An ImageIO class to read the MRC file format. The MRC file format frequently has the extension ".mrc" or ".rec". It is used frequently for electron microscopy and is an emerging standard for cryo-electron tomography and molecular imaging. The format is used to represent 2D, 3D images along with 2D tilt series for tomography. More...

#include <itkMRCImageIO.h>

Inheritance diagram for itk::MRCImageIO:

Collaboration diagram for itk::MRCImageIO:

List of all members.

Public Types
typedef std::vector< std::string >	ArrayOfExtensionsType
typedef vcl_size_t	BufferSizeType
enum	ByteOrder { BigEndian, LittleEndian, OrderNotApplicable }
typedef SmartPointer< const Self >	ConstPointer
enum	FileType { ASCII, Binary, TypeNotApplicable }
typedef long	IndexValueType
enum	IOComponentType { UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT, INT, ULONG, LONG, FLOAT, DOUBLE, CSHORT, CINT, CFLOAT, CDOUBLE }
enum	IOPixelType { UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR, POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D, COMPLEX, FIXEDARRAY, MATRIX }
typedef SmartPointer< Self >	Pointer
typedef MRCImageIO	Self
typedef std::streamoff	SizeType
typedef unsigned long	SizeValueType
typedef StreamingImageIOBase	Superclass

Public Member Functions
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
unsigned long	AddObserver (const EventObject &event, Command *)
unsigned long	AddObserver (const EventObject &event, Command *) const
virtual bool	CanReadFile (const char *)
virtual bool	CanStreamRead (void)
virtual bool	CanStreamWrite (void)
virtual bool	CanWriteFile (const char *)
	Returns true if this ImageIO can write the specified file.
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual void	DebugOff () const
virtual void	DebugOn () const
virtual void	Delete ()
virtual ImageIORegion	GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const
virtual const bool &	GetAbortGenerateData ()
virtual unsigned int	GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
virtual ByteOrder	GetByteOrder () const
std::string	GetByteOrderAsString (ByteOrder) const
Command *	GetCommand (unsigned long tag)
virtual unsigned int	GetComponentSize () const
virtual IOComponentType	GetComponentType () const
std::string	GetComponentTypeAsString (IOComponentType) const
virtual const std::type_info &	GetComponentTypeInfo () const
bool	GetDebug () const
virtual std::vector< double >	GetDefaultDirection (unsigned int i) const
virtual unsigned int	GetDimensions (unsigned int i) const
virtual std::vector< double >	GetDirection (unsigned int i) const
virtual const char *	GetFileName () const
virtual FileType	GetFileType () const
std::string	GetFileTypeAsString (FileType) const
SizeType	GetImageSizeInBytes () const
SizeType	GetImageSizeInComponents () const
SizeType	GetImageSizeInPixels () const
virtual const ImageIORegion &	GetIORegion ()
MetaDataDictionary &	GetMetaDataDictionary (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
virtual unsigned long	GetMTime () const
virtual const char *	GetNameOfClass () const
virtual const unsigned int &	GetNumberOfComponents ()
virtual unsigned int	GetNumberOfDimensions () const
virtual double	GetOrigin (unsigned int i) const
virtual SizeType	GetPixelStride () const
virtual IOPixelType	GetPixelType () const
std::string	GetPixelTypeAsString (IOPixelType) const
virtual const float &	GetProgress ()
virtual int	GetReferenceCount () 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
virtual bool	GetUseCompression () const
virtual bool	GetUseStreamedReading () const
virtual bool	GetUseStreamedWriting () const
bool	HasObserver (const EventObject &event) const
void	InvokeEvent (const EventObject &)
void	InvokeEvent (const EventObject &) const
virtual void	Modified () const
void	Print (std::ostream &os, Indent indent=0) const
virtual void	Read (void *buffer)
virtual void	ReadImageInformation ()
virtual void	Register () const
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
virtual void	SetAbortGenerateData (bool _arg)
virtual void	SetByteOrder (const ByteOrder _arg)
void	SetByteOrderToBigEndian ()
void	SetByteOrderToLittleEndian ()
virtual void	SetComponentType (const IOComponentType _arg)
void	SetDebug (bool debugFlag) const
virtual void	SetDimensions (unsigned int i, unsigned int dim)
virtual void	SetDirection (unsigned int i, std::vector< double > &direction)
virtual void	SetDirection (unsigned int i, vnl_vector< double > &direction)
virtual void	SetFileName (const char *_arg)
virtual void	SetFileType (const FileType _arg)
void	SetFileTypeToASCII ()
void	SetFileTypeToBinary ()
virtual void	SetIORegion (ImageIORegion _arg)
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetNumberOfComponents (unsigned int _arg)
void	SetNumberOfDimensions (unsigned int)
virtual void	SetOrigin (unsigned int i, double origin)
virtual void	SetPixelType (const IOPixelType _arg)
virtual bool	SetPixelTypeInfo (const std::type_info &ptype)
virtual void	SetProgress (float _arg)
virtual void	SetReferenceCount (int)
virtual void	SetSpacing (unsigned int i, double spacing)
virtual void	SetUseCompression (bool _arg)
virtual void	SetUseStreamedReading (bool _arg)
virtual void	SetUseStreamedWriting (bool _arg)
virtual bool	SupportsDimension (unsigned long dim)
virtual void	UnRegister () const
virtual void	UpdateOutputData ()
void	UpdateProgress (float amount)
virtual void	UseCompressionOff ()
virtual void	UseCompressionOn ()
virtual void	UseStreamedReadingOff ()
virtual void	UseStreamedReadingOn ()
virtual void	UseStreamedWritingOff ()
virtual void	UseStreamedWritingOn ()
virtual void	Write (const void *buffer)
virtual void	WriteImageInformation (void)

Static Public Member Functions
static void	BreakOnError ()
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static Pointer	New ()
static void	SetGlobalWarningDisplay (bool flag)

Static Public Attributes
static const char *	m_MetaDataHeaderName = "MRCHeader"

Protected Types
typedef int	InternalReferenceCountType

Protected Member Functions
	MRCImageIO ()
void	AddSupportedReadExtension (const char *extension)
void	AddSupportedWriteExtension (const char *extension)
void	ComputeStrides ()
virtual void	GenerateData ()
virtual unsigned int	GetActualNumberOfSplitsForWritingCanStreamWrite (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion) const
SizeType	GetComponentStride () const
virtual SizeType	GetDataPosition (void) const
	Returns the byte offset into the file where the data is located.
virtual SizeType	GetHeaderSize (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
virtual void	OpenFileForReading (std::ifstream &os, const char *filename)
	Opens a file for reading and random access.
virtual void	OpenFileForWriting (std::ofstream &os, const char *filename, bool truncate)
	Opens a file for writing and random access.
virtual void	PrintHeader (std::ostream &os, Indent indent) const
bool	PrintObservers (std::ostream &os, Indent indent) const
void	PrintSelf (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
void	ReadBufferAsASCII (std::istream &os, void *buffer, IOComponentType ctype, SizeType numberOfBytesToBeRead)
virtual bool	ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)
	Reimplemented from super class to get around 2GB read/write limitation.
virtual bool	RequestedToStream (void) const
	Returns true if GetIORegion is not the same size as the largest region give by GetNumberOfDimensions.
virtual void	Reset (const bool freeDynamic=true)
void	Resize (const unsigned int numDimensions, const unsigned int *dimensions)
virtual bool	StreamReadBufferAsBinary (std::istream &os, void *buffer)
	Reads the set IORegion from os into buffer.
virtual bool	StreamWriteBufferAsBinary (std::ostream &os, const void *buffer)
	Writes the set IORegion from buffer into os.
void	WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentType ctype, SizeType numberOfBytesToWrite)
virtual bool	WriteBufferAsBinary (std::ostream &is, const void *buffer, SizeType num)
	Reimplemented from super class to get around 2GB read/write limitation.

Protected Attributes
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
InternalReferenceCountType	m_ReferenceCount
SimpleFastMutexLock	m_ReferenceCountLock
std::vector< double >	m_Spacing
std::vector< SizeType >	m_Strides
bool	m_UseCompression
bool	m_UseStreamedReading
bool	m_UseStreamedWriting

Private Member Functions
	MRCImageIO (const Self &)
void	InternalReadImageInformation (std::ifstream &is)
void	operator= (const Self &)
void	UpdateHeaderFromImageIO (void)
template<typename TPixelType >
void	UpdateHeaderWithMinMaxMean (const TPixelType *bufferBegin)
void	UpdateHeaderWithMinMaxMean (const void *bufferBegin)
virtual void	WriteImageInformation (const void *bufferBegin)

Private Attributes
MRCHeaderObject::Pointer	m_MRCHeader

Detailed Description

An ImageIO class to read the MRC file format. The MRC file format frequently has the extension ".mrc" or ".rec". It is used frequently for electron microscopy and is an emerging standard for cryo-electron tomography and molecular imaging. The format is used to represent 2D, 3D images along with 2D tilt series for tomography.

The header of the file can contain important information which can not be represented in an Image. Therefor the header is placed into the MetaDataDictionary of "this". The key to access this is MetaDataHeaderName ( fix me when renamed ).

See also:: MRCHeaderObject MetaDataDictionary

This implementation is designed to support IO Streaming of arbitrary regions.

As with all ImageIOs this class is designed to work with ImageFileReader and ImageFileWriter, so its direct use is discouraged.

See also:: ImageFileWriter ImageFileReader ImageIOBase

Definition at line 53 of file itkMRCImageIO.h.

Member Typedef Documentation

typedef std::vector< std::string > itk::ImageIOBase::ArrayOfExtensionsType

inherited

Type for the list of strings to be used for extensions.

Definition at line 388 of file itkImageIOBase.h.

typedef vcl_size_t itk::ImageIOBase::BufferSizeType

inherited

Type for representing size of bytes, and or positions along a memory buffer

Definition at line 256 of file itkImageIOBase.h.

typedef SmartPointer<const Self> itk::LightProcessObject::ConstPointer

inherited

Reimplemented from itk::Object.

Definition at line 78 of file itkLightProcessObject.h.

typedef long itk::ImageIOBase::IndexValueType

inherited

Types for managing image size and image index components.

Reimplemented in itk::PhilipsRECImageIO.

Definition at line 71 of file itkImageIOBase.h.

typedef int itk::LightObject::InternalReferenceCountType

protectedinherited

Define the type of the reference count according to the target. This allows the use of atomic operations

Definition at line 137 of file itkLightObject.h.

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

Reimplemented from itk::StreamingImageIOBase.

Definition at line 60 of file itkMRCImageIO.h.

typedef MRCImageIO itk::MRCImageIO::Self

Standard class typedefs.

Reimplemented from itk::StreamingImageIOBase.

