ITK  5.2.0
Insight Toolkit
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

#include <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 ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = ImageIOBase
 
using Superclass = LightProcessObject
 
using IndexValueType = ::itk::IndexValueType
 
using SizeValueType = ::itk::SizeValueType
 
using IOComponentEnum = itk::IOComponentEnum
 
using IOFileEnum = itk::IOFileEnum
 
using IOByteOrderEnum = itk::IOByteOrderEnum
 
using SizeType = ::itk::intmax_t
 
using BufferSizeType = ::itk::OffsetValueType
 
using ArrayOfExtensionsType = std::vector< std::string >
 
- 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
 
virtual ::itk::LightObject::Pointer CreateAnother () const
 
virtual const char * GetNameOfClass () const
 
void Read (void *buffer) override
 
void ReadImageInformation () override
 
void Write (const void *) override
 
void WriteImageInformation () override
 
- Public Member Functions inherited from itk::ImageIOBase
virtual void SetFileName (const char *_arg)
 
virtual const char * GetFileName () const
 
void SetNumberOfDimensions (unsigned int)
 
virtual unsigned int GetNumberOfDimensions () const
 
virtual void SetDimensions (unsigned int i, SizeValueType dim)
 
virtual SizeValueType GetDimensions (unsigned int i) const
 
virtual void SetOrigin (unsigned int i, double origin)
 
virtual double GetOrigin (unsigned int i) const
 
virtual void SetSpacing (unsigned int i, double spacing)
 
virtual double GetSpacing (unsigned int i) const
 
virtual void SetDirection (unsigned int i, const std::vector< double > &direction)
 
virtual void SetDirection (unsigned int i, const vnl_vector< double > &direction)
 
virtual std::vector< double > GetDirection (unsigned int i) const
 
virtual std::vector< double > GetDefaultDirection (unsigned int i) const
 
virtual void SetIORegion (ImageIORegion _arg)
 
virtual const ImageIORegionGetIORegion () const
 
virtual void SetPixelType (const ::itk::CommonEnums::IOPixel _arg)
 
virtual ::itk::CommonEnums::IOPixel GetPixelType () const
 
virtual void SetComponentType (const IOComponentEnum _arg)
 
virtual IOComponentEnum GetComponentType () const
 
virtual const std::type_info & GetComponentTypeInfo () 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 SetCompressionLevel (int _arg)
 
virtual int GetCompressionLevel () const
 
virtual void SetCompressor (std::string _c)
 
virtual const std::string & GetCompressor () const
 
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 bool GetIsReadAsScalarPlusPalette () const
 
virtual void SetFileType (const IOFileEnum _arg)
 
virtual IOFileEnum GetFileType () const
 
void SetFileTypeToASCII ()
 
void SetFileTypeToBinary ()
 
virtual void SetByteOrder (const IOByteOrderEnum _arg)
 
virtual IOByteOrderEnum GetByteOrder () const
 
void SetByteOrderToBigEndian ()
 
void SetByteOrderToLittleEndian ()
 
std::string GetFileTypeAsString (IOFileEnum) const
 
std::string GetByteOrderAsString (IOByteOrderEnum) const
 
virtual SizeType GetPixelStride () const
 
SizeType GetImageSizeInPixels () const
 
SizeType GetImageSizeInBytes () const
 
SizeType GetImageSizeInComponents () const
 
virtual unsigned int GetComponentSize () const
 
virtual bool CanStreamRead ()
 
virtual bool CanStreamWrite ()
 
virtual bool SupportsDimension (unsigned long dim)
 
virtual ImageIORegion GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const
 
virtual unsigned int GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
 
virtual ImageIORegion GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
 
const ArrayOfExtensionsTypeGetSupportedReadExtensions () const
 
const ArrayOfExtensionsTypeGetSupportedWriteExtensions () const
 
template<typename TPixel >
void SetTypeInfo (const TPixel *)
 
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 > *)
 
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 > *)
 
- 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 SetProgress (float _arg)
 
virtual const float & GetProgress () const
 
void UpdateProgress (float amount)
 
virtual void UpdateOutputData ()
 
- 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
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary ()
 
const MetaDataDictionaryGetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStampGetTimeStamp () 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)
 
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
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 (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 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 override
 
 ~Bruker2dseqImageIO () override
 
- Protected Member Functions inherited from itk::ImageIOBase
 ImageIOBase ()
 
 ~ImageIOBase () override
 
virtual const ImageRegionSplitterBaseGetImageRegionSplitter () const
 
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
 
virtual void InternalSetCompressor (const std::string &COMPRESSOR)
 
virtual void Reset (const bool freeDynamic=true)
 
void Resize (const unsigned int numDimensions, const unsigned int *dimensions)
 
virtual unsigned int GetPixelSize () const
 
void ComputeStrides ()
 
SizeType GetComponentStride () const
 
SizeType GetRowStride () const
 
SizeType GetSliceStride () const
 
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 WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentEnum ctype, SizeType numberOfBytesToWrite)
 
virtual void ReadBufferAsASCII (std::istream &os, void *buffer, IOComponentEnum ctype, SizeType numberOfBytesToBeRead)
 
bool ReadBufferAsBinary (std::istream &os, void *buffer, SizeType numberOfBytesToBeRead)
 
void AddSupportedReadExtension (const char *extension)
 
void AddSupportedWriteExtension (const char *extension)
 
void SetSupportedReadExtensions (const ArrayOfExtensionsType &)
 
void SetSupportedWriteExtensions (const ArrayOfExtensionsType &)
 
virtual unsigned int GetActualNumberOfSplitsForWritingCanStreamWrite (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion) const
 
virtual ImageIORegion GetSplitRegionForWritingCanStreamWrite (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion) const
 
- Protected Member Functions inherited from itk::LightProcessObject
 LightProcessObject ()
 
 ~LightProcessObject () override
 
virtual void GenerateData ()
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
 ~Object () override
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &time)
 
- 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 *buffer, SizeValueType numberOfPixels)
 

Private Attributes

IOByteOrderEnum m_MachineByteOrder
 
IOComponentEnum m_OnDiskComponentType { IOComponentEnum::UCHAR }
 

Additional Inherited Members

- Protected Attributes inherited from itk::ImageIOBase
IOPixelEnum m_PixelType { IOPixelEnum::SCALAR }
 
IOComponentEnum m_ComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }
 
IOByteOrderEnum m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }
 
IOFileEnum m_FileType { IOFileEnum::TypeNotApplicable }
 
bool m_Initialized
 
std::string m_FileName
 
unsigned int m_NumberOfComponents
 
unsigned int m_NumberOfDimensions { 0 }
 
bool m_UseCompression { false }
 
int m_CompressionLevel { 30 }
 
int m_MaximumCompressionLevel { 100 }
 
std::string m_Compressor { "uninitialized" }
 
bool m_UseStreamedReading
 
bool m_UseStreamedWriting
 
bool m_ExpandRGBPalette
 
bool m_IsReadAsScalarPlusPalette
 
bool m_WritePalette
 
ImageIORegion m_IORegion
 
std::vector< SizeValueTypem_Dimensions
 
std::vector< double > m_Spacing
 
std::vector< double > m_Origin
 
std::vector< std::vector< double > > m_Direction
 
std::vector< SizeTypem_Strides
 
- Protected Attributes inherited from itk::LightObject
std::atomic< int > m_ReferenceCount
 

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://hdl.handle.net/1926/1381

Author
Tobias C Wood, King's College London 2017

Definition at line 79 of file itkBruker2dseqImageIO.h.

Member Typedef Documentation

◆ ConstPointer

Definition at line 88 of file itkBruker2dseqImageIO.h.

◆ Pointer

Definition at line 87 of file itkBruker2dseqImageIO.h.

◆ Self

Definition at line 85 of file itkBruker2dseqImageIO.h.

◆ Superclass

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.

◆ CreateAnother()

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.

◆ GetNameOfClass()

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

Run-time type information (and related methods).

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

Types for managing image size and image index components.

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 *  buffer,
SizeValueType  numberOfPixels 
)
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: