Dipole Fit Data implementation. More...

#include <dipole_fit_data.h>

Public Types
typedef QSharedPointer< DipoleFitData >	SPtr
typedef QSharedPointer< const DipoleFitData >	ConstSPtr

Public Member Functions
	DipoleFitData ()
virtual	~DipoleFitData ()

Static Public Member Functions
static int	setup_forward_model (DipoleFitData d, MNELIB::MNECTFCompDataSet comp_data, FWDLIB::FwdCoilSet *comp_coils)
static std::unique_ptr< MNELIB::MNECovMatrix >	ad_hoc_noise (FWDLIB::FwdCoilSet meg, FWDLIB::FwdCoilSet eeg, float grad_std, float mag_std, float eeg_std)
static int	make_projection (const QList< QString > &projnames, const QList< FIFFLIB::FiffChInfo > &chs, int nch, MNELIB::MNEProjOp **res)
static int	scale_noise_cov (DipoleFitData *f, int nave)
static int	scale_dipole_fit_noise_cov (DipoleFitData *f, int nave)
static int	select_dipole_fit_noise_cov (DipoleFitData *f, mshMegEegData d)
static DipoleFitData *	setup_dipole_fit_data (const QString &mriname, const QString &measname, const QString &bemname, Eigen::Vector3f r0, FWDLIB::FwdEegSphereModel eeg_model, int accurate_coils, const QString &badname, const QString &noisename, float grad_std, float mag_std, float eeg_std, float mag_reg, float grad_reg, float eeg_reg, int diagnoise, const QList< QString > &projnames, int include_meg, int include_eeg)
static bool	fit_one (DipoleFitData fit, GuessData guess, float time, float *B, int verbose, ECD &res)
static int	compute_dipole_field (DipoleFitData d, float rd, int whiten, float **fwd)
static DipoleForward *	dipole_forward_one (DipoleFitData d, float rd, DipoleForward *old)

Public Attributes
std::unique_ptr< FIFFLIB::FiffCoordTrans >	mri_head_t
std::unique_ptr< FIFFLIB::FiffCoordTrans >	meg_head_t
int	coord_frame
QList< FIFFLIB::FiffChInfo >	chs
int	nmeg
int	neeg
QStringList	ch_names
std::unique_ptr< FIFFLIB::FiffSparseMatrix >	pick
std::unique_ptr< FWDLIB::FwdCoilSet >	meg_coils
std::unique_ptr< FWDLIB::FwdCoilSet >	eeg_els
float	r0 [3]
QString	bemname
std::unique_ptr< FWDLIB::FwdEegSphereModel >	eeg_model
std::unique_ptr< FWDLIB::FwdBemModel >	bem_model
dipoleFitFuncs	sphere_funcs
dipoleFitFuncs	bem_funcs
dipoleFitFuncs	funcs
dipoleFitFuncs	mag_dipole_funcs
int	fixed_noise
std::unique_ptr< MNELIB::MNECovMatrix >	noise_orig
std::unique_ptr< MNELIB::MNECovMatrix >	noise
int	nave
std::unique_ptr< MNELIB::MNEProjOp >	proj
int	column_norm
int	fit_mag_dipoles
FitDipUserRec *	user

Detailed Description

Dipole Fit Data implementation.

Implements the dipole fit data parser (Replaces *dipoleFitData,dipoleFitDataRec struct of MNE-C fit_types.h).

Definition at line 122 of file dipole_fit_data.h.

Member Typedef Documentation

◆ ConstSPtr

typedef QSharedPointer<const DipoleFitData> INVERSELIB::DipoleFitData::ConstSPtr

Const shared pointer type for DipoleFitData.

Definition at line 126 of file dipole_fit_data.h.

◆ SPtr

typedef QSharedPointer<DipoleFitData> INVERSELIB::DipoleFitData::SPtr

Shared pointer type for DipoleFitData.

Definition at line 125 of file dipole_fit_data.h.

Constructor & Destructor Documentation

◆ DipoleFitData()

DipoleFitData::DipoleFitData ( )

explicit

Default Constructor

Definition at line 3297 of file dipole_fit_data.cpp.

◆ ~DipoleFitData()

DipoleFitData::~DipoleFitData ( )

virtual

Destructs the Dipole Fit Data Refactored: free_dipole_fit_data (dipole_fit_setup.c)

Definition at line 3318 of file dipole_fit_data.cpp.

Member Function Documentation

◆ ad_hoc_noise()

std::unique_ptr< MNECovMatrix > DipoleFitData::ad_hoc_noise	(	FWDLIB::FwdCoilSet *	meg,
		FWDLIB::FwdCoilSet *	eeg,
		float	grad_std,
		float	mag_std,
		float	eeg_std )

static

Definition at line 3488 of file dipole_fit_data.cpp.

◆ compute_dipole_field()

int DipoleFitData::compute_dipole_field	(	DipoleFitData *	d,
		float *	rd,
		int	whiten,
		float **	fwd )

static

Definition at line 4725 of file dipole_fit_data.cpp.

◆ dipole_forward_one()

DipoleForward * DipoleFitData::dipole_forward_one	(	DipoleFitData *	d,
		float *	rd,
		DipoleForward *	old )

static

Definition at line 4264 of file dipole_fit_data.cpp.

◆ fit_one()

bool DipoleFitData::fit_one	(	DipoleFitData *	fit,
		GuessData *	guess,
		float	time,
		float *	B,
		int	verbose,
		ECD &	res )

static

Fit a single dipole to the given data Refactored: fit_one (fit_dipoles.c)

Parameters

[in]	fit	Precomputed fitting data.
[in]	guess	The initial guesses.
[in]	time	Which time is it?.
[in]	B	The field to fit.
[in]	verbose.
[in]	res	The fitted dipole.

Definition at line 4597 of file dipole_fit_data.cpp.

◆ make_projection()

int DipoleFitData::make_projection	(	const QList< QString > &	projnames,
		const QList< FIFFLIB::FiffChInfo > &	chs,
		int	nch,
		MNELIB::MNEProjOp **	res )

static

Definition at line 3539 of file dipole_fit_data.cpp.

◆ scale_dipole_fit_noise_cov()

int DipoleFitData::scale_dipole_fit_noise_cov	(	DipoleFitData *	f,
		int	nave )

static

Definition at line 3656 of file dipole_fit_data.cpp.

◆ scale_noise_cov()

int DipoleFitData::scale_noise_cov	(	DipoleFitData *	f,
		int	nave )

static

Definition at line 3616 of file dipole_fit_data.cpp.

◆ select_dipole_fit_noise_cov()

int DipoleFitData::select_dipole_fit_noise_cov	(	DipoleFitData *	f,
		mshMegEegData	d )

static

Definition at line 3706 of file dipole_fit_data.cpp.

◆ setup_dipole_fit_data()

DipoleFitData * DipoleFitData::setup_dipole_fit_data	(	const QString &	mriname,
		const QString &	measname,
		const QString &	bemname,
		Eigen::Vector3f *	r0,
		FWDLIB::FwdEegSphereModel *	eeg_model,
		int	accurate_coils,
		const QString &	badname,
		const QString &	noisename,
		float	grad_std,
		float	mag_std,
		float	eeg_std,
		float	mag_reg,
		float	grad_reg,
		float	eeg_reg,
		int	diagnoise,
		const QList< QString > &	projnames,
		int	include_meg,
		int	include_eeg )

static

Parameters

mriname	This gives the MRI/head transform.
measname	This gives the MEG/head transform and sensor locations.
bemname	BEM model.
r0	Sphere model origin in head coordinates (optional).
eeg_model	EEG sphere model definition.
accurate_coils	Use accurate coil definitions?.
badname	Bad channels list.
noisename	Noise covariance matrix.
grad_std	Standard deviations for the ad-hoc noise cov (planar gradiometers).
mag_std	Ditto for magnetometers.
eeg_std	Ditto for EEG.
mag_reg	Noise-covariance regularization factors.
diagnoise	Use only the diagonal elements of the noise-covariance matrix.
projnames	SSP file names.
include_meg	Include MEG in the fitting?.

Definition at line 3787 of file dipole_fit_data.cpp.

◆ setup_forward_model()

int DipoleFitData::setup_forward_model	(	DipoleFitData *	d,
		MNELIB::MNECTFCompDataSet *	comp_data,
		FWDLIB::FwdCoilSet *	comp_coils )

static

Definition at line 3329 of file dipole_fit_data.cpp.

Member Data Documentation

◆ bem_funcs

dipoleFitFuncs INVERSELIB::DipoleFitData::bem_funcs

These are the BEM forward functions.

Definition at line 224 of file dipole_fit_data.h.

◆ bem_model

std::unique_ptr<FWDLIB::FwdBemModel> INVERSELIB::DipoleFitData::bem_model

BEM model definition.

Definition at line 221 of file dipole_fit_data.h.

◆ bemname

QString INVERSELIB::DipoleFitData::bemname

Using a BEM?.

Definition at line 218 of file dipole_fit_data.h.

◆ ch_names

QStringList INVERSELIB::DipoleFitData::ch_names

List of all channel names.

Definition at line 213 of file dipole_fit_data.h.

◆ chs

QList<FIFFLIB::FiffChInfo> INVERSELIB::DipoleFitData::chs

Channels.

Definition at line 210 of file dipole_fit_data.h.

◆ column_norm

int INVERSELIB::DipoleFitData::column_norm

What kind of column normalization to apply to the forward solution.

Definition at line 233 of file dipole_fit_data.h.

◆ coord_frame

int INVERSELIB::DipoleFitData::coord_frame

Common coordinate frame.

Definition at line 209 of file dipole_fit_data.h.

◆ eeg_els

std::unique_ptr<FWDLIB::FwdCoilSet> INVERSELIB::DipoleFitData::eeg_els

EEG electrode definitions.

Definition at line 216 of file dipole_fit_data.h.

◆ eeg_model

std::unique_ptr<FWDLIB::FwdEegSphereModel> INVERSELIB::DipoleFitData::eeg_model

EEG sphere model definition.

Definition at line 220 of file dipole_fit_data.h.

◆ fit_mag_dipoles

int INVERSELIB::DipoleFitData::fit_mag_dipoles

Fit magnetic dipoles?.

Definition at line 234 of file dipole_fit_data.h.

◆ fixed_noise

int INVERSELIB::DipoleFitData::fixed_noise

Were fixed noise values used rather than a noise-covariance matrix read from a file.

Definition at line 228 of file dipole_fit_data.h.

◆ funcs

dipoleFitFuncs INVERSELIB::DipoleFitData::funcs

Points to one of the two above.

Definition at line 225 of file dipole_fit_data.h.

◆ mag_dipole_funcs

dipoleFitFuncs INVERSELIB::DipoleFitData::mag_dipole_funcs

Functions to fit a magnetic dipole.

Definition at line 226 of file dipole_fit_data.h.

◆ meg_coils

std::unique_ptr<FWDLIB::FwdCoilSet> INVERSELIB::DipoleFitData::meg_coils

MEG coil definitions.

Definition at line 215 of file dipole_fit_data.h.

◆ meg_head_t

std::unique_ptr<FIFFLIB::FiffCoordTrans> INVERSELIB::DipoleFitData::meg_head_t

MEG <-> head coordinate transformation.

Definition at line 208 of file dipole_fit_data.h.

◆ mri_head_t

std::unique_ptr<FIFFLIB::FiffCoordTrans> INVERSELIB::DipoleFitData::mri_head_t

MRI <-> head coordinate transformation.

Definition at line 207 of file dipole_fit_data.h.

◆ nave

int INVERSELIB::DipoleFitData::nave

How many averages does this correspond to?.

Definition at line 231 of file dipole_fit_data.h.

◆ neeg

int INVERSELIB::DipoleFitData::neeg

How many EEG.

Definition at line 212 of file dipole_fit_data.h.

◆ nmeg

int INVERSELIB::DipoleFitData::nmeg

How many MEG.

Definition at line 211 of file dipole_fit_data.h.

◆ noise

std::unique_ptr<MNELIB::MNECovMatrix> INVERSELIB::DipoleFitData::noise

Noise covariance matrix (weighted to take the selection into account).

Definition at line 230 of file dipole_fit_data.h.

◆ noise_orig

std::unique_ptr<MNELIB::MNECovMatrix> INVERSELIB::DipoleFitData::noise_orig

Noise covariance matrix (original, currently unused).

Definition at line 229 of file dipole_fit_data.h.

◆ pick

std::unique_ptr<FIFFLIB::FiffSparseMatrix> INVERSELIB::DipoleFitData::pick

Matrix to pick data from the full data set which may contain channels we are not interested in (currently unused).

Definition at line 214 of file dipole_fit_data.h.

◆ proj

std::unique_ptr<MNELIB::MNEProjOp> INVERSELIB::DipoleFitData::proj

The projection operator to use.

Definition at line 232 of file dipole_fit_data.h.

◆ r0

float INVERSELIB::DipoleFitData::r0[3]

Sphere model origin.

Definition at line 217 of file dipole_fit_data.h.

◆ sphere_funcs

dipoleFitFuncs INVERSELIB::DipoleFitData::sphere_funcs

These are the sphere model forward functions.

Definition at line 223 of file dipole_fit_data.h.

◆ user

FitDipUserRec* INVERSELIB::DipoleFitData::user

Non-owning pointer to dipole fit workspace (set during fit_one).

Definition at line 235 of file dipole_fit_data.h.

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

src/libraries/inverse/dipoleFit/dipole_fit_data.h
src/libraries/inverse/dipoleFit/dipole_fit_data.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

Constructor & Destructor Documentation

◆ DipoleFitData()

◆ ~DipoleFitData()

Member Function Documentation

◆ ad_hoc_noise()

◆ compute_dipole_field()

◆ dipole_forward_one()

◆ fit_one()

◆ make_projection()

◆ scale_dipole_fit_noise_cov()

◆ scale_noise_cov()

◆ select_dipole_fit_noise_cov()

◆ setup_dipole_fit_data()

◆ setup_forward_model()

Member Data Documentation

◆ bem_funcs

◆ bem_model

◆ bemname

◆ ch_names

◆ chs

◆ column_norm

◆ coord_frame

◆ eeg_els

◆ eeg_model

◆ fit_mag_dipoles

◆ fixed_noise

◆ funcs

◆ mag_dipole_funcs

◆ meg_coils

◆ meg_head_t

◆ mri_head_t

◆ nave

◆ neeg

◆ nmeg

◆ noise

◆ noise_orig

◆ pick

◆ proj

◆ r0

◆ sphere_funcs

◆ user