inv_dipole_fit_data.cpp

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//=============================================================================================================
 
//=============================================================================================================
// INCLUDES
//=============================================================================================================
 
#include <fwd/fwd_types.h>
 
#include "inv_dipole_fit_data.h"
#include "inv_guess_data.h"
#include <mne/mne_meas_data.h>
#include <mne/mne_meas_data_set.h>
#include <mne/mne_proj_item.h>
#include <mne/mne_cov_matrix.h>
#include "inv_ecd.h"
 
#include <fiff/fiff_stream.h>
#include <fiff/fiff_info.h>
#include <fiff/fiff_coord_trans.h>
#include <fwd/fwd_bem_model.h>
#include <mne/mne_surface.h>
 
#include <fwd/fwd_comp_data.h>
 
#include <math/simplex_algorithm.h>
#include <math/sphere.h>
 
#include <Eigen/Dense>
 
#include <QFile>
#include <QTextStream>
#include <QCoreApplication>
#include <QDebug>
 
#include <cmath>
 
using namespace Eigen;
using namespace FIFFLIB;
using namespace MNELIB;
using namespace FWDLIB;
using namespace INVLIB;
 
constexpr int FAIL = -1;
constexpr int OK = 0;
 
//=============================================================================================================
// DEFINE MEMBER METHODS
//=============================================================================================================
 
InvDipoleFitData::InvDipoleFitData()
: coord_frame(FIFFV_COORD_UNKNOWN)
, nmeg(0)
, neeg(0)
, r0(Eigen::Vector3f::Zero())
, funcs(nullptr)
, fixed_noise(false)
, nave(1)
, column_norm(COLUMN_NORM_NONE)
, fit_mag_dipoles(false)
, user(nullptr)
{
}
 
//=============================================================================================================
 
InvDipoleFitData::~InvDipoleFitData()
{
    // unique_ptr members auto-cleanup (including sphere_funcs, bem_funcs, mag_dipole_funcs)
}
 
//=============================================================================================================

int InvDipoleFitData::setup_forward_model(InvDipoleFitData* d, MNECTFCompDataSet* comp_data, FwdCoilSet* comp_coils)
{
    dipoleFitFuncsRec* f;
    int fit_sphere_to_bem = true;
 
    if (!d->bemname.isEmpty()) {
        /*
         * Set up the boundary-element model
         */
        QString bemsolname = FwdBemModel::fwd_bem_make_bem_sol_name(d->bemname);
        d->bemname = bemsolname;
 
        qInfo("\nSetting up the BEM model using %s...", d->bemname.toUtf8().constData());
        qInfo("\nLoading surfaces...");
        d->bem_model = FwdBemModel::fwd_bem_load_three_layer_surfaces(d->bemname);
        if (d->bem_model) {
            qInfo("Three-layer model surfaces loaded.");
        } else {
            d->bem_model = FwdBemModel::fwd_bem_load_homog_surface(d->bemname);
            if (!d->bem_model)
                return FAIL;
            qInfo("Homogeneous model surface loaded.");
        }
        if (d->neeg > 0 && d->bem_model->nsurf == 1) {
            qCritical("Cannot use a homogeneous model in EEG calculations.");
            return FAIL;
        }
        qInfo("\nLoading the solution matrix...");
        if (d->bem_model->fwd_bem_load_recompute_solution(d->bemname, FWD_BEM_UNKNOWN, false) == FAIL)
            return FAIL;
        qInfo("Employing the head->MRI coordinate transform with the BEM model.");
        Q_ASSERT(d->mri_head_t);
        if (d->bem_model->fwd_bem_set_head_mri_t(*d->mri_head_t) == FAIL)
            return FAIL;
        qInfo("BEM model %s is now set up", d->bem_model->sol_name.toUtf8().constData());
        /*
         * Find the best-fitting sphere
         */
        if (fit_sphere_to_bem) {
            MNESurface* inner_skull;
            float simplex_size = 2e-2f;
            float R;
            VectorXf r0_vec;
 
            if ((inner_skull = d->bem_model->fwd_bem_find_surface(FIFFV_BEM_SURF_ID_BRAIN)) == nullptr)
                return FAIL;
 
            if (!UTILSLIB::Sphere::fit_sphere_to_points(inner_skull->rr, simplex_size, r0_vec, R))
                return FAIL;
            d->r0 = r0_vec.head<3>();
 
            FiffCoordTrans::apply_trans(d->r0.data(), *d->mri_head_t, true);
            qInfo("Fitted sphere model origin : %6.1f %6.1f %6.1f mm rad = %6.1f mm.",
                  1000 * d->r0[0], 1000 * d->r0[1], 1000 * d->r0[2], 1000 * R);
        }
        d->bem_funcs = std::make_unique<dipoleFitFuncsRec>();
        f = d->bem_funcs.get();
        if (d->nmeg > 0) {
            /*
           * Use the new compensated field computation
           * It works the same way independent of whether or not the compensation is in effect
           */
            auto comp = FwdCompData::fwd_make_comp_data(comp_data, d->meg_coils.get(), comp_coils,
                                                        FwdBemModel::fwd_bem_field, nullptr, nullptr, d->bem_model.get());
            if (!comp)
                return FAIL;
            qInfo("Compensation setup done.");
 
            qInfo("MEG solution matrix...");
            if (d->bem_model->fwd_bem_specify_coils(d->meg_coils.get()) == FAIL)
                return FAIL;
            if (d->bem_model->fwd_bem_specify_coils(comp->comp_coils.get()) == FAIL)
                return FAIL;
            qInfo("[done]");
 
