void save_fib(const std::string& ext)
{
std::string output_name = file_name;
output_name += ext;
begin_prog("saving data");
gz_mat_write mat_writer(output_name.c_str());
save_to_file(mat_writer);
voxel.end(mat_writer);
std::string final_report = voxel.report.c_str();
final_report += voxel.recon_report.str();
mat_writer.write("report",final_report.c_str(),1,final_report.length());
}
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());
}
}
