#include <itkGDCMSeriesFileNames.h>

Inheritance diagram for itk::GDCMSeriesFileNames:

Collaboration diagram for itk::GDCMSeriesFileNames:

Public Types
typedef SmartPointer< Self >	Pointer
typedef GDCMSeriesFileNames	Self
typedef ProcessObject	Superclass
Public Types inherited from itk::ProcessObject
typedef SmartPointer< const Self >	ConstPointer
typedef DataObject::DataObjectIdentifierType	DataObjectIdentifierType
typedef DataObject::Pointer	DataObjectPointer
typedef std::vector < DataObjectPointer >	DataObjectPointerArray
typedef DataObjectPointerArray::size_type	DataObjectPointerArraySizeType
typedef std::vector < DataObjectIdentifierType >	NameArray
Public Types inherited from itk::Object
Public Types inherited from itk::LightObject

Public Member Functions
void	AddSeriesRestriction (const std::string &tag)
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
const FilenamesContainer &	GetFileNames (const std::string serie)
const FilenamesContainer &	GetInputFileNames ()
virtual const char *	GetNameOfClass () const
const FilenamesContainer &	GetOutputFileNames ()
gdcm::SerieHelper *	GetSeriesHelper (void)
const SerieUIDContainer &	GetSeriesUIDs ()
bool	GetUseSeriesDetails (void)
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	RecursiveOff ()

virtual void	SetLoadSequences (bool _arg)
virtual bool	GetLoadSequences () const
virtual void	LoadSequencesOn ()
virtual void	LoadSequencesOff ()
Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
virtual void	EnlargeOutputRequestedRegion (DataObject *)
virtual const bool &	GetAbortGenerateData ()
NameArray	GetInputNames () const
MultiThreader *	GetMultiThreader () const
DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const
DataObjectPointerArraySizeType	GetNumberOfInputs () const
DataObjectPointerArraySizeType	GetNumberOfOutputs () const
virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const
NameArray	GetOutputNames () const
virtual const float &	GetProgress ()
NameArray	GetRequiredInputNames () const
bool	HasInput (const DataObjectIdentifierType &key) const
bool	HasOutput (const DataObjectIdentifierType &key) const
virtual DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType idx)
virtual DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)
virtual void	PrepareOutputs ()
virtual void	PropagateRequestedRegion (DataObject *output)
virtual void	ResetPipeline ()
virtual void	SetAbortGenerateData (bool _arg)
virtual void	SetProgress (float _arg)
virtual void	Update ()
virtual void	UpdateLargestPossibleRegion ()
virtual void	UpdateOutputData (DataObject *output)
virtual void	UpdateOutputInformation ()
void	UpdateProgress (float amount)
DataObjectPointerArray	GetInputs ()
DataObjectPointerArray	GetOutputs ()
DataObjectPointerArray	GetIndexedInputs ()
DataObjectPointerArray	GetIndexedOutputs ()
DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const
virtual void	SetReleaseDataFlag (bool flag)
virtual bool	GetReleaseDataFlag () const
void	ReleaseDataFlagOn ()
void	ReleaseDataFlagOff ()
virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)
virtual const bool &	GetReleaseDataBeforeUpdateFlag ()
virtual void	ReleaseDataBeforeUpdateFlagOn ()
virtual void	ReleaseDataBeforeUpdateFlagOff ()
virtual void	SetNumberOfThreads (ThreadIdType _arg)
virtual const ThreadIdType &	GetNumberOfThreads ()
Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)
unsigned long	AddObserver (const EventObject &event, Command *) const
virtual void	DebugOff () const
virtual void	DebugOn () const
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
MetaDataDictionary &	GetMetaDataDictionary (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
virtual unsigned long	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
virtual void	Register () const
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int)
virtual void	UnRegister () const
Public Member Functions inherited from itk::LightObject
virtual void	Delete ()
virtual int	GetReferenceCount () const
	itkCloneMacro (Self)
void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()
Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)
virtual void	AddOutput (DataObject *output)
bool	AddRequiredInputName (const DataObjectIdentifierType &)
virtual void	CacheInputReleaseDataFlags ()
virtual void	GenerateData ()
virtual void	GenerateInputRequestedRegion ()
virtual void	GenerateOutputInformation ()
virtual void	GenerateOutputRequestedRegion (DataObject *output)
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs ()
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs ()
bool	IsIndexedName (const DataObjectIdentifierType &) const
bool	IsRequiredInputName (const DataObjectIdentifierType &) const
	itkLegacyMacro (virtual void RemoveInput(DataObject *input))
	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))
	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))
	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))
DataObjectPointerArraySizeType	MakeIndexFromName (const DataObjectIdentifierType &) const
DataObjectIdentifierType	MakeNameFromIndex (DataObjectPointerArraySizeType) const
	ProcessObject ()
virtual void	PropagateResetPipeline ()
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 num, DataObject *input)
virtual void	SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)
void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
virtual void	SetOutput (const DataObjectIdentifierType &key, DataObject *output)
virtual void	SetPrimaryInput (DataObject *input)
virtual void	SetPrimaryOutput (DataObject *output)
void	SetRequiredInputNames (const NameArray &)
virtual void	VerifyInputInformation ()
virtual void	VerifyPreconditions ()
	~ProcessObject ()
DataObject *	GetInput (const DataObjectIdentifierType &key)
const DataObject *	GetInput (const DataObjectIdentifierType &key) const
DataObject *	GetInput (DataObjectPointerArraySizeType)
const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const
DataObject *	GetPrimaryInput ()
const DataObject *	GetPrimaryInput () const
DataObject *	GetOutput (const DataObjectIdentifierType &key)
const DataObject *	GetOutput (const DataObjectIdentifierType &key) const
DataObject *	GetOutput (DataObjectPointerArraySizeType idx)
const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const
DataObject *	GetPrimaryOutput ()
const DataObject *	GetPrimaryOutput () const
virtual void	PushBackInput (const DataObject *input)
virtual void	PopBackInput ()
virtual void	PushFrontInput (const DataObject *input)
virtual void	PopFrontInput ()
Protected Member Functions inherited from itk::Object
	Object ()
bool	PrintObservers (std::ostream &os, Indent indent) const
virtual void	SetTimeStamp (const TimeStamp &time)
virtual	~Object ()
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 Member Functions
	GDCMSeriesFileNames (const Self &)
void	operator= (const Self &)

Private Attributes
std::string	m_InputDirectory
FilenamesContainer	m_InputFileNames
bool	m_LoadPrivateTags
bool	m_LoadSequences
std::string	m_OutputDirectory
FilenamesContainer	m_OutputFileNames
bool	m_Recursive
gdcm::SerieHelper *	m_SerieHelper
SerieUIDContainer	m_SeriesUIDs
bool	m_UseSeriesDetails
virtual void	SetLoadPrivateTags (bool _arg)
virtual bool	GetLoadPrivateTags () const
virtual void	LoadPrivateTagsOn ()
virtual void	LoadPrivateTagsOff ()
	GDCMSeriesFileNames ()
	~GDCMSeriesFileNames ()
void	PrintSelf (std::ostream &os, Indent indent) const

Additional Inherited Members
Protected Attributes inherited from itk::ProcessObject
bool	m_Updating
TimeStamp	m_OutputInformationMTime

Detailed Description

Generate a sequence of filenames from a DICOM series.

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

Extract Image Orientation & Image Position from DICOM images, and then calculate the ordering based on the 3D coordinate of the slice
If for some reason this information is not found or failed, another strategy is used: the ordering is based on 'Image Number'
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().

Definition at line 53 of file itkGDCMSeriesFileNames.h.

Member Typedef Documentation

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

Reimplemented from itk::ProcessObject.

Definition at line 59 of file itkGDCMSeriesFileNames.h.

typedef GDCMSeriesFileNames itk::GDCMSeriesFileNames::Self

Standard class typedefs.

Reimplemented from itk::ProcessObject.

Definition at line 57 of file itkGDCMSeriesFileNames.h.

typedef ProcessObject itk::GDCMSeriesFileNames::Superclass

Reimplemented from itk::ProcessObject.

Definition at line 58 of file itkGDCMSeriesFileNames.h.

Constructor & Destructor Documentation

itk::GDCMSeriesFileNames::GDCMSeriesFileNames ( )

protected

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.

itk::GDCMSeriesFileNames::~GDCMSeriesFileNames ( )

protected

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.

itk::GDCMSeriesFileNames::GDCMSeriesFileNames ( const Self & )

private

Member Function Documentation

void itk::GDCMSeriesFileNames::AddSeriesRestriction ( const std::string & tag )

inline

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)

Definition at line 154 of file itkGDCMSeriesFileNames.h.

virtual::itk::LightObject::Pointer itk::GDCMSeriesFileNames::CreateAnother ( void ) 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.

const FilenamesContainer& 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.

const FilenamesContainer& 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

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.

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.

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

virtual

Run-time type information (and related methods).

Reimplemented from itk::ProcessObject.

const FilenamesContainer& itk::GDCMSeriesFileNames::GetOutputFileNames ( )

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

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

virtual

Recursively parse the input directory

gdcm::SerieHelper* itk::GDCMSeriesFileNames::GetSeriesHelper ( void )

inline

Returns a pointer to the SeriesHelper class. This access allows the files as gdcm dicom objects in a series to be queried for dicom tag values prior to reading the series. Such querying is useful to determine which series should be read - e.g., to determine which is the T2 scan, etc.

Definition at line 143 of file itkGDCMSeriesFileNames.h.

const SerieUIDContainer& 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.

bool itk::GDCMSeriesFileNames::GetUseSeriesDetails ( void )

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 132 of file itkGDCMSeriesFileNames.h.

virtual void itk::GDCMSeriesFileNames::LoadPrivateTagsOff ( )

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.

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.

virtual void itk::GDCMSeriesFileNames::LoadSequencesOff ( )

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.

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.

static Pointer itk::GDCMSeriesFileNames::New ( )

static

Method for creation through the object factory.

Reimplemented from itk::Object.

void itk::GDCMSeriesFileNames::operator= ( const Self & )

private

Time when GenerateOutputInformation was last called.

Reimplemented from itk::ProcessObject.

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

protectedvirtual

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.

Reimplemented from itk::ProcessObject.

virtual void itk::GDCMSeriesFileNames::RecursiveOff ( )

virtual

Recursively parse the input directory

virtual void itk::GDCMSeriesFileNames::RecursiveOn ( )

virtual

Recursively parse the input directory

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

inline

Set the directory that contains the DICOM series.

Definition at line 76 of file itkGDCMSeriesFileNames.h.

void itk::GDCMSeriesFileNames::SetInputDirectory ( const char * name )

Set the directory that contains the DICOM series.

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

Set the directory that contains the DICOM series.

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.

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.

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

inline

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

Definition at line 87 of file itkGDCMSeriesFileNames.h.

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

virtual

Recursively parse the input directory

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

std::string itk::GDCMSeriesFileNames::m_InputDirectory

private

Contains the input directory where the DICOM serie is found

Definition at line 186 of file itkGDCMSeriesFileNames.h.

FilenamesContainer itk::GDCMSeriesFileNames::m_InputFileNames

private

Internal structure to keep the list of input/output filenames

Definition at line 192 of file itkGDCMSeriesFileNames.h.

bool itk::GDCMSeriesFileNames::m_LoadPrivateTags

private

Definition at line 204 of file itkGDCMSeriesFileNames.h.

bool itk::GDCMSeriesFileNames::m_LoadSequences

private

Definition at line 203 of file itkGDCMSeriesFileNames.h.

std::string itk::GDCMSeriesFileNames::m_OutputDirectory

private

Contains the output directory where the DICOM serie should be written

Definition at line 189 of file itkGDCMSeriesFileNames.h.

FilenamesContainer itk::GDCMSeriesFileNames::m_OutputFileNames

private

Definition at line 193 of file itkGDCMSeriesFileNames.h.

bool itk::GDCMSeriesFileNames::m_Recursive

private

Definition at line 202 of file itkGDCMSeriesFileNames.h.

gdcm::SerieHelper* itk::GDCMSeriesFileNames::m_SerieHelper

private

Internal structure to order serie from one directory

Definition at line 196 of file itkGDCMSeriesFileNames.h.

SerieUIDContainer itk::GDCMSeriesFileNames::m_SeriesUIDs

private

Internal structure to keep the list of series UIDs

Definition at line 199 of file itkGDCMSeriesFileNames.h.

bool itk::GDCMSeriesFileNames::m_UseSeriesDetails

private

Definition at line 201 of file itkGDCMSeriesFileNames.h.

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

itkGDCMSeriesFileNames.h

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation