Generate a sequence of filenames from a DICOM series. More...

#include <itkGDCMSeriesFileNames.h>

Inheritance diagram for itk::GDCMSeriesFileNames:

Collaboration diagram for itk::GDCMSeriesFileNames:

Public Types
typedef SmartPointer< const Self >	ConstPointer
typedef SmartPointer< Self >	Pointer
typedef GDCMSeriesFileNames	Self
typedef Object	Superclass
Public Member Functions
void	AddSeriesRestriction (const std::string &tag)
virtual LightObject::Pointer	CreateAnother () const
virtual void	DebugOff () const
virtual void	DebugOn () const
virtual void	Delete ()
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
const FilenamesContainer &	GetFileNames (const std::string serie)
const FilenamesContainer &	GetInputFileNames ()
MetaDataDictionary &	GetMetaDataDictionary (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
virtual unsigned long	GetMTime () const
virtual const char *	GetNameOfClass () const
const FilenamesContainer &	GetOutputFileNames ()
virtual int	GetReferenceCount () const
gdcm::SerieHelper *	GetSeriesHelper (void)
const SerieUIDContainer &	GetSeriesUIDs ()
bool	GetUseSeriesDetails (void)
bool	HasObserver (const EventObject &event) const
void	InvokeEvent (const EventObject &)
void	InvokeEvent (const EventObject &) const
virtual void	Modified () const
void	Print (std::ostream &os, Indent indent=0) const
virtual void	Register () const
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetDirectory (std::string const &name)
void	SetInputDirectory (std::string const &name)
void	SetInputDirectory (const char *name)
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int)
void	SetUseSeriesDetails (bool useSeriesDetails)
virtual void	UnRegister () const


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 ()


virtual void	SetLoadPrivateTags (bool _arg)
virtual bool	GetLoadPrivateTags () const
virtual void	LoadPrivateTagsOn ()
virtual void	LoadPrivateTagsOff ()


unsigned long	AddObserver (const EventObject &event, Command *)
unsigned long	AddObserver (const EventObject &event, Command *) const
Static Public Member Functions
static void	BreakOnError ()
static Pointer	New ()


static void	SetGlobalWarningDisplay (bool flag)
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOn ()
static void	GlobalWarningDisplayOff ()
Protected Types


typedef int	InternalReferenceCountType
Protected Member Functions
	GDCMSeriesFileNames ()
bool	PrintObservers (std::ostream &os, Indent indent) const
void	PrintSelf (std::ostream &os, Indent indent) const
	~GDCMSeriesFileNames ()


virtual void	PrintHeader (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
Protected Attributes
InternalReferenceCountType	m_ReferenceCount
SimpleFastMutexLock	m_ReferenceCountLock

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)

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 'Image 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().

Definition at line 52 of file itkGDCMSeriesFileNames.h.

Member Typedef Documentation

typedef SmartPointer<const Self> itk::Object::ConstPointer [inherited]

Reimplemented from itk::LightObject.

Definition at line 51 of file itkObject.h.

typedef int itk::LightObject::InternalReferenceCountType [protected, inherited]

Define the type of the reference count according to the target. This allows the use of atomic operations

Definition at line 139 of file itkLightObject.h.

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

Reimplemented from itk::Object.

Definition at line 58 of file itkGDCMSeriesFileNames.h.

typedef GDCMSeriesFileNames itk::GDCMSeriesFileNames::Self

Standard class typedefs.

Reimplemented from itk::Object.

Definition at line 56 of file itkGDCMSeriesFileNames.h.

typedef Object itk::GDCMSeriesFileNames::Superclass

Reimplemented from itk::Object.

Definition at line 57 of file itkGDCMSeriesFileNames.h.

Constructor & Destructor Documentation

itk::GDCMSeriesFileNames::GDCMSeriesFileNames ( ) [protected]

itk::GDCMSeriesFileNames::~GDCMSeriesFileNames ( ) [protected]

Member Function Documentation

unsigned long itk::Object::AddObserver	(	const EventObject &	event,
		Command *
	)			`[inherited]`

Allow people to add/remove/invoke observers (callbacks) to any ITK object. This is an implementation of the subject/observer design pattern. An observer is added by specifying an event to respond to and an itk::Command to execute. It returns an unsigned long tag which can be used later to remove the event or retrieve the command. The memory for the Command becomes the responsibility of this object, so don't pass the same instance of a command to two different objects

unsigned long itk::Object::AddObserver	(	const EventObject &	event,
		Command *
	)			const `[inherited]`

Allow people to add/remove/invoke observers (callbacks) to any ITK object. This is an implementation of the subject/observer design pattern. An observer is added by specifying an event to respond to and an itk::Command to execute. It returns an unsigned long tag which can be used later to remove the event or retrieve the command. The memory for the Command becomes the responsibility of this object, so don't pass the same instance of a command to two different objects

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 153 of file itkGDCMSeriesFileNames.h.

static void itk::LightObject::BreakOnError ( ) [static, inherited]

This method is called when itkExceptionMacro executes. It allows the debugger to break on error.

virtual LightObject::Pointer itk::Object::CreateAnother ( ) const [virtual, inherited]

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::LightObject.

virtual void itk::Object::DebugOff ( ) const [virtual, inherited]

Turn debugging output off.

virtual void itk::Object::DebugOn ( ) const [virtual, inherited]

Turn debugging output on.

virtual void itk::LightObject::Delete ( ) [virtual, inherited]

Delete an itk object. This method should always be used to delete an object when the new operator was used to create it. Using the C delete method will not work with reference counting.

Command* itk::Object::GetCommand ( unsigned long tag ) [inherited]

Get the command associated with the given tag. NOTE: This returns a pointer to a Command, but it is safe to asign this to a Command::Pointer. Since Command inherits from LightObject, at this point in the code, only a pointer or a reference to the Command can be used.

bool itk::Object::GetDebug ( ) const [inherited]

Get the value of the debug flag.

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.

static bool itk::Object::GetGlobalWarningDisplay ( ) [static, inherited]

This is a global flag that controls whether any debug, warning or error messages are displayed.

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.

const MetaDataDictionary& itk::Object::GetMetaDataDictionary ( void ) const [inherited]

Returns:: A constant reference to this objects MetaDataDictionary.

MetaDataDictionary& itk::Object::GetMetaDataDictionary ( void ) [inherited]

Returns:: A reference to this objects MetaDataDictionary.

Warning:: This reference may be changed.

virtual unsigned long itk::Object::GetMTime ( ) const [virtual, inherited]

Return this objects modified time.

Referenced by itk::SpatialObject< ::itk::GetMeshDimension< TMesh >::PointDimension >::GetObjectMTime().

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

Run-time type information (and related methods).

Reimplemented from itk::Object.

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

virtual int itk::LightObject::GetReferenceCount ( ) const [inline, virtual, inherited]

Gets the reference count on this object.

Definition at line 106 of file itkLightObject.h.

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 142 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 131 of file itkGDCMSeriesFileNames.h.

static void itk::Object::GlobalWarningDisplayOff ( ) [inline, static, inherited]

This is a global flag that controls whether any debug, warning or error messages are displayed.

Definition at line 100 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

static void itk::Object::GlobalWarningDisplayOn ( ) [inline, static, inherited]

This is a global flag that controls whether any debug, warning or error messages are displayed.

Definition at line 98 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

bool itk::Object::HasObserver ( const EventObject & event ) const [inherited]

Return true if an observer is registered for this event.

void itk::Object::InvokeEvent ( const EventObject & ) [inherited]

Call Execute on all the Commands observing this event id.

void itk::Object::InvokeEvent ( const EventObject & ) const [inherited]

Call Execute on all the Commands observing this event id. The actions triggered by this call doesn't modify this object.

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.

virtual void itk::Object::Modified ( ) const [virtual, inherited]

Update the modification time for this object. Many filters rely on the modification time to determine if they need to recompute their data.

Referenced by itk::NarrowBandImageFilterBase< TInputImage, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::InsertNarrowBandNode(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetCenter(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetMatrix(), itk::NarrowBandImageFilterBase< TInputImage, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::SetNarrowBand(), itk::NarrowBandImageFilterBase< TInputImage, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::SetNarrowBandInnerRadius(), itk::NarrowBandImageFilterBase< TInputImage, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::SetNarrowBandTotalRadius(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetOffset(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetRealThresholds(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetThresholds(), itk::Statistics::GoodnessOfFitFunctionBase< TInputHistogram >::SetTotalObservedScale(), and itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetTranslation().

static Pointer itk::GDCMSeriesFileNames::New ( ) [static]

Method for creation through the object factory.

Reimplemented from itk::Object.

void itk::LightObject::Print	(	std::ostream &	os,
		Indent	indent = `0`
	)			const `[inherited]`

Cause the object to print itself out.

Referenced by itk::WeakPointer< ProcessObject >::Print().

virtual void itk::LightObject::PrintHeader	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual, inherited]`

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.

bool itk::Object::PrintObservers	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, inherited]`

void itk::GDCMSeriesFileNames::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual]`

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::Object.

virtual void itk::LightObject::PrintTrailer	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual, inherited]`

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.

virtual void itk::GDCMSeriesFileNames::RecursiveOff ( ) [virtual]

Recursively parse the input directory

virtual void itk::GDCMSeriesFileNames::RecursiveOn ( ) [virtual]

Recursively parse the input directory

virtual void itk::Object::Register ( ) const [virtual, inherited]

Increase the reference count (mark as used by another object).

Reimplemented from itk::LightObject.

void itk::Object::RemoveAllObservers ( ) [inherited]

Remove all observers .

void itk::Object::RemoveObserver ( unsigned long tag ) [inherited]

Remove the observer with this tag value.

void itk::Object::SetDebug ( bool debugFlag ) const [inherited]

Set the value of the debug flag. A non-zero value turns debugging on.

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

Set the directory that contains the DICOM series.

Definition at line 75 of file itkGDCMSeriesFileNames.h.

static void itk::Object::SetGlobalWarningDisplay ( bool flag ) [static, inherited]

This is a global flag that controls whether any debug, warning or error messages are displayed.

Referenced by itk::Object::GlobalWarningDisplayOff(), and itk::Object::GlobalWarningDisplayOn().

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

Set the directory that contains the DICOM series.

void itk::GDCMSeriesFileNames::SetInputDirectory ( const char * 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::Object::SetMetaDataDictionary ( const MetaDataDictionary & rhs ) [inherited]

Returns:: Set the MetaDataDictionary

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

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

Definition at line 86 of file itkGDCMSeriesFileNames.h.

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

Recursively parse the input directory

virtual void itk::Object::SetReferenceCount ( int ) [virtual, inherited]

Sets the reference count (use with care)

Reimplemented from itk::LightObject.

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

virtual void itk::Object::UnRegister ( ) const [virtual, inherited]

Decrease the reference count (release by another object).

Reimplemented from itk::LightObject.

Member Data Documentation

InternalReferenceCountType itk::LightObject::m_ReferenceCount [mutable, protected, inherited]

Number of uses of this object by other objects.

Definition at line 144 of file itkLightObject.h.

SimpleFastMutexLock itk::LightObject::m_ReferenceCountLock [mutable, protected, inherited]

Mutex lock to protect modification to the reference count

Definition at line 147 of file itkLightObject.h.

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

itkGDCMSeriesFileNames.h

itk::GDCMSeriesFileNames Class Reference [Input and Output Filters]

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

itk::GDCMSeriesFileNames Class Reference
[Input and Output Filters]