ITK  4.8.0
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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::Bruker2DSEQImageIO Class Reference
Input and Output Filters | Module ITKReview

#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:

  1. a text file, named 'subject'
  2. 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:

  1. an 'imnd' or 'method' text file, containing parameters used in setting up and acquiring the data from the scanner
  2. an 'acqp' (ACquisition Parameter) text file, with further details of the acquisition parameters used for that run
  3. a large 'fid' file, that contains the raw, unreconstructed MR Free Induction Decay data
  4. a subdirectory 'pdata' (Processed Data), that contains any reconstructions of the data into images
  5. 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:

  1. 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.
  2. a 'reco' text file, containing some details of the reconstruction.
  3. a 'meta' text file, which I think contains information for the display of the 2dseq file within ParaVision.
  4. 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) override
 
virtual bool CanWriteFile (const char *) override
 
virtual ::itk::LightObject::Pointer CreateAnother () const
 
virtual const char * GetNameOfClass () const
 
virtual void Read (void *buffer) override
 
virtual void ReadImageInformation () override
 
virtual void Write (const void *) override
 
virtual 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 (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 ()
 
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
 
virtual void Register () const override
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag)
 
void SetDebug (bool debugFlag) const
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
virtual void SetReferenceCount (int) override
 
virtual 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

 Bruker2DSEQImageIO ()
 
virtual void PrintSelf (std::ostream &os, Indent indent) const 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 () 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 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
AtomicInt< int > m_ReferenceCount
 

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)
overridevirtual

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

Author
Don C. Bigler
Parameters
FileNameToReadThe 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 *  )
inlineoverridevirtual

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 ( ) 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
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.

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

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::Bruker2DSEQImageIO::ReadImageInformation ( )
overridevirtual

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 *  )
inlineoverridevirtual

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  )
inlineoverridevirtual

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.

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