#include <itkFreeSurferBinaryMeshIO.h>

Inheritance diagram for itk::FreeSurferBinaryMeshIO:

Collaboration diagram for itk::FreeSurferBinaryMeshIO:

Public Types
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = FreeSurferBinaryMeshIO

using	SizeValueType = Superclass::SizeValueType

using	StreamOffsetType = Superclass::StreamOffsetType

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

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

virtual const char *	GetNameOfClass () const

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 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

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	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

unsigned int	GetComponentSize (IOComponentEnum componentType) const

std::string	GetComponentTypeAsString (IOComponentEnum) const

std::string	GetPixelTypeAsString (IOPixelEnum) const

virtual void	SetFileType (const IOFileEnum _arg)

virtual IOFileEnum	GetFileType () const

void	SetFileTypeToASCII ()

void	SetFileTypeToBinary ()

virtual void	SetByteOrder (const IOByteOrderEnum _arg)

virtual IOByteOrderEnum	GetByteOrder () const

void	SetByteOrderToBigEndian ()

void	SetByteOrderToLittleEndian ()

virtual void	SetUseCompression (bool _arg)

virtual bool	GetUseCompression () const

virtual void	UseCompressionOn ()

virtual void	UseCompressionOff ()

std::string	GetFileTypeAsString (IOFileEnum) const

std::string	GetByteOrderAsString (IOByteOrderEnum) const

const ArrayOfExtensionsType &	GetSupportedReadExtensions () const

const ArrayOfExtensionsType &	GetSupportedWriteExtensions () const

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	SetProgress (float _arg)

virtual const float &	GetProgress () const

void	UpdateProgress (float amount)

virtual void	UpdateOutputData ()

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)

unsigned long	AddObserver (const EventObject &event, Command *) const

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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

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 void	Delete ()

virtual int	GetReferenceCount () const

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 val)

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

static Pointer	New ()

Protected Member Functions
void	CloseFile ()

	FreeSurferBinaryMeshIO ()

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)

template<typename T >
void	WritePointData (T *buffer, std::ofstream &outputFile)

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

	~FreeSurferBinaryMeshIO () override

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

	~MeshIOBase () override=default

void	AddSupportedReadExtension (const char *extension)

void	AddSupportedWriteExtension (const char *extension)

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

template<typename T >
void	ReadBufferAsBinary (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
	LightProcessObject ()

	~LightProcessObject () override

virtual void	GenerateData ()

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

	~Object () override

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

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

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
StreamOffsetType	m_FilePosition { 0 }

itk::uint32_t	m_FileTypeIdentifier { 0 }

std::ifstream	m_InputFile

Additional Inherited Members
Protected Attributes inherited from itk::MeshIOBase
IOByteOrderEnum	m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }

IOFileEnum	m_FileType { IOFileEnum::ASCII }

std::string	m_FileName

bool	m_UseCompression { false }

IOComponentEnum	m_PointComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

IOComponentEnum	m_CellComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

IOComponentEnum	m_PointPixelComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

IOComponentEnum	m_CellPixelComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

IOPixelEnum	m_PointPixelType { IOPixelEnum::SCALAR }

IOPixelEnum	m_CellPixelType { IOPixelEnum::SCALAR }

unsigned int	m_NumberOfPointPixelComponents { 0 }

unsigned int	m_NumberOfCellPixelComponents { 0 }

unsigned int	m_PointDimension { 3 }

SizeValueType	m_NumberOfPoints

SizeValueType	m_NumberOfCells

SizeValueType	m_NumberOfPointPixels

SizeValueType	m_NumberOfCellPixels

SizeValueType	m_CellBufferSize

bool	m_UpdatePoints { false }

bool	m_UpdateCells { false }

bool	m_UpdatePointData { false }

bool	m_UpdateCellData { false }

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

Detailed Description

This class defines how to read Freesurfer binary surface file format. To use IO factory, define the suffix as *.fsb.

Definition at line 38 of file itkFreeSurferBinaryMeshIO.h.

Member Typedef Documentation

◆ ConstPointer

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

Definition at line 46 of file itkFreeSurferBinaryMeshIO.h.

◆ Pointer

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

Definition at line 47 of file itkFreeSurferBinaryMeshIO.h.

◆ Self

using itk::FreeSurferBinaryMeshIO::Self = FreeSurferBinaryMeshIO

Standard class type aliases.

Definition at line 44 of file itkFreeSurferBinaryMeshIO.h.

◆ SizeValueType

using itk::FreeSurferBinaryMeshIO::SizeValueType = Superclass::SizeValueType

Definition at line 49 of file itkFreeSurferBinaryMeshIO.h.

◆ StreamOffsetType

using itk::FreeSurferBinaryMeshIO::StreamOffsetType = Superclass::StreamOffsetType

Definition at line 50 of file itkFreeSurferBinaryMeshIO.h.

◆ Superclass

using itk::FreeSurferBinaryMeshIO::Superclass = MeshIOBase

Definition at line 45 of file itkFreeSurferBinaryMeshIO.h.

Constructor & Destructor Documentation

◆ FreeSurferBinaryMeshIO()

itk::FreeSurferBinaryMeshIO::FreeSurferBinaryMeshIO ( )

protected

◆ ~FreeSurferBinaryMeshIO()

itk::FreeSurferBinaryMeshIO::~FreeSurferBinaryMeshIO ( )

overrideprotected

Member Function Documentation

◆ CanReadFile()

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

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.

◆ CanWriteFile()

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

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.

◆ CloseFile()

void itk::FreeSurferBinaryMeshIO::CloseFile ( )

protected

◆ CreateAnother()

virtual::itk::LightObject::Pointer itk::FreeSurferBinaryMeshIO::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.

◆ GetNameOfClass()

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::MeshIOBase.

◆ New()

static Pointer itk::FreeSurferBinaryMeshIO::New ( )

static

Method for creation through the object factory.

◆ OpenFile()

void itk::FreeSurferBinaryMeshIO::OpenFile ( )

protected

◆ PrintSelf()

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

overrideprotectedvirtual

Big or Little Endian, and the type of the file. (May be ignored.)

Reimplemented from itk::MeshIOBase.

◆ ReadCellData()

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

overridevirtual

Big or Little Endian, and the type of the file. (May be ignored.)

Implements itk::MeshIOBase.

◆ ReadCells()

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

overridevirtual

Big or Little Endian, and the type of the file. (May be ignored.)

Implements itk::MeshIOBase.

◆ ReadCellsBuffer()

template<typename TInput , typename TOutput >

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

inlineprotected

Read cells from a data buffer, used when writting mesh

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

Definition at line 156 of file itkFreeSurferBinaryMeshIO.h.

◆ ReadMeshInformation()

void itk::FreeSurferBinaryMeshIO::ReadMeshInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::MeshIOBase.

◆ ReadPointData()

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

overridevirtual

Big or Little Endian, and the type of the file. (May be ignored.)

Implements itk::MeshIOBase.

◆ ReadPoints()

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

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::MeshIOBase.

◆ Write()

void itk::FreeSurferBinaryMeshIO::Write ( )

overridevirtual

Big or Little Endian, and the type of the file. (May be ignored.)

Implements itk::MeshIOBase.

◆ WriteCellData()

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

overridevirtual

Big or Little Endian, and the type of the file. (May be ignored.)

Implements itk::MeshIOBase.

◆ WriteCells() [1/2]

template<typename T >

void itk::FreeSurferBinaryMeshIO::WriteCells	(	T *	buffer,
		std::ofstream &	outputFile
	)

inlineprotected

Write cells to utput stream

Definition at line 140 of file itkFreeSurferBinaryMeshIO.h.

References itk::ByteSwapper< T >::SwapWriteRangeFromSystemToBigEndian().

◆ WriteCells() [2/2]

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

overridevirtual

Big or Little Endian, and the type of the file. (May be ignored.)

Implements itk::MeshIOBase.

◆ WriteMeshInformation()

void itk::FreeSurferBinaryMeshIO::WriteMeshInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::MeshIOBase.

◆ WritePointData() [1/2]

template<typename T >

void itk::FreeSurferBinaryMeshIO::WritePointData	(	T *	buffer,
		std::ofstream &	outputFile
	)

inlineprotected

Write points to output stream

Definition at line 176 of file itkFreeSurferBinaryMeshIO.h.

References itk::ByteSwapper< T >::SwapWriteRangeFromSystemToBigEndian().

◆ WritePointData() [2/2]

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

overridevirtual

Big or Little Endian, and the type of the file. (May be ignored.)

Implements itk::MeshIOBase.

◆ WritePoints() [1/2]

template<typename T >

void itk::FreeSurferBinaryMeshIO::WritePoints	(	T *	buffer,
		std::ofstream &	outputFile
	)

inlineprotected

Write points to output stream

Definition at line 120 of file itkFreeSurferBinaryMeshIO.h.

References itk::ByteSwapper< T >::SwapWriteRangeFromSystemToBigEndian().

◆ WritePoints() [2/2]

void itk::FreeSurferBinaryMeshIO::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_FilePosition

StreamOffsetType itk::FreeSurferBinaryMeshIO::m_FilePosition { 0 }

private

Definition at line 203 of file itkFreeSurferBinaryMeshIO.h.

◆ m_FileTypeIdentifier

itk::uint32_t itk::FreeSurferBinaryMeshIO::m_FileTypeIdentifier { 0 }

private

Definition at line 204 of file itkFreeSurferBinaryMeshIO.h.

◆ m_InputFile

std::ifstream itk::FreeSurferBinaryMeshIO::m_InputFile

private

Definition at line 205 of file itkFreeSurferBinaryMeshIO.h.

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

itkFreeSurferBinaryMeshIO.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConstPointer

◆ Pointer

◆ Self

◆ SizeValueType

◆ StreamOffsetType

◆ Superclass

Constructor & Destructor Documentation

◆ FreeSurferBinaryMeshIO()

◆ ~FreeSurferBinaryMeshIO()

Member Function Documentation

◆ CanReadFile()

◆ CanWriteFile()

◆ CloseFile()

◆ CreateAnother()

◆ GetNameOfClass()

◆ New()

◆ OpenFile()

◆ PrintSelf()

◆ ReadCellData()

◆ ReadCells()

◆ ReadCellsBuffer()

◆ ReadMeshInformation()

◆ ReadPointData()

◆ ReadPoints()

◆ Write()

◆ WriteCellData()

◆ WriteCells() [1/2]

◆ WriteCells() [2/2]

◆ WriteMeshInformation()

◆ WritePointData() [1/2]

◆ WritePointData() [2/2]

◆ WritePoints() [1/2]

◆ WritePoints() [2/2]

Member Data Documentation

◆ m_FilePosition

◆ m_FileTypeIdentifier

◆ m_InputFile