lsWriteVisualizationMesh.hpp

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#pragma once
 
#ifdef VIENNALS_USE_VTK // this class needs vtk support
 
#include <vtkAppendFilter.h>
#include <vtkAppendPolyData.h>
#include <vtkCellData.h>
#include <vtkDataSetTriangleFilter.h>
#include <vtkFloatArray.h>
#include <vtkGeometryFilter.h>
#include <vtkIncrementalOctreePointLocator.h>
#include <vtkIntArray.h>
#include <vtkPointData.h>
#include <vtkProbeFilter.h>
#include <vtkRectilinearGrid.h>
#include <vtkSmartPointer.h>
#include <vtkTableBasedClipDataSet.h>
#include <vtkTriangleFilter.h>
#include <vtkUnstructuredGrid.h>
#include <vtkXMLPolyDataWriter.h>
#include <vtkXMLUnstructuredGridWriter.h>
 
#include <hrleDenseIterator.hpp>
 
#include <lsBooleanOperation.hpp>
#include <lsDomain.hpp>
#include <lsMaterialMap.hpp>
#include <lsPreCompileMacros.hpp>
#include <unordered_map>
#include <utility>
 
// #define LS_TO_VISUALIZATION_DEBUG
#ifdef LS_TO_VISUALIZATION_DEBUG
#include <vtkXMLRectilinearGridWriter.h>
#endif
 
namespace viennals {
 
using namespace viennacore;

template <class T, int D> class WriteVisualizationMesh {
  typedef typename Domain<T, D>::DomainType hrleDomainType;
  using LevelSetsType = std::vector<SmartPointer<Domain<T, D>>>;
  LevelSetsType levelSets;
  SmartPointer<MaterialMap> materialMap = nullptr;
  std::string fileName;
  bool extractVolumeMesh = true;
  bool extractHullMesh = false;
  bool bottomRemoved = false;
  bool writeToFile = true;
  double LSEpsilon = 1e-2;
  std::unordered_map<std::string, std::vector<double>> metaData;
 
  vtkSmartPointer<vtkUnstructuredGrid> volumeVTK;
  vtkSmartPointer<vtkPolyData> hullVTK;

  static void removeDuplicatePoints(vtkSmartPointer<vtkPolyData> &polyData,
                                    const double tolerance) {
 
    vtkSmartPointer<vtkPolyData> newPolyData =
        vtkSmartPointer<vtkPolyData>::New();
    vtkSmartPointer<vtkIncrementalOctreePointLocator> ptInserter =
        vtkSmartPointer<vtkIncrementalOctreePointLocator>::New();
    ptInserter->SetTolerance(tolerance);
 
    vtkSmartPointer<vtkPoints> newPoints = vtkSmartPointer<vtkPoints>::New();
 
    // get bounds
    double gridBounds[6];
    polyData->GetBounds(gridBounds);
 
    // start point insertion from original points
    std::vector<vtkIdType> newPointIds;
    newPointIds.reserve(polyData->GetNumberOfPoints());
    ptInserter->InitPointInsertion(newPoints, gridBounds);
 
    // make new point list
    for (vtkIdType pointId = 0; pointId < polyData->GetNumberOfPoints();
         ++pointId) {
      vtkIdType globalPtId = 0;
      ptInserter->InsertUniquePoint(polyData->GetPoint(pointId), globalPtId);
      newPointIds.push_back(globalPtId);
    }
 
    // now set the new points to the unstructured grid
    newPolyData->SetPoints(newPoints);
 
    // go through all cells and change point ids to match the new ids
    vtkSmartPointer<vtkCellArray> oldCells = polyData->GetPolys();
    vtkSmartPointer<vtkCellArray> newCells =
        vtkSmartPointer<vtkCellArray>::New();
 
    vtkSmartPointer<vtkIdList> cellPoints = vtkSmartPointer<vtkIdList>::New();
    oldCells->InitTraversal();
    while (oldCells->GetNextCell(cellPoints)) {
      for (vtkIdType pointId = 0; pointId < cellPoints->GetNumberOfIds();
           ++pointId) {
        cellPoints->SetId(pointId, newPointIds[cellPoints->GetId(pointId)]);
      }
      // insert same cell with new points
      newCells->InsertNextCell(cellPoints);
    }
 
    newPolyData->SetPolys(newCells);
 
