bool FiffEvoked::read(QIODevice& p_IODevice, FiffEvoked& p_FiffEvoked, QVariant setno, QPair<QVariant,QVariant> baseline, bool proj, fiff_int_t p_aspect_kind)
{
p_FiffEvoked.clear();
//
// Open the file
//
FiffStream::SPtr t_pStream(new FiffStream(&p_IODevice));
QString t_sFileName = t_pStream->streamName();
printf("Reading %s ...\n",t_sFileName.toUtf8().constData());
FiffDirTree t_Tree;
QList<FiffDirEntry> t_Dir;
if(!t_pStream->open(t_Tree, t_Dir))
return false;
//
// Read the measurement info
//
FiffInfo info;
FiffDirTree meas;
if(!t_pStream->read_meas_info(t_Tree, info, meas))
return false;
info.filename = t_sFileName; //move fname storage to read_meas_info member function
//
// Locate the data of interest
//
QList<FiffDirTree> processed = meas.dir_tree_find(FIFFB_PROCESSED_DATA);
if (processed.size() == 0)
{
qWarning("Could not find processed data");
return false;
}
//
QList<FiffDirTree> evoked_node = meas.dir_tree_find(FIFFB_EVOKED);
if (evoked_node.size() == 0)
{
qWarning("Could not find evoked data");
return false;
}
// convert setno to an integer
if(!setno.isValid())
{
if (evoked_node.size() > 1)
{
QStringList comments;
QList<fiff_int_t> aspect_kinds;
QString t;
if(!t_pStream->get_evoked_entries(evoked_node, comments, aspect_kinds, t))
t = QString("None found, must use integer");
qWarning("%d datasets present, setno parameter must be set. Candidate setno names:\n%s", evoked_node.size(), t.toLatin1().constData());
return false;
}
else
setno = 0;
}
else
{
// find string-based entry
bool t_bIsInteger = true;
setno.toInt(&t_bIsInteger);
if(!t_bIsInteger)
{
if(p_aspect_kind != FIFFV_ASPECT_AVERAGE && p_aspect_kind != FIFFV_ASPECT_STD_ERR)
{
qWarning("kindStat must be \"FIFFV_ASPECT_AVERAGE\" or \"FIFFV_ASPECT_STD_ERR\"");
return false;
}
QStringList comments;
QList<fiff_int_t> aspect_kinds;
QString t;
t_pStream->get_evoked_entries(evoked_node, comments, aspect_kinds, t);
bool found = false;
for(qint32 i = 0; i < comments.size(); ++i)
{
if(comments[i].compare(setno.toString()) == 0 && p_aspect_kind == aspect_kinds[i])
{
setno = i;
found = true;
break;
}
}
if(!found)
{
qWarning() << "setno " << setno << " (" << p_aspect_kind << ") not found, out of found datasets:\n " << t;
return false;
}
}
}
if (setno.toInt() >= evoked_node.size() || setno.toInt() < 0)
{
qWarning("Data set selector out of range");
return false;
}
FiffDirTree my_evoked = evoked_node[setno.toInt()];
//
// Identify the aspects
//
QList<FiffDirTree> aspects = my_evoked.dir_tree_find(FIFFB_ASPECT);
if(aspects.size() > 1)
printf("\tMultiple (%d) aspects found. Taking first one.\n", aspects.size());
FiffDirTree my_aspect = aspects[0];
//
// Now find the data in the evoked block
//
fiff_int_t nchan = 0;
float sfreq = -1.0f;
QList<FiffChInfo> chs;
fiff_int_t kind, pos, first=0, last=0;
FiffTag::SPtr t_pTag;
QString comment("");
qint32 k;
for (k = 0; k < my_evoked.nent; ++k)
{
kind = my_evoked.dir[k].kind;
pos = my_evoked.dir[k].pos;
switch (kind)
{
case FIFF_COMMENT:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
comment = t_pTag->toString();
break;
case FIFF_FIRST_SAMPLE:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
first = *t_pTag->toInt();
break;
case FIFF_LAST_SAMPLE:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
last = *t_pTag->toInt();
break;
case FIFF_NCHAN:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
nchan = *t_pTag->toInt();
break;
case FIFF_SFREQ:
FiffTag::read_tag(t_pStream.data(),t_pTag,pos);
sfreq = *t_pTag->toFloat();
break;
case FIFF_CH_INFO:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
chs.append( t_pTag->toChInfo() );
break;
}
}
if (comment.isEmpty())
comment = QString("No comment");
//
// Local channel information?
//
if (nchan > 0)
{
if (chs.size() == 0)
{
qWarning("Local channel information was not found when it was expected.");
return false;
}
if (chs.size() != nchan)
{
qWarning("Number of channels and number of channel definitions are different.");
return false;
}
info.chs = chs;
info.nchan = nchan;
printf("\tFound channel information in evoked data. nchan = %d\n",nchan);
if (sfreq > 0.0f)
info.sfreq = sfreq;
}
qint32 nsamp = last-first+1;
printf("\tFound the data of interest:\n");
printf("\t\tt = %10.2f ... %10.2f ms (%s)\n", 1000*(float)first/info.sfreq, 1000*(float)last/info.sfreq,comment.toUtf8().constData());
if (info.comps.size() > 0)
printf("\t\t%d CTF compensation matrices available\n", info.comps.size());
//
// Read the data in the aspect block
//
fiff_int_t aspect_kind = -1;
fiff_int_t nave = -1;
QList<FiffTag> epoch;
for (k = 0; k < my_aspect.nent; ++k)
{
kind = my_aspect.dir[k].kind;
pos = my_aspect.dir[k].pos;
switch (kind)
{
case FIFF_COMMENT:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
comment = t_pTag->toString();
break;
case FIFF_ASPECT_KIND:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
aspect_kind = *t_pTag->toInt();
break;
case FIFF_NAVE:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
nave = *t_pTag->toInt();
break;
case FIFF_EPOCH:
FiffTag::read_tag(t_pStream.data(), t_pTag, pos);
epoch.append(FiffTag(t_pTag.data()));
break;
}
}
if (nave == -1)
nave = 1;
printf("\t\tnave = %d - aspect type = %d\n", nave, aspect_kind);
qint32 nepoch = epoch.size();
MatrixXd all_data;
if (nepoch == 1)
{
//
// Only one epoch
//
all_data = epoch[0].toFloatMatrix().cast<double>();
all_data.transposeInPlace();
//
// May need a transpose if the number of channels is one
//
if (all_data.cols() == 1 && info.nchan == 1)
all_data.transposeInPlace();
}
else
{
//
// Put the old style epochs together
//
all_data = epoch[0].toFloatMatrix().cast<double>();
all_data.transposeInPlace();
qint32 oldsize;
for (k = 1; k < nepoch; ++k)
{
oldsize = all_data.rows();
MatrixXd tmp = epoch[k].toFloatMatrix().cast<double>();
tmp.transposeInPlace();
all_data.conservativeResize(oldsize+tmp.rows(), all_data.cols());
all_data.block(oldsize, 0, tmp.rows(), tmp.cols()) = tmp;
}
}
if (all_data.cols() != nsamp)
{
qWarning("Incorrect number of samples (%d instead of %d)", (int) all_data.cols(), nsamp);
return false;
}
//
// Calibrate
//
printf("\n\tPreprocessing...\n");
printf("\t%d channels remain after picking\n",info.nchan);
typedef Eigen::Triplet<double> T;
std::vector<T> tripletList;
tripletList.reserve(info.nchan);
for(k = 0; k < info.nchan; ++k)
tripletList.push_back(T(k, k, info.chs[k].cal));
SparseMatrix<double> cals(info.nchan, info.nchan);
cals.setFromTriplets(tripletList.begin(), tripletList.end());
all_data = cals * all_data;
RowVectorXf times = RowVectorXf(last-first+1);
for (k = 0; k < times.size(); ++k)
times[k] = ((float)(first+k)) / info.sfreq;
//
// Set up projection
//
if(info.projs.size() == 0 || !proj)
{
printf("\tNo projector specified for these data.\n");
p_FiffEvoked.proj = MatrixXd();
}
else
{
// Create the projector
MatrixXd projection;
qint32 nproj = info.make_projector(projection);
if(nproj == 0)
{
printf("\tThe projection vectors do not apply to these channels\n");
p_FiffEvoked.proj = MatrixXd();
}
else
{
printf("\tCreated an SSP operator (subspace dimension = %d)\n", nproj);
