#include <itkFreeSurferAsciiMeshIO.h>

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 37 of file itkFreeSurferAsciiMeshIO.h.

Inheritance diagram for itk::FreeSurferAsciiMeshIO:

Collaboration diagram for itk::FreeSurferAsciiMeshIO:

Public Types
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = FreeSurferAsciiMeshIO

using	SizeValueType = Superclass::SizeValueType

using	Superclass = MeshIOBase

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

using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = MeshIOBase

using	SizeValueType = IdentifierType

using	StreamOffsetType = std::streamoff

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 *fileName) override

bool	CanWriteFile (const char *fileName) override

const char *	GetNameOfClass () const override

void	ReadCellData (void *buffer) override

void	ReadCells (void *buffer) override

void	ReadMeshInformation () override

void	ReadPointData (void *buffer) override

void	ReadPoints (void *buffer) override

void	Write () override

void	WriteCellData (void *buffer) override

void	WriteCells (void *buffer) override

void	WriteMeshInformation () override

void	WritePointData (void *buffer) override

void	WritePoints (void *buffer) override

Public Member Functions inherited from itk::MeshIOBase
virtual bool	CanReadFile (const char *)=0

virtual bool	CanWriteFile (const char *)=0

std::string	GetByteOrderAsString (IOByteOrderEnum) const

unsigned int	GetComponentSize (IOComponentEnum componentType) const

std::string	GetComponentTypeAsString (IOComponentEnum) const

std::string	GetFileTypeAsString (IOFileEnum) const

const char *	GetNameOfClass () const override

std::string	GetPixelTypeAsString (IOPixelEnum) const

const ArrayOfExtensionsType &	GetSupportedReadExtensions () const

const ArrayOfExtensionsType &	GetSupportedWriteExtensions () const

virtual void	ReadCellData (void *buffer)=0

virtual void	ReadCells (void *buffer)=0

virtual void	ReadMeshInformation ()=0

virtual void	ReadPointData (void *buffer)=0

virtual void	ReadPoints (void *buffer)=0

void	SetByteOrderToBigEndian ()

void	SetByteOrderToLittleEndian ()

void	SetFileTypeToASCII ()

void	SetFileTypeToBinary ()

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

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

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

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

template<typename T , unsigned int VRows, unsigned int VColumns>
void	SetPixelType (const Matrix< T, VRows, VColumns > &, bool usePointPixel=true)

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

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

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

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

template<typename T >
void	SetPixelType (const T &, 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)

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

virtual void	Write ()=0

virtual void	WriteCellData (void *buffer)=0

virtual void	WriteCells (void *buffer)=0

virtual void	WriteMeshInformation ()=0

virtual void	WritePointData (void *buffer)=0

virtual void	WritePoints (void *buffer)=0

virtual void	SetFileName (const char *_arg)

virtual const char *	GetFileName () const

virtual void	SetPointPixelType (const itk::CommonEnums::IOPixel _arg)

virtual itk::CommonEnums::IOPixel	GetPointPixelType () const

virtual void	SetCellPixelType (const itk::CommonEnums::IOPixel _arg)

virtual itk::CommonEnums::IOPixel	GetCellPixelType () const

virtual void	SetPointComponentType (const itk::CommonEnums::IOComponent _arg)

virtual itk::CommonEnums::IOComponent	GetPointComponentType () const

virtual void	SetCellComponentType (const itk::CommonEnums::IOComponent _arg)

virtual itk::CommonEnums::IOComponent	GetCellComponentType () const

virtual void	SetPointPixelComponentType (const itk::CommonEnums::IOComponent _arg)

virtual itk::CommonEnums::IOComponent	GetPointPixelComponentType () const

virtual void	SetCellPixelComponentType (const itk::CommonEnums::IOComponent _arg)

virtual itk::CommonEnums::IOComponent	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	UpdatePointsOn ()

virtual void	SetUpdateCells (bool _arg)

virtual bool	GetUpdateCells () const

virtual void	UpdateCellsOn ()

virtual void	SetUpdatePointData (bool _arg)

virtual bool	GetUpdatePointData () const

virtual void	UpdatePointDataOn ()

virtual void	SetUpdateCellData (bool _arg)

virtual bool	GetUpdateCellData () const

virtual void	UpdateCellDataOn ()

virtual void	SetFileType (const IOFileEnum _arg)

virtual IOFileEnum	GetFileType () const

virtual void	SetByteOrder (const IOByteOrderEnum _arg)

virtual IOByteOrderEnum	GetByteOrder () const

virtual void	SetUseCompression (bool _arg)

virtual bool	GetUseCompression () const

virtual void	UseCompressionOn ()

