ITK  4.4.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Private Types | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
itk::VoxBoCUBImageIO Class Reference
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#include <itkVoxBoCUBImageIO.h>

+ Inheritance diagram for itk::VoxBoCUBImageIO:
+ Collaboration diagram for itk::VoxBoCUBImageIO:

Detailed Description

Read VoxBoCUBImage file format.

A generic reader and writer object for VoxBo files. Basically it provides uniform access to gzip and normal files

Author
Burstein, Pablo D.; Yushkevich, Paul; Gee, James C.

This implementation was contributed as a paper to the Insight Journal http://hdl.handle.net/1926/303

Definition at line 50 of file itkVoxBoCUBImageIO.h.

Public Types

typedef SmartPointer< Self > Pointer
 
typedef VoxBoCUBImageIO Self
 
typedef ImageIOBase Superclass
 
- Public Types inherited from itk::ImageIOBase
typedef std::vector< std::string > ArrayOfExtensionsType
 
typedef ::itk::OffsetValueType BufferSizeType
 
enum  ByteOrder {
  BigEndian,
  LittleEndian,
  OrderNotApplicable
}
 
enum  FileType {
  ASCII,
  Binary,
  TypeNotApplicable
}
 
typedef ::itk::IndexValueType IndexValueType
 
enum  IOComponentType {
  UNKNOWNCOMPONENTTYPE,
  UCHAR,
  CHAR,
  USHORT,
  SHORT,
  UINT,
  INT,
  ULONG,
  LONG,
  FLOAT,
  DOUBLE
}
 
enum  IOPixelType {
  UNKNOWNPIXELTYPE,
  SCALAR,
  RGB,
  RGBA,
  OFFSET,
  VECTOR,
  POINT,
  COVARIANTVECTOR,
  SYMMETRICSECONDRANKTENSOR,
  DIFFUSIONTENSOR3D,
  COMPLEX,
  FIXEDARRAY,
  MATRIX
}
 
typedef SmartPointer< Self > Pointer
 
typedef ImageIOBase Self
 
typedef ::itk::intmax_t SizeType
 
typedef ::itk::SizeValueType SizeValueType
 
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 *)
 
virtual bool CanWriteFile (const char *)
 
virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
virtual const char * GetNameOfClass () const
 
void PrintSelf (std::ostream &os, Indent indent) const
 
virtual void Read (void *buffer)
 
virtual void ReadImageInformation ()
 
 VoxBoCUBImageIO ()
 
virtual void Write (const void *buffer)
 
virtual void WriteImageInformation ()
 
 ~VoxBoCUBImageIO ()
 
- Public Member Functions inherited from itk::ImageIOBase
virtual bool CanStreamRead ()
 
virtual bool CanStreamWrite ()
 
virtual ImageIORegion GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const
 
virtual unsigned int GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
 
std::string GetByteOrderAsString (ByteOrder) const
 
virtual unsigned int GetComponentSize () const
 
virtual IOComponentType GetComponentType () const
 
virtual const std::type_info & GetComponentTypeInfo () const
 
virtual std::vector< double > GetDefaultDirection (unsigned int i) const
 
virtual itk::SizeValueType GetDimensions (unsigned int i) const
 
virtual std::vector< double > GetDirection (unsigned int i) const
 
std::string GetFileTypeAsString (FileType) const
 
SizeType GetImageSizeInBytes () const
 
SizeType GetImageSizeInComponents () const
 
SizeType GetImageSizeInPixels () const
 
virtual unsigned int GetNumberOfDimensions () const
 
virtual double GetOrigin (unsigned int i) const
 
virtual SizeType GetPixelStride () const
 
virtual double GetSpacing (unsigned int i) const
 
virtual ImageIORegion GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
 
const ArrayOfExtensionsType & GetSupportedReadExtensions () const
 
const ArrayOfExtensionsType & GetSupportedWriteExtensions () const
 
void SetByteOrderToLittleEndian ()
 
virtual void SetComponentType (const IOComponentType _arg)
 
virtual void SetDirection (unsigned int i, std::vector< double > &direction)
 
virtual void SetDirection (unsigned int i, vnl_vector< double > &direction)
 
void SetFileTypeToBinary ()
 
void SetNumberOfDimensions (unsigned int)
 
virtual void SetOrigin (unsigned int i, double origin)
 
template<class TPixel , unsigned VLength>
void SetPixelTypeInfo (const SymmetricSecondRankTensor< TPixel, VLength > *)
 
template<typename TPixel >
void SetPixelTypeInfo (const DiffusionTensor3D< TPixel > *)
 
template<typename TPixel , unsigned VLength>
void SetPixelTypeInfo (const Matrix< TPixel, VLength, VLength > *)
 
template<typename TPixel >
void SetPixelTypeInfo (const std::complex< TPixel > *)
 
template<unsigned VLength>
void SetPixelTypeInfo (const Offset< VLength > *)
 
virtual void SetSpacing (unsigned int i, double spacing)
 
template<typename TPixel >
void SetTypeInfo (const TPixel *)
 
virtual bool SupportsDimension (unsigned long dim)
 
virtual void SetFileName (const char *_arg)
 
virtual const char * GetFileName () const
 
virtual void SetDimensions (unsigned int i, unsigned int dim)
 
virtual void SetIORegion (ImageIORegion _arg)
 
virtual const ImageIORegion & GetIORegion ()
 
virtual void SetPixelType (const IOPixelType _arg)
 
virtual IOPixelType GetPixelType () const
 
virtual void SetNumberOfComponents (unsigned int _arg)
 
virtual const unsigned int & GetNumberOfComponents ()
 
virtual void SetUseCompression (bool _arg)
 
virtual bool GetUseCompression () const
 
virtual void UseCompressionOn ()
 
virtual void UseCompressionOff ()
 
virtual void SetUseStreamedReading (bool _arg)
 
virtual bool GetUseStreamedReading () const
 
virtual void UseStreamedReadingOn ()
 
virtual void UseStreamedReadingOff ()
 
virtual void SetUseStreamedWriting (bool _arg)
 
virtual bool GetUseStreamedWriting () const
 
virtual void UseStreamedWritingOn ()
 
virtual void UseStreamedWritingOff ()
 
virtual void SetFileType (const FileType _arg)
 
virtual FileType GetFileType () const
 
void SetFileTypeToASCII ()
 
virtual void SetByteOrder (const ByteOrder _arg)
 
virtual ByteOrder GetByteOrder () const
 
void SetByteOrderToBigEndian ()
 
template<typename TPixel >
void SetPixelTypeInfo (const TPixel *)
 
template<typename TPixel >
void SetPixelTypeInfo (const RGBPixel< TPixel > *)
 
template<typename TPixel >
void SetPixelTypeInfo (const RGBAPixel< TPixel > *)
 
template<typename TPixel , unsigned VLength>
void SetPixelTypeInfo (const Vector< TPixel, VLength > *)
 
template<typename TPixel >
void SetPixelTypeInfo (const VariableLengthVector< TPixel > *)
 
template<typename TPixel , unsigned VLength>
void SetPixelTypeInfo (const CovariantVector< TPixel, VLength > *)
 
template<typename TPixel , unsigned VLength>
void SetPixelTypeInfo (const FixedArray< TPixel, VLength > *)
 
- 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 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
 
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 ()
 
- Static Public Member Functions inherited from itk::ImageIOBase
static std::string GetComponentTypeAsString (IOComponentType)
 
static IOComponentType GetComponentTypeFromString (const std::string &typeString)
 
static std::string GetPixelTypeAsString (IOPixelType)
 
static IOPixelType GetPixelTypeFromString (const std::string &pixelString)
 
- 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 ()
 

Private Types

typedef std::map
< OrientationFlags,
std::string > 		InverseOrientationMap
 
typedef
SpatialOrientation::ValidCoordinateOrientationFlags 		OrientationFlags
 
typedef std::map< std::string,
OrientationFlags > 		OrientationMap
 

Private Member Functions

bool CheckExtension (const char *, bool &isCompressed)
 
