/**
* 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);
// Command Line Parser
QCommandLineParser parser;
parser.setApplicationDescription("Read Epochs 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 evokedIdxOption("aveIdx", "The average <index> to choose from the average file.", "index", "3");
QCommandLineOption pickAllOption("pickAll", "Pick all channels.", "pickAll", "true");
QCommandLineOption keepCompOption("keepComp", "Keep compensators.", "keepComp", "false");
QCommandLineOption destCompsOption("destComps", "<Destination> of the compensator which is to be calculated.", "destination", "0");
parser.addOption(inputOption);
parser.addOption(eventsFileOption);
parser.addOption(evokedIdxOption);
parser.addOption(pickAllOption);
parser.addOption(keepCompOption);
parser.addOption(destCompsOption);
parser.process(a);
//Load data
QString t_fileRawName = parser.value(inputOption);
QFile t_fileRaw(t_fileRawName);
qint32 event = parser.value(evokedIdxOption).toInt();
QString t_sEventName = parser.value(eventsFileOption);
float fTMin = -1.5f;
float fTMax = 1.5f;
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;
}
// Setup for reading the raw data
FiffRawData raw(t_fileRaw);
MNE::setup_compensators(raw, dest_comp, keep_comp);
RowVectorXi picks;
if (pick_all) {
// Pick all
picks.resize(raw.info.nchan);
for(qint32 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);
}
// Read the events
MatrixXi events;
MNE::read_events(t_sEventName,
t_fileRawName,
events);
// Read the epochs and reject epochs with EOG higher than 250e-06
MNEEpochDataList data = MNEEpochDataList::readEpochs(raw,
events,
fTMin,
fTMax,
event,
250.0*0.0000010,
"eog",
picks);
// Drop rejected epochs
data.dropRejected();
// Generate a evoked from the epochs
FiffEvoked evoked = data.average(raw.info,
raw.first_samp,
raw.last_samp);
return a.exec();
}
