ITK
4.3.0
Insight Segmentation and Registration Toolkit
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#include <itkBruker2DSEQImageIO.h>
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:
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:
Within each of the run directories (e.g. 010005-m00.5X1/5) there are the following:
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:
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 Member Functions | |
virtual bool | CanReadFile (const char *FileNameToRead) |
virtual bool | CanWriteFile (const char *) |
virtual ::itk::LightObject::Pointer | CreateAnother (void) const |
virtual const char * | GetNameOfClass () const |
virtual void | Read (void *buffer) |
virtual void | ReadImageInformation () |
virtual void | Write (const void *) |
virtual void | WriteImageInformation () |
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 unsigned int | 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, std::vector< double > &direction) |
virtual void | SetDirection (unsigned int i, vnl_vector< double > &direction) |
void | SetFileTypeToBinary () |
void | SetNumberOfDimensions (unsigned int) |
virtual void | SetOrigin (unsigned int i, double origin) |
template<class 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 () |
virtual void | SetPixelType (const IOPixelType _arg) |
virtual IOPixelType | GetPixelType () const |
virtual void | SetNumberOfComponents (unsigned int _arg) |
virtual const unsigned int & | GetNumberOfComponents () |
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 () |
virtual void | SetAbortGenerateData (bool _arg) |
virtual void | UpdateOutputData () |
void | UpdateProgress (float amount) |
virtual void | SetProgress (float _arg) |
virtual const float & | GetProgress () |
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 |
void | RemoveAllObservers () |
void | RemoveObserver (unsigned long tag) |
void | SetDebug (bool debugFlag) const |
void | SetMetaDataDictionary (const MetaDataDictionary &rhs) |
virtual void | SetReferenceCount (int) |
virtual void | UnRegister () 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 () | |
void | PrintSelf (std::ostream &os, Indent indent) const |
~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 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 | 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 |
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.
Standard class typedefs.
Definition at line 119 of file itkBruker2DSEQImageIO.h.
Definition at line 116 of file itkBruker2DSEQImageIO.h.
Definition at line 120 of file itkBruker2DSEQImageIO.h.
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Determine if the file can be read with this ImageIO implementation.
FileNameToRead | The name of the file to test for reading. |
Implements itk::ImageIOBase.
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Determine if the file can be written with this ImageIO implementation. FileNameToWrite The name of the file to test for writing.
Implements itk::ImageIOBase.
Definition at line 160 of file itkBruker2DSEQImageIO.h.
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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.
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Run-time type information (and related methods).
Reimplemented from itk::ImageIOBase.
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Method for creation through the object factory.
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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.
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Reads the data from disk into the memory buffer provided.
Implements itk::ImageIOBase.
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Set the spacing and dimension information for the set filename.
Implements itk::ImageIOBase.
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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.
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Set the spacing and dimension information for the set filename.
Implements itk::ImageIOBase.
Definition at line 166 of file itkBruker2DSEQImageIO.h.
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Definition at line 190 of file itkBruker2DSEQImageIO.h.