ITK  5.0.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | Static Private Attributes | List of all members
itk::MetaImageIO Class Reference

#include <itkMetaImageIO.h>

+ Inheritance diagram for itk::MetaImageIO:
+ Collaboration diagram for itk::MetaImageIO:

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 40 of file itkMetaImageIO.h.

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
 
enum  ByteOrder {
  BigEndian,
  LittleEndian,
  OrderNotApplicable
}
 
using ConstPointer = SmartPointer< const Self >
 
enum  FileType {
  ASCII,
  Binary,
  TypeNotApplicable
}
 
using IndexValueType = ::itk::IndexValueType
 
enum  IOComponentType {
  UNKNOWNCOMPONENTTYPE,
  UCHAR,
  CHAR,
  USHORT,
  SHORT,
  UINT,
  INT,
  ULONG,
  LONG,
  ULONGLONG,
  LONGLONG,
  FLOAT,
  DOUBLE
}
 
enum  IOPixelType {
  UNKNOWNPIXELTYPE,
  SCALAR,
  RGB,
  RGBA,
  OFFSET,
  VECTOR,
  POINT,
  COVARIANTVECTOR,
  SYMMETRICSECONDRANKTENSOR,
  DIFFUSIONTENSOR3D,
  COMPLEX,
  FIXEDARRAY,
  MATRIX
}
 
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
 
virtual ::itk::LightObject::Pointer CreateAnother () const
 
ImageIORegion GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const override
 
unsigned int GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) override
 
MetaImage * GetMetaImagePointer ()
 
virtual const char * GetNameOfClass () const
 
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 (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 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 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 ArrayOfExtensionsTypeGetSupportedReadExtensions () const
 
const ArrayOfExtensionsTypeGetSupportedWriteExtensions () const
 
void SetByteOrderToLittleEndian ()
 
virtual void SetComponentType (const IOComponentType _arg)
 
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)
 
template<typename 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 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 ImageIORegionGetIORegion () const
 
virtual void SetPixelType (const IOPixelType _arg)
 
virtual IOPixelType 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 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 SetExpandRGBPalette (bool _arg)
 
virtual bool GetExpandRGBPalette () const
 
virtual void ExpandRGBPaletteOn ()
 
virtual void ExpandRGBPaletteOff ()
 
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 () 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 *)
 
unsigned long AddObserver (const EventObject &event, Command *) const
 
virtual void DebugOff () const
 
virtual void DebugOn () const
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary ()
 
const MetaDataDictionaryGetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStampGetTimeStamp () 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 SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
void SetReferenceCount (int) override
 
void UnRegister () const noexceptoverride
 
virtual void SetObjectName (std::string _arg)
 
virtual const std::string & GetObjectName () 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 void SetDefaultDoublePrecision (unsigned int precision)
 
static unsigned int GetDefaultDoublePrecision ()
 
- 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 ()
 

Protected Member Functions

 MetaImageIO ()
 
void PrintSelf (std::ostream &os, Indent indent) const override
 
 ~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 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 &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 () override
 
virtual bool HasSupportedReadExtension (const char *fileName, bool ignoreCase=true)
 
virtual bool HasSupportedWriteExtension (const char *fileName, bool ignoreCase=true)
 
- 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 &time)
 
 ~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 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
ByteOrder m_ByteOrder
 
IOComponentType m_ComponentType
 
std::vector< SizeValueTypem_Dimensions
 
std::vector< std::vector
< double > > 
m_Direction
 
bool m_ExpandRGBPalette
 
std::string m_FileName
 
FileType m_FileType
 
bool m_Initialized
 
ImageIORegion m_IORegion
 
bool m_IsReadAsScalarPlusPalette
 
unsigned int m_NumberOfComponents
 
unsigned int m_NumberOfDimensions
 
std::vector< double > m_Origin
 
IOPixelType m_PixelType
 
std::vector< double > m_Spacing
 
std::vector< SizeTypem_Strides
 
bool m_UseCompression
 
bool m_UseStreamedReading
 
bool m_UseStreamedWriting
 
- Protected Attributes inherited from itk::LightObject
std::atomic< int > m_ReferenceCount
 

Member Typedef Documentation

Definition at line 48 of file itkMetaImageIO.h.

Standard class type aliases.

Definition at line 46 of file itkMetaImageIO.h.

Definition at line 47 of file itkMetaImageIO.h.

Constructor & Destructor Documentation

itk::MetaImageIO::MetaImageIO ( )
protected
itk::MetaImageIO::~MetaImageIO ( )
overrideprotected

Member Function Documentation

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

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

Implements itk::ImageIOBase.

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 126 of file itkMetaImageIO.h.

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 141 of file itkMetaImageIO.h.

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

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

Implements itk::ImageIOBase.

virtual::itk::LightObject::Pointer itk::MetaImageIO::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.

ImageIORegion itk::MetaImageIO::GenerateStreamableReadRegionFromRequestedRegion ( const ImageIORegion requested) 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.

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 excepetion 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 restictive conditions then they should be checked

Reimplemented from itk::ImageIOBase.

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.

MetaImage* itk::MetaImageIO::GetMetaImagePointer ( )
virtual const char* itk::MetaImageIO::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

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

Derieved classes should overload this method to return a compatible region

Reimplemented from itk::ImageIOBase.

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

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

Warning
this is only used when streaming is on.
static Pointer itk::MetaImageIO::New ( )
static

Method for creation through the object factory.

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.

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

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

void itk::MetaImageIO::ReadImageInformation ( )
overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

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

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.

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

set the precision in the MetaImage member

Definition at line 100 of file itkMetaImageIO.h.

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

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

Warning
this is only used when streaming is on.
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 61 of file itkMetaImageIO.h.

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.

void itk::MetaImageIO::WriteImageInformation ( )
overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

Member Data Documentation

unsigned int itk::MetaImageIO::m_DefaultDoublePrecision
staticprivate

Definition at line 183 of file itkMetaImageIO.h.

MetaImage itk::MetaImageIO::m_MetaImage
private

Definition at line 179 of file itkMetaImageIO.h.

unsigned int itk::MetaImageIO::m_SubSamplingFactor
private

Definition at line 181 of file itkMetaImageIO.h.


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