/**
* 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);
// QFile t_fileIn("./MNE-sample-data/MEG/sample/sample_audvis_raw.fif");
// QFile t_fileIn("./MNE-sample-data/MEG/test_output.fif");
QFile t_fileIn("./MNE-sample-data/MEG/sample/sample_write/test_output.fif");
QFile t_fileOut("./MNE-sample-data/MEG/sample/sample_write/test_output2.fif");
// QFile t_fileOut("./MNE-sample-data/MEG/test_output2.fif");
//
// Setup for reading the raw data
//
FiffRawData raw(t_fileIn);
//
// Set up pick list: MEG + STI 014 - bad channels
//
//
bool want_meg = true;
bool want_eeg = false;
bool want_stim = false;
QStringList include;
include << "STI 014";
// MatrixXi picks = Fiff::pick_types(raw.info, want_meg, want_eeg, want_stim, include, raw.info.bads);
MatrixXi picks = raw.info.pick_types(want_meg, want_eeg, want_stim, include, raw.info.bads); // prefer member function
if(picks.cols() == 0)
{
include.clear();
include << "STI101" << "STI201" << "STI301";
// 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
if(picks.cols() == 0)
{
printf("channel list may need modification\n");
return -1;
}
}
//
RowVectorXd cals;
FiffStream::SPtr outfid = Fiff::start_writing_raw(t_fileOut,raw.info, cals/*, picks*/);
//
// Set up the reading parameters
//
fiff_int_t from = raw.first_samp;
fiff_int_t to = raw.last_samp;
float quantum_sec = 10.0f;//read and write in 10 sec junks
fiff_int_t quantum = ceil(quantum_sec*raw.info.sfreq);
//
// To read the whole file at once set
//
//quantum = to - from + 1;
//
//
// Read and write all the data
//
bool first_buffer = true;
fiff_int_t first, last;
MatrixXd data;
MatrixXd times;
for(first = from; first < to; first+=quantum)
{
last = first+quantum-1;
if (last > to)
{
last = to;
}
if (!raw.read_raw_segment(data,times,first,last/*,picks*/))
{
printf("error during read_raw_segment\n");
return -1;
}
//
// You can add your own miracle here
//
printf("Writing...");
if (first_buffer)
{
if (first > 0)
outfid->write_int(FIFF_FIRST_SAMPLE,&first);
first_buffer = false;
}
outfid->write_raw_buffer(data,cals);
printf("[done]\n");
}
outfid->finish_writing_raw();
printf("Finished\n");
return 0;//a.exec();
}
bool FiffDigPointSet::readFromStream(FiffStream::SPtr &p_pStream, FiffDigPointSet &p_Dig)
{
//
// Open the file, create directory
//
bool open_here = false;
if (!p_pStream->device()->isOpen()) {
QString t_sFileName = p_pStream->streamName();
if(!p_pStream->open())
return false;
printf("Opening header data %s...\n",t_sFileName.toUtf8().constData());
open_here = true;
}
//
// Read the measurement info
//
//read_hpi_info(p_pStream,p_Tree, info);
fiff_int_t kind = -1;
fiff_int_t pos = -1;
FiffTag::SPtr t_pTag;
//
// Locate the Electrodes
//
QList<FiffDirNode::SPtr> isotrak = p_pStream->dirtree()->dir_tree_find(FIFFB_ISOTRAK);
fiff_int_t coord_frame = FIFFV_COORD_HEAD;
FiffCoordTrans dig_trans;
qint32 k = 0;
if (isotrak.size() == 1)
{
for (k = 0; k < isotrak[0]->nent(); ++k)
{
kind = isotrak[0]->dir[k]->kind;
pos = isotrak[0]->dir[k]->pos;
if (kind == FIFF_DIG_POINT)
{
p_pStream->read_tag(t_pTag, pos);
p_Dig.m_qListDigPoint.append(t_pTag->toDigPoint());
}
else
{
if (kind == FIFF_MNE_COORD_FRAME)
{
p_pStream->read_tag(t_pTag, pos);
qDebug() << "NEEDS To BE DEBBUGED: FIFF_MNE_COORD_FRAME" << t_pTag->getType();
coord_frame = *t_pTag->toInt();
}
else if (kind == FIFF_COORD_TRANS)
{
p_pStream->read_tag(t_pTag, pos);
qDebug() << "NEEDS To BE DEBBUGED: FIFF_COORD_TRANS" << t_pTag->getType();
dig_trans = t_pTag->toCoordTrans();
}
}
}
}
for(k = 0; k < p_Dig.size(); ++k)
{
p_Dig[k].coord_frame = coord_frame;
}
//
// All kinds of auxliary stuff
//
if(open_here)
{
p_pStream->close();
}
return true;
}
bool FiffDirTree::copy_tree(FiffStream::SPtr p_pStreamIn, FiffId& in_id, QList<FiffDirTree>& p_Nodes, FiffStream::SPtr p_pStreamOut)
{
if(p_Nodes.size() <= 0)
return false;
qint32 k, p;
for(k = 0; k < p_Nodes.size(); ++k)
{
p_pStreamOut->start_block(p_Nodes[k].block);//8
if (p_Nodes[k].id.version != -1)
{
if (in_id.version != -1)
p_pStreamOut->write_id(FIFF_PARENT_FILE_ID, in_id);//9
p_pStreamOut->write_id(FIFF_BLOCK_ID);//10
p_pStreamOut->write_id(FIFF_PARENT_BLOCK_ID, p_Nodes[k].id);//11
}
for (p = 0; p < p_Nodes[k].nent; ++p)
{
//
// Do not copy these tags
//
if(p_Nodes[k].dir[p].kind == FIFF_BLOCK_ID || p_Nodes[k].dir[p].kind == FIFF_PARENT_BLOCK_ID || p_Nodes[k].dir[p].kind == FIFF_PARENT_FILE_ID)
continue;
//
// Read and write tags, pass data through transparently
//
if (!p_pStreamIn->device()->seek(p_Nodes[k].dir[p].pos)) //fseek(fidin, nodes(k).dir(p).pos, 'bof') == -1
{
printf("Could not seek to the tag\n");
return false;
}
//ToDo this is the same like read_tag
FiffTag::SPtr tag(new FiffTag());
//QDataStream in(fidin);
FiffStream::SPtr in = p_pStreamIn;
in->setByteOrder(QDataStream::BigEndian);
//
// Read fiff tag header from stream
//
*in >> tag->kind;
*in >> tag->type;
qint32 size;
*in >> size;
tag->resize(size);
*in >> tag->next;
//
// Read data when available
//
if (tag->size() > 0)
{
in->readRawData(tag->data(), tag->size());
FiffTag::convert_tag_data(tag,FIFFV_BIG_ENDIAN,FIFFV_NATIVE_ENDIAN);
}
//QDataStream out(p_pStreamOut);
FiffStream::SPtr out = p_pStreamOut;
out->setByteOrder(QDataStream::BigEndian);
*out << (qint32)tag->kind;
*out << (qint32)tag->type;
*out << (qint32)tag->size();
*out << (qint32)FIFFV_NEXT_SEQ;
out->writeRawData(tag->data(),tag->size());
}
for(p = 0; p < p_Nodes[k].nchild; ++p)
{
QList<FiffDirTree> childList;
childList << p_Nodes[k].children[p];
FiffDirTree::copy_tree(p_pStreamIn, in_id, childList, p_pStreamOut);
}
p_pStreamOut->end_block(p_Nodes[k].block);
}
return true;
}
