ITK  4.13.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
itk::SCIFIOImageIO Class Reference

#include <itkSCIFIOImageIO.h>

+ Inheritance diagram for itk::SCIFIOImageIO:
+ Collaboration diagram for itk::SCIFIOImageIO:

Detailed Description

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:

Note that none of the above are required at build time. By default, the Bio-Formats Java libraries (bioformats_package.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:

Definition at line 80 of file itkSCIFIOImageIO.h.

Public Types

typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef SCIFIOImageIO Self
 
typedef ImageIOBase Superclass
 
- Public Types inherited from itk::StreamingImageIOBase
typedef SmartPointer< SelfPointer
 
typedef StreamingImageIOBase Self
 
typedef ImageIOBase Superclass
 
- Public Types inherited from itk::ImageIOBase
typedef std::vector< std::string > ArrayOfExtensionsType
 
typedef ::itk::OffsetValueType BufferSizeType
 
enum  ByteOrder {
  BigEndian,
  LittleEndian,
  OrderNotApplicable
}
 
enum  FileType {
  ASCII,
  Binary,
  TypeNotApplicable
}
 
typedef ::itk::IndexValueType IndexValueType
 
enum  IOComponentType {
  UNKNOWNCOMPONENTTYPE,
  UCHAR,
  CHAR,
  USHORT,
  SHORT,
  UINT,
  INT,
  ULONG,
  LONG,
  ULONGLONG,
  LONGLONG,
  FLOAT,
  DOUBLE
}
 
enum  IOPixelType {
  UNKNOWNPIXELTYPE,
  SCALAR,
  RGB,
  RGBA,
  OFFSET,
  VECTOR,
  POINT,
  COVARIANTVECTOR,
  SYMMETRICSECONDRANKTENSOR,
  DIFFUSIONTENSOR3D,
  COMPLEX,
  FIXEDARRAY,
  MATRIX
}
 
typedef SmartPointer< SelfPointer
 
typedef ImageIOBase Self
 
typedef ::itk::intmax_t SizeType
 
typedef ::itk::SizeValueType SizeValueType
 
typedef LightProcessObject Superclass
 
- Public Types inherited from itk::LightProcessObject
typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef LightProcessObject Self
 
typedef Object Superclass
 
- Public Types inherited from itk::Object
typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef Object Self
 
typedef LightObject Superclass
 
- Public Types inherited from itk::LightObject
typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef LightObject Self
 

Public Member Functions

virtual bool CanReadFile (const char *FileNameToRead) override
 
virtual bool CanWriteFile (const char *FileNameToWrite) override
 
virtual ::itk::LightObject::Pointer CreateAnother () const
 
virtual const char * GetNameOfClass () const
 
virtual int GetSeriesCount ()
 
virtual void Read (void *buffer) override
 
virtual void ReadImageInformation () override
 
virtual bool SetSeries (int series)
 
virtual bool SupportsDimension (unsigned long dim) override
 
virtual void Write (const void *buffer) override
 
virtual void WriteImageInformation () override
 
- Public Member Functions inherited from itk::StreamingImageIOBase
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
 
- Public Member Functions inherited from itk::ImageIOBase
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 ArrayOfExtensionsTypeGetSupportedReadExtensions () const
 
const ArrayOfExtensionsTypeGetSupportedWriteExtensions () const
 
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 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 ImageIORegionGetIORegion () 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 > *)
 
- 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 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 *)
 
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
 
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
 
- 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 (IOComponentType)
 
static IOComponentType GetComponentTypeFromString (const std::string &typeString)
 
static std::string GetPixelTypeAsString (IOPixelType)
 
static IOPixelType 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

virtual SizeType GetHeaderSize () const override
 
 SCIFIOImageIO ()
 
 ~SCIFIOImageIO ()
 
- Protected Member Functions inherited from itk::StreamingImageIOBase
virtual SizeType GetDataPosition (void) const
 
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)
 
- 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 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
 
- Protected Member Functions inherited from itk::LightProcessObject
virtual void GenerateData ()
 
 LightProcessObject ()
 
 ~LightProcessObject () override
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &time)
 
virtual ~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 PrintTrailer (std::ostream &os, Indent indent) const
 
virtual ~LightObject ()
 

Private Member Functions

void CheckError (std::string message)
 
bool CheckJavaPath (std::string javaHome, std::string &javaCmd)
 
void CreateJavaProcess ()
 
void DestroyJavaProcess ()
 
std::string FindDimensionOrder (const ImageIORegion &region)
 
int itkToSCIFIOPixelType (ImageIOBase::IOComponentType cmp)
 
std::string RemoveFinalSlash (std::string path) const
 
ImageIOBase::IOComponentType scifioToITKComponentType (int pixelType)
 
char ** toCArray (std::vector< std::string > &args)
 
std::string WaitForNewLines (int pipedatalength)
 

Private Attributes

std::vector< std::string > m_Args
 
char ** m_Argv
 
MetaDataDictionary m_MetaDataDictionary
 
itksysProcess_Pipe_Handle m_Pipe [2]
 
itksysProcess * m_Process
 

Additional Inherited Members

- Protected Attributes inherited from itk::ImageIOBase
ByteOrder m_ByteOrder
 
IOComponentType m_ComponentType
 
std::vector< SizeValueTypem_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< SizeTypem_Strides
 
bool m_UseCompression
 
bool m_UseStreamedReading
 
bool m_UseStreamedWriting
 
- Protected Attributes inherited from itk::LightObject
AtomicInt< int > m_ReferenceCount
 

Member Typedef Documentation

Definition at line 86 of file itkSCIFIOImageIO.h.

