#include <itkBruker2dseqImageIO.h>

Detailed Description

Class that defines how to read Bruker file format.

The following is a brief description of the Bruker file format.

Within the directory representing a 'session' on the scanner, data is laid out thus:

session/ 1/ <- Series/Acquisition number method <- An important header file acqp <- Another important header fid <- Raw data other unimportant files pdata/ 1/ <- Reconstruction number (may be multiple) 2dseq <- Reconstructed data visu_pars <- Most important header reco <- Mostly duplicated in visu_pars procs <- Unimportant header id <- Unimportant header 2/ ...

The minimum required data to read the image is the '2dseq' and 'visu_pars' file. To use this reader, specify the 2dseq file as the filename. It will check for the existence of the visu_pars file. If both these exist, the file is opened. If the other header files exist (method, acqp, etc.) in the correct locations then they will be read and added to the meta-data dictionary, but they are not used to read the image data itself.

This class supports reading only.

This file reader has been updated for ParaVision 6 2dseq files. The original code was written by Don C. Bigler at Penn State in 2004. It has been significantly changed, as Bruker also changed the format for ParaVision 6. In particular a new header file, 'visu_pars' was introduced that means that multiple headers no longer need to be read in order to read the '2dseq' file. However, if the other Bruker headers are still present they are read and added to the meta-data in case users wish to extract data from them.

The original implementation was contributed as a paper to the Insight Journal https://doi.org/10.54294/o8w4c0

Author: Tobias C Wood, King's College London 2017

Definition at line 79 of file itkBruker2dseqImageIO.h.

Inheritance diagram for itk::Bruker2dseqImageIO:

Collaboration diagram for itk::Bruker2dseqImageIO:

Public Types
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = Bruker2dseqImageIO

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 *) override

const char *	GetNameOfClass () const override

void	Read (void *buffer) override

void	ReadImageInformation () override

void	Write (const void *) override

void	WriteImageInformation () override

Public Member Functions inherited from itk::ImageIOBase
virtual bool	CanStreamRead ()

virtual bool	CanStreamWrite ()

virtual ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const

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	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 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	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 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
	Bruker2dseqImageIO ()

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

	~Bruker2dseqImageIO () 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
void	SwapBytesIfNecessary (void *buff, SizeValueType components)

Private Attributes
IOByteOrderEnum	m_MachineByteOrder {}

IOComponentEnum	m_OnDiskComponentType { IOComponentEnum::UCHAR }

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

◆ ConstPointer

using itk::Bruker2dseqImageIO::ConstPointer = SmartPointer<const Self>

Definition at line 88 of file itkBruker2dseqImageIO.h.

◆ Pointer

using itk::Bruker2dseqImageIO::Pointer = SmartPointer<Self>

Definition at line 87 of file itkBruker2dseqImageIO.h.

◆ Self

using itk::Bruker2dseqImageIO::Self = Bruker2dseqImageIO

Definition at line 85 of file itkBruker2dseqImageIO.h.

◆ Superclass

using itk::Bruker2dseqImageIO::Superclass = ImageIOBase

Definition at line 86 of file itkBruker2dseqImageIO.h.

Constructor & Destructor Documentation

◆ Bruker2dseqImageIO()

itk::Bruker2dseqImageIO::Bruker2dseqImageIO ( )

protected

◆ ~Bruker2dseqImageIO()

itk::Bruker2dseqImageIO::~Bruker2dseqImageIO ( )

overrideprotected

Member Function Documentation

◆ CanReadFile()

bool itk::Bruker2dseqImageIO::CanReadFile ( const char * FileNameToRead )

overridevirtual

Determine if the necessary files exist to read the specified 2dseq file. Returns true if all required files exist.

Implements itk::ImageIOBase.

◆ CanWriteFile()

bool itk::Bruker2dseqImageIO::CanWriteFile ( const char * )

inlineoverridevirtual

Writing files has not been implemented for Bruker 2dseq. This function will always return false.

Implements itk::ImageIOBase.

Definition at line 112 of file itkBruker2dseqImageIO.h.

◆ GetNameOfClass()

const char* itk::Bruker2dseqImageIO::GetNameOfClass ( ) const

overridevirtual

See also: LightObject::GetNameOfClass()

Reimplemented from itk::ImageIOBase.

◆ New()

static Pointer itk::Bruker2dseqImageIO::New ( )

static

New macro for creation of through a SmartPointer.

◆ PrintSelf()

void itk::Bruker2dseqImageIO::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::Bruker2dseqImageIO::Read ( void * buffer )

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

◆ ReadImageInformation()

void itk::Bruker2dseqImageIO::ReadImageInformation ( )

overridevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

◆ SwapBytesIfNecessary()

void itk::Bruker2dseqImageIO::SwapBytesIfNecessary	(	void *	buff,
		SizeValueType	components
	)

private

◆ Write()

void itk::Bruker2dseqImageIO::Write ( const void * )

inlineoverridevirtual

Not implemented - does nothing

Implements itk::ImageIOBase.

Definition at line 126 of file itkBruker2dseqImageIO.h.

◆ WriteImageInformation()

void itk::Bruker2dseqImageIO::WriteImageInformation ( )

inlineoverridevirtual

Not implemented.

Implements itk::ImageIOBase.

Definition at line 119 of file itkBruker2dseqImageIO.h.

Member Data Documentation

◆ m_MachineByteOrder

IOByteOrderEnum itk::Bruker2dseqImageIO::m_MachineByteOrder {}

private

Definition at line 143 of file itkBruker2dseqImageIO.h.

◆ m_OnDiskComponentType

IOComponentEnum itk::Bruker2dseqImageIO::m_OnDiskComponentType { IOComponentEnum::UCHAR }

private

Definition at line 142 of file itkBruker2dseqImageIO.h.

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

itkBruker2dseqImageIO.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ ConstPointer

◆ Pointer

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ Bruker2dseqImageIO()

◆ ~Bruker2dseqImageIO()

Member Function Documentation

◆ CanReadFile()

◆ CanWriteFile()

◆ GetNameOfClass()

◆ New()

◆ PrintSelf()

◆ Read()

◆ ReadImageInformation()

◆ SwapBytesIfNecessary()

◆ Write()

◆ WriteImageInformation()

Member Data Documentation

◆ m_MachineByteOrder

◆ m_OnDiskComponentType