Public Member Functions inherited from itk::LightProcessObject
virtual void	AbortGenerateDataOn ()

virtual const bool &	GetAbortGenerateData () const

const char *	GetNameOfClass () const override

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 *cmd) const

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

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

const char *	GetNameOfClass () const override

virtual const TimeStamp &	GetTimeStamp () 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) const

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexcept override

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
Pointer	Clone () const

virtual Pointer	CreateAnother () const

virtual void	Delete ()

virtual const char *	GetNameOfClass () const

virtual int	GetReferenceCount () const

void	Print (std::ostream &os, Indent indent=0) const

virtual void	Register () const

virtual void	SetReferenceCount (int)

virtual void	UnRegister () const noexcept

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 val)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Protected Member Functions
void	CloseFile ()

	FreeSurferAsciiMeshIO ()

void	OpenFile ()

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=T{})

	~FreeSurferAsciiMeshIO () override


template<typename T >
void	WritePoints (T *buffer, std::ofstream &outputFile, T label=T{})

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

void	AddSupportedWriteExtension (const char *extension)

	MeshIOBase ()

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

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

	~MeshIOBase () override=default

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, CellGeometryEnum type)

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

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

Protected Member Functions inherited from itk::LightProcessObject
virtual void	GenerateData ()

	LightProcessObject ()

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

	~LightProcessObject () override

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

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

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

	~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	PrintSelf (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
IOByteOrderEnum	m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }

SizeValueType	m_CellBufferSize {}

IOComponentEnum	m_CellComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

IOComponentEnum	m_CellPixelComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

IOPixelEnum	m_CellPixelType { IOPixelEnum::SCALAR }

std::string	m_FileName {}

IOFileEnum	m_FileType { IOFileEnum::ASCII }

unsigned int	m_NumberOfCellPixelComponents { 0 }

SizeValueType	m_NumberOfCellPixels {}

SizeValueType	m_NumberOfCells {}

unsigned int	m_NumberOfPointPixelComponents { 0 }

SizeValueType	m_NumberOfPointPixels {}

SizeValueType	m_NumberOfPoints {}

IOComponentEnum	m_PointComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

unsigned int	m_PointDimension { 3 }

IOComponentEnum	m_PointPixelComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

IOPixelEnum	m_PointPixelType { IOPixelEnum::SCALAR }

bool	m_UpdateCellData { false }

bool	m_UpdateCells { false }

bool	m_UpdatePointData { false }

bool	m_UpdatePoints { false }

bool	m_UseCompression { false }

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}

Member Typedef Documentation

◆ ConstPointer

using itk::FreeSurferAsciiMeshIO::ConstPointer = SmartPointer<const Self>

Definition at line 45 of file itkFreeSurferAsciiMeshIO.h.

◆ Pointer

using itk::FreeSurferAsciiMeshIO::Pointer = SmartPointer<Self>

Definition at line 46 of file itkFreeSurferAsciiMeshIO.h.

◆ Self

using itk::FreeSurferAsciiMeshIO::Self = FreeSurferAsciiMeshIO

Standard class type aliases.

Definition at line 43 of file itkFreeSurferAsciiMeshIO.h.

◆ SizeValueType

using itk::FreeSurferAsciiMeshIO::SizeValueType = Superclass::SizeValueType

Definition at line 48 of file itkFreeSurferAsciiMeshIO.h.

◆ Superclass

using itk::FreeSurferAsciiMeshIO::Superclass = MeshIOBase

Definition at line 44 of file itkFreeSurferAsciiMeshIO.h.

Constructor & Destructor Documentation

◆ FreeSurferAsciiMeshIO()

itk::FreeSurferAsciiMeshIO::FreeSurferAsciiMeshIO ( )

protected

◆ ~FreeSurferAsciiMeshIO()

itk::FreeSurferAsciiMeshIO::~FreeSurferAsciiMeshIO ( )

overrideprotected

Member Function Documentation

◆ CanReadFile()

bool itk::FreeSurferAsciiMeshIO::CanReadFile ( const char * fileName )

overridevirtual

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

Parameters

fileName 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.

◆ CanWriteFile()

bool itk::FreeSurferAsciiMeshIO::CanWriteFile ( const char * fileName )

overridevirtual

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

Parameters

fileName 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.

◆ CloseFile()

void itk::FreeSurferAsciiMeshIO::CloseFile ( )

protected

◆ GetNameOfClass()

const char * itk::FreeSurferAsciiMeshIO::GetNameOfClass ( ) const

overridevirtual

See also: LightObject::GetNameOfClass()

Reimplemented from itk::MeshIOBase.

◆ New()

static Pointer itk::FreeSurferAsciiMeshIO::New ( )

static

Method for creation through the object factory.

◆ OpenFile()

void itk::FreeSurferAsciiMeshIO::OpenFile ( )

protected

◆ PrintSelf()

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.

◆ ReadCellData()

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

overridevirtual

Implements itk::MeshIOBase.

◆ ReadCells()

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

overridevirtual

Implements itk::MeshIOBase.

◆ ReadCellsBuffer()

template<typename TInput , typename TOutput >

void itk::FreeSurferAsciiMeshIO::ReadCellsBuffer	(	TInput *	input,
		TOutput *	output
	)

inlineprotected

Read cells from a data buffer, used when writing cells

point identifiers start from the third elements, first element is cellType, the second is numberOfPoints

Definition at line 157 of file itkFreeSurferAsciiMeshIO.h.

◆ ReadMeshInformation()

void itk::FreeSurferAsciiMeshIO::ReadMeshInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::MeshIOBase.

◆ ReadPointData()

void itk::FreeSurferAsciiMeshIO::ReadPointData ( void * buffer )

overridevirtual

Implements itk::MeshIOBase.

◆ ReadPoints()

void itk::FreeSurferAsciiMeshIO::ReadPoints ( void * buffer )

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::MeshIOBase.

◆ Write()

void itk::FreeSurferAsciiMeshIO::Write ( )

overridevirtual

Implements itk::MeshIOBase.

◆ WriteCellData()

void itk::FreeSurferAsciiMeshIO::WriteCellData ( void * buffer )

overridevirtual

Implements itk::MeshIOBase.

◆ WriteCells() [1/2]

template<typename T >

void itk::FreeSurferAsciiMeshIO::WriteCells	(	T *	buffer,
		std::ofstream &	outputFile,
		T	label = `T{}`
	)

inlineprotected

Definition at line 135 of file itkFreeSurferAsciiMeshIO.h.

◆ WriteCells() [2/2]

void itk::FreeSurferAsciiMeshIO::WriteCells ( void * buffer )

overridevirtual

Implements itk::MeshIOBase.

◆ WriteMeshInformation()

void itk::FreeSurferAsciiMeshIO::WriteMeshInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::MeshIOBase.

◆ WritePointData()

void itk::FreeSurferAsciiMeshIO::WritePointData ( void * buffer )

overridevirtual

Implements itk::MeshIOBase.

◆ WritePoints() [1/2]

template<typename T >

void itk::FreeSurferAsciiMeshIO::WritePoints	(	T *	buffer,
		std::ofstream &	outputFile,
		T	label = `T{}`
	)

inlineprotected

Write points to output stream

Definition at line 118 of file itkFreeSurferAsciiMeshIO.h.

◆ WritePoints() [2/2]

void itk::FreeSurferAsciiMeshIO::WritePoints ( void * buffer )

overridevirtual

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

Implements itk::MeshIOBase.

Member Data Documentation

◆ m_InputFile

std::ifstream itk::FreeSurferAsciiMeshIO::m_InputFile {}

private

Definition at line 187 of file itkFreeSurferAsciiMeshIO.h.

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

itkFreeSurferAsciiMeshIO.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ ConstPointer

◆ Pointer

◆ Self

◆ SizeValueType

◆ Superclass

Constructor & Destructor Documentation

◆ FreeSurferAsciiMeshIO()

◆ ~FreeSurferAsciiMeshIO()

Member Function Documentation

◆ CanReadFile()

◆ CanWriteFile()

◆ CloseFile()

◆ GetNameOfClass()

◆ New()

◆ OpenFile()

◆ PrintSelf()

◆ ReadCellData()

◆ ReadCells()

◆ ReadCellsBuffer()

◆ ReadMeshInformation()

◆ ReadPointData()

◆ ReadPoints()

◆ Write()

◆ WriteCellData()

◆ WriteCells() [1/2]

◆ WriteCells() [2/2]

◆ WriteMeshInformation()

◆ WritePointData()

◆ WritePoints() [1/2]

◆ WritePoints() [2/2]

Member Data Documentation

◆ m_InputFile