Multiregion IDs in .ele files following tetrahedralization

[bobbydawson]

I have been trying to implement TetGen in libigl and am struggling to produce an .ele file similar to what TetGen produces as a standalone program. Specifically, I would like the tetrahedra to have accurate region IDs. When I run the following code, the .ele file that is produced has exactly one tetrahedron with region ID = 2, with all others equal to 1. I am using the seed point to initialize the two regions as I understand it, but this might be the issue. The "Trabeculae_shell.obj" and "Endosteum_shell_inner.obj" are watertight, non-intersecting nested meshes, with the latter enveloping the former (both attached). Any help would be much appreciated.

#include <igl/read_triangle_mesh.h>
#include <igl/copyleft/cgal/CSGTree.h>
#include <igl/opengl/glfw/Viewer.h>
#include <igl/jet.h>
#include <Eigen/Core>

#include <igl/copyleft/tetgen/tetrahedralize.h>

int main(int argc, char * argv[])
{
  using namespace Eigen;
  using namespace igl::copyleft::cgal;
  using namespace std;
  using namespace igl;

  // Define Mesh structure
  struct Mesh {
      Eigen::MatrixXd V;
      Eigen::MatrixXi F;
  };


  // Load meshes using read_triangle_mesh
  std::vector<std::string> mesh_files = {"Trabeculae_shell.obj", "Endosteum_shell_inner.obj"};
  std::vector<Mesh> meshes;

  for (const auto& file : mesh_files) {
      Mesh mesh;
      igl::read_triangle_mesh(file, mesh.V, mesh.F);
      meshes.push_back(mesh);
  }

  Eigen::MatrixXd V_all;
  Eigen::MatrixXi F_all;

  // Merge all meshes into V_all and F_all
  for (auto &mesh : meshes) {
      int offset = V_all.rows();
      V_all.conservativeResize(V_all.rows() + mesh.V.rows(), 3);
      F_all.conservativeResize(F_all.rows() + mesh.F.rows(), 3);

      V_all.block(offset, 0, mesh.V.rows(), 3) = mesh.V;
      F_all.block(offset, 0, mesh.F.rows(), 3) = mesh.F.array() + offset;
  }

  Eigen::MatrixXd V_tet;
  Eigen::MatrixXi T;

  Eigen::VectorXi VM,FM;
  Eigen::MatrixXd H;
  Eigen::MatrixXd R(2, 5);
  Eigen::VectorXi TM,TR,PT;
  Eigen::MatrixXi FT,TN;
  int num_regions;

  Eigen::RowVector3d trabec_point(0.146617, 0.09489, 0.204463);
  Eigen::RowVector3d endo_point(0.00708, 0.065277, 0.058339);

  R.row(0) << trabec_point(0), trabec_point(1), trabec_point(2), 1, 0;
  R.row(1) << endo_point(0), endo_point(1), endo_point(2), 2, 0;

  // Tetrahedralize
  igl::copyleft::tetgen::tetrahedralize(V_all, F_all, H, VM, FM, R, "pYA", V_tet, T, F_all, TM, TR, TN, PT, FT, num_regions);
  std::cout << "number of regions: " << num_regions << std::endl;
  int x = 0;
  int num_reg_1 = 0;
  int num_reg_2 = 0;
  for (int i = 0; i < T.rows(); ++i) {
    if (TR(i) != x) {
      std::cout << "Tetrahedron " << i << " is in Region " << TR(i) << std::endl;
      x = TR(i);
    }
    if (TR(i) == 1) {
      num_reg_1++;
    }
    else if (TR(i) == 2) {
      num_reg_2++;
    }
  }
  std::cout << "number of tetrahedra in region 1: " << num_reg_1 << std::endl;
  std::cout << "number of tetrahedra in region 2: " << num_reg_2 << std::endl;

  // Prepare the TetGenIO structure for saving
  tetgenio outmesh;

  // Fill with vertices
  outmesh.numberofpoints = V_tet.rows();
  outmesh.pointlist = new REAL[outmesh.numberofpoints * 3];
  for (int i = 0; i < V_tet.rows(); ++i) {
      for (int j = 0; j < 3; ++j) {
          outmesh.pointlist[i * 3 + j] = V_tet(i, j);
      }
  }

  // Fill with tetrahedra
  outmesh.numberoftetrahedra = T.rows();
  outmesh.tetrahedronlist = new int[outmesh.numberoftetrahedra * 4];
  for (int i = 0; i < T.rows(); ++i) {
      for (int j = 0; j < 4; ++j) {
          outmesh.tetrahedronlist[i * 4 + j] = T(i, j) + 1;  // TetGen is 1-indexed
      }
  }

  outmesh.numberofregions = num_regions;
  outmesh.regionlist = new REAL[outmesh.numberofregions * 5];

  for (int i = 0; i < outmesh.numberofregions; ++i) {
      for (int j = 0; j < 5; ++j) {
          outmesh.regionlist[i * 5 + j] = R(i, j);
      }
  }

  outmesh.numberoftetrahedronattributes = 1;
  outmesh.tetrahedronattributelist = new REAL[outmesh.numberoftetrahedra];
  for (int i = 0; i < outmesh.numberoftetrahedra; ++i) {
      outmesh.tetrahedronattributelist[i] = TR(i);
  }


  // Save to .node and .ele files
  outmesh.save_nodes("output_file");
  outmesh.save_elements("output_file");

  // Cleanup
  delete[] outmesh.pointlist;
  delete[] outmesh.tetrahedronlist;

  delete[] outmesh.regionlist;
  delete[] outmesh.tetrahedronattributelist;



  igl::opengl::glfw::Viewer viewer;
  viewer.data().set_mesh(V_tet, F_all);
  viewer.data().add_points(trabec_point, Eigen::RowVector3d(1,0,0)); // red for trabec_point
  viewer.data().add_points(endo_point, Eigen::RowVector3d(0,1,0));   // green for endo_point
  viewer.launch();

}

Endosteum_shell_inner.zip
Trabeculae_shell.zip