Definition at line 58 of file itkMRCImageIO.h.

typedef std::streamoff itk::ImageIOBase::SizeType

inherited

Type for representing size of bytes, and or positions along a file

Definition at line 253 of file itkImageIOBase.h.

typedef unsigned long itk::ImageIOBase::SizeValueType

inherited

Definition at line 75 of file itkImageIOBase.h.

typedef StreamingImageIOBase itk::MRCImageIO::Superclass

Reimplemented from itk::StreamingImageIOBase.

Definition at line 59 of file itkMRCImageIO.h.

Member Enumeration Documentation

enum itk::ImageIOBase::ByteOrder

inherited

Enums used to specify byte order; whether Big Endian or Little Endian. Some subclasses use this, some ignore it.

Enumerator:

BigEndian
LittleEndian
OrderNotApplicable

Reimplemented in otb::BSQImageIO, otb::LUMImageIO, otb::MWImageIO, and otb::RADImageIO.

Definition at line 207 of file itkImageIOBase.h.

enum itk::ImageIOBase::FileType

inherited

Enums used to specify write style: whether binary or ASCII. Some subclasses use this, some ignore it.

Enumerator:

ASCII
Binary
TypeNotApplicable

Definition at line 203 of file itkImageIOBase.h.

enum itk::ImageIOBase::IOComponentType

inherited

Enums used to manipulate the component type. The component type refers to the actual storage class associated with either a SCALAR pixel type or elements of a compound pixel.

Enumerator:

UNKNOWNCOMPONENTTYPE
UCHAR
CHAR
USHORT
SHORT
UINT
INT
ULONG
LONG
FLOAT
DOUBLE
CSHORT
CINT
CFLOAT
CDOUBLE

Definition at line 94 of file itkImageIOBase.h.

enum itk::ImageIOBase::IOPixelType

inherited

Enums used to manipulate the pixel type. The pixel type provides context for automatic data conversions (for instance, RGB to SCALAR, VECTOR to SCALAR).

Enumerator:

UNKNOWNPIXELTYPE
SCALAR
RGB
RGBA
OFFSET
VECTOR
POINT
COVARIANTVECTOR
SYMMETRICSECONDRANKTENSOR
DIFFUSIONTENSOR3D
COMPLEX
FIXEDARRAY
MATRIX

Definition at line 86 of file itkImageIOBase.h.

Constructor & Destructor Documentation

itk::MRCImageIO::MRCImageIO ( )

protected

Definition at line 39 of file itkMRCImageIO.cxx.

References itk::ImageIOBase::AddSupportedReadExtension(), itk::ImageIOBase::AddSupportedWriteExtension(), itk::ImageIOBase::SetFileTypeToBinary(), itk::ImageIOBase::SetNumberOfComponents(), and itk::ImageIOBase::SetNumberOfDimensions().

itk::MRCImageIO::MRCImageIO ( const Self & )

private

Member Function Documentation

virtual void itk::LightProcessObject::AbortGenerateDataOff ( )

virtualinherited

virtual void itk::LightProcessObject::AbortGenerateDataOn ( )

virtualinherited

Turn on and off the AbortGenerateData flag.

unsigned long itk::Object::AddObserver	(	const EventObject &	event,
		Command *	cmd
	)

inherited

Allow people to add/remove/invoke observers (callbacks) to any ITK object. This is an implementation of the subject/observer design pattern. An observer is added by specifying an event to respond to and an itk::Command to execute. It returns an unsigned long tag which can be used later to remove the event or retrieve the command. The memory for the Command becomes the responsibility of this object, so don't pass the same instance of a command to two different objects

Definition at line 389 of file itkObject.cxx.

References itk::SubjectImplementation::AddObserver().

Referenced by otb::StreamingImageVirtualWriter< TInputImage >::GenerateData(), itk::ProgressAccumulator::RegisterInternalFilter(), otb::ImageFileWriter< TInputImage >::Update(), and otb::WriterWatcherBase::WriterWatcherBase().

unsigned long itk::Object::AddObserver	(	const EventObject &	event,
		Command *	cmd
	)		const

inherited

Definition at line 401 of file itkObject.cxx.

References itk::SubjectImplementation::AddObserver().

void itk::ImageIOBase::AddSupportedReadExtension ( const char * extension )

protectedinherited

Insert an extension to the list of supported extensions for reading.

Definition at line 78 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_SupportedReadExtensions.

Referenced by itk::AnalyzeImageIO::AnalyzeImageIO(), itk::BioRadImageIO::BioRadImageIO(), itk::BMPImageIO::BMPImageIO(), otb::BSQImageIO::BSQImageIO(), itk::PNGImageIO::CanReadFile(), itk::JPEGImageIO::JPEGImageIO(), itk::LSMImageIO::LSMImageIO(), otb::LUMImageIO::LUMImageIO(), itk::MetaImageIO::MetaImageIO(), MRCImageIO(), otb::MWImageIO::MWImageIO(), itk::NiftiImageIO::NiftiImageIO(), otb::RADImageIO::RADImageIO(), itk::TIFFImageIO::TIFFImageIO(), otb::TileMapImageIO::TileMapImageIO(), and itk::VTKImageIO2::VTKImageIO2().

void itk::ImageIOBase::AddSupportedWriteExtension ( const char * extension )

protectedinherited

Insert an extension to the list of supported extensions for writing.

Definition at line 83 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_SupportedWriteExtensions.

Referenced by itk::AnalyzeImageIO::AnalyzeImageIO(), itk::BioRadImageIO::BioRadImageIO(), itk::BMPImageIO::BMPImageIO(), otb::BSQImageIO::BSQImageIO(), itk::PNGImageIO::CanReadFile(), itk::JPEGImageIO::JPEGImageIO(), itk::LSMImageIO::LSMImageIO(), otb::LUMImageIO::LUMImageIO(), itk::MetaImageIO::MetaImageIO(), MRCImageIO(), otb::MWImageIO::MWImageIO(), itk::NiftiImageIO::NiftiImageIO(), otb::RADImageIO::RADImageIO(), itk::TIFFImageIO::TIFFImageIO(), otb::TileMapImageIO::TileMapImageIO(), and itk::VTKImageIO2::VTKImageIO2().

void itk::LightObject::BreakOnError ( )

staticinherited

This method is called when itkExceptionMacro executes. It allows the debugger to break on error.

Definition at line 149 of file itkLightObject.cxx.

bool itk::MRCImageIO::CanReadFile ( const char * )

virtual

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

Implements itk::ImageIOBase.

Definition at line 58 of file itkMRCImageIO.cxx.

References itk::magicMAP, itk::StreamingImageIOBase::OpenFileForReading(), and itk::StreamingImageIOBase::ReadBufferAsBinary().

bool itk::StreamingImageIOBase::CanStreamRead ( void )

virtualinherited

Determine if the ImageIO can stream reading from this file. Default is false.

Reimplemented from itk::ImageIOBase.

Definition at line 306 of file itkStreamingImageIOBase.cxx.

bool itk::StreamingImageIOBase::CanStreamWrite ( void )

virtualinherited

Determine if the ImageIO can stream writing to this file. Default is false.

There are two types of non exclusive streaming: pasteing subregions, and iterative If true then

Reimplemented from itk::ImageIOBase.

Definition at line 311 of file itkStreamingImageIOBase.cxx.

bool itk::MRCImageIO::CanWriteFile ( const char * fname )

virtual

Returns true if this ImageIO can write the specified file.

The methods verifies that the file extension is known to be supported by this class.

Implements itk::ImageIOBase.

Definition at line 342 of file itkMRCImageIO.cxx.

void itk::ImageIOBase::ComputeStrides ( )

protectedinherited

Calculates the different strides (distance from one thing to the next). Upon return, strides[0] = bytes to get to the next component of a pixel, strides[1] = bytes to get to the next pixel in x direction, strides[2] = bytes to get to the next row in y direction, strides[3] = bytes to get to the next slice in z direction, etc.

Definition at line 540 of file itkImageIOBase.cxx.

References itk::ImageIOBase::GetComponentSize(), itk::ImageIOBase::m_Dimensions, itk::ImageIOBase::m_NumberOfComponents, itk::ImageIOBase::m_NumberOfDimensions, and itk::ImageIOBase::m_Strides.

Referenced by itk::MINC2ImageIO::ReadImageInformation(), itk::PhilipsRECImageIO::ReadImageInformation(), itk::AnalyzeImageIO::ReadImageInformation(), and itk::ImageIOBase::Resize().

virtual::itk::LightObject::Pointer itk::MRCImageIO::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::Object::DebugOff ( ) const

virtualinherited

Turn debugging output off.

Definition at line 253 of file itkObject.cxx.

void itk::Object::DebugOn ( ) const

virtualinherited

Turn debugging output on.

Definition at line 242 of file itkObject.cxx.

void itk::LightObject::Delete ( )

virtualinherited

Delete an itk object. This method should always be used to delete an object when the new operator was used to create it. Using the C delete method will not work with reference counting.

Delete a itk object. This method should always be used to delete an object when the new operator was used to create it. Using the C++ delete method will not work with reference counting.

Definition at line 88 of file itkLightObject.cxx.

virtual void itk::LightProcessObject::GenerateData ( void )

inlineprotectedvirtualinherited

This method causes the filter to generate its output.

Reimplemented in itk::ImageKmeansModelEstimator< TInputImage, TMembershipFunction >, itk::ClassifierBase< TDataContainer >, itk::ClassifierBase< TInputImage >, itk::ClassifierBase< TSample >, itk::ClassifierBase< itk::Statistics::ListSample< TInputImage::PixelType > >, itk::ImageClassifierBase< TInputImage, TClassifiedImage >, itk::LevelSetNeighborhoodExtractor< TLevelSet >, itk::ImageModelEstimatorBase< TInputImage, TMembershipFunction >, itk::ImageGaussianModelEstimator< TInputImage, TMembershipFunction, TTrainingImage >, itk::Statistics::SampleClassifier< TSample >, itk::Statistics::SampleClassifier< itk::Statistics::ListSample< TInputImage::PixelType > >, otb::SVMClassifier< TSample, TLabel >, itk::Statistics::SampleClassifierWithMask< TSample, TMaskSample >, and otb::SVMMarginSampler< TSample, TModel >.

Definition at line 121 of file itkLightProcessObject.h.

ImageIORegion itk::StreamingImageIOBase::GenerateStreamableReadRegionFromRequestedRegion ( const ImageIORegion & requested ) const

virtualinherited

Method for supporting streaming. Given a requested region, determine what could be the region that we can read from the file. This is called the streamable region, which will be equal or smaller than the LargestPossibleRegion (unless it was dimensionaly clipped) and greater or equal to the RequestedRegion

the resulting IORegion may be a greater dimensions the the requested IORegion, if the the derived class is unable to read the requested region. For example if the file has a size of [ 10, 10, 10] but the requested region is [10, 10] the return may be 3 dimensions.

Given a requested region, determine what could be the region that we can read from the file. This is called the streamable region, which will be smaller than the LargestPossibleRegion and greater or equal to the RequestedRegion

Reimplemented from itk::ImageIOBase.

Definition at line 420 of file itkStreamingImageIOBase.cxx.

References itk::ImageIOBase::m_Dimensions, itk::ImageIOBase::m_NumberOfDimensions, itk::ImageIOBase::m_UseStreamedReading, itk::ImageIORegion::SetIndex(), and itk::ImageIORegion::SetSize().

virtual const bool& itk::LightProcessObject::GetAbortGenerateData ( )

virtualinherited

Get the AbortGenerateData flag for the process object. Process objects may handle premature termination of execution in different ways.

unsigned int itk::StreamingImageIOBase::GetActualNumberOfSplitsForWriting	(	unsigned int	numberOfRequestedSplits,
		const ImageIORegion &	pasteRegion,
		const ImageIORegion &	largestPossibleRegion
	)

virtualinherited

Before this method is called all the configuration will be done, that is Streaming/PasteRegion/Compression/Filename etc If pasting is being used the number of requested splits is for that region not the largest. The derived ImageIO class should verify that the file is capable of being writen with this configuration. If pasted is enabled and is not support or does not work with the file, then an excepetion should be thrown.

The default implementation depends on CanStreamWrite. If false then 1 is returned (unless pasting is indicated), so that the whole file will be updated in one region. If true then its assumed that any arbitrary region can be writen to any file. So the users request will be respected. If a derived class has more restictive conditions then they should be checked

Reimplemented from itk::ImageIOBase.

Definition at line 318 of file itkStreamingImageIOBase.cxx.

References itk::LightProcessObject::CreateAnother(), itk::ImageIOBase::GetActualNumberOfSplitsForWritingCanStreamWrite(), itk::ImageIOBase::GetComponentType(), itk::ImageIOBase::GetDimensions(), itk::ImageIOBase::GetDirection(), itk::ImageIOBase::GetNumberOfComponents(), itk::ImageIOBase::GetNumberOfDimensions(), itk::ImageIOBase::GetOrigin(), itk::ImageIOBase::GetPixelType(), itk::SmartPointer< TObjectType >::GetPointer(), itk::ImageIOBase::GetSpacing(), and itk::ImageIOBase::m_FileName.

unsigned int itk::ImageIOBase::GetActualNumberOfSplitsForWritingCanStreamWrite	(	unsigned int	numberOfRequestedSplits,
		const ImageIORegion &	pasteRegion
	)		const

protectedvirtualinherited

an implementation of ImageRegionSplitter:GetNumberOfSplits

Reimplemented in otb::TileMapImageIO.

Definition at line 1093 of file itkImageIOBase.cxx.

References itk::ImageIORegion::GetImageDimension(), itk::ImageIORegion::GetSize(), and itk::value_type().

Referenced by itk::StreamingImageIOBase::GetActualNumberOfSplitsForWriting(), itk::MetaImageIO::GetActualNumberOfSplitsForWriting(), and itk::ImageIOBase::GetActualNumberOfSplitsForWriting().

virtual ByteOrder itk::ImageIOBase::GetByteOrder ( ) const

virtualinherited

Referenced by itk::NrrdImageIO::Write().

std::string itk::ImageIOBase::GetByteOrderAsString ( ByteOrder t ) const

inherited

Convenience method returns the ByteOrder as a string. This can be used for writing output files.

Definition at line 739 of file itkImageIOBase.cxx.

References itk::ImageIOBase::BigEndian, itk::ImageIOBase::LittleEndian, and itk::ImageIOBase::OrderNotApplicable.

Referenced by otb::ONERAImageIO::InternalReadImageInformation(), otb::ONERAImageIO::InternalWriteImageInformation(), and itk::ImageIOBase::PrintSelf().

Command * itk::Object::GetCommand ( unsigned long tag )

inherited

Get the command associated with the given tag. NOTE: This returns a pointer to a Command, but it is safe to asign this to a Command::Pointer. Since Command inherits from LightObject, at this point in the code, only a pointer or a reference to the Command can be used.

Definition at line 414 of file itkObject.cxx.

References itk::Object::GetCommand(), and NULL.

Referenced by itk::Object::GetCommand().

unsigned int itk::ImageIOBase::GetComponentSize ( ) const

virtualinherited

Compute the size (in bytes) of the components of a pixel. For example, and RGB pixel of unsigned char would have a component size of 1 byte. This method can be invoked only after the component type is set.

Reimplemented in itk::IPLCommonImageIO.

Definition at line 683 of file itkImageIOBase.cxx.

References itk::ImageIOBase::CDOUBLE, itk::ImageIOBase::CFLOAT, itk::ImageIOBase::CHAR, itk::ImageIOBase::CINT, itk::ImageIOBase::CSHORT, itk::ImageIOBase::DOUBLE, itk::ImageIOBase::FLOAT, itk::ImageIOBase::INT, itk::ImageIOBase::LONG, itk::ImageIOBase::m_ComponentType, itk::ImageIOBase::SHORT, itk::ImageIOBase::UCHAR, itk::ImageIOBase::UINT, itk::ImageIOBase::ULONG, itk::ImageIOBase::UNKNOWNCOMPONENTTYPE, and itk::ImageIOBase::USHORT.

Referenced by itk::ImageIOBase::ComputeStrides(), itk::ImageIOBase::GetPixelSize(), otb::ONERAImageIO::InternalReadImageInformation(), itk::VTKImageIO::Read(), itk::VTKImageIO2::Read(), otb::RADImageIO::Read(), otb::LUMImageIO::Read(), otb::MWImageIO::Read(), otb::BSQImageIO::Read(), otb::JPEG2000ImageIO::ReadImageInformation(), otb::MWImageIO::ReadImageInformation(), otb::RADImageIO::ReadImageInformation(), otb::LUMImageIO::ReadImageInformation(), otb::BSQImageIO::ReadImageInformation(), itk::VTKImageIO::Write(), itk::VTKImageIO2::Write(), otb::MWImageIO::Write(), otb::RADImageIO::Write(), otb::LUMImageIO::Write(), otb::BSQImageIO::Write(), otb::LUMImageIO::WriteImageInformation(), otb::RADImageIO::WriteImageInformation(), otb::MWImageIO::WriteImageInformation(), otb::BSQImageIO::WriteImageInformation(), and otb::JPEG2000ImageIO::WriteImageInformation().

ImageIOBase::SizeType itk::ImageIOBase::GetComponentStride ( ) const

protectedinherited

Convenient method for accessing number of bytes to get to the next pixel component. Returns m_Strides[0].

Definition at line 584 of file itkImageIOBase.cxx.

virtual IOComponentType itk::ImageIOBase::GetComponentType ( ) const

virtualinherited

std::string itk::ImageIOBase::GetComponentTypeAsString ( IOComponentType t ) const

inherited

Convenience method returns the IOComponentType as a string. This can be used for writing output files.

Definition at line 755 of file itkImageIOBase.cxx.

References itk::ImageIOBase::CDOUBLE, itk::ImageIOBase::CFLOAT, itk::ImageIOBase::CHAR, itk::ImageIOBase::CINT, itk::ImageIOBase::CSHORT, itk::ImageIOBase::DOUBLE, itk::ImageIOBase::FLOAT, itk::ImageIOBase::INT, itk::ImageIOBase::LONG, itk::ImageIOBase::SHORT, itk::ImageIOBase::UCHAR, itk::ImageIOBase::UINT, itk::ImageIOBase::ULONG, itk::ImageIOBase::UNKNOWNCOMPONENTTYPE, and itk::ImageIOBase::USHORT.

Referenced by otb::ONERAImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalReadImageInformation(), itk::GDCMImageIO::PrintSelf(), itk::ImageIOBase::PrintSelf(), itk::NiftiImageIO::Read(), UpdateHeaderFromImageIO(), itk::VTKImageIO::Write(), otb::RADImageIO::WriteImageInformation(), and itk::VTKImageIO2::WriteImageInformation().

const std::type_info & itk::ImageIOBase::GetComponentTypeInfo ( ) const

virtualinherited

Reimplemented in itk::IPLCommonImageIO.

Definition at line 183 of file itkImageIOBase.cxx.

References itk::ImageIOBase::CDOUBLE, itk::ImageIOBase::CFLOAT, itk::ImageIOBase::CHAR, itk::ImageIOBase::CINT, itk::ImageIOBase::CSHORT, itk::ImageIOBase::DOUBLE, itk::ImageIOBase::FLOAT, itk::ImageIOBase::INT, itk::ImageIOBase::LONG, itk::ImageIOBase::m_ComponentType, itk::ImageIOBase::SHORT, itk::ImageIOBase::UCHAR, itk::ImageIOBase::UINT, itk::ImageIOBase::ULONG, itk::ImageIOBase::UNKNOWNCOMPONENTTYPE, and itk::ImageIOBase::USHORT.

virtual SizeType itk::StreamingImageIOBase::GetDataPosition ( void ) const

inlineprotectedvirtualinherited

Returns the byte offset into the file where the data is located.

The default implementation is to return the header size.

Definition at line 153 of file itkStreamingImageIOBase.h.

Referenced by itk::StreamingImageIOBase::StreamWriteBufferAsBinary().

bool itk::Object::GetDebug ( ) const

inherited

Get the value of the debug flag.

Definition at line 264 of file itkObject.cxx.

Referenced by otb::ogr::ImageReference< double >::GetDebug().

std::vector< double > itk::ImageIOBase::GetDefaultDirection ( unsigned int k ) const

virtualinherited

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

Return the directions that this particular ImageIO would use by default in the case the recipient image dimension is smaller than the dimension of the image in file.

Reimplemented in itk::AnalyzeImageIO.

Definition at line 1276 of file itkImageIOBase.cxx.

Referenced by itk::AnalyzeImageIO::GetDefaultDirection().

virtual unsigned int itk::ImageIOBase::GetDimensions ( unsigned int i ) const

inlinevirtualinherited

Definition at line 107 of file itkImageIOBase.h.

Referenced by itk::StreamingImageIOBase::GetActualNumberOfSplitsForWriting(), itk::MetaImageIO::GetActualNumberOfSplitsForWriting(), itk::NrrdImageIO::Read(), itk::MetaImageIO::Read(), itk::MINC2ImageIO::Read(), itk::StreamingImageIOBase::RequestedToStream(), itk::MINC2ImageIO::SetSliceScalingFromLocalScaling(), itk::StreamingImageIOBase::StreamWriteBufferAsBinary(), itk::NrrdImageIO::Write(), itk::VTKImageIO::Write(), itk::MINC2ImageIO::Write(), itk::VTKImageIO2::WriteImageInformation(), and itk::PNGImageIO::WriteSlice().

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

inlinevirtualinherited

Reimplemented in itk::AnalyzeImageIO.

Definition at line 130 of file itkImageIOBase.h.

Referenced by itk::StreamingImageIOBase::GetActualNumberOfSplitsForWriting(), itk::MetaImageIO::GetActualNumberOfSplitsForWriting(), itk::AnalyzeImageIO::GetDirection(), itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(), and itk::NrrdImageIO::Write().

virtual const char* itk::ImageIOBase::GetFileName ( ) const

virtualinherited

Referenced by itk::MetaImageIO::GetActualNumberOfSplitsForWriting(), itk::ImageIOBase::GetActualNumberOfSplitsForWriting(), itk::TIFFImageIO::InternalWrite(), itk::PNGImageIO::Read(), itk::JPEGImageIO::Read(), itk::NrrdImageIO::Read(), itk::MetaImageIO::Read(), itk::NiftiImageIO::Read(), itk::BMPImageIO::ReadImageInformation(), itk::NrrdImageIO::ReadImageInformation(), itk::JPEGImageIO::ReadImageInformation(), itk::MetaImageIO::ReadImageInformation(), itk::IPLCommonImageIO::ReadImageInformation(), itk::AnalyzeImageIO::ReadImageInformation(), itk::NiftiImageIO::SetImageIOMetadataFromNIfTI(), itk::NrrdImageIO::Write(), and itk::PNGImageIO::WriteSlice().

virtual FileType itk::ImageIOBase::GetFileType ( ) const

virtualinherited

Referenced by itk::VTKImageIO::InternalReadImageInformation(), itk::VTKImageIO2::InternalReadImageInformation(), itk::NrrdImageIO::Write(), itk::VTKImageIO::Write(), and itk::VTKImageIO2::WriteImageInformation().

std::string itk::ImageIOBase::GetFileTypeAsString ( FileType t ) const

inherited

Convenience method returns the FileType as a string. This can be used for writing output files.

Definition at line 723 of file itkImageIOBase.cxx.

References itk::ImageIOBase::ASCII, itk::ImageIOBase::Binary, and itk::ImageIOBase::TypeNotApplicable.

Referenced by itk::ImageIOBase::PrintSelf().

bool itk::Object::GetGlobalWarningDisplay ( )

staticinherited

Get the value of the global debug output control flag.

Definition at line 381 of file itkObject.cxx.

MRCImageIO::SizeType itk::MRCImageIO::GetHeaderSize ( void ) const

protectedvirtual

Overloaded to return the actually header size of the file specified. The header must be read before this methods is called.

Implements itk::StreamingImageIOBase.

Definition at line 104 of file itkMRCImageIO.cxx.

References itk::SmartPointer< TObjectType >::IsNull(), and m_MRCHeader.

ImageIOBase::SizeType itk::ImageIOBase::GetImageSizeInBytes ( ) const

inherited

Return the number of bytes in the image.

Definition at line 577 of file itkImageIOBase.cxx.

Referenced by itk::BioRadImageIO::Read(), itk::GiplImageIO::Read(), itk::VTKImageIO::Read(), itk::VTKImageIO2::Read(), itk::VoxBoCUBImageIO::Read(), itk::StimulateImageIO::Read(), itk::PhilipsRECImageIO::Read(), itk::AnalyzeImageIO::Read(), itk::Bruker2DSEQImageIO::Read(), itk::DICOMImageIO2::ReadDataCallback(), itk::BioRadImageIO::Write(), itk::VTKImageIO::Write(), itk::VTKImageIO2::Write(), itk::StimulateImageIO::Write(), and itk::GDCMImageIO::Write().

ImageIOBase::SizeType itk::ImageIOBase::GetImageSizeInComponents ( ) const

inherited

Return the number of pixels times the number of components in the image.

Definition at line 570 of file itkImageIOBase.cxx.

Referenced by itk::BioRadImageIO::Read(), itk::VTKImageIO::Read(), itk::VTKImageIO2::Read(), itk::NiftiImageIO::Read(), itk::StimulateImageIO::Read(), itk::BioRadImageIO::Write(), itk::VTKImageIO::Write(), itk::VTKImageIO2::Write(), and itk::StimulateImageIO::Write().

ImageIOBase::SizeType itk::ImageIOBase::GetImageSizeInPixels ( ) const

inherited

Return the number of pixels in the image.

Definition at line 555 of file itkImageIOBase.cxx.

Referenced by itk::MetaImageIO::Read(), itk::AnalyzeImageIO::Read(), itk::VTKImageIO::Write(), and itk::VTKImageIO2::WriteImageInformation().

virtual const ImageIORegion& itk::ImageIOBase::GetIORegion ( )

virtualinherited

MetaDataDictionary & itk::Object::GetMetaDataDictionary ( void )

inherited

Returns:: A reference to this objects MetaDataDictionary.

Warning:: This reference may be changed.

Reimplemented in otb::ImageMetadataInterfaceBase.

Definition at line 532 of file itkObject.cxx.

References NULL.

const MetaDataDictionary & itk::Object::GetMetaDataDictionary ( void ) const

inherited

Returns:: A constant reference to this objects MetaDataDictionary.

Reimplemented in otb::ImageMetadataInterfaceBase.

Definition at line 543 of file itkObject.cxx.

References NULL.

unsigned long itk::Object::GetMTime ( void ) const

virtualinherited

Return this objects modified time.

Return the modification for this object.

Definition at line 286 of file itkObject.cxx.

Referenced by itk::DeformationFieldSource< TOutputImage >::GetMTime(), itk::BoundingBox< TPointIdentifier, VPointDimension, TCoordRep, TPointsContainer >::GetMTime(), itk::InverseDeformationFieldImageFilter< TInputImage, TOutputImage >::GetMTime(), itk::TransformToDeformationFieldSource< TOutputImage, TTransformPrecisionType >::GetMTime(), itk::VectorResampleImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType >::GetMTime(), itk::SpatialObject< TDimension >::GetMTime(), itk::ResampleImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType >::GetMTime(), itk::SpatialObject< ::itk::GetMeshDimension< TMesh >::PointDimension >::GetObjectMTime(), otb::Function::NoStretchRenderingFunction< TPixel, TRGBPixel, TPixelRepresentationFunction, TTransferFunction >::Initialize(), otb::Function::StandardRenderingFunction< TPixel, TRGBPixel, TPixelRepresentationFunction, TTransferFunction >::Initialize(), itk::VTKImageExportBase::PipelineModifiedCallback(), and itk::ProcessObject::UpdateOutputInformation().

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::StreamingImageIOBase.

Referenced by ReadImageInformation().

virtual const unsigned int& itk::ImageIOBase::GetNumberOfComponents ( )

virtualinherited

virtual unsigned int itk::ImageIOBase::GetNumberOfDimensions ( ) const

virtualinherited

Referenced by itk::Brains2MaskImageIO::CanReadFile(), itk::ImageSeriesReader< TOutputImage >::ComputeMovingDimensionIndex(), itk::StreamingImageIOBase::GetActualNumberOfSplitsForWriting(), itk::MetaImageIO::GetActualNumberOfSplitsForWriting(), itk::VTKImageIO2::InternalReadImageInformation(), itk::PNGImageIO::Read(), itk::GiplImageIO::Read(), itk::NrrdImageIO::Read(), otb::ONERAImageIO::Read(), itk::MetaImageIO::Read(), itk::NiftiImageIO::Read(), itk::PhilipsRECImageIO::Read(), itk::Bruker2DSEQImageIO::Read(), itk::MetaImageIO::ReadImageInformation(), itk::AnalyzeImageIO::ReadImageInformation(), itk::Bruker2DSEQImageIO::ReadImageInformation(), itk::StreamingImageIOBase::RequestedToStream(), UpdateHeaderFromImageIO(), itk::BioRadImageIO::Write(), itk::VTKImageIO::Write(), itk::NrrdImageIO::Write(), itk::JPEGImageIO::Write(), itk::StimulateImageIO::Write(), and itk::VTKImageIO2::WriteImageInformation().

virtual double itk::ImageIOBase::GetOrigin ( unsigned int i ) const

inlinevirtualinherited

Definition at line 113 of file itkImageIOBase.h.

Referenced by itk::StreamingImageIOBase::GetActualNumberOfSplitsForWriting(), itk::MetaImageIO::GetActualNumberOfSplitsForWriting(), otb::TileMapImageIO::GetActualNumberOfSplitsForWritingCanStreamWrite(), otb::TileMapImageIO::GetSplitRegionForWritingCanStreamWrite(), itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(), itk::NrrdImageIO::Write(), itk::MINC2ImageIO::Write(), otb::TileMapImageIO::Write(), and itk::VTKImageIO2::WriteImageInformation().

unsigned int itk::ImageIOBase::GetPixelSize ( ) const

protectedvirtualinherited

Compute the size (in bytes) of the pixel. For example, and RGB pixel of unsigned char would have size 3 bytes.

Definition at line 669 of file itkImageIOBase.cxx.

References itk::ImageIOBase::GetComponentSize(), itk::ImageIOBase::GetNumberOfComponents(), itk::ImageIOBase::m_ComponentType, itk::ImageIOBase::m_PixelType, itk::ImageIOBase::UNKNOWNCOMPONENTTYPE, and itk::ImageIOBase::UNKNOWNPIXELTYPE.

Referenced by otb::JPEG2000ImageIO::ReadImageInformation(), otb::MWImageIO::ReadImageInformation(), otb::RADImageIO::ReadImageInformation(), otb::LUMImageIO::ReadImageInformation(), otb::BSQImageIO::ReadImageInformation(), itk::StreamingImageIOBase::StreamWriteBufferAsBinary(), otb::LUMImageIO::WriteImageInformation(), otb::RADImageIO::WriteImageInformation(), otb::MWImageIO::WriteImageInformation(), otb::BSQImageIO::WriteImageInformation(), and otb::JPEG2000ImageIO::WriteImageInformation().

ImageIOBase::SizeType itk::ImageIOBase::GetPixelStride ( ) const

virtualinherited

Convenient method for accessing the number of bytes to get to the next pixel. Returns m_Strides[1];

Please note that this methods depends the private methods ComputeStrides being called, otherwise this is the incorrect value.

Definition at line 591 of file itkImageIOBase.cxx.

virtual IOPixelType itk::ImageIOBase::GetPixelType ( ) const

virtualinherited

Referenced by itk::AnalyzeImageIO::DefineHeaderObjectDataType(), itk::StreamingImageIOBase::GetActualNumberOfSplitsForWriting(), itk::MetaImageIO::GetActualNumberOfSplitsForWriting(), otb::ONERAImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalWriteImageInformation(), itk::NrrdImageIO::Read(), itk::NiftiImageIO::Read(), itk::ImageIOBase::SetPixelTypeInfo(), UpdateHeaderFromImageIO(), itk::NrrdImageIO::Write(), itk::VTKImageIO::Write(), and itk::VTKImageIO2::WriteImageInformation().

std::string itk::ImageIOBase::GetPixelTypeAsString ( IOPixelType t ) const

inherited

Convenience method returns the IOPixelType as a string. This can be used for writing output files.

Definition at line 796 of file itkImageIOBase.cxx.

References itk::ImageIOBase::COMPLEX, itk::ImageIOBase::COVARIANTVECTOR, itk::ImageIOBase::DIFFUSIONTENSOR3D, itk::ImageIOBase::OFFSET, itk::ImageIOBase::POINT, itk::ImageIOBase::RGB, itk::ImageIOBase::RGBA, itk::ImageIOBase::SCALAR, itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR, itk::ImageIOBase::UNKNOWNPIXELTYPE, and itk::ImageIOBase::VECTOR.

Referenced by otb::ONERAImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalWriteImageInformation(), itk::ImageIOBase::PrintSelf(), UpdateHeaderFromImageIO(), and otb::RADImageIO::WriteImageInformation().

virtual const float& itk::LightProcessObject::GetProgress ( )

virtualinherited

Get the execution progress of a process object. The progress is a floating number between (0,1), 0 meaning no progress; 1 meaning the filter has completed execution.

virtual int itk::LightObject::GetReferenceCount ( ) const

inlinevirtualinherited

Gets the reference count on this object.

Definition at line 105 of file itkLightObject.h.

ImageIOBase::SizeType itk::ImageIOBase::GetRowStride ( ) const

protectedinherited

Convenient method for accessing the number of bytes to get to the next row. Returns m_Strides[2].

Definition at line 598 of file itkImageIOBase.cxx.

ImageIOBase::SizeType itk::ImageIOBase::GetSliceStride ( ) const

protectedinherited

Convenient method for accessing the number of bytes to get to the next slice. Returns m_Strides[3].

Definition at line 605 of file itkImageIOBase.cxx.

virtual double itk::ImageIOBase::GetSpacing ( unsigned int i ) const

inlinevirtualinherited

Definition at line 121 of file itkImageIOBase.h.

Referenced by itk::StreamingImageIOBase::GetActualNumberOfSplitsForWriting(), itk::MetaImageIO::GetActualNumberOfSplitsForWriting(), itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(), itk::NrrdImageIO::Write(), itk::MINC2ImageIO::Write(), and itk::VTKImageIO2::WriteImageInformation().

ImageIORegion itk::ImageIOBase::GetSplitRegionForWriting	(	unsigned int	ithPiece,
		unsigned int	numberOfActualSplits,
		const ImageIORegion &	pasteRegion,
		const ImageIORegion &	largestPossibleRegion
	)

virtualinherited

returns the ith IORegion

numberOfActualSplits should be the value returned from GetActualNumberOfSplitsForWriting with the same parameters

Derieved classes should overload this method to return a compatible region

Reimplemented in itk::MetaImageIO.

Definition at line 1200 of file itkImageIOBase.cxx.

References itk::ImageIOBase::CanStreamWrite(), and itk::ImageIOBase::GetSplitRegionForWritingCanStreamWrite().

ImageIORegion itk::ImageIOBase::GetSplitRegionForWritingCanStreamWrite	(	unsigned int	ithPiece,
		unsigned int	numberOfActualSplits,
		const ImageIORegion &	pasteRegion
	)		const

protectedvirtualinherited

an implementation of ImageRegionSplitter:GetSplit

Reimplemented in otb::TileMapImageIO.

Definition at line 1143 of file itkImageIOBase.cxx.

References itk::ImageIORegion::GetImageDimension(), itk::ImageIORegion::GetIndex(), itk::ImageIORegion::GetSize(), itk::ImageIORegion::SetIndex(), itk::ImageIORegion::SetSize(), and itk::value_type().

Referenced by itk::MetaImageIO::GetSplitRegionForWriting(), and itk::ImageIOBase::GetSplitRegionForWriting().

const ImageIOBase::ArrayOfExtensionsType & itk::ImageIOBase::GetSupportedReadExtensions ( ) const

inherited

This method returns an array with the list of filename extensions supported for reading by this ImageIO class. This is intended to facilitate GUI and application level integration.

Definition at line 73 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_SupportedReadExtensions.

const ImageIOBase::ArrayOfExtensionsType & itk::ImageIOBase::GetSupportedWriteExtensions ( ) const

inherited

This method returns an array with the list of filename extensions supported for writing by this ImageIO class. This is intended to facilitate GUI and application level integration.

Definition at line 67 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_SupportedWriteExtensions.

virtual bool itk::ImageIOBase::GetUseCompression ( ) const

virtualinherited

Referenced by itk::MetaImageIO::GetActualNumberOfSplitsForWriting(), and itk::NrrdImageIO::Write().

virtual bool itk::ImageIOBase::GetUseStreamedReading ( ) const

virtualinherited

virtual bool itk::ImageIOBase::GetUseStreamedWriting ( ) const

virtualinherited

static void itk::Object::GlobalWarningDisplayOff ( )

inlinestaticinherited

Definition at line 100 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

Referenced by itk::OutputWindow::DisplayText(), itk::Win32OutputWindow::PromptText(), and itk::Win32OutputWindow::WndProc().

static void itk::Object::GlobalWarningDisplayOn ( )

inlinestaticinherited

Definition at line 98 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

bool itk::Object::HasObserver ( const EventObject & event ) const

inherited

Return true if an observer is registered for this event.

Definition at line 467 of file itkObject.cxx.

void itk::MRCImageIO::InternalReadImageInformation ( std::ifstream & is )

private

Definition at line 236 of file itkMRCImageIO.cxx.

References itk::ImageIOBase::m_FileName, m_MRCHeader, New(), itk::StreamingImageIOBase::OpenFileForReading(), and itk::StreamingImageIOBase::ReadBufferAsBinary().

Referenced by ReadImageInformation().

void itk::Object::InvokeEvent ( const EventObject & event )

inherited

Call Execute on all the Commands observing this event id.

Definition at line 446 of file itkObject.cxx.

Referenced by otb::Wrapper::Application::AddProcess(), itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::IterateThreaderCallback(), and itk::VTKImageExportBase::UpdateDataCallback().

void itk::Object::InvokeEvent ( const EventObject & event ) const

inherited

Call Execute on all the Commands observing this event id. The actions triggered by this call doesn't modify this object.

Definition at line 457 of file itkObject.cxx.

void itk::Object::Modified ( void ) const

virtualinherited

Update the modification time for this object. Many filters rely on the modification time to determine if they need to recompute their data.

Make sure this object's modified time is greater than all others.

Definition at line 297 of file itkObject.cxx.

static Pointer itk::MRCImageIO::New ( )

static

Method for creation through the object factory.

Reimplemented from itk::LightProcessObject.

Referenced by InternalReadImageInformation(), and UpdateHeaderFromImageIO().

void itk::StreamingImageIOBase::OpenFileForReading	(	std::ifstream &	os,
		const char *	filename
	)

protectedvirtualinherited

Opens a file for reading and random access.

The stream is closed if it's already opened. If an error is encountered then an exception will be thrown.

Definition at line 246 of file itkStreamingImageIOBase.cxx.

Referenced by itk::VTKImageIO2::CanReadFile(), CanReadFile(), itk::VTKImageIO2::InternalReadImageInformation(), InternalReadImageInformation(), itk::VTKImageIO2::Read(), and itk::VTKImageIO2::ReadHeaderSize().

void itk::StreamingImageIOBase::OpenFileForWriting	(	std::ofstream &	os,
		const char *	filename,
		bool	truncate
	)

protectedvirtualinherited

Opens a file for writing and random access.

Parameters:

truncate if true then the file is truncated

The stream is closed if it's already opened. If an error is encountered then an exception will be thrown.

Definition at line 271 of file itkStreamingImageIOBase.cxx.

References itk::ImageIOBase::m_FileName.

Referenced by itk::VTKImageIO2::Write(), itk::VTKImageIO2::WriteImageInformation(), and WriteImageInformation().

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

private

Reimplemented from itk::StreamingImageIOBase.

void itk::LightObject::Print	(	std::ostream &	os,
		Indent	indent = `0`
	)		const

inherited

Cause the object to print itself out.

Avoid DLL boundary problems. This function will be common to all itk objects. It just calls the header/self/trailer virtual print methods, which can be overriden by subclasses (any itk object).

Definition at line 135 of file itkLightObject.cxx.

References itk::Indent::GetNextIndent().

Referenced by itk::operator<<().

void itk::LightObject::PrintHeader	(	std::ostream &	os,
		Indent	indent
	)		const

protectedvirtualinherited

Define a default print header for all objects.

Definition at line 320 of file itkLightObject.cxx.

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

protectedinherited

Definition at line 478 of file itkObject.cxx.

void itk::MRCImageIO::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.

Chaining method to print an object's instance variables, as well as its superclasses.

Reimplemented from itk::StreamingImageIOBase.

Definition at line 53 of file itkMRCImageIO.cxx.

References itk::StreamingImageIOBase::PrintSelf().

void itk::LightObject::PrintTrailer	(	std::ostream &	os,
		Indent	indent
	)		const

protectedvirtualinherited

Define a default print trailer for all objects.

Definition at line 331 of file itkLightObject.cxx.

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

virtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

Definition at line 288 of file itkMRCImageIO.cxx.

References itk::ByteSwapper< T >::SwapRangeFromSystemToBigEndian(), and itk::ByteSwapper< T >::SwapRangeFromSystemToLittleEndian().

void itk::ImageIOBase::ReadBufferAsASCII	(	std::istream &	os,
		void *	buffer,
		IOComponentType	ctype,
		ImageIOBase::SizeType	numComp
	)

protectedinherited

Convenient method to read a buffer as ASCII text.

Definition at line 981 of file itkImageIOBase.cxx.

References itk::ImageIOBase::CDOUBLE, itk::ImageIOBase::CFLOAT, itk::ImageIOBase::CHAR, itk::ImageIOBase::CINT, itk::ImageIOBase::CSHORT, itk::ImageIOBase::DOUBLE, itk::ImageIOBase::FLOAT, itk::ImageIOBase::INT, itk::ImageIOBase::LONG, itk::ReadBuffer(), itk::ImageIOBase::SHORT, itk::ImageIOBase::UCHAR, itk::ImageIOBase::UINT, itk::ImageIOBase::ULONG, and itk::ImageIOBase::USHORT.

Referenced by itk::VTKImageIO::Read(), and itk::VTKImageIO2::Read().

bool itk::StreamingImageIOBase::ReadBufferAsBinary	(	std::istream &	is,
		void *	buffer,
		StreamingImageIOBase::SizeType	num
	)

protectedvirtualinherited

Reimplemented from super class to get around 2GB read/write limitation.

Todo:: Move this method to itk::ImageIOBase

Reimplemented from itk::ImageIOBase.

Definition at line 117 of file itkStreamingImageIOBase.cxx.

References itk::ImageIOBase::m_FileName.

Referenced by CanReadFile(), InternalReadImageInformation(), and itk::VTKImageIO2::Read().

void itk::MRCImageIO::ReadImageInformation ( )

virtual

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

Implements itk::ImageIOBase.

Definition at line 114 of file itkMRCImageIO.cxx.

void itk::Object::Register ( ) const

virtualinherited

Increase the reference count (mark as used by another object).

Reimplemented from itk::LightObject.

Definition at line 309 of file itkObject.cxx.

Referenced by itk::ObjectFactoryBase::RegisterFactory().

void itk::Object::RemoveAllObservers ( )

inherited

Remove all observers .

Definition at line 435 of file itkObject.cxx.

void itk::Object::RemoveObserver ( unsigned long tag )

inherited

Remove the observer with this tag value.

Definition at line 425 of file itkObject.cxx.

Referenced by otb::StreamingImageVirtualWriter< TInputImage >::GenerateData(), and otb::ImageFileWriter< TInputImage >::Update().

bool itk::StreamingImageIOBase::RequestedToStream ( void ) const

protectedvirtualinherited

Returns true if GetIORegion is not the same size as the largest region give by GetNumberOfDimensions.

This compares the IORegion to the size of the image in the file. With out regaurd to the dimensions of either, if the images represent the same region then false is returned.

Definition at line 443 of file itkStreamingImageIOBase.cxx.

References itk::ImageIOBase::GetDimensions(), itk::ImageIOBase::GetIORegion(), itk::ImageIOBase::GetNumberOfDimensions(), itk::ImageIORegion::SetIndex(), and itk::ImageIORegion::SetSize().

Referenced by itk::VTKImageIO2::Read(), and itk::VTKImageIO2::Write().

void itk::ImageIOBase::Reset ( const bool freeDynamic = true )

protectedvirtualinherited

Return the object to an initialized state, ready to be used

Definition at line 46 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_Dimensions, itk::ImageIOBase::m_FileName, itk::ImageIOBase::m_Initialized, itk::ImageIOBase::m_NumberOfComponents, itk::ImageIOBase::m_NumberOfDimensions, itk::ImageIOBase::m_Strides, itk::ImageIOBase::m_UseCompression, itk::ImageIOBase::m_UseStreamedReading, and itk::ImageIOBase::m_UseStreamedWriting.

Referenced by itk::ImageIOBase::ImageIOBase().

void itk::ImageIOBase::Resize	(	const unsigned int	numDimensions,
		const unsigned int *	dimensions
	)

protectedinherited

Resize the ImageIOBase object to new dimensions.

Definition at line 88 of file itkImageIOBase.cxx.

References itk::ImageIOBase::ComputeStrides(), itk::ImageIOBase::m_Dimensions, itk::ImageIOBase::m_NumberOfDimensions, and NULL.

virtual void itk::LightProcessObject::SetAbortGenerateData ( bool _arg )

virtualinherited

Set the AbortGenerateData flag for the process object. Process objects may handle premature termination of execution in different ways.

virtual void itk::ImageIOBase::SetByteOrder ( const ByteOrder _arg )

virtualinherited

These methods indicate the byte ordering of the file you are trying to read in. These methods will then either swap or not swap the bytes depending on the byte ordering of the machine it is being run on. For example, reading in a BigEndian file on a BigEndian machine will result in no swapping. Trying to read the same file on a LittleEndian machine will result in swapping. Note: most UNIX machines are BigEndian while PC's and VAX's are LittleEndian. So if the file you are reading in was generated on a VAX or PC, SetByteOrderToLittleEndian() otherwise SetByteOrderToBigEndian(). Some ImageIOBase subclasses ignore these methods.

Referenced by itk::NrrdImageIO::ReadImageInformation().

void itk::ImageIOBase::SetByteOrderToBigEndian ( )

inlineinherited

Definition at line 235 of file itkImageIOBase.h.

Referenced by itk::NrrdImageIO::ReadImageInformation(), itk::VoxBoCUBImageIO::ReadImageInformation(), and ReadImageInformation().

void itk::ImageIOBase::SetByteOrderToLittleEndian ( )

inlineinherited

Definition at line 239 of file itkImageIOBase.h.

Referenced by itk::NrrdImageIO::ReadImageInformation(), itk::VoxBoCUBImageIO::ReadImageInformation(), and ReadImageInformation().

virtual void itk::ImageIOBase::SetComponentType ( const IOComponentType _arg )

virtualinherited

Set/Get the component type of the image. This is always a native type.

Referenced by otb::LUMImageIO::InternalReadHeaderInformation(), otb::BSQImageIO::InternalReadHeaderInformation(), otb::RADImageIO::InternalReadHeaderInformation(), otb::MWImageIO::InternalReadHeaderInformation(), itk::VTKImageIO::InternalReadImageInformation(), itk::BioRadImageIO::InternalReadImageInformation(), itk::VTKImageIO2::InternalReadImageInformation(), itk::StimulateImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalReadImageInformation(), itk::GDCMImageIO::InternalReadImageInformation(), itk::itkSetPixelType(), itk::DICOMImageIO2::ReadImageInformation(), otb::MSTARImageIO::ReadImageInformation(), itk::NrrdImageIO::ReadImageInformation(), otb::JPEG2000ImageIO::ReadImageInformation(), itk::MetaImageIO::ReadImageInformation(), itk::MINC2ImageIO::ReadImageInformation(), ReadImageInformation(), otb::TileMapImageIO::ReadImageInformation(), itk::VTKImageIO2::SetPixelTypeFromString(), and itk::ImageIOBase::SetPixelTypeInfo().

void itk::Object::SetDebug ( bool debugFlag ) const

inherited

Set the value of the debug flag. A non-zero value turns debugging on.

Definition at line 275 of file itkObject.cxx.

void itk::ImageIOBase::SetDimensions	(	unsigned int	i,
		unsigned int	dim
	)

virtualinherited

Set/Get the image dimensions in the x, y, z, etc. directions. GetDimensions() is typically used after reading the data; the SetDimensions() is used prior to writing the data.

Definition at line 102 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_Dimensions, and itk::Object::Modified().

Referenced by itk::VTKImageIO2::InternalReadImageInformation(), itk::DICOMImageIO2::ReadImageInformation(), itk::NrrdImageIO::ReadImageInformation(), itk::MetaImageIO::ReadImageInformation(), itk::MINC2ImageIO::ReadImageInformation(), itk::IPLCommonImageIO::ReadImageInformation(), itk::PhilipsRECImageIO::ReadImageInformation(), itk::AnalyzeImageIO::ReadImageInformation(), and itk::Bruker2DSEQImageIO::ReadImageInformation().

void itk::ImageIOBase::SetDirection	(	unsigned int	i,
		std::vector< double > &	direction
	)

virtualinherited

Set/Get the image direction on an axis-by-axis basis. The SetDirection() method is required when writing the image.

Definition at line 147 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_Direction, and itk::Object::Modified().

void itk::ImageIOBase::SetDirection	(	unsigned int	i,
		vnl_vector< double > &	direction
	)

virtualinherited

Definition at line 162 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_Direction, and itk::Object::Modified().

virtual void itk::ImageIOBase::SetFileName ( const char * _arg )

virtualinherited

Set/Get the name of the file to be read.

Referenced by itk::SiemensVisionImageIO::CanReadFile().

virtual void itk::ImageIOBase::SetFileType ( const FileType _arg )

virtualinherited

These methods control whether the file is written binary or ASCII. Many file formats (i.e., subclasses) ignore this flag.

Referenced by itk::MetaImageIO::ReadImageInformation().

void itk::ImageIOBase::SetFileTypeToASCII ( )

inlineinherited

Definition at line 213 of file itkImageIOBase.h.

Referenced by itk::VTKImageIO::InternalReadImageInformation(), itk::VTKImageIO2::InternalReadImageInformation(), and itk::NrrdImageIO::ReadImageInformation().

void itk::ImageIOBase::SetFileTypeToBinary ( )

inlineinherited

Definition at line 217 of file itkImageIOBase.h.

Referenced by otb::LUMImageIO::InternalReadHeaderInformation(), otb::BSQImageIO::InternalReadHeaderInformation(), otb::RADImageIO::InternalReadHeaderInformation(), otb::MWImageIO::InternalReadHeaderInformation(), itk::VTKImageIO::InternalReadImageInformation(), itk::VTKImageIO2::InternalReadImageInformation(), otb::ONERAImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalWriteImageInformation(), MRCImageIO(), itk::NrrdImageIO::ReadImageInformation(), otb::JPEG2000ImageIO::ReadImageInformation(), otb::TileMapImageIO::ReadImageInformation(), otb::RADImageIO::WriteImageInformation(), and otb::BSQImageIO::WriteImageInformation().

void itk::Object::SetGlobalWarningDisplay ( bool val )

staticinherited

This is a global flag that controls whether any debug, warning or error messages are displayed.

Set the value of the global debug output control flag.

Definition at line 370 of file itkObject.cxx.

Referenced by itk::Object::GlobalWarningDisplayOff(), and itk::Object::GlobalWarningDisplayOn().

virtual void itk::ImageIOBase::SetIORegion ( ImageIORegion _arg )

virtualinherited

Specify the region of the image data to either read or write. The IORegion specifies the part of the image to read or write. Regions are defined with an index and a size vector. These vectors define the start (lower-left corner) and length of the region within the image. Make sure that the IORegion lies within the image.

void itk::Object::SetMetaDataDictionary ( const MetaDataDictionary & rhs )

inherited

Returns:: Set the MetaDataDictionary

Reimplemented in otb::ImageMetadataInterfaceBase.

Definition at line 554 of file itkObject.cxx.

References NULL.

Referenced by otb::VectorImage< TPixel, VImageDimension >::CopyInformation(), and otb::Image< TPixel, VImageDimension >::CopyInformation().

virtual void itk::ImageIOBase::SetNumberOfComponents ( unsigned int _arg )

virtualinherited

Set/Get the number of components per pixel in the image. This may be set by the reading process. For SCALAR pixel types, NumberOfComponents will be 1. For other pixel types, NumberOfComponents will be greater than or equal to one.

void itk::ImageIOBase::SetNumberOfDimensions ( unsigned int dim )

inherited

Set/Get the number of independent variables (dimensions) in the image being read or written. Note this is not necessarily what is written, rather the IORegion controls that.

Definition at line 610 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_Dimensions, itk::ImageIOBase::m_Direction, itk::ImageIOBase::m_NumberOfDimensions, itk::ImageIOBase::m_Origin, itk::ImageIOBase::m_Spacing, itk::ImageIOBase::m_Strides, itk::Object::Modified(), itk::ImageIOBase::SetDirection(), itk::ImageIOBase::SetOrigin(), and itk::ImageIOBase::SetSpacing().

void itk::ImageIOBase::SetOrigin	(	unsigned int	i,
		double	origin
	)

virtualinherited

Set/Get the image origin on a axis-by-axis basis. The SetOrigin() method is required when writing the image.

Definition at line 117 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_Origin, and itk::Object::Modified().

Referenced by itk::Brains2MaskImageIO::CanReadFile(), itk::VTKImageIO2::InternalReadImageInformation(), itk::GE5ImageIO::ModifyImageInformation(), itk::DICOMImageIO2::ReadImageInformation(), itk::NrrdImageIO::ReadImageInformation(), itk::MetaImageIO::ReadImageInformation(), itk::MINC2ImageIO::ReadImageInformation(), itk::Bruker2DSEQImageIO::ReadImageInformation(), and itk::ImageIOBase::SetNumberOfDimensions().

virtual void itk::ImageIOBase::SetPixelType ( const IOPixelType _arg )

virtualinherited

Set/Get the type of the pixel. The PixelTypes provides context to the IO mechanisms for data conversions. PixelTypes can be SCALAR, RGB, RGBA, VECTOR, COVARIANTVECTOR, POINT, INDEX. If the PIXELTYPE is SCALAR, then the NumberOfComponents should be 1. Anyother of PIXELTYPE will have more than one component.

bool itk::ImageIOBase::SetPixelTypeInfo ( const std::type_info & ptype )

virtualinherited

SetPixelTypeInfo is used by writers to convert from an ITK strongly typed pixel to a ImageIO (weaker) typed pixel. This function sets these PixelType, ComponentType, and NumberOfComponents based on RTTI type_info structure passed in. The function returns false if the pixel type is not supported.

Definition at line 476 of file itkImageIOBase.cxx.

Referenced by itk::RawImageIO< TPixel, VImageDimension >::RawImageIO().

virtual void itk::LightProcessObject::SetProgress ( float _arg )

virtualinherited

Set the execution progress of a process object. The progress is a floating number between (0,1), 0 meaning no progress; 1 meaning the filter has completed execution.

void itk::Object::SetReferenceCount ( int ref )

virtualinherited

Sets the reference count (use with care)

If there is a delete method, invoke it.

Reimplemented from itk::LightObject.

Definition at line 347 of file itkObject.cxx.

void itk::ImageIOBase::SetSpacing	(	unsigned int	i,
		double	spacing
	)

virtualinherited

Set/Get the image spacing on an axis-by-axis basis. The SetSpacing() method is required when writing the image.

Definition at line 132 of file itkImageIOBase.cxx.

References itk::ImageIOBase::m_Spacing, and itk::Object::Modified().

Referenced by itk::VTKImageIO2::InternalReadImageInformation(), itk::GE5ImageIO::ModifyImageInformation(), itk::DICOMImageIO2::ReadImageInformation(), itk::NrrdImageIO::ReadImageInformation(), itk::MetaImageIO::ReadImageInformation(), itk::MINC2ImageIO::ReadImageInformation(), itk::IPLCommonImageIO::ReadImageInformation(), itk::PhilipsRECImageIO::ReadImageInformation(), itk::AnalyzeImageIO::ReadImageInformation(), itk::Bruker2DSEQImageIO::ReadImageInformation(), and itk::ImageIOBase::SetNumberOfDimensions().

virtual void itk::ImageIOBase::SetUseCompression ( bool _arg )

virtualinherited

Set/Get a boolean to use the compression or not.

virtual void itk::ImageIOBase::SetUseStreamedReading ( bool _arg )

virtualinherited

Set/Get a boolean to use streaming while reading or not.

virtual void itk::ImageIOBase::SetUseStreamedWriting ( bool _arg )

virtualinherited

Set/Get a boolean to use streaming while writing or not.

bool itk::StreamingImageIOBase::StreamReadBufferAsBinary	(	std::istream &	os,
		void *	buffer
	)

protectedvirtualinherited

Reads the set IORegion from os into buffer.

Parameters:

os	is an istream presumed to be opened for reading in binary mode
buffer	is pointer to an allocated block of memory suitable to hold the IORegion of the pixel type

This methods relies on GetDataPosition to determin where the data is located in the file. It uses m_IORegion to determin the requested region to read.

The files data is assumed to be unpadded and continuous in the file for the size of the image in the dimensions of the m_IORegion. This means that the image file could be broken into slices, but not blocks for this methods to be used.

Definition at line 38 of file itkStreamingImageIOBase.cxx.

Referenced by itk::VTKImageIO2::Read().

bool itk::StreamingImageIOBase::StreamWriteBufferAsBinary	(	std::ostream &	os,
		const void *	buffer
	)

protectedvirtualinherited

Writes the set IORegion from buffer into os.

Parameters:

os	is an ostream presumed to be opened for writing and reading
buffer	is a pointer to the data in a continuous block for the region

This methods relies on GetDataPosition to determin where the data is located in the file. It usesy m_IORegion determin the requested region to written.

Definition at line 173 of file itkStreamingImageIOBase.cxx.

References itk::StreamingImageIOBase::GetDataPosition(), itk::ImageIOBase::GetDimensions(), itk::ImageIORegion::GetImageDimension(), itk::ImageIORegion::GetIndex(), itk::ImageIOBase::GetPixelSize(), itk::ImageIORegion::GetSize(), itk::ImageIORegion::IsInside(), itk::ImageIOBase::m_FileName, itk::ImageIOBase::m_IORegion, and itk::StreamingImageIOBase::WriteBufferAsBinary().

Referenced by itk::VTKImageIO2::Write().

virtual bool itk::ImageIOBase::SupportsDimension ( unsigned long dim )

inlinevirtualinherited

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 in itk::RawImageIO< TPixel, VImageDimension >, itk::MetaImageIO, and itk::NrrdImageIO.

Definition at line 337 of file itkImageIOBase.h.

void itk::Object::UnRegister ( ) const

virtualinherited

Decrease the reference count (release by another object).

If there is a delete method, invoke it.

Reimplemented from itk::LightObject.

Definition at line 324 of file itkObject.cxx.

Referenced by itk::Object::New(), and itk::ObjectFactoryBase::UnRegisterFactory().

void itk::MRCImageIO::UpdateHeaderFromImageIO ( void )

private

Definition at line 354 of file itkMRCImageIO.cxx.

Referenced by WriteImageInformation().

template<typename TPixelType >

void itk::MRCImageIO::UpdateHeaderWithMinMaxMean ( const TPixelType * bufferBegin )

inlineprivate

Definition at line 122 of file itkMRCImageIO.h.

References itk::min_max_element().

Referenced by WriteImageInformation().

void itk::MRCImageIO::UpdateHeaderWithMinMaxMean ( const void * bufferBegin )

private

Definition at line 474 of file itkMRCImageIO.cxx.

References itk::MRCHeaderObject::Header::mode.

void itk::LightProcessObject::UpdateOutputData ( void )

virtualinherited

Actually generate new output.

GenerateData this object - we have not aborted yet, and our progress before we start to execute is 0.0.

 If we ended due to aborting, push the progress up to 1.0 (since
 it probably didn't end there)

Definition at line 77 of file itkLightProcessObject.cxx.

void itk::LightProcessObject::UpdateProgress ( float amount )

inherited

Update the progress of the process object. If a ProgressMethod exists, executes it. Then set the Progress ivar to amount. The parameter amount should range between (0,1).

Definition at line 51 of file itkLightProcessObject.cxx.

virtual void itk::ImageIOBase::UseCompressionOff ( )

virtualinherited

virtual void itk::ImageIOBase::UseCompressionOn ( )

virtualinherited

virtual void itk::ImageIOBase::UseStreamedReadingOff ( )

virtualinherited

virtual void itk::ImageIOBase::UseStreamedReadingOn ( )

virtualinherited

Referenced by otb::TileMapImageIO::TileMapImageIO().

virtual void itk::ImageIOBase::UseStreamedWritingOff ( )

virtualinherited

virtual void itk::ImageIOBase::UseStreamedWritingOn ( )

virtualinherited

Referenced by otb::TileMapImageIO::TileMapImageIO().

void itk::MRCImageIO::Write ( const void * buffer )

virtual

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.

Definition at line 546 of file itkMRCImageIO.cxx.

void itk::ImageIOBase::WriteBufferAsASCII	(	std::ostream &	os,
		const void *	buffer,
		IOComponentType	ctype,
		ImageIOBase::SizeType	numComp
	)

protectedinherited

Convenient method to write a buffer as ASCII text.

Definition at line 843 of file itkImageIOBase.cxx.

References itk::ImageIOBase::CDOUBLE, itk::ImageIOBase::CFLOAT, itk::ImageIOBase::CHAR, itk::ImageIOBase::CINT, itk::ImageIOBase::CSHORT, itk::ImageIOBase::DOUBLE, itk::ImageIOBase::FLOAT, itk::ImageIOBase::INT, itk::ImageIOBase::LONG, itk::ImageIOBase::SHORT, itk::ImageIOBase::UCHAR, itk::ImageIOBase::UINT, itk::ImageIOBase::ULONG, and itk::ImageIOBase::USHORT.

Referenced by itk::VTKImageIO::Write(), and itk::VTKImageIO2::Write().

bool itk::StreamingImageIOBase::WriteBufferAsBinary	(	std::ostream &	is,
		const void *	buffer,
		StreamingImageIOBase::SizeType	num
	)

protectedvirtualinherited

Reimplemented from super class to get around 2GB read/write limitation.

Todo:: Move this methods to itk::ImageIOBase

Definition at line 146 of file itkStreamingImageIOBase.cxx.

References itk::ImageIOBase::m_FileName.

Referenced by itk::StreamingImageIOBase::StreamWriteBufferAsBinary(), and itk::VTKImageIO2::Write().

virtual void itk::MRCImageIO::WriteImageInformation ( void )

inlinevirtual

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

Implements itk::ImageIOBase.

Definition at line 70 of file itkMRCImageIO.h.

void itk::MRCImageIO::WriteImageInformation ( const void * bufferBegin )

privatevirtual

Definition at line 457 of file itkMRCImageIO.cxx.

References itk::ImageIOBase::m_FileName, m_MRCHeader, itk::StreamingImageIOBase::OpenFileForWriting(), UpdateHeaderFromImageIO(), and UpdateHeaderWithMinMaxMean().

Member Data Documentation

ByteOrder itk::ImageIOBase::m_ByteOrder

protectedinherited

Big or Little Endian, and the type of the file. (May be ignored.)

Definition at line 416 of file itkImageIOBase.h.

