Read series of image files into a SimpleITK image. More...

#include <sitkImageSeriesReader.h>

Inheritance diagram for itk::simple::ImageSeriesReader:

Collaboration diagram for itk::simple::ImageSeriesReader:

Public Types
typedef ImageSeriesReader	Self

Public Types inherited from itk::simple::ImageReaderBase
typedef ImageReaderBase	Self

Public Types inherited from itk::simple::ProcessObject
typedef ProcessObject	Self

Public Member Functions
Image	Execute ()

const std::vector< std::string > &	GetFileNames () const

std::string	GetMetaData (unsigned int slice, const std::string &key) const
	Get the value of a meta-data dictionary entry as a string. More...

bool	GetMetaDataDictionaryArrayUpdate ()

std::vector< std::string >	GetMetaDataKeys (unsigned int slice) const
	Get the meta-data dictionary keys for a slice. More...

virtual std::string	GetName () const

bool	HasMetaDataKey (unsigned int slice, const std::string &key) const
	Query a meta-data dictionary for the existence of a key. More...

	ImageSeriesReader ()

Self &	MetaDataDictionaryArrayUpdateOff ()

Self &	MetaDataDictionaryArrayUpdateOn ()

Self &	SetFileNames (const std::vector< std::string > &fileNames)

Self &	SetMetaDataDictionaryArrayUpdate (bool metaDataDictionaryArrayUpdate)

virtual std::string	ToString () const

virtual	~ImageSeriesReader ()

Public Member Functions inherited from itk::simple::ImageReaderBase
virtual std::vector< std::string >	GetRegisteredImageIOs () const
	Get a vector of the names of registered itk ImageIOs. More...

	ImageReaderBase ()

virtual	~ImageReaderBase ()

Self &	SetOutputPixelType (PixelIDValueEnum pixelID)
	Set/Get The output PixelType of the image. More...

PixelIDValueEnum	GetOutputPixelType (void) const
	Set/Get The output PixelType of the image. More...

virtual Self &	SetLoadPrivateTags (bool loadPrivateTags)
	Set/Get loading private DICOM tags into Image's MetaData. More...

virtual bool	GetLoadPrivateTags () const
	Set/Get loading private DICOM tags into Image's MetaData. More...

virtual void	LoadPrivateTagsOn ()
	Set/Get loading private DICOM tags into Image's MetaData. More...

virtual void	LoadPrivateTagsOff ()
	Set/Get loading private DICOM tags into Image's MetaData. More...

virtual Self &	SetImageIO (const std::string &imageio)
	Set/Get name of ImageIO to use. More...

virtual std::string	GetImageIO (void) const
	Set/Get name of ImageIO to use. More...

Public Member Functions inherited from itk::simple::ProcessObject
virtual void	Abort ()

virtual int	AddCommand (itk::simple::EventEnum event, itk::simple::Command &cmd)
	Add a Command Object to observer the event. More...

virtual float	GetProgress () const
	An Active Measurement of the progress of execution. More...

virtual bool	HasCommand (itk::simple::EventEnum event) const
	Query of this object has any registered commands for event. More...

	ProcessObject ()

virtual void	RemoveAllCommands ()
	Remove all registered commands. More...

virtual	~ProcessObject ()

virtual void	DebugOn ()

virtual void	DebugOff ()

virtual bool	GetDebug () const

virtual void	SetDebug (bool debugFlag)

virtual void	SetNumberOfThreads (unsigned int n)

virtual unsigned int	GetNumberOfThreads () const

Static Public Member Functions
static std::vector< std::string >	GetGDCMSeriesFileNames (const std::string &directory, const std::string &seriesID="", bool useSeriesDetails=false, bool recursive=false, bool loadSequences=false)
	Generate a sequence of filenames from a directory with a DICOM data set and a series ID. More...

static std::vector< std::string >	GetGDCMSeriesIDs (const std::string &directory)
	Get all the seriesIDs from a DICOM data set. More...

Static Public Member Functions inherited from itk::simple::ProcessObject
static bool	GetGlobalDefaultDebug ()

static void	GlobalDefaultDebugOff ()

static void	GlobalDefaultDebugOn ()

static void	SetGlobalDefaultDebug (bool debugFlag)

static void	GlobalWarningDisplayOn ()

static void	GlobalWarningDisplayOff ()

static void	SetGlobalWarningDisplay (bool flag)

static bool	GetGlobalWarningDisplay ()

static void	SetGlobalDefaultNumberOfThreads (unsigned int n)

static unsigned int	GetGlobalDefaultNumberOfThreads ()

static double	GetGlobalDefaultCoordinateTolerance ()
	Access the global tolerance to determine congruent spaces. More...

static void	SetGlobalDefaultCoordinateTolerance (double)
	Access the global tolerance to determine congruent spaces. More...

static double	GetGlobalDefaultDirectionTolerance ()
	Access the global tolerance to determine congruent spaces. More...

static void	SetGlobalDefaultDirectionTolerance (double)
	Access the global tolerance to determine congruent spaces. More...

Protected Member Functions
template<class TImageType >
Image	ExecuteInternal (itk::ImageIOBase *)

Protected Member Functions inherited from itk::simple::ImageReaderBase
unsigned int	GetDimensionFromImageIO (const std::string &fileName, unsigned int i)

unsigned int	GetDimensionFromImageIO (const itk::ImageIOBase *iobase, unsigned int i)

itk::SmartPointer< ImageIOBase >	GetImageIOBase (const std::string &fileName)

void	GetPixelIDFromImageIO (const std::string &fileName, PixelIDValueType &outPixelType, unsigned int &outDimensions)

void	GetPixelIDFromImageIO (const itk::ImageIOBase *iobase, PixelIDValueType &outPixelType, unsigned int &outDimensions)

Protected Member Functions inherited from itk::simple::ProcessObject
virtual unsigned long	AddITKObserver (const itk::EventObject &, itk::Command *)

virtual itk::ProcessObject *	GetActiveProcess ()

virtual void	OnActiveProcessDelete ()

virtual void	onCommandDelete (const itk::simple::Command *cmd) SITK_NOEXCEPT

virtual void	PreUpdate (itk::ProcessObject *p)

virtual void	RemoveITKObserver (EventCommand &e)

Protected Member Functions inherited from itk::simple::NonCopyable
	NonCopyable ()

Private Types
typedef Image(Self::*	MemberFunctionType) (itk::ImageIOBase *)

Private Attributes
std::vector< std::string >	m_FileNames

itk::ProcessObject *	m_Filter

nsstd::auto_ptr< detail::MemberFunctionFactory< MemberFunctionType > >	m_MemberFactory

bool	m_MetaDataDictionaryArrayUpdate

nsstd::function< std::string(int, const std::string &)>	m_pfGetMetaData

nsstd::function< std::vector< std::string >int)>	m_pfGetMetaDataKeys

nsstd::function< bool(int, const std::string &)>	m_pfHasMetaDataKey

Friends
struct	detail::MemberFunctionAddressor< MemberFunctionType >

Additional Inherited Members
Static Protected Member Functions inherited from itk::simple::ProcessObject
template<class TImageType >
static TImageType::ConstPointer	CastImageToITK (const Image &img)

template<class TImageType >
static Image	CastITKToImage (TImageType *img)

template<class TPixelType , unsigned int VImageDimension, unsigned int VLength, template< typename, unsigned int > class TVector>
static Image	CastITKToImage (itk::Image< TVector< TPixelType, VLength >, VImageDimension > *img)

static const itk::EventObject &	GetITKEventObject (EventEnum e)

template<typename T >
static std::ostream &	ToStringHelper (std::ostream &os, const T &v)

static std::ostream &	ToStringHelper (std::ostream &os, const char &v)

static std::ostream &	ToStringHelper (std::ostream &os, const signed char &v)

static std::ostream &	ToStringHelper (std::ostream &os, const unsigned char &v)

Detailed Description

Read series of image files into a SimpleITK image.

For some image formats such as DICOM, images also contain associated meta-data (e.g. imaging modality, patient name etc.). By default the reader does not load this information (saves time). To load the meta-data you will need to explicitly configure the reader, MetaDataDictionaryArrayUpdateOn, and possibly specify that you also want to load the private meta-data LoadPrivateTagsOn.

Once the image series is read the meta-data is directly accessible from the reader.

See also: itk::simple::ReadImage for the procedural interface

Examples:: DicomSeriesReader/DicomSeriesReader.cxx.

Definition at line 45 of file sitkImageSeriesReader.h.

Member Typedef Documentation

typedef Image(Self::* itk::simple::ImageSeriesReader::MemberFunctionType) (itk::ImageIOBase *)

private

Definition at line 156 of file sitkImageSeriesReader.h.

typedef ImageSeriesReader itk::simple::ImageSeriesReader::Self

Definition at line 49 of file sitkImageSeriesReader.h.

Constructor & Destructor Documentation

virtual itk::simple::ImageSeriesReader::~ImageSeriesReader ( )

virtual

itk::simple::ImageSeriesReader::ImageSeriesReader ( )

Member Function Documentation

Image itk::simple::ImageSeriesReader::Execute ( )

virtual

Implements itk::simple::ImageReaderBase.

Examples:: DicomSeriesReader/DicomSeriesReader.cxx.

template<class TImageType >

Image itk::simple::ImageSeriesReader::ExecuteInternal ( itk::ImageIOBase * )

protected

const std::vector<std::string>& itk::simple::ImageSeriesReader::GetFileNames ( ) const

static std::vector<std::string> itk::simple::ImageSeriesReader::GetGDCMSeriesFileNames	(	const std::string &	directory,
		const std::string &	seriesID = `""`,
		bool	useSeriesDetails = `false`,
		bool	recursive = `false`,
		bool	loadSequences = `false`
	)

static

Generate a sequence of filenames from a directory with a DICOM data set and a series ID.

This method generates a sequence of filenames whose filenames point to DICOM files. The data set may contain multiple series. The seriesID string is used to select a specific series. The ordering of the filenames is based on one of several strategies, which will read all images in the directory ( assuming there is only one study/series ).

