#include <itkCovarianceSampleFilter.h>

Inheritance diagram for itk::Statistics::CovarianceSampleFilter< TSample >:

Collaboration diagram for itk::Statistics::CovarianceSampleFilter< TSample >:

Detailed Description

template<typename TSample>
class itk::Statistics::CovarianceSampleFilter< TSample >

Calculates the covariance matrix of the target sample data.

The filter calculates first the sample mean and use it in the covariance calculation. The covariance is computed as follows Let $\Sigma$ denotes covariance matrix for the sample, then: When $x_{i}$ is $i$ th component of a measurement vector $\vec x$ , $\mu_{i}$ is the $i$ th component of the $\vec\mu$ , and the $\sigma_{ij}$ is the $ij$ th component $\Sigma$ , $\sigma_{ij} = (x_{i} - \mu_{i})(x_{j} - \mu_{j})$

This estimator is an unbiased one, because it divisor in the covariance computation takes into account that one degree of freedom has been taken for computing the mean.

Without the plugged in mean vector, this calculator will perform the single pass mean and covariance calculation algorithm.

Examples:: Examples/Statistics/BayesianPluginClassifier.cxx, and Examples/Statistics/SampleStatistics.cxx.

Definition at line 52 of file itkCovarianceSampleFilter.h.

Public Types
typedef SmartPointer< const Self >	ConstPointer

typedef SimpleDataObjectDecorator < MatrixType >	MatrixDecoratedType

typedef VariableSizeMatrix < MeasurementRealType >	MatrixType

typedef NumericTraits < MeasurementType >::RealType	MeasurementRealType

typedef SampleType::MeasurementType	MeasurementType

typedef SimpleDataObjectDecorator < MeasurementVectorRealType >	MeasurementVectorDecoratedType

typedef NumericTraits < MeasurementVectorType > ::RealType	MeasurementVectorRealType

typedef SampleType::MeasurementVectorSizeType	MeasurementVectorSizeType

typedef SampleType::MeasurementVectorType	MeasurementVectorType

typedef MeasurementVectorDecoratedType	OutputType

typedef SmartPointer< Self >	Pointer

typedef TSample	SampleType

typedef CovarianceSampleFilter	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
const MatrixType	GetCovarianceMatrix () const

const MatrixDecoratedType *	GetCovarianceMatrixOutput () const

const SampleType *	GetInput () const

const MeasurementVectorRealType	GetMean () const

const MeasurementVectorDecoratedType *	GetMeanOutput () const

MeasurementVectorSizeType	GetMeasurementVectorSize () const

void	SetInput (const SampleType *sample)

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 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)

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

Protected Types
typedef DataObject::Pointer	DataObjectPointer

typedef ProcessObject::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

Protected Member Functions
	CovarianceSampleFilter ()

virtual void	GenerateData () override

virtual DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType idx) override

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

virtual	~CovarianceSampleFilter () 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	GenerateInputRequestedRegion ()

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

virtual void	PopBackInput ()

virtual void	PopFrontInput ()

	ProcessObject ()

virtual void	PropagateResetPipeline ()

virtual void	PushBackInput (const DataObject *input)

virtual void	PushFrontInput (const DataObject *input)

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	VerifyInputInformation ()

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 ()

virtual const char *	GetNameOfClass () const

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

static Pointer	New ()

Additional Inherited Members
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 ()

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

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

Member Typedef Documentation

template<typename TSample >

typedef SmartPointer< const Self > itk::Statistics::CovarianceSampleFilter< TSample >::ConstPointer

Definition at line 60 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef DataObject::Pointer itk::Statistics::CovarianceSampleFilter< TSample >::DataObjectPointer

protected

DataObject pointer

Definition at line 122 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef ProcessObject::DataObjectPointerArraySizeType itk::Statistics::CovarianceSampleFilter< TSample >::DataObjectPointerArraySizeType

protected

Definition at line 124 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef SimpleDataObjectDecorator< MatrixType > itk::Statistics::CovarianceSampleFilter< TSample >::MatrixDecoratedType

VariableSizeMatrix is not a DataObject, we need to decorate it to push it down a ProcessObject's pipeline

Definition at line 100 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef VariableSizeMatrix< MeasurementRealType > itk::Statistics::CovarianceSampleFilter< TSample >::MatrixType

Type of covariance matrix output

Definition at line 93 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef NumericTraits< MeasurementType >::RealType itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementRealType

Type of a floating point measurement component value

Definition at line 81 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef SampleType::MeasurementType itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementType

Type of measurement vector component value

Definition at line 75 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef SimpleDataObjectDecorator< MeasurementVectorRealType > itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementVectorDecoratedType

MeasurementVector is not a DataObject, we need to decorate it to push it down a ProcessObject's pipeline

Definition at line 109 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef NumericTraits< MeasurementVectorType >::RealType itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementVectorRealType

Type of a measurement vector, holding floating point values

Definition at line 78 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef SampleType::MeasurementVectorSizeType itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementVectorSizeType

Type of the length of each measurement vector

Definition at line 72 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef SampleType::MeasurementVectorType itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementVectorType

Type of each measurement vector in sample

Definition at line 65 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef MeasurementVectorDecoratedType itk::Statistics::CovarianceSampleFilter< TSample >::OutputType

Definition at line 111 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef SmartPointer< Self > itk::Statistics::CovarianceSampleFilter< TSample >::Pointer

Definition at line 59 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef TSample itk::Statistics::CovarianceSampleFilter< TSample >::SampleType

Definition at line 61 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef CovarianceSampleFilter itk::Statistics::CovarianceSampleFilter< TSample >::Self

Standard class typedefs.

Definition at line 57 of file itkCovarianceSampleFilter.h.

template<typename TSample >

typedef ProcessObject itk::Statistics::CovarianceSampleFilter< TSample >::Superclass

Definition at line 58 of file itkCovarianceSampleFilter.h.

Constructor & Destructor Documentation

template<typename TSample >

itk::Statistics::CovarianceSampleFilter< TSample >::CovarianceSampleFilter ( )

protected

template<typename TSample >

virtual itk::Statistics::CovarianceSampleFilter< TSample >::~CovarianceSampleFilter ( )

overrideprotectedvirtual

Member Function Documentation

template<typename TSample >

virtual::itk::LightObject::Pointer itk::Statistics::CovarianceSampleFilter< TSample >::CreateAnother ( ) const

virtual

Standard Macros

Reimplemented from itk::Object.

Reimplemented in itk::Statistics::WeightedCovarianceSampleFilter< TSample >.

template<typename TSample >

virtual void itk::Statistics::CovarianceSampleFilter< TSample >::GenerateData ( void )

overrideprotectedvirtual

This method causes the filter to generate its output.

Reimplemented from itk::ProcessObject.

Reimplemented in itk::Statistics::WeightedCovarianceSampleFilter< TSample >.

template<typename TSample >

const MatrixType itk::Statistics::CovarianceSampleFilter< TSample >::GetCovarianceMatrix ( ) const

Return the covariance matrix

template<typename TSample >

const MatrixDecoratedType* itk::Statistics::CovarianceSampleFilter< TSample >::GetCovarianceMatrixOutput ( ) const

template<typename TSample >

const SampleType* itk::Statistics::CovarianceSampleFilter< TSample >::GetInput ( ) const

Method to get the sample

template<typename TSample >

const MeasurementVectorRealType itk::Statistics::CovarianceSampleFilter< TSample >::GetMean ( ) const

Return the mean vector

template<typename TSample >

const MeasurementVectorDecoratedType* itk::Statistics::CovarianceSampleFilter< TSample >::GetMeanOutput ( ) const

template<typename TSample >

MeasurementVectorSizeType itk::Statistics::CovarianceSampleFilter< TSample >::GetMeasurementVectorSize ( ) const

template<typename TSample >

virtual const char* itk::Statistics::CovarianceSampleFilter< TSample >::GetNameOfClass ( ) const

virtual

Standard Macros

Reimplemented from itk::ProcessObject.

Reimplemented in itk::Statistics::WeightedCovarianceSampleFilter< TSample >.

template<typename TSample >

virtual DataObjectPointer itk::Statistics::CovarianceSampleFilter< TSample >::MakeOutput ( DataObjectPointerArraySizeType idx )

overrideprotectedvirtual

Make a DataObject of the correct type to used as the specified output.

Every ProcessObject subclass must be able to create a DataObject that can be used as a specified output. This method is automatically called when DataObject::DisconnectPipeline() is called. DataObject::DisconnectPipeline, disconnects a data object from being an output of its current source. When the data object is disconnected, the ProcessObject needs to construct a replacement output data object so that the ProcessObject is in a valid state. So DataObject::DisconnectPipeline eventually calls ProcessObject::MakeOutput. Note that MakeOutput always returns a itkSmartPointer to a DataObject. ImageSource and MeshSource override this method to create the correct type of image and mesh respectively. If a filter has multiple outputs of different types, then that filter must provide an implementation of MakeOutput().

Reimplemented from itk::ProcessObject.

template<typename TSample >

static Pointer itk::Statistics::CovarianceSampleFilter< TSample >::New ( )

static

Standard Macros

template<typename TSample >

virtual void itk::Statistics::CovarianceSampleFilter< TSample >::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const

overrideprotectedvirtual

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::ProcessObject.

Reimplemented in itk::Statistics::WeightedCovarianceSampleFilter< TSample >.

template<typename TSample >

void itk::Statistics::CovarianceSampleFilter< TSample >::SetInput ( const SampleType * sample )