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ITK
4.13.0
Insight Segmentation and Registration Toolkit
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#include <itkStreamingImageIOBase.h>
A base class for specific ImageIO file formats which support streaming.
This class overloads the methods needed to enable streaming. These methods are utilized by the ImageFileReader and ImageFileWriter. The implementation supports streaming of an arbitrary sized region as well as pasting to new or existing file ( of the same name, size, and pixel type ).
Additionally low level IO methods are provided to read and write an IORegion from a file.
This implementation was taken fron the Insight Joural: https://hdl.handle.net/10380/3171
Definition at line 52 of file itkStreamingImageIOBase.h.
Public Member Functions | |
virtual bool | CanStreamRead (void) override |
virtual bool | CanStreamWrite (void) override |
virtual ImageIORegion | GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const override |
virtual unsigned int | GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) override |
virtual const char * | GetNameOfClass () const |
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virtual bool | CanReadFile (const char *)=0 |
virtual bool | CanWriteFile (const char *)=0 |
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 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 bool | GetIsReadAsScalarPlusPalette () 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 |
virtual void | Read (void *buffer)=0 |
virtual void | ReadImageInformation ()=0 |
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 | 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 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 | SetExpandRGBPalette (bool _arg) |
virtual bool | GetExpandRGBPalette () const |
virtual void | ExpandRGBPaletteOn () |
virtual void | ExpandRGBPaletteOff () |
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 > *) |
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virtual void | AbortGenerateDataOff () |
virtual void | AbortGenerateDataOn () |
virtual ::itk::LightObject::Pointer | CreateAnother () const |
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 |
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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 |
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virtual void | Delete () |
virtual int | GetReferenceCount () const |
itkCloneMacro (Self) | |
void | Print (std::ostream &os, Indent indent=0) const |
Protected Member Functions | |
virtual SizeType | GetDataPosition (void) const |
virtual SizeType | GetHeaderSize (void) const =0 |
virtual void | PrintSelf (std::ostream &os, Indent indent) const override |
virtual bool | ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num) |
virtual bool | RequestedToStream () const |
StreamingImageIOBase () | |
virtual bool | StreamReadBufferAsBinary (std::istream &os, void *buffer) |
virtual bool | StreamWriteBufferAsBinary (std::ostream &os, const void *buffer) |
virtual bool | WriteBufferAsBinary (std::ostream &is, const void *buffer, SizeType num) |
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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 () override | |
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virtual void | GenerateData () |
LightProcessObject () | |
~LightProcessObject () override | |
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Object () | |
bool | PrintObservers (std::ostream &os, Indent indent) const |
virtual void | SetTimeStamp (const TimeStamp &time) |
virtual | ~Object () override |
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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 () |
Additional Inherited Members | |
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static std::string | GetComponentTypeAsString (IOComponentType) |
static IOComponentType | GetComponentTypeFromString (const std::string &typeString) |
static std::string | GetPixelTypeAsString (IOPixelType) |
static IOPixelType | GetPixelTypeFromString (const std::string &pixelString) |
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static Pointer | New () |
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static bool | GetGlobalWarningDisplay () |
static void | GlobalWarningDisplayOff () |
static void | GlobalWarningDisplayOn () |
static Pointer | New () |
static void | SetGlobalWarningDisplay (bool flag) |
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static void | BreakOnError () |
static Pointer | New () |
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ByteOrder | m_ByteOrder |
IOComponentType | m_ComponentType |
std::vector< SizeValueType > | m_Dimensions |
std::vector< std::vector < double > > | m_Direction |
bool | m_ExpandRGBPalette |
std::string | m_FileName |
FileType | m_FileType |
bool | m_Initialized |
ImageIORegion | m_IORegion |
bool | m_IsReadAsScalarPlusPalette |
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 |
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AtomicInt< int > | m_ReferenceCount |
typedef SmartPointer< Self > itk::StreamingImageIOBase::Pointer |
Definition at line 58 of file itkStreamingImageIOBase.h.
