void LegOdoCommon::getCovariance(LegOdoCommonMode mode_current, bool delta_certain,
  Eigen::MatrixXd &cov_legodo, Eigen::VectorXi &z_indices){
  
  // Determine which velocity variance to use
  double R_legodo_vxyz_current = R_legodo_vxyz_;
  double R_legodo_vang_current = R_legodo_vang_;
  if (!delta_certain){
    R_legodo_vxyz_current = R_legodo_vxyz_uncertain_;
    R_legodo_vang_current = R_legodo_vang_uncertain_;
  }
  
  Eigen::VectorXd R_legodo;
  if (mode_current == MODE_LIN_AND_ROT_RATE) {
    z_indices.resize(6);
    R_legodo.resize(6);
  }else if (mode_current == MODE_LIN_RATE){
    z_indices.resize(3);
    R_legodo.resize(3);
  }else if (mode_current == MODE_POSITION_AND_LIN_RATE){
    z_indices.resize(6);
    R_legodo.resize(6);
  }

  // Initialize covariance matrix based on mode.
  if (mode_current == MODE_LIN_AND_ROT_RATE) {
    R_legodo(0) = bot_sq(R_legodo_vxyz_current);
    R_legodo(1) = bot_sq(R_legodo_vxyz_current);
    R_legodo(2) = bot_sq(R_legodo_vxyz_current);
    R_legodo(3) = bot_sq(R_legodo_vang_current);
    R_legodo(4) = bot_sq(R_legodo_vang_current);
    R_legodo(5) = bot_sq(R_legodo_vang_current);
    
    z_indices.head<3>() = eigen_utils::RigidBodyState::velocityInds();
    z_indices.tail<3>() = eigen_utils::RigidBodyState::angularVelocityInds();
  }else if (mode_current == MODE_LIN_RATE){
    R_legodo(0) = bot_sq(R_legodo_vxyz_current);
    R_legodo(1) = bot_sq(R_legodo_vxyz_current);
    R_legodo(2) = bot_sq(R_legodo_vxyz_current);
    
    z_indices.head<3>() = eigen_utils::RigidBodyState::velocityInds();
  }else if (mode_current == MODE_POSITION_AND_LIN_RATE){
    R_legodo(0) = bot_sq(R_legodo_xyz_);
    R_legodo(1) = bot_sq(R_legodo_xyz_);
    R_legodo(2) = bot_sq(R_legodo_xyz_);
    R_legodo(3) = bot_sq(R_legodo_vxyz_current);
    R_legodo(4) = bot_sq(R_legodo_vxyz_current);
    R_legodo(5) = bot_sq(R_legodo_vxyz_current);
    
    z_indices.head<3>() = eigen_utils::RigidBodyState::positionInds();
    z_indices.tail<3>() = eigen_utils::RigidBodyState::velocityInds();    
  }
  
  cov_legodo = R_legodo.asDiagonal();

}
void FunctionApproximator::getParameterVectorMask(const std::set<std::string> selected_values_labels, Eigen::VectorXi& selected_mask) const {
  if (checkModelParametersInitialized())
    model_parameters_->getParameterVectorMask(selected_values_labels,selected_mask);
  else
    selected_mask.resize(0);
  
};
Exemple #3
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Eigen::VectorXi
readLabelFromFile(const std::string &file, int padding)
{

    // check if file exists
    boost::filesystem::path path = file;
    if ( ! (boost::filesystem::exists ( path ) && boost::filesystem::is_regular_file(path)) )
        throw std::runtime_error ("Given file path to read Matrix does not exist!");

    std::ifstream in (file.c_str (), std::ifstream::in);

    char linebuf[819200];



    Eigen::VectorXi Vector;

    in.getline (linebuf, 819200);
        std::string line (linebuf);
        std::vector < std::string > strs_2;
        boost::split (strs_2, line, boost::is_any_of (" "));
        Vector.resize(strs_2.size()-1);
        for (int i = 0; i < strs_2.size()-1; i++)
            Vector ( i) = static_cast<int> (atof (strs_2[i].c_str ()));

    return Vector;
}
Exemple #4
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int main(int argc, char *argv[])
{
  using namespace std;
  using namespace Eigen;

  // Load a mesh in OFF format
  igl::readOFF("../shared/bumpy.off", V, F);

  // Threshold faces with high anisotropy
  b.resize(1);
  b << 0;
  bc.resize(1,3);
  bc << 1,1,1;

  igl::Viewer viewer;

  // Interpolate the field and plot
  key_down(viewer, '4', 0);

  // Plot the mesh
  viewer.data.set_mesh(V, F);
  viewer.callback_key_down = &key_down;

  // Disable wireframe
  viewer.core.show_lines = false;

  // Launch the viewer
  viewer.launch();
}
Exemple #5
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void EigsGen::findMatchedIndex(const Eigen::VectorXcd &target,
                               const Eigen::VectorXcd &collection,
                               Eigen::VectorXi &result)
{
    int nfound = 0;
    int maxn = target.size();
    if(result.size() < maxn)
        result.resize(maxn);
    for(int i = 0; i < collection.size(); i++)
    {
        int j;
        for(j = 0; j < maxn; j++)
        {
            if(abs(collection[i] - target[j]) < 1e-8 * abs(target[j]))
                break;
        }
        if(j < maxn)
        {
            result[nfound] = i;
            nfound++;
            if(collection[i].imag() != 0)
            {
                i++;
                result[nfound] = i;
                nfound++;
            }
        }
        if(nfound >= maxn)  break;
    }
    if(result.size() > nfound)
        result.conservativeResize(nfound);
}
void parse_rhs(
  const int nrhs, 
  const mxArray *prhs[], 
  Eigen::MatrixXd & V,
  Eigen::MatrixXi & Ele,
  Eigen::MatrixXd & Q,
  Eigen::MatrixXd & bb_mins,
  Eigen::MatrixXd & bb_maxs,
  Eigen::VectorXi & elements)
{
  using namespace std;
  using namespace igl;
  using namespace igl::matlab;
  mexErrMsgTxt(nrhs >= 3, "The number of input arguments must be >=3.");

  const int dim = mxGetN(prhs[0]);
  mexErrMsgTxt(dim == 3 || dim == 2,
    "Mesh vertex list must be #V by 2 or 3 list of vertex positions");

  mexErrMsgTxt(dim+1 == mxGetN(prhs[1]),
    "Mesh \"face\" simplex size must equal dimension+1");

  parse_rhs_double(prhs,V);
  parse_rhs_index(prhs+1,Ele);
  parse_rhs_double(prhs+2,Q);
  mexErrMsgTxt(Q.cols() == dim,"Dimension of Q should match V");
  if(nrhs > 3)
  {
    mexErrMsgTxt(nrhs >= 6, "The number of input arguments must be 3 or >=6.");
    parse_rhs_double(prhs+3,bb_mins);
    if(bb_mins.size()>0)
    {
      mexErrMsgTxt(bb_mins.cols() == dim,"Dimension of bb_mins should match V");
      mexErrMsgTxt(bb_mins.rows() >= Ele.rows(),"|bb_mins| should be > |Ele|");
    }
    parse_rhs_double(prhs+4,bb_maxs);
    mexErrMsgTxt(bb_maxs.cols() == bb_mins.cols(),
      "|bb_maxs| should match |bb_mins|");
    mexErrMsgTxt(bb_mins.rows() == bb_maxs.rows(),
      "|bb_mins| should match |bb_maxs|");
    parse_rhs_index(prhs+5,elements);
    mexErrMsgTxt(elements.cols() == 1,"Elements should be column vector");
    mexErrMsgTxt(bb_mins.rows() == elements.rows(),
      "|bb_mins| should match |elements|");
  }else
  {
    // Defaults
    bb_mins.resize(0,dim);
    bb_maxs.resize(0,dim);
    elements.resize(0,1);
  }
}
Exemple #7
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    template<typename T> Eigen::VectorXi vectorToIntEigenVector( T &array )
    {
        Eigen::VectorXi eigenVector;

