Class that defines how to read HDF5 file format. HDF5 IMAGE FILE FORMAT - As much information as I can determine from sourceforge.net/projects/HDF5lib.
- Author
- Kent Williams
HDF5 paths for elements in file
- N is dimension of image
- \/ITKVersion ITK Library Version string
- \/HDFVersion HDF Version String
- \/ITKImage Root Image Group
- \/ITKImage\/<name> name is arbitrary, but to parallel Transform I/O keep an image in a subgroup. The idea is to parallel transform file structure.
- \/ITKImage\/<name>\/Origin N-D point double
- \/ITKImage\/<name>\/Directions N N-vectors double
- \/ITKImage\/<name>\/Spacing N-vector double
- \/ITKImage\/<name>\/Dimensions N-vector itk::SizeValueType
- \/ITKImage\/<name>\/VoxelType String representing voxel type. This can be inferred from the VoxelData type info, but it makes the file more user friendly with respect to HDF5 viewers.
- \/ITKImage\/<name>\/VoxelData multi-dim array of voxel data in the case of non-scalar voxel type, keep voxel components together, to make loading possible without
- \/ITKImage\/<name>\/MetaData Group for storing metadata from MetaDataDictionary
- \/ITKImage\/<name>\/MetaData\/<item-name> Dataset containing data for item-name in the MetaDataDictionary re-arrangement.
Definition at line 86 of file itkHDF5ImageIO.h.
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bool | CanReadFile (const char *FileNameToRead) override |
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bool | CanWriteFile (const char *name) override |
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const char * | GetNameOfClass () const override |
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void | Read (void *buffer) override |
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void | ReadImageInformation () override |
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void | Write (const void *buffer) override |
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void | WriteImageInformation () override |
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bool | CanStreamRead () override |
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bool | CanStreamWrite () override |
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ImageIORegion | GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requestedRegion) const override |
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unsigned int | GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) override |
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const char * | GetNameOfClass () const override |
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virtual bool | CanReadFile (const char *)=0 |
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virtual bool | CanStreamRead () |
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virtual bool | CanStreamWrite () |
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virtual bool | CanWriteFile (const char *)=0 |
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virtual ImageIORegion | GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const |
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virtual unsigned int | GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) |
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std::string | GetByteOrderAsString (IOByteOrderEnum) const |
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virtual unsigned int | GetComponentSize () const |
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virtual IOComponentEnum | GetComponentType () const |
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virtual const std::type_info & | GetComponentTypeInfo () const |
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virtual int | GetCompressionLevel () const |
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virtual const std::string & | GetCompressor () const |
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virtual std::vector< double > | GetDefaultDirection (unsigned int k) const |
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virtual SizeValueType | GetDimensions (unsigned int i) const |
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virtual std::vector< double > | GetDirection (unsigned int i) const |
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std::string | GetFileTypeAsString (IOFileEnum) const |
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SizeType | GetImageSizeInBytes () const |
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SizeType | GetImageSizeInComponents () const |
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SizeType | GetImageSizeInPixels () const |
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virtual bool | GetIsReadAsScalarPlusPalette () const |
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const char * | GetNameOfClass () const override |
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virtual unsigned int | GetNumberOfDimensions () const |
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virtual double | GetOrigin (unsigned int i) const |
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virtual SizeType | GetPixelStride () const |
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virtual double | GetSpacing (unsigned int i) const |
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virtual ImageIORegion | GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) |
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const ArrayOfExtensionsType & | GetSupportedReadExtensions () const |
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const ArrayOfExtensionsType & | GetSupportedWriteExtensions () const |
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virtual void | Read (void *buffer)=0 |
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virtual void | ReadImageInformation ()=0 |
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void | SetByteOrderToLittleEndian () |
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virtual void | SetComponentType (const IOComponentEnum _arg) |
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virtual void | SetCompressionLevel (int _arg) |
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virtual void | SetCompressor (std::string _c) |
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virtual void | SetDirection (unsigned int i, const std::vector< double > &direction) |
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virtual void | SetDirection (unsigned int i, const vnl_vector< double > &direction) |
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void | SetFileTypeToBinary () |
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void | SetNumberOfDimensions (unsigned int) |
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virtual void | SetOrigin (unsigned int i, double origin) |
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virtual void | SetSpacing (unsigned int i, double spacing) |
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template<typename TPixel > |
void | SetTypeInfo (const TPixel *) |
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virtual bool | SupportsDimension (unsigned long dim) |
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virtual void | Write (const void *buffer)=0 |
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virtual void | WriteImageInformation ()=0 |
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virtual void | SetFileName (const char *_arg) |
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virtual const char * | GetFileName () const |
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virtual void | SetDimensions (unsigned int i, SizeValueType dim) |
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virtual void | SetIORegion (ImageIORegion _arg) |
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virtual const ImageIORegion & | GetIORegion () const |
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virtual void | SetPixelType (const itk::CommonEnums::IOPixel _arg) |
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virtual itk::CommonEnums::IOPixel | GetPixelType () const |
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virtual void | SetNumberOfComponents (unsigned int _arg) |
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virtual const unsigned int & | GetNumberOfComponents () const |
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virtual void | SetUseCompression (bool _arg) |
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virtual bool | GetUseCompression () const |
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virtual void | UseCompressionOn () |
