#include <itkBruker2DSEQImageIO.h>

Inheritance diagram for itk::Bruker2DSEQImageIO:

Collaboration diagram for itk::Bruker2DSEQImageIO:

Detailed Description

Class that defines how to read Bruker file format. Bruker IMAGE FILE FORMAT - The following is a brief description of the Bruker file format taken from:

Author: Don C. Bigler http://www.mrc-cbu.cam.ac.uk/Imaging/Common/brukerformat.shtml.

For the Bruker format, a single scanning session is stored in its own directory. The directory is named according to the subject name or number, as typed in by the scanner operator. The directory name usually specifies the subject name/number and which session this is for that subject. Thus, a typical directory name would be

    010005-m00.5X1

where '010005' is the WBIC subject number of the subject, the 00 of 'm00' means this is the first scanning session that subject number of the session for that subject, on that day (1). The first two letters specify the day, since some arbitrary base date - set in the Bruker software.

The WBIC number (e.g. 010005) in turn is made up of the year the subject was first scanned (01 = 2001) and where that subject is in the sequence of new numbers allocated (5 = 5th subject in the year 2001 who has needed a new subject number).

Within the session directory (e.g 010005-m00.5X1), there are:

a text file, named 'subject'
A subdirectory numbered 1, 2, 3 etc, for each saved run of data acquisition in that session

Within each of the run directories (e.g. 010005-m00.5X1/5) there are the following:

an 'imnd' or 'method' text file, containing parameters used in setting up and acquiring the data from the scanner
an 'acqp' (ACquisition Parameter) text file, with further details of the acquisition parameters used for that run
a large 'fid' file, that contains the raw, unreconstructed MR Free Induction Decay data
a subdirectory 'pdata' (Processed Data), that contains any reconstructions of the data into images
various other files, including the 'pulseprogram' and 'grdprog.r' gradient programs

Within each of the 'pdata' subdirectories (e.g 01001-m00.5X1/5/pdata), there are numbered subdirectories (1,2,3 etc) for each new reconstruction of the raw data into images. There is usually only one such reconstruction, in subdirectory '1'.

Within each reconstruction directory (e.g 01001-m00.5X1/5/pdata/1), there are:

a '2dseq' file. This is the 3D (structural etc) or 4D (FMRI) image file. It is simply a binary block of data, which could simply be renamed as 'myscan.img' to make an acceptable Analyze .img file.
a 'reco' text file, containing some details of the reconstruction.
a 'meta' text file, which I think contains information for the display of the 2dseq file within ParaVision.
a 'd3proc' file, containing image size definition parameters, inter alia.

The 'reco', 'acqp', 'd3proc', and '2dseq' files are required for this reader. It will look for these files in the directory structure described above. The path and filename of the '2dseq' file must be the name of the file to read (see CanReadFile). This class supports reading only.

Definition at line 113 of file itkBruker2DSEQImageIO.h.

Public Types
typedef VectorContainer < unsigned int, double >	ACQEchoTimeContainerType

typedef VectorContainer < unsigned int, double >	ACQInversionTimeContainerType

typedef VectorContainer < unsigned int, double >	ACQRepetitionTimeContainerType

typedef VectorContainer < unsigned int, double >	ACQSliceSepnContainerType

typedef SmartPointer< Self >	Pointer

typedef VectorContainer < unsigned int, double >	RECOFOVContainerType

typedef VectorContainer < unsigned int, int >	RECOTranspositionContainerType

typedef Bruker2DSEQImageIO	Self

typedef ImageIOBase	SuperClass

typedef ImageIOBase	Superclass

Public Types inherited from itk::ImageIOBase
typedef std::vector< std::string >	ArrayOfExtensionsType

typedef ::itk::OffsetValueType	BufferSizeType

enum	ByteOrder { BigEndian, LittleEndian, OrderNotApplicable }

enum	FileType { ASCII, Binary, TypeNotApplicable }

typedef ::itk::IndexValueType	IndexValueType

enum	IOComponentType { UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT, INT, ULONG, LONG, FLOAT, DOUBLE }

enum	IOPixelType { UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR, POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D, COMPLEX, FIXEDARRAY, MATRIX }

typedef SmartPointer< Self >	Pointer

typedef ImageIOBase	Self

typedef ::itk::intmax_t	SizeType

typedef ::itk::SizeValueType	SizeValueType

typedef LightProcessObject	Superclass

Public Types inherited from itk::LightProcessObject
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef LightProcessObject	Self

typedef Object	Superclass

Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef Object	Self

typedef LightObject	Superclass

Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef LightObject	Self

Public Member Functions
virtual bool	CanReadFile (const char *FileNameToRead) ITK_OVERRIDE

virtual bool	CanWriteFile (const char *) ITK_OVERRIDE

virtual ::itk::LightObject::Pointer	CreateAnother (void) const

virtual const char *	GetNameOfClass () const

virtual void	Read (void *buffer) ITK_OVERRIDE

virtual void	ReadImageInformation () ITK_OVERRIDE

virtual void	Write (const void *) ITK_OVERRIDE

virtual void	WriteImageInformation () ITK_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 (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 itk::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 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 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, unsigned int dim)

virtual void	SetIORegion (ImageIORegion _arg)

virtual const ImageIORegion &	GetIORegion () 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	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

Command *	GetCommand (unsigned long tag)

bool	GetDebug () const

MetaDataDictionary &	GetMetaDataDictionary (void)

const MetaDataDictionary &	GetMetaDataDictionary (void) 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

virtual void	Register () const ITK_OVERRIDE

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int) ITK_OVERRIDE

virtual void	UnRegister () const ITK_OVERRIDE

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
	Bruker2DSEQImageIO ()

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

	~Bruker2DSEQImageIO ()

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 (void) 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 ()

Protected Member Functions inherited from itk::LightProcessObject
virtual void	GenerateData ()

	LightProcessObject ()

	~LightProcessObject ()

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &time)

virtual	~Object ()

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
	Bruker2DSEQImageIO (const Self &)

void	operator= (const Self &)

void	SwapBytesIfNecessary (void *buffer, SizeValueType numberOfPixels)

Private Attributes
ImageIOBase::ByteOrder	m_MachineByteOrder

Additional Inherited Members
Protected Types inherited from itk::LightObject
typedef int	InternalReferenceCountType

Protected Attributes inherited from itk::ImageIOBase
ByteOrder	m_ByteOrder

IOComponentType	m_ComponentType

std::vector< SizeValueType >	m_Dimensions

std::vector< std::vector < double > >	m_Direction

std::string	m_FileName

FileType	m_FileType

bool	m_Initialized

ImageIORegion	m_IORegion

unsigned int	m_NumberOfComponents

unsigned int	m_NumberOfDimensions

std::vector< double >	m_Origin

IOPixelType	m_PixelType

std::vector< double >	m_Spacing

std::vector< SizeType >	m_Strides

bool	m_UseCompression

bool	m_UseStreamedReading

bool	m_UseStreamedWriting

Protected Attributes inherited from itk::LightObject
InternalReferenceCountType	m_ReferenceCount

SimpleFastMutexLock	m_ReferenceCountLock

Member Typedef Documentation

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::ACQEchoTimeContainerType

Definition at line 132 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::ACQInversionTimeContainerType

Definition at line 134 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::ACQRepetitionTimeContainerType

Definition at line 133 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::ACQSliceSepnContainerType

Definition at line 135 of file itkBruker2DSEQImageIO.h.

typedef SmartPointer< Self > itk::Bruker2DSEQImageIO::Pointer

Definition at line 121 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, double > itk::Bruker2DSEQImageIO::RECOFOVContainerType

Special types used for Bruker meta data.

Definition at line 127 of file itkBruker2DSEQImageIO.h.

typedef VectorContainer< unsigned int, int > itk::Bruker2DSEQImageIO::RECOTranspositionContainerType

Definition at line 131 of file itkBruker2DSEQImageIO.h.

typedef Bruker2DSEQImageIO itk::Bruker2DSEQImageIO::Self

Standard class typedefs.

Definition at line 119 of file itkBruker2DSEQImageIO.h.

typedef ImageIOBase itk::Bruker2DSEQImageIO::SuperClass

Definition at line 116 of file itkBruker2DSEQImageIO.h.

typedef ImageIOBase itk::Bruker2DSEQImageIO::Superclass

Definition at line 120 of file itkBruker2DSEQImageIO.h.

Constructor & Destructor Documentation

itk::Bruker2DSEQImageIO::Bruker2DSEQImageIO ( )

protected

itk::Bruker2DSEQImageIO::~Bruker2DSEQImageIO ( )

protected

itk::Bruker2DSEQImageIO::Bruker2DSEQImageIO ( const Self & )

private

Member Function Documentation

virtual bool itk::Bruker2DSEQImageIO::CanReadFile ( const char * FileNameToRead )

virtual

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

Author: Don C. Bigler

Parameters

FileNameToRead The name of the file to test for reading.

Returns: Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

virtual bool itk::Bruker2DSEQImageIO::CanWriteFile ( const char * )

inlinevirtual

Determine if the file can be written with this ImageIO implementation. FileNameToWrite The name of the file to test for writing.

Author: Don C. Bigler

Postcondition: This function will always return false (Not implemented).

Returns: Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

Definition at line 160 of file itkBruker2DSEQImageIO.h.

virtual::itk::LightObject::Pointer itk::Bruker2DSEQImageIO::CreateAnother ( void ) 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.

virtual const char* itk::Bruker2DSEQImageIO::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

static Pointer itk::Bruker2DSEQImageIO::New ( )

static

Method for creation through the object factory.

void itk::Bruker2DSEQImageIO::operator= ( const Self & )

private

virtual void itk::Bruker2DSEQImageIO::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const

protectedvirtual

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.

virtual void itk::Bruker2DSEQImageIO::Read ( void * buffer )

virtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::Bruker2DSEQImageIO::ReadImageInformation ( )

virtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

void itk::Bruker2DSEQImageIO::SwapBytesIfNecessary	(	void *	buffer,
		SizeValueType	numberOfPixels
	)

private

virtual void itk::Bruker2DSEQImageIO::Write ( const void * )

inlinevirtual

Writes the data to disk from the memory buffer provided. Make sure that the IORegions has been set properly.

Implements itk::ImageIOBase.

Definition at line 173 of file itkBruker2DSEQImageIO.h.

virtual void itk::Bruker2DSEQImageIO::WriteImageInformation ( void )

inlinevirtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

Definition at line 166 of file itkBruker2DSEQImageIO.h.

Member Data Documentation

ImageIOBase::ByteOrder itk::Bruker2DSEQImageIO::m_MachineByteOrder

private

Definition at line 190 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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation