ITK  4.6.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Protected Types | Protected Member Functions | Private Member Functions | List of all members
itk::Statistics::CovarianceSampleFilter< TSample > Class Template Reference
Module ITKStatistics

#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:
Statistics/BayesianPluginClassifier.cxx, and 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 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
 
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
 

Protected Types

typedef DataObject::Pointer DataObjectPointer
 
typedef
ProcessObject::DataObjectPointerArraySizeType 		DataObjectPointerArraySizeType
 
- Protected Types inherited from itk::LightObject
typedef int InternalReferenceCountType
 

Protected Member Functions

 CovarianceSampleFilter ()
 
virtual void GenerateData () ITK_OVERRIDE
 
virtual DataObjectPointer MakeOutput (DataObjectPointerArraySizeType idx) ITK_OVERRIDE
 
virtual void PrintSelf (std::ostream &os, Indent indent) const ITK_OVERRIDE
 
virtual ~CovarianceSampleFilter ()
 
- 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

 CovarianceSampleFilter (const Self &)
 
void operator= (const Self &)
 
virtual const char * GetNameOfClass () const
 
virtual ::itk::LightObject::Pointer CreateAnother (void) 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
InternalReferenceCountType m_ReferenceCount
 
SimpleFastMutexLock m_ReferenceCountLock
 

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 ( )
protectedvirtual
template<typename TSample >
itk::Statistics::CovarianceSampleFilter< TSample >::CovarianceSampleFilter ( const Self &  )
private

Member Function Documentation

template<typename TSample >
virtual::itk::LightObject::Pointer itk::Statistics::CovarianceSampleFilter< TSample >::CreateAnother ( void  ) 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  )
protectedvirtual

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)
protectedvirtual

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 >
void itk::Statistics::CovarianceSampleFilter< TSample >::operator= ( const Self &  )
private
template<typename TSample >
virtual void itk::Statistics::CovarianceSampleFilter< TSample >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
protectedvirtual

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)
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