itk::NiftiImageIO Class Reference

#include <itkNiftiImageIO.h>

Inheritance diagram for itk::NiftiImageIO:

Collaboration diagram for itk::NiftiImageIO:

Public Types
using	Pointer = SmartPointer< Self >
using	Self = NiftiImageIO
using	Superclass = ImageIOBase
Public Types inherited from itk::ImageIOBase
using	ConstPointer = SmartPointer< const Self >
using	Pointer = SmartPointer< Self >
using	Self = ImageIOBase
using	Superclass = LightProcessObject
using	IndexValueType = ::itk::IndexValueType
using	SizeValueType = ::itk::SizeValueType
using	IOComponentEnum = itk::IOComponentEnum
using	IOFileEnum = itk::IOFileEnum
using	IOByteOrderEnum = itk::IOByteOrderEnum
using	SizeType = ::itk::intmax_t
using	BufferSizeType = ::itk::OffsetValueType
using	ArrayOfExtensionsType = std::vector< std::string >
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 *FileNameToRead) override
bool	CanWriteFile (const char *FileNameToWrite) override
virtual ::itk::LightObject::Pointer	CreateAnother () const
NiftiImageIOEnums::NiftiFileEnum	DetermineFileType (const char *FileNameToRead)
ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requestedRegion) const override
virtual const char *	GetNameOfClass () const
void	Read (void *buffer) override
void	ReadImageInformation () override
void	Write (const void *buffer) override
void	WriteImageInformation () override
Public Member Functions inherited from itk::ImageIOBase
virtual void	SetFileName (const char *_arg)
virtual const char *	GetFileName () const
void	SetNumberOfDimensions (unsigned int)
virtual unsigned int	GetNumberOfDimensions () const
virtual void	SetDimensions (unsigned int i, SizeValueType dim)
virtual SizeValueType	GetDimensions (unsigned int i) const
virtual void	SetOrigin (unsigned int i, double origin)
virtual double	GetOrigin (unsigned int i) const
virtual void	SetSpacing (unsigned int i, double spacing)
virtual double	GetSpacing (unsigned int i) const
virtual void	SetDirection (unsigned int i, const std::vector< double > &direction)
virtual void	SetDirection (unsigned int i, const vnl_vector< double > &direction)
virtual std::vector< double >	GetDirection (unsigned int i) const
virtual std::vector< double >	GetDefaultDirection (unsigned int k) const
virtual void	SetIORegion (ImageIORegion _arg)
virtual const ImageIORegion &	GetIORegion () const
virtual void	SetPixelType (const ::itk::CommonEnums::IOPixel _arg)
virtual ::itk::CommonEnums::IOPixel	GetPixelType () const
virtual void	SetComponentType (const IOComponentEnum _arg)
virtual IOComponentEnum	GetComponentType () const
virtual const std::type_info &	GetComponentTypeInfo () const
virtual void	SetNumberOfComponents (unsigned int _arg)
virtual const unsigned int &	GetNumberOfComponents () const
virtual void	SetUseCompression (bool _arg)
virtual bool	GetUseCompression () const
virtual void	UseCompressionOn ()
virtual void	UseCompressionOff ()
virtual void	SetCompressionLevel (int _arg)
virtual int	GetCompressionLevel () const
virtual void	SetCompressor (std::string _c)
virtual const std::string &	GetCompressor () const
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	SetExpandRGBPalette (bool _arg)
virtual bool	GetExpandRGBPalette () const
virtual void	ExpandRGBPaletteOn ()
virtual void	ExpandRGBPaletteOff ()
virtual void	SetWritePalette (bool _arg)
virtual bool	GetWritePalette () const
virtual void	WritePaletteOn ()
virtual void	WritePaletteOff ()
virtual bool	GetIsReadAsScalarPlusPalette () 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 ()
std::string	GetFileTypeAsString (IOFileEnum) const
std::string	GetByteOrderAsString (IOByteOrderEnum) const
virtual SizeType	GetPixelStride () const
SizeType	GetImageSizeInPixels () const
SizeType	GetImageSizeInBytes () const
SizeType	GetImageSizeInComponents () const
virtual unsigned int	GetComponentSize () const
virtual bool	CanStreamRead ()
virtual bool	CanStreamWrite ()
virtual bool	SupportsDimension (unsigned long dim)
virtual unsigned int	GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
virtual ImageIORegion	GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
const ArrayOfExtensionsType &	GetSupportedReadExtensions () const
const ArrayOfExtensionsType &	GetSupportedWriteExtensions () const
template<typename TPixel >
void	SetTypeInfo (const TPixel *)
template<typename TPixel >
void	SetPixelTypeInfo (const TPixel *)
template<typename TPixel >
void	SetPixelTypeInfo (const RGBPixel< TPixel > *)
template<typename TPixel >
void	SetPixelTypeInfo (const RGBAPixel< TPixel > *)
template<unsigned VLength>
void	SetPixelTypeInfo (const Offset< VLength > *)
template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const Vector< TPixel, VLength > *)
template<typename TCoordRep , unsigned NPointDimension>
void	SetPixelTypeInfo (const Point< TCoordRep, NPointDimension > *)
template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const CovariantVector< TPixel, VLength > *)
template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const SymmetricSecondRankTensor< TPixel, VLength > *)
template<typename TPixel >
void	SetPixelTypeInfo (const DiffusionTensor3D< TPixel > *)
template<typename TPixel >
void	SetPixelTypeInfo (const std::complex< TPixel > *)
template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const FixedArray< TPixel, VLength > *)
template<typename TPixel >
void	SetPixelTypeInfo (const VariableLengthVector< TPixel > *)
template<typename TValue >
void	SetPixelTypeInfo (const Array< TValue > *)
template<typename TPixel , unsigned VLength>
void	SetPixelTypeInfo (const Matrix< TPixel, VLength, VLength > *)
template<typename TValue >
void	SetPixelTypeInfo (const VariableSizeMatrix< TValue > *)
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::ImageIOBase
static std::string	GetComponentTypeAsString (IOComponentEnum)
static IOComponentEnum	GetComponentTypeFromString (const std::string &typeString)
static std::string	GetPixelTypeAsString (IOPixelEnum)
static IOPixelEnum	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 val)
Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()
static Pointer	New ()
const std::unique_ptr< NiftiImageProxy >	m_NiftiImageHolder
NiftiImageProxy &	m_NiftiImage
double	m_RescaleSlope { 1.0 }
double	m_RescaleIntercept { 0.0 }
IOComponentEnum	m_OnDiskComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }
NiftiImageIOEnums::Analyze75Flavor	m_LegacyAnalyze75Mode
virtual void	SetRescaleSlope (double _arg)
virtual void	SetRescaleIntercept (double _arg)
virtual void	SetLegacyAnalyze75Mode (NiftiImageIOEnums::Analyze75Flavor _arg)
virtual NiftiImageIOEnums::Analyze75Flavor	GetLegacyAnalyze75Mode () const
	NiftiImageIO ()
	~NiftiImageIO () override
void	PrintSelf (std::ostream &os, Indent indent) const override
virtual bool	GetUseLegacyModeForTwoFileWriting () const
unsigned int	getSFormCodeFromDictionary () const
unsigned int	getQFormCodeFromDictionary () const
bool	MustRescale () const
void	DefineHeaderObjectDataType ()
void	SetNIfTIOrientationFromImageIO (unsigned short int origdims, unsigned short int dims)
void	SetImageIOOrientationFromNIfTI (unsigned short int dims)
void	SetImageIOMetadataFromNIfTI ()

