itk::GDCMSeriesFileNames Class Reference

#include <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
virtual ::itk::LightObject::Pointer	CreateAnother () const
const FileNamesContainerType &	GetInputFileNames ()
virtual const char *	GetNameOfClass () const
void	SetDirectory (std::string const &name)
void	SetInputDirectory (const char *name)
void	SetInputDirectory (std::string const &name)
Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
virtual void	EnlargeOutputRequestedRegion (DataObject *)
virtual const bool &	GetAbortGenerateData () const
DataObjectPointerArray	GetIndexedInputs ()
DataObjectPointerArray	GetIndexedOutputs ()
NameArray	GetInputNames () const
DataObjectPointerArray	GetInputs ()
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	PropagateRequestedRegion (DataObject *output)
virtual void	ResetPipeline ()
virtual void	SetAbortGenerateData (bool _arg)
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	ReleaseDataBeforeUpdateFlagOff ()
virtual void	SetNumberOfWorkUnits (ThreadIdType _arg)
virtual const ThreadIdType &	GetNumberOfWorkUnits () const
MultiThreaderType *	GetMultiThreader () const
void	SetMultiThreader (MultiThreaderType *threader)
virtual void	PrepareOutputs ()
Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)
unsigned long	AddObserver (const EventObject &event, Command *) const
unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const
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)
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 ()
std::string	m_InputDirectory = ""
std::string	m_OutputDirectory = ""
FileNamesContainerType	m_InputFileNames
FileNamesContainerType	m_OutputFileNames
std::unique_ptr< gdcm::SerieHelper >	m_SerieHelper
SeriesUIDContainerType	m_SeriesUIDs
bool	m_UseSeriesDetails = true
bool	m_Recursive = false
bool	m_LoadSequences = false
bool	m_LoadPrivateTags = false
void	SetOutputDirectory (std::string const &name)
const FileNamesContainerType &	GetOutputFileNames ()
const FileNamesContainerType &	GetFileNames (const std::string serie)
const SeriesUIDContainerType &	GetSeriesUIDs ()
virtual void	SetRecursive (bool _arg)
virtual bool	GetRecursive () const
virtual void	RecursiveOn ()
virtual void	RecursiveOff ()
void	SetUseSeriesDetails (bool useSeriesDetails)
bool	GetUseSeriesDetails () const
void	AddSeriesRestriction (const std::string &tag)
virtual void	SetLoadSequences (bool _arg)
virtual bool	GetLoadSequences () const
virtual void	LoadSequencesOn ()
virtual void	LoadSequencesOff ()
virtual void	SetLoadPrivateTags (bool _arg)
virtual bool	GetLoadPrivateTags () const
virtual void	LoadPrivateTagsOn ()
virtual void	LoadPrivateTagsOff ()
	GDCMSeriesFileNames ()
	~GDCMSeriesFileNames () override
void	PrintSelf (std::ostream &os, Indent indent) const override

Additional Inherited Members
Protected Member Functions inherited from itk::ProcessObject
	ProcessObject ()
	~ProcessObject () override
DataObject *	GetInput (const DataObjectIdentifierType &key)
const DataObject *	GetInput (const DataObjectIdentifierType &key) const
DataObject *	GetInput (DataObjectPointerArraySizeType idx)
const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const
virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)
virtual void	SetNthInput (DataObjectPointerArraySizeType idx, DataObject *input)
virtual void	AddInput (DataObject *input)
virtual void	PushBackInput (const DataObject *input)
virtual void	PopBackInput ()
virtual void	PushFrontInput (const DataObject *input)
virtual void	PopFrontInput ()
virtual void	RemoveInput (const DataObjectIdentifierType &key)
virtual void	RemoveInput (DataObjectPointerArraySizeType)
DataObject *	GetPrimaryInput ()
const DataObject *	GetPrimaryInput () const
virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)
virtual const char *	GetPrimaryInputName () const
virtual void	SetPrimaryInput (DataObject *object)
void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const
bool	RemoveRequiredInputName (const DataObjectIdentifierType &)
bool	IsRequiredInputName (const DataObjectIdentifierType &) const
void	SetRequiredInputNames (const NameArray &)
bool	AddRequiredInputName (const DataObjectIdentifierType &)
bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
void	AddOptionalInputName (const DataObjectIdentifierType &)
void	AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
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
virtual void	SetOutput (const DataObjectIdentifierType &name, DataObject *output)
virtual void	RemoveOutput (const DataObjectIdentifierType &key)
DataObject *	GetPrimaryOutput ()
const DataObject *	GetPrimaryOutput () const
virtual void	SetPrimaryOutput (DataObject *object)
virtual void	SetNthOutput (DataObjectPointerArraySizeType idx, DataObject *output)
virtual void	AddOutput (DataObject *output)
virtual void	RemoveOutput (DataObjectPointerArraySizeType idx)
virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const
void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const
DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const
DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const
DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const
bool	IsIndexedInputName (const DataObjectIdentifierType &) const
bool	IsIndexedOutputName (const DataObjectIdentifierType &) const
virtual void	VerifyPreconditions () ITKv5_CONST
virtual void	VerifyInputInformation () ITKv5_CONST
virtual void	GenerateInputRequestedRegion ()
virtual void	GenerateOutputRequestedRegion (DataObject *output)
virtual void	GenerateOutputInformation ()
virtual void	GenerateData ()
virtual void	PropagateResetPipeline ()
virtual void	ReleaseInputs ()
virtual void	CacheInputReleaseDataFlags ()
virtual void	RestoreInputReleaseDataFlags ()
virtual bool	GetThreaderUpdateProgress () const
virtual void	ThreaderUpdateProgressOn ()
virtual void	ThreaderUpdateProgressOff ()
virtual void	SetThreaderUpdateProgress (bool arg)
Protected Member Functions inherited from itk::Object
	Object ()
	~Object () override
bool	PrintObservers (std::ostream &os, Indent indent) const
virtual void	SetTimeStamp (const TimeStamp &timeStamp)
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 ()
Static Protected Member Functions inherited from itk::ProcessObject
static constexpr float	progressFixedToFloat (uint32_t fixed)
static uint32_t	progressFloatToFixed (float f)
Protected Attributes inherited from itk::ProcessObject
bool	m_Updating
TimeStamp	m_OutputInformationMTime
Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount

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.

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

Contains the input directory where the DICOM serie is found

~GDCMSeriesFileNames()

itk::GDCMSeriesFileNames::~GDCMSeriesFileNames ( )

overrideprotected

Contains the input directory where the DICOM serie is found

Member Function Documentation

AddSeriesRestriction()

void itk::GDCMSeriesFileNames::AddSeriesRestriction

(

const std::string &

tag

)

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

Warning

User need to set SetUseSeriesDetails(true)

CreateAnother()

virtual::itk::LightObject::Pointer itk::GDCMSeriesFileNames::CreateAnother ( ) const

virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

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

Contains the input directory where the DICOM serie is found

GetLoadSequences()

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

virtual

Contains the input directory where the DICOM serie is found

GetNameOfClass()

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

virtual

Run-time type information (and related methods).

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

Contains the input directory where the DICOM serie is found

GetSeriesUIDs()

const SeriesUIDContainerType& itk::GDCMSeriesFileNames::GetSeriesUIDs

(

)

Returns a vector containing all the UIDs found when parsing the direcory specified via SetDirectory. If no direcory 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.

LoadPrivateTagsOff()

virtual void itk::GDCMSeriesFileNames::LoadPrivateTagsOff ( )

virtual

Contains the input directory where the DICOM serie is found

LoadPrivateTagsOn()

virtual void itk::GDCMSeriesFileNames::LoadPrivateTagsOn ( )

virtual

Contains the input directory where the DICOM serie is found

LoadSequencesOff()

virtual void itk::GDCMSeriesFileNames::LoadSequencesOff ( )

virtual

Contains the input directory where the DICOM serie is found

LoadSequencesOn()

virtual void itk::GDCMSeriesFileNames::LoadSequencesOn ( )

virtual

Contains the input directory where the DICOM serie is found

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

Contains the input directory where the DICOM serie is found

Reimplemented from itk::ProcessObject.

RecursiveOff()

virtual void itk::GDCMSeriesFileNames::RecursiveOff ( )

virtual

Contains the input directory where the DICOM serie is found

RecursiveOn()

virtual void itk::GDCMSeriesFileNames::RecursiveOn ( )

virtual

Contains the input directory where the DICOM serie is found

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 serie 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 serie 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

Contains the input directory where the DICOM serie is found

Definition at line 219 of file itkGDCMSeriesFileNames.h.

m_LoadSequences

bool itk::GDCMSeriesFileNames::m_LoadSequences = false

private

Contains the input directory where the DICOM serie is found

Definition at line 218 of file itkGDCMSeriesFileNames.h.

m_OutputDirectory

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

private

Contains the output directory where the DICOM serie should be written

Definition at line 204 of file itkGDCMSeriesFileNames.h.

m_OutputFileNames

FileNamesContainerType itk::GDCMSeriesFileNames::m_OutputFileNames

private

Contains the input directory where the DICOM serie is found

Definition at line 208 of file itkGDCMSeriesFileNames.h.

m_Recursive

bool itk::GDCMSeriesFileNames::m_Recursive = false

private

Contains the input directory where the DICOM serie is found

Definition at line 217 of file itkGDCMSeriesFileNames.h.

m_SerieHelper

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

private

Internal structure to order serie 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

Contains the input directory where the DICOM serie is found

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