covariance data More...

#include <fiff_cov.h>

Public Types
typedef QSharedPointer< FiffCov >	SPtr
typedef QSharedPointer< const FiffCov >	ConstSPtr
typedef QSharedDataPointer< FiffCov >	SDPtr

Public Member Functions
	FiffCov ()
	FiffCov (QIODevice &p_IODevice)
	FiffCov (const FiffCov &p_FiffCov)
	~FiffCov ()
void	clear ()
bool	isEmpty () const
FiffCov	pick_channels (const QStringList &p_include=defaultQStringList, const QStringList &p_exclude=defaultQStringList)
FiffCov	prepare_noise_cov (const FiffInfo &p_info, const QStringList &p_chNames) const
FiffCov	regularize (const FiffInfo &p_info, double p_fMag=0.1, double p_fGrad=0.1, double p_fEeg=0.1, bool p_bProj=true, QStringList p_exclude=defaultQStringList) const
bool	save (const QString &fileName) const
FiffCov &	operator= (const FiffCov &rhs)

Static Public Member Functions
static FiffCov	compute_from_epochs (const FiffRawData &raw, const Eigen::MatrixXi &events, const QList< int > &eventCodes, float tmin, float tmax, float bmin=0.0f, float bmax=0.0f, bool doBaseline=false, bool removeMean=true, unsigned int ignoreMask=0, float delay=0.0f)
static FiffCov	computeGrandAverage (const QList< FiffCov > &covs)

Public Attributes
fiff_int_t	kind
Eigen::VectorXi	chClass
bool	diag
fiff_int_t	dim
QStringList	names
Eigen::MatrixXd	data
QList< FiffProj >	projs
QStringList	bads
fiff_int_t	nfree
Eigen::VectorXd	eig
Eigen::MatrixXd	eigvec

Friends
std::ostream &	operator<< (std::ostream &out, const FIFFLIB::FiffCov &p_FiffCov)

Detailed Description

covariance data

Fiff cov data, which corresponds to a covariance data matrix

Definition at line 83 of file fiff_cov.h.

Inheritance diagram for FIFFLIB::FiffCov:

Member Typedef Documentation

◆ ConstSPtr

typedef QSharedPointer<const FiffCov> FIFFLIB::FiffCov::ConstSPtr

Const shared pointer type for FiffCov.

Definition at line 87 of file fiff_cov.h.

◆ SDPtr

typedef QSharedDataPointer<FiffCov> FIFFLIB::FiffCov::SDPtr

Shared data pointer type for FiffCov.

Definition at line 88 of file fiff_cov.h.

◆ SPtr

typedef QSharedPointer<FiffCov> FIFFLIB::FiffCov::SPtr

Shared pointer type for FiffCov.

Definition at line 86 of file fiff_cov.h.

Constructor & Destructor Documentation

◆ FiffCov() [1/3]

FiffCov::FiffCov ( )

Constructs the covariance data matrix.

Definition at line 75 of file fiff_cov.cpp.

◆ FiffCov() [2/3]

FiffCov::FiffCov ( QIODevice & p_IODevice )

Constructs a covariance data matrix, by reading from a IO device.

Parameters

[in] p_IODevice IO device to read from the evoked data set.

Definition at line 87 of file fiff_cov.cpp.

◆ FiffCov() [3/3]

FiffCov::FiffCov ( const FiffCov & p_FiffCov )

Copy constructor.

Parameters

[in] p_FiffCov Covariance data matrix which should be copied.

Definition at line 110 of file fiff_cov.cpp.

◆ ~FiffCov()

FiffCov::~FiffCov ( )

Destroys the covariance data matrix.

Definition at line 129 of file fiff_cov.cpp.

Member Function Documentation

◆ clear()

void FiffCov::clear ( )

Initializes the covariance data matrix.

Definition at line 135 of file fiff_cov.cpp.

◆ compute_from_epochs()

FiffCov FiffCov::compute_from_epochs	(	const FiffRawData &	raw,
		const Eigen::MatrixXi &	events,
		const QList< int > &	eventCodes,
		float	tmin,
		float	tmax,
		float	bmin = 0.0f,
		float	bmax = 0.0f,
		bool	doBaseline = false,
		bool	removeMean = true,
		unsigned int	ignoreMask = 0,
		float	delay = 0.0f )

static

Compute a noise covariance matrix from raw data based on event-locked epochs. Ported from compute_cov.c (MNE-C).

Parameters

[in]	raw	The raw data.
[in]	events	Event matrix (nEvents x 3): [sample, before, after].
[in]	eventCodes	Which event codes to include.
[in]	tmin	Start of time window relative to event (seconds).
[in]	tmax	End of time window relative to event (seconds).
[in]	bmin	Baseline start (seconds, relative to event). Only used if doBaseline is true.
[in]	bmax	Baseline end (seconds, relative to event). Only used if doBaseline is true.
[in]	doBaseline	Whether to apply baseline correction before covariance computation.
[in]	removeMean	Whether to remove sample mean from the covariance estimate.
[in]	ignoreMask	Bit mask ANDed away from event codes before matching (default: 0 = no masking).
[in]	delay	Delay in seconds applied to the event sample before extracting the epoch (default: 0).

Returns: The computed noise covariance matrix, or empty FiffCov on failure.

Definition at line 486 of file fiff_cov.cpp.

◆ computeGrandAverage()

FiffCov FiffCov::computeGrandAverage ( const QList< FiffCov > & covs )

static

Compute a weighted grand-average covariance from multiple covariance matrices, weighting each by its degrees of freedom (nfree).

Parameters

[in] covs List of covariance matrices to combine.

Returns: The grand-average covariance matrix, or empty FiffCov if covs is empty.

Definition at line 627 of file fiff_cov.cpp.

◆ isEmpty()

bool FIFFLIB::FiffCov::isEmpty ( ) const

inline

True if FIFF covariance is empty.

Returns: true if FIFF covariance is empty.

Definition at line 264 of file fiff_cov.h.

◆ operator=()

FiffCov & FiffCov::operator= ( const FiffCov & rhs )

Assignment Operator

Parameters

[in] rhs FiffCov which should be assigned.

Returns: the copied covariance matrix.

Definition at line 465 of file fiff_cov.cpp.

◆ pick_channels()

FiffCov FiffCov::pick_channels	(	const QStringList &	p_include = defaultQStringList,
		const QStringList &	p_exclude = defaultQStringList )

python pick_channels_cov

Pick channels from covariance matrix

Parameters

[in]	p_include	List of channels to include (if empty, include all available). (optional).
[in]	p_exclude	Channels to exclude (if empty, do not exclude any). (optional).

Returns: Covariance solution restricted to selected channels.

Definition at line 151 of file fiff_cov.cpp.

◆ prepare_noise_cov()

FiffCov FiffCov::prepare_noise_cov	(	const FiffInfo &	p_info,
		const QStringList &	p_chNames ) const

Prepare noise covariance matrix. Before creating inverse operator.

Parameters

[in]	p_info	measurement info.
[in]	p_chNames	Channels which should be taken into account.

Returns: the prepared noise covariance matrix.

Definition at line 179 of file fiff_cov.cpp.

◆ regularize()

FiffCov FiffCov::regularize	(	const FiffInfo &	p_info,
		double	p_fMag = 0.1,
		double	p_fGrad = 0.1,
		double	p_fEeg = 0.1,
		bool	p_bProj = true,
		QStringList	p_exclude = defaultQStringList ) const

Regularize noise covariance matrix

This method works by adding a constant to the diagonal for each channel type separatly. Special care is taken to keep the rank of the data constant.

Parameters

[in]	p_info	The measurement info (used to get channel types and bad channels).
[in]	p_fMag	Regularization factor for MEG magnetometers.
[in]	p_fGrad	Regularization factor for MEG gradiometers.
[in]	p_fEeg	Regularization factor for EEG.
[in]	p_bProj	Apply or not projections to keep rank of data.
[in]	p_exclude	List of channels to mark as bad. If None, bads channels are extracted from both info['bads'] and cov['bads'].

Returns: the regularized covariance matrix.

Definition at line 326 of file fiff_cov.cpp.

◆ save()

bool FiffCov::save ( const QString & fileName ) const

Save this covariance matrix to a FIFF file.

Parameters

[in] fileName Output file path.

Returns: true on success.

Definition at line 601 of file fiff_cov.cpp.

◆ operator<<

std::ostream & operator<<	(	std::ostream &	out,
		const FIFFLIB::FiffCov &	p_FiffCov )

friend

overloading the stream out operator<<

Parameters

[in]	out	The stream to which the fiff covariance should be assigned to.
[in]	p_FiffCov	FiffCov which should be assigned to the stream.

Returns: the stream with the attached fiff covariance matrix.

Definition at line 271 of file fiff_cov.h.

Member Data Documentation

◆ bads

QStringList FIFFLIB::FiffCov::bads

List of bad channels.

Definition at line 253 of file fiff_cov.h.

◆ chClass

Eigen::VectorXi FIFFLIB::FiffCov::chClass

Channel classification vector.

Definition at line 247 of file fiff_cov.h.

◆ data

Eigen::MatrixXd FIFFLIB::FiffCov::data

Covariance data.

Definition at line 251 of file fiff_cov.h.

◆ diag

bool FIFFLIB::FiffCov::diag

If the covariance is stored in a diagonal order.

Definition at line 248 of file fiff_cov.h.

◆ dim

fiff_int_t FIFFLIB::FiffCov::dim

Dimension of the covariance (dim x dim).

Definition at line 249 of file fiff_cov.h.

◆ eig

Eigen::VectorXd FIFFLIB::FiffCov::eig

Vector of eigenvalues.

Definition at line 255 of file fiff_cov.h.

◆ eigvec

Eigen::MatrixXd FIFFLIB::FiffCov::eigvec

Matrix of eigenvectors (each row represents an eigenvector).

Definition at line 256 of file fiff_cov.h.

◆ kind

fiff_int_t FIFFLIB::FiffCov::kind

Covariance kind -> fiff_constants.h.

Definition at line 246 of file fiff_cov.h.

◆ names

QStringList FIFFLIB::FiffCov::names

Channel names.

Definition at line 250 of file fiff_cov.h.

◆ nfree

fiff_int_t FIFFLIB::FiffCov::nfree

Number of degrees of freedom.

Definition at line 254 of file fiff_cov.h.

◆ projs

QList<FiffProj> FIFFLIB::FiffCov::projs

List of available ssp projectors.

Definition at line 252 of file fiff_cov.h.

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

src/libraries/fiff/fiff_cov.h
src/libraries/fiff/fiff_cov.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SDPtr

◆ SPtr

Constructor & Destructor Documentation

◆ FiffCov() [1/3]

◆ FiffCov() [2/3]

◆ FiffCov() [3/3]

◆ ~FiffCov()

Member Function Documentation

◆ clear()

◆ compute_from_epochs()

◆ computeGrandAverage()

◆ isEmpty()

◆ operator=()

◆ pick_channels()

◆ prepare_noise_cov()

◆ regularize()

◆ save()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ bads

◆ chClass

◆ data

◆ diag

◆ dim

◆ eig

◆ eigvec

◆ kind

◆ names

◆ nfree

◆ projs