Class to calculate covariance and correlation. More...

#include <mitkCorrelationCalculator.h>

Inheritance diagram for mitk::CorrelationCalculator< T >:

Collaboration diagram for mitk::CorrelationCalculator< T >:

Public Types
enum	ParcelMode { UseAverageTimeSeries, UseMaximumCorrelation, UseAverageCorrelation }
	The ParcelMode enum defines how to define the correlation between two parcels. More...

Public Member Functions
	mitkClassMacroItkParent (CorrelationCalculator, itk::Object)

Pointer	Clone () const

std::vector< double >	ExtractAverageTimeSeriesOfParcel (int parcelValue)
	Extracts the average time series from a roi defined by the parcellation image. More...

void	DoWholeCorrelation ()
	Create a #voxel x #voxel correlation matrix. More...

void	DoParcelCorrelation (ParcelMode mode=UseAverageTimeSeries)
	Create a #parcel x #parcel correlation matrix. More...

virtual void	Modified ()
	Marks average time series as invalid and calls superclass modified. More...

const vnl_matrix< double > *	GetCorrelationMatrix () const

const std::map< unsigned int, int > *	GetLabelOrderMap () const

mitk::ConnectomicsNetwork::Pointer	GetConnectomicsNetwork ()

virtual void	SetParcellationImage (mitk::Image::Pointer _arg)

virtual void	SetTimeSeriesImage (mitk::Image::Pointer _arg)

Static Public Member Functions
static Pointer	New ()

static double	CalculatePearsonCorrelationCoefficient (const std::vector< T > &one, const std::vector< T > &two)
	Calculate and return the pearson correlation coefficient for two vectors of data. More...

static double	CalculateCovariance (const std::vector< T > &one, const std::vector< T > &two)
	Calculates the covariance of two vectors of data. More...

Protected Member Functions
virtual void	Modified () const override

	CorrelationCalculator ()

virtual	~CorrelationCalculator ()

template<typename TPixel , unsigned int VImageDimension>
void	ExtractAllAverageTimeSeries (itk::Image< TPixel, VImageDimension > *itkTimeSeriesImage)

void	ExtractCenterOfMassForParcels ()

double	GetParcelCorrelation (const int &parcelA, const int &parcelB, ParcelMode &mode) const

Protected Attributes
bool	m_InvalidTimeSeries

mitk::Image::Pointer	m_ParcellationImage

mitk::Image::Pointer	m_TimeSeriesImage

std::map< int, std::vector< double > >	m_AverageTimeSeries

std::map< int, std::vector< std::vector< T > > >	m_ParcelTimeSeries

std::map< int, mitk::Point3D >	m_ParcelCenterOfMass

vnl_matrix< double >	m_CorrelationMatrix

std::map< unsigned int, int >	m_LabelOrderMap

Detailed Description

template<class T>
class mitk::CorrelationCalculator< T >

Class to calculate covariance and correlation.

In addition to static functions to calculate covariance and correlation, this class offers capability to set a time series image and optionally a parcellation image and calculate a correlation matrix.

Whole correlation only needs a time series image and will return a #voxel x #voxel matrix where each voxel's time series is correlated against the time series of each other voxel.

Parcel correlation will compute an average time series for each parcel of a parcellation image and create a #parcel x #parcel correlation matrix.

Please note that time series images are assumed to be 4D and parcellation images integer valued and 3D.

Definition at line 48 of file mitkCorrelationCalculator.h.

Member Enumeration Documentation

template<class T >

enum mitk::CorrelationCalculator::ParcelMode

The ParcelMode enum defines how to define the correlation between two parcels.

Available choices are:

UseAverageTimeSeries - Average time series across the parcel, correlate average time series between parcels
UseMaximumCorrelation - Correlate all voxels of the parcels with each other, use maximum correlation
UseAverageCorrelation - Correlate all voxels of the parcels with each other, use average correlation

Enumerator
UseAverageTimeSeries
UseMaximumCorrelation
UseAverageCorrelation

Definition at line 68 of file mitkCorrelationCalculator.h.

Constructor & Destructor Documentation

template<class T >

mitk::CorrelationCalculator< T >::CorrelationCalculator ( )

protected

template<class T >

virtual mitk::CorrelationCalculator< T >::~CorrelationCalculator ( )

protectedvirtual

Member Function Documentation

template<class T >

static double mitk::CorrelationCalculator< T >::CalculateCovariance	(	const std::vector< T > &	one,
		const std::vector< T > &	two
	)

static

Calculates the covariance of two vectors of data.

Expects two vectors of the same length and data type and returns the covariance of the two. Variance can be calculated by providing the same data vector twice.

Parameters

one	first data vector
two	second data vector

Returns: covariance of the two

template<class T >

static double mitk::CorrelationCalculator< T >::CalculatePearsonCorrelationCoefficient	(	const std::vector< T > &	one,
		const std::vector< T > &	two
	)

static

Calculate and return the pearson correlation coefficient for two vectors of data.

