mne_surface.cpp

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//=============================================================================================================
 
//=============================================================================================================
// INCLUDES
//=============================================================================================================
 
#include "mne_surface.h"
#include "mne_source_space.h"
#include "mne_triangle.h"
#include "mne_proj_data.h"
 
#include <fiff/fiff_stream.h>
#include <fiff/fiff_coord_trans.h>
 
#include <QFile>
 
#define _USE_MATH_DEFINES
#include <math.h>
 
#include <Eigen/Dense>
 
//=============================================================================================================
// USED NAMESPACES
//=============================================================================================================
 
using namespace Eigen;
using namespace FIFFLIB;
using namespace MNELIB;
 
//=============================================================================================================
 
#ifndef TRUE
#define TRUE 1
#endif
 
#ifndef FALSE
#define FALSE 0
#endif
 
#ifndef FAIL
#define FAIL -1
#endif
 
#ifndef OK
#define OK 0
#endif
 
#define X_17 0
#define Y_17 1
#define Z_17 2
 
#define VEC_DOT_17(x,y) ((x)[X_17]*(y)[X_17] + (x)[Y_17]*(y)[Y_17] + (x)[Z_17]*(y)[Z_17])
#define VEC_LEN_17(x) sqrt(VEC_DOT_17(x,x))
#define VEC_DIFF_17(from,to,diff) {\
    (diff)[X_17] = (to)[X_17] - (from)[X_17];\
    (diff)[Y_17] = (to)[Y_17] - (from)[Y_17];\
    (diff)[Z_17] = (to)[Z_17] - (from)[Z_17];\
    }
#define VEC_COPY_17(to,from) {\
    (to)[X_17] = (from)[X_17];\
    (to)[Y_17] = (from)[Y_17];\
    (to)[Z_17] = (from)[Z_17];\
    }
 
//=============================================================================================================
// DEFINE MEMBER METHODS
//=============================================================================================================
 
MNESurface::MNESurface()
{
}
 
//=============================================================================================================
 
MNESurface::~MNESurface()
{
}
 
//=============================================================================================================
// Const geometry methods
//=============================================================================================================
 
double MNESurface::sum_solids(const Eigen::Vector3f& from) const
{
    int k;
    double tot_angle, angle;
    for (k = 0, tot_angle = 0.0; k < ntri; k++) {
        angle = solid_angle(from, tris[k]);
        tot_angle += angle;
    }
    return tot_angle;
}
 
//=============================================================================================================
 
void MNESurface::triangle_coords(const Eigen::Vector3f& r, int tri, float &x, float &y, float &z) const
{
    double rr[3];
    double a, b, c, v1, v2, det;
    const MNETriangle* this_tri;
 
    this_tri = &tris[tri];
 
    VEC_DIFF_17(this_tri->r1, r, rr);
    z = VEC_DOT_17(rr, this_tri->nn);
 
    a = VEC_DOT_17(this_tri->r12, this_tri->r12);
    b = VEC_DOT_17(this_tri->r13, this_tri->r13);
    c = VEC_DOT_17(this_tri->r12, this_tri->r13);
 
    v1 = VEC_DOT_17(rr, this_tri->r12);
    v2 = VEC_DOT_17(rr, this_tri->r13);
 
    det = a * b - c * c;
 
    x = (b * v1 - c * v2) / det;
    y = (a * v2 - c * v1) / det;
}
 
//=============================================================================================================
 
int MNESurface::nearest_triangle_point(const Eigen::Vector3f& r, const MNEProjData *user, int tri, float &x, float &y, float &z) const
{
    double p, q, p0, q0, t0;
    double rr[3];
    double a, b, c, v1, v2, det;
    double best, dist, dist0;
    const MNEProjData* pd = user;
    const MNETriangle* this_tri;
 
    this_tri = &tris[tri];
    VEC_DIFF_17(this_tri->r1, r, rr);
    dist = VEC_DOT_17(rr, this_tri->nn);
 
    if (pd) {
        if (!pd->act[tri])
            return FALSE;
        a = pd->a[tri];
        b = pd->b[tri];
        c = pd->c[tri];
    }
    else {
        a = VEC_DOT_17(this_tri->r12, this_tri->r12);
        b = VEC_DOT_17(this_tri->r13, this_tri->r13);
        c = VEC_DOT_17(this_tri->r12, this_tri->r13);
    }
 
    v1 = VEC_DOT_17(rr, this_tri->r12);
    v2 = VEC_DOT_17(rr, this_tri->r13);
 
    det = a * b - c * c;
 
    p = (b * v1 - c * v2) / det;
    q = (a * v2 - c * v1) / det;
 
    if (p >= 0.0 && p <= 1.0 &&
            q >= 0.0 && q <= 1.0 &&
            q <= 1.0 - p) {
        x = p;
        y = q;
        z = dist;
        return TRUE;
    }
    /*
     * Side 1 -> 2
     */
    p0 = p + 0.5 * (q * c) / a;
    if (p0 < 0.0) p0 = 0.0;
    else if (p0 > 1.0) p0 = 1.0;
    q0 = 0.0;
    dist0 = sqrt((p - p0) * (p - p0) * a +
                 (q - q0) * (q - q0) * b +
                 (p - p0) * (q - q0) * c +
                 dist * dist);
    best = dist0;
    x = p0;
    y = q0;
    z = dist0;
    /*
     * Side 2 -> 3
     */
    t0 = 0.5 * ((2.0 * a - c) * (1.0 - p) + (2.0 * b - c) * q) / (a + b - c);
    if (t0 < 0.0) t0 = 0.0;
    else if (t0 > 1.0) t0 = 1.0;
    p0 = 1.0 - t0;
    q0 = t0;
    dist0 = sqrt((p - p0) * (p - p0) * a +
                 (q - q0) * (q - q0) * b +
                 (p - p0) * (q - q0) * c +
                 dist * dist);
    if (dist0 < best) {
        best = dist0;
        x = p0;
        y = q0;
        z = dist0;
    }
    /*
     * Side 1 -> 3
     */
    p0 = 0.0;
    q0 = q + 0.5 * (p * c) / b;
    if (q0 < 0.0) q0 = 0.0;
    else if (q0 > 1.0) q0 = 1.0;
    dist0 = sqrt((p - p0) * (p - p0) * a +
                 (q - q0) * (q - q0) * b +
                 (p - p0) * (q - q0) * c +
                 dist * dist);
    if (dist0 < best) {
        best = dist0;
        x = p0;
        y = q0;
        z = dist0;
    }
    return TRUE;
}
 
//=============================================================================================================
 
int MNESurface::nearest_triangle_point(const Eigen::Vector3f& r, int tri, float &x, float &y, float &z) const
{
    return nearest_triangle_point(r, nullptr, tri, x, y, z);
}
 
//=============================================================================================================
 
Eigen::Vector3f MNESurface::project_to_triangle(int tri, float p, float q) const
{
    const MNETriangle* this_tri = &tris[tri];
 
    return Eigen::Vector3f(
        this_tri->r1 + p * this_tri->r12 + q * this_tri->r13
    );
}
 
//=============================================================================================================
 
Eigen::Vector3f MNESurface::project_to_triangle(int best, const Eigen::Vector3f& r) const
{
    float p, q, dist;
    nearest_triangle_point(r, best, p, q, dist);
    return project_to_triangle(best, p, q);
}
 
//=============================================================================================================
 
int MNESurface::project_to_surface(const MNEProjData *proj_data, const Eigen::Vector3f& r, float &distp) const
{
    float dist;
    float p, q;
    float p0, q0, dist0;
    int best;
    int k;
 
    p0 = q0 = 0.0;
    dist0 = 0.0;
    for (best = -1, k = 0; k < ntri; k++) {
        if (nearest_triangle_point(r, proj_data, k, p, q, dist)) {
            if (best < 0 || std::fabs(dist) < std::fabs(dist0)) {
                dist0 = dist;
                best = k;
                p0 = p;
                q0 = q;
            }
        }
    }
    distp = dist0;
    return best;
}
 
//=============================================================================================================
 
void MNESurface::find_closest_on_surface_approx(const PointsT& r, int np_points,
                                                 Eigen::VectorXi& nearest_tri,
                                                 Eigen::VectorXf& dist, int nstep) const
{
    MNEProjData* p = new MNEProjData(this);
    int k, was;
 
    printf("%s for %d points %d steps...", nearest_tri[0] < 0 ? "Closest" : "Approx closest", np_points, nstep);
 
    for (k = 0; k < np_points; k++) {
        was = nearest_tri[k];
        Eigen::Vector3f pt = Eigen::Map<const Eigen::Vector3f>(r.row(k).data());
        decide_search_restriction(*p, nearest_tri[k], nstep, pt);
        nearest_tri[k] = project_to_surface(p, pt, dist[k]);
        if (nearest_tri[k] < 0) {
            decide_search_restriction(*p, -1, nstep, pt);
            nearest_tri[k] = project_to_surface(p, pt, dist[k]);
        }
    }
    (void)was;
 
    printf("[done]\n");
    delete p;
}
 
//=============================================================================================================
 
void MNESurface::decide_search_restriction(MNEProjData& p,
                                           int approx_best,
                                           int nstep,
                                           const Eigen::Vector3f& r) const
{
    int k;
    float diff[3], dist_val, mindist;
    int minvert;
 
    for (k = 0; k < ntri; k++)
        p.act[k] = FALSE;
 
    if (approx_best < 0) {
        mindist = 1000.0;
        minvert = 0;
        for (k = 0; k < np; k++) {
            VEC_DIFF_17(r, &rr(k, 0), diff);
            dist_val = VEC_LEN_17(diff);
            if (dist_val < mindist && nneighbor_tri[k] > 0) {
                mindist = dist_val;
                minvert = k;
            }
        }
    }
    else {
        const MNETriangle* this_tri = &tris[approx_best];
        VEC_DIFF_17(r, this_tri->r1, diff);
        mindist = VEC_LEN_17(diff);
        minvert = this_tri->vert[0];
 
        VEC_DIFF_17(r, this_tri->r2, diff);
        dist_val = VEC_LEN_17(diff);
        if (dist_val < mindist) {
            mindist = dist_val;
            minvert = this_tri->vert[1];
        }
        VEC_DIFF_17(r, this_tri->r3, diff);
        dist_val = VEC_LEN_17(diff);
        if (dist_val < mindist) {
            mindist = dist_val;
            minvert = this_tri->vert[2];
        }
    }
 
    activate_neighbors(minvert, p.act, nstep);
 
    for (k = 0, p.nactive = 0; k < ntri; k++)
        if (p.act[k])
            p.nactive++;
}
 
//=============================================================================================================
 
void MNESurface::activate_neighbors(int start, Eigen::VectorXi &act, int nstep) const
{
    int k;
 
    if (nstep == 0)
        return;
 
    for (k = 0; k < nneighbor_tri[start]; k++)
        act[neighbor_tri[start][k]] = TRUE;
    for (k = 0; k < nneighbor_vert[start]; k++)
        activate_neighbors(neighbor_vert[start][k], act, nstep - 1);
}
 
//=============================================================================================================
// Static factory methods
//=============================================================================================================
 
MNESurface* MNESurface::read_bem_surface(const QString& name, int which, int add_geometry, float *sigmap)
{
    return read_bem_surface(name, which, add_geometry, sigmap, true);
}
 
//=============================================================================================================
 
MNESurface* MNESurface::read_bem_surface2(const QString& name, int which, int add_geometry, float *sigmap)
{
    return read_bem_surface(name, which, add_geometry, sigmap, FALSE);
}
 
//=============================================================================================================
 
MNESurface* MNESurface::read_bem_surface(const QString& name, int which, int add_geometry, float *sigmap, bool check_too_many_neighbors)
{
    QFile file(name);
    FiffStream::SPtr stream(new FiffStream(&file));
 
    QList<FiffDirNode::SPtr> surfs;
    QList<FiffDirNode::SPtr> bems;
    FiffDirNode::SPtr node;
    FiffTag::UPtr t_pTag;
 
    int     id = -1;
    int     nnode, ntri_count;
    MNESurface* s = NULL;
    int k;
    MatrixXf tmp_node_normals;
    int coord_frame = FIFFV_COORD_MRI;
    float sigma = -1.0;
    MatrixXf tmp_nodes;
    MatrixXi tmp_triangles;
 
    if (!stream->open())
        goto bad;
 
    bems = stream->dirtree()->dir_tree_find(FIFFB_BEM);
    if (bems.size() > 0) {
        node = bems[0];
        if (node->find_tag(stream, FIFF_BEM_COORD_FRAME, t_pTag)) {
            coord_frame = *t_pTag->toInt();
        }
    }
    surfs = stream->dirtree()->dir_tree_find(FIFFB_BEM_SURF);
    if (surfs.size() == 0) {
        printf("No BEM surfaces found in %s", name.toUtf8().constData());
        goto bad;
    }
    if (which >= 0) {
        for (k = 0; k < surfs.size(); ++k) {
            node = surfs[k];
            if (node->find_tag(stream, FIFF_BEM_SURF_ID, t_pTag)) {
                id = *t_pTag->toInt();
                if (id == which)
                    break;
            }
        }
        if (id != which) {
            printf("Desired surface not found in %s", name.toUtf8().constData());
            goto bad;
        }
    }
    else
        node = surfs[0];
 
    if (!node->find_tag(stream, FIFF_BEM_SURF_NNODE, t_pTag))
        goto bad;
    nnode = *t_pTag->toInt();
 
    if (!node->find_tag(stream, FIFF_BEM_SURF_NTRI, t_pTag))
        goto bad;
    ntri_count = *t_pTag->toInt();
 
    if (!node->find_tag(stream, FIFF_BEM_SURF_NODES, t_pTag))
        goto bad;
    tmp_nodes = t_pTag->toFloatMatrix().transpose();
 
    if (node->find_tag(stream, FIFF_BEM_SURF_NORMALS, t_pTag)) {
        tmp_node_normals = t_pTag->toFloatMatrix().transpose();
    }
 
    if (!node->find_tag(stream, FIFF_BEM_SURF_TRIANGLES, t_pTag))
        goto bad;
    tmp_triangles = t_pTag->toIntMatrix().transpose();
 
    if (node->find_tag(stream, FIFF_MNE_COORD_FRAME, t_pTag)) {
        coord_frame = *t_pTag->toInt();
    }
    else if (node->find_tag(stream, FIFF_BEM_COORD_FRAME, t_pTag)) {
        coord_frame = *t_pTag->toInt();
    }
    if (node->find_tag(stream, FIFF_BEM_SIGMA, t_pTag)) {
        sigma = *t_pTag->toFloat();
    }
 
    stream->close();
 
    s = new MNESurface();
    tmp_triangles.array() -= 1;
    s->itris       = tmp_triangles;
    s->id          = which;
    s->sigma       = sigma;
    s->coord_frame = coord_frame;
    s->rr          = tmp_nodes;
    s->nn          = tmp_node_normals;
    s->ntri        = ntri_count;
    s->np          = nnode;
    s->type        = FIFFV_MNE_SPACE_SURFACE;
    s->nuse_tri    = 0;
    s->tot_area    = 0.0;
    s->dist_limit  = -1.0;
    s->vol_dims[0] = s->vol_dims[1] = s->vol_dims[2] = 0;
    s->MRI_vol_dims[0] = s->MRI_vol_dims[1] = s->MRI_vol_dims[2] = 0;
    s->cm[0] = s->cm[1] = s->cm[2] = 0.0;
 
    if (add_geometry) {
        if (check_too_many_neighbors) {
            if (s->add_geometry_info(s->nn.rows() == 0) != OK)
                goto bad;
        }
        else {
            if (s->add_geometry_info2(s->nn.rows() == 0) != OK)
                goto bad;
        }
    }
    else if (s->nn.rows() == 0) {
        if (s->add_vertex_normals() != OK)
            goto bad;
    }
    else
        s->add_triangle_data();
 
    s->nuse   = s->np;
    s->inuse  = Eigen::VectorXi::Ones(s->np);
    s->vertno = Eigen::VectorXi::LinSpaced(s->np, 0, s->np - 1);
    if (sigmap)
        *sigmap = sigma;
 
    return s;
 
bad : {
        stream->close();
        if (s)
            delete s;
        return NULL;
    }
}