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

#include <itkLabelGeometryImageFilter.h>

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

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

Classes
class	LabelGeometry
	Geometry stored per label. More...
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 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 (void) 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)
	typedef (Concept::HasNumericTraits< PixelType >) InputHasNumericTraitsCheck
Static Public Member Functions
static Pointer	New ()
Static Public Attributes
static const unsigned int	ImageDimension = TLabelImage::ImageDimension
Protected Member Functions
void	GenerateData ()

	LabelGeometryImageFilter ()
	~LabelGeometryImageFilter ()
void	PrintSelf (std::ostream &os, Indent indent) const
Private Member Functions
bool	CalculateOrientedBoundingBoxVertices (vnl_symmetric_eigensystem< double > eig, LabelGeometry &m_LabelGeometry)
	LabelGeometryImageFilter (const Self &)
void	operator= (const Self &)
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

Detailed Description

template<class TLabelImage, class 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 http://hdl.handle.net/1926/1493

Wiki Examples:

All Examples

Get geometric properties of labeled regions in an image

Definition at line 79 of file itkLabelGeometryImageFilter.h.