pyWrap.hpp

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#include <pybind11/iostream.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
 
// all header files which define API functions
#include <lsAdvect.hpp>
#include <lsBooleanOperation.hpp>
#include <lsCalculateCurvatures.hpp>
#include <lsCalculateNormalVectors.hpp>
#include <lsCalculateVisibilities.hpp>
#include <lsCheck.hpp>
#include <lsCompareArea.hpp>
#include <lsCompareNarrowBand.hpp>
#include <lsCompareSparseField.hpp>
#include <lsConvexHull.hpp>
#include <lsDetectFeatures.hpp>
#include <lsDomain.hpp>
#include <lsExpand.hpp>
#include <lsExtrude.hpp>
#include <lsFileFormats.hpp>
#include <lsFromMesh.hpp>
#include <lsFromSurfaceMesh.hpp>
#include <lsFromVolumeMesh.hpp>
#include <lsGeometricAdvect.hpp>
#include <lsGeometricAdvectDistributions.hpp>
#include <lsGeometries.hpp>
#include <lsMakeGeometry.hpp>
#include <lsMarkVoidPoints.hpp>
#include <lsMaterialMap.hpp>
#include <lsMesh.hpp>
#include <lsPointData.hpp>
#include <lsPrune.hpp>
#include <lsReader.hpp>
#include <lsReduce.hpp>
#include <lsRemoveStrayPoints.hpp>
#include <lsSlice.hpp>
#include <lsToDiskMesh.hpp>
#include <lsToMesh.hpp>
#include <lsToSurfaceMesh.hpp>
#include <lsToVoxelMesh.hpp>
#include <lsTransformMesh.hpp>
#include <lsVTKReader.hpp>
#include <lsVTKWriter.hpp>
#include <lsVelocityField.hpp>
#include <lsVersion.hpp>
#include <lsWriteVisualizationMesh.hpp>
#include <lsWriter.hpp>
 
#include <vcLogger.hpp>
#include <vcSmartPointer.hpp>
 
using namespace viennals;
namespace py = pybind11;
 
// always use double for python export
typedef double T;
 
PYBIND11_DECLARE_HOLDER_TYPE(TemplateType, SmartPointer<TemplateType>);
 
// GeometricAdvectDistribution
template <int D>
class PylsGeometricAdvectDistribution
    : public GeometricAdvectDistribution<T, D> {
  typedef std::array<viennahrle::CoordType, 3> vectorType;
  typedef std::array<viennahrle::CoordType, 6> boundsType;
  typedef GeometricAdvectDistribution<T, D> ClassType;
  using GeometricAdvectDistribution<T, D>::GeometricAdvectDistribution;
 
public:
  bool isInside(const vectorType &initial, const vectorType &candidate,
                double eps = 0.) const override {
    PYBIND11_OVERLOAD(bool, ClassType, isInside, initial, candidate, eps);
  }
 
  T getSignedDistance(const vectorType &initial, const vectorType &candidate,
                      unsigned long initialPointId) const override {
    PYBIND11_OVERLOAD_PURE(T, ClassType, getSignedDistance, initial, candidate,
                           initialPointId);
  }
 
  boundsType getBounds() const override {
    PYBIND11_OVERLOAD_PURE(boundsType, ClassType, getBounds);
  }
};
 
template <int D> void bindApi(py::module &module) {
  // Also wrap hrleGrid so it can be used to create new LevelSets
  py::class_<viennahrle::Grid<D>>(module, "hrleGrid");
 
  // Domain
  py::class_<Domain<T, D>, SmartPointer<Domain<T, D>>>(module, "Domain")
      // constructors
      .def(py::init(&SmartPointer<Domain<T, D>>::template New<>))
      .def(
          py::init(
              &SmartPointer<Domain<T, D>>::template New<viennahrle::CoordType>),
          py::arg("gridDelta") = 1.0)
      //  .def(py::init(
      //      &SmartPointer<Domain<T, D>>::New<viennahrle::CoordType *,
      //                                       BoundaryConditionEnum *>))
      .def(py::init([](std::array<viennahrle::CoordType, 2 * D> bounds,
                       std::array<BoundaryConditionEnum, D> bcs,
                       viennahrle::CoordType gridDelta) {
             return SmartPointer<Domain<T, D>>::New(bounds.data(), bcs.data(),
                                                    gridDelta);
           }),
           py::arg("bounds"), py::arg("boundaryConditions"),
           py::arg("gridDelta") = 1.0)
      .def(py::init(&SmartPointer<Domain<T, D>>::template New<
                    std::vector<viennahrle::CoordType>, std::vector<unsigned>,
                    viennahrle::CoordType>),
           py::arg("bounds"), py::arg("boundaryConditions"),
           py::arg("gridDelta") = 1.0)
      //  .def(py::init(
      //      &SmartPointer<Domain<T, D>>::New<Domain<T,
      //      D>::PointValueVectorType,
      //                                       viennahrle::CoordType *,
      //                                       BoundaryConditionEnum *>))
      //  .def(py::init(&SmartPointer<Domain<T, D>>::New<
      //                      Domain<T, D>::PointValueVectorType,
      //                      viennahrle::CoordType
      //                      *, BoundaryConditionEnum *,
      //                      viennahrle::CoordType>))
      .def(py::init(&SmartPointer<Domain<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(py::init(
          &SmartPointer<Domain<T, D>>::template New<viennahrle::Grid<D> &>))
      // methods
      .def("deepCopy", &Domain<T, D>::deepCopy,
           "Copy lsDomain in this lsDomain.")
      .def("getNumberOfSegments", &Domain<T, D>::getNumberOfSegments,
           "Get the number of segments, the level set structure is divided "
           "into.")
      .def("getNumberOfPoints", &Domain<T, D>::getNumberOfPoints,
           "Get the number of defined level set values.")
      .def("getLevelSetWidth", &Domain<T, D>::getLevelSetWidth,
           "Get the number of layers of level set points around the explicit "
           "surface.")
      .def("setLevelSetWidth", &Domain<T, D>::setLevelSetWidth,
           "Set the number of layers of level set points which should be "
           "stored around the explicit surface.")
      .def("clearMetaData", &Domain<T, D>::clearMetaData,
           "Clear all metadata stored in the level set.")
      // allow filehandle to be passed and default to python standard output
      .def(
          "print",
          [](Domain<T, D> &d, py::object fileHandle) {
            if (!(py::hasattr(fileHandle, "write") &&
                  py::hasattr(fileHandle, "flush"))) {
              throw py::type_error(
                  "MyClass::read_from_file_like_object(file): incompatible "
                  "function argument:  `file` must be a file-like object, but "
                  "`" +
                  (std::string)(py::repr(fileHandle)) + "` provided");
            }
            py::detail::pythonbuf buf(fileHandle);
            std::ostream stream(&buf);
            d.print(stream);
          },
          py::arg("stream") = py::module::import("sys").attr("stdout"));
 
  // Advect
  py::class_<Advect<T, D>, SmartPointer<Advect<T, D>>>(module, "Advect")
      // constructors
      .def(py::init(&SmartPointer<Advect<T, D>>::template New<>))
      .def(py::init(&SmartPointer<Advect<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(py::init(
          &SmartPointer<Advect<T, D>>::template New<
              SmartPointer<Domain<T, D>> &, SmartPointer<VelocityField<T>> &>))
      // getters and setters
      .def("insertNextLevelSet", &Advect<T, D>::insertNextLevelSet,
           "Insert next level set to use for advection.")
      .def("setVelocityField", &Advect<T, D>::setVelocityField,
           "Set the velocity to use for advection.")
      .def("setAdvectionTime", &Advect<T, D>::setAdvectionTime,
           "Set the time until when the level set should be advected.")
      .def("setTimeStepRatio", &Advect<T, D>::setTimeStepRatio,
           "Set the maximum time step size relative to grid size. Advection is "
           "only stable for <0.5.")
      .def("setCalculateNormalVectors",
           &Advect<T, D>::setCalculateNormalVectors,
           "Set whether normal vectors are needed for the supplied velocity "
           "field.")
      .def("setIgnoreVoids", &Advect<T, D>::setIgnoreVoids,
           "Set whether voids in the geometry should be ignored during "
           "advection or not.")
      .def("getAdvectedTime", &Advect<T, D>::getAdvectedTime,
           "Get the time passed during advection.")
      .def("getNumberOfTimeSteps", &Advect<T, D>::getNumberOfTimeSteps,
           "Get how many advection steps were performed after the last apply() "
           "call.")
      .def("getTimeStepRatio", &Advect<T, D>::getTimeStepRatio,
           "Get the time step ratio used for advection.")
      .def("getCurrentTimeStep", &Advect<T, D>::getCurrentTimeStep,
           "Get the current time step.")
      .def("getCalculateNormalVectors",
           &Advect<T, D>::getCalculateNormalVectors,
           "Get whether normal vectors are computed during advection.")
      .def("setIntegrationScheme", &Advect<T, D>::setIntegrationScheme,
           "Set the integration scheme to use during advection.")
      .def("setDissipationAlpha", &Advect<T, D>::setDissipationAlpha,
           "Set the dissipation value to use for Lax Friedrichs integration.")
      .def("prepareLS", &Advect<T, D>::prepareLS, "Prepare the level-set.")
      // need scoped release since we are calling a python method from
      // parallelised C++ code here
      .def("apply", &Advect<T, D>::apply,
           py::call_guard<py::gil_scoped_release>(), "Perform advection.")
      .def("applyIntegration", &Advect<T, D>::applyIntegration,
           py::call_guard<py::gil_scoped_release>(),
           "Apply the integration scheme and calculate rates and maximum time "
           "step, but it do **not** move the surface.");
 
