ITK  6.0.0
Insight Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | List of all members

#include <itkFreeSurferBinaryMeshIO.h>

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 39 of file 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
 
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 ArrayOfExtensionsTypeGetSupportedReadExtensions () const
 
const ArrayOfExtensionsTypeGetSupportedWriteExtensions () 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
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary ()
 
const MetaDataDictionaryGetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
const char * GetNameOfClass () const override
 
virtual const TimeStampGetTimeStamp () 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 ()
 
 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
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

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 }
 
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

Definition at line 47 of file itkFreeSurferBinaryMeshIO.h.

◆ Pointer

Definition at line 48 of file itkFreeSurferBinaryMeshIO.h.

◆ Self

Standard class type aliases.

Definition at line 45 of file itkFreeSurferBinaryMeshIO.h.

◆ SizeValueType

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

Definition at line 50 of file itkFreeSurferBinaryMeshIO.h.

◆ StreamOffsetType

Definition at line 51 of file itkFreeSurferBinaryMeshIO.h.

◆ Superclass

Definition at line 46 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
fileNameThe 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
fileNameThe 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

◆ GetNameOfClass()

const char * itk::FreeSurferBinaryMeshIO::GetNameOfClass ( ) const
overridevirtual
See also
LightObject::GetNameOfClass()

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

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

Implements itk::MeshIOBase.

◆ ReadCells()

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

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 writing mesh

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

Definition at line 154 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

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

Implements itk::MeshIOBase.

◆ WriteCellData()

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

Implements itk::MeshIOBase.

◆ WriteCells() [1/2]

template<typename T >
void itk::FreeSurferBinaryMeshIO::WriteCells ( T *  buffer,
std::ofstream &  outputFile 
)
inlineprotected

Write cells to output stream

Definition at line 140 of file itkFreeSurferBinaryMeshIO.h.

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

◆ WriteCells() [2/2]

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

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 174 of file itkFreeSurferBinaryMeshIO.h.

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

◆ WritePointData() [2/2]

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

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 121 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 200 of file itkFreeSurferBinaryMeshIO.h.

◆ m_FileTypeIdentifier

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

Definition at line 201 of file itkFreeSurferBinaryMeshIO.h.

◆ m_InputFile

std::ifstream itk::FreeSurferBinaryMeshIO::m_InputFile {}
private

Definition at line 202 of file itkFreeSurferBinaryMeshIO.h.


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