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virtual void | SetUseStreamedReading (bool _arg) |
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virtual bool | GetUseStreamedReading () const |
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virtual void | UseStreamedReadingOn () |
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virtual void | SetUseStreamedWriting (bool _arg) |
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virtual bool | GetUseStreamedWriting () const |
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virtual void | UseStreamedWritingOn () |
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virtual void | SetExpandRGBPalette (bool _arg) |
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virtual bool | GetExpandRGBPalette () const |
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virtual void | ExpandRGBPaletteOn () |
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virtual void | SetWritePalette (bool _arg) |
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virtual bool | GetWritePalette () const |
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virtual void | WritePaletteOn () |
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virtual void | SetFileType (const IOFileEnum _arg) |
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virtual IOFileEnum | GetFileType () const |
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void | SetFileTypeToASCII () |
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virtual void | SetByteOrder (const IOByteOrderEnum _arg) |
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virtual IOByteOrderEnum | GetByteOrder () const |
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void | SetByteOrderToBigEndian () |
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template<typename TPixel > |
void | SetPixelTypeInfo (const TPixel *) |
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template<typename TPixel > |
void | SetPixelTypeInfo (const RGBPixel< TPixel > *) |
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template<typename TPixel > |
void | SetPixelTypeInfo (const RGBAPixel< TPixel > *) |
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template<unsigned int VLength> |
void | SetPixelTypeInfo (const Offset< VLength > *) |
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template<typename TPixel , unsigned int VLength> |
void | SetPixelTypeInfo (const Vector< TPixel, VLength > *) |
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template<typename TCoordRep , unsigned int VPointDimension> |
void | SetPixelTypeInfo (const Point< TCoordRep, VPointDimension > *) |
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template<typename TPixel , unsigned int VLength> |
void | SetPixelTypeInfo (const CovariantVector< TPixel, VLength > *) |
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template<typename TPixel , unsigned int VLength> |
void | SetPixelTypeInfo (const SymmetricSecondRankTensor< TPixel, VLength > *) |
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template<typename TPixel > |
void | SetPixelTypeInfo (const DiffusionTensor3D< TPixel > *) |
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template<typename TPixel > |
void | SetPixelTypeInfo (const std::complex< TPixel > *) |
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template<typename TPixel , unsigned int VLength> |
void | SetPixelTypeInfo (const FixedArray< TPixel, VLength > *) |
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template<typename TPixel > |
void | SetPixelTypeInfo (const VariableLengthVector< TPixel > *) |
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template<typename TValue > |
void | SetPixelTypeInfo (const Array< TValue > *) |
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template<typename TPixel , unsigned int VLength> |
void | SetPixelTypeInfo (const Matrix< TPixel, VLength, VLength > *) |
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template<typename TValue > |
void | SetPixelTypeInfo (const VariableSizeMatrix< TValue > *) |
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virtual void | AbortGenerateDataOn () |
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virtual const bool & | GetAbortGenerateData () const |
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const char * | GetNameOfClass () const override |
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virtual void | SetAbortGenerateData (bool _arg) |
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virtual void | UpdateOutputData () |
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void | UpdateProgress (float amount) |
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virtual void | SetProgress (float _arg) |
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virtual const float & | GetProgress () const |
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unsigned long | AddObserver (const EventObject &event, Command *cmd) const |
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unsigned long | AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const |
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LightObject::Pointer | CreateAnother () const override |
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virtual void | DebugOff () const |
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virtual void | DebugOn () const |
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Command * | GetCommand (unsigned long tag) |
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bool | GetDebug () const |
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MetaDataDictionary & | GetMetaDataDictionary () |
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const MetaDataDictionary & | GetMetaDataDictionary () const |
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virtual ModifiedTimeType | GetMTime () const |
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const char * | GetNameOfClass () const override |
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virtual const TimeStamp & | GetTimeStamp () const |
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bool | HasObserver (const EventObject &event) const |
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void | InvokeEvent (const EventObject &) |
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void | InvokeEvent (const EventObject &) const |
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virtual void | Modified () const |
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void | Register () const override |
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void | RemoveAllObservers () |
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void | RemoveObserver (unsigned long tag) const |
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void | SetDebug (bool debugFlag) const |
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void | SetReferenceCount (int) override |
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void | UnRegister () const noexcept override |
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void | SetMetaDataDictionary (const MetaDataDictionary &rhs) |
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void | SetMetaDataDictionary (MetaDataDictionary &&rrhs) |
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virtual void | SetObjectName (std::string _arg) |
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virtual const std::string & | GetObjectName () const |
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Pointer | Clone () const |
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virtual Pointer | CreateAnother () const |
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virtual void | Delete () |
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virtual const char * | GetNameOfClass () const |
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virtual int | GetReferenceCount () const |
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void | Print (std::ostream &os, Indent indent=0) const |
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virtual void | Register () const |
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virtual void | SetReferenceCount (int) |
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virtual void | UnRegister () const noexcept |
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SizeType | GetHeaderSize () const override |
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| HDF5ImageIO () |
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void | PrintSelf (std::ostream &os, Indent indent) const override |
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| ~HDF5ImageIO () override |
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virtual SizeType | GetDataPosition () const |
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virtual SizeType | GetHeaderSize () const =0 |
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void | PrintSelf (std::ostream &os, Indent indent) const override |
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virtual bool | ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num) |
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virtual bool | RequestedToStream () const |
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| StreamingImageIOBase () |
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virtual bool | StreamReadBufferAsBinary (std::istream &file, void *_buffer) |
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virtual bool | StreamWriteBufferAsBinary (std::ostream &file, const void *_buffer) |
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virtual bool | WriteBufferAsBinary (std::ostream &os, const void *buffer, SizeType num) |
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void | AddSupportedReadExtension (const char *extension) |
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void | AddSupportedWriteExtension (const char *extension) |
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void | ComputeStrides () |
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virtual unsigned int | GetActualNumberOfSplitsForWritingCanStreamWrite (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion) const |
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SizeType | GetComponentStride () const |
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virtual const ImageRegionSplitterBase * | GetImageRegionSplitter () const |
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virtual unsigned int | GetPixelSize () const |
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SizeType | GetRowStride () const |
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SizeType | GetSliceStride () const |
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virtual ImageIORegion | GetSplitRegionForWritingCanStreamWrite (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion) const |
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| ImageIOBase () |
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virtual void | InternalSetCompressor (const std::string &_compressor) |
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virtual void | OpenFileForReading (std::ifstream &inputStream, const std::string &filename, bool ascii=false) |
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virtual void | OpenFileForWriting (std::ofstream &outputStream, const std::string &filename, bool truncate=true, bool ascii=false) |
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void | PrintSelf (std::ostream &os, Indent indent) const override |
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virtual void | ReadBufferAsASCII (std::istream &is, void *buffer, IOComponentEnum ctype, SizeType numComp) |
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bool | ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num) |
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virtual void | Reset (const bool freeDynamic=true) |
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void | Resize (const unsigned int numDimensions, const unsigned int *dimensions) |
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void | SetSupportedReadExtensions (const ArrayOfExtensionsType &) |
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void | SetSupportedWriteExtensions (const ArrayOfExtensionsType &) |
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virtual void | WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentEnum ctype, SizeType numComp) |
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| ~ImageIOBase () override |
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virtual bool | HasSupportedReadExtension (const char *fileName, bool ignoreCase=true) |
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virtual bool | HasSupportedWriteExtension (const char *fileName, bool ignoreCase=true) |
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virtual void | SetMaximumCompressionLevel (int) |
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virtual int | GetMaximumCompressionLevel () const |
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virtual void | GenerateData () |
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| LightProcessObject () |
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void | PrintSelf (std::ostream &os, Indent indent) const override |
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| ~LightProcessObject () override |
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| Object () |
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bool | PrintObservers (std::ostream &os, Indent indent) const |
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void | PrintSelf (std::ostream &os, Indent indent) const override |
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virtual void | SetTimeStamp (const TimeStamp &timeStamp) |
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| ~Object () override |
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virtual LightObject::Pointer | InternalClone () const |
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| LightObject () |
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virtual void | PrintHeader (std::ostream &os, Indent indent) const |
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virtual void | PrintSelf (std::ostream &os, Indent indent) const |
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virtual void | PrintTrailer (std::ostream &os, Indent indent) const |
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virtual | ~LightObject () |
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std::vector< std::vector< double > > | ReadDirections (const std::string &path) |
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template<typename TScalar > |
TScalar | ReadScalar (const std::string &DataSetName) |
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std::string | ReadString (const std::string &path) |
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template<typename TScalar > |
std::vector< TScalar > | ReadVector (const std::string &DataSetName) |
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void | ResetToInitialState () |
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void | SetupStreaming (H5::DataSpace *imageSpace, H5::DataSpace *slabSpace) |
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template<typename TType > |
void | StoreMetaData (MetaDataDictionary *metaDict, const std::string &HDFPath, const std::string &name, unsigned long numElements) |
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void | WriteDirections (const std::string &path, const std::vector< std::vector< double > > &dir) |
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template<typename TType > |
bool | WriteMeta (const std::string &name, MetaDataObjectBase *metaObjBase) |
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template<typename TType > |
bool | WriteMetaArray (const std::string &name, MetaDataObjectBase *metaObjBase) |
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void | WriteScalar (const std::string &path, const bool value) |
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void | WriteScalar (const std::string &path, const long long value) |
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void | WriteScalar (const std::string &path, const long value) |
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template<typename TScalar > |
void | WriteScalar (const std::string &path, const TScalar &value) |
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void | WriteScalar (const std::string &path, const unsigned long long value) |
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void | WriteScalar (const std::string &path, const unsigned long value) |
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void | WriteString (const std::string &path, const char *s) |
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void | WriteString (const std::string &path, const std::string &value) |
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template<typename TScalar > |
void | WriteVector (const std::string &path, const std::vector< TScalar > &vec) |
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