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::NiftiImageIO Class Reference
Input and Output Filters | Module ITKIONIFTI

#include <itkNiftiImageIO.h>

+ Inheritance diagram for itk::NiftiImageIO:
+ Collaboration diagram for itk::NiftiImageIO:

List of all members.

Public Types

typedef SmartPointer< Self > Pointer
typedef NiftiImageIO 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 ::itk::intmax_t SizeType
typedef ::itk::SizeValueType SizeValueType
- Public Types inherited from itk::LightProcessObject
typedef SmartPointer< const Self > ConstPointer
- 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 ImageIORegion GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requestedRegion) const
virtual const char * GetNameOfClass () const
virtual void Read (void *buffer)
virtual void ReadImageInformation ()
virtual void Write (const void *buffer)
virtual void WriteImageInformation ()
- Public Member Functions inherited from itk::ImageIOBase
virtual bool CanStreamRead ()
virtual bool CanStreamWrite ()
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 unsigned int 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 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 ()
- 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)

Protected Member Functions

virtual bool GetUseLegacyModeForTwoFileWriting (void) const
- 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 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 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

void DefineHeaderObjectDataType ()
bool MustRescale ()
 NiftiImageIO (const Self &)
void operator= (const Self &)
void SetImageIOMetadataFromNIfTI ()
void SetImageIOOrientationFromNIfTI (unsigned short int dims)
void SetNIfTIOrientationFromImageIO (unsigned short int origdims, unsigned short int dims)

Private Attributes

bool m_LegacyAnalyze75Mode
nifti_image * m_NiftiImage
IOComponentType m_OnDiskComponentType
double m_RescaleIntercept
double m_RescaleSlope
virtual void SetLegacyAnalyze75Mode (bool _arg)
virtual bool GetLegacyAnalyze75Mode () const
 NiftiImageIO ()
 ~NiftiImageIO ()
void PrintSelf (std::ostream &os, Indent indent) const

Additional Inherited Members

- 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

Detailed Description

Class that defines how to read Nifti file format. Nifti IMAGE FILE FORMAT - As much information as I can determine from sourceforge.net/projects/Niftilib.

Author:
Hans J. Johnson

Definition at line 44 of file itkNiftiImageIO.h.

Member Typedef Documentation

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

Reimplemented from itk::ImageIOBase.

Definition at line 50 of file itkNiftiImageIO.h.

typedef NiftiImageIO itk::NiftiImageIO::Self

Standard class typedefs.

Reimplemented from itk::ImageIOBase.

Definition at line 48 of file itkNiftiImageIO.h.

typedef ImageIOBase itk::NiftiImageIO::Superclass

Reimplemented from itk::ImageIOBase.

Definition at line 49 of file itkNiftiImageIO.h.

Constructor & Destructor Documentation

itk::NiftiImageIO::NiftiImageIO ( )
protected

A mode to allow the Nifti filter to read and write to the LegacyAnalyze75 format as interpreted by the nifti library maintainers. This format does not properly respect the file orientation fields. The itkAnalyzeImageIO file reader/writer should be used to match the Analyze75 file definitions as specified by the Mayo Clinic BIR laboratory. By default this is set to false.

itk::NiftiImageIO::~NiftiImageIO ( )
protected

A mode to allow the Nifti filter to read and write to the LegacyAnalyze75 format as interpreted by the nifti library maintainers. This format does not properly respect the file orientation fields. The itkAnalyzeImageIO file reader/writer should be used to match the Analyze75 file definitions as specified by the Mayo Clinic BIR laboratory. By default this is set to false.

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

Member Function Documentation

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

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

Author:
Hans J Johnson
Parameters:
FileNameToReadThe name of the file to test for reading.
Postcondition:
Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
Returns:
Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

virtual bool itk::NiftiImageIO::CanWriteFile ( const char *  FileNameToWrite)
virtual

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

Parameters:
FileNameToWriteThe name of the file to test for writing.
Author:
Hans J. Johnson
Postcondition:
Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite
Returns:
Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

virtual::itk::LightObject::Pointer itk::NiftiImageIO::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.

void itk::NiftiImageIO::DefineHeaderObjectDataType ( )
private
virtual ImageIORegion itk::NiftiImageIO::GenerateStreamableReadRegionFromRequestedRegion ( const ImageIORegion &  requestedRegion) const
virtual

Calculate the region of the image that can be efficiently read in response to a given requested region.

Reimplemented from itk::ImageIOBase.

virtual bool itk::NiftiImageIO::GetLegacyAnalyze75Mode ( ) const
virtual

A mode to allow the Nifti filter to read and write to the LegacyAnalyze75 format as interpreted by the nifti library maintainers. This format does not properly respect the file orientation fields. The itkAnalyzeImageIO file reader/writer should be used to match the Analyze75 file definitions as specified by the Mayo Clinic BIR laboratory. By default this is set to false.

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

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

virtual bool itk::NiftiImageIO::GetUseLegacyModeForTwoFileWriting ( void  ) const
inlineprotectedvirtual

Definition at line 109 of file itkNiftiImageIO.h.

bool itk::NiftiImageIO::MustRescale ( )
private
static Pointer itk::NiftiImageIO::New ( )
static

Method for creation through the object factory.

Reimplemented from itk::LightProcessObject.

void itk::NiftiImageIO::operator= ( const Self &  )
private

This method causes the filter to generate its output.

Reimplemented from itk::ImageIOBase.

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

A mode to allow the Nifti filter to read and write to the LegacyAnalyze75 format as interpreted by the nifti library maintainers. This format does not properly respect the file orientation fields. The itkAnalyzeImageIO file reader/writer should be used to match the Analyze75 file definitions as specified by the Mayo Clinic BIR laboratory. By default this is set to false.

Reimplemented from itk::ImageIOBase.

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

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::NiftiImageIO::ReadImageInformation ( )
virtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

void itk::NiftiImageIO::SetImageIOMetadataFromNIfTI ( )
private
void itk::NiftiImageIO::SetImageIOOrientationFromNIfTI ( unsigned short int  dims)
private
virtual void itk::NiftiImageIO::SetLegacyAnalyze75Mode ( bool  _arg)
virtual

A mode to allow the Nifti filter to read and write to the LegacyAnalyze75 format as interpreted by the nifti library maintainers. This format does not properly respect the file orientation fields. The itkAnalyzeImageIO file reader/writer should be used to match the Analyze75 file definitions as specified by the Mayo Clinic BIR laboratory. By default this is set to false.

void itk::NiftiImageIO::SetNIfTIOrientationFromImageIO ( unsigned short int  origdims,
unsigned short int  dims 
)
private
virtual void itk::NiftiImageIO::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::NiftiImageIO::WriteImageInformation ( )
virtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

Member Data Documentation

bool itk::NiftiImageIO::m_LegacyAnalyze75Mode
private

Definition at line 128 of file itkNiftiImageIO.h.

nifti_image* itk::NiftiImageIO::m_NiftiImage
private

Definition at line 121 of file itkNiftiImageIO.h.

IOComponentType itk::NiftiImageIO::m_OnDiskComponentType
private

Definition at line 126 of file itkNiftiImageIO.h.

double itk::NiftiImageIO::m_RescaleIntercept
private

Definition at line 124 of file itkNiftiImageIO.h.

double itk::NiftiImageIO::m_RescaleSlope
private

Definition at line 123 of file itkNiftiImageIO.h.

The documentation for this class was generated from the following file:
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Generated on Wed Jul 11 2012 00:18:40 for ITK by doxygen 1.8.1