ITK  4.2.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes
itk::FreeSurferBinaryMeshIO Class Reference
Input and Output Filters | Module ITKIOMesh

#include <itkFreeSurferBinaryMeshIO.h>

+ Inheritance diagram for itk::FreeSurferBinaryMeshIO:
+ Collaboration diagram for itk::FreeSurferBinaryMeshIO:

List of all members.

Public Types

typedef SmartPointer< const Self > ConstPointer
typedef SmartPointer< Self > Pointer
typedef FreeSurferBinaryMeshIO Self
typedef Superclass::SizeValueType SizeValueType
typedef
Superclass::StreamOffsetType 		StreamOffsetType
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
}
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
}
- Public Types inherited from itk::LightProcessObject
- Public Types inherited from itk::Object
- Public Types inherited from itk::LightObject

Public Member Functions

virtual bool CanReadFile (const char *FileNameToRead)
virtual bool CanWriteFile (const char *FileNameToWrite)
virtual ::itk::LightObject::Pointer CreateAnother (void) const
virtual const char * GetNameOfClass () const
virtual void ReadCellData (void *buffer)
virtual void ReadCells (void *buffer)
virtual void ReadMeshInformation ()
virtual void ReadPointData (void *buffer)
virtual void ReadPoints (void *buffer)
virtual void Write ()
virtual void WriteCellData (void *buffer)
virtual void WriteCells (void *buffer)
virtual void WriteMeshInformation ()
virtual void WritePointData (void *buffer)
virtual void WritePoints (void *buffer)
- 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 ()
virtual void SetAbortGenerateData (bool _arg)
virtual void UpdateOutputData ()
void UpdateProgress (float amount)
virtual void SetProgress (float _arg)
virtual const float & GetProgress ()
- 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 (void)
const MetaDataDictionary & GetMetaDataDictionary (void) const
virtual unsigned long 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
void RemoveAllObservers ()
void RemoveObserver (unsigned long tag)
void SetDebug (bool debugFlag) const
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void SetReferenceCount (int)
virtual void UnRegister () 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 ()

Protected Member Functions

void CloseFile ()
 FreeSurferBinaryMeshIO ()
void OpenFile ()
void PrintSelf (std::ostream &os, Indent indent) const
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)
virtual ~FreeSurferBinaryMeshIO ()
- Protected Member Functions inherited from itk::MeshIOBase
void AddSupportedReadExtension (const char *extension)
void AddSupportedWriteExtension (const char *extension)
 MeshIOBase ()
template<class T >
void ReadBufferAsBinary (T *buffer, std::ifstream &inputFile, SizeValueType numberOfComponents)
virtual ~MeshIOBase ()
template<class T >
void ReadBufferAsAscii (T *buffer, std::ifstream &inputFile, SizeValueType numberOfComponents)
template<class T >
void WriteBufferAsAscii (T *buffer, std::ofstream &outputFile, SizeValueType numberOfLines, SizeValueType numberOfComponents)
template<class TOutput , class TInput >
void WriteBufferAsBinary (TInput *buffer, std::ofstream &outputFile, SizeValueType numberOfComponents)
template<class TInput , class TOutput >
void ReadCellsBuffer (TInput *input, TOutput *output, MeshIOBase::CellGeometryType type)
template<class TInput , class TOutput >
void WriteCellsBuffer (TInput *input, TOutput *output, CellGeometryType cellType, unsigned int numberOfPoints, SizeValueType numberOfCells)
template<class TInput , class TOutput >
void WriteCellsBuffer (TInput *input, TOutput *output, CellGeometryType cellType, SizeValueType numberOfCells)
- Protected Member Functions inherited from itk::LightProcessObject
 LightProcessObject ()
 ~LightProcessObject ()
virtual void GenerateData ()
- 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 ()

Private Member Functions

 FreeSurferBinaryMeshIO (const Self &)
void operator= (const Self &)

Private Attributes

StreamOffsetType m_FilePosition
itk::uint32_t m_FileTypeIdentifier
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
unsigned int m_PointDimension
IOComponentType m_PointPixelComponentType
IOPixelType m_PointPixelType
bool m_UpdateCellData
bool m_UpdateCells
bool m_UpdatePointData
bool m_UpdatePoints
bool m_UseCompression

Detailed Description

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

Definition at line 37 of file itkFreeSurferBinaryMeshIO.h.

Member Typedef Documentation

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

Reimplemented from itk::MeshIOBase.

Definition at line 43 of file itkFreeSurferBinaryMeshIO.h.

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

Reimplemented from itk::MeshIOBase.

