Exemple #1
0
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);
}
Exemple #2
0
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);
                }

            }
        }
    }
}
Exemple #3
0
    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());

        }


    }