std::pair<float,float> evaluate_fib( const tipl::geometry<3>& dim, float otsu, const fib_fa_type& fib_fa, fun dir, bool check_trajectory = true) { float connection_count = 0; std::vector<std::vector<unsigned char> > connected(fib_fa.size()); for(unsigned int index = 0;index < connected.size();++index) connected[index].resize(dim.size()); evaluate_connection(dim,otsu,fib_fa,dir,[&](unsigned int pos1,char fib1,unsigned int pos2,char fib2) { connected[fib1][pos1] = 1; connected[fib2][pos2] = 1; connection_count += fib_fa[fib2][pos2]; // no need to add fib1 because it will be counted if fib2 becomes fib1 },check_trajectory); unsigned char num_fib = fib_fa.size(); float no_connection_count = 0; for(tipl::pixel_index<3> index(dim);index < dim.size();++index) { for(unsigned int i = 0;i < num_fib;++i) if(fib_fa[i][index.index()] > otsu && !connected[i][index.index()]) no_connection_count += fib_fa[i][index.index()]; } return std::make_pair(connection_count,no_connection_count); }
void evaluate_connection( const tipl::geometry<3>& dim, float otsu, const fib_fa_type& fib_fa, fun1 dir, fun2 f, bool check_trajectory = true) { unsigned char num_fib = fib_fa.size(); char dx[13] = {1,0,0,1,1,0, 1, 1, 0, 1,-1, 1, 1}; char dy[13] = {0,1,0,1,0,1,-1, 0, 1, 1, 1,-1, 1}; char dz[13] = {0,0,1,0,1,1, 0,-1,-1, 1, 1, 1,-1}; std::vector<tipl::vector<3> > dis(13); for(unsigned int i = 0;i < 13;++i) { dis[i] = tipl::vector<3>(dx[i],dy[i],dz[i]); dis[i].normalize(); } for(tipl::pixel_index<3> index(dim);index < dim.size();++index) { if(fib_fa[0][index.index()] <= otsu) continue; for(unsigned char fib1 = 0;fib1 < num_fib;++fib1) { if(fib_fa[fib1][index.index()] <= otsu) break; for(unsigned int j = 0;j < 2;++j) for(unsigned int i = 0;i < 13;++i) { tipl::vector<3,int> pos; pos = j ? tipl::vector<3,int>(index[0] + dx[i],index[1] + dy[i],index[2] + dz[i]) :tipl::vector<3,int>(index[0] - dx[i],index[1] - dy[i],index[2] - dz[i]); if(!dim.is_valid(pos)) continue; tipl::pixel_index<3> other_index(pos[0],pos[1],pos[2],dim); if(check_trajectory) { if(std::abs(dir(index.index(),fib1)*dis[i]) <= 0.8665) continue; for(unsigned char fib2 = 0;fib2 < num_fib;++fib2) if(fib_fa[fib2][other_index.index()] > otsu && std::abs(dir(other_index.index(),fib2)*dis[i]) > 0.8665) f(index.index(),fib1,other_index.index(),fib2); } else { for(unsigned char fib2 = 0;fib2 < num_fib;++fib2) if(fib_fa[fib2][other_index.index()] > otsu && std::abs(dir(other_index.index(),fib2)*dir(index.index(),fib1)) > 0.8665) f(index.index(),fib1,other_index.index(),fib2); } } } } }
void createLayout(const char* file_name, float fa_value, const std::vector<float>& angle_iteration, unsigned int repeat_num, unsigned int phantom_width, unsigned int boundary) { float iso_fraction = 0.2f; float fiber_fraction = 1.0f-iso_fraction; dim[0] = phantom_width+boundary+boundary; dim[1] = phantom_width+boundary+boundary; dim[2] = std::max<int>(1,angle_iteration.size())*repeat_num; unsigned int total_size = dim.size(); std::vector<float> fa[2]; std::vector<float> gfa; std::vector<short> findex[2]; models.resize(total_size); fa[0].resize(total_size); fa[1].resize(total_size); gfa.resize(total_size); findex[0].resize(total_size); findex[1].resize(total_size); unsigned int main_fiber_index = ti.discretize(tipl::vector<3>(1.0,0.0,0.0)); std::fill(models.begin(),models.end(),(MixGaussianModel*)0); begin_prog("creating layout"); if(angle_iteration.empty()) // use 0 to 90 degrees crossing for (unsigned int n = 0,index = 0; n < repeat_num; ++n) { if (!check_prog(index,total_size)) break; float fa2 = fa_value*fa_value; //fa*fa = (r*r-2*r+1)/(r*r+2) float r = (1.0+fa_value*std::sqrt(3-2*fa2))/(1-fa2); float l2 = mean_dif*3.0/(2.0+r); float l1 = r*l2; for (unsigned int y = 0; y < dim[1]; ++y) { for (unsigned int x = 0; x < dim[0]; ++x,++index) { if (x >= boundary && x < boundary+phantom_width && y >= boundary && y < boundary+phantom_width) { float xf = ((float)x - boundary + 1)/((float)phantom_width);//from 0.02 to 1.00 xf = 1.0f-xf;//0.00 to 0.98 xf = 0.5f+0.5f*xf;//0.50 to 0.99 float angle = ((float)y - boundary)/((float)phantom_width);//0.00 to 0.98 angle = 1.0f-angle;//0.02 to 1.00 angle *= float(M_PI*0.5f);//1.8 degrees 90 degrees models[index] = new MixGaussianModel(l1,l2,mean_dif,angle, fiber_fraction*xf, fiber_fraction*(1.0-xf)); fa[0][index] = fiber_fraction*xf; fa[1][index] = fiber_fraction*(1.0-xf); gfa[index] = fa_value; findex[0][index] = main_fiber_index; findex[1][index] = ti.discretize(tipl::vector<3>(std::cos(angle),std::sin(angle),0.0)); } } } } else for (unsigned int j = 0,index = 0; j < angle_iteration.size(); ++j) for (unsigned int n = 0; n < repeat_num; ++n) { if (!check_prog(index,total_size)) break; float inner_angle = angle_iteration[j]*M_PI/180.0; float fa2 = fa_value*fa_value; //fa*fa = (r*r-2*r+1)/(r*r+2) float r = (1.0+fa_value*std::sqrt(3-2*fa2))/(1-fa2); float l2 = mean_dif*3.0/(2.0+r); float l1 = r*l2; for (unsigned int y = 0; y < dim[1]; ++y) { for (unsigned int x = 0; x < dim[0]; ++x,++index) { if (x >= boundary && x < boundary+phantom_width && y >= boundary && y < boundary+phantom_width) { if(inner_angle >= 0.0) models[index] = new MixGaussianModel(l1,l2,mean_dif,inner_angle,0.5,0.5); else models[index] = new GaussianDispersion(l1,l2,mean_dif,inner_angle,1.0); fa[0][index] = fiber_fraction/2.0; fa[1][index] = fiber_fraction/2.0; gfa[index] = fa_value; findex[0][index] = main_fiber_index; findex[1][index] = ti.discretize(tipl::vector<3>(std::cos(inner_angle),std::sin(inner_angle),0.0)); } } } } set_title("Generating images"); std::string fib_file_name(file_name); fib_file_name += ".layout.fib"; gz_mat_write mat_writer(file_name),mat_layout(fib_file_name.c_str()); // output dimension { mat_writer.write("dimension",&*dim.begin(),1,3); mat_layout.write("dimension",&*dim.begin(),1,3); } // output vexol size { float vs[3] = {1.0,1.0,1.0}; mat_writer.write("voxel_size",vs,1,3); mat_layout.write("voxel_size",vs,1,3); } // output b_table { std::vector<float> buffer; buffer.reserve(bvalues.size()*4); for (unsigned int index = 0; index < bvalues.size(); ++index) { buffer.push_back(bvalues[index]); std::copy(bvectors[index].begin(),bvectors[index].end(),std::back_inserter(buffer)); } mat_writer.write("b_table",&*buffer.begin(),4,bvalues.size()); } // output images { std::vector<short> buffer(models.size()); begin_prog("generating images"); for (unsigned int index = 0; check_prog(index,bvectors.size()); ++index) { for (unsigned int i = 0; i < models.size(); ++i) { if (models[i]) buffer[i] = encodeNoise((*models[i])(bvalues[index]/1000.0,bvectors[index])*spin_density*0.5); // 0.5 volume of water else buffer[i] = encodeNoise(spin_density*exp(-bvalues[index]*0.0016)); // water its coefficient is 0.0016 mm?/s } std::ostringstream out; out << "image" << index; mat_writer.write(out.str().c_str(),&*buffer.begin(),1,buffer.size()); } } // output layout { std::vector<float> float_data; std::vector<short> short_data; ti.save_to_buffer(float_data,short_data); mat_layout.write("odf_vertices",&*float_data.begin(),3,ti.vertices_count); mat_layout.write("odf_faces",&*short_data.begin(),3,ti.faces.size()); mat_layout.write("fa0",&*fa[0].begin(),1,fa[0].size()); mat_layout.write("fa1",&*fa[1].begin(),1,fa[1].size()); mat_layout.write("gfa",&*gfa.begin(),1,gfa.size()); mat_layout.write("index0",&*findex[0].begin(),1,findex[0].size()); mat_layout.write("index1",&*findex[1].begin(),1,findex[1].size()); } }