  py::class_<lsInternal::StencilLocalLaxFriedrichsScalar<T, D, 1>>(
      module, "StencilLocalLaxFriedrichsScalar")
      .def_static(
          "setMaxDissipation",
          &lsInternal::StencilLocalLaxFriedrichsScalar<T, D,
                                                       1>::setMaxDissipation,
          py::arg("maxDissipation"));
 
  module.def("PrepareStencilLocalLaxFriedrichs",
             &PrepareStencilLocalLaxFriedrichs<T, D>, py::arg("levelSets"),
             py::arg("isDepo"));
 
  module.def("FinalizeStencilLocalLaxFriedrichs",
             &FinalizeStencilLocalLaxFriedrichs<T, D>, py::arg("levelSets"));
 
  // BooleanOperation
  py::class_<BooleanOperation<T, D>, SmartPointer<BooleanOperation<T, D>>>(
      module, "BooleanOperation")
      // constructors
      .def(py::init(&SmartPointer<BooleanOperation<T, D>>::template New<>))
      .def(py::init(&SmartPointer<BooleanOperation<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(
          py::init(&SmartPointer<BooleanOperation<T, D>>::template New<
                   SmartPointer<Domain<T, D>> &, SmartPointer<Domain<T, D>> &>))
      // some constructors need lambda to work: seems to be an issue with
      // implicit move constructor
      .def(py::init(
          [](SmartPointer<Domain<T, D>> &domain, BooleanOperationEnum op) {
            return SmartPointer<BooleanOperation<T, D>>::New(domain, op);
          }))
      .def(py::init([](SmartPointer<Domain<T, D>> &domainA,
                       SmartPointer<Domain<T, D>> &domainB,
                       BooleanOperationEnum op) {
        return SmartPointer<BooleanOperation<T, D>>::New(domainA, domainB, op);
      }))
      // methods
      .def("setLevelset", &BooleanOperation<T, D>::setLevelSet,
           "Set levelset on which the boolean operation should be performed.")
      .def("setSecondLevelSet", &BooleanOperation<T, D>::setSecondLevelSet,
           "Set second levelset for boolean operation.")
      .def("setBooleanOperation", &BooleanOperation<T, D>::setBooleanOperation,
           "Set which type of boolean operation should be performed.")
      .def("apply", &BooleanOperation<T, D>::apply,
           "Perform the boolean operation.");
 
  py::class_<CalculateCurvatures<T, D>,
             SmartPointer<CalculateCurvatures<T, D>>>(module,
                                                      "CalculateCurvatures")
      // constructors
      .def(py::init(&SmartPointer<CalculateCurvatures<T, D>>::template New<>))
      .def(py::init(&SmartPointer<CalculateCurvatures<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      // some constructors need lambda to work: seems to be an issue with
      // implicit move constructor
      .def(py::init([](SmartPointer<Domain<T, D>> &domain, CurvatureEnum type) {
        return SmartPointer<CalculateCurvatures<T, D>>::New(domain, type);
      }))
      // methods
      .def("setLevelSet", &CalculateCurvatures<T, D>::setLevelSet,
           "Set levelset for which to calculate the curvatures.")
      .def("setCurvatureType", &CalculateCurvatures<T, D>::setCurvatureType,
           "Set which method to use for calculation: Defaults to mean "
           "curvature.")
      .def("setMaxValue", &CalculateCurvatures<T, D>::setMaxValue,
           "Curvatures will be calculated for all LS values < maxValue.")
      .def("apply", &CalculateCurvatures<T, D>::apply,
           "Perform normal vector calculation.");
 
  // CalculateNormalVectors
  py::class_<CalculateNormalVectors<T, D>,
             SmartPointer<CalculateNormalVectors<T, D>>>(
      module, "CalculateNormalVectors")
      // constructors
      .def(
          py::init(&SmartPointer<CalculateNormalVectors<T, D>>::template New<>))
      .def(py::init(&SmartPointer<CalculateNormalVectors<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      // methods
      .def("setLevelSet", &CalculateNormalVectors<T, D>::setLevelSet,
           "Set levelset for which to calculate normal vectors.")
      .def("apply", &CalculateNormalVectors<T, D>::apply,
           "Perform normal vector calculation.");
 
  // CalculateVisibilities
  py::class_<CalculateVisibilities<T, D>,
             SmartPointer<CalculateVisibilities<T, D>>>(module,
                                                        "CalculateVisibilities")
      .def(py::init(
          &SmartPointer<CalculateVisibilities<T, D>>::template New<
              SmartPointer<Domain<T, D>> &, const Vec3D<T> &, std::string>))
      .def("apply", &CalculateVisibilities<T, D>::apply);
 
  // Check
  py::class_<Check<T, D>, SmartPointer<Check<T, D>>>(module, "Check")
      // constructors
      .def(py::init(&SmartPointer<Check<T, D>>::template New<>))
      .def(py::init(&SmartPointer<Check<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      // methods
      .def("setLevelSet", &Check<T, D>::setLevelSet,
           "Set levelset for which to calculate normal vectors.")
      .def("apply", &Check<T, D>::apply, "Perform check.");
 
  // PointCloud
  py::class_<PointCloud<T, D>, SmartPointer<PointCloud<T, D>>>(module,
                                                               "PointCloud")
      // constructors
      .def(py::init(&SmartPointer<PointCloud<T, D>>::template New<
                    const std::vector<VectorType<T, D>> &>))
      // methods
      .def("insertNextPoint",
           (void(PointCloud<T, D>::*)(const VectorType<T, D> &)) &
               PointCloud<T, D>::insertNextPoint);
 
  // ConvexHull
  py::class_<ConvexHull<T, D>, SmartPointer<ConvexHull<T, D>>>(module,
                                                               "ConvexHull")
      // constructors
      .def(py::init(&SmartPointer<ConvexHull<T, D>>::template New<>))
      .def(py::init(&SmartPointer<ConvexHull<T, D>>::template New<
                    SmartPointer<Mesh<T>> &, SmartPointer<PointCloud<T, D>> &>))
      // methods
      .def("setMesh", &ConvexHull<T, D>::setMesh,
           "Set mesh object where the generated mesh should be stored.")
      .def("setPointCloud", &ConvexHull<T, D>::setPointCloud,
           "Set point cloud used to generate mesh.")
      .def("apply", &ConvexHull<T, D>::apply, "Generate Hull.");
 
  // DetectFeatures
  py::class_<DetectFeatures<T, D>, SmartPointer<DetectFeatures<T, D>>>(
      module, "DetectFeatures")
      // constructors
      .def(py::init(&SmartPointer<DetectFeatures<T, D>>::template New<>))
      .def(py::init(&SmartPointer<DetectFeatures<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(py::init(&SmartPointer<DetectFeatures<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, T>))
      // some constructors need lambda to work: seems to be an issue with
      // implicit move constructor
      .def(py::init([](SmartPointer<Domain<T, D>> &domain, T maxValue,
                       FeatureDetectionEnum type) {
        return SmartPointer<DetectFeatures<T, D>>::New(domain, maxValue, type);
      }))
      .def("setDetectionThreshold",
           &DetectFeatures<T, D>::setDetectionThreshold,
           "Set the curvature value above which a point is considered a "
           "feature.")
      .def("setDetectionMethod", &DetectFeatures<T, D>::setDetectionMethod,
           "Set which method to use to detect features. Defaults to Curvature.")
      .def("apply", &DetectFeatures<T, D>::apply, "Detect features.");
 
  // GeometricAdvect
  py::class_<GeometricAdvect<T, D>, SmartPointer<GeometricAdvect<T, D>>>(
      module, "GeometricAdvect")
      // constructors
      .def(py::init(&SmartPointer<GeometricAdvect<T, D>>::template New<>))
      .def(py::init(
          &SmartPointer<GeometricAdvect<T, D>>::template New<
              SmartPointer<Domain<T, D>> &,
              SmartPointer<
                  GeometricAdvectDistribution<viennahrle::CoordType, D>> &>))
      // methods
      .def("setLevelSet", &GeometricAdvect<T, D>::setLevelSet,
           "Set levelset to advect.")
      .def(
          "setAdvectionDistribution",
          &GeometricAdvect<T, D>::template setAdvectionDistribution<
              PylsGeometricAdvectDistribution<D>>,
          "Set advection distribution to use as kernel for the fast advection.")
      .def("apply", &GeometricAdvect<T, D>::apply,
           py::call_guard<py::gil_scoped_release>(), "Perform advection.");
 