        size_t N_elements = array.size();

        eigenVector.resize( N_elements );

        for ( size_t i = 0; i < N_elements; i++ )
            eigenVector( i ) = array[i];

        return eigenVector;
    }
IGL_INLINE void igl::signed_distance_pseudonormal(
  const Eigen::MatrixXd & P,
  const Eigen::MatrixXd & V,
  const Eigen::MatrixXi & F,
  const AABB<Eigen::MatrixXd,3> & tree,
  const Eigen::MatrixXd & FN,
  const Eigen::MatrixXd & VN,
  const Eigen::MatrixXd & EN,
  const Eigen::VectorXi & EMAP,
  Eigen::VectorXd & S,
  Eigen::VectorXi & I,
  Eigen::MatrixXd & C,
  Eigen::MatrixXd & N)
{
  using namespace Eigen;
  const size_t np = P.rows();
  S.resize(np,1);
  I.resize(np,1);
  N.resize(np,3);
  C.resize(np,3);
# pragma omp parallel for if(np>1000)
  for(size_t p = 0;p<np;p++)
  {
    double s,sqrd;
    RowVector3d n,c;
    int i = -1;
    RowVector3d q = P.row(p);
    signed_distance_pseudonormal(tree,V,F,FN,VN,EN,EMAP,q,s,sqrd,i,c,n);
    S(p) = s*sqrt(sqrd);
    I(p) = i;
    N.row(p) = n;
    C.row(p) = c;
  }
//  igl::AABB<MatrixXd,3> tree_P;
//  MatrixXi J = VectorXi::LinSpaced(P.rows(),0,P.rows()-1);
//  tree_P.init(P,J);
//  tree.squared_distance(V,F,tree_P,P,J,S,I,C);
//# pragma omp parallel for if(np>1000)
//  for(size_t p = 0;p<np;p++)
//  {
//    RowVector3d c = C.row(p);
//    RowVector3d q = P.row(p);
//    const int f = I(p);
//    double s;
//    RowVector3d n;
//    pseudonormal_test(V,F,FN,VN,EN,EMAP,q,f,c,s,n);
//    N.row(p) = n;
//    S(p) = s*sqrt(S(p));
//  }

}
Exemple #9
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void readSamples(const std::string &fname, Eigen::VectorXi &samples)
{
  int numSamples;
  FILE *fp = fopen(fname.c_str(),"r");
  if (fscanf(fp, "%d", &numSamples)!=1)
  {
    fclose(fp);
    return;
  }
  samples.resize(numSamples,1);
  int vali;
  for (int i =0; i<numSamples; ++i)
  {
    if (fscanf(fp, "%d", &vali)!=1 || vali<0)
    {
      fclose(fp);
      samples.resize(0,1);
      return;
    }
    samples[i]=vali;
  }
  fclose(fp);
  
}
Exemple #10
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int main(int argc, char *argv[])
{
  using namespace Eigen;
  using namespace std;
  MatrixXd V;
  MatrixXi F;
  igl::readOFF(TUTORIAL_SHARED_PATH "/cheburashka.off",V,F);

  // Plot the mesh
  igl::opengl::glfw::Viewer viewer;
  viewer.data().set_mesh(V, F);
  viewer.data().show_lines = false;
  viewer.callback_key_down = &key_down;

  // One fixed point
  b.resize(1,1);
  // point on belly.
  b<<2556;
  bc.resize(1,1);
  bc<<1;

  // Construct Laplacian and mass matrix
  SparseMatrix<double> L,M,Minv;
  igl::cotmatrix(V,F,L);
  igl::massmatrix(V,F,igl::MASSMATRIX_TYPE_VORONOI,M);
  //M = (M/M.diagonal().maxCoeff()).eval();
  igl::invert_diag(M,Minv);
  // Bi-Laplacian
  Q = L.transpose() * (Minv * L);
  // Zero linear term
  B = VectorXd::Zero(V.rows(),1);

  // Lower and upper bound
  lx = VectorXd::Zero(V.rows(),1);
  ux = VectorXd::Ones(V.rows(),1);

  // Equality constraint constrain solution to sum to 1
  Beq.resize(1,1);
  Beq(0) = 0.08;
  Aeq = M.diagonal().sparseView().transpose();
  // (Empty inequality constraints)
  solve(viewer);
  cout<<
    "Press '.' to increase scale and resolve."<<endl<<
    "Press ',' to decrease scale and resolve."<<endl;

  viewer.launch();
}
Exemple #11
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void Dmp::getParameterVectorMask(const std::set<std::string> selected_values_labels, Eigen::VectorXi& selected_mask) const
{
  cout << __FILE__ << ":" << __LINE__ << ":Here" << endl;

  selected_mask.resize(getParameterVectorAllSize());
  selected_mask.fill(0);
  
  int offset = 0;
  VectorXi cur_mask;
  for (int dd=0; dd<dim_orig(); dd++)
  {
    function_approximators_[dd]->getParameterVectorMask(selected_values_labels,cur_mask);
    selected_mask.segment(offset,cur_mask.size()) = cur_mask;
    offset += cur_mask.size();
  }
  //nnn Check for multi-dim dmps