Referenced by itk::AnalyzeImageIO::AnalyzeImageIO(), itk::BioRadImageIO::BioRadImageIO(), itk::BMPImageIO::BMPImageIO(), itk::Bruker2DSEQImageIO::Bruker2DSEQImageIO(), otb::BSQImageIO::BSQImageIO(), otb::ONERAImageIO::CanReadFile(), itk::GiplImageIO::CanReadFile(), itk::Brains2MaskImageIO::CanReadFile(), itk::AnalyzeImageIO::CanReadFile(), itk::DICOMImageIO2::DICOMImageIO2(), itk::GDCMImageIO::GDCMImageIO(), itk::GiplImageIO::GiplImageIO(), otb::ONERAImageIO::InternalReadImageInformation(), otb::ONERAImageIO::InternalWriteImageInformation(), itk::LSMImageIO::LSMImageIO(), otb::LUMImageIO::LUMImageIO(), itk::MetaImageIO::MetaImageIO(), otb::MSTARImageIO::MSTARImageIO(), otb::MWImageIO::MWImageIO(), otb::ONERAImageIO::ONERAImageIO(), itk::PhilipsRECImageIO::PhilipsRECImageIO(), itk::ImageIOBase::PrintSelf(), otb::RADImageIO::RADImageIO(), itk::RawImageIO< TPixel, VImageDimension >::RawImageIO(), itk::GiplImageIO::ReadImageInformation(), itk::PhilipsRECImageIO::ReadImageInformation(), itk::AnalyzeImageIO::ReadImageInformation(), itk::Bruker2DSEQImageIO::ReadImageInformation(), itk::StimulateImageIO::StimulateImageIO(), itk::PhilipsRECImageIO::SwapBytesIfNecessary(), itk::AnalyzeImageIO::SwapBytesIfNecessary(), itk::Bruker2DSEQImageIO::SwapBytesIfNecessary(), itk::AnalyzeImageIO::SwapHeaderBytesIfNecessary(), itk::VoxBoCUBImageIO::VoxBoCUBImageIO(), itk::VTKImageIO::VTKImageIO(), itk::VTKImageIO2::VTKImageIO2(), otb::RADImageIO::WriteImageInformation(), otb::MWImageIO::WriteImageInformation(), and otb::BSQImageIO::WriteImageInformation().

IOComponentType itk::ImageIOBase::m_ComponentType

protectedinherited

Used internally to keep track of the type of the component. It is set when ComputeStrides() is invoked.

Definition at line 413 of file itkImageIOBase.h.

std::vector< SizeValueType > itk::ImageIOBase::m_Dimensions

protectedinherited

The array which stores the number of pixels in the x, y, z directions.

Definition at line 446 of file itkImageIOBase.h.

std::vector<std::vector<double> > itk::ImageIOBase::m_Direction

protectedinherited

The arrays which store the direction cosines of the image.

Definition at line 456 of file itkImageIOBase.h.

Referenced by itk::GDCMImageIO::InternalReadImageInformation(), itk::ImageIOBase::SetDirection(), itk::ImageIOBase::SetNumberOfDimensions(), itk::MINC2ImageIO::Write(), and itk::GDCMImageIO::Write().

std::string itk::ImageIOBase::m_FileName

protectedinherited

Filename to read

Definition at line 423 of file itkImageIOBase.h.

FileType itk::ImageIOBase::m_FileType

protectedinherited

Definition at line 417 of file itkImageIOBase.h.

Referenced by itk::BioRadImageIO::BioRadImageIO(), itk::GDCMImageIO::GDCMImageIO(), itk::LSMImageIO::LSMImageIO(), itk::MetaImageIO::MetaImageIO(), itk::ImageIOBase::PrintSelf(), itk::RawImageIO< TPixel, VImageDimension >::RawImageIO(), itk::VTKImageIO::Read(), itk::VTKImageIO2::Read(), itk::StimulateImageIO::StimulateImageIO(), itk::VTKImageIO::VTKImageIO(), itk::VTKImageIO2::VTKImageIO2(), itk::VTKImageIO::Write(), and itk::VTKImageIO2::Write().

bool itk::ImageIOBase::m_Initialized

protectedinherited

Does the ImageIOBase object have enough info to be of use?

Definition at line 420 of file itkImageIOBase.h.

Referenced by itk::ImageIOBase::Reset().

ImageIORegion itk::ImageIOBase::m_IORegion

protectedinherited

The region to read or write. The region contains information about the data within the region to read or write.

Definition at line 443 of file itkImageIOBase.h.

Referenced by itk::ImageIOBase::PrintSelf(), itk::MetaImageIO::Read(), and itk::StreamingImageIOBase::StreamWriteBufferAsBinary().

const char * itk::MRCImageIO::m_MetaDataHeaderName = "MRCHeader"

static

Todo:: Move to itkIOCommon with the other MetaDataDictionary keys, likely rename the symbol to something like ITK_MRCHHeader. (remember to fix class doc too)

Definition at line 101 of file itkMRCImageIO.h.

Referenced by ReadImageInformation().

MRCHeaderObject::Pointer itk::MRCImageIO::m_MRCHeader

private

Definition at line 153 of file itkMRCImageIO.h.

Referenced by GetHeaderSize(), InternalReadImageInformation(), ReadImageInformation(), UpdateHeaderFromImageIO(), and WriteImageInformation().

unsigned int itk::ImageIOBase::m_NumberOfComponents

protectedinherited

Stores the number of components per pixel. This will be 1 for grayscale images, 3 for RGBPixel images, and 4 for RGBPixelA images.

Definition at line 427 of file itkImageIOBase.h.

Referenced by itk::BioRadImageIO::BioRadImageIO(), itk::ImageIOBase::ComputeStrides(), itk::LSMImageIO::FillZeissStruct(), otb::JPEG2000ImageIO::LoadTileData(), itk::ImageIOBase::PrintSelf(), itk::GDCMImageIO::Read(), itk::MetaImageIO::ReadImageInformation(), itk::ImageIOBase::Reset(), and itk::GDCMImageIO::Write().

unsigned int itk::ImageIOBase::m_NumberOfDimensions

protectedinherited

The number of independent dimensions in the image.

Definition at line 430 of file itkImageIOBase.h.

Referenced by itk::ImageIOBase::ComputeStrides(), itk::LSMImageIO::FillZeissStruct(), itk::StreamingImageIOBase::GenerateStreamableReadRegionFromRequestedRegion(), itk::VTKImageIO::InternalReadImageInformation(), itk::BioRadImageIO::InternalReadImageInformation(), itk::VTKImageIO2::InternalReadImageInformation(), itk::StimulateImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalReadImageInformation(), itk::TIFFImageIO::InternalWrite(), itk::DICOMImageIO2::PrintSelf(), itk::ImageIOBase::PrintSelf(), itk::LSMImageIO::ReadImageInformation(), itk::MetaImageIO::ReadImageInformation(), itk::ImageIOBase::Reset(), itk::ImageIOBase::Resize(), itk::ImageIOBase::SetNumberOfDimensions(), itk::LSMImageIO::Write(), itk::BioRadImageIO::Write(), itk::TIFFImageIO::Write(), itk::StimulateImageIO::Write(), itk::GDCMImageIO::Write(), and itk::PNGImageIO::WriteSlice().

std::vector<double> itk::ImageIOBase::m_Origin

protectedinherited

The array which stores the origin of the image.

Definition at line 453 of file itkImageIOBase.h.

Referenced by itk::BMPImageIO::BMPImageIO(), otb::BSQImageIO::BSQImageIO(), otb::GDALImageIO::GDALImageIO(), itk::VTKImageIO::InternalReadImageInformation(), itk::StimulateImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalReadImageInformation(), itk::GDCMImageIO::InternalReadImageInformation(), otb::GDALImageIO::InternalWriteImageInformation(), otb::JPEG2000ImageIO::JPEG2000ImageIO(), itk::JPEGImageIO::JPEGImageIO(), otb::LUMImageIO::LUMImageIO(), otb::MSTARImageIO::MSTARImageIO(), otb::MWImageIO::MWImageIO(), otb::ONERAImageIO::ONERAImageIO(), itk::PNGImageIO::PNGImageIO(), itk::DICOMImageIO2::PrintSelf(), itk::ImageIOBase::PrintSelf(), otb::RADImageIO::RADImageIO(), itk::RawImageIO< TPixel, VImageDimension >::RawImageIO(), itk::TIFFImageIO::ReadImageInformation(), itk::GiplImageIO::ReadImageInformation(), itk::PNGImageIO::ReadImageInformation(), itk::JPEGImageIO::ReadImageInformation(), otb::JPEG2000ImageIO::ReadImageInformation(), itk::VoxBoCUBImageIO::ReadImageInformation(), ReadImageInformation(), otb::TileMapImageIO::ReadImageInformation(), itk::NiftiImageIO::SetImageIOOrientationFromNIfTI(), itk::ImageIOBase::SetNumberOfDimensions(), itk::ImageIOBase::SetOrigin(), itk::TIFFImageIO::TIFFImageIO(), otb::TileMapImageIO::TileMapImageIO(), UpdateHeaderFromImageIO(), itk::VTKImageIO::Write(), itk::StimulateImageIO::Write(), and itk::GDCMImageIO::Write().

IOPixelType itk::ImageIOBase::m_PixelType

protectedinherited

Used internally to keep track of the type of the pixel.

Definition at line 409 of file itkImageIOBase.h.

InternalReferenceCountType itk::LightObject::m_ReferenceCount

mutableprotectedinherited

Number of uses of this object by other objects.

Definition at line 141 of file itkLightObject.h.

SimpleFastMutexLock itk::LightObject::m_ReferenceCountLock

mutableprotectedinherited

Mutex lock to protect modification to the reference count

Definition at line 144 of file itkLightObject.h.

std::vector<double> itk::ImageIOBase::m_Spacing

protectedinherited

The array which stores the spacing of pixels in the x, y, z directions.

Definition at line 450 of file itkImageIOBase.h.

std::vector< SizeType > itk::ImageIOBase::m_Strides

protectedinherited

Stores the number of bytes it takes to get to the next 'thing' e.g. component, pixel, row, slice, etc.

Definition at line 460 of file itkImageIOBase.h.

Referenced by itk::ImageIOBase::ComputeStrides(), itk::ImageIOBase::Reset(), itk::ImageIOBase::SetNumberOfDimensions(), and itk::MINC2ImageIO::Write().

bool itk::ImageIOBase::m_UseCompression

protectedinherited

Should we compress the data?

Definition at line 433 of file itkImageIOBase.h.

Referenced by otb::GDALImageIO::GDALImageIO(), itk::TIFFImageIO::InternalWrite(), itk::JPEGImageIO::JPEGImageIO(), itk::PNGImageIO::PNGImageIO(), itk::ImageIOBase::PrintSelf(), itk::ImageIOBase::Reset(), otb::TileMapImageIO::TileMapImageIO(), itk::LSMImageIO::Write(), itk::GDCMImageIO::Write(), and itk::PNGImageIO::WriteSlice().

bool itk::ImageIOBase::m_UseStreamedReading

protectedinherited

Should we use streaming for reading

Definition at line 436 of file itkImageIOBase.h.

Referenced by itk::StreamingImageIOBase::GenerateStreamableReadRegionFromRequestedRegion(), itk::ImageIOBase::PrintSelf(), and itk::ImageIOBase::Reset().

bool itk::ImageIOBase::m_UseStreamedWriting

protectedinherited

Should we use streaming for writing

Definition at line 439 of file itkImageIOBase.h.

Referenced by itk::ImageIOBase::PrintSelf(), and itk::ImageIOBase::Reset().

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

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Static Public Member Functions

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Protected Types

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