    // conserve all cell data
    // TODO transfer point data as well (do with "InsertTuples (vtkIdList
    // *dstIds, vtkIdList *srcIds, vtkAbstractArray *source) override)" of
    // vtkDataArray class)
    newPolyData->GetCellData()->ShallowCopy(polyData->GetCellData());
 
    // set ugrid to the newly created grid
    polyData = newPolyData;
  }

  static void removeDuplicatePoints(vtkSmartPointer<vtkUnstructuredGrid> &ugrid,
                                    const double tolerance) {
 
    vtkSmartPointer<vtkUnstructuredGrid> newGrid =
        vtkSmartPointer<vtkUnstructuredGrid>::New();
    vtkSmartPointer<vtkIncrementalOctreePointLocator> ptInserter =
        vtkSmartPointer<vtkIncrementalOctreePointLocator>::New();
    ptInserter->SetTolerance(tolerance);
 
    vtkSmartPointer<vtkPoints> newPoints = vtkSmartPointer<vtkPoints>::New();
 
    // get bounds
    double gridBounds[6];
    ugrid->GetBounds(gridBounds);
 
    // start point insertion from original points
    std::vector<vtkIdType> newPointIds;
    newPointIds.reserve(ugrid->GetNumberOfPoints());
    ptInserter->InitPointInsertion(newPoints, gridBounds);
 
    // make new point list
    for (vtkIdType pointId = 0; pointId < ugrid->GetNumberOfPoints();
         ++pointId) {
      vtkIdType globalPtId = 0;
      ptInserter->InsertUniquePoint(ugrid->GetPoint(pointId), globalPtId);
      newPointIds.push_back(globalPtId);
    }
 
    // now set the new points to the unstructured grid
    newGrid->SetPoints(newPoints);
 
    // go through all cells and change point ids to match the new ids
    for (vtkIdType cellId = 0; cellId < ugrid->GetNumberOfCells(); ++cellId) {
      vtkSmartPointer<vtkIdList> cellPoints = vtkSmartPointer<vtkIdList>::New();
      ugrid->GetCellPoints(cellId, cellPoints);
      for (vtkIdType pointId = 0; pointId < cellPoints->GetNumberOfIds();
           ++pointId) {
        cellPoints->SetId(pointId, newPointIds[cellPoints->GetId(pointId)]);
      }
      // insert same cell with new points
      newGrid->InsertNextCell(ugrid->GetCell(cellId)->GetCellType(),
                              cellPoints);
    }
 
    // conserve all cell data
    // TODO transfer point data as well (do with "InsertTuples (vtkIdList
    // *dstIds, vtkIdList *srcIds, vtkAbstractArray *source) override)" of
    // vtkDataArray class)
    newGrid->GetCellData()->ShallowCopy(ugrid->GetCellData());
 
    // set ugrid to the newly created grid
    ugrid = newGrid;
  }

  static void
  removeDegenerateTetras(vtkSmartPointer<vtkUnstructuredGrid> &ugrid) {
    vtkSmartPointer<vtkUnstructuredGrid> newGrid =
        vtkSmartPointer<vtkUnstructuredGrid>::New();
 
    // need to copy material numbers
    vtkSmartPointer<vtkIntArray> materialNumberArray =
        vtkSmartPointer<vtkIntArray>::New();
    materialNumberArray->SetNumberOfComponents(1);
    materialNumberArray->SetName("Material");
 
    // see if material is defined
    int arrayIndex;
    vtkDataArray *matArray =
        ugrid->GetCellData()->GetArray("Material", arrayIndex);
    const int &materialArrayIndex = arrayIndex;
 
    // go through all cells and delete those with duplicate entries
    for (vtkIdType cellId = 0; cellId < ugrid->GetNumberOfCells(); ++cellId) {
      vtkSmartPointer<vtkIdList> cellPoints = vtkSmartPointer<vtkIdList>::New();
      ugrid->GetCellPoints(cellId, cellPoints);
      bool isDuplicate = false;
      for (vtkIdType pointId = 0; pointId < cellPoints->GetNumberOfIds();
           ++pointId) {
        for (vtkIdType nextId = pointId + 1;
             nextId < cellPoints->GetNumberOfIds(); ++nextId) {
          // if they are the same, remove the cell
          if (cellPoints->GetId(pointId) == cellPoints->GetId(nextId))
            isDuplicate = true;
        }
      }
      if (!isDuplicate) {
        // insert same cell if no degenerate points
        newGrid->InsertNextCell(ugrid->GetCell(cellId)->GetCellType(),
                                cellPoints);
        // if material was defined before, use it now
        if (materialArrayIndex >= 0)
          materialNumberArray->InsertNextValue(matArray->GetTuple1(cellId));
      }
    }
 
    // just take the old points and point data
    newGrid->SetPoints(ugrid->GetPoints());
    newGrid->GetPointData()->ShallowCopy(ugrid->GetPointData());
    // set material cell data
    newGrid->GetCellData()->SetScalars(materialNumberArray);
 
    ugrid = newGrid;
  }
 
  // This function takes a levelset and converts it to a vtkRectilinearGrid
  // The full domain contains values, which are capped at numLayers * gridDelta
  // gridExtraPoints layers of grid points are added to the domain according to
  // boundary conditions
  template <int gridExtraPoints = 0>
  vtkSmartPointer<vtkRectilinearGrid>
  LS2RectiLinearGrid(SmartPointer<Domain<T, D>> levelSet, const double LSOffset,
                     int infiniteMinimum = std::numeric_limits<int>::max(),
                     int infiniteMaximum = -std::numeric_limits<int>::max()) {
 
    auto &grid = levelSet->getGrid();
    auto &domain = levelSet->getDomain();
    double gridDelta = grid.getGridDelta();
    int numLayers = levelSet->getLevelSetWidth();
 
    vtkSmartPointer<vtkFloatArray>
        coords[3]; // needs to be 3 because vtk only knows 3D
    int gridMin = 0, gridMax = 0;
    // int openJumpDirection = -1; // direction above the open boundary
    // direction
 
    // fill grid with offset depending on orientation
    for (unsigned i = 0; i < D; ++i) {
      coords[i] = vtkSmartPointer<vtkFloatArray>::New();
 
      if (grid.getBoundaryConditions(i) ==
          Domain<T, D>::BoundaryType::INFINITE_BOUNDARY) {
        // add one to gridMin and gridMax for numerical stability
        gridMin = std::min(domain.getMinRunBreak(i), infiniteMinimum) -
                  1; // choose the smaller number so that for first levelset the
                     // overall minimum can be chosen
        gridMax = std::max(domain.getMaxRunBreak(i), infiniteMaximum) + 1;
 
        // openJumpDirection = i + 1;
      } else {
        gridMin = grid.getMinGridPoint(i) - gridExtraPoints;
        gridMax = grid.getMaxGridPoint(i) + gridExtraPoints;
      }
 
      for (int x = gridMin; x <= gridMax; ++x) {
        coords[i]->InsertNextValue(x * gridDelta);
      }
    }
 
    // if we work in 2D, just add 1 grid point at origin
    if (D == 2) {
      coords[2] = vtkSmartPointer<vtkFloatArray>::New();
      coords[2]->InsertNextValue(0);
    }
 
    vtkSmartPointer<vtkRectilinearGrid> rgrid =
        vtkSmartPointer<vtkRectilinearGrid>::New();
 
    rgrid->SetDimensions(coords[0]->GetNumberOfTuples(),
                         coords[1]->GetNumberOfTuples(),
                         coords[2]->GetNumberOfTuples());
    rgrid->SetXCoordinates(coords[0]);
    rgrid->SetYCoordinates(coords[1]);
    rgrid->SetZCoordinates(coords[2]);
 
    // bool fixBorderPoints = (gridExtraPoints != 0);
 
    // need to save the current position one dimension above open boundary
    // direction, so we can register a jump in the open boundary direction when
    // it occurs, so we can fix the LS value as follows: if remove_bottom==true,
    // we need to flip the sign otherwise the sign stays the same
    // int currentOpenIndex =
    //     it.getIndices()[(openJumpDirection < D) ? openJumpDirection : 0];
 