p_FiffEvoked.proj = projection;
}
// The projection items have been activated
FiffProj::activate_projs(info.projs);
}
if(p_FiffEvoked.proj.rows() > 0)
{
all_data = p_FiffEvoked.proj * all_data;
printf("\tSSP projectors applied to the evoked data\n");
}
// Run baseline correction
all_data = MNEMath::rescale(all_data, times, baseline, QString("mean"));
printf("Applying baseline correction ... (mode: mean)");
// Put it all together
p_FiffEvoked.info = info;
p_FiffEvoked.nave = nave;
p_FiffEvoked.aspect_kind = aspect_kind;
p_FiffEvoked.first = first;
p_FiffEvoked.last = last;
p_FiffEvoked.comment = comment;
p_FiffEvoked.times = times;
p_FiffEvoked.data = all_data;
return true;
}
bool FiffEvokedSet::read(QIODevice& p_IODevice, FiffEvokedSet& p_FiffEvokedSet, QPair<QVariant,QVariant> baseline, bool proj)
{
p_FiffEvokedSet.clear();
//
// Open the file
//
FiffStream::SPtr t_pStream(new FiffStream(&p_IODevice));
QString t_sFileName = t_pStream->streamName();
printf("Exploring %s ...\n",t_sFileName.toUtf8().constData());
FiffDirTree t_Tree;
QList<FiffDirEntry> t_Dir;
if(!t_pStream->open(t_Tree, t_Dir))
return false;
//
// Read the measurement info
//
FiffDirTree meas;
if(!t_pStream->read_meas_info(t_Tree, p_FiffEvokedSet.info, meas))
return false;
p_FiffEvokedSet.info.filename = t_sFileName; //move fname storage to read_meas_info member function
//
// Locate the data of interest
//
QList<FiffDirTree> processed = meas.dir_tree_find(FIFFB_PROCESSED_DATA);
if (processed.size() == 0)
{
qWarning("Could not find processed data");
return false;
}
//
QList<FiffDirTree> evoked_node = meas.dir_tree_find(FIFFB_EVOKED);
if (evoked_node.size() == 0)
{
qWarning("Could not find evoked data");
return false;
}
QStringList comments;
QList<fiff_int_t> aspect_kinds;
QString t;
if(!t_pStream->get_evoked_entries(evoked_node, comments, aspect_kinds, t))
t = QString("None found, must use integer");
printf("\tFound %d datasets\n", evoked_node.size());
for(qint32 i = 0; i < comments.size(); ++i)
{
QFile t_file(p_FiffEvokedSet.info.filename);
printf(">> Processing %s <<\n", comments[i].toLatin1().constData());
FiffEvoked t_FiffEvoked;
if(FiffEvoked::read(t_file, t_FiffEvoked, i, baseline, proj))
p_FiffEvokedSet.evoked.push_back(t_FiffEvoked);
}
return true;
//### OLD MATLAB oriented implementation ###
// data.clear();
// if (setno < 0)
// {
// printf("Data set selector must be positive\n");
// return false;
// }
// //
// // Open the file
// //
// FiffStream::SPtr t_pStream(new FiffStream(&p_IODevice));
// QString t_sFileName = t_pStream->streamName();
// printf("Reading %s ...\n",t_sFileName.toUtf8().constData());
// FiffDirTree t_Tree;
// QList<FiffDirEntry> t_Dir;
// if(!t_pStream->open(t_Tree, t_Dir))
// {
// if(t_pStream)
// delete t_pStream;
// return false;
// }
// //
// // Read the measurement info
// //
// FiffInfo info;// = NULL;
// FiffDirTree meas;
// if(!t_pStream->read_meas_info(t_Tree, info, meas))
// return false;
// info.filename = t_sFileName; //move fname storage to read_meas_info member function
// //
// // Locate the data of interest
// //
// QList<FiffDirTree> processed = meas.dir_tree_find(FIFFB_PROCESSED_DATA);
// if (processed.size() == 0)
// {
// if(t_pStream)
// delete t_pStream;
// printf("Could not find processed data\n");
// return false;
// }
// //
// QList<FiffDirTree> evoked = meas.dir_tree_find(FIFFB_EVOKED);