Standard class typedefs.
Definition at line 56 of file itkStreamingImageIOBase.h.
Definition at line 57 of file itkStreamingImageIOBase.h.
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protected |
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overridevirtual |
Determine if the ImageIO can stream reading from the current settings. Default is false. If this is queried after the header of the file has been read then it will indicate if that file can be streamed
Reimplemented from itk::ImageIOBase.
Reimplemented in itk::VTKImageIO.
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overridevirtual |
Determine if the ImageIO can stream write from the current settings.
There are two types of non exclusive streaming: pasteing subregions, and iterative
Reimplemented from itk::ImageIOBase.
Reimplemented in itk::JPEG2000ImageIO, and itk::VTKImageIO.
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overridevirtual |
Method for supporting streaming. Given a requested region, determine what could be the region that we can read from the file. This is called the streamable region, which will be equal or smaller than the LargestPossibleRegion (unless it was dimensionaly clipped) and greater or equal to the RequestedRegion
the resulting IORegion may be a greater dimensions the the requested IORegion, if the the derived class is unable to read the requested region. For example if the file has a size of [ 10, 10, 10] but the requested region is [10, 10] the return may be 3 dimensions.
Reimplemented from itk::ImageIOBase.
Reimplemented in itk::JPEG2000ImageIO.
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overridevirtual |
Before this method is called all the configuration will be done, that is Streaming/PasteRegion/Compression/Filename etc If pasting is being used the number of requested splits is for that region not the largest. The derived ImageIO class should verify that the file is capable of being written with this configuration. If pasted is enabled and is not support or does not work with the file, then an excepetion should be thrown.
The default implementation depends on CanStreamWrite. If false then 1 is returned (unless pasting is indicated), so that the whole file will be updated in one region. If true then its assumed that any arbitrary region can be written to any file. So the users request will be respected. If a derived class has more restictive conditions then they should be checked
Reimplemented from itk::ImageIOBase.
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inlineprotectedvirtual |
Returns the byte offset into the file where the data is located.
The default implementation is to return the header size.
Definition at line 153 of file itkStreamingImageIOBase.h.
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protectedpure virtual |
Returns the size of the header in the file.
Implemented in itk::HDF5ImageIO, itk::SCIFIOImageIO, itk::MRCImageIO, itk::VTKImageIO, and itk::JPEG2000ImageIO.
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virtual |
Run-time type information (and related methods).
Reimplemented from itk::ImageIOBase.
Reimplemented in itk::HDF5ImageIO, itk::SCIFIOImageIO, itk::MRCImageIO, itk::VTKImageIO, and itk::JPEG2000ImageIO.
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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.
Reimplemented in itk::HDF5ImageIO, itk::JPEG2000ImageIO, itk::VTKImageIO, and itk::MRCImageIO.
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protectedvirtual |
Reimplemented from super class to get around 2GB read/write limitation.
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protectedvirtual |
Returns true if GetIORegion is not the same size as the largest region give by GetNumberOfDimensions.
This compares the IORegion to the size of the image in the file. With out regaurd to the dimensions of either, if the images represent the same region then false is returned.
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protectedvirtual |
Reads the set IORegion from os into buffer.
os | is an istream presumed to be opened for reading in binary mode |
buffer | is pointer to an allocated block of memory suitable to hold the IORegion of the pixel type |
This methods relies on GetDataPosition to determin where the data is located in the file. It uses m_IORegion to determin the requested region to read.
The files data is assumed to be unpadded and continuous in the file for the size of the image in the dimensions of the m_IORegion. This means that the image file could be broken into slices, but not blocks for this methods to be used.
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protectedvirtual |
Writes the set IORegion from buffer into os.
os | is an ostream presumed to be opened for writing and reading |
buffer | is a pointer to the data in a continuous block for the region |
This methods relies on GetDataPosition to determin where the data is located in the file. It usesy m_IORegion determin the requested region to written.
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protectedvirtual |
Reimplemented from super class to get around 2GB read/write limitation.