    // Make array to store signed distance function
    auto const numGridPoints = rgrid->GetNumberOfPoints();
    vtkSmartPointer<vtkFloatArray> signedDistances =
        vtkSmartPointer<vtkFloatArray>::New();
    signedDistances->SetNumberOfComponents(1);
    signedDistances->SetNumberOfTuples(numGridPoints);
    signedDistances->SetName("SignedDistances");
 
#pragma omp parallel
    {
      // use dense iterator to got to every index location
      viennahrle::ConstDenseIterator<typename Domain<T, D>::DomainType> it(
          levelSet->getDomain());
 
#pragma omp for
      for (vtkIdType pointId = 0; pointId < numGridPoints; ++pointId) {
        // iterate until all grid points have a signed distance value
 
        double p[3];
        rgrid->GetPoint(pointId, p);
        // create index vector
        viennahrle::Index<D> indices(grid.globalCoordinates2GlobalIndices(p));
 
        // write the corresponding LSValue
        T value;
 
        // if indices are outside of domain map to local indices
        if (grid.isOutsideOfDomain(indices)) {
          indices = grid.globalIndices2LocalIndices(indices);
          // fixBorderPoints = true;
          // signedDistances->InsertNextValue(
          // signedDistances->GetDataTypeValueMax());
        }
 
        it.goToIndices(indices);
        if (it.getValue() == Domain<T, D>::POS_VALUE) {
          value = numLayers;
        } else if (it.getValue() == Domain<T, D>::NEG_VALUE) {
          value = -numLayers;
        } else {
          value = it.getValue() + LSOffset;
        }
 
        // if (removeBottom) {
        //   // if we jump from one end of the domain to the other and are not
        //   // already in the new run, we need to fix the sign of the run
        //   if (currentOpenIndex != indices[openJumpDirection]) {
        //     currentOpenIndex = indices[openJumpDirection];
        //     if (indices >= it.getIndices()) {
        //       value = -value;
        //     }
        //   }
        // }
 
        signedDistances->SetValue(pointId, value * gridDelta);
        // signedDistances->InsertNextValue(value * gridDelta);
      }
 
      // // advance iterator until it is at correct point
      // while (compare(it_l.end_indices(), indices) < 0) {
      //   it_l.next();
      //   if (it_l.is_finished())
      //     break;
      // }
      // // now move iterator with pointId to get to next point
      // switch (compare(it_l.end_indices(), indices)) {
      // case 0:
      //   it_l.next();
      // default:
      //   ++pointId;
      // }
      // }
    }
 
    // now need to go through again to fix border points, this is done by
    // mapping existing points onto the points outside the domain according
    // to the correct boundary conditions
    // if (fixBorderPoints) {
    //   vtkIdType pointId = 0;
    //   while ((pointId < rgrid->GetNumberOfPoints())) {
    //     if (signedDistances->GetValue(pointId) ==
    //         signedDistances->GetDataTypeValueMax()) {
    //       double p[3];
    //       rgrid->GetPoint(pointId, p);
 
    //       // create index vector
    //       viennahrle::Index<D> indices(
    //           grid.globalCoordinates2GlobalIndices(p));
 
    //       // vector for mapped point inside domain
    //       viennahrle::Index<D> localIndices =
    //           grid.globalIndices2LocalIndices(indices);
 
    //       // now find ID of point we need to take value from
    //       int originalPointId = 0;
    //       for (int i = D - 1; i >= 0; --i) {
    //         originalPointId *=
    //             coords[i]->GetNumberOfTuples(); // extent in direction
    //         originalPointId += localIndices[i] - indices[i];
    //       }
    //       originalPointId += pointId;
 
    //       // now put value of mapped point in global point
    //       signedDistances->SetValue(pointId,
    //                                 signedDistances->GetValue(originalPointId));
    //     }
    //     ++pointId;
    //   }
    // }
 
    // Add the SignedDistances to the grid
    rgrid->GetPointData()->SetScalars(signedDistances);
 
    return rgrid;
  }
 
  void addMetaDataToVTK(vtkDataSet *data) const {
    if (metaData.empty()) {
      return;
    }
 
