#include <itkAnalyzeImageIO.h>

Inheritance diagram for itk::AnalyzeImageIO:

Collaboration diagram for itk::AnalyzeImageIO:

Public Types
typedef SmartPointer< Self >	Pointer
typedef AnalyzeImageIO	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 ::itk::intmax_t	SizeType
typedef ::itk::SizeValueType	SizeValueType
Public Types inherited from itk::LightProcessObject
typedef SmartPointer< const Self >	ConstPointer
Public Types inherited from itk::Object
Public Types inherited from itk::LightObject

Public Member Functions
virtual bool	CanReadFile (const char *FileNameToRead)
virtual bool	CanWriteFile (const char *FileNameToWrite)
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual std::vector< double >	GetDefaultDirection (unsigned int i) const
virtual std::vector< double >	GetDirection (unsigned int i) 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::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 unsigned int	GetDimensions (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 unsigned long	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::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)

Protected Member Functions
	AnalyzeImageIO ()
void	PrintSelf (std::ostream &os, Indent indent) const
	~AnalyzeImageIO ()
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 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
	LightProcessObject ()
	~LightProcessObject ()
virtual void	GenerateData ()
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 Types
enum	ValidAnalyzeOrientationFlags

Private Member Functions
	AnalyzeImageIO (const Self &)
ImageIOBase::ByteOrder	CheckAnalyzeEndian (const struct dsr &temphdr)
void	DefineHeaderObjectDataType (void)
void	operator= (const Self &)
void	SwapBytesIfNecessary (void *buffer, SizeType numberOfPixels)
void	SwapHeaderBytesIfNecessary (struct dsr *const imageheader)

Private Attributes
struct dsr	m_Hdr
ImageIOBase::ByteOrder	m_MachineByteOrder

Additional Inherited Members
Protected Attributes inherited from itk::ImageIOBase
ByteOrder	m_ByteOrder
IOComponentType	m_ComponentType
std::vector< SizeValueType >	m_Dimensions
std::vector< std::vector < double > >	m_Direction
std::string	m_FileName
FileType	m_FileType
bool	m_Initialized
ImageIORegion	m_IORegion
unsigned int	m_NumberOfComponents
unsigned int	m_NumberOfDimensions
std::vector< double >	m_Origin
IOPixelType	m_PixelType
std::vector< double >	m_Spacing
std::vector< SizeType >	m_Strides
bool	m_UseCompression
bool	m_UseStreamedReading
bool	m_UseStreamedWriting

Detailed Description

Class that defines how to read Analyze file format. Analyze IMAGE FILE FORMAT - As much information as I can determine from the Medical image formats web site, and the Analyze75.pdf file provided from the Mayo clinic. A special note of thanks to Dennis P. Hanson (dph@m.nosp@m.ayo..nosp@m.edu) for his generous contributions in getting this information correct.

Author:

Hans J. Johnson Analyze image file sets consist of at least 2 files: REQUIRED:

an image file ([basename].img or [basename].img.gz or [basename].img.Z) This contains the binary represenation of the raw voxel values. If the file is uncompressed, it should be of of size (sizeof(storagetype)*NX*NY*NZ(*NT). The format of the image file is very simple; containing usually uncompressed voxel data for the images in one of the several possible voxel formats:
- 1 bit packed binary (slices begin on byte boundaries)
- 8 bit (unsigned char) gray scale unless .lkup file present
- 16 bit signed short
- 32 bit signed integers or float
- 24 bit RGB, 8 bits per channel
a header file ([basename].hdr) This a 348 byte file 99.99% of all images that contains a binary represenation of the C-struct defined in this file. The analyze 7.5 header structure may, however, be extended beyond this minimal definition to encompase site specific information, and would have more than 348 bytes. Given that the ability to extend the header has rarely been used, this implementation of the Analyze 7.5 file will only read the first 348 bytes into the structure defined in this file, and all informaiton beyond the 348 bytes will be ignored. OPTIONAL:
a color lookup file ([basename].lkup) The .lkup file is a plain ASCII text file that contains 3 integer values between 0 and 255 on each line. Each line of the lkup file represents one color table entry for the Red, Green and Blue color components, respectively. The total dynamic range of the image is divided by the number of colors in color table to determine mapping of the image through these colors.
For example, an 8-color 'rainbow colors' lookup table is represented as:

255 0 0 255 128 0 255 255 0 128 255 0 0 255 0 0 0 255 128 0 255

255 0 255

an object file ([basename].obj) A specially formated file with a mapping between object name and image code used to associate image voxel locations with a label. This file is run length encoded to save disk storage.

Definition at line 92 of file itkAnalyzeImageIO.h.

Member Typedef Documentation

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

Reimplemented from itk::ImageIOBase.

