#include <itkCovarianceSampleFilter.h>

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 53 of file itkCovarianceSampleFilter.h.

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

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

Public Types
using	ConstPointer = SmartPointer< const Self >

using	DataObjectPointer = DataObject::Pointer

using	DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType

using	MatrixDecoratedType = SimpleDataObjectDecorator< MatrixType >

using	MatrixType = VariableSizeMatrix< MeasurementRealType >

using	MeasurementRealType = typename NumericTraits< MeasurementType >::RealType

using	MeasurementType = typename SampleType::MeasurementType

using	MeasurementVectorDecoratedType = SimpleDataObjectDecorator< MeasurementVectorRealType >

using	MeasurementVectorRealType = typename NumericTraits< MeasurementVectorType >::RealType

using	MeasurementVectorSizeType = typename SampleType::MeasurementVectorSizeType

using	MeasurementVectorType = typename SampleType::MeasurementVectorType

using	OutputType = MeasurementVectorDecoratedType

using	Pointer = SmartPointer< Self >

using	SampleType = TSample

using	Self = CovarianceSampleFilter

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
const MatrixType	GetCovarianceMatrix () const

const MatrixDecoratedType *	GetCovarianceMatrixOutput () const

const SampleType *	GetInput () const

const MeasurementVectorRealType	GetMean () const

const MeasurementVectorDecoratedType *	GetMeanOutput () const

MeasurementVectorSizeType	GetMeasurementVectorSize () const

DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType index) override

void	SetInput (const SampleType *sample)

Public Member Functions inherited from itk::ProcessObject
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 float	GetProgress () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

void	IncrementProgress (float increment)

virtual DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)

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 val)

virtual bool	GetReleaseDataFlag () const

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual const bool &	GetReleaseDataBeforeUpdateFlag () const

virtual void	ReleaseDataBeforeUpdateFlagOn ()

virtual void	SetNumberOfWorkUnits (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfWorkUnits () const

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *cmd) const

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

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) const

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexcept override

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
Pointer	Clone () const

virtual void	Delete ()

virtual int	GetReferenceCount () const

void	Print (std::ostream &os, Indent indent=0) const

Protected Member Functions
	CovarianceSampleFilter ()

void	GenerateData () override

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

	~CovarianceSampleFilter () override=default

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

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 idx, DataObject *input)

virtual void	SetNthOutput (DataObjectPointerArraySizeType idx, DataObject *output)

void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)

void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

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

virtual void	SetPrimaryInput (DataObject *object)

virtual void	SetPrimaryOutput (DataObject *object)

void	SetRequiredInputNames (const NameArray &)

virtual void	VerifyInputInformation () const

virtual void	VerifyPreconditions () 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 i)

const DataObject *	GetOutput (DataObjectPointerArraySizeType i) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

virtual bool	GetThreaderUpdateProgress () const

virtual void	ThreaderUpdateProgressOn ()

virtual void	SetThreaderUpdateProgress (bool arg)

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

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

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

	~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 ()

const char *	GetNameOfClass () const override

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 val)

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

static Pointer	New ()

Static Protected Member Functions inherited from itk::ProcessObject
template<typename TSourceObject >
static void	MakeRequiredOutputs (TSourceObject &sourceObject, const DataObjectPointerArraySizeType numberOfRequiredOutputs)

static constexpr float	progressFixedToFloat (uint32_t fixed)

static uint32_t	progressFloatToFixed (float f)

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime {}

bool	m_Updating {}

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

Member Typedef Documentation

◆ ConstPointer

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::ConstPointer = SmartPointer<const Self>

Definition at line 62 of file itkCovarianceSampleFilter.h.

◆ DataObjectPointer

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::DataObjectPointer = DataObject::Pointer

DataObject pointer

Definition at line 126 of file itkCovarianceSampleFilter.h.

◆ DataObjectPointerArraySizeType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType

Definition at line 128 of file itkCovarianceSampleFilter.h.

◆ MatrixDecoratedType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::MatrixDecoratedType = SimpleDataObjectDecorator<MatrixType>

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

Definition at line 105 of file itkCovarianceSampleFilter.h.

◆ MatrixType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::MatrixType = VariableSizeMatrix<MeasurementRealType>

Type of covariance matrix output

Definition at line 97 of file itkCovarianceSampleFilter.h.

◆ MeasurementRealType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementRealType = typename NumericTraits<MeasurementType>::RealType

Type of a floating point measurement component value

Definition at line 83 of file itkCovarianceSampleFilter.h.

◆ MeasurementType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementType = typename SampleType::MeasurementType

Type of measurement vector component value

Definition at line 77 of file itkCovarianceSampleFilter.h.

◆ MeasurementVectorDecoratedType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementVectorDecoratedType = SimpleDataObjectDecorator<MeasurementVectorRealType>

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

Definition at line 116 of file itkCovarianceSampleFilter.h.

◆ MeasurementVectorRealType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementVectorRealType = typename NumericTraits<MeasurementVectorType>::RealType

Type of a measurement vector, holding floating point values

Definition at line 80 of file itkCovarianceSampleFilter.h.

◆ MeasurementVectorSizeType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementVectorSizeType = typename SampleType::MeasurementVectorSizeType

Type of the length of each measurement vector

Definition at line 74 of file itkCovarianceSampleFilter.h.

◆ MeasurementVectorType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::MeasurementVectorType = typename SampleType::MeasurementVectorType

Type of each measurement vector in sample

Definition at line 71 of file itkCovarianceSampleFilter.h.

◆ OutputType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::OutputType = MeasurementVectorDecoratedType

Definition at line 119 of file itkCovarianceSampleFilter.h.

◆ Pointer

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::Pointer = SmartPointer<Self>

Definition at line 61 of file itkCovarianceSampleFilter.h.

◆ SampleType

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::SampleType = TSample

Definition at line 63 of file itkCovarianceSampleFilter.h.

◆ Self

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::Self = CovarianceSampleFilter

Standard class type aliases.

Definition at line 59 of file itkCovarianceSampleFilter.h.

◆ Superclass

template<typename TSample >

using itk::Statistics::CovarianceSampleFilter< TSample >::Superclass = ProcessObject

Definition at line 60 of file itkCovarianceSampleFilter.h.

Constructor & Destructor Documentation

◆ CovarianceSampleFilter()

template<typename TSample >

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

protected

◆ ~CovarianceSampleFilter()

template<typename TSample >

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

overrideprotecteddefault

Member Function Documentation

◆ GenerateData()

template<typename TSample >

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

overrideprotectedvirtual

This method causes the filter to generate its output.

Reimplemented from itk::ProcessObject.

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

◆ GetCovarianceMatrix()

template<typename TSample >

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

Return the covariance matrix

◆ GetCovarianceMatrixOutput()

template<typename TSample >

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

◆ GetInput()

template<typename TSample >

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

Method to get the sample

◆ GetMean()

template<typename TSample >

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

Return the mean vector

◆ GetMeanOutput()

template<typename TSample >

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

◆ GetMeasurementVectorSize()

template<typename TSample >

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

◆ GetNameOfClass()

template<typename TSample >

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

overridevirtual

See also: LightObject::GetNameOfClass()

Reimplemented from itk::ProcessObject.

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

◆ MakeOutput()

template<typename TSample >

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

overridevirtual

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.

◆ New()

template<typename TSample >

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

static

See also: LightObject::GetNameOfClass()

◆ PrintSelf()

template<typename TSample >

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.

◆ SetInput()

template<typename TSample >

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

The documentation for this class was generated from the following file:

itkCovarianceSampleFilter.h

Detailed Description

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

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Member Typedef Documentation

◆ ConstPointer

◆ DataObjectPointer

◆ DataObjectPointerArraySizeType

◆ MatrixDecoratedType

◆ MatrixType

◆ MeasurementRealType

◆ MeasurementType

◆ MeasurementVectorDecoratedType

◆ MeasurementVectorRealType

◆ MeasurementVectorSizeType

◆ MeasurementVectorType

◆ OutputType

◆ Pointer

◆ SampleType

◆ Self

◆ Superclass

Constructor & Destructor Documentation

◆ CovarianceSampleFilter()

◆ ~CovarianceSampleFilter()

Member Function Documentation

◆ GenerateData()

◆ GetCovarianceMatrix()

◆ GetCovarianceMatrixOutput()

◆ GetInput()

◆ GetMean()

◆ GetMeanOutput()

◆ GetMeasurementVectorSize()

◆ GetNameOfClass()

◆ MakeOutput()

◆ New()

◆ PrintSelf()

◆ SetInput()

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