ITK 6.0.0
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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
Data Processing Objects » Filters » Input and Output Filters | Group IO » Module ITKIONIFTI

#include <itkNiftiImageIO.h>

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 https://analyzedirect.com/support/10.0Documents/Analyze_Resource_01.pdf

Definition at line 106 of file 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 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 *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
 
const char * GetNameOfClass () const override
 
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 (NiftiImageIOEnums::Analyze75Flavor _arg)
 
virtual NiftiImageIOEnums::Analyze75Flavor GetLegacyAnalyze75Mode () const
 
virtual void SetConvertRASVectors (bool _arg)
 
virtual bool GetConvertRASVectors () const
 
virtual void ConvertRASVectorsOn ()
 
virtual void ConvertRASVectorsOff ()
 
virtual void SetConvertRASDisplacementVectors (bool _arg)
 
virtual bool GetConvertRASDisplacementVectors () const
 
virtual void ConvertRASDisplacementVectorsOn ()
 
virtual void ConvertRASDisplacementVectorsOff ()
 
virtual void SetSFORM_Permissive (bool _arg)
 
virtual bool GetSFORM_Permissive () const
 
virtual void SFORM_PermissiveOn ()
 
virtual void SFORM_PermissiveOff ()
 
- 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 (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
 
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 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 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 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 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 SetWritePalette (bool _arg)
 
virtual bool GetWritePalette () const
 
virtual void WritePaletteOn ()
 
virtual void WritePaletteOff ()
 
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 TCoordinate, unsigned int VPointDimension>
void SetPixelTypeInfo (const Point< TCoordinate, 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 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 *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
 
const char * GetNameOfClass () const override
 
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 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

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

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

Private Attributes

bool m_ConvertRAS { false }
 
bool m_ConvertRASDisplacementVectors { true }
 
bool m_ConvertRASVectors { false }
 
NiftiImageIOEnums::Analyze75Flavor m_LegacyAnalyze75Mode {}
 
NiftiImageProxy & m_NiftiImage
 
const std::unique_ptr< NiftiImageProxy > m_NiftiImageHolder
 
IOComponentEnum m_OnDiskComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }
 
double m_RescaleIntercept { 0.0 }
 
double m_RescaleSlope { 1.0 }
 
bool m_SFORM_Corrected { false }
 
bool m_SFORM_Permissive
 

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::NiftiImageIO::Pointer = SmartPointer<Self>

Definition at line 114 of file itkNiftiImageIO.h.

◆ Self

using itk::NiftiImageIO::Self = NiftiImageIO

Standard class type aliases.

Definition at line 112 of file itkNiftiImageIO.h.

◆ Superclass

using itk::NiftiImageIO::Superclass = ImageIOBase

Definition at line 113 of file itkNiftiImageIO.h.

Constructor & Destructor Documentation

◆ NiftiImageIO()

itk::NiftiImageIO::NiftiImageIO ( )
protected

Referenced by GetNameOfClass().

◆ ~NiftiImageIO()

itk::NiftiImageIO::~NiftiImageIO ( )
overrideprotected

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
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.

◆ CanWriteFile()

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.

◆ ConvertRASDisplacementVectorsOff()

virtual void itk::NiftiImageIO::ConvertRASDisplacementVectorsOff ( )
virtual

Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and LPS (ITK convention) when reading or writing a "displacement vector" file (intent code: 1006).

This flag is enabled by default. Disabling it may be useful to avoid unnecessary conversions in applications that uses RAS coordinate system.

To write a vector image as displacement vector: set "intent_code" to "1006" in the metadata dictionary of the input image.

itk::MetaDataDictionary& dictionary = image->GetMetaDataDictionary();
itk::EncapsulateMetaData<std::string>(dictionary, "intent_code", "1006");
itk::MetaDataDictionary
Provides a mechanism for storing a collection of arbitrary data types.
Definition itkMetaDataDictionary.h:55
itk::EncapsulateMetaData
void EncapsulateMetaData(MetaDataDictionary &Dictionary, const std::string &key, const T &invalue)
Definition itkMetaDataObject.h:218

◆ ConvertRASDisplacementVectorsOn()

virtual void itk::NiftiImageIO::ConvertRASDisplacementVectorsOn ( )
virtual

Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and LPS (ITK convention) when reading or writing a "displacement vector" file (intent code: 1006).

This flag is enabled by default. Disabling it may be useful to avoid unnecessary conversions in applications that uses RAS coordinate system.

To write a vector image as displacement vector: set "intent_code" to "1006" in the metadata dictionary of the input image.

itk::MetaDataDictionary& dictionary = image->GetMetaDataDictionary();
itk::EncapsulateMetaData<std::string>(dictionary, "intent_code", "1006");

◆ ConvertRASVectorsOff()

virtual void itk::NiftiImageIO::ConvertRASVectorsOff ( )
virtual

Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and LPS (ITK convention) when reading or writing a generic vector image file (intent code: 1007).

This flag is disabled by default because vectors may store non-spatial information.

By default an ITK vector image is written to NIFTI file as a generic vector image, unless "intent_code" field is set explicitly to set to "1006" (displacement vector).

◆ ConvertRASVectorsOn()

virtual void itk::NiftiImageIO::ConvertRASVectorsOn ( )
virtual

Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and LPS (ITK convention) when reading or writing a generic vector image file (intent code: 1007).

This flag is disabled by default because vectors may store non-spatial information.

By default an ITK vector image is written to NIFTI file as a generic vector image, unless "intent_code" field is set explicitly to set to "1006" (displacement vector).

◆ 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

◆ 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
FileNameToReadThe 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.

◆ GetConvertRASDisplacementVectors()

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

Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and LPS (ITK convention) when reading or writing a "displacement vector" file (intent code: 1006).

This flag is enabled by default. Disabling it may be useful to avoid unnecessary conversions in applications that uses RAS coordinate system.

To write a vector image as displacement vector: set "intent_code" to "1006" in the metadata dictionary of the input image.

itk::MetaDataDictionary& dictionary = image->GetMetaDataDictionary();
itk::EncapsulateMetaData<std::string>(dictionary, "intent_code", "1006");

◆ GetConvertRASVectors()

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

Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and LPS (ITK convention) when reading or writing a generic vector image file (intent code: 1007).

This flag is disabled by default because vectors may store non-spatial information.

By default an ITK vector image is written to NIFTI file as a generic vector image, unless "intent_code" field is set explicitly to set to "1006" (displacement vector).

◆ GetLegacyAnalyze75Mode()

virtual NiftiImageIOEnums::Analyze75Flavor 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 by configuration option ITK_NIFTI_IO_ANALYZE_FLAVOR

◆ GetNameOfClass()

const char * itk::NiftiImageIO::GetNameOfClass ( ) const
overridevirtual
See also
LightObject::GetNameOfClass()

Reimplemented from itk::ImageIOBase.

References itk::NiftiImageIOEnums::Analyze75, NiftiImageIO(), itk::NiftiImageIOEnums::OneFileNifti, itk::NiftiImageIOEnums::OtherOrError, and itk::NiftiImageIOEnums::TwoFileNifti.

◆ getQFormCodeFromDictionary()

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

◆ GetSFORM_Permissive()

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

Allow to read nifti files with non-orthogonal sform

◆ getSFormCodeFromDictionary()

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

◆ GetUseLegacyModeForTwoFileWriting()

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

Definition at line 248 of file itkNiftiImageIO.h.

◆ MustRescale()

bool itk::NiftiImageIO::MustRescale ( ) const
private

◆ 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

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::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.

◆ SetConvertRASDisplacementVectors()

virtual void itk::NiftiImageIO::SetConvertRASDisplacementVectors ( bool _arg)
virtual

Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and LPS (ITK convention) when reading or writing a "displacement vector" file (intent code: 1006).

This flag is enabled by default. Disabling it may be useful to avoid unnecessary conversions in applications that uses RAS coordinate system.

To write a vector image as displacement vector: set "intent_code" to "1006" in the metadata dictionary of the input image.

itk::MetaDataDictionary& dictionary = image->GetMetaDataDictionary();
itk::EncapsulateMetaData<std::string>(dictionary, "intent_code", "1006");

◆ SetConvertRASVectors()

virtual void itk::NiftiImageIO::SetConvertRASVectors ( bool _arg)
virtual

Enable conversion of vector coordinates between RAS coordinate system (in NIFTI file) and LPS (ITK convention) when reading or writing a generic vector image file (intent code: 1007).

This flag is disabled by default because vectors may store non-spatial information.

By default an ITK vector image is written to NIFTI file as a generic vector image, unless "intent_code" field is set explicitly to set to "1006" (displacement vector).

◆ SetImageIOMetadataFromNIfTI()

void itk::NiftiImageIO::SetImageIOMetadataFromNIfTI ( )
private

◆ SetImageIOOrientationFromNIfTI()

void itk::NiftiImageIO::SetImageIOOrientationFromNIfTI ( unsigned short dims,
double spacingscale,
double timingscale )
private

◆ 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 origdims,
unsigned short dims )
private

◆ 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.

◆ SetSFORM_Permissive()

virtual void itk::NiftiImageIO::SetSFORM_Permissive ( bool _arg)
virtual

Allow to read nifti files with non-orthogonal sform

◆ SFORM_PermissiveOff()

virtual void itk::NiftiImageIO::SFORM_PermissiveOff ( )
virtual

Allow to read nifti files with non-orthogonal sform

◆ SFORM_PermissiveOn()

virtual void itk::NiftiImageIO::SFORM_PermissiveOn ( )
virtual

Allow to read nifti files with non-orthogonal sform

◆ 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_ConvertRAS

bool itk::NiftiImageIO::m_ConvertRAS { false }
private

Definition at line 291 of file itkNiftiImageIO.h.

◆ m_ConvertRASDisplacementVectors

bool itk::NiftiImageIO::m_ConvertRASDisplacementVectors { true }
private

Definition at line 293 of file itkNiftiImageIO.h.

◆ m_ConvertRASVectors

bool itk::NiftiImageIO::m_ConvertRASVectors { false }
private

Definition at line 292 of file itkNiftiImageIO.h.

◆ m_LegacyAnalyze75Mode

NiftiImageIOEnums::Analyze75Flavor itk::NiftiImageIO::m_LegacyAnalyze75Mode {}
private

Definition at line 297 of file itkNiftiImageIO.h.

◆ m_NiftiImage

NiftiImageProxy& itk::NiftiImageIO::m_NiftiImage
private

Definition at line 286 of file itkNiftiImageIO.h.

◆ m_NiftiImageHolder

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

Definition at line 284 of file itkNiftiImageIO.h.

◆ m_OnDiskComponentType

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

Definition at line 295 of file itkNiftiImageIO.h.

◆ m_RescaleIntercept

double itk::NiftiImageIO::m_RescaleIntercept { 0.0 }
private

Definition at line 289 of file itkNiftiImageIO.h.

◆ m_RescaleSlope

double itk::NiftiImageIO::m_RescaleSlope { 1.0 }
private

Definition at line 288 of file itkNiftiImageIO.h.

◆ m_SFORM_Corrected

bool itk::NiftiImageIO::m_SFORM_Corrected { false }
private

Definition at line 300 of file itkNiftiImageIO.h.

◆ m_SFORM_Permissive

bool itk::NiftiImageIO::m_SFORM_Permissive
private

Definition at line 299 of file itkNiftiImageIO.h.

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