volume<float> draw_mesh_bis(const volume<float>& image, const Mesh &m) { double xdim = (double) image.xdim(); double ydim = (double) image.ydim(); double zdim = (double) image.zdim(); double mininc = min(xdim,min(ydim,zdim)) * .5; volume<float> res = image; double max = image.max(); for (list<Triangle*>::const_iterator i = m._triangles.begin(); i!=m._triangles.end(); i++) { Vec n = (*(*i)->get_vertice(0) - *(*i)->get_vertice(1)); double d = n.norm(); n.normalize(); for (double j=0; j<=d; j+=mininc) { Pt p = (*i)->get_vertice(1)->get_coord() + j* n; draw_segment_bis(res, p, (*i)->get_vertice(2)->get_coord(), max); } } return res; }
//writes externall skull computed from image on output. void t1only_write_ext_skull(volume<float> & output_inskull, volume<float> & output_outskull, volume<float> & output_outskin, const volume<float> & t1, const Mesh & m, const trMatrix & M) { int glob_counter = 0; int rem_counter = 0; const double xdim = t1.xdim(); const double ydim = t1.ydim(); const double zdim = t1.zdim(); double imax = t1.max(); if (imax == 0) imax = 1; volume<short> meshimage; copyconvert(t1, meshimage); meshimage = 0; draw_mesh(meshimage, m); for (vector<Mpoint*>::const_iterator i = m._points.begin(); i != m._points.end(); i++) { (*i)->data.clear(); double max_neighbour = 0; const Vec normal = (*i)->local_normal(); const Vec n = Vec(normal.X/xdim, normal.Y/ydim, normal.Z/zdim); for (list<Mpoint*>::const_iterator nei = (*i)->_neighbours.begin(); nei != (*i)->_neighbours.end(); nei++) max_neighbour = Max(((**i) - (**nei)).norm(), max_neighbour); max_neighbour = ceil((max_neighbour)/2); const Pt mpoint((*i)->get_coord().X/xdim,(*i)->get_coord().Y/ydim,(*i)->get_coord().Z/zdim); for (int ck = (int)floor(mpoint.Z - max_neighbour/zdim); ck <= (int)floor(mpoint.Z + max_neighbour/zdim); ck++) for (int cj = (int)floor(mpoint.Y - max_neighbour/ydim); cj <= (int)floor(mpoint.Y + max_neighbour/ydim); cj++) for (int ci = (int)floor(mpoint.X - max_neighbour/xdim); ci <= (int)floor(mpoint.X + max_neighbour/xdim); ci++) { bool compute = false; const Pt point(ci, cj, ck); const Pt realpoint(ci*xdim, cj*ydim, ck*zdim); if (meshimage(ci, cj, ck) == 1) { double mindist = 10000; for (list<Mpoint*>::const_iterator nei = (*i)->_neighbours.begin(); nei != (*i)->_neighbours.end(); nei++) mindist = Min(((realpoint) - (**nei)).norm(), mindist); if (mindist >= ((realpoint) - (**i)).norm()) compute = true; } if (compute) { glob_counter ++; vector<double> val; if (!special_case(realpoint, normal, M)) val = t1only_co_ext(t1, point, n); else { val = t1only_special_extract(t1, point, n); } if (val.size() == 3) { Pt opoint(point.X, point.Y, point.Z); Vec on(n.X, n.Y, n.Z); Pt c0 = opoint + val[0]*on; Pt c1 = opoint + val[1]*on; Pt c2 = opoint + val[2]*on; output_inskull((int)floor(c0.X + .5) + infxm,(int) floor(c0.Y + .5) + infym,(int) floor(c0.Z + .5) + infzm) +=1; output_outskull((int)floor(c1.X + .5) + infxm,(int) floor(c1.Y + .5) + infym,(int) floor(c1.Z + .5) + infzm)+=1; output_outskin((int)floor(c2.X + .5) + infxm,(int) floor(c2.Y + .5) + infym,(int) floor(c2.Z + .5) + infzm) +=1; } else { rem_counter++; if (val.size()==1) { Pt opoint(point.X, point.Y, point.Z); Vec on(n.X, n.Y, n.Z); Pt c0 = opoint + val[0]*on; output_outskin((int)floor(c0.X + .5) + infxm,(int) floor(c0.Y + .5) + infym,(int) floor(c0.Z + .5) + infzm) +=1; } } } } } if (verbose.value()) { cout<<" nb of profiles : "<<glob_counter<<endl; cout<<" removed profiles : "<<100. * rem_counter/(double) glob_counter<<"%"<<endl; } }
bet_parameters adjust_initial_mesh(const volume<float> & image, Mesh& m, const double & rad = 0., const double xpara=0., const double ypara=0., const double zpara=0.) { bet_parameters bp; double xdim = image.xdim(); double ydim = image.ydim(); double zdim = image.zdim(); double t2, t98, t; //computing t2 && t98 // cout<<"computing robust min && max begins"<<endl; bp.min = image.min(); bp.max = image.max(); t2 = image.robustmin(); t98 = image.robustmax(); //t2=32.; //t98=16121.; // cout<<"computing robust min && max ends"<<endl; t = t2 + .1*(t98 - t2); bp.t98 = t98; bp.t2 = t2; bp.t = t; // cout<<"t2 "<<t2<<" t98 "<<t98<<" t "<<t<<endl; // cout<<"computing center && radius begins"<<endl; //finds the COG Pt center(0, 0, 0); double counter = 0; if (xpara == 0. & ypara==0. & zpara==0.) { double tmp = t - t2; for (int k=0; k<image.zsize(); k++) for (int j=0; j<image.ysize(); j++) for (int i=0; i<image.xsize(); i++) { double c = image(i, j, k ) - t2; if (c > tmp) { c = min(c, t98 - t2); counter+=c; center += Pt(c*i*xdim, c*j*ydim, c*k*zdim); } } center=Pt(center.X/counter, center.Y/counter, center.Z/counter); //cout<<counter<<endl; // cout<<"cog "<<center.X<<" "<<center.Y<<" "<<center.Z<<endl; } else center=Pt(xpara, ypara, zpara); bp.cog = center; if (rad == 0.) { double radius=0; counter=0; double scale=xdim*ydim*zdim; for (int k=0; k<image.zsize(); k++) for (int j=0; j<image.ysize(); j++) for (int i=0; i<image.xsize(); i++) { double c = image(i, j, k); if (c > t) { counter+=1; } } radius = pow (.75 * counter*scale/M_PI, 1.0/3.0); // cout<<radius<<endl; bp.radius = radius; } else (bp.radius = rad); m.translation(center.X, center.Y, center.Z); m.rescale (bp.radius/2, center); // cout<<"computing center && radius ends"<<endl; //computing tm // cout<<"computing tm begins"<<endl; vector<double> vm; for (int k=0; k<image.zsize(); k++) for (int j=0; j<image.ysize(); j++) for (int i=0; i<image.xsize(); i++) { double d = image.value(i, j, k); Pt p(i*xdim, j*ydim, k*zdim); if (d > t2 && d < t98 && ((p - center)|(p - center)) < bp.radius * bp.radius) vm.push_back(d); } int med = (int) floor(vm.size()/2.); // cout<<"before sort"<<endl; nth_element(vm.begin(), vm.begin() + med - 1, vm.end()); //partial_sort(vm.begin(), vm.begin() + med + 1, vm.end()); //double tm = vm[med]; double tm=(*max_element(vm.begin(), vm.begin() + med)); // cout<<"tm "<<tm<<endl; bp.tm = tm; // cout<<"computing tm ends"<<endl; return bp; }