#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 77 of file itkLabelGeometryImageFilter.h.

Classes
class	LabelGeometry

Public Types
using	AxesLengthType = itk::FixedArray< RealType, Self::ImageDimension >

using	BoundingBoxFloatType = itk::FixedArray< float, Self::ImageDimension *2 >

using	BoundingBoxType = itk::FixedArray< typename LabelIndexType::IndexValueType, Self::ImageDimension *2 >

using	BoundingBoxVerticesType = std::vector< LabelPointType >

using	ConstPointer = SmartPointer< const Self >

using	DataObjectPointer = typename DataObject::Pointer

using	IndexArrayType = itk::FixedArray< typename LabelIndexType::IndexValueType, Self::ImageDimension >

using	IndexType = typename TIntensityImage::IndexType

using	InputImagePointer = typename TIntensityImage::Pointer

using	IntensityImageType = TIntensityImage

using	LabelImagePointer = typename TLabelImage::Pointer

using	LabelImageType = TLabelImage

using	LabelIndexType = typename TLabelImage::IndexType

using	LabelIndicesType = std::vector< LabelIndexType >

using	LabelPixelType = typename TLabelImage::PixelType

using	LabelPointType = typename TLabelImage::PointType

using	LabelRegionType = typename TLabelImage::RegionType

using	LabelSizeType = typename TLabelImage::SizeType

using	LabelsType = std::vector< LabelPixelType >

using	MapConstIterator = typename itksys::hash_map< LabelPixelType, LabelGeometry >::const_iterator

using	MapIterator = typename itksys::hash_map< LabelPixelType, LabelGeometry >::iterator

using	MapType = itksys::hash_map< LabelPixelType, LabelGeometry >

using	MatrixType = vnl_matrix< double >

using	PixelType = typename TIntensityImage::PixelType

using	Pointer = SmartPointer< Self >

using	RealObjectType = SimpleDataObjectDecorator< RealType >

using	RealType = typename NumericTraits< PixelType >::RealType

using	RegionType = typename TIntensityImage::RegionType

using	Self = LabelGeometryImageFilter

using	SizeType = typename TIntensityImage::SizeType

using	Superclass = ImageToImageFilter< TLabelImage, TIntensityImage >

using	VectorType = std::vector< double >

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

using	InputImageConstPointer = typename InputImageType::ConstPointer

using	InputImagePixelType = typename InputImageType::PixelType

using	InputImagePointer = typename InputImageType::Pointer

using	InputImageRegionType = typename InputImageType::RegionType

using	InputImageType = TLabelImage

using	OutputImagePixelType = typename Superclass::OutputImagePixelType

using	OutputImageRegionType = typename Superclass::OutputImageRegionType

using	Pointer = SmartPointer< Self >

using	Self = ImageToImageFilter

using	Superclass = ImageSource< TIntensityImage >

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

using	DataObjectIdentifierType = Superclass::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	DataObjectPointerArraySizeType = Superclass::DataObjectPointerArraySizeType

using	OutputImagePixelType = typename OutputImageType::PixelType

using	OutputImagePointer = typename OutputImageType::Pointer

using	OutputImageRegionType = typename OutputImageType::RegionType

using	OutputImageType = TIntensityImage

using	Pointer = SmartPointer< Self >

using	Self = ImageSource

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 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

void	PopBackInput () override

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)

OutputImageType *	GetOutput ()

const OutputImageType *	GetOutput () const

virtual void	GraftOutput (DataObject *output)

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

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

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

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)

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 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	SetNumberOfWorkUnits (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfWorkUnits () 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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexceptoverride

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
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 constexpr unsigned int	ImageDimension = TLabelImage::ImageDimension

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

static constexpr unsigned int	OutputImageDimension

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

Protected Member Functions
void	GenerateData () override

	LabelGeometryImageFilter ()

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

	~LabelGeometryImageFilter () override=default

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)

void	GenerateInputRequestedRegion () override

	ImageToImageFilter ()

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

void	VerifyInputInformation () ITKv5_CONST 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 ()

void	ClassicMultiThread (ThreadFunctionType callbackFunction)

void	GenerateData () override

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

	ImageSource ()

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

	~ImageSource () override=default

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

virtual void	DynamicThreadedGenerateData (const OutputImageRegionType &outputRegionForThread)

virtual bool	GetDynamicMultiThreading () const

virtual void	SetDynamicMultiThreading (bool _arg)

virtual void	DynamicMultiThreadingOn ()

virtual void	DynamicMultiThreadingOff ()

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

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 () ITKv5_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 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)

	~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

Additional Inherited Members
Protected Types inherited from itk::ImageToImageFilter< TLabelImage, TIntensityImage >
using	InputToOutputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::OutputImageDimension, Self::InputImageDimension >

using	OutputToInputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::InputImageDimension, Self::OutputImageDimension >

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

static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	ThreaderCallback (void *arg)

Protected Attributes inherited from itk::ImageSource< TIntensityImage >
bool	m_DynamicMultiThreading

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount