bool MNESourceEstimate::read(QIODevice &p_IODevice, MNESourceEstimate& p_stc)
{
QSharedPointer<QDataStream> t_pStream(new QDataStream(&p_IODevice));
t_pStream->setFloatingPointPrecision(QDataStream::SinglePrecision);
t_pStream->setByteOrder(QDataStream::BigEndian);
t_pStream->setVersion(QDataStream::Qt_5_0);
if(!t_pStream->device()->open(QIODevice::ReadOnly))
return false;
QFile* t_pFile = qobject_cast<QFile*>(&p_IODevice);
if(t_pFile)
printf("Reading source estimate from %s...", t_pFile->fileName().toUtf8().constData());
else
printf("Reading source estimate...");
// read start time in ms
*t_pStream >> p_stc.tmin;
p_stc.tmin /= 1000;
// read sampling rate in ms
*t_pStream >> p_stc.tstep;
p_stc.tstep /= 1000;
// read number of vertices
quint32 t_nVertices;
*t_pStream >> t_nVertices;
p_stc.vertices = VectorXi(t_nVertices);
// read the vertex indices
for(quint32 i = 0; i < t_nVertices; ++i)
*t_pStream >> p_stc.vertices[i];
// read the number of timepts
quint32 t_nTimePts;
*t_pStream >> t_nTimePts;
//
// read the data
//
p_stc.data = MatrixXd(t_nVertices, t_nTimePts);
for(qint32 i = 0; i < p_stc.data.array().size(); ++i)
{
float value;
*t_pStream >> value;
p_stc.data.array()(i) = value;
}
//Update time vector
p_stc.update_times();
// close the file
t_pStream->device()->close();
printf("[done]\n");
return true;
}
/**
* 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 app(argc, argv);
// Command Line Parser
QCommandLineParser parser;
parser.setApplicationDescription("Compute Inverse Powell RAP-MUSIC Example");
parser.addHelpOption();
QCommandLineOption fwdFileOption("fwd", "Path to forward solution <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
QCommandLineOption evokedFileOption("ave", "Path to evoked <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
QCommandLineOption subjectDirectoryOption("subjDir", "Path to subject <directory>.", "directory", "./MNE-sample-data/subjects");
QCommandLineOption subjectOption("subj", "Selected <subject>.", "subject", "sample");
QCommandLineOption stcFileOption("stcOut", "Path to stc <file>, which is to be written.", "file", "");//"RapMusic.stc");
QCommandLineOption numDipolePairsOption("numDip", "<number> of dipole pairs to localize.", "number", "1");
QCommandLineOption doMovieOption("doMovie", "Create overlapping movie.", "doMovie", "false");
QCommandLineOption annotOption("annotType", "Annotation type <type>.", "type", "aparc.a2009s");
QCommandLineOption surfOption("surfType", "Surface type <type>.", "type", "orig");
parser.addOption(fwdFileOption);
parser.addOption(evokedFileOption);
parser.addOption(subjectDirectoryOption);
parser.addOption(subjectOption);
parser.addOption(stcFileOption);
parser.addOption(numDipolePairsOption);
parser.addOption(doMovieOption);
parser.addOption(annotOption);
parser.addOption(surfOption);
parser.process(app);
// Parse command line parameters
QFile t_fileFwd(parser.value(fwdFileOption));
QFile t_fileEvoked(parser.value(evokedFileOption));
QString subject(parser.value(subjectOption));
QString subjectDir(parser.value(subjectDirectoryOption));
AnnotationSet t_annotationSet(subject, 2, parser.value(annotOption), subjectDir);
SurfaceSet t_surfSet(subject, 2, parser.value(surfOption), subjectDir);
QString t_sFileNameStc(parser.value(stcFileOption));
qint32 numDipolePairs = parser.value(numDipolePairsOption).toInt();
bool doMovie = false;
if(parser.value(doMovieOption) == "false" || parser.value(doMovieOption) == "0") {
doMovie = false;
} else if(parser.value(doMovieOption) == "true" || parser.value(doMovieOption) == "1") {
doMovie = true;
}
qDebug() << "Start calculation with stc:" << t_sFileNameStc;
// Load data
fiff_int_t setno = 0;
QPair<QVariant, QVariant> baseline(QVariant(), 0);
FiffEvoked evoked(t_fileEvoked, setno, baseline);
if(evoked.isEmpty())
return 1;
std::cout << "evoked first " << evoked.first << "; last " << evoked.last << std::endl;
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
QStringList ch_sel_names = t_Fwd.info.ch_names;
FiffEvoked pickedEvoked = evoked.pick_channels(ch_sel_names);
//
// Cluster forward solution;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 20);//40);
// std::cout << "Size " << t_clusteredFwd.sol->data.rows() << " x " << t_clusteredFwd.sol->data.cols() << std::endl;
// std::cout << "Clustered Fwd:\n" << t_clusteredFwd.sol->data.row(0) << std::endl;
PwlRapMusic t_pwlRapMusic(t_clusteredFwd, false, numDipolePairs);
int iWinSize = 200;
if(doMovie) {
t_pwlRapMusic.setStcAttr(iWinSize, 0.6);
}
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;
}
std::cout << "source estimated" << std::endl;
if(sourceEstimate.isEmpty())
return 1;
View3D::SPtr testWindow = View3D::SPtr(new View3D());
Data3DTreeModel::SPtr p3DDataModel = Data3DTreeModel::SPtr(new Data3DTreeModel());
testWindow->setModel(p3DDataModel);
p3DDataModel->addSurfaceSet(parser.value(subjectOption), "HemiLRSet", t_surfSet, t_annotationSet);
QList<BrainRTSourceLocDataTreeItem*> rtItemList = p3DDataModel->addSourceData(parser.value(subjectOption), "HemiLRSet", sourceEstimate, t_clusteredFwd);
//Init some rt related values for right visual data
for(int i = 0; i < rtItemList.size(); ++i) {
rtItemList.at(i)->setLoopState(true);
rtItemList.at(i)->setTimeInterval(17);
rtItemList.at(i)->setNumberAverages(1);
rtItemList.at(i)->setStreamingActive(true);
rtItemList.at(i)->setNormalization(QVector3D(0.01,0.5,1.0));
rtItemList.at(i)->setVisualizationType("Annotation based");
rtItemList.at(i)->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 app.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);
//############################# Data location and configs - Change if necessary ############################################
//source localization type
QString method("MNE"); //"MNE" | "dSPM" | "sLORETA"
//Choose which epoch to take - i.e. for every 4th epoch set to 4
int averageIterator = 1;
bool doRawTrialLocalization = false;
//measurement data location (data location must always has same directory structure - see dropbox folder for more information)
//QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2013_12_05_Lorenz_Esch_001");
//QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_01_10_Lorenz_Esch_002");
//QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_01_14_Lorenz_Esch_003");
//QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_01_28_Lorenz_Esch_004");
//QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_02_04_Lorenz_Esch_005");
//QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_02_05_Uwe_Graichen_006");
QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_02_07_Lorenz_Esch_007");
//QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_02_24_Lorenz_Esch_008");
//QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_02_25_Christoph_Dinh_009");
//QString data_location("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_03_17_Lorenz_Esch_010");
//Forward solution
//QFile t_fileFwd("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/Lorenz-131212-Duke128-fwd.fif");
//QFile t_fileFwd("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/Lorenz-140112-Duke128-fwd.fif");
//QFile t_fileFwd("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/Lorenz-140114-Duke128-fwd.fif");
//QFile t_fileFwd("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/Lorenz-140123-Duke128-fwd.fif");
QFile t_fileFwd("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/Lorenz-140128-Duke128-fwd.fif");
//Surface generated by freesurfer
SurfaceSet t_surfSet("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/surface/lh.white", "D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/surface/rh.white");
//AnnotationSet (See Destrieux paper)
AnnotationSet t_annotationSet("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/atlas/lh.aparc.a2009s.annot", "D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/atlas/rh.aparc.a2009s.annot");
//////////////////////////////////////////// Interesting start ////////////////////////////////////////////////////////////////////
//********************************** Involuntary Tapping ***********************************//
//time read around events - note: trigger point is the pressing of the button, not the atual
// float tmin = -2.0f;
// float tmax = 2.0f;
// //Filtered 7-14Hz left tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_involuntary_left_tapping_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_involuntary_left_tapping_131_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_involuntary_left_tapping_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_involuntary_left_tapping_filtered_7_14_Averaged_");
// //Filtered 7-14Hz right tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_involuntary_right_tapping_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEEG_data_001_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_involuntary_right_tapping_136_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_involuntary_right_tapping_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_involuntary_right_tapping_filtered_7_14_Averaged_");
// //Filtered 0.7-40Hz left tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_involuntary_left_tapping_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_involuntary_left_tapping_131_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_involuntary_left_tapping_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_involuntary_left_tapping_filtered_07_40_Averaged_");
// //Filtered 0.7-40Hz right tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_involuntary_right_tapping_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_involuntary_right_tapping_136_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_involuntary_right_tapping_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_involuntary_right_tapping_filtered_07_40_Averaged_");
//////////////////////////////////////////// Interesting end ////////////////////////////////////////////////////////////////////
//********************************** Voluntary Tapping ***********************************//
// //time read around events - note: trigger point is the pressing of the button, not the atual
// float tmin = -1.0f;
// float tmax = 1.0f;
// //Original left tapping - no filtering DC still present
// QString t_sRawFileNameRel ("/Original/EEG_data_001_right_tapping_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_base_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_right_tapping_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_right_tapping_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_right_tapping_Averaged_");
// //Filtered 0.6-40Hz left tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_left_tapping_filtered_06_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_left_tapping_filtered_06_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_left_tapping_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_left_tapping_filtered_06_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_left_tapping_filtered_06_40_Averaged_");
// //Filtered 0.6-40Hz right tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_right_tapping_filtered_06_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_right_tapping_filtered_06_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_right_tapping_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_right_tapping_filtered_06_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_right_tapping_filtered_06_40_Averaged_");
// //Filtered 7-14Hz left tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_voluntary_left_tapping_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_tapping_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_voluntary_left_tapping_artefact_reduction_-1_1_0.002_71_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_left_tapping_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_voluntary_left_tapping_filtered_7_14_Averaged_");
// //Filtered 7-14Hz right tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_voluntary_right_tapping_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_tapping_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_voluntary_right_tapping_artefact_reduction_-1_1_0.003_69_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_right_tapping_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_voluntary_right_tapping_filtered_7_14_Averaged_");
// //Filtered 0.7-40Hz left tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_voluntary_left_tapping_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_tapping_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_voluntary_left_tapping_222_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_left_tapping_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_voluntary_left_tapping_filtered_07_40_Averaged_");
// //Filtered 0.7-40Hz right tapping
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_voluntary_right_tapping_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_tapping_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_voluntary_right_tapping_184_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_right_tapping_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_voluntary_right_tapping_filtered_07_40_Averaged_");
//********************************** Medianus stimulation **********************************//
// //time read around events - note: trigger point is the pressing of the button, not the atual
// float tmin = -1.0f;
// float tmax = 1.0f;
// //Original left medianus stimulation - no filtering DC still present
// QString t_sRawFileNameRel ("/Original/EEG_data_002_medianus_left_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_medianus_base_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_medianus_left_240_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_medianus_left_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_medianus_left_Averaged_");
// //Original right medianus stimulation - no filtering DC still present
// QString t_sRawFileNameRel ("/Original/EEG_data_002_medianus_right_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_medianus_base_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_medianus_right_295_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_medianus_right_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_medianus_right_Averaged_");
// //Filtered 0.7-40Hz left medianus stimulation
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_medianus_left_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_medianus_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_medianus_left_artefact_reduction_-1_1_0.002_80_raw-eve.fif"); // ("EEG_data_002_medianus_left_raw-eve")
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_medianus_left_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_medianus_left_filtered_07_40_Averaged_");
// //Filtered 0.7-40Hz right medianus stimulation
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_medianus_right_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_medianus_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_medianus_right_artefact_reduction_-1_1_0.0025_93_raw-eve.fif"); // ("EEG_data_002_medianus_right_raw-eve")
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_medianus_right_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_medianus_right_filtered_07_40_Averaged_");
// //Filtered 7-14Hz left medianus stimulation
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_medianus_left_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_medianus_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_medianus_left_artefact_reduction_-1_1_0.002_80_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_medianus_left_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_medianus_left_filtered_7_14_Averaged_");
// //Filtered 7-14Hz right medianus stimulation
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_medianus_right_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_medianus_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_medianus_right_artefact_reduction_-1_1_0.0025_93_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_medianus_right_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_medianus_right_filtered_7_14_Averaged_");
//*************************** Voluntary opposing finger movement **************************//
// //time read around events - note: trigger point is the pressing of the button, not the atual
// float tmin = -0.3f;
// float tmax = 0.1f;
// //Original left opposing finger movement - no filtering DC still present
// QString t_sRawFileNameRel ("/Original/EEG_data_001_voluntary_left_opposing_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_base_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_voluntary_left_opposing_89_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_left_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_voluntary_left_Averaged_");
// //Original right opposing finger movement - no filtering DC still present
// QString t_sRawFileNameRel ("/Original/EEG_data_001_voluntary_right_opposing_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_base_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_voluntary_right_opposing_90_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_right_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_voluntary_right_Averaged_");
// //Filtered 7-14Hz left voluntary finger opposing
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_voluntary_left_opposing_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_opposing_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_voluntary_left_opposing_154_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_left_opposing_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_voluntary_left_opposing_filtered_7_14_Averaged_");
// //Filtered 7-14Hz right voluntary finger opposing
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_voluntary_right_opposing_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_opposing_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_voluntary_right_opposing_135_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_right_opposing_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_voluntary_right_opposing_filtered_7_14_Averaged_");
// //Filtered 0.7-40Hz left voluntary finger opposing
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_voluntary_left_opposing_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_opposing_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_voluntary_left_opposing_137_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_left_opposing_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_voluntary_left_opposing_filtered_07_40_Averaged_");
// //Filtered 0.7-40Hz right voluntary finger opposing
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_voluntary_right_opposing_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_voluntary_opposing_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_voluntary_right_opposing_135_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_voluntary_right_opposing_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_voluntary_right_opposing_filtered_07_40_Averaged_");
//*************************** Involuntary opposing finger movement **************************//
//time read around events - note: trigger point is the pressing of the button
float tmin = -1.0f;
float tmax = 1.0f;
// //Filtered 7-14Hz left involuntary finger opposing
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_involuntary_left_opposing_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_involuntary_left_opposing_137_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_involuntary_left_opposing_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_involuntary_left_opposing_filtered_7_14_Averaged_");
// //Filtered 7-14Hz right involuntary finger opposing
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_involuntary_right_opposing_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_involuntary_right_opposing_150_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_involuntary_right_opposing_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_involuntary_right_opposing_filtered_7_14_Averaged_");
// //Filtered 0.7-40Hz left involuntary finger opposing
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_involuntary_left_opposing_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_involuntary_left_opposing_137_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_involuntary_left_opposing_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_involuntary_left_opposing_filtered_07_40_Averaged_");
//Filtered 0.7-40Hz right involuntary finger opposing
QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_001_involuntary_right_opposing_filtered_07_40_raw.fif");
QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_001_base_filtered_07_40_raw-cov.fif");
QString t_sEventFileNameRel("/Processed/events/EEG_data_001_involuntary_right_opposing_150_raw-eve.fif");
QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_involuntary_right_opposing_filtered_07_40_Averaged_");
QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_involuntary_right_opposing_filtered_07_40_Averaged_");
//*************************** Motor imagery **************************//
// //time read around events - note: trigger point is the pressing of the button, not the atual
// float tmin = -1.0f;
// float tmax = 6.0f;
// //Filtered 7-14Hz left MI
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_left_MI_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_002_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_left_MI_filtered_100_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_left_MI_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_left_MI_filtered_7_14_Averaged_");
// //Filtered 7-14Hz right MI
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_right_MI_filtered_7_14_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_002_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_right_MI_filtered_105_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_right_MI_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_right_MI_filtered_7_14_Averaged_");
// //Filtered 0.7-40Hz left MI
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_left_MI_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_002_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_left_MI_filtered_100_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_left_MI_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_left_MI_filtered_07_40_Averaged_");
// //Filtered 0.7-40Hz right MI
// QString t_sRawFileNameRel ("/Processed/filtered/EEG_data_002_right_MI_filtered_07_40_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_002_base_filtered_07_40_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_002_right_MI_filtered_105_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_right_MI_filtered_07_40_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_002_right_MI_filtered_07_40_Averaged_");
//*************************** BCI lefti right in one file finger tapping **************************//
// //time read around events - note: trigger point is the pressing of the button, not the atual
// float tmin = -1.0f;
// float tmax = 1.0f;
// //Filtered 7-14Hz left MI
// QString t_sRawFileNameRel ("/Original/EEG_data_001_voluntary_left_right_tapping_raw.fif");
// QString t_sCovFileNameRel ("/Processed/covariance/EEG_data_002_base_filtered_7_14_raw-cov.fif");
// QString t_sEventFileNameRel("/Processed/events/EEG_data_001_voluntary_left_right_tapping_234_raw-eve.fif");
// QString t_sStcFileNameRel ("/Processed/stc/SourceLoc_left_MI_filtered_7_14_Averaged_");
// QString t_sAvrFileNameRel ("/Processed/averaged/EEG_data_001_voluntary_right_tapping_raw_Averaged_");
//##########################################################################################################################
//Create final location dirs and files
QFile t_fileRaw(t_sRawFileNameRel.prepend(data_location));
QFile t_fileCov(t_sCovFileNameRel.prepend(data_location));
QString t_sEventName = t_sEventFileNameRel.prepend(data_location);
qint32 event = 1; //254-right trigger | 253-left trigger | 252-beep | 1-old eventfile value for trigger
qint32 k, p;
fiff_int_t dest_comp = 0;
bool keep_comp = false;
bool pick_all = false;
//
// 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 = false;
bool want_eeg = true;
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 = 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;
}
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());
}
}
//
// 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
//
//Only take first finger movement of each tapping session (each tapping session consists of 4 seperate finger movement)
// VectorXi vecSel(1);
// vecSel << 60;
if(count<averageIterator)
averageIterator = count;
VectorXi vecSel(count/averageIterator);
int i;
for(i=0; i<count/averageIterator; i++)
vecSel[i] = i*averageIterator;
// Add number of averages read from the eventfile to the file name
t_sAvrFileNameRel.append(t_sAvrFileNameRel.number(tmin));
t_sAvrFileNameRel.append("_");
t_sAvrFileNameRel.append(t_sAvrFileNameRel.number(tmax));
t_sAvrFileNameRel.append("_");
t_sAvrFileNameRel.append(t_sAvrFileNameRel.number(i));
t_sAvrFileNameRel.append(".fif");
QString t_sAvrFileName = t_sAvrFileNameRel.prepend(data_location);
t_sStcFileNameRel.append(t_sStcFileNameRel.number(tmin));
t_sStcFileNameRel.append("_");
t_sStcFileNameRel.append(t_sStcFileNameRel.number(tmax));
t_sStcFileNameRel.append("_");
t_sStcFileNameRel.append(t_sStcFileNameRel.number(i));
t_sStcFileNameRel.append("_");
t_sStcFileNameRel.append(method.append(".stc"));
QString t_sFileNameStc = t_sStcFileNameRel.prepend(data_location);
std::cout << "Select following epochs to average:\n" << vecSel << std::endl;
raw.info.filename = QString(""); //this need to be done in order to write a new file. otherwise some of the info contents are not getting copied correctly from raw.info (i.e. digitizer data)
FiffEvoked evoked = data.average(raw.info, tmin*raw.info.sfreq, floor(tmax*raw.info.sfreq + 0.5), vecSel);
//Write averaged data to file
QFile m_fileOut(t_sAvrFileName);
RowVectorXd m_cals;
FiffStream::SPtr m_pOutfid = Fiff::start_writing_raw(m_fileOut, raw.info, m_cals);
fiff_int_t first = 0;
m_pOutfid->write_int(FIFF_FIRST_SAMPLE, &first);
//m_pOutfid->finish_writing_raw();
Eigen::MatrixXd eData = evoked.data;
Eigen::MatrixXd matValue = MatrixXd::Zero(eData.rows()+10, eData.cols());
matValue.block(0,0,128,matValue.cols()) = evoked.data;
m_pOutfid->write_raw_buffer(matValue, m_cals);
m_pOutfid->finish_writing_raw();
//################################# Source Estimate start ##########################################
double snr = 0.1f;//1.0f;//3.0f;//0.1f;//3.0f;
QString t_sFileNameClusteredInv("");
// Parse command line parameters
for(qint32 i = 0; i < argc; ++i)
{
if(strcmp(argv[i], "-snr") == 0 || strcmp(argv[i], "--snr") == 0)
{
if(i + 1 < argc)
snr = atof(argv[i+1]);
}
else if(strcmp(argv[i], "-method") == 0 || strcmp(argv[i], "--method") == 0)
{
if(i + 1 < argc)
method = QString::fromUtf8(argv[i+1]);
}
else if(strcmp(argv[i], "-inv") == 0 || strcmp(argv[i], "--inv") == 0)
{
if(i + 1 < argc)
t_sFileNameClusteredInv = QString::fromUtf8(argv[i+1]);
}
else if(strcmp(argv[i], "-stc") == 0 || strcmp(argv[i], "--stc") == 0)
{
if(i + 1 < argc)
t_sFileNameStc = QString::fromUtf8(argv[i+1]);
}
}
double lambda2 = 1.0 / pow(snr, 2);
qDebug() << "Start calculation with: SNR" << snr << "; Lambda" << lambda2 << "; Method" << method << "; stc:" << t_sFileNameStc;
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;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 20);//40); % Use multithreading
//MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 10);//40);
//MNEForwardSolution t_clusteredFwd = t_Fwd;
//
// Find rows of interest in stc files
//
QFile wrtFWD ("./mne_x_plugins/resources/tmsi/fwd_clustered.txt");
wrtFWD.open(QIODevice::WriteOnly | QIODevice::Text);
QTextStream out(&wrtFWD);
//Read vertnos
VectorXi vertno_left = t_clusteredFwd.src[0].vertno;
VectorXi vertno_right = t_clusteredFwd.src[1].vertno;
out<<"Vertno Left Hemi:"<<endl<<endl;
for(int i=0; i<vertno_left.rows(); i++)
out<<vertno_left[i]<<endl;
out<<endl<<"Vertno right Hemi:"<<endl<<endl;
for(int i=0; i<vertno_right.rows(); i++)
out<<vertno_right[i]<<endl;
//Read corresponding labels
VectorXi labelIds_left = t_annotationSet[0].getLabelIds();
out<<endl<<endl<<"labelIds_left:"<<endl<<endl;
for(int i=0; i<labelIds_left.rows(); i++)
out<<labelIds_left[i]<<endl;
VectorXi labelIds_right = t_annotationSet[1].getLabelIds();
out<<endl<<endl<<"labelIds_right:"<<endl<<endl;
for(int i=0; i<labelIds_right.rows(); i++)
out<<labelIds_right[i]<<endl;
//Find interesting rows in stc files
// Left hemisphere
QFile wrtFWD_28_left ("./mne_x_plugins/resources/tmsi/fwd_clustered_postcentral_28_Left.txt");
wrtFWD_28_left.open(QIODevice::WriteOnly | QIODevice::Text);
QTextStream out_28_left(&wrtFWD_28_left);
QFile wrtFWD_29_left ("./mne_x_plugins/resources/tmsi/fwd_clustered_precentral_29_Left.txt");
wrtFWD_29_left.open(QIODevice::WriteOnly | QIODevice::Text);
QTextStream out_29_left(&wrtFWD_29_left);
QFile wrtFWD_45_left ("./mne_x_plugins/resources/tmsi/fwd_clustered_central_45_Left.txt");
wrtFWD_45_left.open(QIODevice::WriteOnly | QIODevice::Text);
QTextStream out_45_left(&wrtFWD_45_left);
QVector<int> interestingRows_Left;
out<<endl<<endl<<"interestingRows_Left (matlab syntax):"<<endl<<endl;
for(int i=0; i<vertno_left.rows() ; i++)
{
//G_postcentral
if(labelIds_left[vertno_left[i]] == 9221140)
{
interestingRows_Left.push_back(i);
out<<"Region 28 - G_postcentral: "<<i+1<<endl;
out_28_left<<i+1<<endl;
}
//G_precentral
if(labelIds_left[vertno_left[i]] == 11832380)
{
interestingRows_Left.push_back(i);
out<<"Region 29 - G_precentral: "<<i+1<<endl;
out_29_left<<i+1<<endl;
}
//S_central
if(labelIds_left[vertno_left[i]] == 660701)
{
interestingRows_Left.push_back(i);
out<<"Region 45 - S_central: "<<i+1<<endl;
out_45_left<<i+1<<endl;
}
}
// Right hemisphere
QFile wrtFWD_28_right ("./mne_x_plugins/resources/tmsi/fwd_clustered_postcentral_28_Right.txt");
wrtFWD_28_right.open(QIODevice::WriteOnly | QIODevice::Text);
QTextStream out_28_right(&wrtFWD_28_right);
QFile wrtFWD_29_right ("./mne_x_plugins/resources/tmsi/fwd_clustered_precentral_29_Right.txt");
wrtFWD_29_right.open(QIODevice::WriteOnly | QIODevice::Text);
QTextStream out_29_right(&wrtFWD_29_right);
QFile wrtFWD_45_right ("./mne_x_plugins/resources/tmsi/fwd_clustered_central_45_Right.txt");
wrtFWD_45_right.open(QIODevice::WriteOnly | QIODevice::Text);
QTextStream out_45_right(&wrtFWD_45_right);
QVector<int> interestingRows_Right;
out<<endl<<endl<<"interestingRows_Right (matlab syntax):"<<endl<<endl;
for(int i=0; i<vertno_right.rows() ; i++)
{
//G_postcentral
if(labelIds_right[vertno_right[i]] == 9221140)
{
interestingRows_Right.push_back(i);
out<<"Region 28 - G_postcentral: "<<i+1+vertno_left.rows()<<endl;
out_28_right<<i+1<<endl;
}
//G_precentral
if(labelIds_right[vertno_right[i]] == 11832380)
{
interestingRows_Right.push_back(i);
out<<"Region 29 - G_precentral: "<<i+1+vertno_left.rows()<<endl;
out_29_right<<i+1<<endl;
}
//S_central
if(labelIds_right[vertno_right[i]] == 660701)
{
interestingRows_Right.push_back(i);
out<<"Region 45 - S_central: "<<i+1+vertno_left.rows()<<endl;
out_45_right<<i+1<<endl;
}
}
wrtFWD_28_left.close();
wrtFWD_29_left.close();
wrtFWD_45_left.close();
wrtFWD_28_right.close();
wrtFWD_29_right.close();
wrtFWD_45_right.close();
wrtFWD.close();
//
// make an inverse operators
//
FiffInfo info = evoked.info;
MNEInverseOperator inverse_operator(info, t_clusteredFwd, noise_cov, 0.2f, 0.8f);
// QFile t_fileInv("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_02_07_Lorenz_Esch_007/Processed/inverse operators/Lorenz-140128-Duke128-eeg-inv.fif");
// MNEInverseOperator inverse_operator(t_fileInv);
//
// save clustered inverse
//
if(!t_sFileNameClusteredInv.isEmpty())
{
QFile t_fileClusteredInverse(t_sFileNameClusteredInv);
inverse_operator.write(t_fileClusteredInverse);
}
//
// Compute inverse solution
//
// Calculate stc for averaged data
MinimumNorm minimumNorm(inverse_operator, lambda2, method);
MNESourceEstimate sourceEstimate = minimumNorm.calculateInverse(evoked);
if(sourceEstimate.isEmpty())
return 1;
// Calculate stc for all trials and write to file - dirty
if(doRawTrialLocalization)
{
MNESourceEstimate sourceEstimate_trial;
for(int i = 0; i<data.size(); i++)
{
QString file_trial_stc_orig = t_sFileNameStc;
QString file_trial_stc_tmp = t_sFileNameStc;
QString stc_trial_sub_folder = file_trial_stc_tmp.remove(0,t_sFileNameStc.indexOf("/So")+1);
stc_trial_sub_folder.remove(".stc");
stc_trial_sub_folder.append("-raw-trials/");
QString dirCheck = data_location;
dirCheck.append("/Processed/stc/");
dirCheck.append(stc_trial_sub_folder);
if(QDir(dirCheck).exists() == false)
QDir().mkdir(dirCheck);
stc_trial_sub_folder.prepend("stc/");
file_trial_stc_orig.replace("stc/", stc_trial_sub_folder);
QString temp;
temp.append("_");
temp.append(temp.number(i));
temp.append(".stc");
file_trial_stc_orig.replace(".stc",temp);
sourceEstimate_trial = minimumNorm.calculateInverse(data[i]->epoch,0,1/info.sfreq);
if(sourceEstimate_trial.isEmpty())
return 1;
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileTrialStc(file_trial_stc_orig);
sourceEstimate_trial.write(t_fileTrialStc);
}
}
}
// 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;
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;
// Write stc to file
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileClusteredStc(t_sFileNameStc);
sourceEstimate.write(t_fileClusteredStc);
}
//############################### 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);
// sourceEstimate = sourceEstimate.reduce(253, 1); //1731
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();
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);
//########################################################################################
//
// Source Estimate START
//
//########################################################################################
QFile t_fileFwd("./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
QFile t_fileCov("./MNE-sample-data/MEG/sample/sample_audvis-cov.fif");
QFile t_fileEvoked("./MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
QString t_sFileClusteredInverse("");//QFile t_fileClusteredInverse("./clusteredInverse-inv.fif");
AnnotationSet t_annotationSet ("sample", 2, "aparc.a2009s", "./MNE-sample-data/subjects");
double snr = 1.0;
double lambda2 = 1.0 / pow(snr, 2);
QString method("dSPM"); //"MNE" | "dSPM" | "sLORETA"
// Load data
fiff_int_t setno = 1;
QPair<QVariant, QVariant> baseline(QVariant(), 0);
FiffEvoked evoked(t_fileEvoked, setno, baseline);
if(evoked.isEmpty())
return 1;
std::cout << "Evoked description: " << evoked.comment.toLatin1().constData() << std::endl;
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;
//
MNEForwardSolution t_clusteredFwd = t_Fwd;//.cluster_forward_solution(t_annotationSet, 40);
//
// make an inverse operators
//
FiffInfo info = evoked.info;
MNEInverseOperator inverse_operator(info, t_clusteredFwd, noise_cov, 0.2f, 0.8f);
if(!t_sFileClusteredInverse.isEmpty())
{
QFile t_fileClusteredInverse(t_sFileClusteredInverse);
inverse_operator.write(t_fileClusteredInverse);
}
//
// Compute inverse solution
//
MinimumNorm minimumNorm(inverse_operator, lambda2, method);
MNESourceEstimate sourceEstimate = minimumNorm.calculateInverse(evoked);
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
//
//########################################################################################
//########################################################################################
//
// Create the test view START
//
//########################################################################################
std::cout<<"Creating BrainView"<<std::endl;
SurfaceSet tSurfSet ("sample", 2, "inflated", "./MNE-sample-data/subjects");
AnnotationSet tAnnotSet ("sample", 2, "aparc.a2009s", "./MNE-sample-data/subjects");
//Surface tSurfRight ("sample", 1, "inflated", "./MNE-sample-data/subjects");
//Annotation tAnnotRight ("sample", 1, "aparc.a2009s", "./MNE-sample-data/subjects");
//Surface tSurfLeft ("sample", 0, "inflated", "./MNE-sample-data/subjects");
//Annotation tAnnotLeft ("sample", 0, "aparc.a2009s", "./MNE-sample-data/subjects");
View3D::SPtr testWindow = View3D::SPtr(new View3D());
//testWindow->addBrainData("HemiLR", tSurfLeft, tAnnotLeft);
//testWindow->addBrainData("HemiLR", tSurfRight, tAnnotRight);
testWindow->addBrainData("HemiLRSet", tSurfSet, tAnnotSet);
// QFile t_File("./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
// MNEForwardSolution t_forwardSolution(t_File);
//testWindow->addBrainData("HemiLRSet", t_forwardSolution);
QList<BrainRTDataTreeItem*> rtItemList = testWindow->addRtBrainData("HemiLRSet", sourceEstimate, t_clusteredFwd);
//testWindow->addRtBrainData("HemiLRSet", sourceEstimate);
//rtItemList.at(0)->addData(sourceEstimate);
testWindow->show();
Control3DWidget::SPtr control3DWidget = Control3DWidget::SPtr(new Control3DWidget());
control3DWidget->setWindowFlags(Qt::WindowStaysOnTopHint);
control3DWidget->setView3D(testWindow);
control3DWidget->show();
//########################################################################################
//
// Create the test view END
//
//########################################################################################
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);
// 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[])
{
QGuiApplication a(argc, argv);
//########################################################################################
// Source Estimate
QFile t_fileFwd("./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
QFile t_fileEvoked("./MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
AnnotationSet t_annotationSet("sample", 2, "aparc.a2009s", "./MNE-sample-data/subjects");
SurfaceSet t_surfSet("sample", 2, "white", "./MNE-sample-data/subjects");
QString t_sFileNameStc("");//"RapMusic.stc");
qint32 numDipolePairs = 7;
bool doMovie = false;//true;
// 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]);
}else if(strcmp(argv[i], "-num") == 0 || strcmp(argv[i], "--num") == 0)
{
if(i + 1 < argc)
numDipolePairs = atof(argv[i+1]);
}
}
qDebug() << "Start calculation with stc:" << t_sFileNameStc;
// Load data
fiff_int_t setno = 0;
QPair<QVariant, QVariant> baseline(QVariant(), 0);
FiffEvoked evoked(t_fileEvoked, setno, baseline);
if(evoked.isEmpty())
return 1;
std::cout << "evoked first " << evoked.first << "; last " << evoked.last << std::endl;
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
QStringList ch_sel_names = t_Fwd.info.ch_names;
FiffEvoked pickedEvoked = evoked.pick_channels(ch_sel_names);
//
// Cluster forward solution;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 20);//40);
// std::cout << "Size " << t_clusteredFwd.sol->data.rows() << " x " << t_clusteredFwd.sol->data.cols() << std::endl;
// std::cout << "Clustered Fwd:\n" << t_clusteredFwd.sol->data.row(0) << std::endl;
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;
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);
InverseView view(t_rapMusic.getSourceSpace(), t_qListLabels, t_qListRGBAs, 24, true, false, false);//true);
if (view.stereoType() != QGLView::RedCyanAnaglyph)
view.camera()->setEyeSeparation(0.3f);
QStringList args = QCoreApplication::arguments();
int w_pos = args.indexOf("-width");
int h_pos = args.indexOf("-height");
if (w_pos >= 0 && h_pos >= 0)
{
bool ok = true;
int w = args.at(w_pos + 1).toInt(&ok);
if (!ok)
{
qWarning() << "Could not parse width argument:" << args;
return 1;
}
int h = args.at(h_pos + 1).toInt(&ok);
if (!ok)
{
qWarning() << "Could not parse height argument:" << args;
return 1;
}
view.resize(w, h);
}
else
{
view.resize(800, 600);
}
view.show();
//Push Estimate
view.pushSourceEstimate(sourceEstimate);
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[])
{
QGuiApplication a(argc, argv);
//########################################################################################
// Source Estimate
QFile t_fileFwd("./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
QFile t_fileCov("./MNE-sample-data/MEG/sample/sample_audvis-cov.fif");
QFile t_fileEvoked("./MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
QFile t_fileClusteredInverse("./clusteredInverse-inv.fif");
double snr = 3.0;
double lambda2 = 1.0 / pow(snr, 2);
QString method("sLORETA"); //"MNE" | "dSPM" | "sLORETA"
// Load data
fiff_int_t setno = 0;
QPair<QVariant, QVariant> baseline(QVariant(), 0);
FiffEvoked evoked(t_fileEvoked, setno, baseline);
if(evoked.isEmpty())
return 1;
std::cout << "Evoked description: " << evoked.comment.toLatin1().constData() << std::endl;
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
AnnotationSet t_annotationSet("./MNE-sample-data/subjects/sample/label/lh.aparc.a2009s.annot", "./MNE-sample-data/subjects/sample/label/rh.aparc.a2009s.annot");
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;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution_ccr(t_annotationSet, 40);
//
// make an inverse operators
//
FiffInfo info = evoked.info;
MNEInverseOperator inverse_operator(info, t_clusteredFwd, noise_cov, 0.2f, 0.8f);
inverse_operator.write(t_fileClusteredInverse);
//
// Compute inverse solution
//
MinimumNorm minimumNorm(inverse_operator, lambda2, method);
MNESourceEstimate sourceEstimate = minimumNorm.calculateInverse(evoked);
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
//########################################################################################
AnnotationSet t_annotSet("./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");
QList<Label> t_qListLabels;
QList<RowVector4i> t_qListRGBAs;
//ToDo overload toLabels using instead of t_surfSet rr of MNESourceSpace
t_annotSet.toLabels(t_surfSet, t_qListLabels, t_qListRGBAs);
InverseView view(minimumNorm.getSourceSpace(), t_qListLabels, t_qListRGBAs, 24, true);
if (view.stereoType() != QGLView::RedCyanAnaglyph)
view.camera()->setEyeSeparation(0.3f);
QStringList args = QCoreApplication::arguments();
int w_pos = args.indexOf("-width");
int h_pos = args.indexOf("-height");
if (w_pos >= 0 && h_pos >= 0)
{
bool ok = true;
int w = args.at(w_pos + 1).toInt(&ok);
if (!ok)
{
qWarning() << "Could not parse width argument:" << args;
return 1;
}
int h = args.at(h_pos + 1).toInt(&ok);
if (!ok)
{
qWarning() << "Could not parse height argument:" << args;
return 1;
}
view.resize(w, h);
}
else
{
view.resize(800, 600);
}
view.setTitle(QString("Online Brain Monitoring - %1").arg(evoked.comment));
view.show();
//Push Estimate
view.pushSourceEstimate(sourceEstimate);
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[])
{
QGuiApplication a(argc, argv);
// QFile t_fileFwd("./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
// QFile t_fileCov("./MNE-sample-data/MEG/sample/sample_audvis-cov.fif");
// 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";
// 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_fileFwd("E:/Data/sl_data/MEG/mind006/mind006_051209_auditory01_raw-oct-6p-fwd.fif");
QFile t_fileCov("E:/Data/sl_data/MEG/mind006/mind006_051209_auditory01_raw-cov.fif");
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";
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");
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;
//
// 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
// 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;
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
double snr = 1.0f;//0.1f;//1.0f;//3.0f;//0.1f;//3.0f;
QString method("dSPM"); //"MNE" | "dSPM" | "sLORETA"
QString t_sFileNameClusteredInv("");
QString t_sFileNameStc("mind006_051209_auditory01.stc");
// Parse command line parameters
for(qint32 i = 0; i < argc; ++i)
{
if(strcmp(argv[i], "-snr") == 0 || strcmp(argv[i], "--snr") == 0)
{
if(i + 1 < argc)
snr = atof(argv[i+1]);
}
else if(strcmp(argv[i], "-method") == 0 || strcmp(argv[i], "--method") == 0)
{
if(i + 1 < argc)
method = QString::fromUtf8(argv[i+1]);
}
else if(strcmp(argv[i], "-inv") == 0 || strcmp(argv[i], "--inv") == 0)
{
if(i + 1 < argc)
t_sFileNameClusteredInv = QString::fromUtf8(argv[i+1]);
}
else if(strcmp(argv[i], "-stc") == 0 || strcmp(argv[i], "--stc") == 0)
{
if(i + 1 < argc)
t_sFileNameStc = QString::fromUtf8(argv[i+1]);
}
}
double lambda2 = 1.0 / pow(snr, 2);
qDebug() << "Start calculation with: SNR" << snr << "; Lambda" << lambda2 << "; Method" << method << "; stc:" << t_sFileNameStc;
// // Load data
// fiff_int_t setno = 1;
// QPair<QVariant, QVariant> baseline(QVariant(), 0);
// FiffEvoked evoked(t_fileEvoked, setno, baseline);
// if(evoked.isEmpty())
// return 1;
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;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution_ccr(t_annotationSet, 20);//40);
//
// 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
MNESourceEstimate sourceEstimate;
QList<qint64> qVecElapsedTime;
for(qint32 i = 0; i < 20; ++i)
{
//Benchmark time
QElapsedTimer timer;
timer.start();
sourceEstimate = minimumNorm.calculateInverse(evoked);
qVecElapsedTime.append(timer.elapsed());
}
double meanTime = 0.0;
for(qint32 i = 0; i < qVecElapsedTime.size(); ++i)
meanTime += qVecElapsedTime[i];
meanTime /= qVecElapsedTime.size();
qDebug() << "MNE calculation took" << meanTime << "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);
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);
InverseView view(minimumNorm.getSourceSpace(), t_qListLabels, t_qListRGBAs, 24, true, false, true);
if (view.stereoType() != QGLView::RedCyanAnaglyph)
view.camera()->setEyeSeparation(0.3f);
QStringList args = QCoreApplication::arguments();
int w_pos = args.indexOf("-width");
int h_pos = args.indexOf("-height");
if (w_pos >= 0 && h_pos >= 0)
{
bool ok = true;
int w = args.at(w_pos + 1).toInt(&ok);
if (!ok)
{
qWarning() << "Could not parse width argument:" << args;
return 1;
}
int h = args.at(h_pos + 1).toInt(&ok);
if (!ok)
{
qWarning() << "Could not parse height argument:" << args;
return 1;
}
view.resize(w, h);
}
else
{
view.resize(800, 600);
}
view.show();
//Push Estimate
view.pushSourceEstimate(sourceEstimate);
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();
}
/**
* 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[])
{
QCoreApplication app(argc, argv);
// Command Line Parser
QCommandLineParser parser;
parser.setApplicationDescription("Inverse MNE Example");
parser.addHelpOption();
QCommandLineOption evokedFileOption("ave", "Path to evoked <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
QCommandLineOption invFileOption("inv", "Path to inverse operator <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-meg-eeg-inv.fif");
QCommandLineOption snrOption("snr", "The <snr> value used for computation.", "snr", "1.0");
QCommandLineOption methodOption("method", "Inverse estimation <method>, i.e., 'MNE', 'dSPM' or 'sLORETA'.", "method", "dSPM");
QCommandLineOption stcFileOption("stcOut", "Path to stc <file>, which is to be written.", "file", "");
parser.addOption(evokedFileOption);
parser.addOption(invFileOption);
parser.addOption(snrOption);
parser.addOption(methodOption);
parser.addOption(stcFileOption);
parser.process(app);
QFile t_fileEvoked(parser.value(evokedFileOption));
QFile t_fileInv(parser.value(invFileOption));
float snr = parser.value(snrOption).toFloat();
QString method(parser.value(methodOption));
QString t_sFileNameStc(parser.value(stcFileOption));
double lambda2 = 1.0 / pow(snr, 2);
qDebug() << "Start calculation with: SNR" << snr << "; Lambda" << lambda2 << "; Method" << method << "; stc:" << t_sFileNameStc;
//
// Read the data first
//
fiff_int_t setno = 0;
QPair<QVariant, QVariant> baseline(QVariant(), 0);
FiffEvoked evoked(t_fileEvoked, setno, baseline);
if(evoked.isEmpty())
return 1;
//
// Then the inverse operator
//
MNEInverseOperator inverse_operator(t_fileInv);
//
// Compute inverse solution
//
MinimumNorm minimumNorm(inverse_operator, lambda2, method);
MNESourceEstimate sourceEstimate = minimumNorm.calculateInverse(evoked);
//
//Results
//
std::cout << "\npart ( block( 0, 0, 10, 10) ) of the inverse solution:\n" << sourceEstimate.data.block(0,0,10,10) << std::endl;
printf("tmin = %f s\n", sourceEstimate.tmin);
printf("tstep = %f s\n", sourceEstimate.tstep);
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileStc(t_sFileNameStc);
sourceEstimate.write(t_fileStc);
//test if everything was written correctly
MNESourceEstimate readSourceEstimate(t_fileStc);
std::cout << "\npart ( block( 0, 0, 10, 10) ) of the inverse solution:\n" << readSourceEstimate.data.block(0,0,10,10) << std::endl;
printf("tmin = %f s\n", readSourceEstimate.tmin);
printf("tstep = %f s\n", readSourceEstimate.tstep);
}
return 0;//app.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[])
{
QCoreApplication a(argc, argv);
// fname_data - Name of the data file
// setno - Data set number
// fname_inv - Inverse operator file name
// nave - Number of averages (scales the noise covariance)
// If negative, the number of averages in the data will be
// used
// lambda2 - The regularization factor
// dSPM - do dSPM?
