void add_end_roi(const image::geometry<3>& geo,
const std::vector<image::vector<3,short> >& points)
{
end.push_back(std::make_shared<Roi>(geo));
for(unsigned int index = 0; index < points.size(); ++index)
end.back()->addPoint(points[index]);
}
void add_terminate_roi(const image::geometry<3>& geo,
const std::vector<image::vector<3,short> >& points)
{
if(!terminate.get())
terminate.reset(new Roi(geo));
for(unsigned int index = 0; index < points.size(); ++index)
terminate->addPoint(points[index]);
}
void thread_run(unsigned char thread_index,unsigned char thread_count,
const std::vector<unsigned char>& mask)
{
unsigned int sum_mask = std::accumulate(mask.begin(),mask.end(),(unsigned int)0)/thread_count;
unsigned int cur = 0;
for(unsigned int voxel_index = thread_index;
voxel_index < dim.size() &&
(thread_index != 0 || check_prog(cur,sum_mask));voxel_index += thread_count)
{
if (!mask[voxel_index])
continue;
cur += mask[voxel_index];
voxel_data[thread_index].init();
voxel_data[thread_index].voxel_index = voxel_index;
for (int index = 0; index < process_list.size(); ++index)
process_list[index].run(*this,voxel_data[thread_index]);
if(prog_aborted())
break;
}
}
std::pair<float,float> evaluate_fib(
const image::geometry<3>& dim,
const std::vector<std::vector<float> >& fib_fa,
const std::vector<std::vector<float> >& fib_dir)
{
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<image::vector<3> > dis(13);
for(unsigned int i = 0;i < 13;++i)
{
dis[i] = image::vector<3>(dx[i],dy[i],dz[i]);
dis[i].normalize();
}
float otsu = *std::max_element(fib_fa[0].begin(),fib_fa[0].end())*0.1;
std::vector<std::vector<unsigned char> > connected(fib_fa.size());
for(unsigned int index = 0;index < connected.size();++index)
connected[index].resize(dim.size());
float connection_count = 0;
for(image::pixel_index<3> index(dim);index < dim.size();++index)
{
if(fib_fa[0][index.index()] <= otsu)
continue;
unsigned int index3 = index.index()+index.index()+index.index();
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)
{
image::vector<3,int> pos;
pos = j ? image::vector<3,int>(index[0] + dx[i],index[1] + dy[i],index[2] + dz[i])
:image::vector<3,int>(index[0] - dx[i],index[1] - dy[i],index[2] - dz[i]);
if(!dim.is_valid(pos))
continue;
image::pixel_index<3> other_index(pos[0],pos[1],pos[2],dim);
unsigned int other_index3 = other_index.index()+other_index.index()+other_index.index();
if(std::abs(image::vector<3>(&fib_dir[fib1][index3])*dis[i]) <= 0.8665)
continue;
for(unsigned char fib2 = 0;fib2 < num_fib;++fib2)
if(fib_fa[fib2][other_index.index()] > otsu &&
std::abs(image::vector<3>(&fib_dir[fib2][other_index3])*dis[i]) > 0.8665)
{
connected[fib1][index.index()] = 1;
connected[fib2][other_index.index()] = 1;
connection_count += fib_fa[fib2][other_index.index()];
}
}
}
}
float no_connection_count = 0;
for(image::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);
}
virtual void init(Voxel& voxel)
{
if(voxel.vs[0] == 0.0 ||
voxel.vs[1] == 0.0 ||
voxel.vs[2] == 0.0)
throw std::runtime_error("No spatial information found in src file. Recreate src file or contact developer for assistance");
begin_prog("normalization");
VG = fa_template_imp.I;
VF = voxel.fa_map;
image::filter::gaussian(voxel.fa_map);
image::filter::gaussian(voxel.fa_map);
image::filter::gaussian(voxel.qa_map);
image::filter::gaussian(voxel.qa_map);
image::normalize(voxel.fa_map,1.0);
image::normalize(voxel.qa_map,1.0);
for(unsigned int index = 0;index < voxel.qa_map.size();++index)
if(voxel.qa_map[index] == 0.0 || voxel.fa_map[index]/voxel.qa_map[index] > 2.5)
VF[index] = 0.0;
image::filter::gaussian(VF);
src_geo = VF.geometry();
image::normalize(VF,1.0);
//VF.save_to_file<image::io::nifti<> >("VF.nii");
image::normalize(VG,1.0);
// get rid of the gray matters
image::minus_constant(VF.begin(),VF.end(),0.3);
image::lower_threshold(VF.begin(),VF.end(),0.00);
image::normalize(VF,1.0);
image::minus_constant(VG.begin(),VG.end(),0.3);
image::lower_threshold(VG.begin(),VG.end(),0.00);
image::normalize(VG,1.0);
VGvs[0] = std::fabs(fa_template_imp.tran[0]);
VGvs[1] = std::fabs(fa_template_imp.tran[5]);
VGvs[2] = std::fabs(fa_template_imp.tran[10]);
image::affine_transform<3,double> arg_min;
// VG: FA TEMPLATE
// VF: SUBJECT QA
arg_min.scaling[0] = voxel.vs[0] / VGvs[0];
arg_min.scaling[1] = voxel.vs[1] / VGvs[1];
arg_min.scaling[2] = voxel.vs[2] / VGvs[2];
voxel_volume_scale = arg_min.scaling[0]*arg_min.scaling[1]*arg_min.scaling[2];
// calculate center of mass
image::vector<3,double> mF = center_of_mass(VF);
image::vector<3,double> mG = center_of_mass(VG);
arg_min.translocation[0] = mG[0]-mF[0]*arg_min.scaling[0];
arg_min.translocation[1] = mG[1]-mF[1]*arg_min.scaling[1];
arg_min.translocation[2] = mG[2]-mF[2]*arg_min.scaling[2];
bool terminated = false;
set_title("linear registration");
begin_prog("conducting registration");
check_prog(0,2);
image::reg::linear(VF,VG,arg_min,image::reg::affine,image::reg::square_error(),terminated,0.25);
check_prog(1,2);
// create VFF the affine transformed VF
image::basic_image<float,3> VFF(VG.geometry());
{
affine = arg_min;
image::reg::linear_get_trans(VF.geometry(),VG.geometry(),affine);
{
std::vector<double> T(16);
affine.save_to_transform(T.begin());
T[15] = 1.0;
math::matrix_inverse(T.begin(),math::dim<4,4>());
affine.load_from_transform(T.begin());
}
image::resample(VF,VFF,affine);
//VFF.save_to_file<image::io::nifti<> >("VFF.nii");
//VG.save_to_file<image::io::nifti<> >("VG.nii");
}
{
switch(voxel.reg_method)
{
case 0:
mni.normalize(VG,VFF);
break;
case 1:
mni.normalize(VG,VFF,12,14,12,4,8);
break;
}
//calculate the goodness of fit
std::vector<float> x,y;
x.reserve(VG.size());
y.reserve(VG.size());
image::interpolation<image::linear_weighting,3> trilinear_interpolation;
for(image::pixel_index<3> index;VG.geometry().is_valid(index);
index.next(VG.geometry()))
if(VG[index.index()] != 0)
{
image::vector<3,double> pos;
mni.warp_coordinate(index,pos);
double value = 0.0;
if(!trilinear_interpolation.estimate(VFF,pos,value))
continue;
x.push_back(VG[index.index()]);
y.push_back(value);
}
R2 = x.empty() ? 0.0 : image::correlation(x.begin(),x.end(),y.begin());
R2 *= R2;
std::cout << "R2 = " << R2 << std::endl;
}
check_prog(2,2);
// setup output bounding box
{
//setBoundingBox(-78,-112,-50,78,76,85,1.0);
float voxel_size = voxel.param[1];
bounding_box_lower[0] = std::floor(-78.0/voxel_size+0.5)*voxel_size;