  assert(offset == getParameterVectorAllSize());   
}
Exemple #12
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void calin::iact_data::instrument_layout::map_channels_using_from_coordinates(
  Eigen::VectorXi& map,
  const std::vector<double>& from_x, const std::vector<double>& from_y,
  const calin::ix::iact_data::instrument_layout::CameraLayout& to,
  double tolerance)
{
  tolerance *= tolerance;
  if(from_x.size() != from_y.size())
    throw std::runtime_error("X and Y coordinate vectors must be same size.");
  map.resize(to.channel_size());
  for(int ichan=0; ichan<to.channel_size(); ichan++) {
    const auto& chan = to.channel(ichan);
    map[ichan] = -1;
    for(unsigned jchan=0; jchan<from_x.size(); jchan++) {
      double d2 = SQR(chan.x()-from_x[jchan])+SQR(chan.y()-from_y[jchan]);
      if(d2 < tolerance) {
        map[ichan] = jchan;
        break;
      }
    }
  }
}
IGL_INLINE void igl::copyleft::cgal::point_mesh_squared_distance(
  const Eigen::MatrixXd & P,
  const CGAL::AABB_tree<
    CGAL::AABB_traits<Kernel, 
      CGAL::AABB_triangle_primitive<Kernel, 
        typename std::vector<CGAL::Triangle_3<Kernel> >::iterator
      >
    >
  > & tree,
  const std::vector<CGAL::Triangle_3<Kernel> > & T,
  Eigen::VectorXd & sqrD,
  Eigen::VectorXi & I,
  Eigen::MatrixXd & C)
{
  typedef CGAL::Triangle_3<Kernel> Triangle_3; 
  typedef typename std::vector<Triangle_3>::iterator Iterator;
  typedef CGAL::AABB_triangle_primitive<Kernel, Iterator> Primitive;
  typedef CGAL::AABB_traits<Kernel, Primitive> AABB_triangle_traits;
  typedef CGAL::AABB_tree<AABB_triangle_traits> Tree;
  typedef typename Tree::Point_and_primitive_id Point_and_primitive_id;
  typedef CGAL::Point_3<Kernel>    Point_3;
  assert(P.cols() == 3);
  const int n = P.rows();
  sqrD.resize(n,1);
  I.resize(n,1);
  C.resize(n,P.cols());
  for(int p = 0;p < n;p++)
  {
    Point_3 query(P(p,0),P(p,1),P(p,2));
    // Find closest point and primitive id
    Point_and_primitive_id pp = tree.closest_point_and_primitive(query);
    Point_3 closest_point = pp.first;
    C(p,0) = CGAL::to_double(closest_point[0]);
    C(p,1) = CGAL::to_double(closest_point[1]);
    C(p,2) = CGAL::to_double(closest_point[2]);
    sqrD(p) = CGAL::to_double((closest_point-query).squared_length());
    I(p) = pp.second - T.begin();
  }
}
Exemple #14
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void calin::iact_data::instrument_layout::map_channels_using_grid(
  Eigen::VectorXi& map,
  const calin::ix::iact_data::instrument_layout::CameraLayout& from,
  const calin::ix::iact_data::instrument_layout::CameraLayout& to)
{
  std::map<unsigned, int> grid_map;
  for(int ichan=0; ichan<from.channel_size(); ichan++) {
    const auto& chan = from.channel(ichan);
    if(chan.pixel_grid_index() >= 0)
      grid_map[chan.pixel_grid_index()] = chan.channel_index();
  }
  map.resize(to.channel_size());
  for(int ichan=0; ichan<to.channel_size(); ichan++) {
    const auto& chan = to.channel(ichan);
    if(chan.pixel_grid_index() < 0)
      map[ichan] = -1;
    else if(grid_map.find(chan.pixel_grid_index()) == grid_map.end())
      map[ichan] = -1;
    else
      map[ichan] = grid_map[chan.pixel_grid_index()];
  }
}
void igl::polyvector_field_one_ring_matchings(const Eigen::PlainObjectBase<DerivedV> &V,
                                              const Eigen::PlainObjectBase<DerivedF> &F,
                                              const std::vector<std::vector<VFType> >& VF,
                                              const Eigen::MatrixXi& E2F,
                                              const Eigen::MatrixXi& F2E,
                                              const Eigen::PlainObjectBase<DerivedTT>& TT,
                                              const Eigen::PlainObjectBase<DerivedM> &match_ab,
                                              const Eigen::PlainObjectBase<DerivedM> &match_ba,
                                              const int vi,
                                              Eigen::MatrixXi &mvi,
                                              Eigen::VectorXi &fi)
{
  int half_degree = match_ab.cols();
  mvi.resize(VF[vi].size()+1,half_degree);
  fi.resize(VF[vi].size()+1,1);
  //start from one face
  //first, check if the vertex is on a boundary
  //then there must be two faces that are on the boundary
  //(other cases not supported)

  int fstart = -1;
  int ind = 0;
  for (int i =0; i<VF[vi].size(); ++i)
  {
    int fi = VF[vi][i];
    for (int  j=0; j<3; ++j)
      if (F(fi,j)==vi && TT(fi,j) == -1)
      {
        ind ++;
        fstart = fi;
        //        break;
      }
  }
  if (ind >1 )
  {
    std::cerr<<"igl::polyvector_field_one_ring_matchings -- vertex "<<vi<< " is on an unusual boundary"<<std::endl;
    exit(1);
  }
  if (fstart == -1)
    fstart = VF[vi][0];
  int current_face = fstart;
  int i =0;
  fi[i] = current_face;
  for (int j=0; j<half_degree; ++j)
    mvi(i,j) = j;

  int next_face = -1;
  while (next_face != fstart && current_face!=-1)
  {
    // look for the vertex
    int j=-1;
    for (unsigned z=0; z<3; ++z)
      if (F(current_face,(z+1)%3) == vi)
      {
        j=z;
        break;
      }
    assert(j!=-1);

    next_face = TT(current_face, j);
    ++i;

    if (next_face == -1)
      mvi.row(i).setConstant(-1);
    else
    {
      // look at the edge between the two faces
      const int &current_edge = F2E(current_face,j);

      for (int k=0; k<half_degree; ++k)
      {
        // check its orientation to determine whether match_ab or match_ba should be used
        if ((E2F(current_edge,0) == current_face) &&
            (E2F(current_edge,1) == next_face) )
        {
          //look at match_ab
          mvi(i,k) = match_ab(current_edge,(mvi(i-1,k))%half_degree);
        }
        else
        {
          assert((E2F(current_edge,1) == current_face) &&
                 (E2F(current_edge,0) == next_face));
          //look at match_ba
          mvi(i,k) = match_ba(current_edge,(mvi(i-1,k))%half_degree);
        }
        if (mvi(i-1,k)>=half_degree)
          mvi(i,k) = (mvi(i,k)+half_degree)%(2*half_degree);
      }
    }
    current_face = next_face;
    fi[i] = current_face;
  }
}
Exemple #16
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IGL_INLINE bool igl::decimate(
  const Eigen::MatrixXd & OV,
  const Eigen::MatrixXi & OF,
  const std::function<void(
    const int,
    const Eigen::MatrixXd &,
    const Eigen::MatrixXi &,
    const Eigen::MatrixXi &,
    const Eigen::VectorXi &,
    const Eigen::MatrixXi &,
    const Eigen::MatrixXi &,
    double &,
    Eigen::RowVectorXd &)> & cost_and_placement,
  const std::function<bool(
      const Eigen::MatrixXd &,
      const Eigen::MatrixXi &,
      const Eigen::MatrixXi &,
      const Eigen::VectorXi &,
      const Eigen::MatrixXi &,
      const Eigen::MatrixXi &,
      const std::set<std::pair<double,int> > &,
      const std::vector<std::set<std::pair<double,int> >::iterator > &,
      const Eigen::MatrixXd &,
      const int,
      const int,
      const int,
      const int,
      const int)> & stopping_condition,
    const std::function<bool(
      const Eigen::MatrixXd &                                         ,/*V*/
      const Eigen::MatrixXi &                                         ,/*F*/
      const Eigen::MatrixXi &                                         ,/*E*/
      const Eigen::VectorXi &                                         ,/*EMAP*/
      const Eigen::MatrixXi &                                         ,/*EF*/
      const Eigen::MatrixXi &                                         ,/*EI*/
      const std::set<std::pair<double,int> > &                        ,/*Q*/
      const std::vector<std::set<std::pair<double,int> >::iterator > &,/*Qit*/
      const Eigen::MatrixXd &                                         ,/*C*/
      const int                                                        /*e*/
      )> & pre_collapse,
    const std::function<void(
      const Eigen::MatrixXd &                                         ,   /*V*/
      const Eigen::MatrixXi &                                         ,   /*F*/
      const Eigen::MatrixXi &                                         ,   /*E*/
      const Eigen::VectorXi &                                         ,/*EMAP*/
      const Eigen::MatrixXi &                                         ,  /*EF*/
      const Eigen::MatrixXi &                                         ,  /*EI*/
      const std::set<std::pair<double,int> > &                        ,   /*Q*/
      const std::vector<std::set<std::pair<double,int> >::iterator > &, /*Qit*/
      const Eigen::MatrixXd &                                         ,   /*C*/
      const int                                                       ,   /*e*/
      const int                                                       ,  /*e1*/
      const int                                                       ,  /*e2*/
      const int                                                       ,  /*f1*/
      const int                                                       ,  /*f2*/
      const bool                                                  /*collapsed*/
      )> & post_collapse,
  const Eigen::MatrixXi & OE,
  const Eigen::VectorXi & OEMAP,
  const Eigen::MatrixXi & OEF,
  const Eigen::MatrixXi & OEI,
  Eigen::MatrixXd & U,
  Eigen::MatrixXi & G,
  Eigen::VectorXi & J,
  Eigen::VectorXi & I
  )
{

  // Decimate 1
  using namespace Eigen;
  using namespace std;
  // Working copies
  Eigen::MatrixXd V = OV;
  Eigen::MatrixXi F = OF;
  Eigen::MatrixXi E = OE;
  Eigen::VectorXi EMAP = OEMAP;
  Eigen::MatrixXi EF = OEF;
  Eigen::MatrixXi EI = OEI;
  typedef std::set<std::pair<double,int> > PriorityQueue;
  PriorityQueue Q;
  std::vector<PriorityQueue::iterator > Qit;
  Qit.resize(E.rows());
  // If an edge were collapsed, we'd collapse it to these points:
  MatrixXd C(E.rows(),V.cols());
  for(int e = 0;e<E.rows();e++)
  {
    double cost = e;
    RowVectorXd p(1,3);
    cost_and_placement(e,V,F,E,EMAP,EF,EI,cost,p);
    C.row(e) = p;
    Qit[e] = Q.insert(std::pair<double,int>(cost,e)).first;
  }
  int prev_e = -1;
  bool clean_finish = false;

  while(true)
  {
    if(Q.empty())
    {
      break;
    }
    if(Q.begin()->first == std::numeric_limits<double>::infinity())
    {
      // min cost edge is infinite cost
      break;
    }
    int e,e1,e2,f1,f2;
    if(collapse_edge(
       cost_and_placement, pre_collapse, post_collapse,
       V,F,E,EMAP,EF,EI,Q,Qit,C,e,e1,e2,f1,f2))
    {
      if(stopping_condition(V,F,E,EMAP,EF,EI,Q,Qit,C,e,e1,e2,f1,f2))
      {
        clean_finish = true;
        break;
      }
    }else
    {
      if(prev_e == e)
      {
        assert(false && "Edge collapse no progress... bad stopping condition?");
        break;
      }
      // Edge was not collapsed... must have been invalid. collapse_edge should
      // have updated its cost to inf... continue
    }
    prev_e = e;
  }
  // remove all IGL_COLLAPSE_EDGE_NULL faces
  MatrixXi F2(F.rows(),3);
  J.resize(F.rows());
  int m = 0;
  for(int f = 0;f<F.rows();f++)
  {
    if(
      F(f,0) != IGL_COLLAPSE_EDGE_NULL || 
      F(f,1) != IGL_COLLAPSE_EDGE_NULL || 
      F(f,2) != IGL_COLLAPSE_EDGE_NULL)
    {
      F2.row(m) = F.row(f);
      J(m) = f;
      m++;
    }
  }
  F2.conservativeResize(m,F2.cols());
  J.conservativeResize(m);
  VectorXi _1;
  remove_unreferenced(V,F2,U,G,_1,I);
  return clean_finish;
}
Exemple #17
0
IGL_INLINE void igl::boundary_loop(
    const Eigen::MatrixXd& V,
    const Eigen::MatrixXi& F,
    Eigen::VectorXi& b)
{
  std::vector<int> bnd;
  bnd.clear();
  std::vector<bool> isVisited(V.rows(),false);

  // Actually mesh only needs to be manifold near boundary, so this is
  // over zealous (see gptoolbox's outline_loop for a more general
  // (and probably faster) implementation)
  assert(is_edge_manifold(V,F) && "Mesh must be manifold");
  Eigen::MatrixXi TT,TTi;
  std::vector<std::vector<int> > VF, VFi;
  igl::triangle_triangle_adjacency(V,F,TT,TTi);
  igl::vertex_triangle_adjacency(V,F,VF,VFi);

  // Extract one boundary edge
  bool done = false;
  for (int i = 0; i < TT.rows() && !done; i++)
  {
    for (int j = 0; j < TT.cols(); j++)
    {
      if (TT(i,j) < 0)
      {
        int idx1, idx2;
        idx1 = F(i,j);
        idx2 = F(i,(j+1) % F.cols());
        bnd.push_back(idx1);
        bnd.push_back(idx2);
        isVisited[idx1] = true;
        isVisited[idx2] = true;
        done = true;
        break;
      }
    }
  }

  // Traverse boundary
  while(1)
  {
    bool changed = false;
    int lastV;
    lastV = bnd[bnd.size()-1];

    for (int i = 0; i < (int)VF[lastV].size(); i++)
    {
      int curr_neighbor = VF[lastV][i];

      if (TT.row(curr_neighbor).minCoeff() < 0.) // Face contains boundary edge
      {
        int idx_lastV_in_face;
        if (F(curr_neighbor,0) == lastV) idx_lastV_in_face = 0;
        if (F(curr_neighbor,1) == lastV) idx_lastV_in_face = 1;
        if (F(curr_neighbor,2) == lastV) idx_lastV_in_face = 2;

        int idx_prev = (idx_lastV_in_face + F.cols()-1) % F.cols();
        int idx_next = (idx_lastV_in_face + 1) % F.cols();
        bool isPrevVisited = isVisited[F(curr_neighbor,idx_prev)];
        bool isNextVisited = isVisited[F(curr_neighbor,idx_next)];

        bool gotBndEdge = false;
        int next_bnd_vertex;
        if (!isNextVisited && TT(curr_neighbor,idx_lastV_in_face) < 0)
        {
          next_bnd_vertex = idx_next;
          gotBndEdge = true;
        }
        else if (!isPrevVisited && TT(curr_neighbor,(idx_lastV_in_face+2) % F.cols()) < 0)
        {
          next_bnd_vertex = idx_prev;
          gotBndEdge = true;
        }

        if (gotBndEdge)
        {
          changed = true;
          bnd.push_back(F(curr_neighbor,next_bnd_vertex));
          isVisited[F(curr_neighbor,next_bnd_vertex)] = true;
          break;
        }
      }
    }

    if (!changed)
      break;
  }

  b.resize(bnd.size());
  for(unsigned i=0;i<bnd.size();++i)
    b(i) = bnd[i];
}
Exemple #18
0
int main(int argc, char * argv[])
{
  using namespace std;
  using namespace Eigen;
  using namespace igl;
  string filename = "../shared/cheburashka.off";
  string skel_filename = "../shared/cheburashka.tgf";
  if(argc < 3)
  {
    cerr<<"Usage:"<<endl<<"    ./example input.obj"<<endl;
    cout<<endl<<"Opening default mesh..."<<endl;
  }else
  {
    // Read and prepare mesh
    filename = argv[1];
    skel_filename = argv[2];
  }

  // print key commands
  cout<<"[Click] and [drag]  Rotate model using trackball."<<endl;
  cout<<"[Z,z]               Snap rotation to canonical view."<<endl;
  cout<<"[⌘ Z]               Undo."<<endl;
  cout<<"[⇧ ⌘ Z]             Redo."<<endl;
  cout<<"[^C,ESC]            Exit."<<endl;

  // dirname, basename, extension and filename
  string d,b,ext,f;
  pathinfo(filename,d,b,ext,f);
  // Convert extension to lower case
  transform(ext.begin(), ext.end(), ext.begin(), ::tolower);
  vector<vector<double > > vV,vN,vTC;
  vector<vector<int > > vF,vFTC,vFN;
  if(ext == "obj")
  {
    // Convert extension to lower case
    if(!igl::readOBJ(filename,vV,vTC,vN,vF,vFTC,vFN))
    {
      return 1;
    }
  }else if(ext == "off")
  {
    // Convert extension to lower case
    if(!igl::readOFF(filename,vV,vF,vN))
    {
      return 1;
    }
  }else if(ext == "wrl")
  {
    // Convert extension to lower case
    if(!igl::readWRL(filename,vV,vF))
    {
      return 1;
    }
  //}else
  //{
  //  // Convert extension to lower case
  //  MatrixXi T;
  //  if(!igl::readMESH(filename,V,T,F))
  //  {
  //    return 1;
  //  }
  //  //if(F.size() > T.size() || F.size() == 0)
  //  {
  //    boundary_facets(T,F);
  //  }
  }
  if(vV.size() > 0)
  {
    if(!list_to_matrix(vV,V))
    {
      return 1;
    }
    polygon_mesh_to_triangle_mesh(vF,F);
  }

  readTGF(skel_filename,C,BE);
  // Recover parent indices because (C,BE) is crappy format for a tree.
  P.resize(BE.rows(),1);
  for(int e = 0;e<BE.rows();e++)
  {
    P(e) = -1;
    for(int f = 0;f<BE.rows();f++)
    {
      if(BE(e,0) == BE(f,1))
      {
        P(e) = f;
      }
    }
  }

  init_weights(V,F,C,BE,W);
  lbs_matrix(V,W,M);

  init_relative();

  // Init glut
  glutInit(&argc,argv);
  if( !TwInit(TW_OPENGL, NULL) )
  {
    // A fatal error occured
    fprintf(stderr, "AntTweakBar initialization failed: %s\n", TwGetLastError());
    return 1;
  }
  // Create a tweak bar
  rebar.TwNewBar("TweakBar");
  rebar.TwAddVarRW("camera_rotation", TW_TYPE_QUAT4D,
    s.camera.m_rotation_conj.coeffs().data(), "open readonly=true");
  TwType RotationTypeTW = ReTwDefineEnumFromString("RotationType",
    "igl_trackball,two-a...-fixed-up");
  rebar.TwAddVarCB( "rotation_type", RotationTypeTW,
    set_rotation_type,get_rotation_type,NULL,"keyIncr=] keyDecr=[");
  rebar.TwAddVarRW("skeleton_on_top", TW_TYPE_BOOLCPP,&skeleton_on_top,"key=O");
  rebar.TwAddVarRW("wireframe", TW_TYPE_BOOLCPP,&wireframe,"key=l");
  TwType SkelStyleTypeTW = ReTwDefineEnumFromString("SkelStyleType",
    "3d,vector-graphics");
  rebar.TwAddVarRW("style",SkelStyleTypeTW,&skel_style,"key=s");
  rebar.load(REBAR_NAME);

  // Init antweakbar
  glutInitDisplayString( "rgba depth double samples>=8 ");
  glutInitWindowSize(glutGet(GLUT_SCREEN_WIDTH)/2.0,glutGet(GLUT_SCREEN_HEIGHT)/2.0);
  glutCreateWindow("upright");
  glutDisplayFunc(display);
  glutReshapeFunc(reshape);
  glutKeyboardFunc(key);
  glutMouseFunc(mouse);
  glutMotionFunc(mouse_drag);
  glutPassiveMotionFunc((GLUTmousemotionfun)TwEventMouseMotionGLUT);
  glutMainLoop();

  return 0;
}
Exemple #19
0
void remesh(const Eigen::MatrixXd &V, const Eigen::MatrixXi &F, const Eigen::VectorXi &M,
            Eigen::MatrixXd &Vout, Eigen::MatrixXi &Fout, Eigen::VectorXi &Mout,
            double e_length) {
  // The boundary vertices.
  double zmin = 1e10;
  double zmax = -1e10;
  for (int i = 0; i < V.rows(); i++) {
    zmin = std::min(zmin, V(i, 2));
    zmax = std::max(zmax, V(i, 2));
  }
  Eigen::VectorXd minV = V.colwise().minCoeff(),
       maxV = V.colwise().maxCoeff();

  // Compute average edge length.
  if (e_length <= 0) {
    e_length = avg_edgeLength(V, F, M);
  }

  // Convert to OpenMesh.
  TriangleMesh tri;
  IGLToOpenMesh(V, F, tri);
  // Do some more setup.
  tri.update_face_normals();
  tri.update_vertex_normals();
  tri.request_vertex_status();
  tri.request_edge_status();
  tri.request_face_status();

  // Check all edges to see if they're protected or not.
  TriangleMesh::EIter e_it;
  for (e_it = tri.edges_begin(); e_it != tri.edges_end(); ++e_it) {
    // Get both vertices.
    TriangleMesh::VHandle v0 = tri.to_vertex_handle(tri.halfedge_handle(*e_it, 0));
    TriangleMesh::VHandle v1 = tri.to_vertex_handle(tri.halfedge_handle(*e_it, 1));
    // See if both are nonoriginal
    if (M(tri.data(v0).getOriginalIndex()) != GLOBAL::nonoriginal_marker &&
        M(tri.data(v1).getOriginalIndex()) != GLOBAL::nonoriginal_marker) {
      tri.data(*e_it).setProtected(true);
    }
    // Also set vertices if they're original.
    if (M(tri.data(v0).getOriginalIndex()) != GLOBAL::nonoriginal_marker) {
      tri.data(v0).setProtected(true);
    }
    if (M(tri.data(v1).getOriginalIndex()) != GLOBAL::nonoriginal_marker) {
      tri.data(v1).setProtected(true);
    }
  }
  
  /*
  // Check for bad vertices.
  for (int i = 0; i < tri.n_vertices(); ++i) {
    TriangleMesh::VertexHandle vv = TriangleMesh::VertexHandle(i);
    const TriangleMesh::Point &pt = tMesh.point(vv);

    // Set statitonary if original marker set.
    if (M(tri.data(vv).getOriginalIndex()) == GLOBAL::original_marker) {
      