  // GeometricAdvectDistributions
  py::class_<GeometricAdvectDistribution<T, D>,
             SmartPointer<GeometricAdvectDistribution<T, D>>,
             PylsGeometricAdvectDistribution<D>>(module,
                                                 "GeometricAdvectDistribution")
      // constructors
      .def(py::init<>())
      // methods
      .def("isInside", &GeometricAdvectDistribution<T, D>::isInside,
           "Check whether passed point is inside the distribution.")
      .def("getSignedDistance",
           &GeometricAdvectDistribution<T, D>::getSignedDistance,
           "Get the signed distance of the passed point to the surface of the "
           "distribution.")
      .def("getBounds", &GeometricAdvectDistribution<T, D>::getBounds,
           "Get the cartesian bounds of the distribution.");
 
  py::class_<SphereDistribution<T, D>, SmartPointer<SphereDistribution<T, D>>,
             GeometricAdvectDistribution<T, D>>(module, "SphereDistribution")
      // constructors
      .def(
          py::init(&SmartPointer<SphereDistribution<T, D>>::template New<T, T>))
      // methods
      .def("isInside", &SphereDistribution<T, D>::isInside,
           "Check whether passed point is inside the distribution.")
      .def("getSignedDistance", &SphereDistribution<T, D>::getSignedDistance,
           "Get the signed distance of the passed point to the surface of the "
           "distribution.")
      .def("getBounds", &SphereDistribution<T, D>::getBounds,
           "Get the cartesian bounds of the distribution.");
 
  py::class_<BoxDistribution<T, D>, SmartPointer<BoxDistribution<T, D>>,
             GeometricAdvectDistribution<T, D>>(module, "BoxDistribution")
      // constructors
      .def(py::init(&SmartPointer<BoxDistribution<T, D>>::template New<
                    const std::array<T, 3>, T>))
      // methods
      .def("isInside", &BoxDistribution<T, D>::isInside,
           "Check whether passed point is inside the distribution.")
      .def("getSignedDistance", &BoxDistribution<T, D>::getSignedDistance,
           "Get the signed distance of the passed point to the surface of the "
           "distribution.")
      .def("getBounds", &BoxDistribution<T, D>::getBounds,
           "Get the cartesian bounds of the distribution.");
 
  // Expand
  py::class_<Expand<T, D>, SmartPointer<Expand<T, D>>>(module, "Expand")
      // constructors
      .def(py::init(&SmartPointer<Expand<T, D>>::template New<>))
      .def(py::init(&SmartPointer<Expand<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(py::init(&SmartPointer<Expand<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, int>))
      // methods
      .def("setLevelSet", &Expand<T, D>::setLevelSet, "Set levelset to expand.")
      .def("setWidth", &Expand<T, D>::setWidth, "Set the width to expand to.")
      .def("apply", &Expand<T, D>::apply, "Perform expansion.");
 
  // FromSurfaceMesh
  py::class_<FromSurfaceMesh<T, D>, SmartPointer<FromSurfaceMesh<T, D>>>(
      module, "FromSurfaceMesh")
      // constructors
      .def(py::init(&SmartPointer<FromSurfaceMesh<T, D>>::template New<>))
      .def(py::init(&SmartPointer<FromSurfaceMesh<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, SmartPointer<Mesh<T>> &>))
      .def(py::init(
          &SmartPointer<FromSurfaceMesh<T, D>>::template New<
              SmartPointer<Domain<T, D>> &, SmartPointer<Mesh<T>> &, bool>))
      // methods
      .def("setLevelSet", &FromSurfaceMesh<T, D>::setLevelSet,
           "Set levelset to read into.")
      .def("setMesh", &FromSurfaceMesh<T, D>::setMesh,
           "Set the mesh to read from.")
      .def("setRemoveBoundaryTriangles",
           static_cast<void (FromSurfaceMesh<T, D>::*)(bool)>(
               &FromSurfaceMesh<T, D>::setRemoveBoundaryTriangles),
           "Set whether to include mesh elements outside of the simulation "
           "domain.")
      .def("setRemoveBoundaryTriangles",
           static_cast<void (FromSurfaceMesh<T, D>::*)(std::array<bool, 3>)>(
               &FromSurfaceMesh<T, D>::setRemoveBoundaryTriangles),
           "Set whether to include mesh elements outside of the simulation "
           "domain.")
      .def("apply", &FromSurfaceMesh<T, D>::apply,
           "Construct a levelset from a surface mesh.");
 
  // FromVolumeMesh
  py::class_<FromVolumeMesh<T, D>, SmartPointer<FromVolumeMesh<T, D>>>(
      module, "FromVolumeMesh")
      // constructors
      .def(py::init(&SmartPointer<FromVolumeMesh<T, D>>::template New<>))
      .def(py::init(&SmartPointer<FromVolumeMesh<T, D>>::template New<
                    typename FromVolumeMesh<T, D>::GridType &,
                    SmartPointer<Mesh<T>> &>))
      .def(py::init(&SmartPointer<FromVolumeMesh<T, D>>::template New<
                    typename FromVolumeMesh<T, D>::GridType &,
                    SmartPointer<Mesh<T>> &, bool>))
      // methods
      .def("setGrid", &FromVolumeMesh<T, D>::setGrid,
           "Set the grid used to read in the level sets.")
      .def("setMesh", &FromVolumeMesh<T, D>::setMesh,
           "Set the mesh to read from.")
      .def("setRemoveBoundaryTriangles",
           &FromVolumeMesh<T, D>::setRemoveBoundaryTriangles,
           "Set whether to include mesh elements outside of the simulation "
           "domain.")
      .def("apply", &FromVolumeMesh<T, D>::apply,
           "Construct a levelset from a volume mesh.");
 
  // FromMesh
  py::class_<FromMesh<T, D>, SmartPointer<FromMesh<T, D>>>(module, "FromMesh")
      .def(py::init(&SmartPointer<FromMesh<T, D>>::template New<>))
      .def(py::init(&SmartPointer<FromMesh<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, SmartPointer<Mesh<T>> &>))
      .def("setMesh", &FromMesh<T, D>::setMesh, "Set the mesh to read from.")
      .def("setSortPointList", &FromMesh<T, D>::setSortPointList)
      .def("apply", &FromMesh<T, D>::apply);
 
  // lsGeometries
  // Sphere
  py::class_<Sphere<T, D>, SmartPointer<Sphere<T, D>>>(module, "Sphere")
      // constructors
      .def(py::init(&SmartPointer<Sphere<T, D>>::template New<
                    const std::vector<T> & /*origin*/, T /*radius*/>),
           py::arg("origin"), py::arg("radius"));
  // Plane
  py::class_<Plane<T, D>, SmartPointer<Plane<T, D>>>(module, "Plane")
      // constructors
      .def(py::init(&SmartPointer<Plane<T, D>>::template New<
                    const std::vector<T> & /*origin*/,
                    const std::vector<T> & /*normal*/>),
           py::arg("origin"), py::arg("normal"));
  // Box
  py::class_<Box<T, D>, SmartPointer<Box<T, D>>>(module, "Box")
      // constructors
      .def(py::init(&SmartPointer<Box<T, D>>::template New<
                    const std::vector<T> & /*minPoint*/,
                    const std::vector<T> & /*maxPoint*/>),
           py::arg("minPoint"), py::arg("maxPoint"));
  // Cylinder
  py::class_<Cylinder<T, D>, SmartPointer<Cylinder<T, D>>>(module, "Cylinder")
      // constructors
      .def(
          py::init(&SmartPointer<Cylinder<T, D>>::template New<
                   const std::vector<T> & /*origin*/,
                   const std::vector<T> & /*axisDirection*/, const T /*height*/,
                   const T /*radius*/, const T /*topRadius*/>),
          py::arg("origin"), py::arg("axisDirection"), py::arg("height"),
          py::arg("radius"), py::arg("topRadius") = 0.);
 
  // MakeGeometry
  py::class_<MakeGeometry<T, D>, SmartPointer<MakeGeometry<T, D>>>(
      module, "MakeGeometry")
      // constructors
      .def(py::init(&SmartPointer<MakeGeometry<T, D>>::template New<>))
      .def(py::init(&SmartPointer<MakeGeometry<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(
          py::init(&SmartPointer<MakeGeometry<T, D>>::template New<
                   SmartPointer<Domain<T, D>> &, SmartPointer<Sphere<T, D>> &>))
      .def(py::init(&SmartPointer<MakeGeometry<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, SmartPointer<Plane<T, D>> &>))
      .def(py::init(&SmartPointer<MakeGeometry<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, SmartPointer<Box<T, D>> &>))
      .def(py::init(
          &SmartPointer<MakeGeometry<T, D>>::template New<
              SmartPointer<Domain<T, D>> &, SmartPointer<Cylinder<T, D>> &>))
      .def(py::init(
          &SmartPointer<MakeGeometry<T, D>>::template New<
              SmartPointer<Domain<T, D>> &, SmartPointer<PointCloud<T, D>> &>))
      // methods
      .def("setLevelSet", &MakeGeometry<T, D>::setLevelSet,
           "Set the levelset in which to create the geometry.")
      .def("setGeometry",
           (void(MakeGeometry<T, D>::*)(SmartPointer<Sphere<T, D>>)) &
               MakeGeometry<T, D>::setGeometry)
      .def("setGeometry",
           (void(MakeGeometry<T, D>::*)(SmartPointer<Plane<T, D>>)) &
               MakeGeometry<T, D>::setGeometry)
      .def("setGeometry",
           (void(MakeGeometry<T, D>::*)(SmartPointer<Box<T, D>>)) &
               MakeGeometry<T, D>::setGeometry)
      .def("setGeometry",
           (void(MakeGeometry<T, D>::*)(SmartPointer<Cylinder<T, D>>)) &
               MakeGeometry<T, D>::setGeometry)
      .def("setGeometry",
           (void(MakeGeometry<T, D>::*)(SmartPointer<PointCloud<T, D>>)) &
               MakeGeometry<T, D>::setGeometry)
      .def("setIgnoreBoundaryConditions",
           (void(MakeGeometry<T, D>::*)(bool)) &
               MakeGeometry<T, D>::setIgnoreBoundaryConditions)
      .def("setIgnoreBoundaryConditions",
           (void(MakeGeometry<T, D>::*)(std::array<bool, 3>)) &
               MakeGeometry<T, D>::setIgnoreBoundaryConditions)
      .def("apply", &MakeGeometry<T, D>::apply, "Generate the geometry.");
 
  // MarkVoidPoints
  py::class_<MarkVoidPoints<T, D>, SmartPointer<MarkVoidPoints<T, D>>>(
      module, "MarkVoidPoints")
      // constructors
      .def(py::init(&SmartPointer<MarkVoidPoints<T, D>>::template New<>))
      .def(py::init(&SmartPointer<MarkVoidPoints<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(py::init(&SmartPointer<MarkVoidPoints<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, bool &>))
      // methods
      .def("setLevelSet", &MarkVoidPoints<T, D>::setLevelSet,
           "Set the levelset to mark void points in.")
      .def("setReverseVoidDetection",
           &MarkVoidPoints<T, D>::setReverseVoidDetection,
           "Reverse the logic of detecting the top surface.")
      .def("setDetectLargestSurface",
           &MarkVoidPoints<T, D>::setDetectLargestSurface,
           "Set that the top surface should be the one with the most connected "
           "LS points.")
      .def("setVoidTopSurface", &MarkVoidPoints<T, D>::setVoidTopSurface,
           "Set the logic by which to choose the surface which is non-void. "
           "All other connected surfaces will then be marked as void points.")
      .def("setSaveComponentsId", &MarkVoidPoints<T, D>::setSaveComponentIds,
           "Save the connectivity information of all LS points in the "
           "pointData of the level set.")
      .def("apply", &MarkVoidPoints<T, D>::apply, "Mark void points.");
 
  // Prune
  py::class_<Prune<T, D>, SmartPointer<Prune<T, D>>>(module, "Prune")
      // constructors
      .def(py::init(&SmartPointer<Prune<T, D>>::template New<>))
      .def(py::init(&SmartPointer<Prune<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      // methods
      .def("setLevelSet", &Prune<T, D>::setLevelSet, "Set levelset to prune.")
      .def("apply", &Prune<T, D>::apply, "Perform pruning operation.");
 
  // Reader
  py::class_<Reader<T, D>, SmartPointer<Reader<T, D>>>(module, "Reader")
      // constructors
      .def(py::init(&SmartPointer<Reader<T, D>>::template New<>))
      .def(py::init(&SmartPointer<Reader<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(py::init(&SmartPointer<Reader<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, std::string>))
      // methods
      .def("setLevelSet", &Reader<T, D>::setLevelSet,
           "Set levelset to write to file.")
      .def("setFileName", &Reader<T, D>::setFileName,
           "Set the filename for the output file.")
      .def("apply", &Reader<T, D>::apply, "Write to file.");
 