Definition at line 98 of file itkAnalyzeImageIO.h.

typedef AnalyzeImageIO itk::AnalyzeImageIO::Self

Standard class typedefs.

Reimplemented from itk::ImageIOBase.

Definition at line 96 of file itkAnalyzeImageIO.h.

typedef ImageIOBase itk::AnalyzeImageIO::Superclass

Reimplemented from itk::ImageIOBase.

Definition at line 97 of file itkAnalyzeImageIO.h.

Member Enumeration Documentation

enum itk::AnalyzeImageIO::ValidAnalyzeOrientationFlags

private

Valid Orientation values for objects

Key Description Origin dims[1] dims[2] dims[3]
=================================================================
0 transverse-unflipped IRP R->L P->A I->S
1 coronal-unflipped IRP R->L I->S P->A
2 sagittal-unflipped IRP P->A I->S R->L
3 transverse-flipped IRA R->L A->P I->S
4 coronal-flipped SRP R->L S->I P->A
5 sagittal-flipped ILP P->A I->S L->R
Where the Origin disignators are with respect to the patient
[(I)nferior|(S)uperior] [(L}eft|(R)ight] [(A)nterior|(P)osterior]
Note:
Key's 0-5 correspond to the Analyze v7.5 orientations, and should not be changed.

Definition at line 167 of file itkAnalyzeImageIO.h.

Constructor & Destructor Documentation

itk::AnalyzeImageIO::AnalyzeImageIO ( )

protected

itk::AnalyzeImageIO::~AnalyzeImageIO ( )

protected

itk::AnalyzeImageIO::AnalyzeImageIO ( const Self & )

private

Member Function Documentation

virtual bool itk::AnalyzeImageIO::CanReadFile ( const char * FileNameToRead )

virtual

Determine if the file can be read with this ImageIO implementation.

Author:: Hans J Johnson

Parameters:

FileNameToRead The name of the file to test for reading.

Postcondition:: Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite

Returns:: Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

virtual bool itk::AnalyzeImageIO::CanWriteFile ( const char * FileNameToWrite )

virtual

Determine if the file can be written with this ImageIO implementation.

Parameters:

FileNameToWrite The name of the file to test for writing.

Author:: Hans J. Johnson

Postcondition:: Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite

Returns:: Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

ImageIOBase::ByteOrder itk::AnalyzeImageIO::CheckAnalyzeEndian ( const struct dsr & temphdr )

private

Author:: Hans J. Johnson Check the endedness of the header file.

Parameters:

temphdr - a reference to the header structure

Returns:: The endedness of the file

virtual::itk::LightObject::Pointer itk::AnalyzeImageIO::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::LightProcessObject.

void itk::AnalyzeImageIO::DefineHeaderObjectDataType ( void )

private

Author:: Hans J. Johnson Defines the header object data type feilds according to Analyze v7.5 specifications

Returns:: nothing

virtual std::vector< double > itk::AnalyzeImageIO::GetDefaultDirection ( unsigned int i ) const

virtual

Return the directions to be assigned by default to recipient images whose dimension is smaller than the image dimension in file.

Reimplemented from itk::ImageIOBase.

virtual std::vector< double > itk::AnalyzeImageIO::GetDirection ( unsigned int i ) const

virtual

Return the directions with a correction for the 2D case.

Reimplemented from itk::ImageIOBase.

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

static Pointer itk::AnalyzeImageIO::New ( )

static

Method for creation through the object factory.

Reimplemented from itk::LightProcessObject.

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

private

This method causes the filter to generate its output.

Reimplemented from itk::ImageIOBase.

void itk::AnalyzeImageIO::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::ImageIOBase.

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

virtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::AnalyzeImageIO::ReadImageInformation ( )

virtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

void itk::AnalyzeImageIO::SwapBytesIfNecessary	(	void *	buffer,
		SizeType	numberOfPixels
	)

private

void itk::AnalyzeImageIO::SwapHeaderBytesIfNecessary ( struct dsr *const imageheader )

private

Author:: Hans J. Johnson Performs byte swapping of the Analyze Image header if necessary.

Parameters:

imageheader An Analyze 7.5 compliant image header.

Returns:: void

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

virtual

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

Implements itk::ImageIOBase.

virtual void itk::AnalyzeImageIO::WriteImageInformation ( )

virtual

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.

Member Data Documentation

struct dsr itk::AnalyzeImageIO::m_Hdr

private

All of the information read in from the header file

Definition at line 241 of file itkAnalyzeImageIO.h.

ImageIOBase::ByteOrder itk::AnalyzeImageIO::m_MachineByteOrder

private

Definition at line 242 of file itkAnalyzeImageIO.h.

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

itkAnalyzeImageIO.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

For example, an 8-color 'rainbow colors' lookup table is represented as:

255 0 255

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation