// transforms a 4D Volume in a SVM samples file, based on a mask
void saveSVMFile(volume4D <float> &volSamples, volume<float> &mask, const char *outputFileName, float minValue, vector <int > &indexes, vector <int> &classes)
{
	FILE *f;
	f = fopen(outputFileName, "wt+");
	if (f != NULL)
	{
		int i, t;
		for (int h = 0; h < indexes.size(); h++)
		{
			// picking the right indexes
			t = indexes[h] - 1;
			i = 0;
			// saving the class value. Remember indexes size is different from classes. classes has the same sime of the number of volumes
			fprintf(f, "%d ", classes[t]);
			for (int z = 0; z < mask.zsize(); z++)
				for (int y = 0; y < mask.ysize(); y++)
					for (int x = 0; x < mask.xsize(); x++)
						if (mask.value(x, y, z) > minValue)
						{
							i++;
							// writing each voxel value in svm format
							fprintf(f, "%d:%f ", i, volSamples.value(x, y, z, t));
						}
			fprintf(f, "\n");
		}
		fclose(f);
	}
}

FnirtFileWriter::FnirtFileWriter(const string&              fname,
				 const volume<float>&       fieldx,                         
			         const volume<float>&       fieldy,                         
			         const volume<float>&       fieldz)
{
  volume<float>  tmp(fieldx.xsize(),fieldx.ysize(),fieldx.zsize());
  tmp.copyproperties(fieldx);
  Matrix         aff = IdentityMatrix(4);

  common_field_construction(fname,tmp,fieldx,fieldy,fieldz,aff);
}

volume<float> inside_mesh(const volume<float> & image, const Mesh& m)
{
  volume<float> res = image;
  int xsize = image.xsize();
  int ysize = image.ysize();
  int zsize = image.zsize();
  volume<short> inside = make_mask_from_mesh(image, m);
  for (int k=0; k<zsize; k++)
    for (int j=0; j<ysize; j++)
      for (int i=0; i<xsize; i++)
	res.value(i, j, k) = (1-inside.value(i, j, k)) * image.value(i, j, k);
  return res;
}

//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;
}

// calculates the mean for each roi
void RoiMeanCalculation::calculateMeans(volume<float> &actualvolume)
{
	if (means.size())
	{
		for (int i = 0; i < means.size(); i++) means[i] = 0;

		for (int z = 0; z < reference.zsize(); z++)
			for (int y = 0; y < reference.ysize(); y++)
				for (int x = 0; x < reference.xsize(); x++)
				{
					float value = reference.value(x, y, z);
					if (value != 0)
					{
						int idx = mapping[value];
						if (idx >= -1)
							means[idx] += actualvolume.value(x, y, z);
					}
				}

		for (int i = 0; i < means.size(); i++)
		{
			if (counts[i]) means[i] = means[i] / (float)counts[i];
		}
	}
}

//extracts profiles in the area around the eyes
vector<double> t1only_special_extract(const volume<float> & t1, const Pt & point, const Vec & n) {
  vector<double> resul;
  resul.clear();
  bool output = true; 
  const double INNER_DEPTH = 3;
  const double OUTER_DEPTH = 100;
  
  Profile pt1;
  for (double d = -INNER_DEPTH; d < OUTER_DEPTH; d+=.5)
    {
      Pt c = point + d * n;
      double tmp1 = t1.interpolate(c.X, c.Y, c.Z);
      pt1.add (d, tmp1);
    }
  pt1.init_roi();

  //outer skin
  double outskin = pt1.last_point_over(pt1.end(), .2);
  double check = pt1.last_point_over(outskin - 1.5, .2);
  if (outskin - check > 2) output = false;
  
  pt1.set_rroi(outskin);
  
  double inskull = pt1.next_point_under(-INNER_DEPTH, .25);
  if (inskull > 5) inskull = 0;
  
  double outskull = pt1.next_point_over(inskull, .35);
  
  resul.push_back(inskull);
  resul.push_back(outskull);
  resul.push_back(outskin);
  
  return resul;
}

void _volume2Sample(svm_model *model, volume<float> &volSample, volume<float> &mask, int sampleSize, float minValue, svm_node * &sample)
{	
	sample=(struct svm_node *) malloc((sampleSize+1)*sizeof(struct svm_node));
    
	int i=0;
    for(int z=0; z < volSample.zsize();z++)
      for(int y=0; y < volSample.ysize();y++)
	     for(int x=0; x < volSample.xsize();x++)
         if (mask.value(x,y,z) > minValue)
		   {
             sample[i].index = (i+1);
		       sample[i].value = volSample.value(x,y,z);
				 i++;
			}
    sample[i].index = -1;
}

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 check_integral(fields &f,
		    linear_integrand_data &d, const volume &v,
		    component cgrid)
{
  double x1 = v.in_direction_min(d.dx);
  double x2 = v.in_direction_max(d.dx);
  double y1 = v.in_direction_min(d.dy);
  double y2 = v.in_direction_max(d.dy);
  double z1 = v.in_direction_min(d.dz);
  double z2 = v.in_direction_max(d.dz);
  
  master_printf("Check %d-dim. %s integral in %s cell with %s integrand...",
		(x2 - x1 > 0) + (y2 - y1 > 0) + (z2 - z1 > 0), 
		component_name(cgrid),
		v.dim == D3 ? "3d" : (v.dim == D2 ? "2d" : 
				       (v.dim == Dcyl ? "cylindrical" 
					: "1d")),
		(d.c == 1.0 && !d.axy && !d.ax && !d.ay && !d.az
		 && !d.axy && !d.ayz && !d.axz) ? "unit" : "linear");
  if (0)
    master_printf("\n... grid_volume (%g,%g,%g) at (%g,%g,%g) with integral (%g, %g,%g,%g, %g,%g,%g, %g)...\n",
		  x2 - x1, y2 - y1, z2 - z1,
		  (x1+x2)/2, (y1+y2)/2, (z1+z2)/2,
		  d.c, d.ax,d.ay,d.az, d.axy,d.ayz,d.axz, d.axyz);

  double sum = real(f.integrate(0, 0, linear_integrand, (void *) &d, v));
  if (fabs(sum - correct_integral(v, d)) > 1e-9 * fabs(sum))
    abort("FAILED: %0.16g instead of %0.16g\n", 
	  (double) sum, correct_integral(v, d));
  master_printf("...PASSED.\n");
}

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;
}

// transforms an array in a volume
void array2Volume(const char *maskFile, float minValue, vector <double> &weightVector, volume<float> &weightVolume)
{
	volume<float> mask;
    if (maskFile != NULL)
    {
      string Maskfile = maskFile;
      read_volume(mask, Maskfile);
    }

	weightVolume.reinitialize(mask.xsize(), mask.ysize(), mask.zsize(), 0, true);
    weightVolume.copyproperties(mask);
	int i = 0;
	for(int z=0;z < mask.zsize();z++)
	   for(int y=0;y < mask.ysize();y++)
		  for(int x=0;x < mask.xsize();x++)
			 if (mask.value(x,y,z) > minValue)
			 {
				 weightVolume.value(x,y,z) = (float) weightVector[i];
				 i++;
			 }
			 else weightVolume.value(x,y,z) = (float) 0.0;
}

void vega::data::hexagonal_prismatic_lattice::fill_volume_cell( volume& v, const prismatic_hexagon_node & node )
{
    static const int hex_pixel_offset[8][2] = { {1, 0}, {2, 0}, {0, 1}, {1, 1}, {2, 1}, {3, 1}, {1, 2}, {2, 2}};

    math::vector3d vertex = node.get_vertex();

    for(size_t h=0;h<8;++h)
    {
        math::vector3d pixel;
        int xx = (int)vertex.x + hex_pixel_offset[h][0];
        int yy = (int)vertex.y + hex_pixel_offset[h][1];
        int zz = (int)vertex.z;
        if( xx >= 0 && yy >= 0 && zz >= 0 && xx < v.get_width() && yy < v.get_height() && zz < v.get_depth() )
        {
#ifndef USE_COLOR_MAP
            v.set_voxel(xx, yy, zz, (voxel)(node.density * 255.f));
#else
            v.set_voxel(xx, yy, zz, (voxel)(node.color.A));
#endif
        }
    }
}

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++);
      }
    }
  }
}

// returns in `output` the best voxels of `region`
void RegionExtraction::regionBestVoxels(RoiMeanCalculation &reference, volume<float>&values, volume<float>&output, int region, int regionSize, float percentage)
{
   vector<roiPoint> roi;
   roi.resize(regionSize);
   greaterRoiPoint greaterFirst;
   int index=0;
   
   // Filter the voxels of the region `region`
   for(int z=0;z<values.zsize();z++)
      for(int y=0;y<values.ysize();y++)
         for(int x=0;x<values.xsize();x++)
         {
            // get the voxel intensity in reference
            int voxelRegion = (int) reference.voxelValues(x,y,z);
            
            // if is the chosen region, records the voxel values (T values or other voxel value)
            if (region == voxelRegion)
            {
               roi[index].value = values.value(x,y,z);
               roi[index].roiValue = region;
               
               roi[index].x=x;
               roi[index].y=y;
               roi[index].z=z;
               index++;
            }
            else values.value(x,y,z)=(float)0.0;
         }
   
   // sorts the vector of values in descending order
   std::sort(roi.begin(), roi.end(), greaterFirst);
   
   // calculates the cut Index. Remember the voxels descending order
   int cutIndex = (int) (roi.size() * percentage + 0.5);
   
   // recording the result in `output`
   for (int j=0; j<=cutIndex;j++)
   {
      output.value(roi[j].x, roi[j].y, roi[j].z) = roi[j].roiValue;
   }
}

static double correct_integral(const volume &v,
			       const linear_integrand_data &data)
{
  direction x = data.dx, y = data.dy, z = data.dz;
  double x1 = v.in_direction_min(x);
  double x2 = v.in_direction_max(x);
  double y1 = v.in_direction_min(y);
  double y2 = v.in_direction_max(y);
  double z1 = v.in_direction_min(z);
  double z2 = v.in_direction_max(z);

  return (data.c * integral1(x1,x2,x) * integral1(y1,y2,y) * integral1(z1,z2,z)
       + data.ax * integralx(x1,x2,x) * integral1(y1,y2,y) * integral1(z1,z2,z)
       + data.ay * integral1(x1,x2,x) * integralx(y1,y2,y) * integral1(z1,z2,z)
       + data.az * integral1(x1,x2,x) * integral1(y1,y2,y) * integralx(z1,z2,z)
      + data.axy * integralx(x1,x2,x) * integralx(y1,y2,y) * integral1(z1,z2,z)
      + data.ayz * integral1(x1,x2,x) * integralx(y1,y2,y) * integralx(z1,z2,z)
      + data.axz * integralx(x1,x2,x) * integral1(y1,y2,y) * integralx(z1,z2,z)
     + data.axyz * integralx(x1,x2,x) * integralx(y1,y2,y) * integralx(z1,z2,z)
	  );
}

vector<double> t1only_co_ext(const volume<float> & t1, const Pt & point, const Vec & n) {
  vector<double> resul;
  resul.clear();
  bool output = true; 
  bool alloutput = true;
  const double INNER_DEPTH = 3;
  const double OUTER_DEPTH = 60;
  
  Profile pt1;
  for (double d = -INNER_DEPTH; d < OUTER_DEPTH; d+=.5)
    {
      Pt c = point + d * n;
      double tmp1 = t1.interpolate(c.X, c.Y, c.Z);
      pt1.add (d, tmp1);
    }
  pt1.init_roi();

  //outer skin

  double outskin = pt1.last_point_over(pt1.end(), .2);
  double check = pt1.last_point_over(outskin - 1.5, .2);
  if (outskin - check > 2) outskin = check;

  const double OUTER_SKIN = outskin;  

  pt1.set_rroi(OUTER_SKIN);

  double inskull = pt1.next_point_under(pt1.begin(), .25);

  pt1.set_lroi(inskull);

  if (alloutput)
    {
      //outer skull
      
      //starting from the skin
      double outskull2 = 0;
      outskull2 = pt1.last_point_over(outskin, .75); 

      outskull2 = pt1.last_point_under(outskull2, .20);

      //starting from the brain
      double minabs = pt1.next_point_under(pt1.begin(), .30);
      if (minabs == -500) output = false;
      minabs = Max(minabs, -INNER_DEPTH);

      double localminabs = minabs;//0
      if (output)
	{
	  bool stop = false;

	  const double lowthreshold = pt1.threshold(.15);

	  const double upthreshold = pt1.threshold(.60);
	  int test = 0;
	  for (vector<pro_pair>::const_iterator i = pt1.v.begin(); i != pt1.v.end(); i++)
	    {
	      if (!stop && (*i).abs>=minabs && i!=pt1.v.end() && i!=pt1.v.begin())
		{
		  if ((*i).val>upthreshold) stop = true; //avoid climbing skin
		  if ((*i).val>lowthreshold) test++;
		  if ((*i).val<lowthreshold) test--;
		  if (test < 0) test=0;
		  if (test == 12) {stop = true;}
		  if ((*i).val<lowthreshold) 
		    {
		      localminabs = (*i).abs;
		    }
		}
	    }
	}

      double outskull = pt1.next_point_over(localminabs, .15);//.20
      
      if (outskull2 - outskull < -2 || outskull2 - outskull >= 2) {output = false;}
      
      if (outskin - outskull2 < 2) output = false;
      
      if (output) 
	{
	  resul.push_back(inskull);
	  resul.push_back(outskull2);
	  resul.push_back(outskin);
	}
      else resul.push_back(outskin);
    }
  
  return resul;
}

//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.........

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.........