C++ volume::ydim方法代码示例

//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;
		  }
	      }
//.........这里部分代码省略.........

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;
      
//.........这里部分代码省略.........

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));
//.........这里部分代码省略.........