//calculates the mask from the mesh by spreading an initial point outside the mesh, and stopping it when the mesh is reached.
volume<short> make_mask_from_mesh(const volume<float> & image, const Mesh& m)
{
// cout<<"make_mask_from_mesh begins"<<endl;
double xdim = (double) image.xdim();
double ydim = (double) image.ydim();
double zdim = (double) image.zdim();
volume<short> mask;
copyconvert(image,mask);
int xsize = mask.xsize();
int ysize = mask.ysize();
int zsize = mask.zsize();
mask = 1;
mask = draw_mesh(mask, m);
vector<Pt> current;
current.clear();
Pt c(0., 0., 0.);
for (vector<Mpoint *>::const_iterator it=m._points.begin(); it!=m._points.end(); it++)
c+=(*it)->get_coord();
c*=(1./m._points.size());
c.X/=xdim; c.Y/=ydim; c.Z/=zdim;
current.push_back(c);
while (!current.empty())
{
Pt pc = current.back();
int x, y, z;
x=(int) pc.X; y=(int) pc.Y; z=(int) pc.Z;
//current.remove(pc);
current.pop_back();
mask.value(x, y, z) = 0;
if (0<=x-1 && mask.value(x-1, y, z)==1) current.push_back(Pt(x-1, y, z));
if (0<=y-1 && mask.value(x, y-1, z)==1) current.push_back(Pt(x, y-1, z));
if (0<=z-1 && mask.value(x, y, z-1)==1) current.push_back(Pt(x, y, z-1));
if (xsize>x+1 && mask.value(x+1, y, z)==1) current.push_back(Pt(x+1, y, z));
if (ysize>y+1 && mask.value(x, y+1, z)==1) current.push_back(Pt(x, y+1, z));
if (zsize>z+1 && mask.value(x, y, z+1)==1) current.push_back(Pt(x, y, z+1));
}
// cout<<"make_mask_from_mesh ends"<<endl;
return mask;
}
void draw_segment(volume<short>& image, const Pt& p1, const Pt& p2)
{
double xdim = (double) image.xdim();
double ydim = (double) image.ydim();
double zdim = (double) image.zdim();
double mininc = min(xdim,min(ydim,zdim)) * .5;
Vec n = p1 - p2;
double d = n.norm();
n.normalize();
for (double i=0; i<=d; i+=mininc)
{
Pt p = p2 + i* n;
image((int) floor((p.X)/xdim +.5),(int) floor((p.Y)/ydim +.5),(int) floor((p.Z)/zdim +.5)) = 1;
}
}
void draw_mesh(volume<short>& image, const Mesh &m)
{
double xdim = (double) image.xdim();
double ydim = (double) image.ydim();
double zdim = (double) image.zdim();
double mininc = min(xdim,min(ydim,zdim)) * .5;
for (list<Triangle*>::const_iterator i = m._triangles.begin(); i!=m._triangles.end(); i++)
{
Vec n = (*(*i)->get_vertice(0) - *(*i)->get_vertice(1));
double d = n.norm();
n.normalize();
for (double j=0; j<=d; j+=mininc)
{
Pt p = (*i)->get_vertice(1)->get_coord() + j* n;
draw_segment(image, p, (*i)->get_vertice(2)->get_coord());
}
}
}
void basisfield::Set(const volume<float>& pfield)
{
if (int(FieldSz_x()) != pfield.xsize() || int(FieldSz_y()) != pfield.ysize() || int(FieldSz_z()) != pfield.zsize()) {
throw BasisfieldException("basisfield::Set:: Matrix size mismatch beween basisfield class and supplied field");
}
if (Vxs_x() != pfield.xdim() || Vxs_y() != pfield.ydim() || Vxs_z() != pfield.zdim()) {
throw BasisfieldException("basisfield::Set:: Voxel size mismatch beween basisfield class and supplied field");
}
volume<float> volume_of_ones(pfield.xsize(),pfield.ysize(),pfield.zsize());
volume_of_ones.copyproperties(pfield);
volume_of_ones = 1.0;
double lambda = 0.001;
ColumnVector y = Jte(pfield,0);
boost::shared_ptr<MISCMATHS::BFMatrix> XtX = JtJ(volume_of_ones);
boost::shared_ptr<MISCMATHS::BFMatrix> BeEn = BendEnergyHess();
XtX->AddToMe(*BeEn,lambda);
ColumnVector coef_roof = XtX->SolveForx(y,SYM_POSDEF,1e-6,500);
SetCoef(coef_roof);
}
void basisfield::AsVolume(volume<float>& vol, FieldIndex fi)
{
if (int(FieldSz_x()) != vol.xsize() || int(FieldSz_y()) != vol.ysize() || int(FieldSz_z()) != vol.zsize()) {
throw BasisfieldException("basisfield::AsVolume:: Matrix size mismatch beween field and volume");
}
if (Vxs_x() != vol.xdim() || Vxs_y() != vol.ydim() || Vxs_z() != vol.zdim()) {
throw BasisfieldException("basisfield::AsVolume:: Voxel size mismatch beween field and volume");
}
if (!coef) {throw BasisfieldException("basisfield::AsVolume: Coefficients undefined");}
if (!UpToDate(fi)) {Update(fi);}
const boost::shared_ptr<NEWMAT::ColumnVector> tmptr = Get(fi);
int vindx=0;
for (unsigned int k=0; k<FieldSz_z(); k++) {
for (unsigned int j=0; j<FieldSz_y(); j++) {
for (unsigned int i=0; i<FieldSz_x(); i++) {
vol(i,j,k) = tmptr->element(vindx++);
}
}
}
}
volume<float> draw_mesh_bis(const volume<float>& image, const Mesh &m)
{
double xdim = (double) image.xdim();
double ydim = (double) image.ydim();
double zdim = (double) image.zdim();
double mininc = min(xdim,min(ydim,zdim)) * .5;
volume<float> res = image;
double max = image.max();
for (list<Triangle*>::const_iterator i = m._triangles.begin(); i!=m._triangles.end(); i++)
{
Vec n = (*(*i)->get_vertice(0) - *(*i)->get_vertice(1));
double d = n.norm();
n.normalize();
for (double j=0; j<=d; j+=mininc)
{
Pt p = (*i)->get_vertice(1)->get_coord() + j* n;
draw_segment_bis(res, p, (*i)->get_vertice(2)->get_coord(), max);
}
}
return res;
}
//writes externall skull computed from image on output.
void t1only_write_ext_skull(volume<float> & output_inskull, volume<float> & output_outskull, volume<float> & output_outskin, const volume<float> & t1, const Mesh & m, const trMatrix & M) {
int glob_counter = 0;
int rem_counter = 0;
const double xdim = t1.xdim();
const double ydim = t1.ydim();
const double zdim = t1.zdim();
double imax = t1.max();
if (imax == 0) imax = 1;
volume<short> meshimage;
copyconvert(t1, meshimage);
meshimage = 0;
draw_mesh(meshimage, m);
for (vector<Mpoint*>::const_iterator i = m._points.begin(); i != m._points.end(); i++)
{
(*i)->data.clear();
double max_neighbour = 0;
const Vec normal = (*i)->local_normal();
const Vec n = Vec(normal.X/xdim, normal.Y/ydim, normal.Z/zdim);
for (list<Mpoint*>::const_iterator nei = (*i)->_neighbours.begin(); nei != (*i)->_neighbours.end(); nei++)
max_neighbour = Max(((**i) - (**nei)).norm(), max_neighbour);
max_neighbour = ceil((max_neighbour)/2);
const Pt mpoint((*i)->get_coord().X/xdim,(*i)->get_coord().Y/ydim,(*i)->get_coord().Z/zdim);
for (int ck = (int)floor(mpoint.Z - max_neighbour/zdim); ck <= (int)floor(mpoint.Z + max_neighbour/zdim); ck++)
for (int cj = (int)floor(mpoint.Y - max_neighbour/ydim); cj <= (int)floor(mpoint.Y + max_neighbour/ydim); cj++)
for (int ci = (int)floor(mpoint.X - max_neighbour/xdim); ci <= (int)floor(mpoint.X + max_neighbour/xdim); ci++)
{
bool compute = false;
const Pt point(ci, cj, ck);
const Pt realpoint(ci*xdim, cj*ydim, ck*zdim);
if (meshimage(ci, cj, ck) == 1)
{
double mindist = 10000;
for (list<Mpoint*>::const_iterator nei = (*i)->_neighbours.begin(); nei != (*i)->_neighbours.end(); nei++)
mindist = Min(((realpoint) - (**nei)).norm(), mindist);
if (mindist >= ((realpoint) - (**i)).norm()) compute = true;
