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());
}
}
