#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:

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 (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:

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.

Public Types
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = SCIFIOImageIO

using	Superclass = ImageIOBase

Public Types inherited from itk::StreamingImageIOBase
using	Pointer = SmartPointer< Self >

using	Self = StreamingImageIOBase

using	Superclass = ImageIOBase

Public Types inherited from itk::ImageIOBase
using	ArrayOfExtensionsType = std::vector< std::string >

using	BufferSizeType = ::itk::OffsetValueType

enum	ByteOrder { BigEndian, LittleEndian, OrderNotApplicable }

using	ConstPointer = SmartPointer< const Self >

enum	FileType { ASCII, Binary, TypeNotApplicable }

using	IndexValueType = ::itk::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 }

using	Pointer = SmartPointer< Self >

using	Self = ImageIOBase

using	SizeType = ::itk::intmax_t

using	SizeValueType = ::itk::SizeValueType

using	Superclass = LightProcessObject

Public Types inherited from itk::LightProcessObject
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = LightProcessObject

using	Superclass = Object

Public Types inherited from itk::Object
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

Public Types inherited from itk::LightObject
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = LightObject

Public Member Functions
bool	CanReadFile (const char *FileNameToRead) override

bool	CanWriteFile (const char *FileNameToWrite) override

virtual ::itk::LightObject::Pointer	CreateAnother () const

virtual const char *	GetNameOfClass () const

virtual int	GetSeriesCount ()

void	Read (void *buffer) override

void	ReadImageInformation () override

virtual bool	SetSeries (int series)

bool	SupportsDimension (unsigned long dim) override

void	Write (const void *buffer) override

void	WriteImageInformation () override

Public Member Functions inherited from itk::StreamingImageIOBase
bool	CanStreamRead () override

bool	CanStreamWrite () override

ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const override

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 ArrayOfExtensionsType &	GetSupportedReadExtensions () const

const ArrayOfExtensionsType &	GetSupportedWriteExtensions () 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 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 > *)

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

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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexceptoverride

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
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
SizeType	GetHeaderSize () const override

	SCIFIOImageIO ()

	~SCIFIOImageIO () override

Protected Member Functions inherited from itk::StreamingImageIOBase
virtual SizeType	GetDataPosition () const

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

virtual bool	HasSupportedReadExtension (const char *fileName, bool ignoreCase=true)

virtual bool	HasSupportedWriteExtension (const char *fileName, bool ignoreCase=true)

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)

	~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 {OrderNotApplicable}

IOComponentType	m_ComponentType {UNKNOWNCOMPONENTTYPE}

std::vector< SizeValueType >	m_Dimensions

std::vector< std::vector < double > >	m_Direction

bool	m_ExpandRGBPalette

std::string	m_FileName

FileType	m_FileType {TypeNotApplicable}

bool	m_Initialized

ImageIORegion	m_IORegion

bool	m_IsReadAsScalarPlusPalette

unsigned int	m_NumberOfComponents

unsigned int	m_NumberOfDimensions {0}

std::vector< double >	m_Origin

IOPixelType	m_PixelType {SCALAR}

std::vector< double >	m_Spacing

std::vector< SizeType >	m_Strides

bool	m_UseCompression

bool	m_UseStreamedReading

bool	m_UseStreamedWriting

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount

Member Typedef Documentation

using itk::SCIFIOImageIO::ConstPointer = SmartPointer<const Self>

Definition at line 86 of file itkSCIFIOImageIO.h.

using itk::SCIFIOImageIO::Pointer = SmartPointer<Self>

Definition at line 85 of file itkSCIFIOImageIO.h.

using itk::SCIFIOImageIO::Self = SCIFIOImageIO

Definition at line 83 of file itkSCIFIOImageIO.h.

using itk::SCIFIOImageIO::Superclass = ImageIOBase

Definition at line 84 of file itkSCIFIOImageIO.h.

Constructor & Destructor Documentation

itk::SCIFIOImageIO::SCIFIOImageIO ( )

protected

itk::SCIFIOImageIO::~SCIFIOImageIO ( )

overrideprotected

Member Function Documentation

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

overridevirtual

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

Implements itk::ImageIOBase.

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

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

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

overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

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

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

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.

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:

itkSCIFIOImageIO.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation