bool MNEForwardSolution::read_one(FiffStream* p_pStream, const FiffDirTree& p_Node, MNEForwardSolution& one)
{
//
// Read all interesting stuff for one forward solution
//
if(p_Node.isEmpty())
return false;
one.clear();
FIFFLIB::FiffTag* t_pTag = NULL;
if(!p_Node.find_tag(p_pStream, FIFF_MNE_SOURCE_ORIENTATION, t_pTag))
{
p_pStream->device()->close();
std::cout << "Source orientation tag not found."; //ToDo: throw error.
return false;
}
one.source_ori = *t_pTag->toInt();
if(!p_Node.find_tag(p_pStream, FIFF_MNE_COORD_FRAME, t_pTag))
{
p_pStream->device()->close();
std::cout << "Coordinate frame tag not found."; //ToDo: throw error.
return false;
}
one.coord_frame = *t_pTag->toInt();
if(!p_Node.find_tag(p_pStream, FIFF_MNE_SOURCE_SPACE_NPOINTS, t_pTag))
{
p_pStream->device()->close();
std::cout << "Number of sources not found."; //ToDo: throw error.
return false;
}
one.nsource = *t_pTag->toInt();
if(!p_Node.find_tag(p_pStream, FIFF_NCHAN, t_pTag))
{
p_pStream->device()->close();
printf("Number of channels not found."); //ToDo: throw error.
return false;
}
one.nchan = *t_pTag->toInt();
if(p_pStream->read_named_matrix(p_Node, FIFF_MNE_FORWARD_SOLUTION, *one.sol.data()))
one.sol->transpose_named_matrix();
else
{
p_pStream->device()->close();
printf("Forward solution data not found ."); //ToDo: throw error.
//error(me,'Forward solution data not found (%s)',mne_omit_first_line(lasterr));
return false;
}
if(p_pStream->read_named_matrix(p_Node, FIFF_MNE_FORWARD_SOLUTION_GRAD, *one.sol_grad.data()))
one.sol_grad->transpose_named_matrix();
else
one.sol_grad->clear();
if (one.sol->data.rows() != one.nchan ||
(one.sol->data.cols() != one.nsource && one.sol->data.cols() != 3*one.nsource))
{
p_pStream->device()->close();
printf("Forward solution matrix has wrong dimensions.\n"); //ToDo: throw error.
//error(me,'Forward solution matrix has wrong dimensions');
return false;
}
if (!one.sol_grad->isEmpty())
{
if (one.sol_grad->data.rows() != one.nchan ||
(one.sol_grad->data.cols() != 3*one.nsource && one.sol_grad->data.cols() != 3*3*one.nsource))
{
p_pStream->device()->close();
printf("Forward solution gradient matrix has wrong dimensions.\n"); //ToDo: throw error.
//error(me,'Forward solution gradient matrix has wrong dimensions');
}
}
if (t_pTag)
delete t_pTag;
return true;
}
bool MNEInverseOperator::read_inverse_operator(QIODevice& p_IODevice, MNEInverseOperator& inv)
{
//
// Open the file, create directory
//
FiffStream::SPtr t_pStream(new FiffStream(&p_IODevice));
printf("Reading inverse operator decomposition from %s...\n",t_pStream->streamName().toUtf8().constData());
FiffDirTree t_Tree;
QList<FiffDirEntry> t_Dir;
if(!t_pStream->open(t_Tree, t_Dir))
return false;
//
// Find all inverse operators
//
QList <FiffDirTree> invs_list = t_Tree.dir_tree_find(FIFFB_MNE_INVERSE_SOLUTION);
if ( invs_list.size()== 0)
{
printf("No inverse solutions in %s\n", t_pStream->streamName().toUtf8().constData());
return false;
}
FiffDirTree* invs = &invs_list[0];
//
// Parent MRI data
//
QList <FiffDirTree> parent_mri = t_Tree.dir_tree_find(FIFFB_MNE_PARENT_MRI_FILE);
if (parent_mri.size() == 0)
{
printf("No parent MRI information in %s", t_pStream->streamName().toUtf8().constData());
return false;
}
printf("\tReading inverse operator info...");
//
// Methods and source orientations
//
FiffTag::SPtr t_pTag;
if (!invs->find_tag(t_pStream.data(), FIFF_MNE_INCLUDED_METHODS, t_pTag))
{
printf("Modalities not found\n");
return false;
}
inv = MNEInverseOperator();
inv.methods = *t_pTag->toInt();
//
if (!invs->find_tag(t_pStream.data(), FIFF_MNE_SOURCE_ORIENTATION, t_pTag))
{
printf("Source orientation constraints not found\n");
return false;
}
inv.source_ori = *t_pTag->toInt();
//
if (!invs->find_tag(t_pStream.data(), FIFF_MNE_SOURCE_SPACE_NPOINTS, t_pTag))
{
printf("Number of sources not found\n");
return false;
}
inv.nsource = *t_pTag->toInt();
inv.nchan = 0;
//
// Coordinate frame
//
if (!invs->find_tag(t_pStream.data(), FIFF_MNE_COORD_FRAME, t_pTag))
{
printf("Coordinate frame tag not found\n");
return false;
}
inv.coord_frame = *t_pTag->toInt();
//
// The actual source orientation vectors
//
if (!invs->find_tag(t_pStream.data(), FIFF_MNE_INVERSE_SOURCE_ORIENTATIONS, t_pTag))
{
printf("Source orientation information not found\n");
return false;
}
// if(inv.source_nn)
// delete inv.source_nn;
inv.source_nn = t_pTag->toFloatMatrix();
inv.source_nn.transposeInPlace();
printf("[done]\n");
//
// The SVD decomposition...
//
printf("\tReading inverse operator decomposition...");
if (!invs->find_tag(t_pStream.data(), FIFF_MNE_INVERSE_SING, t_pTag))
{
printf("Singular values not found\n");
return false;
}
// if(inv.sing)
// delete inv.sing;
inv.sing = Map<VectorXf>(t_pTag->toFloat(), t_pTag->size()/4).cast<double>();
inv.nchan = inv.sing.rows();
//
// The eigenleads and eigenfields
//
inv.eigen_leads_weighted = false;
if(!t_pStream->read_named_matrix(*invs, FIFF_MNE_INVERSE_LEADS, *inv.eigen_leads.data()))
{
inv.eigen_leads_weighted = true;
if(!t_pStream->read_named_matrix(*invs, FIFF_MNE_INVERSE_LEADS_WEIGHTED, *inv.eigen_leads.data()))
{
printf("Error reading eigenleads named matrix.\n");
return false;
}
}
//
// Having the eigenleads as columns is better for the inverse calculations
//
inv.eigen_leads->transpose_named_matrix();
if(!t_pStream->read_named_matrix(*invs, FIFF_MNE_INVERSE_FIELDS, *inv.eigen_fields.data()))
{
printf("Error reading eigenfields named matrix.\n");
return false;
}
printf("[done]\n");
//
// Read the covariance matrices
//
if(t_pStream->read_cov(*invs, FIFFV_MNE_NOISE_COV, *inv.noise_cov.data()))
{
printf("\tNoise covariance matrix read.\n");
}
else
{
printf("\tError: Not able to read noise covariance matrix.\n");
return false;
}
if(t_pStream->read_cov(*invs, FIFFV_MNE_SOURCE_COV, *inv.source_cov.data()))
{
printf("\tSource covariance matrix read.\n");
}
else
{
printf("\tError: Not able to read source covariance matrix.\n");
return false;
}
//
// Read the various priors
//
if(t_pStream->read_cov(*invs, FIFFV_MNE_ORIENT_PRIOR_COV, *inv.orient_prior.data()))
{
printf("\tOrientation priors read.\n");
}
else
inv.orient_prior->clear();
if(t_pStream->read_cov(*invs, FIFFV_MNE_DEPTH_PRIOR_COV, *inv.depth_prior.data()))
{
printf("\tDepth priors read.\n");
}
else
{
inv.depth_prior->clear();
}
if(t_pStream->read_cov(*invs, FIFFV_MNE_FMRI_PRIOR_COV, *inv.fmri_prior.data()))
{
printf("\tfMRI priors read.\n");
}
else
{
inv.fmri_prior->clear();
}
//
// Read the source spaces
//
if(!MNESourceSpace::readFromStream(t_pStream, false, t_Tree, inv.src))
{
printf("\tError: Could not read the source spaces.\n");
return false;
}
for (qint32 k = 0; k < inv.src.size(); ++k)
inv.src[k].id = MNESourceSpace::find_source_space_hemi(inv.src[k]);
//
// Get the MRI <-> head coordinate transformation
//
FiffCoordTrans mri_head_t;// = NULL;
if (!parent_mri[0].find_tag(t_pStream.data(), FIFF_COORD_TRANS, t_pTag))
{
printf("MRI/head coordinate transformation not found\n");
return false;
}
else
{
mri_head_t = t_pTag->toCoordTrans();
if (mri_head_t.from != FIFFV_COORD_MRI || mri_head_t.to != FIFFV_COORD_HEAD)
{
mri_head_t.invert_transform();
if (mri_head_t.from != FIFFV_COORD_MRI || mri_head_t.to != FIFFV_COORD_HEAD)
{
printf("MRI/head coordinate transformation not found");
// if(mri_head_t)
// delete mri_head_t;
return false;
}
}
}
inv.mri_head_t = mri_head_t;
//
// get parent MEG info
//
t_pStream->read_meas_info_base(t_Tree, inv.info);
//
// Transform the source spaces to the correct coordinate frame
// if necessary
//
if (inv.coord_frame != FIFFV_COORD_MRI && inv.coord_frame != FIFFV_COORD_HEAD)
printf("Only inverse solutions computed in MRI or head coordinates are acceptable");
//
// Number of averages is initially one
//
inv.nave = 1;
//
// We also need the SSP operator
//
inv.projs = t_pStream->read_proj(t_Tree);
//
// Some empty fields to be filled in later
//
// inv.proj = []; % This is the projector to apply to the data
// inv.whitener = []; % This whitens the data
// inv.reginv = []; % This the diagonal matrix implementing
// % regularization and the inverse
// inv.noisenorm = []; % These are the noise-normalization factors
//
if(!inv.src.transform_source_space_to(inv.coord_frame, mri_head_t))
{
printf("Could not transform source space.\n");
}
printf("\tSource spaces transformed to the inverse solution coordinate frame\n");
//
// Done!
//
return true;
}