ITK  4.4.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | List of all members
itk::LSMImageIO Class Reference

#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< SelfPointer
 
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< SelfPointer
 
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< 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 *)
 
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 ArrayOfExtensionsTypeGetSupportedReadExtensions () const
 
const ArrayOfExtensionsTypeGetSupportedWriteExtensions () 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 ImageIORegionGetIORegion ()
 
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
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary (void)
 
const MetaDataDictionaryGetMetaDataDictionary (void) 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
 
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

Definition at line 52 of file itkLSMImageIO.h.

Standard class typedefs.

Definition at line 50 of file itkLSMImageIO.h.

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: