itk::GDCMSeriesFileNames Class Reference

#include <itkGDCMSeriesFileNames.h>

Detailed Description

Generate a sequence of filenames from a DICOM series.

This class generates a sequence of files whose filenames point to a DICOM file. The ordering is based on the following strategy: Read all images in the directory (assuming there is only one study/series)

1. Extract Image Orientation & Image Position from DICOM images, and then calculate the ordering based on the 3D coordinate of the slice.
2. If for some reason this information is not found or failed, another strategy is used: the ordering is based on 'Instance Number'.
3. If this strategy also failed, then the filenames are ordered by lexicographical order.

If multiple volumes are being grouped as a single series for your DICOM objects, you may want to try calling SetUseSeriesDetails(true) prior to calling SetDirectory().

Examples

Examples/IO/DicomSeriesReadGaussianImageWrite.cxx, Examples/IO/DicomSeriesReadImageWrite2.cxx, Examples/IO/DicomSeriesReadPrintTags.cxx, Examples/IO/DicomSeriesReadSeriesWrite.cxx, SphinxExamples/src/IO/GDCM/ReadAndPrintDICOMTags/Code.cxx, SphinxExamples/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Code.cxx, and SphinxExamples/src/IO/GDCM/ResampleDICOMSeries/Code.cxx.

Definition at line 63 of file itkGDCMSeriesFileNames.h.

Inheritance diagram for itk::GDCMSeriesFileNames:

Collaboration diagram for itk::GDCMSeriesFileNames:

Public Types
using	FileNamesContainerType = FilenamesContainer
using	Pointer = SmartPointer< Self >
using	Self = GDCMSeriesFileNames
using	SeriesUIDContainerType = SerieUIDContainer
using	Superclass = ProcessObject
Public Types inherited from itk::ProcessObject
using	ConstPointer = SmartPointer< const Self >
using	DataObjectIdentifierType = DataObject::DataObjectIdentifierType
using	DataObjectPointer = DataObject::Pointer
using	DataObjectPointerArray = std::vector< DataObjectPointer >
using	DataObjectPointerArraySizeType = DataObjectPointerArray::size_type
using	MultiThreaderType = MultiThreaderBase
using	NameArray = std::vector< DataObjectIdentifierType >
using	Pointer = SmartPointer< Self >
using	Self = ProcessObject
using	Superclass = Object
Public Types inherited from itk::Object
using	ConstPointer = SmartPointer< const Self >
using	Pointer = SmartPointer< Self >
using	Self = Object
using	Superclass = LightObject
Public Types inherited from itk::LightObject
using	ConstPointer = SmartPointer< const Self >
using	Pointer = SmartPointer< Self >
using	Self = LightObject

Public Member Functions
void	AddSeriesRestriction (const std::string &tag)
const FileNamesContainerType &	GetFileNames (const std::string serie)
const FileNamesContainerType &	GetInputFileNames ()
const char *	GetNameOfClass () const override
const FileNamesContainerType &	GetOutputFileNames ()
const SeriesUIDContainerType &	GetSeriesUIDs ()
bool	GetUseSeriesDetails () const
void	SetDirectory (std::string const &name)
void	SetInputDirectory (const char *name)
void	SetInputDirectory (std::string const &name)
void	SetUseSeriesDetails (bool useSeriesDetails)
void	SetOutputDirectory (std::string const &name)
virtual void	SetRecursive (bool _arg)
virtual bool	GetRecursive () const
virtual void	RecursiveOn ()
virtual void	SetLoadSequences (bool _arg)
virtual bool	GetLoadSequences () const
virtual void	LoadSequencesOn ()
virtual void	SetLoadPrivateTags (bool _arg)
virtual bool	GetLoadPrivateTags () const
virtual void	LoadPrivateTagsOn ()
Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOn ()
virtual void	EnlargeOutputRequestedRegion (DataObject *)
virtual const bool &	GetAbortGenerateData () const
DataObjectPointerArray	GetIndexedInputs ()
DataObjectPointerArray	GetIndexedOutputs ()
NameArray	GetInputNames () const
DataObjectPointerArray	GetInputs ()
MultiThreaderType *	GetMultiThreader () const
DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const
DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const
DataObjectPointerArraySizeType	GetNumberOfInputs () const
DataObjectPointerArraySizeType	GetNumberOfOutputs () const
virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const
NameArray	GetOutputNames () const
DataObjectPointerArray	GetOutputs ()
virtual float	GetProgress () const
NameArray	GetRequiredInputNames () const
bool	HasInput (const DataObjectIdentifierType &key) const
bool	HasOutput (const DataObjectIdentifierType &key) const
void	IncrementProgress (float increment)
virtual DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)
virtual DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType idx)
virtual void	PrepareOutputs ()
virtual void	PropagateRequestedRegion (DataObject *output)
virtual void	ResetPipeline ()
virtual void	SetAbortGenerateData (bool _arg)
void	SetMultiThreader (MultiThreaderType *threader)
virtual void	Update ()
virtual void	UpdateLargestPossibleRegion ()
virtual void	UpdateOutputData (DataObject *output)
virtual void	UpdateOutputInformation ()
void	UpdateProgress (float progress)
virtual void	SetReleaseDataFlag (bool val)
virtual bool	GetReleaseDataFlag () const
void	ReleaseDataFlagOn ()
void	ReleaseDataFlagOff ()
virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)
virtual const bool &	GetReleaseDataBeforeUpdateFlag () const
virtual void	ReleaseDataBeforeUpdateFlagOn ()
virtual void	SetNumberOfWorkUnits (ThreadIdType _arg)
virtual const ThreadIdType &	GetNumberOfWorkUnits () const
Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *cmd) const
unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const
LightObject::Pointer	CreateAnother () const override
virtual void	DebugOff () const
virtual void	DebugOn () const
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
MetaDataDictionary &	GetMetaDataDictionary ()
const MetaDataDictionary &	GetMetaDataDictionary () const
virtual ModifiedTimeType	GetMTime () const
virtual const TimeStamp &	GetTimeStamp () const
bool	HasObserver (const EventObject &event) const
void	InvokeEvent (const EventObject &)
void	InvokeEvent (const EventObject &) const
virtual void	Modified () const
void	Register () const override
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag) const
void	SetDebug (bool debugFlag) const
void	SetReferenceCount (int) override
void	UnRegister () const noexcept override
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)
virtual void	SetObjectName (std::string _arg)
virtual const std::string &	GetObjectName () const
Public Member Functions inherited from itk::LightObject
Pointer	Clone () const
virtual void	Delete ()
virtual int	GetReferenceCount () const
void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static Pointer	New ()
static void	SetGlobalWarningDisplay (bool val)
Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()
static Pointer	New ()

Protected Member Functions
	GDCMSeriesFileNames ()
void	PrintSelf (std::ostream &os, Indent indent) const override
	~GDCMSeriesFileNames () override
Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)
void	AddOptionalInputName (const DataObjectIdentifierType &)
void	AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
virtual void	AddOutput (DataObject *output)
bool	AddRequiredInputName (const DataObjectIdentifierType &)
bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
virtual void	CacheInputReleaseDataFlags ()
virtual void	GenerateData ()
virtual void	GenerateInputRequestedRegion ()
virtual void	GenerateOutputInformation ()
virtual void	GenerateOutputRequestedRegion (DataObject *output)
DataObject *	GetInput (const DataObjectIdentifierType &key)
const DataObject *	GetInput (const DataObjectIdentifierType &key) const
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const
bool	IsIndexedInputName (const DataObjectIdentifierType &) const
bool	IsIndexedOutputName (const DataObjectIdentifierType &) const
bool	IsRequiredInputName (const DataObjectIdentifierType &) const
DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const
DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const
DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const
DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const
virtual void	PopBackInput ()
virtual void	PopFrontInput ()
	ProcessObject ()
virtual void	PropagateResetPipeline ()
virtual void	PushBackInput (const DataObject *input)
virtual void	PushFrontInput (const DataObject *input)
virtual void	ReleaseInputs ()
virtual void	RemoveInput (const DataObjectIdentifierType &key)
virtual void	RemoveInput (DataObjectPointerArraySizeType)
virtual void	RemoveOutput (const DataObjectIdentifierType &key)
virtual void	RemoveOutput (DataObjectPointerArraySizeType idx)
bool	RemoveRequiredInputName (const DataObjectIdentifierType &)
virtual void	RestoreInputReleaseDataFlags ()
virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)
virtual void	SetNthInput (DataObjectPointerArraySizeType idx, DataObject *input)
virtual void	SetNthOutput (DataObjectPointerArraySizeType idx, DataObject *output)
void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
virtual void	SetOutput (const DataObjectIdentifierType &name, DataObject *output)
virtual void	SetPrimaryInput (DataObject *object)
virtual void	SetPrimaryOutput (DataObject *object)
void	SetRequiredInputNames (const NameArray &)
virtual void	VerifyInputInformation () const
virtual void	VerifyPreconditions () const
	~ProcessObject () override
DataObject *	GetInput (DataObjectPointerArraySizeType idx)
const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const
DataObject *	GetPrimaryInput ()
const DataObject *	GetPrimaryInput () const
virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)
virtual const char *	GetPrimaryInputName () const
DataObject *	GetOutput (const DataObjectIdentifierType &key)
const DataObject *	GetOutput (const DataObjectIdentifierType &key) const
virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)
virtual const char *	GetPrimaryOutputName () const
DataObject *	GetOutput (DataObjectPointerArraySizeType i)
const DataObject *	GetOutput (DataObjectPointerArraySizeType i) const
DataObject *	GetPrimaryOutput ()
const DataObject *	GetPrimaryOutput () const
virtual bool	GetThreaderUpdateProgress () const
virtual void	ThreaderUpdateProgressOn ()
virtual void	SetThreaderUpdateProgress (bool arg)
Protected Member Functions inherited from itk::Object
	Object ()
bool	PrintObservers (std::ostream &os, Indent indent) const
virtual void	SetTimeStamp (const TimeStamp &timeStamp)
	~Object () override
Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const
	LightObject ()
virtual void	PrintHeader (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
virtual	~LightObject ()

Private Attributes
std::string	m_InputDirectory = ""
FileNamesContainerType	m_InputFileNames {}
bool	m_LoadPrivateTags = false
bool	m_LoadSequences = false
std::string	m_OutputDirectory = ""
FileNamesContainerType	m_OutputFileNames {}
bool	m_Recursive = false
std::unique_ptr< gdcm::SerieHelper >	m_SerieHelper
SeriesUIDContainerType	m_SeriesUIDs {}
bool	m_UseSeriesDetails = true

Additional Inherited Members
Static Protected Member Functions inherited from itk::ProcessObject
template<typename TSourceObject >
static void	MakeRequiredOutputs (TSourceObject &sourceObject, const DataObjectPointerArraySizeType numberOfRequiredOutputs)
static constexpr float	progressFixedToFloat (uint32_t fixed)
static uint32_t	progressFloatToFixed (float f)
Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime {}
bool	m_Updating {}
Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}

Member Typedef Documentation

FileNamesContainerType

using itk::GDCMSeriesFileNames::FileNamesContainerType = FilenamesContainer

Type of the container that holds the file names in the series.

Definition at line 74 of file itkGDCMSeriesFileNames.h.

Pointer

using itk::GDCMSeriesFileNames::Pointer = SmartPointer<Self>

Definition at line 71 of file itkGDCMSeriesFileNames.h.

Self

using itk::GDCMSeriesFileNames::Self = GDCMSeriesFileNames

Standard class type aliases.

Definition at line 69 of file itkGDCMSeriesFileNames.h.

SeriesUIDContainerType

using itk::GDCMSeriesFileNames::SeriesUIDContainerType = SerieUIDContainer

Type of the container that holds the UID's for the series.

Definition at line 77 of file itkGDCMSeriesFileNames.h.

Superclass

using itk::GDCMSeriesFileNames::Superclass = ProcessObject

Definition at line 70 of file itkGDCMSeriesFileNames.h.

Constructor & Destructor Documentation

GDCMSeriesFileNames()

itk::GDCMSeriesFileNames::GDCMSeriesFileNames ( )

protected

~GDCMSeriesFileNames()

itk::GDCMSeriesFileNames::~GDCMSeriesFileNames ( )

overrideprotected

Member Function Documentation

AddSeriesRestriction()

void itk::GDCMSeriesFileNames::AddSeriesRestriction

(

const std::string &

tag

)

Add more restriction on the selection of a Series. This follows the same approach as SetUseSeriesDetails, but allows a user to add even more DICOM tags to take into account for subrefining a set of DICOM files into multiple series. The tag format is "group|element" of a DICOM tag.

Warning

UseSeriesDetails needs to be set to true.

GetFileNames()

const FileNamesContainerType& itk::GDCMSeriesFileNames::GetFileNames

(

const std::string

serie

)

Returns a vector containing the series' file names. The file names are ordered by the strategy define in header. All DICOM files have the same exact UID equal to the one user's specified. An extended UID may be returned/used if SetUseSeriesDetails(true) has been called.

GetInputFileNames()

const FileNamesContainerType& itk::GDCMSeriesFileNames::GetInputFileNames

(

)

Returns a vector containing the series' file names. The file names are ordered by the strategy define in header. No sorting is done based on UID

GetLoadPrivateTags()

virtual bool itk::GDCMSeriesFileNames::GetLoadPrivateTags ( ) const

virtual

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

GetLoadSequences()

virtual bool itk::GDCMSeriesFileNames::GetLoadSequences ( ) const

virtual

Parse any sequences in the DICOM file. Defaults to false to skip sequences. This makes loading DICOM files faster when sequences are not needed.

GetNameOfClass()

const char* itk::GDCMSeriesFileNames::GetNameOfClass ( ) const

overridevirtual

See also

LightObject::GetNameOfClass()

Reimplemented from itk::ProcessObject.

GetOutputFileNames()

const FileNamesContainerType& itk::GDCMSeriesFileNames::GetOutputFileNames

(

)

Returns a vector containing the series' file names. The file names are ordered in the same exact order as the input one. This could be dangerous if the writing has changed 3rd position or some other DICOM tag in the header

GetRecursive()

virtual bool itk::GDCMSeriesFileNames::GetRecursive ( ) const

virtual

Recursively parse the input directory. Must be set before the call to SetInputDirectory().

GetSeriesUIDs()

const SeriesUIDContainerType& itk::GDCMSeriesFileNames::GetSeriesUIDs

(

)

Returns a vector containing all the UIDs found when parsing the directory specified via SetDirectory. If no directory is specified return an empty vector. An extended UID may be returned/used if SetUseSeriesDetails(true) has been called.

GetUseSeriesDetails()

bool itk::GDCMSeriesFileNames::GetUseSeriesDetails ( ) const

inline

Returns true if using 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

Definition at line 161 of file itkGDCMSeriesFileNames.h.

LoadPrivateTagsOn()

virtual void itk::GDCMSeriesFileNames::LoadPrivateTagsOn ( )

virtual

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

LoadSequencesOn()

virtual void itk::GDCMSeriesFileNames::LoadSequencesOn ( )

virtual

Parse any sequences in the DICOM file. Defaults to false to skip sequences. This makes loading DICOM files faster when sequences are not needed.

New()

static Pointer itk::GDCMSeriesFileNames::New ( )

static

Method for creation through the object factory.

PrintSelf()

void itk::GDCMSeriesFileNames::PrintSelf ( std::ostream &  os, Indent  indent  ) const

overrideprotectedvirtual

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::ProcessObject.

