SourceEstimate MinimumNorm::calculateInverse(const FiffEvoked &p_fiffEvoked, bool pick_normal) const
{
//
// Set up the inverse according to the parameters
//
qint32 nave = p_fiffEvoked.nave;
if(!m_inverseOperator.check_ch_names(p_fiffEvoked.info))
{
qWarning("Channel name check failed.");
return SourceEstimate();
}
MNEInverseOperator inv = m_inverseOperator.prepare_inverse_operator(nave, m_fLambda, m_bdSPM, m_bsLORETA);
//
// Pick the correct channels from the data
//
FiffEvoked t_fiffEvoked = p_fiffEvoked.pick_channels(inv.noise_cov->names);
printf("Picked %d channels from the data\n",t_fiffEvoked.info.nchan);
printf("Computing inverse...");
MatrixXd K;
SparseMatrix<double> noise_norm;
QList<VectorXi> vertno;
Label label;
inv.assemble_kernel(label, m_sMethod, pick_normal, K, noise_norm, vertno);
MatrixXd sol = K * t_fiffEvoked.data; //apply imaging kernel
if (inv.source_ori == FIFFV_MNE_FREE_ORI)
{
printf("combining the current components...");
MatrixXd sol1(sol.rows()/3,sol.cols());
for(qint32 i = 0; i < sol.cols(); ++i)
{
VectorXd* tmp = MNEMath::combine_xyz(sol.block(0,i,sol.rows(),1));
sol1.block(0,i,sol.rows()/3,1) = tmp->cwiseSqrt();
delete tmp;
}
sol.resize(sol1.rows(),sol1.cols());
sol = sol1;
}
if (m_bdSPM)
{
printf("(dSPM)...");
sol = inv.noisenorm*sol;
}
else if (m_bsLORETA)
{
printf("(sLORETA)...");
sol = inv.noisenorm*sol;
}
printf("[done]\n");
//Results
float tmin = ((float)t_fiffEvoked.first) / t_fiffEvoked.info.sfreq;
float tstep = 1/t_fiffEvoked.info.sfreq;
QList<VectorXi> t_qListVertices;
for(qint32 h = 0; h < inv.src.size(); ++h)
t_qListVertices.push_back(inv.src[h].vertno);
return SourceEstimate(sol, t_qListVertices, tmin, tstep);
}
void RtAve::generateEvoked(double dTriggerType)
{
QMutexLocker locker(&m_qMutex);
if(m_mapStimAve[dTriggerType].isEmpty()) {
return;
}
//Init evoked
FiffEvoked evoked;
int iEvokedIdx = -1;
for(int i = 0; i < m_pStimEvokedSet->evoked.size(); ++i) {
if(m_pStimEvokedSet->evoked.at(i).comment == QString::number(dTriggerType)) {
evoked = m_pStimEvokedSet->evoked.at(i);
iEvokedIdx = i;
break;
}
}
//If the evoked is not yet present add it here
if(iEvokedIdx == -1) {
float T = 1.0/m_pFiffInfo->sfreq;
evoked.setInfo(*m_pFiffInfo.data());
evoked.baseline = m_pairBaselineSec;
evoked.times.resize(m_iPreStimSamples + m_iPostStimSamples);
evoked.times[0] = -T*m_iPreStimSamples;
for(int i = 1; i < evoked.times.size(); ++i)
evoked.times[i] = evoked.times[i-1] + T;
evoked.first = evoked.times[0];
evoked.last = evoked.times[evoked.times.size()-1];
evoked.comment = QString::number(dTriggerType);
}
// Generate final evoked
MatrixXd finalAverage = MatrixXd::Zero(m_mapStimAve[dTriggerType].first().rows(), m_iPreStimSamples+m_iPostStimSamples);
if(m_iAverageMode == 0) {
for(int i = 0; i < m_mapStimAve[dTriggerType].size(); ++i) {
finalAverage += m_mapStimAve[dTriggerType].at(i);
}
if(m_mapStimAve[dTriggerType].isEmpty()) {
finalAverage = finalAverage/1;
} else {
finalAverage = finalAverage/m_mapStimAve[dTriggerType].size();
}
if(m_bDoBaselineCorrection) {
finalAverage = MNEMath::rescale(finalAverage, evoked.times, m_pairBaselineSec, QString("mean"));
}
evoked.data = finalAverage;
if(m_mapNumberCalcAverages[dTriggerType] < m_iNumAverages) {
m_mapNumberCalcAverages[dTriggerType]++;
}
evoked.nave = m_mapNumberCalcAverages[dTriggerType];
} else if(m_iAverageMode == 1) {
MatrixXd tempMatrix = m_mapStimAve[dTriggerType].last();
if(m_bDoBaselineCorrection) {
tempMatrix = MNEMath::rescale(tempMatrix, evoked.times, m_pairBaselineSec, QString("mean"));
}
evoked += tempMatrix;
m_mapNumberCalcAverages[dTriggerType]++;
}
//Add new data to evoked data set
if(iEvokedIdx != -1) {
//Evoked data is already present
m_pStimEvokedSet->evoked[iEvokedIdx] = evoked;
} else {
//Evoked data is not present yet
m_pStimEvokedSet->evoked.append(evoked);
}
}
/**
* The function main marks the entry point of the program.
* By default, main has the storage class extern.
*
* @param [in] argc (argument count) is an integer that indicates how many arguments were entered on the command line when the program was started.
* @param [in] argv (argument vector) is an array of pointers to arrays of character objects. The array objects are null-terminated strings, representing the arguments that were entered on the command line when the program was started.
* @return the value that was set to exit() (which is 0 if exit() is called via quit()).
*/
int main(int argc, char *argv[])
{
QApplication a(argc, argv);
// Command Line Parser
QCommandLineParser parser;
parser.setApplicationDescription("Clustered Inverse Raw Example");
parser.addHelpOption();
QCommandLineOption inputOption("fileIn", "The input file <in>.", "in", "./MNE-sample-data/MEG/sample/sample_audvis_raw.fif");
QCommandLineOption surfOption("surfType", "Surface type <type>.", "type", "inflated");
QCommandLineOption annotOption("annotType", "Annotation type <type>.", "type", "aparc.a2009s");
QCommandLineOption subjectOption("subject", "Selected subject <subject>.", "subject", "sample");
QCommandLineOption subjectPathOption("subjectPath", "Selected subject path <subjectPath>.", "subjectPath", "./MNE-sample-data/subjects");
QCommandLineOption fwdOption("fwd", "Path to forwad solution <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
QCommandLineOption covFileOption("cov", "Path to the covariance <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-cov.fif");
QCommandLineOption evokedIndexOption("aveIdx", "The average <index> to choose from the average file.", "index", "1");
QCommandLineOption eventsFileOption("eve", "Path to the event <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis_raw-eve.fif");
QCommandLineOption hemiOption("hemi", "Selected hemisphere <hemi>.", "hemi", "2");
QCommandLineOption methodOption("method", "Inverse estimation <method>, i.e., 'MNE', 'dSPM' or 'sLORETA'.", "method", "dSPM");//"MNE" | "dSPM" | "sLORETA"
QCommandLineOption snrOption("snr", "The SNR value used for computation <snr>.", "snr", "1.0");//3.0;//0.1;//3.0;
QCommandLineOption invFileOutOption("invOut", "Path to inverse <file>, which is to be written.", "file", "");
QCommandLineOption stcFileOutOption("stcOut", "Path to stc <file>, which is to be written.", "file", "");
QCommandLineOption keepCompOption("keepComp", "Keep compensators.", "keepComp", "false");
QCommandLineOption pickAllOption("pickAll", "Pick all channels.", "pickAll", "true");
QCommandLineOption destCompsOption("destComps", "<Destination> of the compensator which is to be calculated.", "destination", "0");
parser.addOption(inputOption);
parser.addOption(surfOption);
parser.addOption(annotOption);
parser.addOption(subjectOption);
parser.addOption(subjectPathOption);
parser.addOption(fwdOption);
parser.addOption(covFileOption);
parser.addOption(evokedIndexOption);
parser.addOption(eventsFileOption);
parser.addOption(hemiOption);
parser.addOption(methodOption);
parser.addOption(snrOption);
parser.addOption(invFileOutOption);
parser.addOption(stcFileOutOption);
parser.addOption(keepCompOption);
parser.addOption(pickAllOption);
parser.addOption(destCompsOption);
parser.process(a);
// Load files
QFile t_fileFwd(parser.value(fwdOption));
QFile t_fileCov(parser.value(covFileOption));
QFile t_fileRaw(parser.value(inputOption));
QString t_sEventName = parser.value(eventsFileOption);
SurfaceSet t_surfSet (parser.value(subjectOption), parser.value(hemiOption).toInt(), parser.value(surfOption), parser.value(subjectPathOption));
AnnotationSet t_annotationSet (parser.value(subjectOption), parser.value(hemiOption).toInt(), parser.value(annotOption), parser.value(subjectPathOption));
qint32 event = parser.value(evokedIndexOption).toInt();
float tmin = -0.2f;
float tmax = 0.4f;
bool keep_comp = false;
if(parser.value(keepCompOption) == "false" || parser.value(keepCompOption) == "0") {
keep_comp = false;
} else if(parser.value(keepCompOption) == "true" || parser.value(keepCompOption) == "1") {
keep_comp = true;
}
fiff_int_t dest_comp = parser.value(destCompsOption).toInt();
bool pick_all = false;
if(parser.value(pickAllOption) == "false" || parser.value(pickAllOption) == "0") {
pick_all = false;
} else if(parser.value(pickAllOption) == "true" || parser.value(pickAllOption) == "1") {
pick_all = true;
}
qint32 k, p;
//
// Setup for reading the raw data
//
FiffRawData raw(t_fileRaw);
RowVectorXi picks;
if (pick_all)
{
//
// Pick all
//
picks.resize(raw.info.nchan);
for(k = 0; k < raw.info.nchan; ++k)
picks(k) = k;
//
}
else
{
QStringList include;
include << "STI 014";
bool want_meg = true;
bool want_eeg = false;
bool want_stim = false;
// picks = Fiff::pick_types(raw.info, want_meg, want_eeg, want_stim, include, raw.info.bads);
picks = raw.info.pick_types(want_meg, want_eeg, want_stim, include, raw.info.bads);//prefer member function
}
QStringList ch_names;
for(k = 0; k < picks.cols(); ++k)
ch_names << raw.info.ch_names[picks(0,k)];
//
// Set up projection
//
if (raw.info.projs.size() == 0)
printf("No projector specified for these data\n");
else
{
//
// Activate the projection items
//
for (k = 0; k < raw.info.projs.size(); ++k)
raw.info.projs[k].active = true;
printf("%d projection items activated\n",raw.info.projs.size());
//
// Create the projector
//
// fiff_int_t nproj = MNE::make_projector_info(raw.info, raw.proj); Using the member function instead
fiff_int_t nproj = raw.info.make_projector(raw.proj);
if (nproj == 0)
{
printf("The projection vectors do not apply to these channels\n");
}
else
{
printf("Created an SSP operator (subspace dimension = %d)\n",nproj);
}
}
//
// Set up the CTF compensator
//
// qint32 current_comp = MNE::get_current_comp(raw.info);
qint32 current_comp = raw.info.get_current_comp();
if (current_comp > 0)
printf("Current compensation grade : %d\n",current_comp);
if (keep_comp)
dest_comp = current_comp;
if (current_comp != dest_comp)
{
qDebug() << "This part needs to be debugged";
if(MNE::make_compensator(raw.info, current_comp, dest_comp, raw.comp))
{
// raw.info.chs = MNE::set_current_comp(raw.info.chs,dest_comp);
raw.info.set_current_comp(dest_comp);
printf("Appropriate compensator added to change to grade %d.\n",dest_comp);
}
else
{
printf("Could not make the compensator\n");
return 0;
}
}
//
// Read the events
//
QFile t_EventFile;
MatrixXi events;
if (t_sEventName.size() == 0)
{
p = t_fileRaw.fileName().indexOf(".fif");
if (p > 0)
{
t_sEventName = t_fileRaw.fileName().replace(p, 4, "-eve.fif");
}
else
{
printf("Raw file name does not end properly\n");
return 0;
}
// events = mne_read_events(t_sEventName);
t_EventFile.setFileName(t_sEventName);
MNE::read_events(t_EventFile, events);
printf("Events read from %s\n",t_sEventName.toUtf8().constData());
}
else
{
//
// Binary file
//
p = t_fileRaw.fileName().indexOf(".fif");
if (p > 0)
{
t_EventFile.setFileName(t_sEventName);
if(!MNE::read_events(t_EventFile, events))
{
printf("Error while read events.\n");
return 0;
}
printf("Binary event file %s read\n",t_sEventName.toUtf8().constData());
}
else
{
//
// Text file
//
printf("Text file %s is not supported jet.\n",t_sEventName.toUtf8().constData());
// try
// events = load(eventname);
// catch
// error(me,mne_omit_first_line(lasterr));
// end
// if size(events,1) < 1
// error(me,'No data in the event file');
// end
// //
// // Convert time to samples if sample number is negative
// //
// for p = 1:size(events,1)
// if events(p,1) < 0
// events(p,1) = events(p,2)*raw.info.sfreq;
// end
// end
// //
// // Select the columns of interest (convert to integers)
// //
// events = int32(events(:,[1 3 4]));
// //
// // New format?
// //
// if events(1,2) == 0 && events(1,3) == 0
// fprintf(1,'The text event file %s is in the new format\n',eventname);
// if events(1,1) ~= raw.first_samp
// error(me,'This new format event file is not compatible with the raw data');
// end
// else
// fprintf(1,'The text event file %s is in the old format\n',eventname);
// //
// // Offset with first sample
// //
// events(:,1) = events(:,1) + raw.first_samp;
// end
}
}
//
// Select the desired events
//
qint32 count = 0;
MatrixXi selected = MatrixXi::Zero(1, events.rows());
for (p = 0; p < events.rows(); ++p)
{
if (events(p,1) == 0 && events(p,2) == event)
{
selected(0,count) = p;
++count;
}
}
selected.conservativeResize(1, count);
if (count > 0)
printf("%d matching events found\n",count);
else
{
printf("No desired events found.\n");
return 0;
}
fiff_int_t event_samp, from, to;
MatrixXd timesDummy;
MNEEpochDataList data;
MNEEpochData* epoch = NULL;
MatrixXd times;
for (p = 0; p < count; ++p)
{
//
// Read a data segment
//
event_samp = events(selected(p),0);
from = event_samp + tmin*raw.info.sfreq;
to = event_samp + floor(tmax*raw.info.sfreq + 0.5);
epoch = new MNEEpochData();
if(raw.read_raw_segment(epoch->epoch, timesDummy, from, to, picks))
{
if (p == 0)
{
times.resize(1, to-from+1);
for (qint32 i = 0; i < times.cols(); ++i)
times(0, i) = ((float)(from-event_samp+i)) / raw.info.sfreq;
}
epoch->event = event;
epoch->tmin = ((float)(from)-(float)(raw.first_samp))/raw.info.sfreq;
epoch->tmax = ((float)(to)-(float)(raw.first_samp))/raw.info.sfreq;
data.append(MNEEpochData::SPtr(epoch));//List takes ownwership of the pointer - no delete need
}
else
{
printf("Can't read the event data segments");
return 0;
}
}
if(data.size() > 0)
{
printf("Read %d epochs, %d samples each.\n",data.size(),(qint32)data[0]->epoch.cols());
//DEBUG
std::cout << data[0]->epoch.block(0,0,10,10) << std::endl;
qDebug() << data[0]->epoch.rows() << " x " << data[0]->epoch.cols();
std::cout << times.block(0,0,1,10) << std::endl;
qDebug() << times.rows() << " x " << times.cols();
}
// Calculate the average
// Option 1 - Random selection
VectorXi vecSel(50);
srand (time(NULL)); // initialize random seed
for(qint32 i = 0; i < vecSel.size(); ++i)
{
qint32 val = rand() % count;
vecSel(i) = val;
}
// //Option 3 - Take all epochs
// VectorXi vecSel(data.size());
// for(qint32 i = 0; i < vecSel.size(); ++i)
// {
// vecSel(i) = i;
// }
// //Option 3 - Manual selection
// VectorXi vecSel(20);
// vecSel << 76, 74, 13, 61, 97, 94, 75, 71, 60, 56, 26, 57, 56, 0, 52, 72, 33, 86, 96, 67;
std::cout << "Select following epochs to average:\n" << vecSel << std::endl;
FiffEvoked evoked = data.average(raw.info, tmin*raw.info.sfreq, floor(tmax*raw.info.sfreq + 0.5), vecSel);
//########################################################################################
// Source Estimate
//
// Settings
//
double snr = parser.value(snrOption).toDouble();
QString method(parser.value(methodOption));
QString t_sFileNameClusteredInv(parser.value(invFileOutOption));
QString t_sFileNameStc(parser.value(stcFileOutOption));
double lambda2 = 1.0 / pow(snr, 2);
qDebug() << "Start calculation with: SNR" << snr << "; Lambda" << lambda2 << "; Method" << method << "; stc:" << t_sFileNameStc;
//
// Load data
//
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
FiffCov noise_cov(t_fileCov);
//
// regularize noise covariance
//
noise_cov = noise_cov.regularize(evoked.info, 0.05, 0.05, 0.1, true);
//
// Cluster forward solution;
//
MatrixXd D;
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 20, D, noise_cov, evoked.info);
//
// make an inverse operators
//
FiffInfo info = evoked.info;
MNEInverseOperator inverse_operator(info, t_clusteredFwd, noise_cov, 0.2f, 0.8f);
//
// save clustered inverse
//
if(!t_sFileNameClusteredInv.isEmpty())
{
QFile t_fileClusteredInverse(t_sFileNameClusteredInv);
inverse_operator.write(t_fileClusteredInverse);
}
//
// Compute inverse solution
//
MinimumNorm minimumNorm(inverse_operator, lambda2, method);
#ifdef BENCHMARK
//
// Set up the inverse according to the parameters
//
minimumNorm.doInverseSetup(vecSel.size(),false);
MNESourceEstimate sourceEstimate;
QList<qint64> qVecElapsedTime;
for(qint32 i = 0; i < 100; ++i)
{
//Benchmark time
QElapsedTimer timer;
timer.start();
sourceEstimate = minimumNorm.calculateInverse(evoked.data, evoked.times(0), evoked.times(1)-evoked.times(0));
qVecElapsedTime.append(timer.elapsed());
}
double meanTime = 0.0;
qint32 offset = 19;
qint32 c = 0;
for(qint32 i = offset; i < qVecElapsedTime.size(); ++i)
{
meanTime += qVecElapsedTime[i];
++c;
}
meanTime /= (double)c;
double varTime = 0;
for(qint32 i = offset; i < qVecElapsedTime.size(); ++i)
varTime += pow(qVecElapsedTime[i] - meanTime,2);
varTime /= (double)c - 1.0f;
varTime = sqrt(varTime);
qDebug() << "MNE calculation took" << meanTime << "+-" << varTime << "ms in average";
#else
MNESourceEstimate sourceEstimate = minimumNorm.calculateInverse(evoked);
#endif
if(sourceEstimate.isEmpty())
return 1;
// View activation time-series
std::cout << "\nsourceEstimate:\n" << sourceEstimate.data.block(0,0,10,10) << std::endl;
std::cout << "time\n" << sourceEstimate.times.block(0,0,1,10) << std::endl;
std::cout << "timeMin\n" << sourceEstimate.times[0] << std::endl;
std::cout << "timeMax\n" << sourceEstimate.times[sourceEstimate.times.size()-1] << std::endl;
std::cout << "time step\n" << sourceEstimate.tstep << std::endl;
//Condition Numbers
// MatrixXd mags(102, t_Fwd.sol->data.cols());
// qint32 count = 0;
// for(qint32 i = 2; i < 306; i += 3)
// {
// mags.row(count) = t_Fwd.sol->data.row(i);
// ++count;
// }
// MatrixXd magsClustered(102, t_clusteredFwd.sol->data.cols());
// count = 0;
// for(qint32 i = 2; i < 306; i += 3)
// {
// magsClustered.row(count) = t_clusteredFwd.sol->data.row(i);
// ++count;
// }
// MatrixXd grads(204, t_Fwd.sol->data.cols());
// count = 0;
// for(qint32 i = 0; i < 306; i += 3)
// {
// grads.row(count) = t_Fwd.sol->data.row(i);
// ++count;
// grads.row(count) = t_Fwd.sol->data.row(i+1);
// ++count;
// }
// MatrixXd gradsClustered(204, t_clusteredFwd.sol->data.cols());
// count = 0;
// for(qint32 i = 0; i < 306; i += 3)
// {
// gradsClustered.row(count) = t_clusteredFwd.sol->data.row(i);
// ++count;
// gradsClustered.row(count) = t_clusteredFwd.sol->data.row(i+1);
// ++count;
// }
VectorXd s;
double t_dConditionNumber = MNEMath::getConditionNumber(t_Fwd.sol->data, s);
double t_dConditionNumberClustered = MNEMath::getConditionNumber(t_clusteredFwd.sol->data, s);
std::cout << "Condition Number:\n" << t_dConditionNumber << std::endl;
std::cout << "Clustered Condition Number:\n" << t_dConditionNumberClustered << std::endl;
std::cout << "ForwardSolution" << t_Fwd.sol->data.block(0,0,10,10) << std::endl;
std::cout << "Clustered ForwardSolution" << t_clusteredFwd.sol->data.block(0,0,10,10) << std::endl;
// double t_dConditionNumberMags = MNEMath::getConditionNumber(mags, s);
// double t_dConditionNumberMagsClustered = MNEMath::getConditionNumber(magsClustered, s);
// std::cout << "Condition Number Magnetometers:\n" << t_dConditionNumberMags << std::endl;
// std::cout << "Clustered Condition Number Magnetometers:\n" << t_dConditionNumberMagsClustered << std::endl;
// double t_dConditionNumberGrads = MNEMath::getConditionNumber(grads, s);
// double t_dConditionNumberGradsClustered = MNEMath::getConditionNumber(gradsClustered, s);
// std::cout << "Condition Number Gradiometers:\n" << t_dConditionNumberGrads << std::endl;
// std::cout << "Clustered Condition Number Gradiometers:\n" << t_dConditionNumberGradsClustered << std::endl;
//Source Estimate end
//########################################################################################
// //only one time point - P100
// qint32 sample = 0;
// for(qint32 i = 0; i < sourceEstimate.times.size(); ++i)
// {
// if(sourceEstimate.times(i) >= 0)
// {
// sample = i;
// break;
// }
// }
// sample += (qint32)ceil(0.106/sourceEstimate.tstep); //100ms
// sourceEstimate = sourceEstimate.reduce(sample, 1);
View3D::SPtr testWindow = View3D::SPtr(new View3D());
Data3DTreeModel::SPtr p3DDataModel = Data3DTreeModel::SPtr(new Data3DTreeModel());
testWindow->setModel(p3DDataModel);
p3DDataModel->addSurfaceSet(parser.value(subjectOption), "MRI", t_surfSet, t_annotationSet);
if(MneEstimateTreeItem* pRTDataItem = p3DDataModel->addSourceData(parser.value(subjectOption), evoked.comment, sourceEstimate, t_clusteredFwd)) {
pRTDataItem->setLoopState(true);
pRTDataItem->setTimeInterval(17);
pRTDataItem->setNumberAverages(1);
pRTDataItem->setStreamingActive(true);
pRTDataItem->setNormalization(QVector3D(0.0,0.5,20.0));
pRTDataItem->setVisualizationType("Smoothing based");
pRTDataItem->setColortable("Hot");
}
testWindow->show();
Control3DWidget::SPtr control3DWidget = Control3DWidget::SPtr(new Control3DWidget());
control3DWidget->init(p3DDataModel, testWindow);
control3DWidget->show();
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileClusteredStc(t_sFileNameStc);
sourceEstimate.write(t_fileClusteredStc);
}
return a.exec();
}
/**
* The function main marks the entry point of the program.
* By default, main has the storage class extern.
*
* @param [in] argc (argument count) is an integer that indicates how many arguments were entered on the command line when the program was started.
* @param [in] argv (argument vector) is an array of pointers to arrays of character objects. The array objects are null-terminated strings, representing the arguments that were entered on the command line when the program was started.
* @return the value that was set to exit() (which is 0 if exit() is called via quit()).
*/
int main(int argc, char *argv[])
{
QApplication a(argc, argv);
QFile t_fileRaw("./MNE-sample-data/MEG/sample/sample_audvis_raw.fif");
QString t_sEventName = "./MNE-sample-data/MEG/sample/sample_audvis_raw-eve.fif";
QFile t_fileFwd("./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
AnnotationSet t_annotationSet("./MNE-sample-data/subjects/sample/label/lh.aparc.a2009s.annot", "./MNE-sample-data/subjects/sample/label/rh.aparc.a2009s.annot");
SurfaceSet t_surfSet("./MNE-sample-data/subjects/sample/surf/lh.white", "./MNE-sample-data/subjects/sample/surf/rh.white");
// QFile t_fileRaw("E:/Data/sl_data/MEG/mind006/mind006_051209_auditory01_raw.fif");
// QString t_sEventName = "E:/Data/sl_data/MEG/mind006/mind006_051209_auditory01_raw-eve.fif";
// QFile t_fileFwd("E:/Data/sl_data/MEG/mind006/mind006_051209_auditory01_raw-oct-6p-fwd.fif");
// AnnotationSet t_annotationSet("E:/Data/sl_data/subjects/mind006/label/lh.aparc.a2009s.annot", "E:/Data/sl_data/subjects/mind006/label/rh.aparc.a2009s.annot");
// SurfaceSet t_surfSet("E:/Data/sl_data/subjects/mind006/surf/lh.white", "E:/Data/sl_data/subjects/mind006/surf/rh.white");
// QFile t_fileRaw("E:/Data/sl_data/MEG/mind006/mind006_051209_median01_raw.fif");
// QString t_sEventName = "E:/Data/sl_data/MEG/mind006/mind006_051209_median01_raw-eve.fif";
// QFile t_fileFwd("E:/Data/sl_data/MEG/mind006/mind006_051209_median01_raw-oct-6-fwd.fif");
// AnnotationSet t_annotationSet("E:/Data/sl_data/subjects/mind006/label/lh.aparc.a2009s.annot", "E:/Data/sl_data/subjects/mind006/label/rh.aparc.a2009s.annot");
// SurfaceSet t_surfSet("E:/Data/sl_data/subjects/mind006/surf/lh.white", "E:/Data/sl_data/subjects/mind006/surf/rh.white");
QString t_sFileNameStc("");//("mind006_051209_auditory01.stc");
bool doMovie = false;//true;
qint32 numDipolePairs = 7;
qint32 event = 1;
float tmin = -0.2f;
float tmax = 0.4f;
bool keep_comp = false;
fiff_int_t dest_comp = 0;
bool pick_all = true;
qint32 k, p;
// Parse command line parameters
for(qint32 i = 0; i < argc; ++i)
{
if(strcmp(argv[i], "-stc") == 0 || strcmp(argv[i], "--stc") == 0)
{
if(i + 1 < argc)
t_sFileNameStc = QString::fromUtf8(argv[i+1]);
}
}
//
// Load data
//
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
//
// Setup for reading the raw data
//
FiffRawData raw(t_fileRaw);
RowVectorXi picks;
if (pick_all)
{
//
// Pick all
//
picks.resize(raw.info.nchan);
for(k = 0; k < raw.info.nchan; ++k)
picks(k) = k;
//
}
else
{
QStringList include;
include << "STI 014";
bool want_meg = true;
bool want_eeg = false;
bool want_stim = false;
picks = raw.info.pick_types(want_meg, want_eeg, want_stim, include, raw.info.bads);//prefer member function
}
QStringList ch_names;
for(k = 0; k < picks.cols(); ++k)
ch_names << raw.info.ch_names[picks(0,k)];
//
// Set up projection
//
if (raw.info.projs.size() == 0)
printf("No projector specified for these data\n");
else
{
//
// Activate the projection items
//
for (k = 0; k < raw.info.projs.size(); ++k)
raw.info.projs[k].active = true;
printf("%d projection items activated\n",raw.info.projs.size());
//
// Create the projector
//
// fiff_int_t nproj = MNE::make_projector_info(raw.info, raw.proj); Using the member function instead
fiff_int_t nproj = raw.info.make_projector(raw.proj);
if (nproj == 0)
{
printf("The projection vectors do not apply to these channels\n");
}
else
{
printf("Created an SSP operator (subspace dimension = %d)\n",nproj);
}
}
//
// Set up the CTF compensator
//
qint32 current_comp = raw.info.get_current_comp();
if (current_comp > 0)
printf("Current compensation grade : %d\n",current_comp);
if (keep_comp)
dest_comp = current_comp;
if (current_comp != dest_comp)
{
qDebug() << "This part needs to be debugged";
if(MNE::make_compensator(raw.info, current_comp, dest_comp, raw.comp))
{
raw.info.set_current_comp(dest_comp);
printf("Appropriate compensator added to change to grade %d.\n",dest_comp);
}
else
{
printf("Could not make the compensator\n");
return 0;
}
}
//
// Read the events
//
QFile t_EventFile;
MatrixXi events;
if (t_sEventName.size() == 0)
{
p = t_fileRaw.fileName().indexOf(".fif");
if (p > 0)
{
t_sEventName = t_fileRaw.fileName().replace(p, 4, "-eve.fif");
}
else
{
printf("Raw file name does not end properly\n");
return 0;
}
// events = mne_read_events(t_sEventName);
t_EventFile.setFileName(t_sEventName);
MNE::read_events(t_EventFile, events);
printf("Events read from %s\n",t_sEventName.toUtf8().constData());
}
else
{
//
// Binary file
//
p = t_fileRaw.fileName().indexOf(".fif");
if (p > 0)
{
t_EventFile.setFileName(t_sEventName);
if(!MNE::read_events(t_EventFile, events))
{
printf("Error while read events.\n");
return 0;
}
printf("Binary event file %s read\n",t_sEventName.toUtf8().constData());
}
else
{
//
// Text file
//
printf("Text file %s is not supported jet.\n",t_sEventName.toUtf8().constData());
// try
// events = load(eventname);
// catch
// error(me,mne_omit_first_line(lasterr));
// end
// if size(events,1) < 1
// error(me,'No data in the event file');
// end
// //
// // Convert time to samples if sample number is negative
// //
// for p = 1:size(events,1)
// if events(p,1) < 0
// events(p,1) = events(p,2)*raw.info.sfreq;
// end
// end
// //
// // Select the columns of interest (convert to integers)
// //
// events = int32(events(:,[1 3 4]));
// //
// // New format?
// //
// if events(1,2) == 0 && events(1,3) == 0
// fprintf(1,'The text event file %s is in the new format\n',eventname);
// if events(1,1) ~= raw.first_samp
// error(me,'This new format event file is not compatible with the raw data');
// end
// else
// fprintf(1,'The text event file %s is in the old format\n',eventname);
// //
// // Offset with first sample
// //
// events(:,1) = events(:,1) + raw.first_samp;
// end
}
}
//
// Select the desired events
//
qint32 count = 0;
MatrixXi selected = MatrixXi::Zero(1, events.rows());
for (p = 0; p < events.rows(); ++p)
{
if (events(p,1) == 0 && events(p,2) == event)
{
selected(0,count) = p;
++count;
}
}
selected.conservativeResize(1, count);
if (count > 0)
printf("%d matching events found\n",count);
else
{
printf("No desired events found.\n");
return 0;
}
fiff_int_t event_samp, from, to;
MatrixXd timesDummy;
MNEEpochDataList data;
MNEEpochData* epoch = NULL;
MatrixXd times;
for (p = 0; p < count; ++p)
{
//
// Read a data segment
//
event_samp = events(selected(p),0);
from = event_samp + tmin*raw.info.sfreq;
to = event_samp + floor(tmax*raw.info.sfreq + 0.5);
epoch = new MNEEpochData();
if(raw.read_raw_segment(epoch->epoch, timesDummy, from, to, picks))
{
if (p == 0)
{
times.resize(1, to-from+1);
for (qint32 i = 0; i < times.cols(); ++i)
times(0, i) = ((float)(from-event_samp+i)) / raw.info.sfreq;
}
epoch->event = event;
epoch->tmin = ((float)(from)-(float)(raw.first_samp))/raw.info.sfreq;
epoch->tmax = ((float)(to)-(float)(raw.first_samp))/raw.info.sfreq;
data.append(MNEEpochData::SPtr(epoch));//List takes ownwership of the pointer - no delete need
}
else
{
printf("Can't read the event data segments");
return 0;
}
}
if(data.size() > 0)
{
printf("Read %d epochs, %d samples each.\n",data.size(),(qint32)data[0]->epoch.cols());
//DEBUG
std::cout << data[0]->epoch.block(0,0,10,10) << std::endl;
qDebug() << data[0]->epoch.rows() << " x " << data[0]->epoch.cols();
std::cout << times.block(0,0,1,10) << std::endl;
qDebug() << times.rows() << " x " << times.cols();
}
//
// calculate the average
//
// //Option 1
// qint32 numAverages = 99;
// VectorXi vecSel(numAverages);
// srand (time(NULL)); // initialize random seed
// for(qint32 i = 0; i < vecSel.size(); ++i)
// {
// qint32 val = rand() % data.size();
// vecSel(i) = val;
// }
//Option 2
// VectorXi vecSel(20);
//// vecSel << 76, 74, 13, 61, 97, 94, 75, 71, 60, 56, 26, 57, 56, 0, 52, 72, 33, 86, 96, 67;
// vecSel << 65, 22, 47, 55, 16, 29, 14, 36, 57, 97, 89, 46, 9, 93, 83, 52, 71, 52, 3, 96;
//Option 3 Newest
// VectorXi vecSel(10);
// vecSel << 0, 96, 80, 55, 66, 25, 26, 2, 55, 58, 6, 88;
VectorXi vecSel(1);
vecSel << 0;
std::cout << "Select following epochs to average:\n" << vecSel << std::endl;
FiffEvoked evoked = data.average(raw.info, tmin*raw.info.sfreq, floor(tmax*raw.info.sfreq + 0.5), vecSel);
QStringList ch_sel_names = t_Fwd.info.ch_names;
FiffEvoked pickedEvoked = evoked.pick_channels(ch_sel_names);
//########################################################################################
// RAP MUSIC Source Estimate
//
// Cluster forward solution;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 20);//40);
//
// Compute inverse solution
//
RapMusic t_rapMusic(t_clusteredFwd, false, numDipolePairs);
if(doMovie)
t_rapMusic.setStcAttr(200,0.5);
MNESourceEstimate sourceEstimate = t_rapMusic.calculateInverse(pickedEvoked);
if(sourceEstimate.isEmpty())
return 1;
// // View activation time-series
// std::cout << "\nsourceEstimate:\n" << sourceEstimate.data.block(0,0,10,10) << std::endl;
// std::cout << "time\n" << sourceEstimate.times.block(0,0,1,10) << std::endl;
// std::cout << "timeMin\n" << sourceEstimate.times[0] << std::endl;
// std::cout << "timeMax\n" << sourceEstimate.times[sourceEstimate.times.size()-1] << std::endl;
// std::cout << "time step\n" << sourceEstimate.tstep << std::endl;
//Source Estimate end
//########################################################################################
// //only one time point - P100
// qint32 sample = 0;
// for(qint32 i = 0; i < sourceEstimate.times.size(); ++i)
// {
// if(sourceEstimate.times(i) >= 0)
// {
// sample = i;
// break;
// }
// }
// sample += (qint32)ceil(0.106/sourceEstimate.tstep); //100ms
// sourceEstimate = sourceEstimate.reduce(sample, 1);
View3D::SPtr testWindow = View3D::SPtr(new View3D());
testWindow->addBrainData("Subject01", "HemiLRSet", t_surfSet, t_annotationSet);
QList<BrainRTSourceLocDataTreeItem*> rtItemList = testWindow->addRtBrainData("Subject01", "HemiLRSet", sourceEstimate, t_clusteredFwd);
testWindow->show();
Control3DWidget::SPtr control3DWidget = Control3DWidget::SPtr(new Control3DWidget());
control3DWidget->setView3D(testWindow);
control3DWidget->show();
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileClusteredStc(t_sFileNameStc);
sourceEstimate.write(t_fileClusteredStc);
}
return a.exec();//1;//a.exec();
}
/**
* The function main marks the entry point of the program.
* By default, main has the storage class extern.
*
* @param [in] argc (argument count) is an integer that indicates how many arguments were entered on the command line when the program was started.
* @param [in] argv (argument vector) is an array of pointers to arrays of character objects. The array objects are null-terminated strings, representing the arguments that were entered on the command line when the program was started.
* @return the value that was set to exit() (which is 0 if exit() is called via quit()).
*/
int main(int argc, char *argv[])
{
QApplication a(argc, argv);
// Command Line Parser
QCommandLineParser parser;
parser.setApplicationDescription("Clustered Inverse Powell Rap Music Raw Example");
parser.addHelpOption();
QCommandLineOption inputOption("fileIn", "The input file <in>.", "in", QCoreApplication::applicationDirPath() + "/MNE-sample-data/MEG/sample/sample_audvis_raw.fif");
QCommandLineOption eventsFileOption("eve", "Path to the event <file>.", "file", QCoreApplication::applicationDirPath() + "/MNE-sample-data/MEG/sample/sample_audvis_raw-eve.fif");
QCommandLineOption fwdOption("fwd", "Path to forwad solution <file>.", "file", QCoreApplication::applicationDirPath() + "/MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
QCommandLineOption surfOption("surfType", "Surface type <type>.", "type", "orig");
QCommandLineOption annotOption("annotType", "Annotation type <type>.", "type", "aparc.a2009s");
QCommandLineOption subjectOption("subject", "Selected subject <subject>.", "subject", "sample");
QCommandLineOption subjectPathOption("subjectPath", "Selected subject path <subjectPath>.", "subjectPath", QCoreApplication::applicationDirPath() + "/MNE-sample-data/subjects");
QCommandLineOption stcFileOption("stcOut", "Path to stc <file>, which is to be written.", "file", "");
QCommandLineOption numDipolePairsOption("numDip", "<number> of dipole pairs to localize.", "number", "7");
QCommandLineOption evokedIdxOption("aveIdx", "The average <index> to choose from the average file.", "index", "1");
QCommandLineOption hemiOption("hemi", "Selected hemisphere <hemi>.", "hemi", "2");
QCommandLineOption doMovieOption("doMovie", "Create overlapping movie.", "doMovie", "false");
QCommandLineOption keepCompOption("keepComp", "Keep compensators.", "keepComp", "false");
QCommandLineOption pickAllOption("pickAll", "Pick all channels.", "pickAll", "true");
QCommandLineOption destCompsOption("destComps", "<Destination> of the compensator which is to be calculated.", "destination", "0");
parser.addOption(inputOption);
parser.addOption(eventsFileOption);
parser.addOption(fwdOption);
parser.addOption(surfOption);
parser.addOption(annotOption);
parser.addOption(subjectOption);
parser.addOption(subjectPathOption);
parser.addOption(stcFileOption);
parser.addOption(numDipolePairsOption);
parser.addOption(evokedIdxOption);
parser.addOption(hemiOption);
parser.addOption(doMovieOption);
parser.addOption(keepCompOption);
parser.addOption(pickAllOption);
parser.addOption(destCompsOption);
parser.process(a);
//Load data
QFile t_fileRaw(parser.value(inputOption));
QString t_sEventName = parser.value(eventsFileOption);
QFile t_fileFwd(parser.value(fwdOption));
SurfaceSet t_surfSet (parser.value(subjectOption), parser.value(hemiOption).toInt(), parser.value(surfOption), parser.value(subjectPathOption));
AnnotationSet t_annotationSet (parser.value(subjectOption), parser.value(hemiOption).toInt(), parser.value(annotOption), parser.value(subjectPathOption));
QString t_sFileNameStc(parser.value(stcFileOption));
qint32 numDipolePairs = parser.value(numDipolePairsOption).toInt();
//Choose average
qint32 event = parser.value(evokedIdxOption).toInt();
float tmin = 0.1f;
float tmax = 0.2f;
bool keep_comp = false;
if(parser.value(keepCompOption) == "false" || parser.value(keepCompOption) == "0") {
keep_comp = false;
} else if(parser.value(keepCompOption) == "true" || parser.value(keepCompOption) == "1") {
keep_comp = true;
}
fiff_int_t dest_comp = parser.value(destCompsOption).toInt();
bool pick_all = false;
if(parser.value(pickAllOption) == "false" || parser.value(pickAllOption) == "0") {
pick_all = false;
} else if(parser.value(pickAllOption) == "true" || parser.value(pickAllOption) == "1") {
pick_all = true;
}
qint32 k, p;
bool doMovie = false;
if(parser.value(doMovieOption) == "false" || parser.value(doMovieOption) == "0") {
pick_all = false;
} else if(parser.value(doMovieOption) == "true" || parser.value(doMovieOption) == "1") {
pick_all = true;
}
//
// Load data
//
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
//
// Setup for reading the raw data
//
FiffRawData raw(t_fileRaw);
RowVectorXi picks;
if (pick_all)
{
//
// Pick all
//
picks.resize(raw.info.nchan);
for(k = 0; k < raw.info.nchan; ++k)
picks(k) = k;
//
}
else
{
QStringList include;
include << "STI 014";
bool want_meg = true;
bool want_eeg = false;
bool want_stim = false;
picks = raw.info.pick_types(want_meg, want_eeg, want_stim, include, raw.info.bads);//prefer member function
}
QStringList ch_names;
for(k = 0; k < picks.cols(); ++k)
ch_names << raw.info.ch_names[picks(0,k)];
//
// Set up projection
//
if (raw.info.projs.size() == 0)
printf("No projector specified for these data\n");
else
{
//
// Activate the projection items
//
for (k = 0; k < raw.info.projs.size(); ++k)
raw.info.projs[k].active = true;
printf("%d projection items activated\n",raw.info.projs.size());
//
// Create the projector
//
// fiff_int_t nproj = MNE::make_projector_info(raw.info, raw.proj); Using the member function instead
fiff_int_t nproj = raw.info.make_projector(raw.proj);
if (nproj == 0)
{
printf("The projection vectors do not apply to these channels\n");
}
else
{
printf("Created an SSP operator (subspace dimension = %d)\n",nproj);
}
}
//
// Set up the CTF compensator
//
qint32 current_comp = raw.info.get_current_comp();
if (current_comp > 0)
printf("Current compensation grade : %d\n",current_comp);
if (keep_comp)
dest_comp = current_comp;
if (current_comp != dest_comp)
{
qDebug() << "This part needs to be debugged";
if(MNE::make_compensator(raw.info, current_comp, dest_comp, raw.comp))
{
raw.info.set_current_comp(dest_comp);
printf("Appropriate compensator added to change to grade %d.\n",dest_comp);
}
else
{
printf("Could not make the compensator\n");
return 0;
}
}
//
// Read the events
//
QFile t_EventFile;
MatrixXi events;
if (t_sEventName.size() == 0)
{
p = t_fileRaw.fileName().indexOf(".fif");
if (p > 0)
{
t_sEventName = t_fileRaw.fileName().replace(p, 4, "-eve.fif");
}
else
{
printf("Raw file name does not end properly\n");
return 0;
}
// events = mne_read_events(t_sEventName);
t_EventFile.setFileName(t_sEventName);
MNE::read_events(t_EventFile, events);
printf("Events read from %s\n",t_sEventName.toUtf8().constData());
}
else
{
//
// Binary file
//
p = t_fileRaw.fileName().indexOf(".fif");
if (p > 0)
{
t_EventFile.setFileName(t_sEventName);
if(!MNE::read_events(t_EventFile, events))
{
printf("Error while read events.\n");
return 0;
}
printf("Binary event file %s read\n",t_sEventName.toUtf8().constData());
}
else
{
//
// Text file
//
printf("Text file %s is not supported jet.\n",t_sEventName.toUtf8().constData());
// try
// events = load(eventname);
// catch
// error(me,mne_omit_first_line(lasterr));
// end
// if size(events,1) < 1
// error(me,'No data in the event file');
// end
// //
// // Convert time to samples if sample number is negative
// //
// for p = 1:size(events,1)
// if events(p,1) < 0
// events(p,1) = events(p,2)*raw.info.sfreq;
// end
// end
// //
// // Select the columns of interest (convert to integers)
// //
// events = int32(events(:,[1 3 4]));
// //
// // New format?
// //
// if events(1,2) == 0 && events(1,3) == 0
// fprintf(1,'The text event file %s is in the new format\n',eventname);
// if events(1,1) ~= raw.first_samp
// error(me,'This new format event file is not compatible with the raw data');
// end
// else
// fprintf(1,'The text event file %s is in the old format\n',eventname);
// //
// // Offset with first sample
// //
// events(:,1) = events(:,1) + raw.first_samp;
// end
}
}
//
// Select the desired events
//
qint32 count = 0;
MatrixXi selected = MatrixXi::Zero(1, events.rows());
for (p = 0; p < events.rows(); ++p)
{
if (events(p,1) == 0 && events(p,2) == event)
{
selected(0,count) = p;
++count;
}
}
selected.conservativeResize(1, count);
if (count > 0)
printf("%d matching events found\n",count);
else
{
printf("No desired events found.\n");
return 0;
}
fiff_int_t event_samp, from, to;
MatrixXd timesDummy;
MNEEpochDataList data;
MNEEpochData* epoch = NULL;
MatrixXd times;
for (p = 0; p < count; ++p)
{
//
// Read a data segment
//
event_samp = events(selected(p),0);
from = event_samp + tmin*raw.info.sfreq;
to = event_samp + floor(tmax*raw.info.sfreq + 0.5);
epoch = new MNEEpochData();
if(raw.read_raw_segment(epoch->epoch, timesDummy, from, to, picks))
{
if (p == 0)
{
times.resize(1, to-from+1);
for (qint32 i = 0; i < times.cols(); ++i)
times(0, i) = ((float)(from-event_samp+i)) / raw.info.sfreq;
}
epoch->event = event;
epoch->tmin = ((float)(from)-(float)(raw.first_samp))/raw.info.sfreq;
epoch->tmax = ((float)(to)-(float)(raw.first_samp))/raw.info.sfreq;
data.append(MNEEpochData::SPtr(epoch));//List takes ownwership of the pointer - no delete need
}
else
{
printf("Can't read the event data segments");
return 0;
}
}
if(data.size() > 0)
{
printf("Read %d epochs, %d samples each.\n",data.size(),(qint32)data[0]->epoch.cols());
// //DEBUG
// std::cout << data[0]->epoch.block(0,0,10,10) << std::endl;
// qDebug() << data[0]->epoch.rows() << " x " << data[0]->epoch.cols();
// std::cout << times.block(0,0,1,10) << std::endl;
// qDebug() << times.rows() << " x " << times.cols();
}
// Calculate the average
// Option 1 - Random selection
VectorXi vecSel(2);
srand (time(NULL)); // initialize random seed
for(qint32 i = 0; i < vecSel.size(); ++i)
{
qint32 val = rand() % count;
vecSel(i) = val;
}
// //Option 3 - Take all epochs
// VectorXi vecSel(data.size());
// for(qint32 i = 0; i < vecSel.size(); ++i)
// {
// vecSel(i) = i;
// }
// //Option 3 - Manual selection
// VectorXi vecSel(20);
// vecSel << 76, 74, 13, 61, 97, 94, 75, 71, 60, 56, 26, 57, 56, 0, 52, 72, 33, 86, 96, 67;
std::cout << "Select following epochs to average:\n" << vecSel << std::endl;
FiffEvoked evoked = data.average(raw.info, tmin*raw.info.sfreq, floor(tmax*raw.info.sfreq + 0.5), vecSel);
QStringList ch_sel_names = t_Fwd.info.ch_names;
FiffEvoked pickedEvoked = evoked.pick_channels(ch_sel_names);
//########################################################################################
// RAP MUSIC Source Estimate
//
// Cluster forward solution;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 20);//40);
//
// Compute inverse solution
//
PwlRapMusic t_pwlRapMusic(t_clusteredFwd, false, numDipolePairs);
#ifdef BENCHMARK
MNESourceEstimate sourceEstimate;
QList<qint64> qVecElapsedTime;
for(qint32 i = 0; i < 100; ++i)
{
//Benchmark time
QElapsedTimer timer;
timer.start();
sourceEstimate = t_pwlRapMusic.calculateInverse(pickedEvoked);
qVecElapsedTime.append(timer.elapsed());
}
double meanTime = 0.0;
qint32 offset = 19;
qint32 c = 0;
for(qint32 i = offset; i < qVecElapsedTime.size(); ++i)
{
meanTime += qVecElapsedTime[i];
++c;
}
meanTime /= (double)c;
double varTime = 0;
for(qint32 i = offset; i < qVecElapsedTime.size(); ++i)
varTime += pow(qVecElapsedTime[i] - meanTime,2);
varTime /= (double)c - 1.0f;
varTime = sqrt(varTime);
qDebug() << "RAP-MUSIC calculation took" << meanTime << "+-" << varTime << "ms in average";
#else
int iWinSize = 200;
if(doMovie) {
t_pwlRapMusic.setStcAttr(iWinSize, 0.6f);
}
MNESourceEstimate sourceEstimate = t_pwlRapMusic.calculateInverse(pickedEvoked);
if(doMovie) {
//Select only the activations once
MatrixXd dataPicked(sourceEstimate.data.rows(), int(std::floor(sourceEstimate.data.cols()/iWinSize)));
for(int i = 0; i < dataPicked.cols(); ++i) {
dataPicked.col(i) = sourceEstimate.data.col(i*iWinSize);
}
sourceEstimate.data = dataPicked;
}
if(sourceEstimate.isEmpty()) {
return 1;
}
#endif
if(sourceEstimate.isEmpty())
return 1;
// // View activation time-series
// std::cout << "\nsourceEstimate:\n" << sourceEstimate.data.block(0,0,10,10) << std::endl;
// std::cout << "time\n" << sourceEstimate.times.block(0,0,1,10) << std::endl;
// std::cout << "timeMin\n" << sourceEstimate.times[0] << std::endl;
// std::cout << "timeMax\n" << sourceEstimate.times[sourceEstimate.times.size()-1] << std::endl;
// std::cout << "time step\n" << sourceEstimate.tstep << std::endl;
//Source Estimate end
//########################################################################################
// //only one time point - P100
// qint32 sample = 0;
// for(qint32 i = 0; i < sourceEstimate.times.size(); ++i)
// {
// if(sourceEstimate.times(i) >= 0)
// {
// sample = i;
// break;
// }
// }
// sample += (qint32)ceil(0.106/sourceEstimate.tstep); //100ms
// sourceEstimate = sourceEstimate.reduce(sample, 1);
AbstractView::SPtr p3DAbstractView = AbstractView::SPtr(new AbstractView());
Data3DTreeModel::SPtr p3DDataModel = p3DAbstractView->getTreeModel();
p3DDataModel->addSurfaceSet(parser.value(subjectOption), evoked.comment, t_surfSet, t_annotationSet);
//Add rt source loc data and init some visualization values
if(MneEstimateTreeItem* pRTDataItem = p3DDataModel->addSourceData(parser.value(subjectOption),
evoked.comment,
sourceEstimate,
t_clusteredFwd,
t_surfSet,
t_annotationSet)) {
pRTDataItem->setLoopState(true);
pRTDataItem->setTimeInterval(17);
pRTDataItem->setNumberAverages(1);
pRTDataItem->setStreamingState(true);
pRTDataItem->setThresholds(QVector3D(0.01f,0.5f,1.0f));
pRTDataItem->setVisualizationType("Annotation based");
pRTDataItem->setColormapType("Hot");
}
p3DAbstractView->show();
QList<Label> t_qListLabels;
QList<RowVector4i> t_qListRGBAs;
//ToDo overload toLabels using instead of t_surfSet rr of MNESourceSpace
t_annotationSet.toLabels(t_surfSet, t_qListLabels, t_qListRGBAs);
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileClusteredStc(t_sFileNameStc);
sourceEstimate.write(t_fileClusteredStc);
}
return a.exec();//1;//a.exec();
}
/**
* The function main marks the entry point of the program.
* By default, main has the storage class extern.
*
* @param [in] argc (argument count) is an integer that indicates how many arguments were entered on the command line when the program was started.
* @param [in] argv (argument vector) is an array of pointers to arrays of character objects. The array objects are null-terminated strings, representing the arguments that were entered on the command line when the program was started.
* @return the value that was set to exit() (which is 0 if exit() is called via quit()).
*/
int main(int argc, char *argv[])
{
QGuiApplication app(argc, argv);
QGuiApplication::setApplicationName("RTC Evaluation");
QGuiApplication::setApplicationVersion("Revision 1");
///////////////////////////////////// #1 CLI Parser /////////////////////////////////////
QCommandLineParser parser;
parser.setApplicationDescription("RTC Evaluation");
parser.addHelpOption();
parser.addVersionOption();
// MEG Source Directory
QCommandLineOption srcDirectoryOption(QStringList() << "s" << "meg-source-directory",
QCoreApplication::translate("main", "Read MEG (fwd, cov, raw, eve) source files from <directory>."),
QCoreApplication::translate("main", "directory"),
"./MNE-sample-data/MEG/sample/");
parser.addOption(srcDirectoryOption);
// Forward Solution File
QCommandLineOption fwdFileOption(QStringList() << "fwd" << "forward-solution",
QCoreApplication::translate("main", "The forward solution <file>."),
QCoreApplication::translate("main", "file"),
"sample_audvis-meg-eeg-oct-6-fwd.fif");
parser.addOption(fwdFileOption);
// Raw MEG File
QCommandLineOption rawFileOption(QStringList() << "raw" << "raw-file",
QCoreApplication::translate("main", "The raw MEG data <file>."),
QCoreApplication::translate("main", "file"),
"sample_audvis_raw.fif");
parser.addOption(rawFileOption);
// Event File
QCommandLineOption eveFileOption(QStringList() << "eve" << "event-file",
QCoreApplication::translate("main", "The event <file>."),
QCoreApplication::translate("main", "file"),
"sample_audvis_raw-eve.fif");
parser.addOption(eveFileOption);
// Event Num
QCommandLineOption evenNumOption(QStringList() << "evenum" << "event-number",
QCoreApplication::translate("main", "The <event number>."),
QCoreApplication::translate("main", "event"),
"1");//2;//3;//4;
parser.addOption(evenNumOption);
// FS Subject Directory
QCommandLineOption subjDirectoryOption(QStringList() << "subjdir" << "subject-directory",
QCoreApplication::translate("main", "The FreeSurfer <subjects directory>."),
QCoreApplication::translate("main", "directory"),
"./MNE-sample-data/subjects");
parser.addOption(subjDirectoryOption);
// FS Subject
QCommandLineOption subjIdOption(QStringList() << "subjid" << "subject-id",
QCoreApplication::translate("main", "The FreeSurfer <subject id>."),
QCoreApplication::translate("main", "subject id"),
"sample");
parser.addOption(subjIdOption);
// Target Directory
QCommandLineOption targetDirectoryOption(QStringList() << "t" << "target-directory",
QCoreApplication::translate("main", "Copy all result files into <directory>."),
QCoreApplication::translate("main", "directory"));
parser.addOption(targetDirectoryOption);
// Target Prefix
QCommandLineOption targetPrefixOption(QStringList() << "p" << "prefix",
QCoreApplication::translate("main", "The result file's <prefix>."),
QCoreApplication::translate("main", "prefix"));
parser.addOption(targetPrefixOption);
// tmin
QCommandLineOption tMinOption(QStringList() << "tmin" << "t-min",
QCoreApplication::translate("main", "The starting time point <tmin>."),
QCoreApplication::translate("main", "tmin"),
"0.1");
parser.addOption(tMinOption);
// tmax
QCommandLineOption tMaxOption(QStringList() << "tmax" << "t-max",
QCoreApplication::translate("main", "The end time point <tmax>."),
QCoreApplication::translate("main", "tmax"),
"0.2");
parser.addOption(tMaxOption);
// Process the actual command line arguments given by the user
parser.process(app);
//////////////////////////////// #2 get parsed values /////////////////////////////////
//Sources
QString sFwdName = parser.value(srcDirectoryOption)+parser.value(fwdFileOption);
qDebug() << "Forward Solution" << sFwdName;
QString sRawName = parser.value(srcDirectoryOption)+parser.value(rawFileOption);
qDebug() << "Raw data" << sRawName;
QString t_sEventName = parser.value(srcDirectoryOption)+parser.value(eveFileOption);
qDebug() << "Events" << t_sEventName;
qint32 eveNum = (qint32)parser.value(evenNumOption).toInt();
qDebug() << "Event Number" << eveNum;
QString t_sSubjectsDir = parser.value(subjDirectoryOption);
qDebug() << "Subjects Directory" << t_sSubjectsDir;
QString t_sSubject = parser.value(subjIdOption);
qDebug() << "Subject" << t_sSubject;
//Targets
QString sTargetDir = parser.value(targetDirectoryOption);
qDebug() << "Target Directory" << sTargetDir;
QString sTargetPrefix = parser.value(targetPrefixOption);
qDebug() << "Target Prefix" << sTargetPrefix;
//Parameters
float tmin = (float)parser.value(tMinOption).toFloat();
qDebug() << "tMin" << tmin;
float tmax = (float)parser.value(tMaxOption).toFloat();
qDebug() << "tMax" << tmax;
QFile t_fileFwd(sFwdName);
//
// Load data
//
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
AnnotationSet t_annotationSet(t_sSubject, 2, "aparc.a2009s", t_sSubjectsDir);
// std::cout << "LabelIDs:\n" << t_annotationSet[0].getColortable().getLabelIds() << std::endl;
//
// Cluster forward solution;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 20);//40);
QFile t_fileRaw(sRawName);
// bool doMovie = false;//true;
qint32 numDipolePairs = 1;
bool keep_comp = false;
fiff_int_t dest_comp = 0;
bool pick_all = true;
qint32 k, p;
//
// Setup for reading the raw data
//
FiffRawData raw(t_fileRaw);
RowVectorXi picks;
if (pick_all)
{
//
// Pick all
//
picks.resize(raw.info.nchan);
for(k = 0; k < raw.info.nchan; ++k)
picks(k) = k;
//
}
else
{
QStringList include;
include << "STI 014";
bool want_meg = true;
bool want_eeg = false;
bool want_stim = false;
picks = raw.info.pick_types(want_meg, want_eeg, want_stim, include, raw.info.bads);//prefer member function
}
QStringList ch_names;
for(k = 0; k < picks.cols(); ++k)
ch_names << raw.info.ch_names[picks(0,k)];
//
// Set up projection
//
if (raw.info.projs.size() == 0)
printf("No projector specified for these data\n");
else
{
//
// Activate the projection items
//
for (k = 0; k < raw.info.projs.size(); ++k)
raw.info.projs[k].active = true;
printf("%d projection items activated\n",raw.info.projs.size());
//
// Create the projector
//
// fiff_int_t nproj = MNE::make_projector_info(raw.info, raw.proj); Using the member function instead
fiff_int_t nproj = raw.info.make_projector(raw.proj);
if (nproj == 0)
{
printf("The projection vectors do not apply to these channels\n");
}
else
{
printf("Created an SSP operator (subspace dimension = %d)\n",nproj);
}
}
//
// Set up the CTF compensator
//
qint32 current_comp = raw.info.get_current_comp();
if (current_comp > 0)
printf("Current compensation grade : %d\n",current_comp);
if (keep_comp)
dest_comp = current_comp;
if (current_comp != dest_comp)
{
qDebug() << "This part needs to be debugged";
if(MNE::make_compensator(raw.info, current_comp, dest_comp, raw.comp))
{
raw.info.set_current_comp(dest_comp);
printf("Appropriate compensator added to change to grade %d.\n",dest_comp);
}
else
{
printf("Could not make the compensator\n");
return 0;
}
}
//
// Read the events
//
QFile t_EventFile;
MatrixXi events;
if (t_sEventName.size() == 0)
{
p = t_fileRaw.fileName().indexOf(".fif");
if (p > 0)
{
t_sEventName = t_fileRaw.fileName().replace(p, 4, "-eve.fif");
}
else
{
printf("Raw file name does not end properly\n");
return 0;
}
// events = mne_read_events(t_sEventName);
t_EventFile.setFileName(t_sEventName);
MNE::read_events(t_EventFile, events);
printf("Events read from %s\n",t_sEventName.toUtf8().constData());
}
else
{
//
// Binary file
//
p = t_fileRaw.fileName().indexOf(".fif");
if (p > 0)
{
t_EventFile.setFileName(t_sEventName);
if(!MNE::read_events(t_EventFile, events))
{
printf("Error while read events.\n");
return 0;
}
printf("Binary event file %s read\n",t_sEventName.toUtf8().constData());
}
else
{
//
// Text file
//
printf("Text file %s is not supported jet.\n",t_sEventName.toUtf8().constData());
// try
// events = load(eventname);
// catch
// error(me,mne_omit_first_line(lasterr));
// end
// if size(events,1) < 1
// error(me,'No data in the event file');
// end
// //
// // Convert time to samples if sample number is negative
// //
// for p = 1:size(events,1)
// if events(p,1) < 0
// events(p,1) = events(p,2)*raw.info.sfreq;
// end
// end
// //
// // Select the columns of interest (convert to integers)
// //
// events = int32(events(:,[1 3 4]));
// //
// // New format?
// //
// if events(1,2) == 0 && events(1,3) == 0
// fprintf(1,'The text event file %s is in the new format\n',eventname);
// if events(1,1) ~= raw.first_samp
// error(me,'This new format event file is not compatible with the raw data');
// end
// else
// fprintf(1,'The text event file %s is in the old format\n',eventname);
// //
// // Offset with first sample
// //
// events(:,1) = events(:,1) + raw.first_samp;
// end
}
}
// std::cout << "Events:\n" << events << std::endl;
//
// Select the desired events
//
qint32 count = 0;
MatrixXi selected = MatrixXi::Zero(1, events.rows());
for (p = 0; p < events.rows(); ++p)
{
if (events(p,1) == 0 && events(p,2) == eveNum)
{
selected(0,count) = p;
++count;
}
}
selected.conservativeResize(1, count);
if (count > 0)
printf("%d matching events found\n",count);
else
{
printf("No desired events found.\n");
return 0;
}
fiff_int_t event_samp, from, to;
MatrixXd timesDummy;
MNEEpochDataList data;
MNEEpochData* epoch = NULL;
MatrixXd times;
for (p = 0; p < count; ++p)
{
//
// Read a data segment
//
event_samp = events(selected(p),0);
from = event_samp + tmin*raw.info.sfreq;
to = event_samp + floor(tmax*raw.info.sfreq + 0.5);
epoch = new MNEEpochData();
if(raw.read_raw_segment(epoch->epoch, timesDummy, from, to, picks))
{
if (p == 0)
{
times.resize(1, to-from+1);
for (qint32 i = 0; i < times.cols(); ++i)
times(0, i) = ((float)(from-event_samp+i)) / raw.info.sfreq;
}
epoch->event = eveNum;
epoch->tmin = ((float)(from)-(float)(raw.first_samp))/raw.info.sfreq;
epoch->tmax = ((float)(to)-(float)(raw.first_samp))/raw.info.sfreq;
data.append(MNEEpochData::SPtr(epoch));//List takes ownwership of the pointer - no delete need
}
else
{
printf("Can't read the event data segments");
return 0;
}
}
if(data.size() > 0)
{
printf("Read %d epochs, %d samples each.\n",data.size(),(qint32)data[0]->epoch.cols());
// //DEBUG
// std::cout << data[0]->epoch.block(0,0,10,10) << std::endl;
// qDebug() << data[0]->epoch.rows() << " x " << data[0]->epoch.cols();
// std::cout << times.block(0,0,1,10) << std::endl;
// qDebug() << times.rows() << " x " << times.cols();
}
//
// Init RAP-MUSIC
//
RapMusic t_rapMusic(t_clusteredFwd, false, numDipolePairs);
//
// calculate the average
//
for(qint32 numAverages = 1; numAverages <= 20; numAverages += 1)
{
for(qint32 it = 0; it <= 30; ++it)
{
//
// calculate the average
//
VectorXi vecSel(numAverages);
srand (time(NULL)); // initialize random seed
for(qint32 i = 0; i < vecSel.size(); ++i)
{
qint32 val = rand() % data.size();
vecSel(i) = val;
}
// std::cout << "Select following epochs to average:\n" << vecSel << std::endl;
// QString sSelFile = QString("aveInfo_%1_%2.txt").arg(numAverages).arg(it);
// std::ofstream selFile(sSelFile.toLatin1().constData());
// if (selFile.is_open())
// {
// selFile << vecSel << '\n';
// }
FiffEvoked evoked = data.average(raw.info, tmin*raw.info.sfreq, floor(tmax*raw.info.sfreq + 0.5), vecSel);
QStringList ch_sel_names = t_Fwd.info.ch_names;
FiffEvoked pickedEvoked = evoked.pick_channels(ch_sel_names);
//########################################################################################
// RAP MUSIC Source Estimate
// if(doMovie)
// t_pwlRapMusic.setStcAttr(200,0.5);
MNESourceEstimate sourceEstimate = t_rapMusic.calculateInverse(pickedEvoked);
// std::cout << "Source Estimate:\n" << sourceEstimate.data << std::endl;
// std::cout << "Source Estimate vertices:\n" << sourceEstimate.vertices << std::endl;
if(!sourceEstimate.isEmpty())
{
QString t_sFileNameStc = sTargetDir+QString("%1_%2_ave_it_%3.stc").arg(sTargetPrefix).arg(numAverages).arg(it);
qDebug() << "Write to:" << t_sFileNameStc;
QDir dir(sTargetDir);
if (!dir.exists()) {
dir.mkpath(".");
}
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileClusteredStc(t_sFileNameStc);
sourceEstimate.write(t_fileClusteredStc);
}
}
}
}
return 0;//app.exec();
}
bool FiffEvoked::read(QIODevice& p_IODevice, FiffEvoked& p_FiffEvoked, QVariant setno, QPair<QVariant,QVariant> baseline, bool proj, fiff_int_t p_aspect_kind)
{
p_FiffEvoked.clear();
//
// Open the file
//
FiffStream::SPtr t_pStream(new FiffStream(&p_IODevice));
QString t_sFileName = t_pStream->streamName();
printf("Reading %s ...\n",t_sFileName.toUtf8().constData());
FiffDirTree t_Tree;
QList<FiffDirEntry> t_Dir;
if(!t_pStream->open(t_Tree, t_Dir))
return false;
//
// Read the measurement info
//
FiffInfo info;
FiffDirTree meas;
if(!t_pStream->read_meas_info(t_Tree, info, meas))
return false;
info.filename = t_sFileName; //move fname storage to read_meas_info member function
//
// Locate the data of interest
//
QList<FiffDirTree> processed = meas.dir_tree_find(FIFFB_PROCESSED_DATA);
if (processed.size() == 0)
{
qWarning("Could not find processed data");
return false;
}
//
QList<FiffDirTree> evoked_node = meas.dir_tree_find(FIFFB_EVOKED);
if (evoked_node.size() == 0)
{
qWarning("Could not find evoked data");
return false;
}
// convert setno to an integer
if(!setno.isValid())
{
if (evoked_node.size() > 1)
{
QStringList comments;
QList<fiff_int_t> aspect_kinds;
QString t;
if(!t_pStream->get_evoked_entries(evoked_node, comments, aspect_kinds, t))
t = QString("None found, must use integer");
qWarning("%d datasets present, setno parameter must be set. Candidate setno names:\n%s", evoked_node.size(), t.toLatin1().constData());
return false;
}
else
setno = 0;
}
else
{
// find string-based entry
bool t_bIsInteger = true;
setno.toInt(&t_bIsInteger);
if(!t_bIsInteger)
{
if(p_aspect_kind != FIFFV_ASPECT_AVERAGE && p_aspect_kind != FIFFV_ASPECT_STD_ERR)
{
qWarning("kindStat must be \"FIFFV_ASPECT_AVERAGE\" or \"FIFFV_ASPECT_STD_ERR\"");
return false;
}
QStringList comments;
QList<fiff_int_t> aspect_kinds;
QString t;
t_pStream->get_evoked_entries(evoked_node, comments, aspect_kinds, t);
bool found = false;
for(qint32 i = 0; i < comments.size(); ++i)
{
if(comments[i].compare(setno.toString()) == 0 && p_aspect_kind == aspect_kinds[i])
{
setno = i;
found = true;
break;
}
}
if(!found)
{
qWarning() << "setno " << setno << " (" << p_aspect_kind << ") not found, out of found datasets:\n " << t;
return false;
}
}
}
if (setno.toInt() >= evoked_node.size() || setno.toInt() < 0)
{
qWarning("Data set selector out of range");
return false;
}
FiffDirTree my_evoked = evoked_node[setno.toInt()];
//
// Identify the aspects
//
QList<FiffDirTree> aspects = my_evoked.dir_tree_find(FIFFB_ASPECT);
if(aspects.size() > 1)
printf("\tMultiple (%d) aspects found. Taking first one.\n", aspects.size());
FiffDirTree my_aspect = aspects[0];
//
// Now find the data in the evoked block
//
fiff_int_t nchan = 0;
float sfreq = -1.0f;
QList<FiffChInfo> chs;
fiff_int_t kind, pos, first=0, last=0;
FiffTag::SPtr t_pTag;
QString comment("");
qint32 k;
for (k = 0; k < my_evoked.nent; ++k)
{
kind = my_evoked.dir[k].kind;
pos = my_evoked.dir[k].pos;
switch (kind)
{
case FIFF_COMMENT:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
comment = t_pTag->toString();
break;
case FIFF_FIRST_SAMPLE:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
first = *t_pTag->toInt();
break;
case FIFF_LAST_SAMPLE:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
last = *t_pTag->toInt();
break;
case FIFF_NCHAN:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
nchan = *t_pTag->toInt();
break;
case FIFF_SFREQ:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
sfreq = *t_pTag->toFloat();
break;
case FIFF_CH_INFO:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
chs.append( t_pTag->toChInfo() );
break;
}
}
if (comment.isEmpty())
comment = QString("No comment");
//
// Local channel information?
//
if (nchan > 0)
{
if (chs.size() == 0)
{
qWarning("Local channel information was not found when it was expected.");
return false;
}
if (chs.size() != nchan)
{
qWarning("Number of channels and number of channel definitions are different.");
return false;
}
info.chs = chs;
info.nchan = nchan;
printf("\tFound channel information in evoked data. nchan = %d\n",nchan);
if (sfreq > 0.0f)
info.sfreq = sfreq;
}
qint32 nsamp = last-first+1;
printf("\tFound the data of interest:\n");
printf("\t\tt = %10.2f ... %10.2f ms (%s)\n", 1000*(float)first/info.sfreq, 1000*(float)last/info.sfreq,comment.toUtf8().constData());
if (info.comps.size() > 0)
printf("\t\t%d CTF compensation matrices available\n", info.comps.size());
//
// Read the data in the aspect block
//
fiff_int_t aspect_kind = -1;
fiff_int_t nave = -1;
QList<FiffTag> epoch;
for (k = 0; k < my_aspect.nent; ++k)
{
kind = my_aspect.dir[k].kind;
pos = my_aspect.dir[k].pos;
switch (kind)
{
case FIFF_COMMENT:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
comment = t_pTag->toString();
break;
case FIFF_ASPECT_KIND:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
aspect_kind = *t_pTag->toInt();
break;
case FIFF_NAVE:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
nave = *t_pTag->toInt();
break;
case FIFF_EPOCH:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
epoch.append(FiffTag(t_pTag.data()));
break;
}
}
if (nave == -1)
nave = 1;
printf("\t\tnave = %d - aspect type = %d\n", nave, aspect_kind);
qint32 nepoch = epoch.size();
MatrixXd all_data;
if (nepoch == 1)
{
//
// Only one epoch
//
all_data = epoch[0].toFloatMatrix().cast<double>();
all_data.transposeInPlace();
//
// May need a transpose if the number of channels is one
//
if (all_data.cols() == 1 && info.nchan == 1)
all_data.transposeInPlace();
}
else
{
//
// Put the old style epochs together
//
all_data = epoch[0].toFloatMatrix().cast<double>();
all_data.transposeInPlace();
qint32 oldsize;
for (k = 1; k < nepoch; ++k)
{
oldsize = all_data.rows();
MatrixXd tmp = epoch[k].toFloatMatrix().cast<double>();
tmp.transposeInPlace();
all_data.conservativeResize(oldsize+tmp.rows(), all_data.cols());
all_data.block(oldsize, 0, tmp.rows(), tmp.cols()) = tmp;
}
}
if (all_data.cols() != nsamp)
{
qWarning("Incorrect number of samples (%d instead of %d)", (int) all_data.cols(), nsamp);
return false;
}
//
// Calibrate
//
printf("\n\tPreprocessing...\n");
printf("\t%d channels remain after picking\n",info.nchan);
typedef Eigen::Triplet<double> T;
std::vector<T> tripletList;
tripletList.reserve(info.nchan);
for(k = 0; k < info.nchan; ++k)
tripletList.push_back(T(k, k, info.chs[k].cal));
SparseMatrix<double> cals(info.nchan, info.nchan);
cals.setFromTriplets(tripletList.begin(), tripletList.end());
all_data = cals * all_data;
RowVectorXf times = RowVectorXf(last-first+1);
for (k = 0; k < times.size(); ++k)
times[k] = ((float)(first+k)) / info.sfreq;
//
// Set up projection
//
if(info.projs.size() == 0 || !proj)
{
printf("\tNo projector specified for these data.\n");
p_FiffEvoked.proj = MatrixXd();
}
else
{
// Create the projector
MatrixXd projection;
qint32 nproj = info.make_projector(projection);
if(nproj == 0)
{
printf("\tThe projection vectors do not apply to these channels\n");
p_FiffEvoked.proj = MatrixXd();
}
else
{
printf("\tCreated an SSP operator (subspace dimension = %d)\n", nproj);
p_FiffEvoked.proj = projection;
}
// The projection items have been activated
FiffProj::activate_projs(info.projs);
}
if(p_FiffEvoked.proj.rows() > 0)
{
all_data = p_FiffEvoked.proj * all_data;
printf("\tSSP projectors applied to the evoked data\n");
}
// Run baseline correction
all_data = MNEMath::rescale(all_data, times, baseline, QString("mean"));
printf("Applying baseline correction ... (mode: mean)");
// Put it all together
p_FiffEvoked.info = info;
p_FiffEvoked.nave = nave;
p_FiffEvoked.aspect_kind = aspect_kind;
p_FiffEvoked.first = first;
p_FiffEvoked.last = last;
p_FiffEvoked.comment = comment;
p_FiffEvoked.times = times;
p_FiffEvoked.data = all_data;
return true;
}