// if (evoked.size() == 0)
// {
// if(t_pStream)
// delete t_pStream;
// printf("Could not find evoked data");
// return false;
// }
// //
// // Identify the aspects
// //
// fiff_int_t naspect = 0;
// fiff_int_t nsaspects = 0;
// qint32 oldsize = 0;
// MatrixXi is_smsh(1,0);
// QList< QList<FiffDirTree> > sets_aspects;
// QList< qint32 > sets_naspect;
// QList<FiffDirTree> saspects;
// qint32 k;
// for (k = 0; k < evoked.size(); ++k)
// {
//// sets(k).aspects = fiff_dir_tree_find(evoked(k),FIFF.FIFFB_ASPECT);
//// sets(k).naspect = length(sets(k).aspects);
// sets_aspects.append(evoked[k].dir_tree_find(FIFFB_ASPECT));
// sets_naspect.append(sets_aspects[k].size());
// if (sets_naspect[k] > 0)
// {
// oldsize = is_smsh.cols();
// is_smsh.conservativeResize(1, oldsize + sets_naspect[k]);
// is_smsh.block(0, oldsize, 1, sets_naspect[k]) = MatrixXi::Zero(1, sets_naspect[k]);
// naspect += sets_naspect[k];
// }
// saspects = evoked[k].dir_tree_find(FIFFB_SMSH_ASPECT);
// nsaspects = saspects.size();
// if (nsaspects > 0)
// {
// sets_naspect[k] += nsaspects;
// sets_aspects[k].append(saspects);
// oldsize = is_smsh.cols();
// is_smsh.conservativeResize(1, oldsize + sets_naspect[k]);
// is_smsh.block(0, oldsize, 1, sets_naspect[k]) = MatrixXi::Ones(1, sets_naspect[k]);
// naspect += nsaspects;
// }
// }
// printf("\t%d evoked data sets containing a total of %d data aspects in %s\n",evoked.size(),naspect,t_sFileName.toUtf8().constData());
// if (setno >= naspect || setno < 0)
// {
// if(t_pStream)
// delete t_pStream;
// printf("Data set selector out of range\n");
// return false;
// }
// //
// // Next locate the evoked data set
// //
// qint32 p = 0;
// qint32 a = 0;
// bool goon = true;
// FiffDirTree my_evoked;
// FiffDirTree my_aspect;
// for(k = 0; k < evoked.size(); ++k)
// {
// for (a = 0; a < sets_naspect[k]; ++a)
// {
// if(p == setno)
// {
// my_evoked = evoked[k];
// my_aspect = sets_aspects[k][a];
// goon = false;
// break;
// }
// ++p;
// }
// if (!goon)
// break;
// }
// //
// // The desired data should have been found but better to check
// //
// if (my_evoked.isEmpty() || my_aspect.isEmpty())
// {
// if(t_pStream)
// delete t_pStream;
// printf("Desired data set not found\n");
// return false;
// }
// //
// // Now find the data in the evoked block
// //
// fiff_int_t nchan = 0;
// float sfreq = -1.0f;
// QList<FiffChInfo> chs;
// fiff_int_t kind, pos, first, last;
// FiffTag* t_pTag = NULL;
// QString comment("");
// for (k = 0; k < my_evoked.nent; ++k)
// {
// kind = my_evoked.dir[k].kind;
// pos = my_evoked.dir[k].pos;
// switch (kind)
// {
// case FIFF_COMMENT:
// FiffTag::read_tag(t_pStream,t_pTag,pos);
// comment = t_pTag->toString();
// break;
// case FIFF_FIRST_SAMPLE:
// FiffTag::read_tag(t_pStream,t_pTag,pos);
// first = *t_pTag->toInt();
// break;
// case FIFF_LAST_SAMPLE:
// FiffTag::read_tag(t_pStream,t_pTag,pos);
// last = *t_pTag->toInt();
// break;
// case FIFF_NCHAN:
// FiffTag::read_tag(t_pStream,t_pTag,pos);
// nchan = *t_pTag->toInt();
// break;
// case FIFF_SFREQ:
// FiffTag::read_tag(t_pStream,t_pTag,pos);
// sfreq = *t_pTag->toFloat();
// break;
// case FIFF_CH_INFO:
// FiffTag::read_tag(t_pStream, t_pTag, pos);
// chs.append( t_pTag->toChInfo() );
// break;
// }
// }
// if (comment.isEmpty())
// comment = QString("No comment");
// //
// // Local channel information?
// //
// if (nchan > 0)
// {
// if (chs.size() == 0)
// {
// if(t_pStream)
// delete t_pStream;
// printf("Local channel information was not found when it was expected.\n");
// return false;
// }
// if (chs.size() != nchan)
// {
// if(t_pStream)
// delete t_pStream;
// printf("Number of channels and number of channel definitions are different\n");
// return false;
// }
// info.chs = chs;
// info.nchan = nchan;
// printf("\tFound channel information in evoked data. nchan = %d\n",nchan);
// if (sfreq > 0.0f)
// info.sfreq = sfreq;
// }
// qint32 nsamp = last-first+1;
// printf("\tFound the data of interest:\n");
// printf("\t\tt = %10.2f ... %10.2f ms (%s)\n", 1000*(float)first/info.sfreq, 1000*(float)last/info.sfreq,comment.toUtf8().constData());
// if (info.comps.size() > 0)
// printf("\t\t%d CTF compensation matrices available\n", info.comps.size());
// //
// // Read the data in the aspect block
// //
// fiff_int_t nepoch = 0;
// fiff_int_t aspect_kind = -1;
// fiff_int_t nave = -1;
// QList<FiffTag*> epoch;
// for (k = 0; k < my_aspect.nent; ++k)
// {
// kind = my_aspect.dir[k].kind;
// pos = my_aspect.dir[k].pos;
// switch (kind)
// {
// case FIFF_COMMENT:
// FiffTag::read_tag(t_pStream, t_pTag, pos);
// comment = t_pTag->toString();
// break;
// case FIFF_ASPECT_KIND:
// FiffTag::read_tag(t_pStream, t_pTag, pos);
// aspect_kind = *t_pTag->toInt();
// break;
// case FIFF_NAVE:
// FiffTag::read_tag(t_pStream, t_pTag, pos);
// nave = *t_pTag->toInt();
// break;
// case FIFF_EPOCH:
// FiffTag::read_tag(t_pStream, t_pTag, pos);
// epoch.append(new FiffTag(t_pTag));
// ++nepoch;
// break;
// }
// }
// if (nave == -1)
// nave = 1;
// printf("\t\tnave = %d aspect type = %d\n", nave, aspect_kind);
// if (nepoch != 1 && nepoch != info.nchan)
// {
// if(t_pStream)
// delete t_pStream;
// printf("Number of epoch tags is unreasonable (nepoch = %d nchan = %d)\n", nepoch, info.nchan);
// return false;
// }
// //
// MatrixXd all;// = NULL;
// if (nepoch == 1)
// {
// //
// // Only one epoch
// //
// all = epoch[0]->toFloatMatrix();
// all.transposeInPlace();
// //
// // May need a transpose if the number of channels is one
// //
// if (all.cols() == 1 && info.nchan == 1)
// all.transposeInPlace();
// }
// else
// {
// //
// // Put the old style epochs together
// //
// all = epoch[0]->toFloatMatrix();
// all.transposeInPlace();
// for (k = 2; k < nepoch; ++k)
// {
// oldsize = all.rows();
// MatrixXd tmp = epoch[k]->toFloatMatrix();
// tmp.transposeInPlace();
// all.conservativeResize(oldsize+tmp.rows(), all.cols());
// all.block(oldsize, 0, tmp.rows(), tmp.cols()) = tmp;
// }
// }
// if (all.cols() != nsamp)
// {
// if(t_pStream)
// delete t_pStream;
// printf("Incorrect number of samples (%d instead of %d)", (int)all.cols(), nsamp);
// return false;
// }
// //
// // Calibrate
// //
// typedef Eigen::Triplet<double> T;
// std::vector<T> tripletList;
// tripletList.reserve(info.nchan);
// for(k = 0; k < info.nchan; ++k)
// tripletList.push_back(T(k, k, info.chs[k].cal));
// SparseMatrix<double> cals(info.nchan, info.nchan);
// cals.setFromTriplets(tripletList.begin(), tripletList.end());
// all = cals * all;
// //
// // Put it all together
// //
// data.info = info;
//// if(data.evoked)
//// delete data.evoked;
// data.evoked.append(FiffEvokedData::SDPtr(new FiffEvokedData()));
// data.evoked[0]->aspect_kind = aspect_kind;
// data.evoked[0]->is_smsh = is_smsh(0,setno);
// if (nave != -1)
// data.evoked[0]->nave = nave;
// else
// data.evoked[0]->nave = 1;
// data.evoked[0]->first = first;
// data.evoked[0]->last = last;
// if (!comment.isEmpty())
// data.evoked[0]->comment = comment;
// //
// // Times for convenience and the actual epoch data
// //
// data.evoked[0]->times = MatrixXd(1, last-first+1);
// for (k = 0; k < data.evoked[0]->times.cols(); ++k)
// data.evoked[0]->times(0, k) = ((float)(first+k)) / info.sfreq;
//// if(data.evoked[0].epochs)
//// delete data.evoked[0]->epochs;
// data.evoked[0]->epochs = all;
// if(t_pStream)
// delete t_pStream;
// return true;
}