RecursiveOn()

virtual void itk::GDCMSeriesFileNames::RecursiveOn ( )

virtual

Recursively parse the input directory. Must be set before the call to SetInputDirectory().

SetDirectory()

void itk::GDCMSeriesFileNames::SetDirectory ( std::string const &  name )

inline

Set the directory that contains the DICOM series.

Definition at line 97 of file itkGDCMSeriesFileNames.h.

SetInputDirectory() [1/2]

void itk::GDCMSeriesFileNames::SetInputDirectory

(

const char *

name

)

Set the directory that contains the DICOM series.

SetInputDirectory() [2/2]

void itk::GDCMSeriesFileNames::SetInputDirectory

(

std::string const &

name

)

Set the directory that contains the DICOM series.

SetLoadPrivateTags()

virtual void itk::GDCMSeriesFileNames::SetLoadPrivateTags ( bool  _arg )

virtual

Parse any private tags in the DICOM file. Defaults to false to skip private tags. This makes loading DICOM files faster when private tags are not needed.

SetLoadSequences()

virtual void itk::GDCMSeriesFileNames::SetLoadSequences ( bool  _arg )

virtual

Parse any sequences in the DICOM file. Defaults to false to skip sequences. This makes loading DICOM files faster when sequences are not needed.

SetOutputDirectory()

void itk::GDCMSeriesFileNames::SetOutputDirectory ( std::string const &  name )

inline

Set the directory where the output DICOM series should be written.

Definition at line 110 of file itkGDCMSeriesFileNames.h.

SetRecursive()

virtual void itk::GDCMSeriesFileNames::SetRecursive ( bool  _arg )

virtual

Recursively parse the input directory. Must be set before the call to SetInputDirectory().

SetUseSeriesDetails()

void itk::GDCMSeriesFileNames::SetUseSeriesDetails

(

bool

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

Member Data Documentation

m_InputDirectory

std::string itk::GDCMSeriesFileNames::m_InputDirectory = ""

private

Contains the input directory where the DICOM series is found

Definition at line 201 of file itkGDCMSeriesFileNames.h.

m_InputFileNames

FileNamesContainerType itk::GDCMSeriesFileNames::m_InputFileNames {}

private

Internal structure to keep the list of input/output filenames

Definition at line 207 of file itkGDCMSeriesFileNames.h.

m_LoadPrivateTags

bool itk::GDCMSeriesFileNames::m_LoadPrivateTags = false

private

Definition at line 219 of file itkGDCMSeriesFileNames.h.

m_LoadSequences

bool itk::GDCMSeriesFileNames::m_LoadSequences = false

private

Definition at line 218 of file itkGDCMSeriesFileNames.h.

m_OutputDirectory

std::string itk::GDCMSeriesFileNames::m_OutputDirectory = ""

private

Contains the output directory where the DICOM series should be written

Definition at line 204 of file itkGDCMSeriesFileNames.h.

m_OutputFileNames

FileNamesContainerType itk::GDCMSeriesFileNames::m_OutputFileNames {}

private

Definition at line 208 of file itkGDCMSeriesFileNames.h.

m_Recursive

bool itk::GDCMSeriesFileNames::m_Recursive = false

private

Definition at line 217 of file itkGDCMSeriesFileNames.h.

m_SerieHelper

std::unique_ptr<gdcm::SerieHelper> itk::GDCMSeriesFileNames::m_SerieHelper

private

Internal structure to order series from one directory

Definition at line 211 of file itkGDCMSeriesFileNames.h.

m_SeriesUIDs

SeriesUIDContainerType itk::GDCMSeriesFileNames::m_SeriesUIDs {}

private

Internal structure to keep the list of series UIDs

Definition at line 214 of file itkGDCMSeriesFileNames.h.

m_UseSeriesDetails

bool itk::GDCMSeriesFileNames::m_UseSeriesDetails = true

private

Definition at line 216 of file itkGDCMSeriesFileNames.h.

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

• itkGDCMSeriesFileNames.h