GenericCUBFileAdaptor * CreateReader (const char *filename)
 
GenericCUBFileAdaptor * CreateWriter (const char *filename)
 
void InitializeOrientationMap ()
 
void operator= (const Self &)
 
void SwapBytesIfNecessary (void *buffer, BufferSizeType numberOfBytes)
 
 VoxBoCUBImageIO (const Self &)
 

Private Attributes

InverseOrientationMap m_InverseOrientationMap
 
OrientationMap m_OrientationMap
 
GenericCUBFileAdaptor * m_Reader
 
GenericCUBFileAdaptor * m_Writer
 

Static Private Attributes

static const char * m_VB_BYTEORDER
 
static const char * m_VB_BYTEORDER_LSB
 
static const char * m_VB_BYTEORDER_MSB
 
static const char * m_VB_DATATYPE
 
static const char * m_VB_DATATYPE_BYTE
 
static const char * m_VB_DATATYPE_DOUBLE
 
static const char * m_VB_DATATYPE_FLOAT
 
static const char * m_VB_DATATYPE_INT
 
static const char * m_VB_DIMENSIONS
 
static const char * m_VB_IDENTIFIER_FILETYPE
 
static const char * m_VB_IDENTIFIER_SYSTEM
 
static const char * m_VB_ORIENTATION
 
static const char * m_VB_ORIGIN
 
static const char * m_VB_SPACING
 

Additional Inherited Members

- Protected Types inherited from itk::LightObject
typedef int InternalReferenceCountType
 
- Protected Member Functions inherited from itk::ImageIOBase
void AddSupportedReadExtension (const char *extension)
 
void AddSupportedWriteExtension (const char *extension)
 
void ComputeStrides ()
 
virtual unsigned int GetActualNumberOfSplitsForWritingCanStreamWrite (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion) const
 
SizeType GetComponentStride () const
 
virtual const
ImageRegionSplitterBase * 		GetImageRegionSplitter (void) const
 
virtual unsigned int GetPixelSize () const
 
SizeType GetRowStride () const
 
SizeType GetSliceStride () const
 
virtual ImageIORegion GetSplitRegionForWritingCanStreamWrite (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion) const
 
 ImageIOBase ()
 
virtual void ReadBufferAsASCII (std::istream &os, void *buffer, IOComponentType ctype, SizeType numberOfBytesToBeRead)
 
bool ReadBufferAsBinary (std::istream &os, void *buffer, SizeType numberOfBytesToBeRead)
 
virtual void Reset (const bool freeDynamic=true)
 
void Resize (const unsigned int numDimensions, const unsigned int *dimensions)
 
virtual void WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentType ctype, SizeType numberOfBytesToWrite)
 
 ~ImageIOBase ()
 
- Protected Attributes inherited from itk::ImageIOBase
ByteOrder m_ByteOrder
 
IOComponentType m_ComponentType
 
std::vector< SizeValueType > m_Dimensions
 
std::vector< std::vector
< double > > 		m_Direction
 
std::string m_FileName
 
FileType m_FileType
 
bool m_Initialized
 
ImageIORegion m_IORegion
 
unsigned int m_NumberOfComponents
 
unsigned int m_NumberOfDimensions
 
std::vector< double > m_Origin
 
IOPixelType m_PixelType
 
std::vector< double > m_Spacing
 
std::vector< SizeType > m_Strides
 
bool m_UseCompression
 
bool m_UseStreamedReading
 
bool m_UseStreamedWriting
 

Member Typedef Documentation

typedef std::map< OrientationFlags, std::string > itk::VoxBoCUBImageIO::InverseOrientationMap
private

Definition at line 111 of file itkVoxBoCUBImageIO.h.

typedef SpatialOrientation::ValidCoordinateOrientationFlags itk::VoxBoCUBImageIO::OrientationFlags
private

Definition at line 109 of file itkVoxBoCUBImageIO.h.

typedef std::map< std::string, OrientationFlags > itk::VoxBoCUBImageIO::OrientationMap
private

Definition at line 110 of file itkVoxBoCUBImageIO.h.