Definition at line 85 of file itkSCIFIOImageIO.h.

Definition at line 83 of file itkSCIFIOImageIO.h.

Definition at line 84 of file itkSCIFIOImageIO.h.

Constructor & Destructor Documentation

itk::SCIFIOImageIO::SCIFIOImageIO ( )
protected
itk::SCIFIOImageIO::~SCIFIOImageIO ( )
protected

Member Function Documentation

virtual bool itk::SCIFIOImageIO::CanReadFile ( const char *  FileNameToRead)
overridevirtual

------------— Read the data--------------—

Implements itk::ImageIOBase.

virtual bool itk::SCIFIOImageIO::CanWriteFile ( const char *  FileNameToWrite)
overridevirtual

------------—Write the data---------------—

Implements itk::ImageIOBase.

void itk::SCIFIOImageIO::CheckError ( std::string  message)
private
bool itk::SCIFIOImageIO::CheckJavaPath ( std::string  javaHome,
std::string &  javaCmd 
)
private
virtual::itk::LightObject::Pointer itk::SCIFIOImageIO::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.

void itk::SCIFIOImageIO::CreateJavaProcess ( )
private
void itk::SCIFIOImageIO::DestroyJavaProcess ( )
private
std::string itk::SCIFIOImageIO::FindDimensionOrder ( const ImageIORegion region)
private
virtual SizeType itk::SCIFIOImageIO::GetHeaderSize ( ) const
inlineoverrideprotectedvirtual

Returns the size of the header in the file.

Implements itk::StreamingImageIOBase.

Definition at line 126 of file itkSCIFIOImageIO.h.

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

RTTI (and related methods)

Reimplemented from itk::StreamingImageIOBase.

virtual int itk::SCIFIOImageIO::GetSeriesCount ( )
virtual
int itk::SCIFIOImageIO::itkToSCIFIOPixelType ( ImageIOBase::IOComponentType  cmp)
inlineprivate

Definition at line 172 of file itkSCIFIOImageIO.h.

static Pointer itk::SCIFIOImageIO::New ( )
static

Method for creation through the object factory

virtual void itk::SCIFIOImageIO::Read ( void *  buffer)
overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::SCIFIOImageIO::ReadImageInformation ( )
overridevirtual

Read the spacing and dimensions of the image. Assumes SetFileName has been called with a valid file name.

Implements itk::ImageIOBase.

std::string itk::SCIFIOImageIO::RemoveFinalSlash ( std::string  path) const
private
ImageIOBase::IOComponentType itk::SCIFIOImageIO::scifioToITKComponentType ( int  pixelType)
inlineprivate

Definition at line 149 of file itkSCIFIOImageIO.h.

virtual bool itk::SCIFIOImageIO::SetSeries ( int  series)
virtual
virtual bool itk::SCIFIOImageIO::SupportsDimension ( unsigned long  dim)
overridevirtual

The different types of ImageIO's can support data of varying dimensionality. For example, some file formats are strictly 2D while others can support 2D, 3D, or even n-D. This method returns true/false as to whether the ImageIO can support the dimension indicated.

Reimplemented from itk::ImageIOBase.

char** itk::SCIFIOImageIO::toCArray ( std::vector< std::string > &  args)
inlineprivate

Definition at line 137 of file itkSCIFIOImageIO.h.

std::string itk::SCIFIOImageIO::WaitForNewLines ( int  pipedatalength)
private
virtual void itk::SCIFIOImageIO::Write ( const void *  buffer)
overridevirtual

Writes the data to disk from the memory buffer provided. Make sure that the IORegions has been set properly. The buffer is cast to a pointer to the beginning of the image data.

Implements itk::ImageIOBase.

virtual void itk::SCIFIOImageIO::WriteImageInformation ( )
overridevirtual

Writes the spacing and dimensions of the image. Assumes SetFileName has been called with a valid file name.

Implements itk::ImageIOBase.

Member Data Documentation

std::vector< std::string > itk::SCIFIOImageIO::m_Args
private

Definition at line 199 of file itkSCIFIOImageIO.h.

char** itk::SCIFIOImageIO::m_Argv
private

Definition at line 200 of file itkSCIFIOImageIO.h.

MetaDataDictionary itk::SCIFIOImageIO::m_MetaDataDictionary
private

Definition at line 198 of file itkSCIFIOImageIO.h.

itksysProcess_Pipe_Handle itk::SCIFIOImageIO::m_Pipe[2]
private

Definition at line 201 of file itkSCIFIOImageIO.h.

itksysProcess* itk::SCIFIOImageIO::m_Process
private

Definition at line 202 of file itkSCIFIOImageIO.h.


The documentation for this class was generated from the following file: