#include <itkLSMImageIO.h>

Inheritance diagram for itk::LSMImageIO:

Collaboration diagram for itk::LSMImageIO:

Detailed Description

ImageIO class for reading LSM (Zeiss) images LSM is a line of confocal laser scanning microscopes produced by the Zeiss company LSM files are essentially extensions of the TIFF multiple image stack file format.

Definition at line 46 of file itkLSMImageIO.h.

Public Types
typedef SmartPointer< Self >	Pointer

typedef LSMImageIO	Self

typedef ImageIOBase	Superclass

Public Types inherited from itk::TIFFImageIO
enum	{ NOFORMAT, RGB_, GRAYSCALE, PALETTE_RGB, PALETTE_GRAYSCALE, OTHER }

enum	{ NoCompression, PackBits, JPEG, Deflate, LZW }

typedef SmartPointer< Self >	Pointer

typedef TIFFImageIO	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, FLOAT, DOUBLE }

enum	IOPixelType { UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR, POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D, COMPLEX, FIXEDARRAY, MATRIX }

typedef SmartPointer< Self >	Pointer

typedef ImageIOBase	Self

typedef ::itk::intmax_t	SizeType

typedef ::itk::SizeValueType	SizeValueType

typedef LightProcessObject	Superclass

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

typedef SmartPointer< Self >	Pointer

typedef LightProcessObject	Self

typedef Object	Superclass

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

typedef SmartPointer< Self >	Pointer

typedef Object	Self

typedef LightObject	Superclass

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

typedef SmartPointer< Self >	Pointer

typedef LightObject	Self

Public Member Functions
virtual bool	CanReadFile (const char *)

virtual bool	CanWriteFile (const char *)

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

virtual const char *	GetNameOfClass () const

virtual void	Read (void *buffer)

virtual void	ReadImageInformation ()

virtual void	Write (const void *buffer)

virtual void	WriteImageInformation ()

Public Member Functions inherited from itk::TIFFImageIO
virtual void	ReadTiles (void *buffer)

virtual void	ReadVolume (void *buffer)

void	SetCompression (int compression)

void	SetCompressionToDeflate ()

void	SetCompressionToJPEG ()

void	SetCompressionToLZW ()

void	SetCompressionToNoCompression ()

void	SetCompressionToPackBits ()

Public Member Functions inherited from itk::ImageIOBase
virtual bool	CanStreamRead ()

virtual bool	CanStreamWrite ()

virtual ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const

virtual unsigned int	GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)

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 itk::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 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, std::vector< double > &direction)

virtual void	SetDirection (unsigned int i, vnl_vector< double > &direction)

void	SetFileTypeToBinary ()

void	SetNumberOfDimensions (unsigned int)

virtual void	SetOrigin (unsigned int i, double origin)

template<class 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	SetFileName (const char *_arg)

virtual const char *	GetFileName () const

virtual void	SetDimensions (unsigned int i, unsigned int dim)

virtual void	SetIORegion (ImageIORegion _arg)

virtual const ImageIORegion &	GetIORegion ()

virtual void	SetPixelType (const IOPixelType _arg)

virtual IOPixelType	GetPixelType () const

virtual void	SetNumberOfComponents (unsigned int _arg)

virtual const unsigned int &	GetNumberOfComponents ()

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	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 ()

virtual void	SetAbortGenerateData (bool _arg)

virtual void	UpdateOutputData ()

void	UpdateProgress (float amount)

virtual void	SetProgress (float _arg)

virtual const float &	GetProgress ()

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 (void)

const MetaDataDictionary &	GetMetaDataDictionary (void) 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

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int)

virtual void	UnRegister () 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::TIFFImageIO
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
	LSMImageIO ()

void	PrintSelf (std::ostream &os, Indent indent) const

	~LSMImageIO ()

Protected Member Functions inherited from itk::TIFFImageIO
bool	CanFindTIFFTag (unsigned int t)

int	EvaluateImageAt (void out, void in)

void	GetColor (int index, unsigned short red, unsigned short green, unsigned short *blue)

unsigned int	GetFormat ()

void	InitializeColors ()

void	InternalWrite (const void *buffer)

void	ReadGenericImage (void *out, unsigned int, unsigned int height)

void *	ReadRawByteFromTag (unsigned int t, short &value_count)

void	ReadTwoSamplesPerPixelImage (void *out, unsigned int, unsigned int height)

	TIFFImageIO ()

	~TIFFImageIO ()

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 (void) 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	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 ()

Protected Member Functions inherited from itk::LightProcessObject
virtual void	GenerateData ()

	LightProcessObject ()

	~LightProcessObject ()

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &time)

virtual	~Object ()

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	FillZeissStruct (char *z)

	LSMImageIO (const Self &)

void	operator= (const Self &)

Additional Inherited Members
Protected Types inherited from itk::LightObject
typedef int	InternalReferenceCountType

Protected Attributes inherited from itk::TIFFImageIO
int	m_Compression

TIFFReaderInternal *	m_InternalImage

Member Typedef Documentation

typedef SmartPointer< Self > itk::LSMImageIO::Pointer

Definition at line 52 of file itkLSMImageIO.h.

typedef LSMImageIO itk::LSMImageIO::Self

Standard class typedefs.

Definition at line 50 of file itkLSMImageIO.h.

typedef ImageIOBase itk::LSMImageIO::Superclass

Definition at line 51 of file itkLSMImageIO.h.

Constructor & Destructor Documentation

itk::LSMImageIO::LSMImageIO ( )

protected

itk::LSMImageIO::~LSMImageIO ( )

protected

itk::LSMImageIO::LSMImageIO ( const Self & )

private

Member Function Documentation

virtual bool itk::LSMImageIO::CanReadFile ( const char * )

virtual

Determine the file type. Returns true if this ImageIO can read the file specified.

Reimplemented from itk::TIFFImageIO.

virtual bool itk::LSMImageIO::CanWriteFile ( const char * )

virtual

Determine the file type. Returns true if this ImageIO can read the file specified.

Reimplemented from itk::TIFFImageIO.

virtual::itk::LightObject::Pointer itk::LSMImageIO::CreateAnother ( void ) 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::TIFFImageIO.

void itk::LSMImageIO::FillZeissStruct ( char * z )

private

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::TIFFImageIO.

static Pointer itk::LSMImageIO::New ( )

static

Method for creation through the object factory.

void itk::LSMImageIO::operator= ( const Self & )

private

void itk::LSMImageIO::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const

protectedvirtual

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::TIFFImageIO.

virtual void itk::LSMImageIO::Read ( void * buffer )

virtual

Reads the data from disk into the memory buffer provided.

Reimplemented from itk::TIFFImageIO.

virtual void itk::LSMImageIO::ReadImageInformation ( )

virtual

Set the spacing and dimesion information for the current filename.

Reimplemented from itk::TIFFImageIO.

virtual void itk::LSMImageIO::Write ( const void * buffer )

virtual

Writes the data to disk from the memory buffer provided. Make sure that the IORegion has been set properly.

Reimplemented from itk::TIFFImageIO.

virtual void itk::LSMImageIO::WriteImageInformation ( void )

inlinevirtual

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

Reimplemented from itk::TIFFImageIO.

Definition at line 80 of file itkLSMImageIO.h.

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

itkLSMImageIO.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation