itk::MetaImageIO Class Reference

#include <itkMetaImageIO.h>

Detailed Description

Read MetaImage file format.

For a detailed description of using this format, please see https://www.itk.org/Wiki/ITK/MetaIO/Documentation

Definition at line 43 of file itkMetaImageIO.h.

Inheritance diagram for itk::MetaImageIO:

Collaboration diagram for itk::MetaImageIO:

Public Types
using	Pointer = SmartPointer< Self >
using	Self = MetaImageIO
using	Superclass = ImageIOBase
Public Types inherited from itk::ImageIOBase
using	ArrayOfExtensionsType = std::vector< std::string >
using	BufferSizeType = itk::OffsetValueType
using	ConstPointer = SmartPointer< const Self >
using	IndexValueType = itk::IndexValueType
using	IOByteOrderEnum = itk::IOByteOrderEnum
using	IOComponentEnum = itk::IOComponentEnum
using	IOFileEnum = itk::IOFileEnum
using	Pointer = SmartPointer< Self >
using	Self = ImageIOBase
using	SizeType = itk::intmax_t
using	SizeValueType = itk::SizeValueType
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 *) override
bool	CanWriteFile (const char *) override
ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requestedRegion) const override
unsigned int	GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) override
MetaImage *	GetMetaImagePointer ()
const char *	GetNameOfClass () const override
ImageIORegion	GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) override
void	Read (void *buffer) override
void	ReadImageInformation () override
virtual void	SetDataFileName (const char *filename)
virtual void	SetDoublePrecision (unsigned int precision)
bool	SupportsDimension (unsigned long) override
void	Write (const void *buffer) override
void	WriteImageInformation () override
bool	CanStreamRead () override
bool	CanStreamWrite () override
virtual void	SetSubSamplingFactor (unsigned int _arg)
virtual unsigned int	GetSubSamplingFactor () const
Public Member Functions inherited from itk::ImageIOBase
std::string	GetByteOrderAsString (IOByteOrderEnum) const
virtual unsigned int	GetComponentSize () const
virtual IOComponentEnum	GetComponentType () const
virtual const std::type_info &	GetComponentTypeInfo () const
virtual int	GetCompressionLevel () const
virtual const std::string &	GetCompressor () const
virtual std::vector< double >	GetDefaultDirection (unsigned int k) const
virtual SizeValueType	GetDimensions (unsigned int i) const
virtual std::vector< double >	GetDirection (unsigned int i) const
std::string	GetFileTypeAsString (IOFileEnum) const
SizeType	GetImageSizeInBytes () const
SizeType	GetImageSizeInComponents () const
SizeType	GetImageSizeInPixels () const
virtual bool	GetIsReadAsScalarPlusPalette () const
virtual unsigned int	GetNumberOfDimensions () const
virtual double	GetOrigin (unsigned int i) const
virtual SizeType	GetPixelStride () const
virtual double	GetSpacing (unsigned int i) const
const ArrayOfExtensionsType &	GetSupportedReadExtensions () const
const ArrayOfExtensionsType &	GetSupportedWriteExtensions () const
void	SetByteOrderToLittleEndian ()
virtual void	SetComponentType (const IOComponentEnum _arg)
virtual void	SetCompressionLevel (int _arg)
virtual void	SetCompressor (std::string _c)
virtual void	SetDirection (unsigned int i, const std::vector< double > &direction)
virtual void	SetDirection (unsigned int i, const vnl_vector< double > &direction)
void	SetFileTypeToBinary ()
void	SetNumberOfDimensions (unsigned int)
virtual void	SetOrigin (unsigned int i, double origin)
virtual void	SetSpacing (unsigned int i, double spacing)
template<typename TPixel >
void	SetTypeInfo (const TPixel *)
virtual void	SetFileName (const char *_arg)
virtual const char *	GetFileName () const
virtual void	SetDimensions (unsigned int i, SizeValueType dim)
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	SetNumberOfComponents (unsigned int _arg)
virtual const unsigned int &	GetNumberOfComponents () const
virtual void	SetUseCompression (bool _arg)
virtual bool	GetUseCompression () const
virtual void	UseCompressionOn ()
virtual void	SetUseStreamedReading (bool _arg)
virtual bool	GetUseStreamedReading () const
virtual void	UseStreamedReadingOn ()
virtual void	SetUseStreamedWriting (bool _arg)
virtual bool	GetUseStreamedWriting () const
virtual void	UseStreamedWritingOn ()
virtual void	SetExpandRGBPalette (bool _arg)
virtual bool	GetExpandRGBPalette () const
virtual void	ExpandRGBPaletteOn ()
virtual void	SetWritePalette (bool _arg)
virtual bool	GetWritePalette () const
virtual void	WritePaletteOn ()
virtual void	SetFileType (const IOFileEnum _arg)
virtual IOFileEnum	GetFileType () const
void	SetFileTypeToASCII ()
virtual void	SetByteOrder (const IOByteOrderEnum _arg)
virtual IOByteOrderEnum	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<unsigned int VLength>
void	SetPixelTypeInfo (const Offset< VLength > *)
template<typename TPixel , unsigned int VLength>
void	SetPixelTypeInfo (const Vector< TPixel, VLength > *)
template<typename TCoordRep , unsigned int VPointDimension>
void	SetPixelTypeInfo (const Point< TCoordRep, VPointDimension > *)
template<typename TPixel , unsigned int VLength>
void	SetPixelTypeInfo (const CovariantVector< TPixel, VLength > *)
template<typename TPixel , unsigned int 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 int 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 int 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	AbortGenerateDataOn ()
virtual const bool &	GetAbortGenerateData () const
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
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) 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 void	Delete ()
virtual int	GetReferenceCount () const
void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()
static void	SetDefaultDoublePrecision (unsigned int precision)
static unsigned int	GetDefaultDoublePrecision ()
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 ()

Protected Member Functions
	MetaImageIO ()
void	PrintSelf (std::ostream &os, Indent indent) const override
template<unsigned int VNRows, unsigned int VNColumns = VNRows>
bool	WriteMatrixInMetaData (std::ostringstream &strs, const MetaDataDictionary &metaDict, const std::string &metaString)
	~MetaImageIO () override
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 () 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	InternalSetCompressor (const std::string &_compressor)
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	ReadBufferAsASCII (std::istream &is, void *buffer, IOComponentEnum ctype, SizeType numComp)
bool	ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)
virtual void	Reset (const bool freeDynamic=true)
void	Resize (const unsigned int numDimensions, const unsigned int *dimensions)
void	SetSupportedReadExtensions (const ArrayOfExtensionsType &)
void	SetSupportedWriteExtensions (const ArrayOfExtensionsType &)
virtual void	WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentEnum ctype, SizeType numComp)
	~ImageIOBase () override
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
Protected Member Functions inherited from itk::LightProcessObject
virtual void	GenerateData ()
	LightProcessObject ()
	~LightProcessObject () override
Protected Member Functions inherited from itk::Object
	Object ()
bool	PrintObservers (std::ostream &os, Indent indent) const
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	PrintTrailer (std::ostream &os, Indent indent) const
virtual	~LightObject ()

Private Member Functions
	itkGetGlobalDeclarationMacro (unsigned int, DefaultDoublePrecision)

Private Attributes
MetaImage	m_MetaImage {}
unsigned int	m_SubSamplingFactor {}

Static Private Attributes
static unsigned int *	m_DefaultDoublePrecision

Additional Inherited Members
Protected Attributes inherited from itk::ImageIOBase
IOByteOrderEnum	m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }
IOComponentEnum	m_ComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }
int	m_CompressionLevel { 30 }
std::string	m_Compressor { "uninitialized" }
std::vector< SizeValueType >	m_Dimensions {}
std::vector< std::vector< double > >	m_Direction {}
bool	m_ExpandRGBPalette {}
std::string	m_FileName {}
IOFileEnum	m_FileType { IOFileEnum::TypeNotApplicable }
bool	m_Initialized {}
ImageIORegion	m_IORegion {}
bool	m_IsReadAsScalarPlusPalette {}
int	m_MaximumCompressionLevel { 100 }
unsigned int	m_NumberOfComponents {}
unsigned int	m_NumberOfDimensions { 0 }
std::vector< double >	m_Origin {}
IOPixelEnum	m_PixelType { IOPixelEnum::SCALAR }
std::vector< double >	m_Spacing {}
std::vector< SizeType >	m_Strides {}
bool	m_UseCompression { false }
bool	m_UseStreamedReading {}
bool	m_UseStreamedWriting {}
bool	m_WritePalette {}
Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}

