int DipoleFit::fit_dipoles( const QString& dataname, MneMeasData* data, DipoleFitData* fit, GuessData* guess, float tmin, float tmax, float tstep, float integ, int verbose, ECDSet& p_set)
{
float *one = MALLOC(data->nchan,float);
float time;
ECDSet set;
ECD dip;
int s;
int report_interval = 10;
set.dataname = dataname;
fprintf(stderr,"Fitting...%c",verbose ? '\n' : '\0');
for (s = 0, time = tmin; time < tmax; s++, time = tmin + s*tstep) {
/*
* Pick the data point
*/
if (mne_get_values_from_data(time,integ,data->current->data,data->current->np,data->nchan,data->current->tmin,
1.0/data->current->tstep,FALSE,one) == FAIL) {
fprintf(stderr,"Cannot pick time: %7.1f ms\n",1000*time);
continue;
}
if (!DipoleFitData::fit_one(fit,guess,time,one,verbose,dip))
printf("t = %7.1f ms : %s\n",1000*time,"error (tbd: catch)");
else {
set.addEcd(dip);
if (verbose)
dip.print(stdout);
else {
if (set.size() % report_interval == 0)
fprintf(stderr,"%d..",set.size());
}
}
}
if (!verbose)
fprintf(stderr,"[done]\n");
FREE(one);
p_set = set;
return OK;
}
ECDView::ECDView(const DipoleFitSettings& dipFitSettings, const ECDSet& ecdSet, QWidget* parent)
: AbstractView(parent)
{
//Read mri transform
QFile file(dipFitSettings.mriname);
ECDSet ecdSetTrans = ecdSet;
if(file.exists()) {
FiffCoordTrans coordTrans(file);
for(int i = 0; i < ecdSet.size() ; ++i) {
MatrixX3f dipoles(1, 3);
//transform location
dipoles(0,0) = ecdSet[i].rd(0);
dipoles(0,1) = ecdSet[i].rd(1);
dipoles(0,2) = ecdSet[i].rd(2);
dipoles = coordTrans.apply_trans(dipoles);
ecdSetTrans[i].rd(0) = dipoles(0,0);
ecdSetTrans[i].rd(1) = dipoles(0,1);
ecdSetTrans[i].rd(2) = dipoles(0,2);
//transform orientation
dipoles(0,0) = ecdSet[i].Q(0);
dipoles(0,1) = ecdSet[i].Q(1);
dipoles(0,2) = ecdSet[i].Q(2);
dipoles = coordTrans.apply_trans(dipoles, false);
ecdSetTrans[i].Q(0) = dipoles(0,0);
ecdSetTrans[i].Q(1) = dipoles(0,1);
ecdSetTrans[i].Q(2) = dipoles(0,2);
}
} else {
qCritical("ECDView::ECDView - Cannot open FiffCoordTrans file");
}
//Add ECD data
m_pData3DModel->addDipoleFitData("sample", QString("Set %1").arg(dipFitSettings.setno), ecdSetTrans);
//Read and show BEM
QFile t_fileBem(dipFitSettings.bemname);
if(t_fileBem.exists()) {
MNEBem t_Bem(t_fileBem);
m_pData3DModel->addBemData("sample", "BEM", t_Bem);
} else {
qCritical("ECDView::ECDView - Cannot open MNEBem file");
}
}
int DipoleFit::fit_dipoles_raw(const QString& dataname, MneRawData* raw, mneChSelection sel, DipoleFitData* fit, GuessData* guess, float tmin, float tmax, float tstep, float integ, int verbose, ECDSet& p_set)
{
float *one = MALLOC(sel->nchan,float);
float sfreq = raw->info->sfreq;
float myinteg = integ > 0.0 ? 2*integ : 0.1;
int overlap = ceil(myinteg*sfreq);
int length = SEG_LEN*sfreq;
int step = length - overlap;
int stepo = step + overlap/2;
int start = raw->first_samp;
int s,picks;
float time,stime;
float **data = ALLOC_CMATRIX(sel->nchan,length);
ECD dip;
ECDSet set;
int report_interval = 10;
set.dataname = dataname;
/*
* Load the initial data segment
*/
stime = start/sfreq;
if (MneRawData::mne_raw_pick_data_filt(raw,sel,start,length,data) == FAIL)
goto bad;
fprintf(stderr,"Fitting...%c",verbose ? '\n' : '\0');
for (s = 0, time = tmin; time < tmax; s++, time = tmin + s*tstep) {
picks = time*sfreq - start;
if (picks > stepo) { /* Need a new data segment? */
start = start + step;
if (MneRawData::mne_raw_pick_data_filt(raw,sel,start,length,data) == FAIL)
goto bad;
picks = time*sfreq - start;
stime = start/sfreq;
}
/*
* Get the values
*/
if (mne_get_values_from_data_ch (time,integ,data,length,sel->nchan,stime,sfreq,FALSE,one) == FAIL) {
fprintf(stderr,"Cannot pick time: %8.3f s\n",time);
continue;
}
/*
* Fit
*/
if (!DipoleFitData::fit_one(fit,guess,time,one,verbose,dip))
qWarning() << "Error";
else {
set.addEcd(dip);
if (verbose)
dip.print(stdout);
else {
if (set.size() % report_interval == 0)
fprintf(stderr,"%d..",set.size());
}
}
}
if (!verbose)
fprintf(stderr,"[done]\n");
FREE_CMATRIX(data);
FREE(one);
p_set = set;
return OK;
bad : {
FREE_CMATRIX(data);
FREE(one);
return FAIL;
}
}
//*************************************************************************************************************
//todo split in initFit where the settings are handed over and the actual fit
ECDSet DipoleFit::calculateFit() const
{
GuessData* guess = NULL;
ECDSet set;
FwdEegSphereModel* eeg_model = NULL;
DipoleFitData* fit_data = NULL;
MneMeasData* data = NULL;
MneRawData* raw = NULL;
mneChSelection sel = NULL;
printf("---- Setting up...\n\n");
if (settings->include_eeg) {
if ((eeg_model = FwdEegSphereModel::setup_eeg_sphere_model(settings->eeg_model_file,settings->eeg_model_name,settings->eeg_sphere_rad)) == NULL)
goto out;
}
if ((fit_data = DipoleFitData::setup_dipole_fit_data( settings->mriname,
settings->measname,
settings->bemname.isEmpty() ? NULL : settings->bemname.toLatin1().data(),
&settings->r0,eeg_model,settings->accurate,
settings->badname,
settings->noisename,
settings->grad_std,settings->mag_std,settings->eeg_std,
settings->mag_reg,settings->grad_reg,settings->eeg_reg,
settings->diagnoise,settings->projnames,settings->include_meg,settings->include_eeg)) == NULL )
goto out;
fit_data->fit_mag_dipoles = settings->fit_mag_dipoles;
if (settings->is_raw) {
int c;
float t1,t2;
printf("\n---- Opening a raw data file...\n\n");
if ((raw = MneRawData::mne_raw_open_file(settings->measname.isEmpty() ? NULL : settings->measname.toLatin1().data(),TRUE,FALSE,&(settings->filter))) == NULL)
goto out;
/*
* A channel selection is needed to access the data
*/
sel = mne_ch_selection_these("fit",fit_data->ch_names,fit_data->nmeg+fit_data->neeg);
mne_ch_selection_assign_chs(sel,raw);
for (c = 0; c < sel->nchan; c++)
if (sel->pick[c] < 0) {
qCritical ("All desired channels were not available");
goto out;
}
printf("\tChannel selection created.\n");
/*
* Let's be a little generous here
*/
t1 = raw->first_samp/raw->info->sfreq;
t2 = (raw->first_samp+raw->nsamp-1)/raw->info->sfreq;
if (settings->tmin < t1 + settings->integ)
settings->tmin = t1 + settings->integ;
if (settings->tmax > t2 - settings->integ)
settings->tmax = t2 - settings->integ;
if (settings->tstep < 0)
settings->tstep = 1.0/raw->info->sfreq;
printf("\tOpened raw data file %s : %d MEG and %d EEG \n",
settings->measname.toLatin1().data(),fit_data->nmeg,fit_data->neeg);
}
else {
printf("\n---- Reading data...\n\n");
if ((data = MneMeasData::mne_read_meas_data(settings->measname,settings->setno,NULL,NULL,
fit_data->ch_names,fit_data->nmeg+fit_data->neeg)) == NULL)
goto out;
if (settings->do_baseline)
data->adjust_baselines(settings->bmin,settings->bmax);
else
printf("\tNo baseline setting in effect.\n");
if (settings->tmin < data->current->tmin + settings->integ/2.0)
settings->tmin = data->current->tmin + settings->integ/2.0;
if (settings->tmax > data->current->tmin + (data->current->np-1)*data->current->tstep - settings->integ/2.0)
settings->tmax = data->current->tmin + (data->current->np-1)*data->current->tstep - settings->integ/2.0;
if (settings->tstep < 0)
settings->tstep = data->current->tstep;
printf("\tRead data set %d from %s : %d MEG and %d EEG \n",
settings->setno,settings->measname.toLatin1().data(),fit_data->nmeg,fit_data->neeg);
if (!settings->noisename.isEmpty()) {
printf("\nScaling the noise covariance...\n");
if (DipoleFitData::scale_noise_cov(fit_data,data->current->nave) == FAIL)
goto out;
}
}
/*
* Proceed to computing the fits
*/
printf("\n---- Computing the forward solution for the guesses...\n\n");
if ((guess = new GuessData( settings->guessname,
settings->guess_surfname,
settings->guess_mindist, settings->guess_exclude, settings->guess_grid, fit_data)) == NULL)
goto out;
fprintf (stderr,"\n---- Fitting : %7.1f ... %7.1f ms (step: %6.1f ms integ: %6.1f ms)\n\n",
1000*settings->tmin,1000*settings->tmax,1000*settings->tstep,1000*settings->integ);
if (raw) {
if (fit_dipoles_raw(settings->measname,raw,sel,fit_data,guess,settings->tmin,settings->tmax,settings->tstep,settings->integ,settings->verbose) == FAIL)
goto out;
}
else {
if (fit_dipoles(settings->measname,data,fit_data,guess,settings->tmin,settings->tmax,settings->tstep,settings->integ,settings->verbose,set) == FAIL)
goto out;
}
printf("%d dipoles fitted\n",set.size());
out : {
return set;
}
}