    }
  }
  */

  // Then, do the remeshing--but only split long edge, collapse short edges, 
  // and equalize valences.
  IsotropicRemeshing ir(e_length);
  //int types = ISOTROPIC_REMESHING_TYPES::SPLIT_LONG_EDGES |
              //ISOTROPIC_REMESHING_TYPES::COLLAPSE_SHORT_EDGES |
              //ISOTROPIC_REMESHING_TYPES::EQUALIZE_VALENCES |
              //ISOTROPIC_REMESHING_TYPES::AREA_EQUALIZATION;
  ir.setBoundingBox(TriangleMesh::Point(maxV(0), maxV(1), maxV(2)),
                    TriangleMesh::Point(minV(0), minV(1), minV(2)));
  int types = ISOTROPIC_REMESHING_TYPES::EQUALIZE_VALENCES |
      ISOTROPIC_REMESHING_TYPES::AREA_EQUALIZATION;
  ir.remesh(&tri, 1, types);

  // Then, copy it all back.
  Eigen::VectorXi origIdx;
  OpenMeshToIGL(tri, Vout, Fout, origIdx);
  // Set the new markers as well.
  Mout.resize(Vout.rows());
  for (int i = 0; i < Vout.rows(); ++i) {
    // If it doesn't correspond to a previous vertex, it's a "nonoriginal".
    if (origIdx(i) == -1) {
      Mout(i) = GLOBAL::nonoriginal_marker;
    } else {
      // Otherwise, it's the same marker as it was before.
      Mout(i) = M(origIdx(i));
      int oidx = origIdx(i);
      double moved = ( V.row(oidx) - Vout.row(i) ).norm();
      if ( moved > GLOBAL::EPS && M(oidx) != GLOBAL::nonoriginal_marker) {
        printf("point %d(m:%d new:%d) moved by %lf\n", oidx, M(oidx), i, moved);
        Mout(i) = 10;
      }
    }
    int oidx = origIdx(i);
    if (Vout(i, 2) - zmin < 0 || 
        zmax - Vout(i, 2) < 0) {
      printf("point %d(%d) moved out of bounds! by %lf vs %lf,%lf (%le,%le)\n",
             oidx, M(oidx), Vout(i, 2), zmin, zmax,
             Vout(i,2) - zmin, zmax - Vout(i,2));
      exit(1);
    }
  }
}
IGL_INLINE bool igl::boundary_conditions(
  const Eigen::MatrixXd & V  ,
  const Eigen::MatrixXi & /*Ele*/,
  const Eigen::MatrixXd & C  ,
  const Eigen::VectorXi & P  ,
  const Eigen::MatrixXi & BE ,
  const Eigen::MatrixXi & CE ,
  Eigen::VectorXi &       b  ,
  Eigen::MatrixXd &       bc )
{
  using namespace Eigen;
  using namespace igl;
  using namespace std;

  if(P.size()+BE.rows() == 0)
  {
    verbose("^%s: Error: no handles found\n",__FUNCTION__);
    return false;
  }


  vector<int> bci;
  vector<int> bcj;
  vector<int> bcv;

  // loop over points
  for(int p = 0;p<P.size();p++)
  {
    VectorXd pos = C.row(P(p));
    // loop over domain vertices
    for(int i = 0;i<V.rows();i++)
    {
      // Find samples just on pos
      //Vec3 vi(V(i,0),V(i,1),V(i,2));
      // EIGEN GOTCHA:
      // double sqrd = (V.row(i)-pos).array().pow(2).sum();
      // Must first store in temporary
      VectorXd vi = V.row(i);
      double sqrd = (vi-pos).squaredNorm();
      if(sqrd <= FLOAT_EPS)
      {
        //cout<<"sum((["<<
        //  V(i,0)<<" "<<
        //  V(i,1)<<" "<<
        //  V(i,2)<<"] - ["<<
        //  pos(0)<<" "<<
        //  pos(1)<<" "<<
        //  pos(2)<<"]).^2) = "<<sqrd<<endl;
        bci.push_back(i);
        bcj.push_back(p);
        bcv.push_back(1.0);
      }
    }
  }

  // loop over bone edges
  for(int e = 0;e<BE.rows();e++)
  {
    // loop over domain vertices
    for(int i = 0;i<V.rows();i++)
    {
      // Find samples from tip up to tail
      VectorXd tip = C.row(BE(e,0));
      VectorXd tail = C.row(BE(e,1));
      // Compute parameter along bone and squared distance
      double t,sqrd;
      project_to_line(
          V(i,0),V(i,1),V(i,2),
          tip(0),tip(1),tip(2),
          tail(0),tail(1),tail(2),
          t,sqrd);
      if(t>=-FLOAT_EPS && t<=(1.0f+FLOAT_EPS) && sqrd<=FLOAT_EPS)
      {
        bci.push_back(i);
        bcj.push_back(P.size()+e);
        bcv.push_back(1.0);
      }
    }
  }

  // Cage edges are not considered yet
  // loop over cage edges
  for(int e = 0;e<CE.rows();e++)
  {
    // loop over domain vertices
    for(int i = 0;i<V.rows();i++)
    {
      // Find samples from tip up to tail
      VectorXd tip = C.row(P(CE(e,0)));
      VectorXd tail = C.row(P(CE(e,1)));
      // Compute parameter along bone and squared distance
      double t,sqrd;
      project_to_line(
          V(i,0),V(i,1),V(i,2),
          tip(0),tip(1),tip(2),
          tail(0),tail(1),tail(2),
          t,sqrd);
      if(t>=-FLOAT_EPS && t<=(1.0f+FLOAT_EPS) && sqrd<=FLOAT_EPS)
      {
        bci.push_back(i);
        bcj.push_back(CE(e,0));
        bcv.push_back(1.0-t);
        bci.push_back(i);
        bcj.push_back(CE(e,1));
        bcv.push_back(t);
      }
    }
  }

  // find unique boundary indices
  vector<int> vb = bci;
  sort(vb.begin(),vb.end());
  vb.erase(unique(vb.begin(), vb.end()), vb.end());

  b.resize(vb.size());
  bc = MatrixXd::Zero(vb.size(),P.size()+BE.rows());
  // Map from boundary index to index in boundary
  map<int,int> bim;
  int i = 0;
  // Also fill in b
  for(vector<int>::iterator bit = vb.begin();bit != vb.end();bit++)
  {
    b(i) = *bit;
    bim[*bit] = i;
    i++;
  }

  // Build BC
  for(i = 0;i < (int)bci.size();i++)
  {
    assert(bim.find(bci[i]) != bim.end());
    bc(bim[bci[i]],bcj[i]) = bcv[i];
  }

  // Normalize accross rows so that conditions sum to one
  for(i = 0;i<bc.rows();i++)
  {
    double sum = bc.row(i).sum();
    assert(sum != 0);
    bc.row(i).array() /= sum;
  }

  if(bc.size() == 0)
  {
    verbose("^%s: Error: boundary conditions are empty.\n",__FUNCTION__);
    return false;
  }

  // If there's only a single boundary condition, the following tests
  // are overzealous.
  if(bc.rows() == 1)
  {
    return true;
  }

  // Check that every Weight function has at least one boundary value of 1 and
  // one value of 0
  for(i = 0;i<bc.cols();i++)
  {
    double min_abs_c = bc.col(i).array().abs().minCoeff();
    double max_c = bc.col(i).maxCoeff();
    if(min_abs_c > FLOAT_EPS)
    {
      verbose("^%s: Error: handle %d does not receive 0 weight\n",__FUNCTION__,i);
      return false;
    }
    if(max_c< (1-FLOAT_EPS))
    {
      verbose("^%s: Error: handle %d does not receive 1 weight\n",__FUNCTION__,i);
      return false;
    }
  }

  return true;
}
IGL_INLINE void igl::signed_distance(
  const Eigen::MatrixXd & P,
  const Eigen::MatrixXd & V,
  const Eigen::MatrixXi & F,
  const SignedDistanceType sign_type,
  Eigen::VectorXd & S,
  Eigen::VectorXi & I,
  Eigen::MatrixXd & C,
  Eigen::MatrixXd & N)
{
  using namespace Eigen;
  using namespace std;
  assert(V.cols() == 3 && "V should have 3d positions");
  assert(P.cols() == 3 && "P should have 3d positions");
  // Only unsigned distance is supported for non-triangles
  if(sign_type != SIGNED_DISTANCE_TYPE_UNSIGNED)
  {
    assert(F.cols() == 3 && "F should have triangles");
  }

  // Prepare distance computation
  AABB<MatrixXd,3> tree;
  tree.init(V,F);

  Eigen::MatrixXd FN,VN,EN;
  Eigen::MatrixXi E;
  Eigen::VectorXi EMAP;
  WindingNumberAABB<Eigen::Vector3d> hier;
  switch(sign_type)
  {
    default:
      assert(false && "Unknown SignedDistanceType");
    case SIGNED_DISTANCE_TYPE_UNSIGNED:
      // do nothing
      break;
    case SIGNED_DISTANCE_TYPE_DEFAULT:
    case SIGNED_DISTANCE_TYPE_WINDING_NUMBER:
      hier.set_mesh(V,F);
      hier.grow();
      break;
    case SIGNED_DISTANCE_TYPE_PSEUDONORMAL:
      // "Signed Distance Computation Using the Angle Weighted Pseudonormal"
      // [Bærentzen & Aanæs 2005]
      per_face_normals(V,F,FN);
      per_vertex_normals(V,F,PER_VERTEX_NORMALS_WEIGHTING_TYPE_ANGLE,FN,VN);
      per_edge_normals(
        V,F,PER_EDGE_NORMALS_WEIGHTING_TYPE_UNIFORM,FN,EN,E,EMAP);
      N.resize(P.rows(),3);
      break;
  }

  S.resize(P.rows(),1);
  I.resize(P.rows(),1);
  C.resize(P.rows(),3);
  for(int p = 0;p<P.rows();p++)
  {
    const RowVector3d q = P.row(p);
    double s,sqrd;
    RowVector3d c;
    int i=-1;
    switch(sign_type)
    {
      default:
        assert(false && "Unknown SignedDistanceType");
      case SIGNED_DISTANCE_TYPE_UNSIGNED:
        s = 1.;
        sqrd = tree.squared_distance(V,F,q,i,c);
        break;
      case SIGNED_DISTANCE_TYPE_DEFAULT:
      case SIGNED_DISTANCE_TYPE_WINDING_NUMBER:
        signed_distance_winding_number(tree,V,F,hier,q,s,sqrd,i,c);
        break;
      case SIGNED_DISTANCE_TYPE_PSEUDONORMAL:
      {
        Eigen::RowVector3d n;
        signed_distance_pseudonormal(tree,V,F,FN,VN,EN,EMAP,q,s,sqrd,i,c,n);
        N.row(p) = n;
        break;
      }
    }
    I(p) = i;
    S(p) = s*sqrt(sqrd);
    C.row(p) = c;
  }
}
Exemple #22
0
// Create a random set of tangent vectors
void generate_constraints()
{
  b.resize(42,1);
  b<<
  663,
  513,
  3872,
  2601,
  3549,
  2721,
  3796,
  594,
  868,
  1730,
  1581,
  3081,
  1471,
  1650,
  454,
  2740,
  2945,
  3808,
  3679,
  3589,
  450,
  2656,
  1791,
  1792,
  2917,
  3744,
  1536,
  2809,
  3866,
  3658,
  1665,
  2670,
  1601,
  1793,
  3614,
  524,
  2877,
  449,
  455,
  3867,
  3871,
  2592;

blevel.setOnes(b.rows(),1);
bc.resize(b.rows(),6);
bc<<
-0.88046298335147721,0.27309862654264377,0.38755912468723769,-0.350632259447135,-0.92528970817792766,-0.14455440005410564,
0.91471470003012889,0.392936119054695,-0.094330397492144599,0.32234487030777614,-0.85027369799342767,-0.41608703787410195,
0.94335566040683105,0.073867667925654024,-0.32345581709658111,0.19950360079371404,-0.90525435056476755,0.37511714710727789,
-0.92054671613540229,0.15077598183983737,0.36036141124232496,-0.27998315313687211,-0.89796618385425386,-0.33950871360506074,
0.88944399663239937,0.23035525634795684,-0.39474780902172396,0.27297422303141039,-0.96047177712172194,0.054580572670497061,
-0.83112706922096102,-0.55599928943162547,0.0096221078617792517,0.52546831822766438,-0.79091522174894457,-0.31358596675362826,
0.90724658517664569,-0.41046292080872998,-0.091781394228251156,-0.34252813327252363,-0.84767620917196618,0.40511667741613094,
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}
Exemple #23
0
// A tet is organized in the following fashion:
//
//       0
//       
//       3       (3 is in the background; 1 and 2 are in the foreground)
//  2        1
//
// So the faces (with counterclockwise normals) are:
// (0 1 3)
// (0 2 1)
// (3 2 0)
// (1 2 3)
//
//
// This method will perform three steps:
// 1. Add all faces, duplicating ones on the interior
// 2. Remove all duplicate verts (might have been caused during #1)
// 3. Remove all duplicate faces
void marching_tets(
  const Eigen::MatrixXd& V,
  const Eigen::MatrixXi& T,
  const Eigen::VectorXd& H,
  double offset,
  Eigen::MatrixXd& NV,
  Eigen::MatrixXi& NF,
  Eigen::VectorXi& I)
{
  min_how_much = 1;
  max_how_much = 0;
  using namespace Eigen;
  using namespace std;

  // Count the faces.
  std::map<std::vector<int>, int> face_counts;
  for (int i = 0; i < T.rows(); ++i) {
    std::vector<std::vector<int> > fs;
    fs.push_back({T(i, 0), T(i, 1), T(i, 3)});
    fs.push_back({T(i, 0), T(i, 2), T(i, 1)});
    fs.push_back({T(i, 3), T(i, 2), T(i, 0)});
    fs.push_back({T(i, 1), T(i, 2), T(i, 3)});
    for (auto &f : fs) {
      std::sort(f.begin(), f.end());
      // Add it to the map.
      face_counts[f]++;
    }
  }

  vector<Eigen::RowVector3i> faces;
  vector<int> faces_markers;
  vector<Eigen::RowVector3d> new_verts;
  int times[6];
  for (int i = 0; i < 6; i++) {
    times[i] = 0;
  }

  // Create data structure.
  MarchingTetsDat dd(V, H, faces, faces_markers, face_counts, new_verts, offset);

  int numEq = 0;