}
if (compute)
{
glob_counter ++;
vector<double> val;
if (!special_case(realpoint, normal, M))
val = t1only_co_ext(t1, point, n);
else
{
val = t1only_special_extract(t1, point, n);
}
if (val.size() == 3)
{
Pt opoint(point.X, point.Y, point.Z);
Vec on(n.X, n.Y, n.Z);
Pt c0 = opoint + val[0]*on;
Pt c1 = opoint + val[1]*on;
Pt c2 = opoint + val[2]*on;
output_inskull((int)floor(c0.X + .5) + infxm,(int) floor(c0.Y + .5) + infym,(int) floor(c0.Z + .5) + infzm) +=1;
output_outskull((int)floor(c1.X + .5) + infxm,(int) floor(c1.Y + .5) + infym,(int) floor(c1.Z + .5) + infzm)+=1;
output_outskin((int)floor(c2.X + .5) + infxm,(int) floor(c2.Y + .5) + infym,(int) floor(c2.Z + .5) + infzm) +=1;
}
else {
rem_counter++;
if (val.size()==1)
{
Pt opoint(point.X, point.Y, point.Z);
Vec on(n.X, n.Y, n.Z);
Pt c0 = opoint + val[0]*on;
output_outskin((int)floor(c0.X + .5) + infxm,(int) floor(c0.Y + .5) + infym,(int) floor(c0.Z + .5) + infzm) +=1;
}
}
}
}
}
if (verbose.value())
{
cout<<" nb of profiles : "<<glob_counter<<endl;
cout<<" removed profiles : "<<100. * rem_counter/(double) glob_counter<<"%"<<endl;
}
}
double standard_step_of_computation(const volume<float> & image, Mesh & m, const int iteration_number, const double E,const double F, const float addsmooth, const float speed, const int nb_iter, const int id, const int od, const bool vol, const volume<short> & mask){
double xdim = image.xdim();
double ydim = image.ydim();
double zdim = image.zdim();
if (nb_iter % 50 == 0)
{
double l2 = 0;
int counter = 0;
for (vector<Mpoint*>::iterator i = m._points.begin(); i!=m._points.end(); i++ )
{
counter++;
l2 += (*i)->medium_distance_of_neighbours();
}
l = l2/counter;
}
if (nb_iter % 100 == 0)
{
for (vector<Mpoint*>::iterator i = m._points.begin(); i!=m._points.end(); i++)
{
Vec n = (*i)->local_normal();
Pt point = (*i)->get_coord();
Pt ipoint(point.X/xdim, point.Y/ydim, point.Z/zdim);
Vec in(n.X/xdim, n.Y/ydim, n.Z/zdim);
double max = 0;
Pt c_m1 = ipoint + (-1) * in;
double current = image.interpolate((c_m1.X),(c_m1.Y),(c_m1.Z));
for (double i2 = 1; i2 < 150; i2+=2)
{
if (max > .1) break;
Pt c_p = ipoint + i2 * in;
double tmpp = image.interpolate((c_p.X),(c_p.Y),(c_p.Z));
double tmp = (tmpp - current) * 100;
max = Max(max, tmp);
current = tmpp;
if (tmpp > .1) {max = 1; break;}
}
if (max < .1)
{
//There is a problem here for precision mode, since with the copy, no guarantee that data is non-zero size
//even if mesh.cpp operator = is modified to copy data, after retesselate "new" points will have zero size data member
if ( (*i)->data.size() ) (*i)->data.pop_back();
(*i)->data.push_back(1);
}
else
{
if ( (*i)->data.size() ) (*i)->data.pop_back();
(*i)->data.push_back(0);
}
}
}
for (vector<Mpoint*>::iterator i = m._points.begin(); i!=m._points.end(); i++)
{
Vec sn, st, u1, u2, u3, u;
double f2, f3=0;
Vec n = (*i)->local_normal();
Vec dv = (*i)->difference_vector();
double tmp = dv|n;
sn = n * tmp;
st = dv - sn;
u1 = st*.5;
double rinv = (2 * fabs(sn|n))/(l*l);
f2 = (1+tanh(F*(rinv - E)))*0.5;
u2 = f2 * sn * addsmooth;
if ((*i)->data.back() == 0)
{
//main term of skull_extraction
{
Pt point = (*i)->get_coord();
Pt ipoint(point.X/xdim, point.Y/ydim, point.Z/zdim);
Vec in(n.X/xdim, n.Y/ydim, n.Z/zdim);
Pt c_m = ipoint + (-1.) * in;
Pt c_p = ipoint + 1. * in;
double tmp = image.interpolate((c_p.X ),( c_p.Y),(c_p.Z));
double gradient = tmp - image.interpolate((c_m.X),(c_m.Y), (c_m.Z));
double tmp2 = gradient*100;
f3 = max(-1., min(tmp2, 1.));
if (tmp2 >= 0 && tmp2 < .1 && tmp < .1 ) f3 = speed;
if (vol)
{
double tmpvol = mask.interpolate((ipoint.X ),(ipoint.Y),(ipoint.Z));
if (tmpvol > .0)
{
f3 = Max(Max(tmpvol*.5, .1), f3);
f2 = 0;
}
}
}
}
else
{
f3 = 0;
Pt point = (*i)->get_coord();
Pt ipoint(point.X/xdim, point.Y/ydim, point.Z/zdim);
double tmpvol = mask.interpolate((ipoint.X ),(ipoint.Y),(ipoint.Z));
if (tmpvol > .0)
{
f3 = Max(tmpvol*.5, .1);
f2 = 0;
}
}
u3 = .05 * f3 * n;
u = u1 + u2 + u3;
(*i)->_update_coord = (*i)->get_coord() + u;
}
m.update();
return (0);
}
double step_of_computation(const volume<float> & image, Mesh & m, const double bet_main_parameter, const int pass, const double increase_smoothing, const int iteration_number, double & l, const double t2, const double tm, const double t, const double E,const double F, const double zcog, const double radius, const double local_th=0., const int d1=7, const int d2=3){
double xdim = image.xdim();
double ydim = image.ydim();
double zdim = image.zdim();
if (iteration_number==50 || iteration_number%100 == 0 )
{
l = 0;
int counter = 0;
for (vector<Mpoint*>::iterator i = m._points.begin(); i!=m._points.end(); i++ )
{
counter++;
l += (*i)->medium_distance_of_neighbours();
}
l/=counter;
}
for (vector<Mpoint*>::iterator i = m._points.begin(); i!=m._points.end(); i++)
{
Vec sn, st, u1, u2, u3, u;
double f2, f3=0;
Vec n = (*i)->local_normal();
Vec dv = (*i)->difference_vector();
double tmp = dv|n;
sn = n * tmp;
st = dv - sn;
u1 = st*.5;
double rinv = (2 * fabs(sn|n))/(l*l);
f2 = (1+tanh(F*(rinv - E)))*0.5;
if (pass > 0)
if (tmp > 0) {
f2*=increase_smoothing;
f2 = Min(f2, 1.);
}
u2 = f2 * sn;
//main term of bet
{
double local_t = bet_main_parameter;
if (local_th != 0.0)
{
local_t = Min(1., Max(0., bet_main_parameter + local_th*((*i)->get_coord().Z - zcog)/radius));
}
double Imin = tm;
double Imax = t;
Pt p = (*i)->get_coord() + (-1)*n;
double iv = p.X/xdim + .5, jv = p.Y/ydim +.5, kv = p.Z/zdim +.5;
if (image.in_bounds((int)iv,(int) jv,(int) kv))
{
double im=image.value((int)iv,(int)jv,(int)kv);
Imin = Min(Imin, im);
Imax = Max(Imax,im);
double nxv=n.X/xdim, nyv=n.Y/ydim, nzv=n.Z/zdim;
int i2=(int)(iv-(d1-1)*nxv), j2 =(int) (jv-(d1-1)*nyv), k2 =(int)(kv-(d1-1)*nzv);
if (image.in_bounds(i2, j2, k2))
{
im=image.value(i2,j2,k2);
Imin = Min(Imin, im);
for (int gi=2; gi<d1; gi++)
{
// the following is a quick calc of Pt p = (*i)->get_coord() + (-gi)*n;
iv-=nxv; jv-=nyv; kv-=nzv;
im = image.value((int) (iv), (int) (jv), (int) (kv));
Imin = Min(Imin, im);
if (gi<d2)
Imax = Max(Imax,im);
}
Imin = Max (t2, Imin);
Imax = Min (tm, Imax);
const double tl = (Imax - t2) * local_t + t2;
if (Imax - t2 > 0)
f3=2*(Imin - tl)/(Imax - t2);
else f3=(Imin - tl)*2;
}
}
}
f3 *= (normal_max_update_fraction * lambda_fit * l);
u3 = f3 * n;
u = u1 + u2 + u3;
//cout<<"l "<<l<<"u1 "<<((u1*n).norm())<<"u2 "<<(u2|n)<<"u3 "<<(u3|n)<<endl;
(*i)->_update_coord = (*i)->get_coord() + u;
}
m.update();
return (0);
}
bet_parameters adjust_initial_mesh(const volume<float> & image, Mesh& m, const double & rad = 0., const double xpara=0., const double ypara=0., const double zpara=0.)
{
bet_parameters bp;
double xdim = image.xdim();
double ydim = image.ydim();
double zdim = image.zdim();
double t2, t98, t;
//computing t2 && t98
// cout<<"computing robust min && max begins"<<endl;
bp.min = image.min();
bp.max = image.max();
t2 = image.robustmin();
t98 = image.robustmax();
//t2=32.;
//t98=16121.;
// cout<<"computing robust min && max ends"<<endl;
t = t2 + .1*(t98 - t2);
bp.t98 = t98;
bp.t2 = t2;
bp.t = t;
// cout<<"t2 "<<t2<<" t98 "<<t98<<" t "<<t<<endl;
// cout<<"computing center && radius begins"<<endl;
//finds the COG
Pt center(0, 0, 0);
double counter = 0;
if (xpara == 0. & ypara==0. & zpara==0.)
{
double tmp = t - t2;
for (int k=0; k<image.zsize(); k++)
for (int j=0; j<image.ysize(); j++)
for (int i=0; i<image.xsize(); i++)
{
double c = image(i, j, k ) - t2;
if (c > tmp)
{
c = min(c, t98 - t2);
counter+=c;
center += Pt(c*i*xdim, c*j*ydim, c*k*zdim);
}
}
center=Pt(center.X/counter, center.Y/counter, center.Z/counter);
//cout<<counter<<endl;
// cout<<"cog "<<center.X<<" "<<center.Y<<" "<<center.Z<<endl;
}
else center=Pt(xpara, ypara, zpara);
bp.cog = center;
if (rad == 0.)
{
double radius=0;
counter=0;
double scale=xdim*ydim*zdim;
for (int k=0; k<image.zsize(); k++)
for (int j=0; j<image.ysize(); j++)
for (int i=0; i<image.xsize(); i++)
{
double c = image(i, j, k);
if (c > t)
{
counter+=1;
}
}
radius = pow (.75 * counter*scale/M_PI, 1.0/3.0);
// cout<<radius<<endl;
bp.radius = radius;
}
else (bp.radius = rad);
m.translation(center.X, center.Y, center.Z);
m.rescale (bp.radius/2, center);
// cout<<"computing center && radius ends"<<endl;
//computing tm
// cout<<"computing tm begins"<<endl;
vector<double> vm;
for (int k=0; k<image.zsize(); k++)
for (int j=0; j<image.ysize(); j++)
for (int i=0; i<image.xsize(); i++)
{
double d = image.value(i, j, k);
Pt p(i*xdim, j*ydim, k*zdim);
if (d > t2 && d < t98 && ((p - center)|(p - center)) < bp.radius * bp.radius)
vm.push_back(d);
}
int med = (int) floor(vm.size()/2.);
// cout<<"before sort"<<endl;
nth_element(vm.begin(), vm.begin() + med - 1, vm.end());
//partial_sort(vm.begin(), vm.begin() + med + 1, vm.end());
//double tm = vm[med];
double tm=(*max_element(vm.begin(), vm.begin() + med));
// cout<<"tm "<<tm<<endl;
bp.tm = tm;
// cout<<"computing tm ends"<<endl;
return bp;
}