This function expects two vectors of the same length and data type and calculates the pearson correlation coefficient.

Parameters

one	first data vector
two	second data vector

Returns: pearson correlation coefficent

template<class T >

Pointer mitk::CorrelationCalculator< T >::Clone ( ) const

template<class T >

void mitk::CorrelationCalculator< T >::DoParcelCorrelation ( ParcelMode mode = UseAverageTimeSeries )

Create a #parcel x #parcel correlation matrix.

template<class T >

void mitk::CorrelationCalculator< T >::DoWholeCorrelation ( )

Create a #voxel x #voxel correlation matrix.

template<class T >

template<typename TPixel , unsigned int VImageDimension>

void mitk::CorrelationCalculator< T >::ExtractAllAverageTimeSeries ( itk::Image< TPixel, VImageDimension > * itkTimeSeriesImage )

protected

template<class T >

std::vector< double > mitk::CorrelationCalculator< T >::ExtractAverageTimeSeriesOfParcel ( int parcelValue )

Extracts the average time series from a roi defined by the parcellation image.

This function requires a parcellation image and a time series image to be set and registered to each other. For each voxel in the time series image it will check whether it is inside the specified parcel of the parcellation image. All inside voxels will be averaged for all time steps and an average time series is returned.

Calculates and saves the averages for all parcellations, to speed up consecutive calls.

Parameters

parcelValue the voxel value of the roi in the parcellation image.

Returns: vector of the average values of the roi for each timestep

template<class T >

void mitk::CorrelationCalculator< T >::ExtractCenterOfMassForParcels ( )

protected

template<class T >

mitk::ConnectomicsNetwork::Pointer mitk::CorrelationCalculator< T >::GetConnectomicsNetwork ( )

template<class T >

const vnl_matrix< double >* mitk::CorrelationCalculator< T >::GetCorrelationMatrix ( ) const

template<class T >

const std::map< unsigned int, int >* mitk::CorrelationCalculator< T >::GetLabelOrderMap ( ) const

template<class T >

double mitk::CorrelationCalculator< T >::GetParcelCorrelation	(	const int &	parcelA,
		const int &	parcelB,
		ParcelMode &	mode
	)		const

protected

template<class T >

mitk::CorrelationCalculator< T >::mitkClassMacroItkParent	(	CorrelationCalculator< T >	,
		itk::Object
	)

template<class T >

virtual void mitk::CorrelationCalculator< T >::Modified ( )

virtual

Marks average time series as invalid and calls superclass modified.

template<class T >

virtual void mitk::CorrelationCalculator< T >::Modified ( ) const

overrideprotectedvirtual

template<class T >

static Pointer mitk::CorrelationCalculator< T >::New ( )

static

template<class T >

virtual void mitk::CorrelationCalculator< T >::SetParcellationImage ( mitk::Image::Pointer _arg )

virtual

template<class T >

virtual void mitk::CorrelationCalculator< T >::SetTimeSeriesImage ( mitk::Image::Pointer _arg )

virtual

Member Data Documentation

template<class T >

std::map< int, std::vector<double> > mitk::CorrelationCalculator< T >::m_AverageTimeSeries

protected

Definition at line 159 of file mitkCorrelationCalculator.h.

template<class T >

vnl_matrix< double > mitk::CorrelationCalculator< T >::m_CorrelationMatrix

protected

Definition at line 164 of file mitkCorrelationCalculator.h.

template<class T >

bool mitk::CorrelationCalculator< T >::m_InvalidTimeSeries

protected

Definition at line 154 of file mitkCorrelationCalculator.h.

template<class T >

std::map< unsigned int, int > mitk::CorrelationCalculator< T >::m_LabelOrderMap

protected

Definition at line 166 of file mitkCorrelationCalculator.h.

template<class T >

std::map< int, mitk::Point3D > mitk::CorrelationCalculator< T >::m_ParcelCenterOfMass

protected

Definition at line 162 of file mitkCorrelationCalculator.h.

template<class T >

mitk::Image::Pointer mitk::CorrelationCalculator< T >::m_ParcellationImage

protected

Definition at line 156 of file mitkCorrelationCalculator.h.

template<class T >

std::map< int, std::vector<std::vector< T > > > mitk::CorrelationCalculator< T >::m_ParcelTimeSeries

protected

Definition at line 160 of file mitkCorrelationCalculator.h.

template<class T >

mitk::Image::Pointer mitk::CorrelationCalculator< T >::m_TimeSeriesImage

protected

Definition at line 157 of file mitkCorrelationCalculator.h.

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

mitkCorrelationCalculator.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<class T> class mitk::CorrelationCalculator< T >

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class T>
class mitk::CorrelationCalculator< T >