ITK  5.4.0
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Public Types | Public Member Functions | Protected Types | Protected Member Functions | List of all members
itk::Statistics::CovarianceSampleFilter< TSample > Class Template Reference
Group Numerics » Module ITKStatistics

#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 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
 
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 *)
 
unsigned long AddObserver (const EventObject &event, Command *) 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)
 
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 Types

using DataObjectPointer = DataObject::Pointer
 
using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType
 

Protected Member Functions

 CovarianceSampleFilter ()
 
void GenerateData () override
 
DataObjectPointer MakeOutput (DataObjectPointerArraySizeType index) 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 () ITKv5_CONST
 
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 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
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
protected

DataObject pointer

Definition at line 132 of file itkCovarianceSampleFilter.h.

◆ DataObjectPointerArraySizeType

template<typename TSample >
using itk::Statistics::CovarianceSampleFilter< TSample >::DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType
protected

Definition at line 134 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)
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.

◆ 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)
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