ImageIO class for reading SDT/SPR (Stimulate) images This format is similar to a MetaImageIO file: The user should specify the .spr file (not the data file : .sdt). More...

#include <itkStimulateImageIO.h>

Inheritance diagram for itk::StimulateImageIO:

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Collaboration diagram for itk::StimulateImageIO:

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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 }
enum	IOPixelType { UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR, POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D, COMPLEX, FIXEDARRAY, MATRIX }
typedef SmartPointer< Self >	Pointer
typedef StimulateImageIO	Self
typedef std::streamoff	SizeType
typedef unsigned long	SizeValueType
typedef ImageIOBase	Superclass
Public Member Functions
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
virtual bool	CanReadFile (const char *)
virtual bool	CanStreamRead ()
virtual bool	CanStreamWrite ()
virtual bool	CanWriteFile (const char *)
virtual LightObject::Pointer	CreateAnother () 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)
std::string	GetByteOrderAsString (ByteOrder) const
Command *	GetCommand (unsigned long tag)
virtual unsigned int	GetComponentSize () const
std::string	GetComponentTypeAsString (IOComponentType) const
bool	GetDebug () const
virtual std::vector< double >	GetDefaultDirection (unsigned int i) const
virtual const float *	GetDisplayRange () const
std::string	GetFileTypeAsString (FileType) const
SizeType	GetImageSizeInBytes () const
SizeType	GetImageSizeInComponents () const
SizeType	GetImageSizeInPixels () const
MetaDataDictionary &	GetMetaDataDictionary (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
virtual unsigned long	GetMTime () const
virtual const char *	GetNameOfClass () const
virtual SizeType	GetPixelStride () const
std::string	GetPixelTypeAsString (IOPixelType) const
virtual int	GetReferenceCount () const
virtual ImageIORegion	GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
const ArrayOfExtensionsType &	GetSupportedReadExtensions () const
const ArrayOfExtensionsType &	GetSupportedWriteExtensions () 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)
void	SetDebug (bool debugFlag) const
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual bool	SetPixelTypeInfo (const std::type_info &ptype)
virtual void	SetReferenceCount (int)
virtual bool	SupportsDimension (unsigned long dim)
virtual void	UnRegister () const
virtual void	UpdateOutputData ()
void	UpdateProgress (float amount)
virtual void	Write (const void *buffer)
virtual void	WriteImageInformation ()


virtual void	SetFileName (const char *_arg)
virtual const char *	GetFileName () const


void	SetNumberOfDimensions (unsigned int)
virtual unsigned int	GetNumberOfDimensions () const


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


virtual void	SetOrigin (unsigned int i, double origin)
virtual double	GetOrigin (unsigned int i) const


virtual void	SetSpacing (unsigned int i, double spacing)
virtual double	GetSpacing (unsigned int i) const


virtual void	SetDirection (unsigned int i, std::vector< double > &direction)
virtual void	SetDirection (unsigned int i, vnl_vector< double > &direction)
virtual std::vector< double >	GetDirection (unsigned int i) const


virtual void	SetIORegion (ImageIORegion _arg)
virtual const ImageIORegion &	GetIORegion ()


virtual void	SetPixelType (const IOPixelType _arg)
virtual IOPixelType	GetPixelType () const


virtual void	SetComponentType (const IOComponentType _arg)
virtual IOComponentType	GetComponentType () const
virtual const std::type_info &	GetComponentTypeInfo () 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 ()
void	SetFileTypeToBinary ()


virtual void	SetByteOrder (const ByteOrder _arg)
virtual ByteOrder	GetByteOrder () const
void	SetByteOrderToBigEndian ()
void	SetByteOrderToLittleEndian ()


virtual void	SetProgress (float _arg)


virtual const float &	GetProgress ()


unsigned long	AddObserver (const EventObject &event, Command *)
unsigned long	AddObserver (const EventObject &event, Command *) const
Static Public Member Functions
static void	BreakOnError ()
static Pointer	New ()


static void	SetGlobalWarningDisplay (bool flag)
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOn ()
static void	GlobalWarningDisplayOff ()
Protected Types


typedef int	InternalReferenceCountType
Protected Member Functions
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 unsigned int	GetPixelSize () const
SizeType	GetRowStride () const
SizeType	GetSliceStride () const
virtual ImageIORegion	GetSplitRegionForWritingCanStreamWrite (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion) const
void	InternalReadImageInformation (std::ifstream &file)
bool	OpenStimulateFileForReading (std::ifstream &os, const char *filename)
bool	OpenStimulateFileForWriting (std::ofstream &os, const char *filename)
bool	PrintObservers (std::ostream &os, Indent indent) const
void	PrintSelf (std::ostream &os, Indent indent) const
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)
	StimulateImageIO ()
void	WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentType ctype, SizeType numberOfBytesToWrite)
	~StimulateImageIO ()


virtual void	PrintHeader (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
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

Detailed Description

ImageIO class for reading SDT/SPR (Stimulate) images This format is similar to a MetaImageIO file: The user should specify the .spr file (not the data file : .sdt).

This is based on the notes from:

http://www.cmrr.umn.edu/stimulate/stimUsersGuide/node57.html

It has been tested on:

ftp://ftp.cmrr.umn.edu/pub/stimulate/data/

Warning:: Beware of the scalar range of some files (See GetDisplayRange).

Author:: Mathieu Malaterre CREATIS team at INSA - Lyon 2002 http://www.creatis.insa-lyon.fr

Definition at line 56 of file itkStimulateImageIO.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 403 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 271 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 [protected, inherited]

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

Definition at line 139 of file itkLightObject.h.

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

Reimplemented from itk::ImageIOBase.

Definition at line 62 of file itkStimulateImageIO.h.

typedef StimulateImageIO itk::StimulateImageIO::Self

Standard class typedefs.

Reimplemented from itk::ImageIOBase.

Definition at line 60 of file itkStimulateImageIO.h.

typedef std::streamoff itk::ImageIOBase::SizeType [inherited]

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

Definition at line 268 of file itkImageIOBase.h.

typedef unsigned long itk::ImageIOBase::SizeValueType [inherited]

Definition at line 76 of file itkImageIOBase.h.

typedef ImageIOBase itk::StimulateImageIO::Superclass

Reimplemented from itk::ImageIOBase.

Definition at line 61 of file itkStimulateImageIO.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

Definition at line 220 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 216 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

Definition at line 95 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 87 of file itkImageIOBase.h.

Constructor & Destructor Documentation

itk::StimulateImageIO::StimulateImageIO ( ) [protected]

itk::StimulateImageIO::~StimulateImageIO ( ) [protected]

Member Function Documentation

virtual void itk::LightProcessObject::AbortGenerateDataOff ( ) [virtual, inherited]

virtual void itk::LightProcessObject::AbortGenerateDataOn ( ) [virtual, inherited]

Turn on and off the AbortGenerateData flag.

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

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

void itk::ImageIOBase::AddSupportedReadExtension ( const char * extension ) [protected, inherited]

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

void itk::ImageIOBase::AddSupportedWriteExtension ( const char * extension ) [protected, inherited]

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

static void itk::LightObject::BreakOnError ( ) [static, inherited]

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

virtual bool itk::StimulateImageIO::CanReadFile ( const char * ) [virtual]

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

Implements itk::ImageIOBase.

virtual bool itk::ImageIOBase::CanStreamRead ( void ) [inline, virtual, inherited]

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

Reimplemented in itk::MetaImageIO, and itk::StreamingImageIOBase.

Definition at line 307 of file itkImageIOBase.h.

virtual bool itk::ImageIOBase::CanStreamWrite ( void ) [inline, virtual, inherited]

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 in itk::MetaImageIO, and itk::StreamingImageIOBase.

Definition at line 331 of file itkImageIOBase.h.

virtual bool itk::StimulateImageIO::CanWriteFile ( const char * ) [virtual]

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

Implements itk::ImageIOBase.

void itk::ImageIOBase::ComputeStrides ( ) [protected, inherited]

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.

virtual LightObject::Pointer itk::Object::CreateAnother ( ) const [virtual, inherited]

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::LightObject.

virtual void itk::Object::DebugOff ( ) const [virtual, inherited]

Turn debugging output off.

virtual void itk::Object::DebugOn ( ) const [virtual, inherited]

Turn debugging output on.

virtual void itk::LightObject::Delete ( ) [virtual, inherited]

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.

virtual void itk::LightProcessObject::GenerateData ( void ) [inline, protected, virtual, inherited]

This method causes the filter to generate its output.

Reimplemented in itk::ClassifierBase< TDataContainer >, itk::ImageClassifierBase< TInputImage, TClassifiedImage >, itk::ImageGaussianModelEstimator< TInputImage, TMembershipFunction, TTrainingImage >, itk::ImageKmeansModelEstimator< TInputImage, TMembershipFunction >, itk::ImageModelEstimatorBase< TInputImage, TMembershipFunction >, itk::LevelSetNeighborhoodExtractor< TLevelSet >, itk::Statistics::SampleClassifier< TSample >, itk::Statistics::SampleClassifierWithMask< TSample, TMaskSample >, itk::ClassifierBase< TInputImage >, and itk::ClassifierBase< TSample >.

Definition at line 123 of file itkLightProcessObject.h.

virtual ImageIORegion itk::ImageIOBase::GenerateStreamableReadRegionFromRequestedRegion ( const ImageIORegion & requested ) const [virtual, inherited]

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.

Reimplemented in itk::MetaImageIO, itk::NiftiImageIO, and itk::StreamingImageIOBase.

virtual const bool& itk::LightProcessObject::GetAbortGenerateData ( ) [virtual, inherited]

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

virtual unsigned int itk::ImageIOBase::GetActualNumberOfSplitsForWriting	(	unsigned int	numberOfRequestedSplits,
		const ImageIORegion &	pasteRegion,
		const ImageIORegion &	largestPossibleRegion
	)			`[virtual, inherited]`

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 in itk::MetaImageIO, and itk::StreamingImageIOBase.

virtual unsigned int itk::ImageIOBase::GetActualNumberOfSplitsForWritingCanStreamWrite	(	unsigned int	numberOfRequestedSplits,
		const ImageIORegion &	pasteRegion
	)			const `[protected, virtual, inherited]`

an implementation of ImageRegionSplitter:GetNumberOfSplits

virtual ByteOrder itk::ImageIOBase::GetByteOrder ( ) const [virtual, inherited]

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.

std::string itk::ImageIOBase::GetByteOrderAsString ( ByteOrder ) const [inherited]

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

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.

virtual unsigned int itk::ImageIOBase::GetComponentSize ( ) const [virtual, inherited]

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.

SizeType itk::ImageIOBase::GetComponentStride ( ) const [protected, inherited]

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

virtual IOComponentType itk::ImageIOBase::GetComponentType ( ) const [virtual, inherited]

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

std::string itk::ImageIOBase::GetComponentTypeAsString ( IOComponentType ) const [inherited]

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

virtual const std::type_info& itk::ImageIOBase::GetComponentTypeInfo ( ) const [virtual, inherited]

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

Reimplemented in itk::IPLCommonImageIO.

bool itk::Object::GetDebug ( ) const [inherited]

Get the value of the debug flag.

virtual std::vector<double> itk::ImageIOBase::GetDefaultDirection ( unsigned int i ) const [virtual, inherited]

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

Reimplemented in itk::AnalyzeImageIO.

virtual unsigned int itk::ImageIOBase::GetDimensions ( unsigned int i ) const [inline, virtual, inherited]

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 109 of file itkImageIOBase.h.

virtual std::vector<double> itk::ImageIOBase::GetDirection ( unsigned int i ) const [inline, virtual, inherited]

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

Reimplemented in itk::AnalyzeImageIO.

Definition at line 135 of file itkImageIOBase.h.

virtual const float* itk::StimulateImageIO::GetDisplayRange ( ) const [virtual]

Two values used for applying intensity windowing to the data set. The pair of numbers represent a low value and a hight value. Pixel values below the low_value will be displayed as black and voxels with values above the high_value will be displayed as white. Pixels with values within the display range are displayed with a grey value that is scaled linearly between the low_value and high_value.

virtual const char* itk::ImageIOBase::GetFileName ( ) const [virtual, inherited]

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

virtual FileType itk::ImageIOBase::GetFileType ( ) const [virtual, inherited]

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

std::string itk::ImageIOBase::GetFileTypeAsString ( FileType ) const [inherited]

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

static bool itk::Object::GetGlobalWarningDisplay ( ) [static, inherited]

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

SizeType itk::ImageIOBase::GetImageSizeInBytes ( ) const [inherited]

Return the number of bytes in the image.

SizeType itk::ImageIOBase::GetImageSizeInComponents ( ) const [inherited]

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

SizeType itk::ImageIOBase::GetImageSizeInPixels ( ) const [inherited]

Return the number of pixels in the image.

virtual const ImageIORegion& itk::ImageIOBase::GetIORegion ( ) [virtual, inherited]

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.

const MetaDataDictionary& itk::Object::GetMetaDataDictionary ( void ) const [inherited]

Returns:: A constant reference to this objects MetaDataDictionary.

MetaDataDictionary& itk::Object::GetMetaDataDictionary ( void ) [inherited]

Returns:: A reference to this objects MetaDataDictionary.

Warning:: This reference may be changed.

virtual unsigned long itk::Object::GetMTime ( ) const [virtual, inherited]

Return this objects modified time.

Referenced by itk::SpatialObject< ::itk::GetMeshDimension< TMesh >::PointDimension >::GetObjectMTime().

virtual const char* itk::StimulateImageIO::GetNameOfClass ( ) const [virtual]

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

virtual const unsigned int& itk::ImageIOBase::GetNumberOfComponents ( ) [virtual, inherited]

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.

virtual unsigned int itk::ImageIOBase::GetNumberOfDimensions ( ) const [virtual, 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.

virtual double itk::ImageIOBase::GetOrigin ( unsigned int i ) const [inline, virtual, inherited]

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

Definition at line 116 of file itkImageIOBase.h.

virtual unsigned int itk::ImageIOBase::GetPixelSize ( ) const [protected, virtual, inherited]

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

virtual SizeType itk::ImageIOBase::GetPixelStride ( ) const [virtual, inherited]

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.

virtual IOPixelType itk::ImageIOBase::GetPixelType ( ) const [virtual, inherited]

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.

std::string itk::ImageIOBase::GetPixelTypeAsString ( IOPixelType ) const [inherited]

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

virtual const float& itk::LightProcessObject::GetProgress ( ) [virtual, inherited]

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 [inline, virtual, inherited]

Gets the reference count on this object.

Definition at line 106 of file itkLightObject.h.

SizeType itk::ImageIOBase::GetRowStride ( ) const [protected, inherited]

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

SizeType itk::ImageIOBase::GetSliceStride ( ) const [protected, inherited]

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

virtual double itk::ImageIOBase::GetSpacing ( unsigned int i ) const [inline, virtual, inherited]

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

Definition at line 125 of file itkImageIOBase.h.

virtual ImageIORegion itk::ImageIOBase::GetSplitRegionForWriting	(	unsigned int	ithPiece,
		unsigned int	numberOfActualSplits,
		const ImageIORegion &	pasteRegion,
		const ImageIORegion &	largestPossibleRegion
	)			`[virtual, inherited]`

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.

virtual ImageIORegion itk::ImageIOBase::GetSplitRegionForWritingCanStreamWrite	(	unsigned int	ithPiece,
		unsigned int	numberOfActualSplits,
		const ImageIORegion &	pasteRegion
	)			const `[protected, virtual, inherited]`

an implementation of ImageRegionSplitter:GetSplit

const 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.

const 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.

virtual bool itk::ImageIOBase::GetUseCompression ( ) const [virtual, inherited]

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

virtual bool itk::ImageIOBase::GetUseStreamedReading ( ) const [virtual, inherited]

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

virtual bool itk::ImageIOBase::GetUseStreamedWriting ( ) const [virtual, inherited]

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

static void itk::Object::GlobalWarningDisplayOff ( ) [inline, static, inherited]

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

Definition at line 100 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

static void itk::Object::GlobalWarningDisplayOn ( ) [inline, static, inherited]

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

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.

void itk::StimulateImageIO::InternalReadImageInformation ( std::ifstream & file ) [protected]

void itk::Object::InvokeEvent ( const EventObject & ) [inherited]

Call Execute on all the Commands observing this event id.

void itk::Object::InvokeEvent ( const EventObject & ) const [inherited]

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

virtual void itk::Object::Modified ( ) const [virtual, inherited]

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

Referenced by itk::NarrowBandImageFilterBase< TInputImage, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::InsertNarrowBandNode(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetCenter(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetMatrix(), itk::NarrowBandImageFilterBase< TInputImage, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::SetNarrowBand(), itk::NarrowBandImageFilterBase< TInputImage, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::SetNarrowBandInnerRadius(), itk::NarrowBandImageFilterBase< TInputImage, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::SetNarrowBandTotalRadius(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetOffset(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetRealThresholds(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetThresholds(), itk::Statistics::GoodnessOfFitFunctionBase< TInputHistogram >::SetTotalObservedScale(), and itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetTranslation().

static Pointer itk::StimulateImageIO::New ( ) [static]

Method for creation through the object factory.

Reimplemented from itk::LightProcessObject.

bool itk::StimulateImageIO::OpenStimulateFileForReading	(	std::ifstream &	os,
		const char *	filename
	)			`[protected]`

bool itk::StimulateImageIO::OpenStimulateFileForWriting	(	std::ofstream &	os,
		const char *	filename
	)			`[protected]`

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

Cause the object to print itself out.

Referenced by itk::WeakPointer< ProcessObject >::Print().

virtual void itk::LightObject::PrintHeader	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual, inherited]`

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.

bool itk::Object::PrintObservers	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, inherited]`

void itk::StimulateImageIO::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual]`

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::LightObject::PrintTrailer	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual, inherited]`

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.

virtual void itk::StimulateImageIO::Read ( void * buffer ) [virtual]

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

void itk::ImageIOBase::ReadBufferAsASCII	(	std::istream &	os,
		void *	buffer,
		IOComponentType	ctype,
		SizeType	numberOfBytesToBeRead
	)			`[protected, inherited]`

Convenient method to read a buffer as ASCII text.

bool itk::ImageIOBase::ReadBufferAsBinary	(	std::istream &	os,
		void *	buffer,
		SizeType	numberOfBytesToBeRead
	)			`[protected, inherited]`

Convenient method to read a buffer as binary. Return true on success.

Reimplemented in itk::StreamingImageIOBase.

virtual void itk::StimulateImageIO::ReadImageInformation ( ) [virtual]

Set the spacing and dimesion information for the current filename.

Implements itk::ImageIOBase.

virtual void itk::Object::Register ( ) const [virtual, inherited]

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

Reimplemented from itk::LightObject.

void itk::Object::RemoveAllObservers ( ) [inherited]

Remove all observers .

void itk::Object::RemoveObserver ( unsigned long tag ) [inherited]

Remove the observer with this tag value.

virtual void itk::ImageIOBase::Reset ( const bool freeDynamic = true ) [protected, virtual, inherited]

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

void itk::ImageIOBase::Resize	(	const unsigned int	numDimensions,
		const unsigned int *	dimensions
	)			`[protected, inherited]`

Resize the ImageIOBase object to new dimensions.

virtual void itk::LightProcessObject::SetAbortGenerateData ( bool _arg ) [virtual, inherited]

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 ) [virtual, inherited]

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.

void itk::ImageIOBase::SetByteOrderToBigEndian ( ) [inline, inherited]

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.

Definition at line 249 of file itkImageIOBase.h.

void itk::ImageIOBase::SetByteOrderToLittleEndian ( ) [inline, inherited]

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.

Definition at line 253 of file itkImageIOBase.h.

virtual void itk::ImageIOBase::SetComponentType ( const IOComponentType _arg ) [virtual, inherited]

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

void itk::Object::SetDebug ( bool debugFlag ) const [inherited]

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

virtual void itk::ImageIOBase::SetDimensions	(	unsigned int	i,
		unsigned int	dim
	)			`[virtual, inherited]`

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.

virtual void itk::ImageIOBase::SetDirection	(	unsigned int	i,
		std::vector< double > &	direction
	)			`[virtual, inherited]`

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

virtual void itk::ImageIOBase::SetDirection	(	unsigned int	i,
		vnl_vector< double > &	direction
	)			`[virtual, inherited]`

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

virtual void itk::ImageIOBase::SetFileName ( const char * _arg ) [virtual, inherited]

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

virtual void itk::ImageIOBase::SetFileType ( const FileType _arg ) [virtual, inherited]

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

void itk::ImageIOBase::SetFileTypeToASCII ( ) [inline, inherited]

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

Definition at line 226 of file itkImageIOBase.h.

void itk::ImageIOBase::SetFileTypeToBinary ( ) [inline, inherited]

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

Definition at line 230 of file itkImageIOBase.h.

static void itk::Object::SetGlobalWarningDisplay ( bool flag ) [static, inherited]

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

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

virtual void itk::ImageIOBase::SetIORegion ( ImageIORegion _arg ) [virtual, inherited]

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

virtual void itk::ImageIOBase::SetNumberOfComponents ( unsigned int _arg ) [virtual, inherited]

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 ) [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.

virtual void itk::ImageIOBase::SetOrigin	(	unsigned int	i,
		double	origin
	)			`[virtual, inherited]`

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

virtual void itk::ImageIOBase::SetPixelType ( const IOPixelType _arg ) [virtual, inherited]

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.

virtual bool itk::ImageIOBase::SetPixelTypeInfo ( const std::type_info & ptype ) [virtual, inherited]

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.

virtual void itk::LightProcessObject::SetProgress ( float _arg ) [virtual, inherited]

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.

virtual void itk::Object::SetReferenceCount ( int ) [virtual, inherited]

Sets the reference count (use with care)

Reimplemented from itk::LightObject.

virtual void itk::ImageIOBase::SetSpacing	(	unsigned int	i,
		double	spacing
	)			`[virtual, inherited]`

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

virtual void itk::ImageIOBase::SetUseCompression ( bool _arg ) [virtual, inherited]

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

virtual void itk::ImageIOBase::SetUseStreamedReading ( bool _arg ) [virtual, inherited]

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

virtual void itk::ImageIOBase::SetUseStreamedWriting ( bool _arg ) [virtual, inherited]

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

virtual bool itk::ImageIOBase::SupportsDimension ( unsigned long dim ) [inline, virtual, inherited]

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

Definition at line 352 of file itkImageIOBase.h.

virtual void itk::Object::UnRegister ( ) const [virtual, inherited]

Decrease the reference count (release by another object).

Reimplemented from itk::LightObject.

virtual void itk::LightProcessObject::UpdateOutputData ( ) [virtual, inherited]

Actually generate new output.

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).

virtual void itk::ImageIOBase::UseCompressionOff ( ) [virtual, inherited]

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

virtual void itk::ImageIOBase::UseCompressionOn ( ) [virtual, inherited]

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

virtual void itk::ImageIOBase::UseStreamedReadingOff ( ) [virtual, inherited]

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

virtual void itk::ImageIOBase::UseStreamedReadingOn ( ) [virtual, inherited]

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

virtual void itk::ImageIOBase::UseStreamedWritingOff ( ) [virtual, inherited]

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

virtual void itk::ImageIOBase::UseStreamedWritingOn ( ) [virtual, inherited]

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

virtual void itk::StimulateImageIO::Write ( const void * buffer ) [virtual]

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

Implements itk::ImageIOBase.

void itk::ImageIOBase::WriteBufferAsASCII	(	std::ostream &	os,
		const void *	buffer,
		IOComponentType	ctype,
		SizeType	numberOfBytesToWrite
	)			`[protected, inherited]`