Interface to the OME SCIFIO Java Library.
This class provides the ability to read and write all the file formats supported by the SCIFIO Java library, including Bio-Formats.
It invokes a Java process via a system call, and uses pipes to communicate with it.
The SCIFIO ImageIO module has the following runtime requirements:
- Java Runtime Environment (JRE)
- SCIFIO Java libraries (i.e., JAR files) – for open file formats. SCIFIO (which stands for "SCientific Image Formats Input and Output) is a framework for image I/O in Java. It is permissively licensed (BSD-2) and includes support for reading and writing several formats.
- Optionally, Bio-Formats Java libraries – for additional file formats. Bio-Formats is an extension of SCIFIO, licensed under the GPL, which provides support for a large number (more than 120) proprietary file formats (PFFs), particularly those in life sciences disciplines.
Note that none of the above are required at build time. By default, the Bio-Formats Java libraries (loci_tools.jar, which is a bundle of all SCIFIO & Bio-Formats libraries including dependencies) are downloaded at build time and placed into the lib/Jars subfolder of the build tree. A distributable JRE is also downloaded at build time.
The following environment variables can optionally be set to control the behavior of the SCIFIO ImageIO plugin – in particular, how it interfaces with the Java Runtime Environment:
- JAVA_HOME - Environment variable to determine the location of the java binary. If not set, "java" must be on the system path.
- SCIFIO_PATH - Specifies the location of the required SCIFIO JAR libraries. If unset, the default behavior is to first check the lib/jars subfolder of the build directory. Failing that, it looks for the same subfolder in the install directory given at build time.
- JAVA_FLAGS - Used to pass any additional desired parameters to the Java execution. This is especially useful to override Java's maximum heap size, but also nice for tweaking the VM in many other ways (e.g., garbage collection settings).
Definition at line 80 of file itkSCIFIOImageIO.h.
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virtual bool | CanReadFile (const char *FileNameToRead) |
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virtual bool | CanWriteFile (const char *FileNameToWrite) |
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virtual ::itk::LightObject::Pointer | CreateAnother (void) const |
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virtual const char * | GetNameOfClass () const |
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virtual int | GetSeriesCount () |
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virtual void | Read (void *buffer) |
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virtual void | ReadImageInformation () |
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virtual bool | SetSeries (int series) |
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virtual bool | SupportsDimension (unsigned long dim) |
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virtual void | Write (const void *buffer) |
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virtual void | WriteImageInformation () |
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virtual bool | CanStreamRead (void) ITK_OVERRIDE |
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virtual bool | CanStreamWrite (void) ITK_OVERRIDE |
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virtual ImageIORegion | GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const ITK_OVERRIDE |
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virtual unsigned int | GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion) ITK_OVERRIDE |
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std::string | GetByteOrderAsString (ByteOrder) const |
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virtual unsigned int | GetComponentSize () const |
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virtual IOComponentType | GetComponentType () const |
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virtual const std::type_info & | GetComponentTypeInfo () const |
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virtual std::vector< double > | GetDefaultDirection (unsigned int i) const |
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virtual itk::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 (FileType) 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 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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void | SetByteOrderToLittleEndian () |
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virtual void | SetComponentType (const IOComponentType _arg) |
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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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template<typename TPixel , unsigned 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 , unsigned VLength> |
void | SetPixelTypeInfo (const Matrix< TPixel, VLength, VLength > *) |
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template<typename TPixel > |
void | SetPixelTypeInfo (const std::complex< TPixel > *) |
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template<unsigned VLength> |
void | SetPixelTypeInfo (const Offset< VLength > *) |
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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 void | SetFileName (const char *_arg) |
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virtual const char * | GetFileName () const |
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virtual void | SetDimensions (unsigned int i, unsigned int 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 IOPixelType _arg) |
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virtual IOPixelType | 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 | UseCompressionOff () |
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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 | UseStreamedReadingOff () |
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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 | UseStreamedWritingOff () |
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virtual void | SetFileType (const FileType _arg) |
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virtual FileType | GetFileType () const |
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void | SetFileTypeToASCII () |
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virtual void | SetByteOrder (const ByteOrder _arg) |
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virtual ByteOrder | 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<typename TPixel , unsigned VLength> |
void | SetPixelTypeInfo (const Vector< TPixel, VLength > *) |
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template<typename TPixel > |
void | SetPixelTypeInfo (const VariableLengthVector< TPixel > *) |
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template<typename TPixel , unsigned VLength> |
void | SetPixelTypeInfo (const CovariantVector< TPixel, VLength > *) |
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template<typename TPixel , unsigned VLength> |
void | SetPixelTypeInfo (const FixedArray< TPixel, VLength > *) |
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virtual void | AbortGenerateDataOff () |
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virtual void | AbortGenerateDataOn () |
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virtual const bool & | GetAbortGenerateData () const |
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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 *) |
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unsigned long | AddObserver (const EventObject &event, Command *) const |
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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 (void) |
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const MetaDataDictionary & | GetMetaDataDictionary (void) const |
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virtual ModifiedTimeType | GetMTime () const |
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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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virtual void | Register () const ITK_OVERRIDE |
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void | RemoveAllObservers () |
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void | RemoveObserver (unsigned long tag) |
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void | SetDebug (bool debugFlag) const |
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void | SetMetaDataDictionary (const MetaDataDictionary &rhs) |
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virtual void | SetReferenceCount (int) ITK_OVERRIDE |
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virtual void | UnRegister () const ITK_OVERRIDE |
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virtual void | SetObjectName (std::string _arg) |
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virtual const std::string & | GetObjectName () const |
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virtual void | Delete () |
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virtual int | GetReferenceCount () const |
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| itkCloneMacro (Self) |
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void | Print (std::ostream &os, Indent indent=0) const |
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virtual SizeType | GetHeaderSize () const |
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| SCIFIOImageIO () |
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| ~SCIFIOImageIO () |
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virtual SizeType | GetDataPosition (void) const |
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virtual void | PrintSelf (std::ostream &os, Indent indent) const ITK_OVERRIDE |
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virtual bool | ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num) |
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virtual bool | RequestedToStream (void) const |
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| StreamingImageIOBase () |
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virtual bool | StreamReadBufferAsBinary (std::istream &os, void *buffer) |
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virtual bool | StreamWriteBufferAsBinary (std::ostream &os, const void *buffer) |
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virtual bool | WriteBufferAsBinary (std::ostream &is, 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 (void) 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 | 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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virtual void | ReadBufferAsASCII (std::istream &os, void *buffer, IOComponentType ctype, SizeType numberOfBytesToBeRead) |
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bool | ReadBufferAsBinary (std::istream &os, void *buffer, SizeType numberOfBytesToBeRead) |
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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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virtual void | WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentType ctype, SizeType numberOfBytesToWrite) |
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| ~ImageIOBase () |
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virtual void | GenerateData () |
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| LightProcessObject () |
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| ~LightProcessObject () |
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| Object () |
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bool | PrintObservers (std::ostream &os, Indent indent) const |
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virtual void | SetTimeStamp (const TimeStamp &time) |
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virtual | ~Object () |
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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 | PrintTrailer (std::ostream &os, Indent indent) const |
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virtual | ~LightObject () |
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