    // add metadata to field data
    vtkSmartPointer<vtkFieldData> fieldData = data->GetFieldData();
    for (const auto &meta : metaData) {
      if (meta.second.empty())
        continue; // skip empty metadata
 
      vtkSmartPointer<vtkFloatArray> metaDataArray =
          vtkSmartPointer<vtkFloatArray>::New();
      metaDataArray->SetName(meta.first.c_str());
      metaDataArray->SetNumberOfValues(meta.second.size());
      for (size_t i = 0; i < meta.second.size(); ++i) {
        metaDataArray->SetValue(i, meta.second[i]);
      }
      fieldData->AddArray(metaDataArray);
    }
  }
 
public:
  WriteVisualizationMesh() = default;
 
  WriteVisualizationMesh(SmartPointer<Domain<T, D>> levelSet) {
    levelSets.push_back(levelSet);
  }

  void insertNextLevelSet(SmartPointer<Domain<T, D>> levelSet) {
    levelSets.push_back(levelSet);
  }
 
  void clearLevelSets() { levelSets.clear(); }

  void setFileName(std::string passedFileName) {
    fileName = std::move(passedFileName);
  }

  void setExtractHullMesh(bool passedExtractHullMesh) {
    extractHullMesh = passedExtractHullMesh;
  }

  void setExtractVolumeMesh(bool passedExtractVolumeMesh) {
    extractVolumeMesh = passedExtractVolumeMesh;
  }
 
  void setWriteToFile(bool passedWriteToFile) {
    writeToFile = passedWriteToFile;
  }
 
  void setMaterialMap(SmartPointer<MaterialMap> passedMaterialMap) {
    materialMap = passedMaterialMap;
  }
 
  void setWrappingLayerEpsilon(double epsilon) { LSEpsilon = epsilon; }
 
  void setMetaData(const std::unordered_map<std::string, std::vector<double>>
                       &passedMetaData) {
    metaData = passedMetaData;
  }
 
  void addMetaData(const std::string &key, double value) {
    metaData[key] = std::vector<double>{value};
  }
 
  void addMetaData(const std::string &key, const std::vector<double> &values) {
    metaData[key] = values;
  }
 
  void addMetaData(
      const std::unordered_map<std::string, std::vector<double>> &newMetaData) {
    for (const auto &pair : newMetaData) {
      metaData[pair.first] = pair.second;
    }
  }
 
  auto getVolumeMesh() const { return volumeVTK; }
 
  auto getHullMesh() const { return hullVTK; }
 
  void apply() {
    // check if level sets have enough layers
    for (unsigned i = 0; i < levelSets.size(); ++i) {
      if (levelSets[i]->getLevelSetWidth() < 2) {
        VIENNACORE_LOG_WARNING(
            "WriteVisualizationMesh: Level Set " + std::to_string(i) +
            " should have a width greater than 1! Conversion might fail!");
      }
    }
 
    // This algorithm peels material regions inward: it starts from the region
    // inside levelSets.back() and repeatedly subdivides that with the earlier
    // level sets.  It therefore requires a NESTED stack, where the last level
    // set encloses every earlier one.
    //
    // A domain may legitimately hold a top level set that does not wrap the
    // others — a LOCOS mask inserted with wrapLowerLevelSet=false, which has to
    // stay a separate body for the mask mechanics.  Passing that in unchanged
    // clips the entire mesh to the mask's own extent, so the substrate and most
    // of the oxide silently vanish from the output.
    //
    // Repair it here with cumulative unions.  This is a no-op on an already
    // nested stack (the union of a set with a subset is that set), so it only
    // affects inputs that would otherwise be rendered wrongly.  The unions are
    // built on deep copies, leaving the caller's level sets untouched.
    if (levelSets.size() > 1) {
      LevelSetsType nested;
      nested.reserve(levelSets.size());
      for (auto &ls : levelSets) {
        auto merged = SmartPointer<Domain<T, D>>::New(ls);
        if (!nested.empty())
          BooleanOperation<T, D>(merged, nested.back(),
                                 BooleanOperationEnum::UNION)
              .apply();
        nested.push_back(merged);
      }
      levelSets = std::move(nested);
    }
 
    const double gridDelta = levelSets[0]->getGrid().getGridDelta();
 
    // store volume for each material
    std::vector<vtkSmartPointer<vtkUnstructuredGrid>> materialMeshes;
    std::vector<unsigned> materialIds;
 
    int totalMinimum = std::numeric_limits<int>::max();
    int totalMaximum = -std::numeric_limits<int>::max();
    for (auto &it : levelSets) {
      if (it->getNumberOfPoints() == 0) {
        continue;
      }
      auto &grid = it->getGrid();
      auto &domain = it->getDomain();
      for (unsigned i = 0; i < D; ++i) {
        if (grid.getBoundaryConditions(i) ==
            Domain<T, D>::BoundaryType::INFINITE_BOUNDARY) {
          totalMinimum = std::min(totalMinimum, domain.getMinRunBreak(i));
          totalMaximum = std::max(totalMaximum, domain.getMaxRunBreak(i));
        }
      }
    }
 
    // create volume mesh for largest LS
    // Use vtkClipDataSet to slice the grid
    vtkSmartPointer<vtkTableBasedClipDataSet> clipper =
        vtkSmartPointer<vtkTableBasedClipDataSet>::New();
    auto topGrid = vtkSmartPointer<vtkRectilinearGrid>::New();
    // if (bottomRemoved) {
    topGrid =
        LS2RectiLinearGrid(levelSets.back(), 0, totalMinimum, totalMaximum);
    // } else {
    //   topGrid = LS2RectiLinearGrid<false>(levelSets.back(), 0,
    //   totalMinimum,
    //                                       totalMaximum);
    // }
#ifdef LS_TO_VISUALIZATION_DEBUG
    {
      auto gwriter = vtkSmartPointer<vtkXMLRectilinearGridWriter>::New();
      gwriter->SetFileName("./grid_0.vtr");
      gwriter->SetInputData(topGrid);
      gwriter->Write();
      std::cout << "Wrote grid 0" << std::endl;
    }
#endif
    clipper->SetInputData(topGrid);
    clipper->InsideOutOn();
    clipper->SetValue(0.0);
    clipper->GenerateClippedOutputOn(); // TODO remove
    clipper->Update();
 
#ifdef LS_TO_VISUALIZATION_DEBUG
    {
      auto gwriter = vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
      gwriter->SetFileName("./clipped.vtu");
      gwriter->SetInputData(clipper->GetClippedOutput());
      gwriter->Write();
      std::cout << "Wrote clipped" << std::endl;
    }
#endif
 
    const bool useMaterialMap = materialMap != nullptr;
    materialMeshes.emplace_back(clipper->GetOutput());
    materialIds.push_back(useMaterialMap ? materialMap->getMaterialId(0) : 0);
 
#ifdef LS_TO_VISUALIZATION_DEBUG
    {
      auto gwriter = vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
      gwriter->SetFileName("./probed_0.vtu");
      gwriter->SetInputData(materialMeshes.front());
      gwriter->Write();
    }
#endif
 
    unsigned counter = 1;
 
    // now cut large volume mesh with all the smaller ones
    for (typename LevelSetsType::const_reverse_iterator it =
             ++levelSets.rbegin();
         it != levelSets.rend(); ++it) {
      if (it->get()->getNumberOfPoints() == 0)
        continue; // ignore empty levelSets
 
      // create grid of next LS with slight offset and project into current
      // mesh
      vtkSmartPointer<vtkRectilinearGrid> rgrid =
          vtkSmartPointer<vtkRectilinearGrid>::New();
      // if (bottomRemoved) {
      rgrid = LS2RectiLinearGrid<1>(*it, -LSEpsilon * counter, totalMinimum,
                                    totalMaximum);
      // } else {
      //   rgrid = LS2RectiLinearGrid<false, 1>(*it, -LSEpsilon * counter,
      //                                        totalMinimum, totalMaximum);
      // }
 
#ifdef LS_TO_VISUALIZATION_DEBUG
      {
        vtkSmartPointer<vtkXMLRectilinearGridWriter> gwriter =
            vtkSmartPointer<vtkXMLRectilinearGridWriter>::New();
        gwriter->SetFileName(
            ("./grid_" + std::to_string(counter) + ".vtr").c_str());
        gwriter->SetInputData(rgrid);
        gwriter->Write();
        std::cout << "Wrote grid " << counter << std::endl;
      }
#endif
 
      // now transfer implicit values to mesh points
      vtkSmartPointer<vtkProbeFilter> probeFilter =
          vtkSmartPointer<vtkProbeFilter>::New();
      probeFilter->SetInputData(materialMeshes.back()); // last element
      probeFilter->SetSourceData(rgrid);
      probeFilter->Update();
 
#ifdef LS_TO_VISUALIZATION_DEBUG
      {
        vtkSmartPointer<vtkXMLUnstructuredGridWriter> gwriter =
            vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
        gwriter->SetFileName(
            ("./probed_" + std::to_string(counter) + ".vtu").c_str());
        gwriter->SetInputData(probeFilter->GetOutput());
        gwriter->Write();
        std::cout << "Wrote unstructured grid " << counter << std::endl;
      }
#endif
 
      // now clip the mesh and save the clipped as the 1st layer and use the
      // inverse for the next layer clipping Use vtkTabelBasedClipDataSet to
      // slice the grid
      vtkSmartPointer<vtkTableBasedClipDataSet> insideClipper =
          vtkSmartPointer<vtkTableBasedClipDataSet>::New();
      insideClipper->SetInputConnection(probeFilter->GetOutputPort());
      insideClipper->GenerateClippedOutputOn();
      insideClipper->Update();
 
      materialMeshes.back() = insideClipper->GetOutput();
      materialMeshes.emplace_back(insideClipper->GetClippedOutput());
      auto material = counter;
      if (useMaterialMap)
        material = materialMap->getMaterialId(counter);
      materialIds.push_back(material);
 
      ++counter;
    }
 
    vtkSmartPointer<vtkAppendFilter> appendFilter =
        vtkSmartPointer<vtkAppendFilter>::New();
 
    vtkSmartPointer<vtkAppendPolyData> hullAppendFilter =
        vtkSmartPointer<vtkAppendPolyData>::New();
 
    for (unsigned i = 0; i < materialMeshes.size(); ++i) {
 
      // write material number in mesh
      vtkSmartPointer<vtkIntArray> materialNumberArray =
          vtkSmartPointer<vtkIntArray>::New();
      materialNumberArray->SetNumberOfComponents(1);
      materialNumberArray->SetName("Material");
      for (unsigned j = 0;
           j <
           materialMeshes[materialMeshes.size() - 1 - i]->GetNumberOfCells();
           ++j) {
        materialNumberArray->InsertNextValue(materialIds[i]);
      }
      materialMeshes[materialMeshes.size() - 1 - i]->GetCellData()->SetScalars(
          materialNumberArray);
 
      // delete all point data, so it is not in ouput
      // TODO this includes signed distance information which could be
      // conserved for debugging also includes wheter a cell was vaild for
      // cutting by the grid
      vtkSmartPointer<vtkPointData> pointData =
          materialMeshes[materialMeshes.size() - 1 - i]->GetPointData();
      const int numberOfArrays = pointData->GetNumberOfArrays();
      for (int j = 0; j < numberOfArrays; ++j) {
        pointData->RemoveArray(0); // remove first array until none are left
      }
 
      // if hull mesh should be exported, create hull for each layer and put
      // them together
      if (extractHullMesh) {
        vtkSmartPointer<vtkGeometryFilter> geoFilter =
            vtkSmartPointer<vtkGeometryFilter>::New();
        geoFilter->SetInputData(materialMeshes[materialMeshes.size() - 1 - i]);
        geoFilter->Update();
        hullAppendFilter->AddInputData(geoFilter->GetOutput());
      }
 
      appendFilter->AddInputData(materialMeshes[materialMeshes.size() - 1 - i]);
    }
 
    // do not need tetrahedral volume mesh if we do not print volume
    volumeVTK = vtkSmartPointer<vtkUnstructuredGrid>::New();
    hullVTK = vtkSmartPointer<vtkPolyData>::New();
    if (extractVolumeMesh) {
      appendFilter->Update();
 
      // remove degenerate points and remove cells which collapse to zero
      // volume then
      volumeVTK = appendFilter->GetOutput();
#ifdef LS_TO_VISUALIZATION_DEBUG
      {
        std::cout << "Before duplicate removal: " << std::endl;
        std::cout << "Points: " << volumeVTK->GetNumberOfPoints() << std::endl;
        std::cout << "Cells: " << volumeVTK->GetNumberOfCells() << std::endl;
        vtkSmartPointer<vtkXMLUnstructuredGridWriter> gwriter =
            vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
        gwriter->SetFileName("before_removal.vtu");
        gwriter->SetInputData(appendFilter->GetOutput());
        gwriter->Update();
      }
#endif
 
      // use 1/1000th of grid spacing for contraction of two similar points,
      // so that tetrahedralisation works correctly
      removeDuplicatePoints(volumeVTK, 1e-3 * gridDelta);
 
#ifdef LS_TO_VISUALIZATION_DEBUG
      {
        std::cout << "After duplicate removal: " << std::endl;
        std::cout << "Points: " << volumeVTK->GetNumberOfPoints() << std::endl;
        std::cout << "Cells: " << volumeVTK->GetNumberOfCells() << std::endl;
        vtkSmartPointer<vtkXMLUnstructuredGridWriter> gwriter =
            vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
        gwriter->SetFileName("after_removal.vtu");
        gwriter->SetInputData(volumeVTK);
        gwriter->Update();
      }
#endif
 
      // change all 3D cells into tetras and all 2D cells to triangles
      vtkSmartPointer<vtkDataSetTriangleFilter> triangleFilter =
          vtkSmartPointer<vtkDataSetTriangleFilter>::New();
      triangleFilter->SetInputData(volumeVTK);
      triangleFilter->Update();
      volumeVTK = triangleFilter->GetOutput();
 
      // now that only tetras are left, remove the ones with degenerate points
      removeDegenerateTetras(volumeVTK);
 
      // add meta data to volume mesh
      addMetaDataToVTK(volumeVTK);
 
      if (writeToFile) {
        auto writer = vtkSmartPointer<vtkXMLUnstructuredGridWriter>::New();
        writer->SetFileName((fileName + "_volume.vtu").c_str());
        // Inline binary rather than VTK's default appended mode: VTK 9.1's
        // reader cannot parse appended data once an array spans more than one
        // 32 kB compression block, so meshes above a few thousand cells are
        // written unreadably by its own reader (and by anything else linking
        // 9.1).  Verified across every appended variant — base64 or raw,
        // compressed or not — all fail to round-trip, while inline binary
        // succeeds at identical file size.
        writer->SetDataModeToBinary();
        writer->SetInputData(volumeVTK);
        writer->Write();
      }
    }
 
    // Now make hull mesh if necessary
    if (extractHullMesh) {
      hullAppendFilter->Update();
      hullVTK = hullAppendFilter->GetOutput();
      // use 1/1000th of grid spacing for contraction of two similar points
      removeDuplicatePoints(hullVTK, 1e-3 * gridDelta);
 
      vtkSmartPointer<vtkTriangleFilter> hullTriangleFilter =
          vtkSmartPointer<vtkTriangleFilter>::New();
      hullTriangleFilter->SetInputData(hullVTK);
      hullTriangleFilter->Update();
 
      hullVTK = hullTriangleFilter->GetOutput();
 
      // add meta data to hull mesh
      addMetaDataToVTK(hullVTK);
 
      if (writeToFile) {
        auto writer = vtkSmartPointer<vtkXMLPolyDataWriter>::New();
        writer->SetFileName((fileName + "_hull.vtp").c_str());
        // See the volume writer above: VTK 9.1 cannot read back its own
        // appended-mode output for multi-block arrays.
        writer->SetDataModeToBinary();
        writer->SetInputData(hullVTK);
        writer->Write();
      } else {
        hullTriangleFilter->Update();
      }
    }
  }
};
 
// add all template specialisations for this class
PRECOMPILE_PRECISION_DIMENSION(WriteVisualizationMesh)
 
} // namespace viennals
 
#endif // VIENNALS_USE_VTK