#include <itkLabelGeometryImageFilter.h>

Inheritance diagram for itk::LabelGeometryImageFilter< TLabelImage, TIntensityImage >:

Collaboration diagram for itk::LabelGeometryImageFilter< TLabelImage, TIntensityImage >:

Detailed Description

template<typename TLabelImage, typename TIntensityImage = TLabelImage>
class itk::LabelGeometryImageFilter< TLabelImage, TIntensityImage >

Given a label map and an optional intensity image, compute geometric features.

This filter enables the measurement of geometric features of all objects in a labeled ND volume. This labeled volume can represent, for instance, a medical image segmented into different anatomical structures or a microscope image segmented into individual cells. This filter is closely related to the itkLabelStatisticsImageFilter, which measures statistics of image regions defined by a labeled mask such as min, max, and mean intensity, intensity standard deviation, and bounding boxes. This filter, however, measures the geometry of the labeled regions themselves.

It calculates features similar to the regionprops command of Matlab. The set of measurements that it enables include: volume, centroid, eigenvalues, eigenvectors, axes lenghts, eccentricity, elongation, orientation, bounding box, oriented bounding box, and rotation matrix. These features are based solely on the labeled mask itself. It also calculates integrated intensity and weighted centroid, which are measured on an intensity image under the labeled mask. These features represent the set of currently calculated features, but the framework of the filter is designed so that it can be easily expanded to measure a wide variety of other features.

Authors: Dirk Padfield and James Miller.

This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://commonfund.nih.gov/bioinformatics.

This filter was contributed in the Insight Journal paper: "A Label Geometry Image Filter for Multiple Object Measurement" by Padfield D., Miller J http://www.insight-journal.org/browse/publication/301 https://hdl.handle.net/1926/1493

Wiki Examples:

Examples:: WikiExamples/ImageProcessing/LabelGeometryImageFilter.cxx.

Definition at line 78 of file itkLabelGeometryImageFilter.h.

Classes
class	LabelGeometry

Public Types
typedef itk::FixedArray < RealType, itkGetStaticConstMacro(ImageDimension) >	AxesLengthType

typedef std::vector < LabelPointType >	BoundingBoxVerticesType

typedef SmartPointer< const Self >	ConstPointer

typedef DataObject::Pointer	DataObjectPointer

typedef itk::FixedArray < typename LabelIndexType::IndexValueType, itkGetStaticConstMacro(ImageDimension) >	IndexArrayType

typedef TIntensityImage::IndexType	IndexType

typedef TIntensityImage::Pointer	InputImagePointer

typedef TIntensityImage	IntensityImageType

typedef TLabelImage::Pointer	LabelImagePointer

typedef TLabelImage	LabelImageType

typedef TLabelImage::IndexType	LabelIndexType

typedef std::vector < LabelIndexType >	LabelIndicesType

typedef TLabelImage::PixelType	LabelPixelType

typedef TLabelImage::PointType	LabelPointType

typedef TLabelImage::RegionType	LabelRegionType

typedef TLabelImage::SizeType	LabelSizeType

typedef std::vector < LabelPixelType >	LabelsType

typedef itksys::hash_map < LabelPixelType, LabelGeometry > ::const_iterator	MapConstIterator

typedef itksys::hash_map < LabelPixelType, LabelGeometry >::iterator	MapIterator

typedef itksys::hash_map < LabelPixelType, LabelGeometry >	MapType

typedef vnl_matrix< double >	MatrixType

typedef TIntensityImage::PixelType	PixelType

typedef SmartPointer< Self >	Pointer

typedef SimpleDataObjectDecorator < RealType >	RealObjectType

typedef NumericTraits < PixelType >::RealType	RealType

typedef TIntensityImage::RegionType	RegionType

typedef LabelGeometryImageFilter	Self

typedef TIntensityImage::SizeType	SizeType

typedef ImageToImageFilter < TLabelImage, TIntensityImage >	Superclass

typedef std::vector< double >	VectorType


typedef itk::FixedArray < typename LabelIndexType::IndexValueType, itkGetStaticConstMacro(ImageDimension)*2 >	BoundingBoxType

typedef itk::FixedArray< float, itkGetStaticConstMacro(ImageDimension)*2 >	BoundingBoxFloatType

Public Types inherited from itk::ImageToImageFilter< TLabelImage, TIntensityImage >
typedef SmartPointer< const Self >	ConstPointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef InputImageType::PixelType	InputImagePixelType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::RegionType	InputImageRegionType

typedef TLabelImage	InputImageType

typedef Superclass::OutputImagePixelType	OutputImagePixelType

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef SmartPointer< Self >	Pointer

typedef ImageToImageFilter	Self

typedef ImageSource < TIntensityImage >	Superclass

Public Types inherited from itk::ImageSource< TIntensityImage >
typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef Superclass::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

typedef OutputImageType::PixelType	OutputImagePixelType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::RegionType	OutputImageRegionType

typedef TIntensityImage	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef ImageSource	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 MultiThreader	MultiThreaderType

typedef std::vector < DataObjectIdentifierType >	NameArray

typedef SmartPointer< Self >	Pointer

typedef ProcessObject	Self

typedef Object	Superclass

Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef Object	Self

typedef LightObject	Superclass

Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef LightObject	Self

Public Member Functions
virtual void	CalculateOrientedBoundingBoxOff ()

virtual void	CalculateOrientedBoundingBoxOn ()

virtual void	CalculateOrientedIntensityRegionsOff ()

virtual void	CalculateOrientedIntensityRegionsOn ()

virtual void	CalculateOrientedLabelRegionsOff ()

virtual void	CalculateOrientedLabelRegionsOn ()

virtual void	CalculatePixelIndicesOff ()

virtual void	CalculatePixelIndicesOn ()

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

AxesLengthType	GetAxesLength (LabelPixelType label) const

BoundingBoxType	GetBoundingBox (LabelPixelType label) const

LabelSizeType	GetBoundingBoxSize (LabelPixelType label) const

RealType	GetBoundingBoxVolume (LabelPixelType label) const

virtual bool	GetCalculateOrientedBoundingBox ()

virtual bool	GetCalculateOrientedIntensityRegions ()

virtual bool	GetCalculateOrientedLabelRegions ()

virtual bool	GetCalculatePixelIndices ()

LabelPointType	GetCentroid (LabelPixelType label) const

RealType	GetEccentricity (LabelPixelType label) const

VectorType	GetEigenvalues (LabelPixelType label) const

MatrixType	GetEigenvectors (LabelPixelType label) const

RealType	GetElongation (LabelPixelType label) const

RealType	GetIntegratedIntensity (LabelPixelType label) const

const TIntensityImage *	GetIntensityInput () const

std::vector< LabelPixelType >	GetLabels () const

RealType	GetMajorAxisLength (LabelPixelType label) const

RealType	GetMinorAxisLength (LabelPixelType label) const

virtual const char *	GetNameOfClass () const

SizeValueType	GetNumberOfLabels () const

SizeValueType	GetNumberOfObjects () const

RealType	GetOrientation (LabelPixelType label) const

LabelPointType	GetOrientedBoundingBoxOrigin (LabelPixelType label) const

LabelPointType	GetOrientedBoundingBoxSize (LabelPixelType label) const

BoundingBoxVerticesType	GetOrientedBoundingBoxVertices (LabelPixelType label) const

RealType	GetOrientedBoundingBoxVolume (LabelPixelType label) const

TIntensityImage *	GetOrientedIntensityImage (LabelPixelType label) const

TLabelImage *	GetOrientedLabelImage (LabelPixelType label) const

LabelIndicesType	GetPixelIndices (LabelPixelType label) const

RegionType	GetRegion (LabelPixelType label) const

MatrixType	GetRotationMatrix (LabelPixelType label) const

SizeValueType	GetVolume (LabelPixelType label) const

LabelPointType	GetWeightedCentroid (LabelPixelType label) const

bool	HasLabel (LabelPixelType label) const

void	SetCalculateOrientedBoundingBox (const bool value)

void	SetCalculateOrientedIntensityRegions (const bool value)

void	SetCalculateOrientedLabelRegions (const bool value)

void	SetCalculatePixelIndices (const bool value)

void	SetIntensityInput (const TIntensityImage *input)

Public Member Functions inherited from itk::ImageToImageFilter< TLabelImage, TIntensityImage >
const InputImageType *	GetInput () const

const InputImageType *	GetInput (unsigned int idx) const

virtual void	PopBackInput () override

virtual void	PopFrontInput () override

virtual void	PushBackInput (const InputImageType *image)

virtual void	PushFrontInput (const InputImageType *image)

virtual void	SetInput (const InputImageType *image)

virtual void	SetInput (unsigned int, const TLabelImage *image)

virtual void	SetCoordinateTolerance (double _arg)

virtual double	GetCoordinateTolerance () const

virtual void	SetDirectionTolerance (double _arg)

virtual double	GetDirectionTolerance () const

Public Member Functions inherited from itk::ImageSource< TIntensityImage >
OutputImageType *	GetOutput (unsigned int idx)

virtual void	GraftNthOutput (unsigned int idx, DataObject *output)

virtual void	GraftOutput (const DataObjectIdentifierType &key, DataObject *output)

OutputImageType *	GetOutput ()

const OutputImageType *	GetOutput () const

virtual void	GraftOutput (DataObject *output)

virtual ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override

virtual ProcessObject::DataObjectPointer	MakeOutput (const ProcessObject::DataObjectIdentifierType &) override

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 ()

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 const float &	GetProgress () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

virtual void	PrepareOutputs ()

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)

void	SetProgress (float progress)

virtual void	SetReleaseDataFlag (bool flag)

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	SetNumberOfThreads (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfThreads () const

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 ()

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

virtual void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int) override

virtual void	UnRegister () const noexceptoverride

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () 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 ()

Static Public Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()

static void	GlobalWarningDisplayOff ()

static void	GlobalWarningDisplayOn ()

static Pointer	New ()

static void	SetGlobalWarningDisplay (bool flag)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Static Public Attributes
static const unsigned int	ImageDimension = TLabelImage::ImageDimension

Static Public Attributes inherited from itk::ImageToImageFilter< TLabelImage, TIntensityImage >
static const unsigned int	InputImageDimension

static const unsigned int	OutputImageDimension

Static Public Attributes inherited from itk::ImageSource< TIntensityImage >
static const unsigned int	OutputImageDimension

Protected Member Functions
void	GenerateData () override

	LabelGeometryImageFilter ()

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

	~LabelGeometryImageFilter ()

Protected Member Functions inherited from itk::ImageToImageFilter< TLabelImage, TIntensityImage >
virtual void	CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)

virtual void	CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)

virtual void	GenerateInputRequestedRegion () override

	ImageToImageFilter ()

virtual void	VerifyInputInformation () override

	~ImageToImageFilter () override

void	PushBackInput (const DataObject *input) override

void	PushFrontInput (const DataObject *input) override

Protected Member Functions inherited from itk::ImageSource< TIntensityImage >
virtual void	AfterThreadedGenerateData ()

virtual void	AllocateOutputs ()

virtual void	BeforeThreadedGenerateData ()

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

	ImageSource ()

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int pieces, OutputImageRegionType &splitRegion)

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)

virtual	~ImageSource () 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	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

	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))

	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))

	itkLegacyMacro (virtual void RemoveInput(DataObject *input))

	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))

DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const

DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const

DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const

DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) 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	VerifyPreconditions ()

	~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 (void) const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName (void) const

DataObject *	GetOutput (DataObjectPointerArraySizeType idx)

const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &time)

virtual	~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 Member Functions
bool	CalculateOrientedBoundingBoxVertices (vnl_symmetric_eigensystem< double > eig, LabelGeometry &m_LabelGeometry)

Private Attributes
LabelsType	m_AllLabels

bool	m_CalculateOrientedBoundingBox

bool	m_CalculateOrientedIntensityRegions

bool	m_CalculateOrientedLabelRegions

bool	m_CalculatePixelIndices

LabelGeometry	m_LabelGeometry

MapType	m_LabelGeometryMapper

SimpleFastMutexLock	m_Mutex

Additional Inherited Members
Protected Types inherited from itk::ImageToImageFilter< TLabelImage, TIntensityImage >
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension) >	InputToOutputRegionCopierType

typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension) >	OutputToInputRegionCopierType

Static Protected Member Functions inherited from itk::ImageSource< TIntensityImage >
static const ImageRegionSplitterBase *	GetGlobalDefaultSplitter ()

static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Protected Attributes inherited from itk::LightObject
AtomicInt< int >	m_ReferenceCount