bounding_box_lower[1] = std::floor(-112.0/voxel_size+0.5)*voxel_size;
bounding_box_lower[2] = std::floor(-50.0/voxel_size+0.5)*voxel_size;
bounding_box_upper[0] = std::floor(78.0/voxel_size+0.5)*voxel_size;
bounding_box_upper[1] = std::floor(76.0/voxel_size+0.5)*voxel_size;
bounding_box_upper[2] = std::floor(85.0/voxel_size+0.5)*voxel_size;
des_geo[0] = (bounding_box_upper[0]-bounding_box_lower[0])/voxel_size+1;//79
des_geo[1] = (bounding_box_upper[1]-bounding_box_lower[1])/voxel_size+1;//95
des_geo[2] = (bounding_box_upper[2]-bounding_box_lower[2])/voxel_size+1;//69
des_offset[0] = bounding_box_lower[0]/VGvs[0]-fa_template_imp.tran[3]/fa_template_imp.tran[0];
des_offset[1] = bounding_box_lower[1]/VGvs[1]-fa_template_imp.tran[7]/fa_template_imp.tran[5];
des_offset[2] = bounding_box_lower[2]/VGvs[2]-fa_template_imp.tran[11]/fa_template_imp.tran[10];
scale[0] = voxel_size/VGvs[0];
scale[1] = voxel_size/VGvs[1];
scale[2] = voxel_size/VGvs[2];
}
begin_prog("q-space diffeomorphic reconstruction");
float sigma = voxel.param[0]; //diffusion sampling length ratio, optimal 1.24
// setup mask
{
// set the current mask to template space
voxel.image_model->set_dimension(des_geo[0],des_geo[1],des_geo[2]);
for(image::pixel_index<3> index;des_geo.is_valid(index);index.next(des_geo))
{
image::vector<3,int> mni_pos(index);
mni_pos *= voxel.param[1];
mni_pos[0] /= VGvs[0];
mni_pos[1] /= VGvs[1];
mni_pos[2] /= VGvs[2];
mni_pos += des_offset;
voxel.image_model->mask[index.index()] =
fa_template_imp.I.at(mni_pos[0],mni_pos[1],mni_pos[2]) > 0.0? 1: 0;
}
}
q_vectors_time.resize(voxel.bvalues.size());
for (unsigned int index = 0; index < voxel.bvalues.size(); ++index)
{
q_vectors_time[index] = voxel.bvectors[index];
q_vectors_time[index] *= std::sqrt(voxel.bvalues[index]*0.01506);// get q in (mm) -1
q_vectors_time[index] *= sigma;
}
b0_index = -1;
if(voxel.half_sphere)
for(unsigned int index = 0;index < voxel.bvalues.size();++index)
if(voxel.bvalues[index] == 0)
b0_index = index;
ptr_images.clear();
for (unsigned int index = 0; index < voxel.image_model->dwi_data.size(); ++index)
ptr_images.push_back(point_image_type((const unsigned short*)voxel.image_model->dwi_data[index],src_geo));
voxel.qa_scaling = voxel.reponse_function_scaling/voxel.vs[0]/voxel.vs[1]/voxel.vs[2];
max_accumulated_qa = 0;
std::fill(voxel.vs.begin(),voxel.vs.end(),voxel.param[1]);
jdet.resize(des_geo.size());
if (voxel.odf_deconvolusion)
{
gqi.init(voxel);
deconvolution.init(voxel);
}
if (voxel.odf_decomposition)
{
gqi.init(voxel);
decomposition.init(voxel);
}
angle_variance = 8; //degress;
angle_variance *= M_PI/180;
angle_variance *= angle_variance;
angle_variance *= 2.0;
}
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 = 0.2;
float fiber_fraction = 1.0-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(image::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 = 1.0-xf;//0.00 to 0.98
xf = 0.5+0.5*xf;//0.50 to 0.99
float angle = ((float)y - boundary)/((float)phantom_width);//0.00 to 0.98
angle = 1.0-angle;//0.02 to 1.00
angle *= M_PI*0.5;//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(image::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(image::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());
}
}