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

#include <itkNiftiImageIO.h>

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

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 42 of file itkNiftiImageIO.h.

Public Types

enum  FileType {
  TwoFileNifti = 2,
  OneFileNifti = 1,
  Analyze75 = 0,
  OtherOrError = -1
}
 
using Pointer = SmartPointer< Self >
 
using Self = NiftiImageIO
 
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 *FileNameToRead) override
 
bool CanWriteFile (const char *FileNameToWrite) override
 
virtual ::itk::LightObject::Pointer CreateAnother () const
 
FileType 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
 
virtual void SetRescaleSlope (double _arg)
 
virtual void SetRescaleIntercept (double _arg)
 
virtual void SetLegacyAnalyze75Mode (bool _arg)
 
virtual bool GetLegacyAnalyze75Mode () const
 
- 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 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
 
virtual ImageIORegion GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
 
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 bool SupportsDimension (unsigned long dim)
 
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 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

virtual bool GetUseLegacyModeForTwoFileWriting () const
 
 NiftiImageIO ()
 
void PrintSelf (std::ostream &os, Indent indent) const override
 
 ~NiftiImageIO () 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 Member Functions

void DefineHeaderObjectDataType ()
 
unsigned int getQFormCodeFromDictionary () const
 
unsigned int getSFormCodeFromDictionary () const
 
bool MustRescale ()
 
void SetImageIOMetadataFromNIfTI ()
 
void SetImageIOOrientationFromNIfTI (unsigned short int dims)
 
void SetNIfTIOrientationFromImageIO (unsigned short int origdims, unsigned short int dims)
 

Private Attributes

bool m_LegacyAnalyze75Mode
 
NiftiImageProxy & m_NiftiImage
 
const std::unique_ptr
< NiftiImageProxy > 
m_NiftiImageHolder
 
IOComponentType m_OnDiskComponentType
 
double m_RescaleIntercept
 
double m_RescaleSlope
 

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 50 of file itkNiftiImageIO.h.

Standard class type aliases.

Definition at line 48 of file itkNiftiImageIO.h.

Definition at line 49 of file itkNiftiImageIO.h.

Member Enumeration Documentation

Possible file formats readable by this ImageIO implementation. Used by DetermineFileType().

Enumerator
TwoFileNifti 

2-file Nifti (consisting of .hdr and .img file).

OneFileNifti 

1-file Nifti (consisting of .nii file).

Analyze75 

Legacy Analyze 7.5 format (consisting of .hdr and .img file).

OtherOrError 

Some other file format, or file system error.

Definition at line 62 of file itkNiftiImageIO.h.

Constructor & Destructor Documentation

itk::NiftiImageIO::NiftiImageIO ( )
protected
itk::NiftiImageIO::~NiftiImageIO ( )
overrideprotected

Member Function Documentation

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
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.

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

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

Parameters
FileNameToWriteThe 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.

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.

void itk::NiftiImageIO::DefineHeaderObjectDataType ( )
private
FileType 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
FileNameToReadThe name of the file to test for reading.
Returns
Returns one of the FileType enumerations.
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.

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. By default this is set to true.

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

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

unsigned int itk::NiftiImageIO::getQFormCodeFromDictionary ( ) const
private
unsigned int itk::NiftiImageIO::getSFormCodeFromDictionary ( ) const
private
virtual bool itk::NiftiImageIO::GetUseLegacyModeForTwoFileWriting ( ) const
inlineprotectedvirtual

Definition at line 142 of file itkNiftiImageIO.h.

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

Method for creation through the object factory.

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

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

void itk::NiftiImageIO::ReadImageInformation ( )
overridevirtual

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. By default this is set to true.

void itk::NiftiImageIO::SetNIfTIOrientationFromImageIO ( unsigned short int  origdims,
unsigned short int  dims 
)
private
virtual void itk::NiftiImageIO::SetRescaleIntercept ( double  _arg)
virtual

Set the slope and intercept for voxel value rescaling.

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

Set the slope and intercept for voxel value rescaling.

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.

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

bool itk::NiftiImageIO::m_LegacyAnalyze75Mode
private

Definition at line 177 of file itkNiftiImageIO.h.

NiftiImageProxy& itk::NiftiImageIO::m_NiftiImage
private

Definition at line 170 of file itkNiftiImageIO.h.

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

Definition at line 164 of file itkNiftiImageIO.h.

IOComponentType itk::NiftiImageIO::m_OnDiskComponentType
private

Definition at line 175 of file itkNiftiImageIO.h.

double itk::NiftiImageIO::m_RescaleIntercept
private

Definition at line 173 of file itkNiftiImageIO.h.

double itk::NiftiImageIO::m_RescaleSlope
private

Definition at line 172 of file itkNiftiImageIO.h.


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