Additional Inherited Members
Protected Member Functions inherited from itk::ImageIOBase
	ImageIOBase ()
	~ImageIOBase () override
virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const
virtual bool	HasSupportedReadExtension (const char *fileName, bool ignoreCase=true)
virtual bool	HasSupportedWriteExtension (const char *fileName, bool ignoreCase=true)
virtual void	SetMaximumCompressionLevel (int)
virtual int	GetMaximumCompressionLevel () const
virtual void	InternalSetCompressor (const std::string &_compressor)
virtual void	Reset (const bool freeDynamic=true)
void	Resize (const unsigned int numDimensions, const unsigned int *dimensions)
virtual unsigned int	GetPixelSize () const
void	ComputeStrides ()
SizeType	GetComponentStride () const
SizeType	GetRowStride () const
SizeType	GetSliceStride () const
virtual void	OpenFileForReading (std::ifstream &inputStream, const std::string &filename, bool ascii=false)
virtual void	OpenFileForWriting (std::ofstream &outputStream, const std::string &filename, bool truncate=true, bool ascii=false)
virtual void	WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentEnum ctype, SizeType numComp)
virtual void	ReadBufferAsASCII (std::istream &is, void *buffer, IOComponentEnum ctype, SizeType numComp)
bool	ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)
void	AddSupportedReadExtension (const char *extension)
void	AddSupportedWriteExtension (const char *extension)
void	SetSupportedReadExtensions (const ArrayOfExtensionsType &)
void	SetSupportedWriteExtensions (const ArrayOfExtensionsType &)
virtual unsigned int	GetActualNumberOfSplitsForWritingCanStreamWrite (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion) const
virtual ImageIORegion	GetSplitRegionForWritingCanStreamWrite (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion) const
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 ()
Protected Attributes inherited from itk::ImageIOBase
IOPixelEnum	m_PixelType { IOPixelEnum::SCALAR }
IOComponentEnum	m_ComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }
IOByteOrderEnum	m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }
IOFileEnum	m_FileType { IOFileEnum::TypeNotApplicable }
bool	m_Initialized
std::string	m_FileName
unsigned int	m_NumberOfComponents
unsigned int	m_NumberOfDimensions { 0 }
bool	m_UseCompression { false }
int	m_CompressionLevel { 30 }
int	m_MaximumCompressionLevel { 100 }
std::string	m_Compressor { "uninitialized" }
bool	m_UseStreamedReading
bool	m_UseStreamedWriting
bool	m_ExpandRGBPalette
bool	m_IsReadAsScalarPlusPalette
bool	m_WritePalette
ImageIORegion	m_IORegion
std::vector< SizeValueType >	m_Dimensions
std::vector< double >	m_Spacing
std::vector< double >	m_Origin
std::vector< std::vector< double > >	m_Direction
std::vector< SizeType >	m_Strides
Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount

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, The University of Iowa 2002 The specification for this file format is taken from the web site http://analyzedirect.com/support/10.0Documents/Analyze_Resource_01.pdf

Definition at line 105 of file itkNiftiImageIO.h.

Member Typedef Documentation

Pointer

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

Definition at line 113 of file itkNiftiImageIO.h.

Self

using itk::NiftiImageIO::Self = NiftiImageIO

Standard class type aliases.

Definition at line 111 of file itkNiftiImageIO.h.

Superclass

using itk::NiftiImageIO::Superclass = ImageIOBase

Definition at line 112 of file itkNiftiImageIO.h.

Constructor & Destructor Documentation

NiftiImageIO()

itk::NiftiImageIO::NiftiImageIO ( )

protected

Set the slope and intercept for voxel value rescaling.

~NiftiImageIO()

itk::NiftiImageIO::~NiftiImageIO ( )

overrideprotected

Set the slope and intercept for voxel value rescaling.

Member Function Documentation

CanReadFile()

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

overridevirtual

Reads the file to determine if it can be read with this ImageIO implementation. Analyze 7.5 format files will only result in true if LegacyAnalyze75Mode is true.

Parameters

FileNameToRead

The 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.

CanWriteFile()

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

overridevirtual

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

Parameters

FileNameToWrite

The name of the file to test for writing.

Postcondition

Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite

Returns

Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

CreateAnother()

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

DefineHeaderObjectDataType()

void itk::NiftiImageIO::DefineHeaderObjectDataType ( )

private

Set the slope and intercept for voxel value rescaling.

DetermineFileType()

NiftiImageIOEnums::NiftiFileEnum itk::NiftiImageIO::DetermineFileType

(

const char *

FileNameToRead

)

Reads the file to determine if it can be read with this ImageIO implementation, and to determine what kind of file it is (Analyze vs NIfTI). Note that the value of LegacyAnalyze75Mode is ignored by this method.

Parameters

FileNameToRead

The name of the file to test for reading.

Returns

Returns one of the IOFileEnum enumerations.

GenerateStreamableReadRegionFromRequestedRegion()

ImageIORegion itk::NiftiImageIO::GenerateStreamableReadRegionFromRequestedRegion ( const ImageIORegion &  requestedRegion ) const

overridevirtual

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

Reimplemented from itk::ImageIOBase.

GetLegacyAnalyze75Mode()

virtual NiftiImageIOEnums::Analyze75Flavor itk::NiftiImageIO::GetLegacyAnalyze75Mode ( ) const

virtual

Set the slope and intercept for voxel value rescaling.

GetNameOfClass()

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

getQFormCodeFromDictionary()

unsigned int itk::NiftiImageIO::getQFormCodeFromDictionary ( ) const

private

Set the slope and intercept for voxel value rescaling.

getSFormCodeFromDictionary()

unsigned int itk::NiftiImageIO::getSFormCodeFromDictionary ( ) const

private

Set the slope and intercept for voxel value rescaling.

GetUseLegacyModeForTwoFileWriting()

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

inlineprotectedvirtual

Set the slope and intercept for voxel value rescaling.

Definition at line 208 of file itkNiftiImageIO.h.

MustRescale()

bool itk::NiftiImageIO::MustRescale ( ) const

private

Set the slope and intercept for voxel value rescaling.

New()

static Pointer itk::NiftiImageIO::New ( )

static

Method for creation through the object factory.

PrintSelf()

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

overrideprotectedvirtual

Set the slope and intercept for voxel value rescaling.

Reimplemented from itk::ImageIOBase.

Read()

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

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

ReadImageInformation()

void itk::NiftiImageIO::ReadImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

SetImageIOMetadataFromNIfTI()

void itk::NiftiImageIO::SetImageIOMetadataFromNIfTI ( )

private

Set the slope and intercept for voxel value rescaling.

SetImageIOOrientationFromNIfTI()

void itk::NiftiImageIO::SetImageIOOrientationFromNIfTI ( unsigned short int  dims )

private

Set the slope and intercept for voxel value rescaling.

SetLegacyAnalyze75Mode()

virtual void itk::NiftiImageIO::SetLegacyAnalyze75Mode ( NiftiImageIOEnums::Analyze75Flavor  _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. By default this is set by configuration option ITK_NIFTI_IO_ANALYZE_FLAVOR

SetNIfTIOrientationFromImageIO()

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

private

Set the slope and intercept for voxel value rescaling.

SetRescaleIntercept()

virtual void itk::NiftiImageIO::SetRescaleIntercept ( double  _arg )

virtual

Set the slope and intercept for voxel value rescaling.

SetRescaleSlope()

virtual void itk::NiftiImageIO::SetRescaleSlope ( double  _arg )

virtual

Set the slope and intercept for voxel value rescaling.

Write()

void itk::NiftiImageIO::Write ( const void *  buffer )

overridevirtual

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

Implements itk::ImageIOBase.

WriteImageInformation()

void itk::NiftiImageIO::WriteImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

For Nifti this does not write a file, it only fills in the appropriate header information.

Implements itk::ImageIOBase.

Member Data Documentation

m_LegacyAnalyze75Mode

NiftiImageIOEnums::Analyze75Flavor itk::NiftiImageIO::m_LegacyAnalyze75Mode

private

Set the slope and intercept for voxel value rescaling.

Definition at line 253 of file itkNiftiImageIO.h.

m_NiftiImage

NiftiImageProxy& itk::NiftiImageIO::m_NiftiImage

private

Set the slope and intercept for voxel value rescaling.

Definition at line 246 of file itkNiftiImageIO.h.

m_NiftiImageHolder

const std::unique_ptr<NiftiImageProxy> itk::NiftiImageIO::m_NiftiImageHolder

private

Set the slope and intercept for voxel value rescaling.

Definition at line 240 of file itkNiftiImageIO.h.

m_OnDiskComponentType

IOComponentEnum itk::NiftiImageIO::m_OnDiskComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }

private

Set the slope and intercept for voxel value rescaling.

Definition at line 251 of file itkNiftiImageIO.h.

m_RescaleIntercept

double itk::NiftiImageIO::m_RescaleIntercept { 0.0 }

private

Set the slope and intercept for voxel value rescaling.

Definition at line 249 of file itkNiftiImageIO.h.

m_RescaleSlope

double itk::NiftiImageIO::m_RescaleSlope { 1.0 }

private

Set the slope and intercept for voxel value rescaling.

Definition at line 248 of file itkNiftiImageIO.h.

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

• itkNiftiImageIO.h