength>
void	SetPixelType (const Vector< T, VLength > &, bool UsePointPixel=true)

template<typename T , unsigned int VLength>
void	SetPixelType (const CovariantVector< T, VLength > &, bool UsePointPixel=true)

template<typename T , unsigned int VLength>
void	SetPixelType (const FixedArray< T, VLength > &, bool UsePointPixel=true)

template<typename T , unsigned int VLength>
void	SetPixelType (const SymmetricSecondRankTensor< T, VLength >, bool UsePointPixel=true)

template<typename T >
void	SetPixelType (const DiffusionTensor3D< T > &, bool UsePointPixel=true)

template<typename T , unsigned int NR, unsigned int NC>
void	SetPixelType (const Matrix< T, NR, NC > &, bool UsePointPixel=true)

template<typename T >
void	SetPixelType (const std::complex< T > &, bool UsePointPixel=true)

template<typename T >
void	SetPixelType (const Array< T > &array, bool UsePointPixel=true)

template<typename T >
void	SetPixelType (const VariableLengthVector< T > &vector, bool UsePointPixel=true)

template<typename T >
void	SetPixelType (const VariableSizeMatrix< T > &matrix, bool UsePointPixel=true)

virtual void	SetFileName (const char *_arg)

virtual const char *	GetFileName () const

virtual void	SetPointPixelType (const IOPixelType _arg)

virtual IOPixelType	GetPointPixelType () const

virtual void	SetCellPixelType (const IOPixelType _arg)

virtual IOPixelType	GetCellPixelType () const

virtual void	SetPointComponentType (const IOComponentType _arg)

virtual IOComponentType	GetPointComponentType () const

virtual void	SetCellComponentType (const IOComponentType _arg)

virtual IOComponentType	GetCellComponentType () const

virtual void	SetPointPixelComponentType (const IOComponentType _arg)

virtual IOComponentType	GetPointPixelComponentType () const

virtual void	SetCellPixelComponentType (const IOComponentType _arg)

virtual IOComponentType	GetCellPixelComponentType () const

virtual void	SetNumberOfPointPixelComponents (unsigned int _arg)

virtual unsigned int	GetNumberOfPointPixelComponents () const

virtual void	SetNumberOfCellPixelComponents (unsigned int _arg)

virtual unsigned int	GetNumberOfCellPixelComponents () const

virtual void	SetPointDimension (unsigned int _arg)

virtual unsigned int	GetPointDimension () const

virtual void	SetNumberOfPoints (SizeValueType _arg)

virtual SizeValueType	GetNumberOfPoints () const

virtual void	SetNumberOfCells (SizeValueType _arg)

virtual SizeValueType	GetNumberOfCells () const

virtual void	SetNumberOfPointPixels (SizeValueType _arg)

virtual SizeValueType	GetNumberOfPointPixels () const

virtual void	SetNumberOfCellPixels (SizeValueType _arg)

virtual SizeValueType	GetNumberOfCellPixels () const

virtual void	SetCellBufferSize (SizeValueType _arg)

virtual SizeValueType	GetCellBufferSize () const

virtual void	SetUpdatePoints (bool _arg)

virtual bool	GetUpdatePoints () const

virtual void	SetUpdateCells (bool _arg)

virtual bool	GetUpdateCells () const

virtual void	SetUpdatePointData (bool _arg)

virtual bool	GetUpdatePointData () const

virtual void	SetUpdateCellData (bool _arg)

virtual bool	GetUpdateCellData () const

virtual void	SetFileType (const FileType _arg)

virtual FileType	GetFileType () const

virtual void	SetByteOrder (const ByteOrder _arg)

virtual ByteOrder	GetByteOrder () const

virtual void	SetUseCompression (bool _arg)

virtual bool	GetUseCompression () const

virtual void	UseCompressionOn ()

virtual void	UseCompressionOff ()

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::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	CloseFile ()

	FreeSurferAsciiMeshIO ()

void	OpenFile ()

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

template<typename TInput , typename TOutput >
void	ReadCellsBuffer (TInput input, TOutput output)

template<typename T >
void	WriteCells (T *buffer, std::ofstream &outputFile, T label=itk::NumericTraits< T >::ZeroValue())

virtual	~FreeSurferAsciiMeshIO () override


template<typename T >
void	WritePoints (T *buffer, std::ofstream &outputFile, T label=itk::NumericTraits< T >::ZeroValue())

Protected Member Functions inherited from itk::MeshIOBase
void	AddSupportedReadExtension (const char *extension)

void	AddSupportedWriteExtension (const char *extension)

	MeshIOBase ()

template<typename T >
void	ReadBufferAsBinary (T *buffer, std::ifstream &inputFile, SizeValueType numberOfComponents)

virtual	~MeshIOBase () override

template<typename T >
void	ReadBufferAsAscii (T *buffer, std::ifstream &inputFile, SizeValueType numberOfComponents)

template<typename T >
void	WriteBufferAsAscii (T *buffer, std::ofstream &outputFile, SizeValueType numberOfLines, SizeValueType numberOfComponents)

template<typename TOutput , typename TInput >
void	WriteBufferAsBinary (TInput *buffer, std::ofstream &outputFile, SizeValueType numberOfComponents)

template<typename TInput , typename TOutput >
void	ReadCellsBuffer (TInput input, TOutput output)

template<typename TInput , typename TOutput >
void	ReadCellsBuffer (TInput input, TOutput output, MeshIOBase::CellGeometryType type)

template<typename TInput , typename TOutput >
void	WriteCellsBuffer (TInput input, TOutput output, CellGeometryType cellType, unsigned int numberOfPoints, SizeValueType numberOfCells)

template<typename TInput , typename TOutput >
void	WriteCellsBuffer (TInput input, TOutput output, CellGeometryType cellType, SizeValueType numberOfCells)

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)

virtual	~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 Attributes
std::ifstream	m_InputFile

Additional Inherited Members
Protected Attributes inherited from itk::MeshIOBase
ByteOrder	m_ByteOrder

SizeValueType	m_CellBufferSize

IOComponentType	m_CellComponentType

IOComponentType	m_CellPixelComponentType

IOPixelType	m_CellPixelType

std::string	m_FileName

FileType	m_FileType

unsigned int	m_NumberOfCellPixelComponents

SizeValueType	m_NumberOfCellPixels

SizeValueType	m_NumberOfCells

unsigned int	m_NumberOfPointPixelComponents

SizeValueType	m_NumberOfPointPixels

SizeValueType	m_NumberOfPoints

IOComponentType	m_PointComponentType

SizeValueType	m_PointDimension

IOComponentType	m_PointPixelComponentType

IOPixelType	m_PointPixelType

bool	m_UpdateCellData

bool	m_UpdateCells

bool	m_UpdatePointData

bool	m_UpdatePoints

bool	m_UseCompression

Protected Attributes inherited from itk::LightObject
AtomicInt< int >	m_ReferenceCount

Member Typedef Documentation

typedef SmartPointer< const Self > itk::FreeSurferAsciiMeshIO::ConstPointer

Definition at line 42 of file itkFreeSurferAsciiMeshIO.h.

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

Definition at line 43 of file itkFreeSurferAsciiMeshIO.h.

typedef FreeSurferAsciiMeshIO itk::FreeSurferAsciiMeshIO::Self

Standard class typedefs.

Definition at line 40 of file itkFreeSurferAsciiMeshIO.h.

typedef Superclass::SizeValueType itk::FreeSurferAsciiMeshIO::SizeValueType

Definition at line 45 of file itkFreeSurferAsciiMeshIO.h.

typedef MeshIOBase itk::FreeSurferAsciiMeshIO::Superclass

Definition at line 41 of file itkFreeSurferAsciiMeshIO.h.

Constructor & Destructor Documentation

itk::FreeSurferAsciiMeshIO::FreeSurferAsciiMeshIO ( )

protected

virtual itk::FreeSurferAsciiMeshIO::~FreeSurferAsciiMeshIO ( )

overrideprotectedvirtual

Member Function Documentation

virtual bool itk::FreeSurferAsciiMeshIO::CanReadFile ( const char * FileNameToRead )

overridevirtual

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

Parameters

FileNameToRead The name of the file to test for reading.

Postcondition: Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite

Returns: Returns true if this MeshIO can read the file specified.

Implements itk::MeshIOBase.

virtual bool itk::FreeSurferAsciiMeshIO::CanWriteFile ( const char * FileNameToWrite )

overridevirtual

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

Parameters

FileNameToWrite The name of the file to test for writing.

Postcondition: Sets classes MeshIOBase::m_FileName variable to be FileNameToWrite

Returns: Returns true if this MeshIO can write the file specified.

Implements itk::MeshIOBase.

void itk::FreeSurferAsciiMeshIO::CloseFile ( )

protected

virtual::itk::LightObject::Pointer itk::FreeSurferAsciiMeshIO::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 const char* itk::FreeSurferAsciiMeshIO::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from itk::MeshIOBase.

static Pointer itk::FreeSurferAsciiMeshIO::New ( )

static

Method for creation through the object factory.

void itk::FreeSurferAsciiMeshIO::OpenFile ( )

protected

virtual void itk::FreeSurferAsciiMeshIO::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::MeshIOBase.

virtual void itk::FreeSurferAsciiMeshIO::ReadCellData ( void * buffer )

overridevirtual

Implements itk::MeshIOBase.

virtual void itk::FreeSurferAsciiMeshIO::ReadCells ( void * buffer )

overridevirtual

Implements itk::MeshIOBase.

template<typename TInput , typename TOutput >