MNE-CPP  0.1.9
A Framework for Electrophysiology
Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
INVERSELIB::DipoleFitData Class Reference

Dipole Fit Data implementation. More...

#include <dipole_fit_data.h>

Public Types

typedef QSharedPointer< DipoleFitDataSPtr
typedef QSharedPointer< const DipoleFitDataConstSPtr

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 MNELIB::MneCovMatrixad_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 DipoleFitDatasetup_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 DipoleForwarddipole_forward_one (DipoleFitData *d, float *rd, DipoleForward *old)

Public Attributes

int coord_frame
QList< FIFFLIB::FiffChInfochs
int nmeg
int neeg
QStringList ch_names
float r0 [3]
QString bemname
dipoleFitFuncs sphere_funcs
dipoleFitFuncs bem_funcs
dipoleFitFuncs funcs
dipoleFitFuncs mag_dipole_funcs
int fixed_noise
int nave
int column_norm
int fit_mag_dipoles
void * user
fitUserFreeFunc user_free

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 109 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 113 of file dipole_fit_data.h.

◆ SPtr

Shared pointer type for DipoleFitData.

Definition at line 112 of file dipole_fit_data.h.

Constructor & Destructor Documentation

◆ DipoleFitData()

DipoleFitData::DipoleFitData ( )

Default Constructor

Definition at line 3337 of file dipole_fit_data.cpp.

◆ ~DipoleFitData()

DipoleFitData::~DipoleFitData ( )

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

Definition at line 3370 of file dipole_fit_data.cpp.

Member Function Documentation

◆ fit_one()

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

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

[in]fitPrecomputed fitting data.
[in]guessThe initial guesses.
[in]timeWhich time is it?.
[in]BThe field to fit.
[in]resThe fitted dipole.

Definition at line 4671 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 
mrinameThis gives the MRI/head transform.
measnameThis gives the MEG/head transform and sensor locations.
bemnameBEM model.
r0Sphere model origin in head coordinates (optional).
eeg_modelEEG sphere model definition.
accurate_coilsUse accurate coil definitions?.
badnameBad channels list.
noisenameNoise covariance matrix.
grad_stdStandard deviations for the ad-hoc noise cov (planar gradiometers).
mag_stdDitto for magnetometers.
eeg_stdDitto for EEG.
mag_regNoise-covariance regularization factors.
diagnoiseUse only the diagonal elements of the noise-covariance matrix.
projnamesSSP file names.
include_megInclude MEG in the fitting?.

Definition at line 3868 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 211 of file dipole_fit_data.h.

◆ bem_model

FWDLIB::FwdBemModel* INVERSELIB::DipoleFitData::bem_model

BEM model definition.

Definition at line 208 of file dipole_fit_data.h.

◆ bemname

QString INVERSELIB::DipoleFitData::bemname

Using a BEM?.

Definition at line 205 of file dipole_fit_data.h.

◆ ch_names

QStringList INVERSELIB::DipoleFitData::ch_names

List of all channel names.

Definition at line 200 of file dipole_fit_data.h.

◆ chs

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


Definition at line 197 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 220 of file dipole_fit_data.h.

◆ coord_frame

int INVERSELIB::DipoleFitData::coord_frame

Common coordinate frame.

Definition at line 196 of file dipole_fit_data.h.

◆ eeg_els

FWDLIB::FwdCoilSet* INVERSELIB::DipoleFitData::eeg_els

EEG electrode definitions.

Definition at line 203 of file dipole_fit_data.h.

◆ eeg_model

FWDLIB::FwdEegSphereModel* INVERSELIB::DipoleFitData::eeg_model

EEG sphere model definition.

Definition at line 207 of file dipole_fit_data.h.

◆ fit_mag_dipoles

int INVERSELIB::DipoleFitData::fit_mag_dipoles

Fit magnetic dipoles?.

Definition at line 221 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 215 of file dipole_fit_data.h.

◆ funcs

dipoleFitFuncs INVERSELIB::DipoleFitData::funcs

Points to one of the two above.

Definition at line 212 of file dipole_fit_data.h.

◆ mag_dipole_funcs

dipoleFitFuncs INVERSELIB::DipoleFitData::mag_dipole_funcs

Functions to fit a magnetic dipole.

Definition at line 213 of file dipole_fit_data.h.

◆ meg_coils

FWDLIB::FwdCoilSet* INVERSELIB::DipoleFitData::meg_coils

MEG coil definitions.

Definition at line 202 of file dipole_fit_data.h.

◆ meg_head_t

FIFFLIB::FiffCoordTransOld* INVERSELIB::DipoleFitData::meg_head_t

MEG <-> head coordinate transformation.

Definition at line 195 of file dipole_fit_data.h.

◆ mri_head_t

FIFFLIB::FiffCoordTransOld* INVERSELIB::DipoleFitData::mri_head_t

MRI <-> head coordinate transformation.

Definition at line 194 of file dipole_fit_data.h.

◆ nave

int INVERSELIB::DipoleFitData::nave

How many averages does this correspond to?.

Definition at line 218 of file dipole_fit_data.h.

◆ neeg

int INVERSELIB::DipoleFitData::neeg

How many EEG.

Definition at line 199 of file dipole_fit_data.h.

◆ nmeg

int INVERSELIB::DipoleFitData::nmeg

How many MEG.

Definition at line 198 of file dipole_fit_data.h.

◆ noise

MNELIB::MneCovMatrix* INVERSELIB::DipoleFitData::noise

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

Definition at line 217 of file dipole_fit_data.h.

◆ noise_orig

MNELIB::MneCovMatrix* INVERSELIB::DipoleFitData::noise_orig

Noise covariance matrix (original).

Definition at line 216 of file dipole_fit_data.h.

◆ pick

FIFFLIB::FiffSparseMatrix* INVERSELIB::DipoleFitData::pick

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

Definition at line 201 of file dipole_fit_data.h.

◆ proj

MNELIB::MneProjOp* INVERSELIB::DipoleFitData::proj

The projection operator to use.

Definition at line 219 of file dipole_fit_data.h.

◆ r0

float INVERSELIB::DipoleFitData::r0[3]

Sphere model origin.

Definition at line 204 of file dipole_fit_data.h.

◆ sphere_funcs

dipoleFitFuncs INVERSELIB::DipoleFitData::sphere_funcs

These are the sphere model forward functions.

Definition at line 210 of file dipole_fit_data.h.

◆ user

void* INVERSELIB::DipoleFitData::user

User data for anything we need.

Definition at line 222 of file dipole_fit_data.h.

◆ user_free

fitUserFreeFunc INVERSELIB::DipoleFitData::user_free

Function to free the above.

Definition at line 223 of file dipole_fit_data.h.

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