// sLORETA - do sLORETA?
// QFile t_fileEvoked("./MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
// QFile t_fileInv("./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-meg-eeg-inv.fif");
QFile t_fileEvoked("E:/Data/sl_data/MEG/mind006/mind006_051209_auditory01_raw-ave.fif");
QFile t_fileInv("E:/Data/sl_data/MEG/mind006/mind006_051209_auditory01_raw-oct-6p-meg-inv.fif");
float snr = 1.0f;
QString method("dSPM"); //"MNE" | "dSPM" | "sLORETA"
QString t_sFileNameStc("");
// Parse command line parameters
for(qint32 i = 0; i < argc; ++i)
{
if(strcmp(argv[i], "-snr") == 0 || strcmp(argv[i], "--snr") == 0)
{
if(i + 1 < argc)
snr = atof(argv[i+1]);
}
else if(strcmp(argv[i], "-method") == 0 || strcmp(argv[i], "--method") == 0)
{
if(i + 1 < argc)
method = QString::fromUtf8(argv[i+1]);
}
else if(strcmp(argv[i], "-stc") == 0 || strcmp(argv[i], "--stc") == 0)
{
if(i + 1 < argc)
t_sFileNameStc = QString::fromUtf8(argv[i+1]);
}
}
double lambda2 = 1.0 / pow(snr, 2);
qDebug() << "Start calculation with: SNR" << snr << "; Lambda" << lambda2 << "; Method" << method << "; stc:" << t_sFileNameStc;
//
// Read the data first
//
fiff_int_t setno = 0;
QPair<QVariant, QVariant> baseline(QVariant(), 0);
FiffEvoked evoked(t_fileEvoked, setno, baseline);
if(evoked.isEmpty())
return 1;
//
// Then the inverse operator
//
MNEInverseOperator inverse_operator(t_fileInv);
//
// Compute inverse solution
//
MinimumNorm minimumNorm(inverse_operator, lambda2, method);
MNESourceEstimate sourceEstimate = minimumNorm.calculateInverse(evoked);
//
//Results
//
std::cout << "\npart ( block( 0, 0, 10, 10) ) of the inverse solution:\n" << sourceEstimate.data.block(0,0,10,10) << std::endl;
printf("tmin = %f s\n", sourceEstimate.tmin);
printf("tstep = %f s\n", sourceEstimate.tstep);
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileStc(t_sFileNameStc);
sourceEstimate.write(t_fileStc);
//test if everything was written correctly
MNESourceEstimate readSourceEstimate(t_fileStc);
std::cout << "\npart ( block( 0, 0, 10, 10) ) of the inverse solution:\n" << readSourceEstimate.data.block(0,0,10,10) << std::endl;
printf("tmin = %f s\n", readSourceEstimate.tmin);
printf("tstep = %f s\n", readSourceEstimate.tstep);
}
return 0;//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");
QFile t_fileFwd("./MNE-sample-data/MEG/sample/sample_audvis-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");
// 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");
// 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");
// QFile t_fileRaw("D:/Dropbox/Masterarbeit DB/Messdaten/mind006/mind006_051209_index01_raw.fif");
// QFile t_fileFwd("D:/Dropbox/Masterarbeit DB/Messdaten/mind006/mind006_051209_index01_raw-oct-6-fwd.fif");
// AnnotationSet t_annotationSet("D:/Dropbox/Masterarbeit DB/Messdaten/mind006/label/lh.aparc.a2009s.annot", "D:/Dropbox/Masterarbeit DB/Messdaten/mind006/label/rh.aparc.a2009s.annot");
// SurfaceSet t_surfSet("D:/Dropbox/Masterarbeit DB/Messdaten/mind006/surf/lh.white", "D:/Dropbox/Masterarbeit DB/Messdaten/mind006/surf/rh.white");
// QString t_sFileNameStc("D:/Dropbox/Masterarbeit DB/Messdaten/mind006/mind006_051209_index01_raw_RAP.stc");
// QFile t_fileRaw("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_03_17_Lorenz_Esch_010/Processed/averaged/EEG_data_001_voluntary_left_tapping_raw_Averaged_-1_1_108.fif");
// QFile t_fileFwd("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/Lorenz-140128-Duke128-fwd.fif");
// AnnotationSet t_annotationSet("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/atlas/lh.aparc.a2009s.annot", "D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/atlas/rh.aparc.a2009s.annot");
// SurfaceSet t_surfSet("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/surface/lh.white", "D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/surface/rh.white");
QString t_sFileNameStc("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_03_17_Lorenz_Esch_010/Processed/stc/EEG_data_001_voluntary_left_tapping_raw_Averaged_-1_1_108_RAP.stc");
// QFile t_fileRaw("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_02_04_Lorenz_Esch_005/Processed/averaged/EEG_data_002_voluntary_right_tapping_filtered_07_40_Averaged_-1_1_184.fif");
// QFile t_fileFwd("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/Lorenz-140128-Duke128-fwd.fif");
// AnnotationSet t_annotationSet("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/atlas/lh.aparc.a2009s.annot", "D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/atlas/rh.aparc.a2009s.annot");
// SurfaceSet t_surfSet("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/surface/lh.white", "D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/surface/rh.white");
// QString t_sFileNameStc("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_02_04_Lorenz_Esch_005/Processed/stc/EEG_data_002_voluntary_right_tapping_filtered_07_40_Averaged_-1_1_184_RAP.stc");
// QFile t_fileRaw("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_03_17_Lorenz_Esch_010/Processed/filtered/EEG_data_001_voluntary_left_right_tapping_filtered_07_40_raw.fif");
// QFile t_fileFwd("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/Lorenz-140128-Duke128-fwd.fif");
// AnnotationSet t_annotationSet("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/atlas/lh.aparc.a2009s.annot", "D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/atlas/rh.aparc.a2009s.annot");
// SurfaceSet t_surfSet("D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/surface/lh.white", "D:/Dropbox/Masterarbeit DB/Messdaten/Forward solutions/surface/rh.white");
// QString t_sFileNameStc("D:/Dropbox/Masterarbeit DB/Messdaten/EEG/2014_03_17_Lorenz_Esch_010/Processed/stc/EEG_data_001_voluntary_left_right_tapping_filtered_07_40_raw_RAP.stc");
qint32 numDipolePairs = 7;
qint32 samplesStcWindow = 300;
float stcOverlap = 0.0f;
qint32 startSample = 0;
qint32 numSample = 40000;
bool in_samples = true;
bool keep_comp = true;
// 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]);
}
}
//
// Read raw data
//
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
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);
QList<Label> t_qListLabelSelection;
//LH
t_qListLabelSelection << t_qListLabels[28] << t_qListLabels[29] << t_qListLabels[45] << t_qListLabels[66];
//RH
t_qListLabelSelection << t_qListLabels[103] << t_qListLabels[104] << t_qListLabels[120]<< t_qListLabels[141];
// std::cout << "t_qListLabels.size " << t_qListLabels.size() << std::endl;
// for(qint32 i = 0; i < t_qListLabels.size(); ++i)
// {
// qDebug() << "Num" << i << t_qListLabels[i].name;
// std::cout << t_qListLabels[i].hemi << std::endl;
// }
MNEForwardSolution t_SelectFwd = t_Fwd.pick_regions(t_qListLabelSelection);
//
// Setup for reading the raw data
//
FiffRawData raw(t_fileRaw);
float from = raw.first_samp + startSample;
float to = from + numSample - 1;
//
// Set up pick list: MEG + STI 014 - bad channels
//
QStringList include;
// include << "STI 014";
bool want_meg = false;
bool want_eeg = true;
bool want_stim = false;
RowVectorXi picks = raw.info.pick_types(want_meg, want_eeg, want_stim, include);//, raw.info.bads);
//
// Set up projection
//
qint32 k = 0;
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 = 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();
qint32 dest_comp = -1;
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 -1;
}
}
//
// Read a data segment
// times output argument is optional
//
bool readSuccessful = false;
MatrixXd data;
MatrixXd times;
if (in_samples)
readSuccessful = raw.read_raw_segment(data, times, (qint32)from, (qint32)to, picks);
else
readSuccessful = raw.read_raw_segment_times(data, times, from, to, picks);
if (!readSuccessful)
{
printf("Could not read raw segment.\n");
return -1;
}
printf("Read %d samples.\n",(qint32)data.cols());
//########################################################################################
// RAP MUSIC Source Estimate
//
// Cluster forward solution;
//
MNEForwardSolution t_clusteredFwd = t_SelectFwd.cluster_forward_solution(t_annotationSet, 20);//t_Fwd.cluster_forward_solution_ccr(t_annotationSet, 20);//40);
//
// Compute inverse solution
//
PwlRapMusic t_pwlRapMusic(t_clusteredFwd, false, numDipolePairs);
MNESourceEstimate sourceEstimate;
float tstep = 1.0f/raw.info.sfreq;
float tmin;
if(in_samples)
tmin = from * tstep;
else
tmin = from;
//
// Rap MUSIC Source estimate
//
sourceEstimate.data = MatrixXd::Zero(t_clusteredFwd.nsource, data.cols());
//Results
sourceEstimate.vertices = VectorXi(t_clusteredFwd.src[0].vertno.size() + t_clusteredFwd.src[1].vertno.size());
sourceEstimate.vertices << t_clusteredFwd.src[0].vertno, t_clusteredFwd.src[1].vertno;
sourceEstimate.times = RowVectorXf::Zero(data.cols());
sourceEstimate.times[0] = tmin;
for(qint32 i = 1; i < sourceEstimate.times.size(); ++i)
sourceEstimate.times[i] = sourceEstimate.times[i-1] + tstep;
sourceEstimate.tmin = tmin;
sourceEstimate.tstep = tstep;
bool first = true;
bool last = false;
qint32 t_iNumSensors = data.rows();
qint32 t_iNumSteps = data.cols();
qint32 t_iSamplesOverlap = (qint32)floor(((float)samplesStcWindow)*stcOverlap);
qint32 t_iSamplesDiscard = t_iSamplesOverlap/2;
MatrixXd measData = MatrixXd::Zero(t_iNumSensors, samplesStcWindow);
qint32 curSample = 0;
qint32 curResultSample = 0;
qint32 stcWindowSize = samplesStcWindow - 2*t_iSamplesDiscard;
while(!last)
{
//Data
if(curSample + samplesStcWindow >= t_iNumSteps) //last
{
last = true;
measData = data.block(0, data.cols()-samplesStcWindow, t_iNumSensors, samplesStcWindow);
}
else
measData = data.block(0, curSample, t_iNumSensors, samplesStcWindow);
curSample += (samplesStcWindow - t_iSamplesOverlap);
if(first)
curSample -= t_iSamplesDiscard; //shift on start t_iSamplesDiscard backwards
//Calculate
MNESourceEstimate stcData = t_pwlRapMusic.calculateInverse(measData, 0.0f, tstep);
//Assign Result
if(last)
stcWindowSize = stcData.data.cols() - curResultSample;
sourceEstimate.data.block(0,curResultSample,sourceEstimate.data.rows(),stcWindowSize) =
stcData.data.block(0,0,stcData.data.rows(),stcWindowSize);
curResultSample += stcWindowSize;
if(first)
first = false;
}
if(sourceEstimate.isEmpty())
return 1;
// Write stc to file
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileClusteredStc(t_sFileNameStc);
sourceEstimate.write(t_fileClusteredStc);
}
//Source Estimate end
//########################################################################################
View3D::SPtr testWindow = View3D::SPtr(new View3D());
testWindow->addBrainData("HemiLRSet", t_surfSet, t_annotationSet);
QList<BrainRTSourceLocDataTreeItem*> rtItemList = testWindow->addRtBrainData("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();
}
/**
* 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 a(argc, argv);
// QFile t_fileRaw("./MNE-sample-data/MEG/sample/sample_audvis_raw.fif");
// QFile t_fileFwd("./MNE-sample-data/MEG/sample/sample_audvis-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");
// 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");
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");
qint32 numDipolePairs = 7;
qint32 samplesStcWindow = 100;
float stcOverlap = 0.0f;
qint32 startSample = 0;
qint32 numSample = 20000;
bool in_samples = true;
bool keep_comp = true;
// 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]);
}
}
//
// Read raw data
//
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
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);
QList<Label> t_qListLabelSelection;
//LH
t_qListLabelSelection << t_qListLabels[28] << t_qListLabels[29] << t_qListLabels[45];
//RH
t_qListLabelSelection << t_qListLabels[103] << t_qListLabels[104] << t_qListLabels[120];
// std::cout << "t_qListLabelsTest.size " << t_qListLabelsTest.size() << std::endl;
// for(qint32 i = 0; i < t_qListLabelSelection.size(); ++i)
// {
// qDebug() << "Num" << i << t_qListLabelSelection[i].name;
// std::cout << t_qListLabelSelection[i].hemi << std::endl;
// }
MNEForwardSolution t_SelectFwd = t_Fwd.pick_regions(t_qListLabelSelection);
//
// Setup for reading the raw data
//
FiffRawData raw(t_fileRaw);
float from = raw.first_samp + startSample;
float to = from + numSample - 1;
//
// Set up pick list: MEG + STI 014 - bad channels
//
QStringList include;
// include << "STI 014";
bool want_meg = true;
bool want_eeg = false;
bool want_stim = false;
RowVectorXi picks = raw.info.pick_types(want_meg, want_eeg, want_stim, include);//, raw.info.bads);
//
// Set up projection
//
qint32 k = 0;
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 = 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();
qint32 dest_comp = -1;
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 -1;
}
}
//
// Read a data segment
// times output argument is optional
//
bool readSuccessful = false;
MatrixXd data;
MatrixXd times;
if (in_samples)
readSuccessful = raw.read_raw_segment(data, times, (qint32)from, (qint32)to, picks);
else
readSuccessful = raw.read_raw_segment_times(data, times, from, to, picks);
if (!readSuccessful)
{
printf("Could not read raw segment.\n");
return -1;
}
printf("Read %d samples.\n",(qint32)data.cols());
//########################################################################################
// RAP MUSIC Source Estimate
//
// Cluster forward solution;
//
MNEForwardSolution t_clusteredFwd = t_SelectFwd.cluster_forward_solution_ccr(t_annotationSet, 20);//t_Fwd.cluster_forward_solution_ccr(t_annotationSet, 20);//40);
//
// Compute inverse solution
//
PwlRapMusic t_pwlRapMusic(t_clusteredFwd, false, numDipolePairs);
MNESourceEstimate sourceEstimate;
float tstep = 1.0f/raw.info.sfreq;
float tmin;
if(in_samples)
tmin = from * tstep;
else
tmin = from;
//
// Rap MUSIC Source estimate
//
sourceEstimate.data = MatrixXd::Zero(t_clusteredFwd.nsource, data.cols());
//Results
sourceEstimate.vertices = VectorXi(t_clusteredFwd.src[0].vertno.size() + t_clusteredFwd.src[1].vertno.size());
sourceEstimate.vertices << t_clusteredFwd.src[0].vertno, t_clusteredFwd.src[1].vertno;
sourceEstimate.times = RowVectorXf::Zero(data.cols());
sourceEstimate.times[0] = tmin;
for(qint32 i = 1; i < sourceEstimate.times.size(); ++i)
sourceEstimate.times[i] = sourceEstimate.times[i-1] + tstep;
sourceEstimate.tmin = tmin;
sourceEstimate.tstep = tstep;
bool first = true;
bool last = false;
qint32 t_iNumSensors = data.rows();
qint32 t_iNumSteps = data.cols();
qint32 t_iSamplesOverlap = (qint32)floor(((float)samplesStcWindow)*stcOverlap);
qint32 t_iSamplesDiscard = t_iSamplesOverlap/2;
MatrixXd measData = MatrixXd::Zero(t_iNumSensors, samplesStcWindow);
qint32 curSample = 0;
qint32 curResultSample = 0;
qint32 stcWindowSize = samplesStcWindow - 2*t_iSamplesDiscard;
while(!last)
{
//Data
if(curSample + samplesStcWindow >= t_iNumSteps) //last
{
last = true;
measData = data.block(0, data.cols()-samplesStcWindow, t_iNumSensors, samplesStcWindow);
}
else
measData = data.block(0, curSample, t_iNumSensors, samplesStcWindow);
curSample += (samplesStcWindow - t_iSamplesOverlap);
if(first)
curSample -= t_iSamplesDiscard; //shift on start t_iSamplesDiscard backwards
//Calculate
MNESourceEstimate stcData = t_pwlRapMusic.calculateInverse(measData, 0.0f, tstep);
//Assign Result
if(last)
stcWindowSize = stcData.data.cols() - curResultSample;
sourceEstimate.data.block(0,curResultSample,sourceEstimate.data.rows(),stcWindowSize) =
stcData.data.block(0,0,stcData.data.rows(),stcWindowSize);
curResultSample += stcWindowSize;
if(first)
first = false;
}
if(sourceEstimate.isEmpty())
return 1;
//Source Estimate end
//########################################################################################
InverseView view(t_pwlRapMusic.getSourceSpace(), t_qListLabels, t_qListRGBAs, 24, true, false, false);//true);
if (view.stereoType() != QGLView::RedCyanAnaglyph)
view.camera()->setEyeSeparation(0.3f);
QStringList args = QCoreApplication::arguments();
int w_pos = args.indexOf("-width");
int h_pos = args.indexOf("-height");
if (w_pos >= 0 && h_pos >= 0)
{
bool ok = true;
int w = args.at(w_pos + 1).toInt(&ok);
if (!ok)
{
qWarning() << "Could not parse width argument:" << args;
return 1;
}
int h = args.at(h_pos + 1).toInt(&ok);
if (!ok)
{
qWarning() << "Could not parse height argument:" << args;
return 1;
}
view.resize(w, h);
}
else
{
view.resize(800, 600);
}
view.show();
//Push Estimate
view.pushSourceEstimate(sourceEstimate);
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 app(argc, argv);
// Command Line Parser
QCommandLineParser parser;
parser.setApplicationDescription("Clustered Inverse Example");
parser.addHelpOption();
QCommandLineOption sampleFwdFileOption("f", "Path to forward solution <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
QCommandLineOption sampleCovFileOption("c", "Path to covariance <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-cov.fif");
QCommandLineOption sampleEvokedFileOption("e", "Path to evoked <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
parser.addOption(sampleFwdFileOption);
parser.addOption(sampleCovFileOption);
parser.addOption(sampleEvokedFileOption);
parser.process(app);
//########################################################################################
// Source Estimate
QFile t_fileFwd(parser.value(sampleFwdFileOption));
QFile t_fileCov(parser.value(sampleCovFileOption));
QFile t_fileEvoked(parser.value(sampleEvokedFileOption));
double snr = 1.0f;//3.0f;//0.1f;//3.0f;
QString method("dSPM"); //"MNE" | "dSPM" | "sLORETA"
QString t_sFileNameClusteredInv("");
QString t_sFileNameStc("");
// Parse command line parameters
for(qint32 i = 0; i < argc; ++i)
{
if(strcmp(argv[i], "-snr") == 0 || strcmp(argv[i], "--snr") == 0)
{
if(i + 1 < argc)
snr = atof(argv[i+1]);
}
else if(strcmp(argv[i], "-method") == 0 || strcmp(argv[i], "--method") == 0)
{
if(i + 1 < argc)
method = QString::fromUtf8(argv[i+1]);
}
else if(strcmp(argv[i], "-inv") == 0 || strcmp(argv[i], "--inv") == 0)
{
if(i + 1 < argc)
t_sFileNameClusteredInv = QString::fromUtf8(argv[i+1]);
}
else if(strcmp(argv[i], "-stc") == 0 || strcmp(argv[i], "--stc") == 0)
{
if(i + 1 < argc)
t_sFileNameStc = QString::fromUtf8(argv[i+1]);
}
}
double lambda2 = 1.0 / pow(snr, 2);
qDebug() << "Start calculation with: SNR" << snr << "; Lambda" << lambda2 << "; Method" << method << "; stc:" << t_sFileNameStc;
// Load data
fiff_int_t setno = 0;
QPair<QVariant, QVariant> baseline(QVariant(), 0);
FiffEvoked evoked(t_fileEvoked, setno, baseline);
if(evoked.isEmpty())
return 1;
std::cout << "evoked first " << evoked.first << "; last " << evoked.last << std::endl;
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
// AnnotationSet t_annotationSet("./MNE-sample-data/subjects/sample/label/lh.aparc.a2009s.annot", "./MNE-sample-data/subjects/sample/label/rh.aparc.a2009s.annot");
// AnnotationSet t_annotationSet("/home/chdinh/sl_data/subjects/mind006/label/lh.aparc.a2009s.annot", "/home/chdinh/sl_data/subjects/mind006/label/rh.aparc.a2009s.annot");
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");
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;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 20);//40);
// std::cout << "Size " << t_clusteredFwd.sol->data.rows() << " x " << t_clusteredFwd.sol->data.cols() << std::endl;
// std::cout << "Clustered Fwd:\n" << t_clusteredFwd.sol->data.row(0) << std::endl;
//
// 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);
MNESourceEstimate sourceEstimate = minimumNorm.calculateInverse(evoked);
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
//########################################################################################
// SurfaceSet t_surfSet("./MNE-sample-data/subjects/sample/surf/lh.white", "./MNE-sample-data/subjects/sample/surf/rh.white");
// SurfaceSet t_surfSet("/home/chdinh/sl_data/subjects/mind006/surf/lh.white", "/home/chdinh/sl_data/subjects/mind006/surf/rh.white");
SurfaceSet t_surfSet("E:/Data/sl_data/subjects/mind006/surf/lh.white", "E:/Data/sl_data/subjects/mind006/surf/rh.white");
// //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("HemiLRSet", t_surfSet, t_annotationSet);
// QList<BrainRTSourceLocDataTreeItem*> rtItemList = testWindow->addRtBrainData("HemiLRSet", sourceEstimate, t_clusteredFwd);
// testWindow->show();
if(!t_sFileNameStc.isEmpty())
{
QFile t_fileClusteredStc(t_sFileNameStc);
sourceEstimate.write(t_fileClusteredStc);
}
//*/
return app.exec();//1;
}
/**
* 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 app(argc, argv);
// Command Line Parser
QCommandLineParser parser;
parser.setApplicationDescription("Compute Inverse Powell RAP-MUSIC Example");
parser.addHelpOption();
QCommandLineOption sampleFwdFileOption("f", "Path to forward solution <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif");
QCommandLineOption sampleEvokedFileOption("e", "Path to evoked <file>.", "file", "./MNE-sample-data/MEG/sample/sample_audvis-ave.fif");
QCommandLineOption sampleSubjectDirectoryOption("d", "Path to subject <directory>.", "directory", "./MNE-sample-data/subjects");
QCommandLineOption sampleSubjectOption("s", "Selected <subject>.", "subject", "sample");
QCommandLineOption stcFileOption("t", "Path to <target> where stc is stored to.", "target", "");//"RapMusic.stc");
QCommandLineOption numDipolePairsOption("n", "<number> of dipole pairs to localize.", "number", "7");
QCommandLineOption doMovieOption("m", "Create overlapping movie.");
parser.addOption(sampleFwdFileOption);
parser.addOption(sampleEvokedFileOption);
parser.addOption(sampleSubjectDirectoryOption);
parser.addOption(sampleSubjectOption);
parser.addOption(stcFileOption);
parser.addOption(numDipolePairsOption);
parser.addOption(doMovieOption);
parser.process(app);
//########################################################################################
// Source Estimate
QFile t_fileFwd(parser.value(sampleFwdFileOption));
QFile t_fileEvoked(parser.value(sampleEvokedFileOption));
QString subject(parser.value(sampleSubjectOption)); QString subjectDir(parser.value(sampleSubjectDirectoryOption));
AnnotationSet t_annotationSet(subject, 2, "aparc.a2009s", subjectDir);
SurfaceSet t_surfSet(subject, 2, "white", subjectDir);
QString t_sFileNameStc(parser.value(stcFileOption));
qint32 numDipolePairs = parser.value(numDipolePairsOption).toInt();
bool doMovie = parser.isSet(doMovieOption);
// 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]);
}else if(strcmp(argv[i], "-num") == 0 || strcmp(argv[i], "--num") == 0)
{
if(i + 1 < argc)
numDipolePairs = atof(argv[i+1]);
}
}
qDebug() << "Start calculation with stc:" << t_sFileNameStc;
// Load data
fiff_int_t setno = 0;
QPair<QVariant, QVariant> baseline(QVariant(), 0);
FiffEvoked evoked(t_fileEvoked, setno, baseline);
if(evoked.isEmpty())
return 1;
std::cout << "evoked first " << evoked.first << "; last " << evoked.last << std::endl;
MNEForwardSolution t_Fwd(t_fileFwd);
if(t_Fwd.isEmpty())
return 1;
QStringList ch_sel_names = t_Fwd.info.ch_names;
FiffEvoked pickedEvoked = evoked.pick_channels(ch_sel_names);
//
// Cluster forward solution;
//
MNEForwardSolution t_clusteredFwd = t_Fwd.cluster_forward_solution(t_annotationSet, 20);//40);
// std::cout << "Size " << t_clusteredFwd.sol->data.rows() << " x " << t_clusteredFwd.sol->data.cols() << std::endl;
// std::cout << "Clustered Fwd:\n" << t_clusteredFwd.sol->data.row(0) << std::endl;
PwlRapMusic t_pwlRapMusic(t_clusteredFwd, false, numDipolePairs);
if(doMovie)
t_pwlRapMusic.setStcAttr(200,0.5);
MNESourceEstimate sourceEstimate = t_pwlRapMusic.calculateInverse(pickedEvoked);
std::cout << "source estimated" << std::endl;
if(sourceEstimate.isEmpty())
return 1;
View3D::SPtr testWindow = View3D::SPtr(new View3D());
testWindow->addBrainData("HemiLRSet", t_surfSet, t_annotationSet);
QList<BrainRTSourceLocDataTreeItem*> rtItemList = testWindow->addRtBrainData("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 app.exec();
}
