#include <itkScalarImageToCooccurrenceMatrixFilter.h>

Inheritance diagram for itk::Statistics::ScalarImageToCooccurrenceMatrixFilter< TImageType, THistogramFrequencyContainer >:

Collaboration diagram for itk::Statistics::ScalarImageToCooccurrenceMatrixFilter< TImageType, THistogramFrequencyContainer >:

Detailed Description

template<typename TImageType, typename THistogramFrequencyContainer = DenseFrequencyContainer2>
class itk::Statistics::ScalarImageToCooccurrenceMatrixFilter< TImageType, THistogramFrequencyContainer >

This class computes a co-occurence matrix (histogram) from a given image and a mask image if provided. Coocurrence matrces are used for image texture description.

This filters creates a grey-level co-occurence matrix from a N-D scalar image. This is the first step in texture description a la Haralick. (See Haralick, R.M., K. Shanmugam and I. Dinstein. 1973. Textural Features for Image Classification. IEEE Transactions on Systems, Man and Cybernetics. SMC-3(6):610-620. See also Haralick, R.M. 1979. Statistical and Structural Approaches to Texture. Proceedings of the IEEE, 67:786-804.)

The basic idea is as follows: Given an image and an offset (e.g. (1, -1) for a 2-d image), grey-level co-occurences are pairs of intensity values for a specific pixel and the pixel at that offset from the specified pixel. These co-occurences can provide information about the visual texture of an image region – for example, an eight-bit image of alternating pixel-wide white and black vertical lines would have a large number of (0, 255) and (255, 0) co-occurences for offset (1, 0).

The offset (or offsets) along which the co-occurences are calculated can be set by the user. Traditionally, only one offset is used per histogram, and offset components in the range [-1, 1] are used. For rotation-invariant features, averages of features computed over several histograms with different offsets are generally used, instead of computing features from one histogram created with several offsets. Additionally, instead of using offsets of two or more pixels in any direction, multy-resulution techniques (e.g. image pyramids) are generally used to deal with texture at different spatial resolutions.

This class calculates a 2-d histogram of all the co-occurence pairs in the given image's requested region, for a given set of offsets. That is, if a given offset falls outside of the requested region at a particular point, that co-occurrence pair will not be added to the matrix.

The number of histogram bins on each axis can be set (defaults to 256). Also, by default the histogram min and max corresponds to the largest and smallest possible pixel value of that pixel type. To customize the histogram bounds for a given image, the max and min pixel values that will be placed in the histogram can be set manually. NB: The min and max are INCLUSIVE.

Further, the type of histogram frequency container used is an optional template parameter. By default, a dense container is used, but for images with little texture or in cases where the user wants more histogram bins, a sparse container can be used for the histogram instead.

WARNING: This probably won't work for pixels of double or long-double type unless you set the histogram min and max manually. This is because the largest histogram bin by default has max value of the largest possible pixel value plus 1. For double and long-double types, whose "RealType" as defined by the NumericTraits class is the same, and thus cannot hold any larger values, this would cause a float overflow.

See Also: MaskedScalarImageToCooccurrenceMatrixFilter; HistogramToTextureFeaturesFilter; ScalarImageTextureCalculator

Author: Zachary Pincus and Glenn Pierce

Definition at line 94 of file itkScalarImageToCooccurrenceMatrixFilter.h.

Public Types
typedef SmartPointer< const Self >	ConstPointer

typedef HistogramType::ConstPointer	HistogramConstPointer

typedef HistogramType::Pointer	HistogramPointer

typedef Histogram < MeasurementType, THistogramFrequencyContainer >	HistogramType

typedef ImageType::ConstPointer	ImageConstPointer

typedef ImageType::Pointer	ImagePointer

typedef TImageType	ImageType

typedef NumericTraits < PixelType >::RealType	MeasurementType

typedef HistogramType::MeasurementVectorType	MeasurementVectorType

typedef ImageType::OffsetType	OffsetType

typedef VectorContainer < unsigned char, OffsetType >	OffsetVector

typedef OffsetVector::ConstPointer	OffsetVectorConstPointer

typedef OffsetVector::Pointer	OffsetVectorPointer

typedef ImageType::PixelType	PixelType

typedef SmartPointer< Self >	Pointer

typedef ImageType::SizeType	RadiusType

typedef ImageType::RegionType	RegionType

typedef ScalarImageToCooccurrenceMatrixFilter	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

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

const ImageType *	GetInput () const

const ImageType *	GetMaskImage () const

virtual PixelType	GetMax () const

virtual PixelType	GetMin () const

virtual const char *	GetNameOfClass () const

const HistogramType *	GetOutput () const

void	SetInput (const ImageType *image)

void	SetMaskImage (const ImageType *image)

void	SetOffset (const OffsetType offset)

void	SetPixelValueMinMax (PixelType min, PixelType max)


virtual void	SetOffsets (const OffsetVector *_arg)

virtual const OffsetVector *	GetOffsets () const


virtual void	SetNumberOfBinsPerAxis (unsigned int _arg)

virtual unsigned int	GetNumberOfBinsPerAxis () const


virtual void	SetNormalize (bool _arg)

virtual bool	GetNormalize () const

virtual void	NormalizeOn ()

virtual void	NormalizeOff ()


virtual void	SetInsidePixelValue (PixelType _arg)

virtual PixelType	GetInsidePixelValue () const

Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()

virtual void	AbortGenerateDataOn ()

virtual void	EnlargeOutputRequestedRegion (DataObject *)

virtual const bool &	GetAbortGenerateData () const

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 () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

virtual DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)

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)

DataObjectPointerArray	GetInputs ()

DataObjectPointerArray	GetOutputs ()

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const

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 (void)

const MetaDataDictionary &	GetMetaDataDictionary (void) 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 ITK_OVERRIDE

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int) ITK_OVERRIDE

virtual void	UnRegister () const ITK_OVERRIDE

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	DefaultBinsPerAxis = 256

Protected Types
typedef DataObject::Pointer	DataObjectPointer

typedef ProcessObject::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

Protected Types inherited from itk::LightObject
typedef int	InternalReferenceCountType

Protected Member Functions
virtual void	FillHistogram (RadiusType radius, RegionType region)

virtual void	FillHistogramWithMask (RadiusType radius, RegionType region, const ImageType *maskImage)

virtual void	GenerateData () ITK_OVERRIDE

virtual DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType idx) ITK_OVERRIDE

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

	ScalarImageToCooccurrenceMatrixFilter ()

virtual	~ScalarImageToCooccurrenceMatrixFilter ()

Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)

virtual void	AddOutput (DataObject *output)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateInputRequestedRegion ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (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)

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	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

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

virtual void	SetPrimaryInput (DataObject *input)

virtual void	SetPrimaryOutput (DataObject *output)

virtual void	VerifyInputInformation ()

virtual void	VerifyPreconditions ()

	~ProcessObject ()

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

DataObject *	GetInput (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

virtual void	PushBackInput (const DataObject *input)

virtual void	PopBackInput ()

virtual void	PushFrontInput (const DataObject *input)

virtual void	PopFrontInput ()

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName (void) const

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const

bool	AddRequiredInputName (const DataObjectIdentifierType &)

bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

bool	RemoveRequiredInputName (const DataObjectIdentifierType &)

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

void	SetRequiredInputNames (const NameArray &)

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 ()

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
void	NormalizeHistogram (void)

void	operator= (const Self &)

	ScalarImageToCooccurrenceMatrixFilter (const Self &)

Private Attributes
PixelType	m_InsidePixelValue

MeasurementVectorType	m_LowerBound

PixelType	m_Max

PixelType	m_Min

bool	m_Normalize

unsigned int	m_NumberOfBinsPerAxis

OffsetVectorConstPointer	m_Offsets

MeasurementVectorType	m_UpperBound

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

bool	m_Updating

Protected Attributes inherited from itk::LightObject
InternalReferenceCountType	m_ReferenceCount

SimpleFastMutexLock	m_ReferenceCountLock