ITK
6.0.0
Insight Toolkit
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#include <itkBruker2dseqImageIO.h>
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
Definition at line 79 of file itkBruker2dseqImageIO.h.
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 | CanReadFile (const char *)=0 |
virtual bool | CanStreamRead () |
virtual bool | CanStreamWrite () |
virtual bool | CanWriteFile (const char *)=0 |
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 |
const char * | GetNameOfClass () const override |
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 |
virtual void | Read (void *buffer)=0 |
virtual void | ReadImageInformation ()=0 |
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 | Write (const void *buffer)=0 |
virtual void | WriteImageInformation ()=0 |
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 TCoordRep , unsigned int VPointDimension> | |
void | SetPixelTypeInfo (const Point< TCoordRep, 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 |
const char * | GetNameOfClass () const override |
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 |
const char * | GetNameOfClass () const override |
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 Pointer | CreateAnother () const |
virtual void | Delete () |
virtual const char * | GetNameOfClass () const |
virtual int | GetReferenceCount () const |
void | Print (std::ostream &os, Indent indent=0) const |
virtual void | Register () const |
virtual void | SetReferenceCount (int) |
virtual void | UnRegister () const noexcept |
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) |
void | PrintSelf (std::ostream &os, Indent indent) const override |
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 () | |
void | PrintSelf (std::ostream &os, Indent indent) const override |
~LightProcessObject () override | |
Protected Member Functions inherited from itk::Object | |
Object () | |
bool | PrintObservers (std::ostream &os, Indent indent) const |
void | PrintSelf (std::ostream &os, Indent indent) const override |
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 | PrintSelf (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 } |
using itk::Bruker2dseqImageIO::ConstPointer = SmartPointer<const Self> |
Definition at line 88 of file itkBruker2dseqImageIO.h.
Definition at line 87 of file itkBruker2dseqImageIO.h.
Definition at line 85 of file itkBruker2dseqImageIO.h.
Definition at line 86 of file itkBruker2dseqImageIO.h.
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protected |
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overrideprotected |
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overridevirtual |
Determine if the necessary files exist to read the specified 2dseq file. Returns true if all required files exist.
Implements itk::ImageIOBase.
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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.
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overridevirtual |
Reimplemented from itk::ImageIOBase.
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static |
New macro for creation of through a SmartPointer.
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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.
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overridevirtual |
Reads the data from disk into the memory buffer provided.
Implements itk::ImageIOBase.
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overridevirtual |
Set the spacing and dimension information for the set filename.
Implements itk::ImageIOBase.
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private |
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inlineoverridevirtual |
Not implemented - does nothing
Implements itk::ImageIOBase.
Definition at line 126 of file itkBruker2dseqImageIO.h.
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inlineoverridevirtual |
Not implemented.
Implements itk::ImageIOBase.
Definition at line 119 of file itkBruker2dseqImageIO.h.
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private |
Definition at line 143 of file itkBruker2dseqImageIO.h.
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private |
Definition at line 142 of file itkBruker2dseqImageIO.h.