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

Definition at line 56 of file itkVoxBoCUBImageIO.h.

typedef VoxBoCUBImageIO itk::VoxBoCUBImageIO::Self

Standard class typedefs.

Definition at line 54 of file itkVoxBoCUBImageIO.h.

typedef ImageIOBase itk::VoxBoCUBImageIO::Superclass

Definition at line 55 of file itkVoxBoCUBImageIO.h.

Constructor & Destructor Documentation

itk::VoxBoCUBImageIO::VoxBoCUBImageIO ( )
itk::VoxBoCUBImageIO::~VoxBoCUBImageIO ( )
itk::VoxBoCUBImageIO::VoxBoCUBImageIO ( const Self &  )
private

Member Function Documentation

virtual bool itk::VoxBoCUBImageIO::CanReadFile ( const char *  )
virtual

Determine the file type. Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

virtual bool itk::VoxBoCUBImageIO::CanWriteFile ( const char *  )
virtual

Determine the file type. Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

bool itk::VoxBoCUBImageIO::CheckExtension ( const char *  ,
bool &  isCompressed 
)
private
virtual::itk::LightObject::Pointer itk::VoxBoCUBImageIO::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.

GenericCUBFileAdaptor* itk::VoxBoCUBImageIO::CreateReader ( const char *  filename)
private
GenericCUBFileAdaptor* itk::VoxBoCUBImageIO::CreateWriter ( const char *  filename)
private
virtual const char* itk::VoxBoCUBImageIO::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

void itk::VoxBoCUBImageIO::InitializeOrientationMap ( )
private
static Pointer itk::VoxBoCUBImageIO::New ( )
static

Method for creation through the object factory.

void itk::VoxBoCUBImageIO::operator= ( const Self &  )
private
void itk::VoxBoCUBImageIO::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
virtual

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::ImageIOBase.

virtual void itk::VoxBoCUBImageIO::Read ( void *  buffer)
virtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::VoxBoCUBImageIO::ReadImageInformation ( )
virtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

void itk::VoxBoCUBImageIO::SwapBytesIfNecessary ( void *  buffer,
BufferSizeType  numberOfBytes 
)
private
virtual void itk::VoxBoCUBImageIO::Write ( const void *  buffer)
virtual

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

Implements itk::ImageIOBase.

virtual void itk::VoxBoCUBImageIO::WriteImageInformation ( )
virtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

Member Data Documentation

InverseOrientationMap itk::VoxBoCUBImageIO::m_InverseOrientationMap
private

Definition at line 114 of file itkVoxBoCUBImageIO.h.

OrientationMap itk::VoxBoCUBImageIO::m_OrientationMap
private

Definition at line 113 of file itkVoxBoCUBImageIO.h.

GenericCUBFileAdaptor* itk::VoxBoCUBImageIO::m_Reader
private

Definition at line 103 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_BYTEORDER
staticprivate

Definition at line 126 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_BYTEORDER_LSB
staticprivate

Definition at line 129 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_BYTEORDER_MSB
staticprivate

Definition at line 128 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE
staticprivate

Definition at line 125 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE_BYTE
staticprivate

Definition at line 130 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE_DOUBLE
staticprivate

Definition at line 133 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE_FLOAT
staticprivate

Definition at line 132 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DATATYPE_INT
staticprivate

Definition at line 131 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_DIMENSIONS
staticprivate

Definition at line 122 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_IDENTIFIER_FILETYPE
staticprivate

Definition at line 121 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_IDENTIFIER_SYSTEM
staticprivate

Definition at line 120 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_ORIENTATION
staticprivate

Definition at line 127 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_ORIGIN
staticprivate

Definition at line 124 of file itkVoxBoCUBImageIO.h.

const char* itk::VoxBoCUBImageIO::m_VB_SPACING
staticprivate

Definition at line 123 of file itkVoxBoCUBImageIO.h.

GenericCUBFileAdaptor * itk::VoxBoCUBImageIO::m_Writer
private

Definition at line 103 of file itkVoxBoCUBImageIO.h.

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