  // Check each tet face, add as needed.
  for (int i = 0; i < T.rows(); ++i) {
    // See if the tet is entirely inside.
    vector<int> inside, outside, inside_t, outside_t, identical;
    for (int j = 0; j < T.cols(); ++j) {
      //if (H(T(i, j)) > offset + 1e-4) {
      if (H(T(i, j)) > offset) {
        outside.push_back(j);
      } else if (H(T(i, j)) < offset) {
        inside.push_back(j);
      } else {
        numEq++;
        identical.push_back(j);
      }

      if (H(T(i, j)) == GLOBAL::outside_temp) {
        outside_t.push_back(j);
      } else if (H(T(i, j)) == GLOBAL::inside_temp) {
        inside_t.push_back(j);
      }
    }

    // Ignore this tet if it's entirely outside.
    if (outside.size() == 4) {
      continue;
    }


    if (outside.size() == 0 && inside.size() == 0) {
      // degenerate, ignore.
      printf("WARNING: degenerate tet face found!!\n");
    } else if (inside.size() == 0 && identical.size() < 3) {
      // Nothing to add.
    } else if (identical.size() == 3) {
      //addOrig(T.row(i), 7, dd.faces, dd.faces_markers);
      // Ignore it if there's only one on the outside.
      //if (inside.size() == 0) continue;
      if (outside.size() == 0) continue;
      times[1]++;
      // Add just a single face (always)
      int i1 = T(i,identical[0]), i2 = T(i,identical[1]), i3 = T(i,identical[2]);
      Eigen::RowVector3i f({i1, i2, i3});
      dd.faces.push_back(f);
      dd.faces_markers.push_back(1);
    } else if (outside.size() == 0) {
      // (these are colored blue)
      times[0]++;
      // (A) Takes care of:
      //   inside: 1, identical: 3 (remove three duplicated faces later)
      //   inside: 2, identical: 2 (remove all four duplicated faces later)
      //   inside: 3, identical: 1 (remove all four duplicated faces later)
      //   inside: 4, identical: 0 (remove all four duplicated faces later)
      case0Out(dd, T.row(i), inside, outside, identical, inside_t, outside_t);
    } else if (inside.size() == 1) {
      // (these are colored green)
      times[2]++;
      // (B) Takes care of:
      //   inside: 1 outside: 3
      //   inside: 1 outside: 2 identical: 1
      //   inside: 1 outside: 1 identical: 2
      //
      case1In(dd, T.row(i), inside, outside, identical, inside_t, outside_t);
    } else if (inside.size() == 3 && outside.size() == 1) {
      // (these are colored orange)
      times[3]++;
      // (C) takes care of:
      //   inside: 3 outside: 1
      //
      case3In1Out(dd, T.row(i), inside, outside, identical, inside_t, outside_t);
    } else if (inside.size() == 2 && outside.size() >= 1) {
      // (these are colored red)
      times[4]++;
      // (D) takes care of:
      //   inside: 2 outside: 1 identical: 1
      //   inside: 2 outside: 2 identical: 0
      //
      case2In2Out(dd, T.row(i), inside, outside, identical, inside_t, outside_t);
    } else {
      times[5]++;
      fprintf(stderr, "WARN: marching tets found something weird, with in:%lu out:%lu\n",
              inside.size(), outside.size());
    }
  }

  printf("Finished marching tets with usages:\n");
  for (int i = 0; i < 6; ++i) {
    printf("  %d: %d\n", i, times[i]);
  }
  printf("how_much is %lf and EPS is %lf\n", min_how_much, GLOBAL::EPS);
  printf("     max is %lf\n", max_how_much);
  printf("Num equal is %d\n", numEq);

  // Copy verts
  NV.resize(V.rows() + new_verts.size(), 3);
  for (int i = 0; i < V.rows(); ++i) {
    NV.row(i) = V.row(i);
  }
  for (int i = 0; i < new_verts.size(); ++i) {
    NV.row(i + V.rows()) = new_verts[i];
  }
  // Set I
  I.resize(NV.rows());
  for (int i = 0; i < I.rows(); ++i) {
    if (i < V.rows()) {
      I(i) = i;
    } else {
      I(i) = -1;
    }
  }
  Eigen::VectorXi facesMarkers;
  facesMarkers.resize(faces.size());
  // Copy faces
  NF.resize(faces.size(), 3);
  for (int i = 0; i < faces.size(); ++i) {
    NF.row(i) = faces[i];
    facesMarkers(i) = faces_markers[i];
  }
  
  Eigen::MatrixXd newV;
  Eigen::MatrixXi newF;
  Eigen::VectorXi SVJ, SVI, I2;
  // Helpers::viewTriMesh(NV, NF, facesMarkers);
  //igl::writeOFF("offset_mesh.off", NV, NF)
  Helpers::writeMeshWithMarkers("offset_mesh", NV, NF, facesMarkers);

  /*
  igl::collapse_small_triangles(NV, NF, 1e-8, newF);
  printf("Collapsed %d small triangles\n", NF.rows() - newF.rows());
  NF = newF;
  */

  ///*
  igl::remove_duplicate_vertices(NV, NF, 1e-20, newV, SVI, SVJ, newF);
  I2.resize(newV.rows());
  I2.setConstant(-1);
  for (int i = 0; i < NV.rows(); ++i) {
    if (I2(SVJ(i)) == -1) {
      I2(SVJ(i)) = I(i);
    } else {
      I2(SVJ(i)) = std::min(I2(SVJ(i)), I(i));
    }
  }
  NF = newF;
  NV = newV;
  I = I2;

  // Now see if we have duplicated faces.
  //igl::resolve_duplicated_faces(NF, newF, SVJ);
  //NF = newF;
  //*/

  // Other option is to do these two:
  // These are bad because sometimes the "small" triangles are not area zero,
  // and doing the removeDuplicates will delete these triangles and make the
  // mesh non-manifold. Better to wait for remeshing later.
  //Helpers::removeDuplicates(NV, NF, I);
  //Helpers::collapseSmallTriangles(NV, NF);

  igl::remove_unreferenced(NV, NF, newV, newF, SVI, SVJ);
  I2.resize(newV.rows());
  I2.setConstant(-1);
  for (int i = 0; i < I2.rows(); ++i) {
    I2(i) = I(SVJ(i));
  }
  I = I2;
  NV = newV;
  NF = newF;


  // orient everything correctly.
  Eigen::VectorXi C;
  igl::orientable_patches(NF, C);
  igl::bfs_orient(NF, newF, C);
  NF = newF;
  igl::orient_outward(NV, NF, C, newF, SVJ);
  NF = newF;
  //igl::writeOFF("offset_mesh_normals.off", NV, NF);

#ifdef DEBUG_MESH
  if (!Helpers::isMeshOkay(NV, NF)) {
    printf("Error: Mesh is not okay at first...\n");
  }
  if (!Helpers::isManifold(NV, NF, I)) {
    printf("Error: Mesh from marching tets not manifold!\n");
    Eigen::VectorXi temp;
    temp.resize(I.rows());
    temp.setZero();
    Helpers::isManifold(NV, NF, temp, true);
    Helpers::viewTriMesh(NV, NF, temp);
    Helpers::writeMeshWithMarkers("marching_tets_manifold", NV, NF, temp);
    cout << "See marching_tets_manifold.off for problems.\n";
    exit(1);
  }
#endif
}