            f->meg_field = FwdCompData::fwd_comp_field;
            f->meg_vec_field = nullptr;
            f->meg_client = comp.get();
            f->meg_comp = std::move(comp);
        }
        if (d->neeg > 0) {
            qInfo("\tEEG solution matrix...");
            if (d->bem_model->fwd_bem_specify_els(d->eeg_els.get()) == FAIL)
                return FAIL;
            qInfo("[done]");
            f->eeg_pot = FwdBemModel::fwd_bem_pot_els;
            f->eeg_vec_pot = nullptr;
            f->eeg_client = d->bem_model.get();
        }
    }
    if (d->neeg > 0 && !d->eeg_model) {
        qCritical("EEG sphere model not defined.");
        return FAIL;
    }
    d->sphere_funcs = std::make_unique<dipoleFitFuncsRec>();
    f = d->sphere_funcs.get();
    if (d->neeg > 0) {
        d->eeg_model->r0 = d->r0;
        f->eeg_pot = FwdEegSphereModel::fwd_eeg_spherepot_coil;
        f->eeg_vec_pot = FwdEegSphereModel::fwd_eeg_spherepot_coil_vec;
        f->eeg_client = d->eeg_model.get();
    }
    if (d->nmeg > 0) {
        /*
         * Use the new compensated field computation
         * It works the same way independent of whether or not the compensation is in effect
         */
        auto comp = FwdCompData::fwd_make_comp_data(comp_data, d->meg_coils.get(), comp_coils,
                                                    FwdBemModel::fwd_sphere_field,
                                                    FwdBemModel::fwd_sphere_field_vec,
                                                    nullptr,
                                                    d->r0.data());
        if (!comp)
            return FAIL;
        f->meg_field = FwdCompData::fwd_comp_field;
        f->meg_vec_field = FwdCompData::fwd_comp_field_vec;
        f->meg_client = comp.get();
        f->meg_comp = std::move(comp);
    }
    qInfo("Sphere model origin : %6.1f %6.1f %6.1f mm.",
          1000 * d->r0[0], 1000 * d->r0[1], 1000 * d->r0[2]);
    /*
       * Finally add the magnetic dipole fitting functions (for special purposes)
       */
    d->mag_dipole_funcs = std::make_unique<dipoleFitFuncsRec>();
    f = d->mag_dipole_funcs.get();
    if (d->nmeg > 0) {
        /*
         * Use the new compensated field computation
         * It works the same way independent of whether or not the compensation is in effect
         */
        auto comp = FwdCompData::fwd_make_comp_data(comp_data, d->meg_coils.get(), comp_coils,
                                                    FwdBemModel::fwd_mag_dipole_field,
                                                    FwdBemModel::fwd_mag_dipole_field_vec,
                                                    nullptr,
                                                    nullptr);
        if (!comp)
            return FAIL;
        f->meg_field = FwdCompData::fwd_comp_field;
        f->meg_vec_field = FwdCompData::fwd_comp_field_vec;
        f->meg_client = comp.get();
        f->meg_comp = std::move(comp);
    }
    f->eeg_pot = FwdBemModel::fwd_mag_dipole_field;
    f->eeg_vec_pot = FwdBemModel::fwd_mag_dipole_field_vec;
    /*
        * Select the appropriate fitting function
        */
    d->funcs = !d->bemname.isEmpty() ? d->bem_funcs.get() : d->sphere_funcs.get();
 
    return OK;
}
 
//=============================================================================================================

std::unique_ptr<MNECovMatrix> InvDipoleFitData::ad_hoc_noise(FwdCoilSet* meg, FwdCoilSet* eeg, float grad_std, float mag_std, float eeg_std)
{
    int nchan;
    Eigen::VectorXd stds;
    QStringList names, ch_names;
    int k, n;
 
    qInfo("Using standard noise values "
          "(MEG grad : %6.1f fT/cm MEG mag : %6.1f fT EEG : %6.1f uV)\n",
          1e13 * grad_std, 1e15 * mag_std, 1e6 * eeg_std);
 
    nchan = 0;
    if (meg)
        nchan = nchan + meg->ncoil();
    if (eeg)
        nchan = nchan + eeg->ncoil();
 
    stds.resize(nchan);
 
    n = 0;
    if (meg) {
        for (k = 0; k < meg->ncoil(); k++, n++) {
            if (meg->coils[k]->is_axial_coil()) {
                stds[n] = static_cast<double>(mag_std) * mag_std;
#ifdef TEST_REF
                if (meg->coils[k]->type == FIFFV_COIL_CTF_REF_MAG ||
                    meg->coils[k]->type == FIFFV_COIL_CTF_REF_GRAD ||
                    meg->coils[k]->type == FIFFV_COIL_CTF_REF_GOFF)
                    stds[n] = 1e6 * stds[n];
#endif
            } else
                stds[n] = static_cast<double>(grad_std) * grad_std;
            ch_names.append(meg->coils[k]->chname);
        }
    }
    if (eeg) {
        for (k = 0; k < eeg->ncoil(); k++, n++) {
            stds[n] = static_cast<double>(eeg_std) * eeg_std;
            ch_names.append(eeg->coils[k]->chname);
        }
    }
    names = ch_names;
    return MNECovMatrix::create(FIFFV_MNE_NOISE_COV, nchan, names, Eigen::VectorXd(), stds);
}
 
//=============================================================================================================
 
int InvDipoleFitData::scale_noise_cov(InvDipoleFitData* f, int nave)
{
    float nave_ratio = static_cast<float>(f->nave) / static_cast<float>(nave);
    int k;
 
    if (!f->noise)
        return OK;
 
    if (f->noise->cov.size() > 0) {
        qInfo("Decomposing the sensor noise covariance matrix...");
        if (f->noise->decompose_eigen() == FAIL)
            return FAIL;
 
        for (k = 0; k < f->noise->ncov * (f->noise->ncov + 1) / 2; k++)
            f->noise->cov[k] = nave_ratio * f->noise->cov[k];
        for (k = 0; k < f->noise->ncov; k++) {
            f->noise->lambda[k] = nave_ratio * f->noise->lambda[k];
            if (f->noise->lambda[k] < 0.0)
                f->noise->lambda[k] = 0.0;
        }
        if (f->noise->add_inv() == FAIL)
            return FAIL;
    } else {
        for (k = 0; k < f->noise->ncov; k++)
            f->noise->cov_diag[k] = nave_ratio * f->noise->cov_diag[k];
        qInfo("Decomposition not needed for a diagonal noise covariance matrix.");
        if (f->noise->add_inv() == FAIL)
            return FAIL;
    }
    qInfo("Effective nave is now %d", nave);
    f->nave = nave;
    return OK;
}
 
//=============================================================================================================
 
int InvDipoleFitData::scale_dipole_fit_noise_cov(InvDipoleFitData* f, int nave)
{
    float nave_ratio = static_cast<float>(f->nave) / static_cast<float>(nave);
    int k;
 
    if (!f->noise)
        return OK;
    if (f->fixed_noise)
        return OK;
 
    if (f->noise->cov.size() > 0) {
        /*
         * Do the decomposition and check that the matrix is positive definite
         */
        qInfo("Decomposing the noise covariance...");
        if (f->noise->cov.size() > 0) {
            if (f->noise->decompose_eigen() == FAIL)
                return FAIL;
            for (k = 0; k < f->noise->ncov; k++) {
                if (f->noise->lambda[k] < 0.0)
                    f->noise->lambda[k] = 0.0;
            }
        }
        for (k = 0; k < f->noise->ncov * (f->noise->ncov + 1) / 2; k++)
            f->noise->cov[k] = nave_ratio * f->noise->cov[k];
        for (k = 0; k < f->noise->ncov; k++) {
            f->noise->lambda[k] = nave_ratio * f->noise->lambda[k];
            if (f->noise->lambda[k] < 0.0)
                f->noise->lambda[k] = 0.0;
        }
        if (f->noise->add_inv() == FAIL)
            return FAIL;
    } else {
        for (k = 0; k < f->noise->ncov; k++)
            f->noise->cov_diag[k] = nave_ratio * f->noise->cov_diag[k];
        qInfo("Decomposition not needed for a diagonal noise covariance matrix.");
        if (f->noise->add_inv() == FAIL)
            return FAIL;
    }
    qInfo("Effective nave is now %d", nave);
    f->nave = nave;
    return OK;
}
 
//=============================================================================================================

int InvDipoleFitData::select_dipole_fit_noise_cov(InvDipoleFitData* f,
                                                  MNEMeasData* meas,
                                                  int nave_in,
                                                  const int* sels)
{
    int nave, j, k;
    float nonsel_w = 30;
    int min_nchan = 20;
 
    if (!f || !f->noise_orig)
        return OK;
    if (!meas)
        nave = 1;
    else {
        if (nave_in < 0)
            nave = meas->current->nave;
        else
            nave = nave_in;
    }
    /*
     * Channel selection
     */
    if (meas && sels) {
        std::vector<float> wVec(f->noise_orig->ncov);
        float* w = wVec.data();
        int nomit_meg, nomit_eeg, nmeg, neeg;
 
        nmeg = neeg = 0;
        nomit_meg = nomit_eeg = 0;
        for (k = 0; k < f->noise_orig->ncov; k++) {
            if (f->noise_orig->ch_class[k] == MNE_COV_CH_EEG)
                neeg++;
            else
                nmeg++;
            /* Check whether this channel is selected in the measurement */
            bool selected = false;
            for (int c = 0; c < meas->nchan; c++) {
                if (QString::compare(f->noise_orig->names[k],
                                     meas->chs[c].ch_name,
                                     Qt::CaseInsensitive) == 0) {
                    selected = sels[c] != 0;
                    break;
                }
            }
            if (selected)
                w[k] = 1.0;
            else {
                w[k] = nonsel_w;
                if (f->noise_orig->ch_class[k] == MNE_COV_CH_EEG)
                    nomit_eeg++;
                else
                    nomit_meg++;
            }
        }
        f->noise.reset();
        if (nmeg > 0 && nmeg - nomit_meg > 0 && nmeg - nomit_meg < min_nchan) {
            qCritical("Too few MEG channels remaining");
            return FAIL;
        }
        if (neeg > 0 && neeg - nomit_eeg > 0 && neeg - nomit_eeg < min_nchan) {
            qCritical("Too few EEG channels remaining");
            return FAIL;
        }
        f->noise = f->noise_orig->dup();
        if (nomit_meg + nomit_eeg > 0) {
            if (f->noise->cov.size() > 0) {
                for (j = 0; j < f->noise->ncov; j++)
                    for (k = 0; k <= j; k++) {
                        f->noise->cov[MNECovMatrix::lt_packed_index(j, k)] *= static_cast<double>(w[j]) * w[k];
                    }
            } else {
                for (j = 0; j < f->noise->ncov; j++) {
                    f->noise->cov_diag[j] *= static_cast<double>(w[j]) * w[j];
                }
            }
        }
    } else {
        if (f->noise && f->nave == nave)
            return OK;
        f->noise = f->noise_orig->dup();
    }
 
    return scale_dipole_fit_noise_cov(f, nave);
}
 
//=============================================================================================================

InvDipoleFitData* InvDipoleFitData::setup_dipole_fit_data(const QString& mriname,
                                                          const QString& measname,
                                                          const QString& bemname,
                                                          Vector3f* r0,
                                                          FwdEegSphereModel* eeg_model,
                                                          int accurate_coils,
                                                          const QString& badname,
                                                          const QString& noisename,
                                                          float grad_std,
                                                          float mag_std,
                                                          float eeg_std,
                                                          float mag_reg,
                                                          float grad_reg,
                                                          float eeg_reg,
                                                          int diagnoise,
                                                          const QList<QString>& projnames,
                                                          int include_meg,
                                                          int include_eeg)
{
    auto res = std::make_unique<InvDipoleFitData>();
    QStringList badlist;
    int nbad = 0;
    QStringList file_bads;
    int file_nbad = 0;
    int coord_frame = FIFFV_COORD_HEAD;
    std::unique_ptr<MNECovMatrix> cov;
    std::unique_ptr<FwdCoilSet> templates;
    std::unique_ptr<MNECTFCompDataSet> comp_data;
    std::unique_ptr<FwdCoilSet> comp_coils;
 
    /*
       * Read the coordinate transformations
       */
    if (!mriname.isEmpty()) {
        res->mri_head_t = std::make_unique<FiffCoordTrans>(FiffCoordTrans::readMriTransform(mriname));
        if (res->mri_head_t->isEmpty())
            return nullptr;
    } else if (!bemname.isEmpty()) {
        qWarning("Source of MRI / head transform required for the BEM model is missing");
        return nullptr;
    } else {
        float move[] = {0.0, 0.0, 0.0};
        float rot[3][3] = {{1.0, 0.0, 0.0},
                           {0.0, 1.0, 0.0},
                           {0.0, 0.0, 1.0}};
        Eigen::Matrix3f rotMat;
        rotMat << rot[0][0], rot[0][1], rot[0][2],
            rot[1][0], rot[1][1], rot[1][2],
            rot[2][0], rot[2][1], rot[2][2];
        Eigen::Vector3f moveVec = Eigen::Map<Eigen::Vector3f>(move);
        res->mri_head_t = std::make_unique<FiffCoordTrans>(FIFFV_COORD_MRI, FIFFV_COORD_HEAD, rotMat, moveVec);
    }
 
    res->mri_head_t->print();
    res->meg_head_t = std::make_unique<FiffCoordTrans>(FiffCoordTrans::readMeasTransform(measname));
    if (res->meg_head_t->isEmpty())
        return nullptr;
    res->meg_head_t->print();
    /*
       * Read the bad channel lists
       */
    if (!badname.isEmpty()) {
        if (!FiffInfoBase::readBadChannelsFromFile(badname, badlist))
            return nullptr;
        nbad = badlist.size();
        qInfo("%d bad channels read from %s.", nbad, badname.toUtf8().data());
    }
    {
        QFile measFile(measname);
        FiffStream::SPtr measStream(new FiffStream(&measFile));
        if (measStream->open()) {
            file_bads = measStream->read_bad_channels(measStream->dirtree());
            file_nbad = file_bads.size();
            measStream->close();
        }
    }
    if (file_nbad > 0) {
        if (badlist.isEmpty())
            nbad = 0;
        for (int k = 0; k < file_nbad; k++) {
            badlist.append(file_bads[k]);
            nbad++;
        }
        file_bads.clear();
        qInfo("%d bad channels read from the data file.", file_nbad);
    }
    qInfo("%d bad channels total.", nbad);
    /*
       * Read the channel information
       */
    if (!FiffInfo::readMegEegChannels(measname,
                                      include_meg,
                                      include_eeg,
                                      badlist,
                                      res->chs,
                                      res->nmeg,
                                      res->neeg))
        return nullptr;
 
    if (res->nmeg > 0)
        qInfo("Will use %3d MEG channels from %s", res->nmeg, measname.toUtf8().data());
    if (res->neeg > 0)
        qInfo("Will use %3d EEG channels from %s", res->neeg, measname.toUtf8().data());
    {
        int nch_total = res->nmeg + res->neeg;
        res->ch_names.clear();
        for (int i = 0; i < nch_total; i++)
            res->ch_names.append(res->chs[i].ch_name);
    }
    /*
       * Make coil definitions
       */
    res->coord_frame = coord_frame;
    if (coord_frame == FIFFV_COORD_HEAD) {
        //#ifdef USE_SHARE_PATH
        //        char *coilfile = mne_compose_mne_name("share/mne","coil_def.dat");
        //#else
        //    const char *path = "setup/mne";
        //    const char *filename = "coil_def.dat";
        //    const char *coilfile = mne_compose_mne_name(path,filename);
 
        //    QString qPath("/usr/pubsw/packages/mne/stable/share/mne/coil_def.dat");
 
        QString qPath = QString(QCoreApplication::applicationDirPath() + "/../resources/general/coilDefinitions/coil_def.dat");
        QFile file(qPath);
        if (!QCoreApplication::startingUp())
            qPath = QCoreApplication::applicationDirPath() + QString("/../resources/general/coilDefinitions/coil_def.dat");
        else if (!file.exists())
            qPath = "../resources/general/coilDefinitions/coil_def.dat";
 
        QByteArray coilfileBytes = qPath.toUtf8();
        const char* coilfile = coilfileBytes.constData();
        //#endif
 
        if (!coilfile)
            return nullptr;
        templates = FwdCoilSet::read_coil_defs(coilfile);
        if (!templates) {
            return nullptr;
        }
 
        Q_ASSERT(res->meg_head_t);
        res->meg_coils = templates->create_meg_coils(res->chs,
                                                     res->nmeg,
                                                     accurate_coils ? FWD_COIL_ACCURACY_ACCURATE : FWD_COIL_ACCURACY_NORMAL,
                                                     *res->meg_head_t);
        if (!res->meg_coils)
            return nullptr;
        res->eeg_els = FwdCoilSet::create_eeg_els(res->chs.mid(res->nmeg),
                                                  res->neeg);
        if (!res->eeg_els)
            return nullptr;
        qInfo("Head coordinate coil definitions created.");
    } else {
        qWarning("Cannot handle computations in %s coordinates", FiffCoordTrans::frame_name(coord_frame).toUtf8().constData());
        return nullptr;
    }
    /*
       * Forward model setup
       */
    res->bemname = bemname;
    if (r0) {
        res->r0 = *r0;
    }
    res->eeg_model.reset(eeg_model);
    /*
       * Compensation data
       */
    comp_data = MNECTFCompDataSet::read(measname);
    if (!comp_data)
        return nullptr;
    if (comp_data->ncomp > 0) { /* Compensation channel information may be needed */
        QList<FiffChInfo> comp_chs;
        int ncomp = 0;
 
        qInfo("%d compensation data sets in %s", comp_data->ncomp, measname.toUtf8().data());
        {
            QFile compFile(measname);
            FiffStream::SPtr compStream(new FiffStream(&compFile));
            if (!compStream->open())
                return nullptr;
            FiffInfo compInfo;
            FiffDirNode::SPtr compInfoNode;
            if (!compStream->read_meas_info(compStream->dirtree(), compInfo, compInfoNode)) {
                compStream->close();
                return nullptr;
            }
            compStream->close();
            for (int k = 0; k < compInfo.chs.size(); k++) {
                if (compInfo.chs[k].kind == FIFFV_REF_MEG_CH) {
                    comp_chs.append(compInfo.chs[k]);
                    ncomp++;
                }
            }
        }
        if (ncomp > 0) {
            comp_coils = templates->create_meg_coils(comp_chs,
                                                     ncomp,
                                                     FWD_COIL_ACCURACY_NORMAL,
                                                     *res->meg_head_t);
            if (!comp_coils) {
                return nullptr;
            }
            qInfo("%d compensation channels in %s", comp_coils->ncoil(), measname.toUtf8().data());
        }
    } else { /* Get rid of the empty data set */
        comp_data.reset();
    }
    /*
       * Ready to set up the forward model
       */
    if (setup_forward_model(res.get(), comp_data.get(), comp_coils.get()) == FAIL)
        return nullptr;
    res->column_norm = COLUMN_NORM_LOC;
    /*
       * Projection data should go here
       */
    if (!MNEProjOp::makeProjection(projnames,
                                   res->chs,
                                   res->nmeg + res->neeg,
                                   res->proj))
        return nullptr;
    if (res->proj && res->proj->nitems > 0) {
        qInfo("Final projection operator is:");
        {
            QTextStream errStream(stderr);
            res->proj->report(errStream, QStringLiteral("\t"));
        }
 
        if (res->proj->assign_channels(res->ch_names, res->nmeg + res->neeg) == FAIL)
            return nullptr;
        if (res->proj->make_proj() == FAIL)
            return nullptr;
    } else
        qInfo("No projection will be applied to the data.");
 
    /*
        * Noise covariance
        */
    if (!noisename.isEmpty()) {
        if ((cov = MNECovMatrix::read(noisename, FIFFV_MNE_SENSOR_COV)) == nullptr)
            return nullptr;
        qInfo("Read a %s noise-covariance matrix from %s",
              cov->cov_diag.size() > 0 ? "diagonal" : "full", noisename.toUtf8().data());
    } else {
        if ((cov = ad_hoc_noise(res->meg_coils.get(), res->eeg_els.get(), grad_std, mag_std, eeg_std)) == nullptr)
            return nullptr;
    }
    res->noise = cov->pick_chs_omit(res->ch_names,
                                    res->nmeg + res->neeg,
                                    true,
                                    res->chs);
    if (!res->noise) {
        return nullptr;
    }
 
    qInfo("Picked appropriate channels from the noise-covariance matrix.");
    cov.reset();
 
    /*
       * Apply the projection operator to the noise-covariance matrix
       */
    if (res->proj && res->proj->nitems > 0 && res->proj->nvec > 0) {
        if (res->proj->apply_cov(res->noise.get()) == FAIL)
            return nullptr;
        qInfo("Projection applied to the covariance matrix.");
    }
 
    /*
       * Force diagonal noise covariance?
       */
    if (diagnoise) {
        res->noise->revert_to_diag();
        qInfo("Using only the main diagonal of the noise-covariance matrix.");
    }
 
    /*
       * Regularize the possibly deficient noise-covariance matrix
       */
    if (res->noise->cov.size() > 0) {
        Eigen::Vector3f regs;
        int do_it;
 
        regs[MNE_COV_CH_MEG_MAG] = mag_reg;
        regs[MNE_COV_CH_MEG_GRAD] = grad_reg;
        regs[MNE_COV_CH_EEG] = eeg_reg;
        /*
         * Classify the channels
         */
        if (res->noise->classify_channels(res->chs,
                                          res->nmeg + res->neeg) == FAIL)
            return nullptr;
        /*
         * Do we need to do anything?
         */
        do_it = 0;
        for (int k = 0; k < res->noise->ncov; k++) {
            if (res->noise->ch_class[k] != MNE_COV_CH_UNKNOWN &&
                regs[res->noise->ch_class[k]] > 0.0)
                do_it++;
        }
        /*
         * Apply regularization if necessary
         */
        if (do_it > 0)
            res->noise->regularize(regs);
        else
            qInfo("No regularization applied to the noise-covariance matrix");
    }
 
    /*
       * Do the decomposition and check that the matrix is positive definite
       */
    qInfo("Decomposing the noise covariance...");
    if (res->noise->cov.size() > 0) {
        if (res->noise->decompose_eigen() == FAIL)
            return nullptr;
        qInfo("Eigenvalue decomposition done.");
        for (int k = 0; k < res->noise->ncov; k++) {
            if (res->noise->lambda[k] < 0.0)
                res->noise->lambda[k] = 0.0;
        }
    } else {
        qInfo("Decomposition not needed for a diagonal covariance matrix.");
        if (res->noise->add_inv() == FAIL)
            return nullptr;
    }
 
    badlist.clear();
    return res.release();
}
 
//=============================================================================================================
 
bool InvDipoleFitData::print_fields(const Eigen::Vector3f& rd,
                                    const Eigen::Vector3f& Q,
                                    float time,
                                    float integ,
                                    InvDipoleFitData& fit,
                                    const MNEMeasData& data,
                                    QTextStream& out)
{
    const int nch = fit.nmeg + fit.neeg;
    if (data.nchan != nch || !data.current) {
        qWarning("print_fields: the data do not hold the %d fit channels", nch);
        return false;
    }
    Eigen::VectorXf measured(nch);
    if (data.current->getValuesAtTime(time, integ, nch, false, measured.data()) == FAIL) {
        qWarning("Cannot pick time: %7.1f ms", 1000 * time);
        return false;
    }
    if (fit.proj && fit.proj->project_vector(measured, true) == FAIL)
        return false;
 
    Eigen::MatrixXf fwd(nch, 3);
    if (compute_dipole_field(fit, rd, false, fwd) == FAIL)
        return false;
    const Eigen::VectorXf predicted = fwd * Q;
 
    for (int k = 0; k < nch; ++k) {
        const double scale = k < fit.nmeg ? 1e15 : 1e6;
        out << fit.ch_names[k] << '\t' << scale * measured[k] << '\t' << scale * predicted[k] << '\n';
    }
    return true;
}
 
//=============================================================================================================

std::unique_ptr<InvDipoleForward> dipole_forward(InvDipoleFitData* d,
                                                 float** rd,
                                                 int ndip,
                                                 std::unique_ptr<InvDipoleForward> old)
{
    std::unique_ptr<InvDipoleForward> res;
    float S[3];
    int k;
    /*
   * Allocate data if necessary
   */
    if (old && old->ndip == ndip && old->nch == d->nmeg + d->neeg) {
        res = std::move(old);
    } else {
        res = std::make_unique<InvDipoleForward>();
        int nch = d->nmeg + d->neeg;
        int m = 3 * ndip;
        res->fwd.resize(m, nch);
        res->uu.resize(m, nch);
        res->vv.resize(m, m);
        res->sing.resize(m);
        res->scales.resize(m);
        res->rd.resize(ndip, 3);
        res->nch = nch;
        res->ndip = ndip;
    }
 
    for (k = 0; k < ndip; k++) {
        res->rd.row(k) = Eigen::Map<const Eigen::Vector3f>(rd[k]).transpose();
        /*
     * Calculate the field of three orthogonal dipoles
     */
        Eigen::MatrixXf this_fwd(d->nmeg + d->neeg, 3);
        Eigen::Map<const Eigen::Vector3f> rd_k(rd[k]);
        if ((InvDipoleFitData::compute_dipole_field(*d, rd_k, true, this_fwd)) == FAIL)
            return nullptr;
        for (int p = 0; p < 3; p++)
            res->fwd.row(3 * k + p) = this_fwd.col(p).transpose();
        /*
     * Choice of column normalization
     * (componentwise normalization is not recommended)
     */
        if (d->column_norm == COLUMN_NORM_LOC || d->column_norm == COLUMN_NORM_COMP) {
            for (int p = 0; p < 3; p++)
                S[p] = res->fwd.row(3 * k + p).squaredNorm();
            if (d->column_norm == COLUMN_NORM_COMP) {
                for (int p = 0; p < 3; p++)
                    res->scales[3 * k + p] = sqrt(S[p]);
            } else {
                /*
     * Divide by three or not?
     */
                res->scales[3 * k + 0] = res->scales[3 * k + 1] = res->scales[3 * k + 2] = sqrt(S[0] + S[1] + S[2]) / 3.0;
            }
            for (int p = 0; p < 3; p++) {
                if (res->scales[3 * k + p] > 0.0) {
                    res->scales[3 * k + p] = 1.0 / res->scales[3 * k + p];
                    res->fwd.row(3 * k + p) *= res->scales[3 * k + p];
                } else
                    res->scales[3 * k + p] = 1.0;
            }
        } else {
            res->scales[3 * k] = 1.0;
            res->scales[3 * k + 1] = 1.0;
            res->scales[3 * k + 2] = 1.0;
        }
    }
 
    /*
   * SVD: A = U · Σ · V^T  where A is m×n (3*ndip × nch)
   *   uu stores right singular vectors (V^T rows, length nch) for data-space projections
   *   vv stores left  singular vectors (U^T rows, length m)   for dipole-moment reconstruction
   */
    {
        int m = 3 * ndip;
        int n = d->nmeg + d->neeg;
        int udim = std::min(m, n);
        JacobiSVD<MatrixXf> svd(res->fwd, ComputeFullU | ComputeFullV);
        res->sing = svd.singularValues();
        res->uu = svd.matrixV().transpose().topRows(udim);
        res->vv = svd.matrixU().transpose().topRows(udim);
    }
 
    return res;
}
 
//=============================================================================================================

std::unique_ptr<InvDipoleForward> InvDipoleFitData::dipole_forward_one(InvDipoleFitData* d,
                                                                       const Eigen::Vector3f& rd,
                                                                       std::unique_ptr<InvDipoleForward> old)
{
    float* rds[1];
    rds[0] = const_cast<float*>(rd.data());
    return dipole_forward(d, rds, 1, std::move(old));
}
 
//=============================================================================================================
// Dipole fitting - evaluation
static float fit_eval(const VectorXf& rd, const void* user)
{
    InvDipoleFitData* fit = const_cast<InvDipoleFitData*>(static_cast<const InvDipoleFitData*>(user));
    InvDipoleForward* fwd;
    FitDipUserRec* fuser = fit->user;
    double Bm2, one;
    int ncomp, c;
 
    fuser->fwd = InvDipoleFitData::dipole_forward_one(fit, rd.head<3>(), std::move(fuser->fwd));
    fwd = fuser->fwd.get();
    ncomp = fwd->sing[2] / fwd->sing[0] > fuser->limit ? 3 : 2;
    if (fuser->report_dim)
        qInfo("ncomp = %d", ncomp);
 
    Eigen::Map<const VectorXf> Bmap(fuser->B, fwd->nch);
    for (c = 0, Bm2 = 0.0; c < ncomp; c++) {
        one = fwd->uu.row(c).dot(Bmap);
        Bm2 = Bm2 + one * one;
    }
    return fuser->B2 - Bm2;
}

static int find_best_guess(const Eigen::Ref<const Eigen::VectorXf>& B,
                           int nch,
                           InvGuessData* guess,
                           float limit,
                           int& bestp,
                           float& goodp)
{
    int k, c;
    double B2, Bm2, this_good, one;
    int best = -1;
    float good = 0.0;
    InvDipoleForward* fwd;
    int ncomp;
 
    B2 = B.squaredNorm();
    for (k = 0; k < guess->nguess; k++) {
        fwd = guess->guess_fwd[k].get();
        if (fwd->nch == nch) {
            ncomp = fwd->sing[2] / fwd->sing[0] > limit ? 3 : 2;
            for (c = 0, Bm2 = 0.0; c < ncomp; c++) {
                one = fwd->uu.row(c).dot(B);
                Bm2 = Bm2 + one * one;
            }
            this_good = 1.0 - (B2 - Bm2) / B2;
            if (this_good > good) {
                best = k;
                good = this_good;
            }
        }
    }
    if (best < 0) {
        qWarning("No reasonable initial guess found.");
        return FAIL;
    }
    bestp = best;
    goodp = good;
    return OK;
}

static MatrixXf make_initial_dipole_simplex(const Eigen::Vector3f& r0,
                                            float size)
{
    /*
   * For this definition of a regular tetrahedron, see
   *
   * http://mathworld.wolfram.com/Tetrahedron.html
   *
   */
    float x = sqrt(3.0f) / 3.0f;
    float r = sqrt(6.0f) / 12.0f;
    float R = 3 * r;
    float d = x / 2.0f;
    float rr[][3] = {{x, 0.0f, -r},
                     {-d, 0.5f, -r},
                     {-d, -0.5f, -r},
                     {0.0f, 0.0f, R}};
 
    MatrixXf simplex = MatrixXf::Zero(4, 3);
 
    for (int j = 0; j < 4; j++) {
        simplex.row(j) = Eigen::Map<const Vector3f>(rr[j]).transpose() * size + r0.transpose();
    }
    return simplex;
}
 
static bool dipole_report_func(int loop,
                               const VectorXf& fitpar,
                               double fval_lo,
                               double fval_hi,
                               double par_diff)
{
    qInfo("loop %d rd %7.2f %7.2f %7.2f fval %g %g par diff %g",
          loop, 1000 * fitpar[0], 1000 * fitpar[1], 1000 * fitpar[2], fval_lo, fval_hi, 1000 * par_diff);
 
    return true;
}

static int fit_Q(InvDipoleFitData* fit,
                 const Eigen::Ref<const Eigen::VectorXf>& B,
                 const Eigen::Vector3f& rd,
                 float limit,
                 Eigen::Vector3f& Q,
                 int& ncomp,
                 float& res)
{
    int c;
    const auto fwd = InvDipoleFitData::dipole_forward_one(fit, rd, nullptr);
    float Bm2, one;
 
    if (!fwd)
        return FAIL;
 
    ncomp = fwd->sing[2] / fwd->sing[0] > limit ? 3 : 2;
 
    Q.setZero();
    for (c = 0, Bm2 = 0.0; c < ncomp; c++) {
        one = fwd->uu.row(c).dot(B);
        Q += (one / fwd->sing[c]) * fwd->vv.row(c).head(3).transpose();
        Bm2 = Bm2 + one * one;
    }
    /*
   * Counteract the effect of column normalization
   */
    for (c = 0; c < 3; c++)
        Q[c] = fwd->scales[c] * Q[c];
    res = B.squaredNorm() - Bm2;
 
    return OK;
}
 
//=============================================================================================================
// Dipole fitting - main entry point
bool InvDipoleFitData::fit_one(InvDipoleFitData* fit,
                               InvGuessData* guess,
                               float time,
                               Eigen::Ref<Eigen::VectorXf> B,
                               int verbose,
                               InvEcd& res)
{
    VectorXf vals(4);                  /* Values at the vertices */
    float limit = 0.2f;                /* (pseudo) radial component omission limit */
    float size = 1e-2f;                /* Size of the initial simplex */
    float ftol[] = {1e-2f, 1e-2f};     /* Tolerances on the the two passes */
    float atol[] = {0.2e-3f, 0.2e-3f}; /* If dipole movement between two iterations is less than this,
                                                  we consider to have converged */
    int ntol = 2;
    int max_eval = 1000;                    /* Limit for fit function evaluations */
    int report_interval = verbose ? 1 : -1; /* How often to report the intermediate result */
 
    int best;
    float good, final_val;
    Eigen::Vector3f rd_final, Q;
    FitDipUserRec user;
    int k, neval, neval_tot, nchan, ncomp;
    int fit_fail;
    Vector3f rd_guess;
 
    nchan = fit->nmeg + fit->neeg;
    user.fwd = nullptr;
 
    if (fit->proj && fit->proj->project_vector(B, true) == FAIL)
        return false;
 
    if (fit->noise->whiten_vector(B, B, nchan) == FAIL)
        return false;
    /*
   * Get the initial guess
   */
    if (find_best_guess(B, nchan, guess, limit, best, good) < 0)
        return false;
 
    user.limit = limit;
    user.B = B.data();
    user.B2 = B.squaredNorm();
    user.fwd = nullptr;
    user.report_dim = false;
    fit->user = &user;
 
    rd_guess = guess->rr.row(best).transpose();
    rd_final = rd_guess;
 
    neval_tot = 0;
    fit_fail = false;
    for (k = 0; k < ntol; k++) {
        /*
     * Do first pass with the sphere model
     */
        if (fit->fit_mag_dipoles)
            fit->funcs = fit->mag_dipole_funcs.get(); // the guesses were computed with these too
        else if (k == 0)
            fit->funcs = fit->sphere_funcs.get();
        else
            fit->funcs = !fit->bemname.isEmpty() ? fit->bem_funcs.get() : fit->sphere_funcs.get();
 
        MatrixXf simplexMat = make_initial_dipole_simplex(rd_guess, size);
        for (int p = 0; p < 4; p++)
            vals[p] = fit_eval(simplexMat.row(p), fit);
 
        // Capture fit pointer in type-safe lambda — no void* needed
        auto cost = [fit](const VectorXf& x) -> float {
            return fit_eval(x, fit);
        };
 
        if (!UTILSLIB::SimplexAlgorithm::simplex_minimize<float>(
                simplexMat,      /* The initial simplex */
                vals,            /* Function values at the vertices */
                ftol[k],         /* Relative convergence tolerance for the target function */
                atol[k],         /* Absolute tolerance for the change in the parameters */
                cost,            /* The cost function (captures fit data) */
                max_eval,        /* Maximum number of function evaluations */
                neval,           /* Number of function evaluations */
                report_interval, /* How often to report (-1 = no_reporting) */
                dipole_report_func)) {
            if (k == 0) {
                return false;
            } else {
                float rv = 2.0f * (vals.maxCoeff() - vals.minCoeff()) / (vals.maxCoeff() + vals.minCoeff());
                qWarning("Warning (t = %8.1f ms) : g = %6.1f %% final val = %7.3f rtol = %f",
                         1000 * time, 100 * (1 - vals[0] / user.B2), vals[0], rv);
                fit_fail = true;
            }
        }
        rd_final = simplexMat.row(0).transpose();
        rd_guess = simplexMat.row(0).transpose();
 
        neval_tot += neval;
        final_val = vals[0];
    }
    /*
   * Confidence limits should be computed here
   */
    /*
   * Compute the dipole moment at the final point
   */
    if (fit_Q(fit, B, rd_final, user.limit, Q, ncomp, final_val) == OK) {
        res.time = time;
        res.valid = true;
        res.rd = rd_final;
        res.Q = Q;
        res.good = 1.0 - final_val / user.B2;
        if (fit_fail)
            res.good = -res.good;
        res.khi2 = final_val;
        if (fit->proj)
            res.nfree = nchan - 3 - ncomp - fit->proj->nvec;
        else
            res.nfree = nchan - 3 - ncomp;
        res.neval = neval_tot;
    } else {
        return false;
    }
 
    return true;
}
 
//=============================================================================================================

int InvDipoleFitData::compute_dipole_field(InvDipoleFitData& d, const Eigen::Vector3f& rd, int whiten, Eigen::Ref<Eigen::MatrixXf> fwd)
{
    static const Eigen::Vector3f Qx(1.0f, 0.0f, 0.0f);
    static const Eigen::Vector3f Qy(0.0f, 1.0f, 0.0f);
    static const Eigen::Vector3f Qz(0.0f, 0.0f, 1.0f);
    int nch = d.nmeg + d.neeg;
    int k;
    /*
   * Compute the fields
   */
    if (d.nmeg > 0) {
        int nmeg = d.meg_coils->ncoil();
        if (d.funcs->meg_vec_field) {
            /*
             * Use the vector field function: computes all three dipole
             * orientations at once. Output is 3 x ncoil, we need nch x 3.
             */
            Eigen::MatrixXf vec_meg(3, nmeg);
            if (d.funcs->meg_vec_field(rd, *d.meg_coils, vec_meg, d.funcs->meg_client) != OK)
                return FAIL;
            fwd.topRows(nmeg) = vec_meg.transpose();
        } else {
            auto fwd0 = fwd.col(0).head(nmeg);
            auto fwd1 = fwd.col(1).head(nmeg);
            auto fwd2 = fwd.col(2).head(nmeg);
            if (d.funcs->meg_field(rd, Qx, *d.meg_coils, fwd0, d.funcs->meg_client) != OK)
                return FAIL;
            if (d.funcs->meg_field(rd, Qy, *d.meg_coils, fwd1, d.funcs->meg_client) != OK)
                return FAIL;
            if (d.funcs->meg_field(rd, Qz, *d.meg_coils, fwd2, d.funcs->meg_client) != OK)
                return FAIL;
        }
    }
 
    if (d.neeg > 0) {
        int neeg = d.eeg_els->ncoil();
        if (d.funcs->eeg_vec_pot) {
            /*
             * Use the vector potential function: computes all three dipole
             * orientations at once. Output is 3 x ncoil, we need nch x 3.
             */
            Eigen::MatrixXf vec_eeg(3, neeg);
            if (d.funcs->eeg_vec_pot(rd, *d.eeg_els, vec_eeg, d.funcs->eeg_client) != OK)
                return FAIL;
            fwd.block(d.nmeg, 0, neeg, 3) = vec_eeg.transpose();
        } else {
            auto fwd0 = fwd.col(0).segment(d.nmeg, neeg);
            auto fwd1 = fwd.col(1).segment(d.nmeg, neeg);
            auto fwd2 = fwd.col(2).segment(d.nmeg, neeg);
            if (d.funcs->eeg_pot(rd, Qx, *d.eeg_els, fwd0, d.funcs->eeg_client) != OK)
                return FAIL;
            if (d.funcs->eeg_pot(rd, Qy, *d.eeg_els, fwd1, d.funcs->eeg_client) != OK)
                return FAIL;
            if (d.funcs->eeg_pot(rd, Qz, *d.eeg_els, fwd2, d.funcs->eeg_client) != OK)
                return FAIL;
        }
    }
 
    /*
   * Apply projection
   */
    for (k = 0; k < 3; k++)
        if (d.proj && d.proj->project_vector(fwd.col(k), true) == FAIL)
            return FAIL;
 
    /*
   * Whiten
   */
    if (d.noise && whiten) {
        for (k = 0; k < 3; k++) {
            auto col_k = fwd.col(k);
            if (d.noise->whiten_vector(col_k, col_k, nch) == FAIL)
                return FAIL;
        }
    }
 
    return OK;
}