Definition at line 44 of file itkFreeSurferBinaryMeshIO.h.

typedef FreeSurferBinaryMeshIO itk::FreeSurferBinaryMeshIO::Self

Standard class typedefs.

Reimplemented from itk::MeshIOBase.

Definition at line 41 of file itkFreeSurferBinaryMeshIO.h.

typedef Superclass::SizeValueType itk::FreeSurferBinaryMeshIO::SizeValueType

Reimplemented from itk::MeshIOBase.

Definition at line 46 of file itkFreeSurferBinaryMeshIO.h.

typedef Superclass::StreamOffsetType itk::FreeSurferBinaryMeshIO::StreamOffsetType

Type for representing size of bytes, and or positions along a file

Reimplemented from itk::MeshIOBase.

Definition at line 47 of file itkFreeSurferBinaryMeshIO.h.

typedef MeshIOBase itk::FreeSurferBinaryMeshIO::Superclass

Reimplemented from itk::MeshIOBase.

Definition at line 42 of file itkFreeSurferBinaryMeshIO.h.

Constructor & Destructor Documentation

itk::FreeSurferBinaryMeshIO::FreeSurferBinaryMeshIO ( )
protected
virtual itk::FreeSurferBinaryMeshIO::~FreeSurferBinaryMeshIO ( )
inlineprotectedvirtual

Definition at line 169 of file itkFreeSurferBinaryMeshIO.h.

itk::FreeSurferBinaryMeshIO::FreeSurferBinaryMeshIO ( const Self &  )
private

Member Function Documentation

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

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

Parameters:
FileNameToReadThe 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::FreeSurferBinaryMeshIO::CanWriteFile ( const char *  FileNameToWrite)
virtual

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

Parameters:
FileNameToWriteThe 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::FreeSurferBinaryMeshIO::CloseFile ( )
protected
virtual::itk::LightObject::Pointer itk::FreeSurferBinaryMeshIO::CreateAnother ( void  ) 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::FreeSurferBinaryMeshIO::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from itk::MeshIOBase.

static Pointer itk::FreeSurferBinaryMeshIO::New ( )
static

Method for creation through the object factory.

Reimplemented from itk::LightProcessObject.

void itk::FreeSurferBinaryMeshIO::OpenFile ( )
protected
void itk::FreeSurferBinaryMeshIO::operator= ( const Self &  )
private

This method causes the filter to generate its output.

Reimplemented from itk::MeshIOBase.

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

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

Implements itk::MeshIOBase.

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

Implements itk::MeshIOBase.

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.

Reimplemented from itk::MeshIOBase.

Definition at line 135 of file itkFreeSurferBinaryMeshIO.h.

virtual void itk::FreeSurferBinaryMeshIO::ReadMeshInformation ( )
virtual

Set the spacing and dimension information for the set filename.

Implements itk::MeshIOBase.

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

Implements itk::MeshIOBase.

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

Reads the data from disk into the memory buffer provided.

Implements itk::MeshIOBase.

virtual void itk::FreeSurferBinaryMeshIO::Write ( )
virtual

Implements itk::MeshIOBase.

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

Implements itk::MeshIOBase.

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

Implements itk::MeshIOBase.

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

Write cells to utput stream

Definition at line 121 of file itkFreeSurferBinaryMeshIO.h.

References itk::uint32_t.

virtual void itk::FreeSurferBinaryMeshIO::WriteMeshInformation ( )
virtual

Set the spacing and dimension information for the set filename.

Implements itk::MeshIOBase.

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

Implements itk::MeshIOBase.

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

Write points to output stream

Definition at line 154 of file itkFreeSurferBinaryMeshIO.h.

virtual void itk::FreeSurferBinaryMeshIO::WritePoints ( void *  buffer)
virtual

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

Implements itk::MeshIOBase.

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

Write points to output stream

Definition at line 103 of file itkFreeSurferBinaryMeshIO.h.

Member Data Documentation

StreamOffsetType itk::FreeSurferBinaryMeshIO::m_FilePosition
private

Definition at line 181 of file itkFreeSurferBinaryMeshIO.h.

itk::uint32_t itk::FreeSurferBinaryMeshIO::m_FileTypeIdentifier
private

Definition at line 182 of file itkFreeSurferBinaryMeshIO.h.

std::ifstream itk::FreeSurferBinaryMeshIO::m_InputFile
private

Definition at line 183 of file itkFreeSurferBinaryMeshIO.h.

The documentation for this class was generated from the following file:
Tarballs of the nightly generated Doxygen documentation are available for the html, xml, and tag file.
Generated on Wed Jul 11 2012 00:03:38 for ITK by doxygen 1.8.1