Member Typedef Documentation

Pointer

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

Definition at line 51 of file itkMetaImageIO.h.

Self

using itk::MetaImageIO::Self = MetaImageIO

Standard class type aliases.

Definition at line 49 of file itkMetaImageIO.h.

Superclass

using itk::MetaImageIO::Superclass = ImageIOBase

Definition at line 50 of file itkMetaImageIO.h.

Constructor & Destructor Documentation

MetaImageIO()

itk::MetaImageIO::MetaImageIO ( )

protected

~MetaImageIO()

itk::MetaImageIO::~MetaImageIO ( )

overrideprotected

Member Function Documentation

CanReadFile()

bool itk::MetaImageIO::CanReadFile ( const char *  )

overridevirtual

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

Implements itk::ImageIOBase.

CanStreamRead()

bool itk::MetaImageIO::CanStreamRead ( )

inlineoverridevirtual

Determine if the ImageIO can stream reading from this file. Only time cannot stream read/write is if compression is used. CanRead must be called prior to this function.

Reimplemented from itk::ImageIOBase.

Definition at line 140 of file itkMetaImageIO.h.

CanStreamWrite()

bool itk::MetaImageIO::CanStreamWrite ( )

inlineoverridevirtual

Determine if the ImageIO can stream writing to this file. Only time cannot stream read/write is if compression is used. Assumes file passes a CanRead call and its pixels are of the same type as the template of the writer. Can verify by first calling CanRead and then CanStreamRead prior to calling CanStreamWrite.

Reimplemented from itk::ImageIOBase.

Definition at line 156 of file itkMetaImageIO.h.

CanWriteFile()

bool itk::MetaImageIO::CanWriteFile ( const char *  )

overridevirtual

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

Implements itk::ImageIOBase.

GenerateStreamableReadRegionFromRequestedRegion()

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

overridevirtual

Method for supporting streaming. Given a requested region, calculate what could be the region that we can read from the file. This is called the streamable region, which will be smaller than the LargestPossibleRegion and greater or equal to the RequestedRegion

Reimplemented from itk::ImageIOBase.

GetActualNumberOfSplitsForWriting()

unsigned int itk::MetaImageIO::GetActualNumberOfSplitsForWriting ( unsigned int  numberOfRequestedSplits, const ImageIORegion &  pasteRegion, const ImageIORegion &  largestPossibleRegion  )

overridevirtual

Before this method is called all the configuration will be done, that is Streaming/PasteRegion/Compression/Filename etc If pasting is being used the number of requested splits is for that region not the largest. The derived ImageIO class should verify that the file is capable of being written with this configuration. If pasted is enabled and is not support or does not work with the file, then an exception should be thrown.

The default implementation depends on CanStreamWrite. If false then 1 is returned (unless pasting is indicated), so that the whole file will be updated in one region. If true then its assumed that any arbitrary region can be written to any file. So the users request will be respected. If a derived class has more restrictive conditions then they should be checked

Reimplemented from itk::ImageIOBase.

GetDefaultDoublePrecision()

static unsigned int itk::MetaImageIO::GetDefaultDoublePrecision ( )

static

Set the default precision when writing out the MetaImage header. MetaImage header contains values stored in memory as double, use this precision when writing out the value. The precision should only be defined in the range [0, 17] since a value of 17 will make the conversion of a double floating-point to text and back exact. This function is not thread safe. Default value after static initialization is 17.

GetMetaImagePointer()

MetaImage* itk::MetaImageIO::GetMetaImagePointer

(

)

GetNameOfClass()

const char* itk::MetaImageIO::GetNameOfClass ( ) const

overridevirtual

See also

LightObject::GetNameOfClass()

Reimplemented from itk::ImageIOBase.

GetSplitRegionForWriting()

ImageIORegion itk::MetaImageIO::GetSplitRegionForWriting ( unsigned int  ithPiece, unsigned int  numberOfActualSplits, const ImageIORegion &  pasteRegion, const ImageIORegion &  largestPossibleRegion  )

overridevirtual

returns the ith IORegion

numberOfActualSplits should be the value returned from GetActualNumberOfSplitsForWriting with the same parameters

Derived classes should overload this method to return a compatible region

Reimplemented from itk::ImageIOBase.

GetSubSamplingFactor()

virtual unsigned int itk::MetaImageIO::GetSubSamplingFactor ( ) const

virtual

Determining the subsampling factor in case we want a coarse version of the image/

Warning

this is only used when streaming is on.

itkGetGlobalDeclarationMacro()

itk::MetaImageIO::itkGetGlobalDeclarationMacro ( unsigned int  , DefaultDoublePrecision    )

private

Only used to synchronize the global variable across static libraries.

New()

static Pointer itk::MetaImageIO::New ( )

static

Method for creation through the object factory.

PrintSelf()

void itk::MetaImageIO::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::ImageIOBase.

Read()

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

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

ReadImageInformation()

void itk::MetaImageIO::ReadImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

SetDataFileName()

virtual void itk::MetaImageIO::SetDataFileName ( const char *  filename )

virtual

Set the filename for the Data file. Setting this will make the Writer to use the non-Local mode and save header and data in independent files

SetDefaultDoublePrecision()

static void itk::MetaImageIO::SetDefaultDoublePrecision ( unsigned int  precision )

static

Set the default precision when writing out the MetaImage header. MetaImage header contains values stored in memory as double, use this precision when writing out the value. The precision should only be defined in the range [0, 17] since a value of 17 will make the conversion of a double floating-point to text and back exact. This function is not thread safe. Default value after static initialization is 17.

SetDoublePrecision()

virtual void itk::MetaImageIO::SetDoublePrecision ( unsigned int  precision )

inlinevirtual

set the precision in the MetaImage member

Definition at line 113 of file itkMetaImageIO.h.

SetSubSamplingFactor()

virtual void itk::MetaImageIO::SetSubSamplingFactor ( unsigned int  _arg )

virtual

Determining the subsampling factor in case we want a coarse version of the image/

Warning

this is only used when streaming is on.

SupportsDimension()

bool itk::MetaImageIO::SupportsDimension ( unsigned long  )

inlineoverridevirtual

The different types of ImageIO's can support data of varying dimensionality. For example, some file formats are strictly 2D while others can support 2D, 3D, or even n-D. This method returns true/false as to whether the ImageIO can support the dimension indicated.

Reimplemented from itk::ImageIOBase.

Definition at line 65 of file itkMetaImageIO.h.

Write()

void itk::MetaImageIO::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::MetaImageIO::WriteImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

WriteMatrixInMetaData()

template<unsigned int VNRows, unsigned int VNColumns>

bool itk::MetaImageIO::WriteMatrixInMetaData ( std::ostringstream &  strs, const MetaDataDictionary &  metaDict, const std::string &  metaString  )

protected

Definition at line 211 of file itkMetaImageIO.h.

References itk::ExposeMetaData().

Member Data Documentation

m_DefaultDoublePrecision

unsigned int* itk::MetaImageIO::m_DefaultDoublePrecision

staticprivate

Definition at line 206 of file itkMetaImageIO.h.

m_MetaImage

MetaImage itk::MetaImageIO::m_MetaImage {}

private

Definition at line 202 of file itkMetaImageIO.h.

m_SubSamplingFactor

unsigned int itk::MetaImageIO::m_SubSamplingFactor {}

private

Definition at line 204 of file itkMetaImageIO.h.

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

• itkMetaImageIO.h