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:

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.

Note: DICOM tags are represented as strings in the meta-data dictionary(s), therefore "0020|000D" and "0020|000d" are different when accessing the tag value. This differs from the hexadecimal numbers they represent, 0020|000D and 0020|000d are equivalent. The ITK meta-data dictionary is string based and uses lower case to represent the hexadecimal number read from disk, so 0020|000d will work as a key and 0020|000D will not be found in the dictionary (results in an exception if attempting to access). It is recommended to use lower case when setting and accessing DICOM tags.; If the pixel type for the returned image is not specified it is deduced from the first image in the series. This approach is computationally efficient and assumes that all images in a series have the same pixel type. In rare situations this is not the case, not all images have the same pixel type. If this leads to a narrowing conversion (e.g. first image pixel type is unsigned int and others are float) the returned image does not represent the data correctly. To resolve such situations, explicitly specify the expected pixel type via the SetOutputPixelType method before reading the series.

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

Examples: DicomSeriesReader/DicomSeriesReader.cxx.

Definition at line 68 of file sitkImageSeriesReader.h.

Public Types
using	Self = ImageSeriesReader

Public Types inherited from itk::simple::ImageReaderBase
using	Self = ImageReaderBase

Public Types inherited from itk::simple::ProcessObject
using	Self = ProcessObject

Public Member Functions
Image	Execute () override
	Set/Get The output PixelType of the image. More...

const std::vector< PathType > &	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...

std::string	GetName () const override

double	GetSpacingWarningRelThreshold () 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< PathType > &fileNames)

Self &	SetMetaDataDictionaryArrayUpdate (bool metaDataDictionaryArrayUpdate)

Self &	SetSpacingWarningRelThreshold (double spacingWarningRelThreshold)

std::string	ToString () const override

	~ImageSeriesReader () override

Public Member Functions inherited from itk::simple::ImageReaderBase
	ImageReaderBase ()

	~ImageReaderBase () override

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

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

virtual std::vector< std::string >	GetRegisteredImageIOs () const
	Get a vector of the names of registered itk ImageIOs. More...

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

virtual bool	GetLoadPrivateTags () const
	Set/Get The output PixelType of the image. More...

virtual void	LoadPrivateTagsOn ()
	Set/Get The output PixelType of the image. More...

virtual void	LoadPrivateTagsOff ()
	Set/Get The output PixelType of the image. More...

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

virtual std::string	GetImageIO () const
	Set/Get The output PixelType of the image. More...

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

virtual int	AddCommand (itk::simple::EventEnum event, const std::function< void()> &func)
	Directly add a callback to observe an event. More...

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

virtual void	SetNumberOfWorkUnits (unsigned int n)

virtual unsigned int	GetNumberOfWorkUnits () const

Static Public Member Functions
static std::vector< PathType >	GetGDCMSeriesFileNames (const PathType &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 PathType &directory, bool useSeriesDetails=false)
	Get all the seriesIDs from a DICOM data set. More...

Static Public Member Functions inherited from itk::simple::ImageReaderBase
static std::string	GetImageIOFromFileName (const PathType &fileName)
	Get the automatic ImageIO from the ImageIOFactory. 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 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...

static bool	SetGlobalDefaultThreader (const std::string &threader)
	Set/Get the default threader used for process objects. More...

static std::string	GetGlobalDefaultThreader ()
	Set/Get the default threader used for process objects. More...

static void	SetGlobalDefaultNumberOfThreads (unsigned int n)

static unsigned int	GetGlobalDefaultNumberOfThreads ()
	Set/Get the default threader used for process objects. More...

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

Protected Member Functions inherited from itk::simple::ImageReaderBase
itk::SmartPointer< ImageIOBase >	GetImageIOBase (const PathType &fileName)
	Set/Get The output PixelType of the image. More...

void	GetPixelIDFromImageIO (const PathType &fileName, PixelIDValueType &outPixelType, unsigned int &outDimensions)
	Set/Get The output PixelType of the image. More...

void	GetPixelIDFromImageIO (const itk::ImageIOBase *iobase, PixelIDValueType &outPixelType, unsigned int &outDimensions)
	Set/Get The output PixelType of the image. More...

unsigned int	GetDimensionFromImageIO (const PathType &filename, unsigned int i)
	Set/Get The output PixelType of the image. More...

unsigned int	GetDimensionFromImageIO (const itk::ImageIOBase *iobase, unsigned int i)
	Set/Get The output PixelType of the image. More...

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) noexcept

virtual void	PreUpdate (itk::ProcessObject *p)

virtual void	RemoveITKObserver (EventCommand &e)

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

	NonCopyable (const NonCopyable &)=delete

NonCopyable &	operator= (const NonCopyable &)=delete

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

Private Attributes
std::vector< PathType >	m_FileNames

itk::ProcessObject *	m_Filter {nullptr}

std::unique_ptr< detail::MemberFunctionFactory< MemberFunctionType > >	m_MemberFactory

bool	m_MetaDataDictionaryArrayUpdate {false}

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

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

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

double	m_SpacingWarningRelThreshold {1e-4}

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

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

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

Member Typedef Documentation

◆ MemberFunctionType

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

private

Definition at line 231 of file sitkImageSeriesReader.h.

◆ Self

using itk::simple::ImageSeriesReader::Self = ImageSeriesReader

Definition at line 71 of file sitkImageSeriesReader.h.

Constructor & Destructor Documentation

◆ ~ImageSeriesReader()

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

override

◆ ImageSeriesReader()

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

Member Function Documentation

◆ Execute()

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

overridevirtual

Set/Get The output PixelType of the image.

By default the value is sitkUnknown, which enable the output pixel type to be same as the file. If the pixel type is specified then the itk::ConvertPixelBuffer will be used to convert the pixels.

Implements itk::simple::ImageReaderBase.

Examples: DicomSeriesReader/DicomSeriesReader.cxx.

◆ ExecuteInternal()

template<class TImageType >

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

protected

◆ GetFileNames()

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

◆ GetGDCMSeriesFileNames()

static std::vector<PathType> itk::simple::ImageSeriesReader::GetGDCMSeriesFileNames	(	const PathType &	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. If the parameter value was obtained from a call to GDCMSeriesIDs, the value of the useSeriesDetails parameter must be the same here and in the call to GDCMSeriesIDs.
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.

◆ GetGDCMSeriesIDs()

static std::vector<std::string> itk::simple::ImageSeriesReader::GetGDCMSeriesIDs	(	const PathType &	directory,
		bool	useSeriesDetails = `false`
	)

static

Get all the seriesIDs from a DICOM data set.

Parameters

directory	The directory that contains the DICOM data set
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. The parameter value must match the value used in the call to GDCMSeriesFileNames.

See also: itk::GDCMSeriesFileNames

◆ GetMetaData()

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 218 of file sitkImageSeriesReader.h.

◆ GetMetaDataDictionaryArrayUpdate()

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

inline

Definition at line 101 of file sitkImageSeriesReader.h.

◆ GetMetaDataKeys()

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 196 of file sitkImageSeriesReader.h.

◆ GetName()

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

inlineoverridevirtual

return user readable name of the filter

Implements itk::simple::ProcessObject.

Definition at line 83 of file sitkImageSeriesReader.h.

◆ GetSpacingWarningRelThreshold()

double itk::simple::ImageSeriesReader::GetSpacingWarningRelThreshold ( ) const

◆ HasMetaDataKey()

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 204 of file sitkImageSeriesReader.h.

◆ MetaDataDictionaryArrayUpdateOff()

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

inline

Definition at line 114 of file sitkImageSeriesReader.h.

◆ MetaDataDictionaryArrayUpdateOn()

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

inline

Set the value of MetaDataDictionaryArrayUpdate to true or false respectively.

Definition at line 109 of file sitkImageSeriesReader.h.

◆ SetFileNames()

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

Examples: DicomSeriesReader/DicomSeriesReader.cxx.

◆ SetMetaDataDictionaryArrayUpdate()

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 95 of file sitkImageSeriesReader.h.

◆ SetSpacingWarningRelThreshold()

Self& itk::simple::ImageSeriesReader::SetSpacingWarningRelThreshold ( double spacingWarningRelThreshold )

Set the relative threshold for issuing warnings about non-uniform sampling.

◆ ToString()

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

overridevirtual

Print ourselves to string

Reimplemented from itk::simple::ImageReaderBase.

Friends And Related Function Documentation

◆ detail::MemberFunctionAddressor< MemberFunctionType >

friend struct detail::MemberFunctionAddressor< MemberFunctionType >

friend

Definition at line 234 of file sitkImageSeriesReader.h.

Member Data Documentation

◆ m_FileNames

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

private

Definition at line 246 of file sitkImageSeriesReader.h.

◆ m_Filter

itk::ProcessObject* itk::simple::ImageSeriesReader::m_Filter {nullptr}

private

Definition at line 243 of file sitkImageSeriesReader.h.

◆ m_MemberFactory

std::unique_ptr<detail::MemberFunctionFactory<MemberFunctionType> > itk::simple::ImageSeriesReader::m_MemberFactory

private

Definition at line 235 of file sitkImageSeriesReader.h.

◆ m_MetaDataDictionaryArrayUpdate

bool itk::simple::ImageSeriesReader::m_MetaDataDictionaryArrayUpdate {false}

private

Definition at line 250 of file sitkImageSeriesReader.h.

◆ m_pfGetMetaData

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

private

Definition at line 240 of file sitkImageSeriesReader.h.

◆ m_pfGetMetaDataKeys

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

private

Definition at line 238 of file sitkImageSeriesReader.h.

◆ m_pfHasMetaDataKey

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

private

Definition at line 239 of file sitkImageSeriesReader.h.

◆ m_SpacingWarningRelThreshold

double itk::simple::ImageSeriesReader::m_SpacingWarningRelThreshold {1e-4}

private

Definition at line 248 of file sitkImageSeriesReader.h.

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

sitkImageSeriesReader.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Friends

Additional Inherited Members

Member Typedef Documentation

◆ MemberFunctionType

◆ Self

Constructor & Destructor Documentation

◆ ~ImageSeriesReader()

◆ ImageSeriesReader()

Member Function Documentation

◆ Execute()

◆ ExecuteInternal()

◆ GetFileNames()

◆ GetGDCMSeriesFileNames()

◆ GetGDCMSeriesIDs()

◆ GetMetaData()

◆ GetMetaDataDictionaryArrayUpdate()

◆ GetMetaDataKeys()

◆ GetName()

◆ GetSpacingWarningRelThreshold()

◆ HasMetaDataKey()

◆ MetaDataDictionaryArrayUpdateOff()

◆ MetaDataDictionaryArrayUpdateOn()

◆ SetFileNames()

◆ SetMetaDataDictionaryArrayUpdate()

◆ SetSpacingWarningRelThreshold()

◆ ToString()

Friends And Related Function Documentation

◆ detail::MemberFunctionAddressor< MemberFunctionType >

Member Data Documentation

◆ m_FileNames

◆ m_Filter

◆ m_MemberFactory

◆ m_MetaDataDictionaryArrayUpdate

◆ m_pfGetMetaData

◆ m_pfGetMetaDataKeys

◆ m_pfHasMetaDataKey

◆ m_SpacingWarningRelThreshold