Parameters

directory	Set the directory that contains the DICOM data set.
recursive	Recursively parse the input directory.
seriesID	Set the name that identifies a particular series. Default value is an empty string which will return the file names associated with the first series found in the directory.
useSeriesDetails	Use additional series information such as ProtocolName and SeriesName to identify when a single SeriesUID contains multiple 3D volumes - as can occur with perfusion and DTI imaging.
loadSequences	Parse any sequences in the DICOM data set. Loading DICOM files is faster when sequences are not needed.

See also: itk::GDCMSeriesFileNames

Examples:: DicomSeriesReader/DicomSeriesReader.cxx.

static std::vector<std::string> itk::simple::ImageSeriesReader::GetGDCMSeriesIDs ( const std::string & directory )

static

Get all the seriesIDs from a DICOM data set.

Parameters

directory The directory that contains the DICOM data set

See also: itk::GDCMSeriesFileNames

std::string itk::simple::ImageSeriesReader::GetMetaData	(	unsigned int	slice,
		const std::string &	key
	)		const

inline

Get the value of a meta-data dictionary entry as a string.

If the key is not in the dictionary then an exception is thrown.

string types in the dictionary are returned as their native string. Other types are printed to string before returning.

Definition at line 146 of file sitkImageSeriesReader.h.

bool itk::simple::ImageSeriesReader::GetMetaDataDictionaryArrayUpdate ( )

inline

Definition at line 69 of file sitkImageSeriesReader.h.

std::vector<std::string> itk::simple::ImageSeriesReader::GetMetaDataKeys ( unsigned int slice ) const

inline

Get the meta-data dictionary keys for a slice.

This is only valid after successful execution of this filter and when MetaDataDictionaryArrayUpdate is true. Each element in the array corresponds to a "slice" or filename read during execution.

If the slice index is out of range, an exception will be thrown.

Returns a vector of keys to the key/value entries in the file's meta-data dictionary. Iterate through with these keys to get the values.

Definition at line 132 of file sitkImageSeriesReader.h.

virtual std::string itk::simple::ImageSeriesReader::GetName ( ) const

inlinevirtual

return user readable name of the filter

Implements itk::simple::ProcessObject.

Definition at line 59 of file sitkImageSeriesReader.h.

bool itk::simple::ImageSeriesReader::HasMetaDataKey	(	unsigned int	slice,
		const std::string &	key
	)		const

inline

Query a meta-data dictionary for the existence of a key.

Definition at line 136 of file sitkImageSeriesReader.h.

Self& itk::simple::ImageSeriesReader::MetaDataDictionaryArrayUpdateOff ( )

inline

Definition at line 74 of file sitkImageSeriesReader.h.

Self& itk::simple::ImageSeriesReader::MetaDataDictionaryArrayUpdateOn ( )

inline

Set the value of MetaDataDictionaryArrayUpdate to true or false respectively.

Definition at line 73 of file sitkImageSeriesReader.h.

Self& itk::simple::ImageSeriesReader::SetFileNames ( const std::vector< std::string > & fileNames )

Examples:: DicomSeriesReader/DicomSeriesReader.cxx.

Self& itk::simple::ImageSeriesReader::SetMetaDataDictionaryArrayUpdate ( bool metaDataDictionaryArrayUpdate )

inline

Set/Get whether the meta-data dictionaries for the slices should be read. Default value is false, because of the additional computation time.

Definition at line 67 of file sitkImageSeriesReader.h.

virtual std::string itk::simple::ImageSeriesReader::ToString ( ) const

virtual

Print ourselves to string

Reimplemented from itk::simple::ImageReaderBase.

Friends And Related Function Documentation

friend struct detail::MemberFunctionAddressor< MemberFunctionType >

friend

Definition at line 159 of file sitkImageSeriesReader.h.

Member Data Documentation

std::vector<std::string> itk::simple::ImageSeriesReader::m_FileNames

private

Definition at line 171 of file sitkImageSeriesReader.h.

itk::ProcessObject* itk::simple::ImageSeriesReader::m_Filter

private

Definition at line 168 of file sitkImageSeriesReader.h.

nsstd::auto_ptr<detail::MemberFunctionFactory<MemberFunctionType> > itk::simple::ImageSeriesReader::m_MemberFactory

private

Definition at line 160 of file sitkImageSeriesReader.h.

bool itk::simple::ImageSeriesReader::m_MetaDataDictionaryArrayUpdate

private

Definition at line 173 of file sitkImageSeriesReader.h.

nsstd::function<std::string(int, const std::string &)> itk::simple::ImageSeriesReader::m_pfGetMetaData

private

Definition at line 165 of file sitkImageSeriesReader.h.

nsstd::function<std::vector<std::string>int)> itk::simple::ImageSeriesReader::m_pfGetMetaDataKeys

private

Definition at line 163 of file sitkImageSeriesReader.h.

nsstd::function<bool(int, const std::string &)> itk::simple::ImageSeriesReader::m_pfHasMetaDataKey

private

Definition at line 164 of file sitkImageSeriesReader.h.

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

sitkImageSeriesReader.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation