virtual void end(Voxel& voxel,gz_mat_write& mat_writer)
{
voxel.recon_report
<< " The percentage of the negative signals was " << (float)100.0*total_negative_value/(float)total_value << "%.";
std::vector<float> b_table(4); // space for b0
for (unsigned int index = 0;index < bvectors.size();++index)
{
b_table.push_back(bvalues.front());
std::copy(bvectors[index].begin(),bvectors[index].end(),std::back_inserter(b_table));
}
mat_writer.write("b_table",&b_table[0],4,b_table.size()/4);
unsigned int image_num = 0;
if(!b0.empty())
{
mat_writer.write("image0",&b0[0],1,b0.size());
++image_num;
}
for (unsigned int index = 0;index < dwi.size();++index)
{
std::ostringstream out;
out << "image" << image_num;
mat_writer.write(out.str().c_str(),&(dwi[index][0]),1,dwi[index].size());
++image_num;
}
}
virtual void end(Voxel& voxel,gz_mat_write& mat_writer)
{
mat_writer.write("fa0",&*voxel.fib_fa.begin(),1,voxel.fib_fa.size());
mat_writer.write("dir0",&*voxel.fib_dir.begin(),1,voxel.fib_dir.size());
mat_writer.write("adc",&*md.begin(),1,md.size());
mat_writer.write("axial_dif",&*d0.begin(),1,d0.size());
mat_writer.write("radial_dif",&*d1.begin(),1,d1.size());
}
virtual void end(Voxel& voxel,gz_mat_write& mat_writer)
{
if (!voxel.odf_deconvolusion)
return;
mat_writer.write("deconvolution_kernel",&*voxel.response_function.begin(),1,voxel.response_function.size());
mat_writer.write("free_water_diffusion",&*voxel.free_water_diffusion.begin(),1,voxel.free_water_diffusion.size());
mat_writer.write("sensitivity_error_percentage",&sensitivity_error_percentage,1,1);
mat_writer.write("specificity_error_percentage",&specificity_error_percentage,1,1);
}
virtual void end(Voxel& voxel,gz_mat_write& mat_writer)
{
if (voxel.need_odf)
{
set_title("output odfs");
for (unsigned int index = 0;index < voxel.template_odfs.size();++index)
{
std::ostringstream out;
out << "odf" << index;
mat_writer.write(out.str().c_str(),&*voxel.template_odfs[index].begin(),
voxel.ti.half_vertices_count,
voxel.template_odfs[index].size()/(voxel.ti.half_vertices_count));
}
}
mat_writer.write("trans",&*voxel.param,4,4);
}
virtual void end(Voxel& voxel,gz_mat_write& mat_writer)
{
set_title("output data");
mat_writer.write("gfa",&*gfa.begin(),1,gfa.size());
if(!voxel.odf_deconvolusion && voxel.z0 + 1.0 != 1.0)
{
mat_writer.write("z0",&voxel.z0,1,1);
std::for_each(iso.begin(),iso.end(),boost::lambda::_1 /= voxel.z0);
for (unsigned int i = 0;i < voxel.max_fiber_number;++i)
std::for_each(fa[i].begin(),fa[i].end(),boost::lambda::_1 /= voxel.z0);
}
mat_writer.write("iso",&*iso.begin(),1,iso.size());
for (unsigned int index = 0;index < voxel.max_fiber_number;++index)
{
std::ostringstream out;
out << index;
std::string num = out.str();
std::string fa_str = "fa";
fa_str += num;
set_title(fa_str.c_str());
mat_writer.write(fa_str.c_str(),&*fa[index].begin(),1,fa[index].size());
}
// output normalized qa
{
float max_qa = 0.0;
for (unsigned int i = 0;i < voxel.max_fiber_number;++i)
max_qa = std::max<float>(*std::max_element(fa[i].begin(),fa[i].end()),max_qa);
if(max_qa != 0.0)
for (unsigned int index = 0;index < voxel.max_fiber_number;++index)
{
std::for_each(fa[index].begin(),fa[index].end(),boost::lambda::_1 /= max_qa);
std::ostringstream out;
out << index;
std::string num = out.str();
std::string fa_str = "nqa";
fa_str += num;
set_title(fa_str.c_str());
mat_writer.write(fa_str.c_str(),&*fa[index].begin(),1,fa[index].size());
}
}
}
virtual void end(Voxel& voxel,gz_mat_write& mat_writer)
{
if (!voxel.odf_decomposition)
return;
if(max_iso + 1.0 != 1.0)
std::for_each(fiber_ratio.begin(),fiber_ratio.end(),boost::lambda::_1 /= max_iso);
mat_writer.write("fiber_ratio",&*fiber_ratio.begin(),1,fiber_ratio.size());
}
virtual void end(Voxel& voxel,gz_mat_write& mat_writer)
{
for(unsigned int index = 0;index < max_length;++index)
{
std::ostringstream out;
out << "pdf_" << index << "um";
mat_writer.write(out.str().c_str(),&*dis[index].begin(),1,dis[index].size());
}
for(unsigned int index = 0;index < max_length;++index)
{
std::ostringstream out;
out << "cdf_" << index << "um";
mat_writer.write(out.str().c_str(),&*cdf[index].begin(),1,cdf[index].size());
}
mat_writer.write("fa0",&*dis[0].begin(),1,dis[0].size());
std::vector<short> index0(voxel.dim.size());
mat_writer.write("index0",&*index0.begin(),1,index0.size());
}
virtual void end(Voxel& voxel,gz_mat_write& mat_writer)
{
for (unsigned int index = 0;index < voxel.max_fiber_number;++index)
{
std::ostringstream out;
out << index;
std::string num = out.str();
std::string index_str = "dir";
index_str += num;
set_title(index_str.c_str());
mat_writer.write(index_str.c_str(),&*dir[index].begin(),1,dir[index].size());
}
}
void save_to_file(gz_mat_write& mat_writer)
{
set_title("saving");
// dimension
{
short dim[3];
dim[0] = voxel.dim[0];
dim[1] = voxel.dim[1];
dim[2] = voxel.dim[2];
mat_writer.write("dimension",dim,1,3);
}
// voxel size
mat_writer.write("voxel_size",&*voxel.vs.begin(),1,3);
std::vector<float> float_data;
std::vector<short> short_data;
voxel.ti.save_to_buffer(float_data,short_data);
mat_writer.write("odf_vertices",&*float_data.begin(),3,voxel.ti.vertices_count);
mat_writer.write("odf_faces",&*short_data.begin(),3,voxel.ti.faces.size());
}
virtual void end(Voxel& voxel,gz_mat_write& mat_writer)
{
if (!voxel.need_odf)
return;
{
set_title("output odfs");
for (unsigned int index = 0;index < odf_data.size();++index)
{
if (!voxel.odf_deconvolusion)
std::for_each(odf_data[index].begin(),odf_data[index].end(),boost::lambda::_1 /= voxel.z0);
std::ostringstream out;
out << "odf" << index;
mat_writer.write(out.str().c_str(),&*odf_data[index].begin(),
voxel.ti.half_vertices_count,
odf_data[index].size()/(voxel.ti.half_vertices_count));
}
odf_data.clear();
}
}
virtual void end(Voxel&,gz_mat_write& mat_writer)
{
if(hgqi)
mat_writer.write("hraw",&hraw[0],1,hraw.size());
}