  // Reduce
  py::class_<Reduce<T, D>, SmartPointer<Reduce<T, D>>>(module, "Reduce")
      // constructors
      .def(py::init(&SmartPointer<Reduce<T, D>>::template New<>))
      .def(py::init(&SmartPointer<Reduce<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(py::init(&SmartPointer<Reduce<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, int>))
      .def(py::init(&SmartPointer<Reduce<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, int, bool>))
      // methods
      .def("setLevelSet", &Reduce<T, D>::setLevelSet, "Set levelset to reduce.")
      .def("setWidth", &Reduce<T, D>::setWidth, "Set the width to reduce to.")
      .def("setNoNewSegment", &Reduce<T, D>::setNoNewSegment,
           "Set whether the levelset should be segmented anew (balanced across "
           "cores) after reduction.")
      .def("apply", &Reduce<T, D>::apply, "Perform reduction.");
 
  // RemoveStrayPoints
  py::class_<RemoveStrayPoints<T, D>, SmartPointer<RemoveStrayPoints<T, D>>>(
      module, "RemoveStrayPoints")
      // constructors
      .def(py::init(&SmartPointer<RemoveStrayPoints<T, D>>::template New<>))
      .def(py::init(&SmartPointer<RemoveStrayPoints<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      // methods
      .def("setLevelSet", &RemoveStrayPoints<T, D>::setLevelSet,
           "Set levelset for stray point removal.")
      .def("setVoidTopSurface", &RemoveStrayPoints<T, D>::setVoidTopSurface,
           "Set the logic by which to choose the surface which should be kept. "
           "All other LS values will be marked as stray points and removed.")
      .def("apply", &RemoveStrayPoints<T, D>::apply, "Remove stray points.");
 
  // ToDiskMesh
  py::class_<ToDiskMesh<T, D>, SmartPointer<ToDiskMesh<T, D>>>(module,
                                                               "ToDiskMesh")
      // constructors
      .def(py::init(&SmartPointer<ToDiskMesh<T, D>>::template New<>))
      .def(py::init(&SmartPointer<ToDiskMesh<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, SmartPointer<Mesh<T>> &>))
      // methods
      .def("setLevelSet", &ToDiskMesh<T, D>::setLevelSet,
           "Set levelset to mesh.")
      .def("setMesh", &ToDiskMesh<T, D>::setMesh, "Set the mesh to generate.")
      .def("apply", &ToDiskMesh<T, D>::apply,
           "Convert the levelset to a surface mesh.");
 
  // ToMesh
  py::class_<ToMesh<T, D>, SmartPointer<ToMesh<T, D>>>(module, "ToMesh")
      // constructors
      .def(py::init(&SmartPointer<ToMesh<T, D>>::template New<>))
      .def(py::init(&SmartPointer<ToMesh<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, SmartPointer<Mesh<T>> &>))
      .def(py::init(
          &SmartPointer<ToMesh<T, D>>::template New<
              SmartPointer<Domain<T, D>> &, SmartPointer<Mesh<T>> &, bool>))
      .def(py::init(&SmartPointer<ToMesh<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, SmartPointer<Mesh<T>> &, bool,
                    bool>))
      // methods
      .def("setLevelSet", &ToMesh<T, D>::setLevelSet, "Set levelset to mesh.")
      .def("setMesh", &ToMesh<T, D>::setMesh, "Set the mesh to generate.")
      .def("setOnlyDefined", &ToMesh<T, D>::setOnlyDefined,
           "Set whether only defined points should be output to the mesh.")
      .def("setOnlyActive", &ToMesh<T, D>::setOnlyActive,
           "Set whether only level set points <0.5 should be output.")
      .def("apply", &ToMesh<T, D>::apply,
           "Convert the levelset to a surface mesh.");
 
  // ToSurfaceMesh
  py::class_<ToSurfaceMesh<T, D>, SmartPointer<ToSurfaceMesh<T, D>>>(
      module, "ToSurfaceMesh")
      // constructors
      .def(py::init(&SmartPointer<ToSurfaceMesh<T, D>>::template New<>))
      .def(py::init(&SmartPointer<ToSurfaceMesh<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, SmartPointer<Mesh<T>> &>))
      // methods
      .def("setLevelSet", &ToSurfaceMesh<T, D>::setLevelSet,
           "Set levelset to mesh.")
      .def("setMesh", &ToSurfaceMesh<T, D>::setMesh,
           "Set the mesh to generate.")
      .def("apply", &ToSurfaceMesh<T, D>::apply,
           "Convert the levelset to a surface mesh.");
 
  // ToVoxelMesh
  py::class_<ToVoxelMesh<T, D>, SmartPointer<ToVoxelMesh<T, D>>>(module,
                                                                 "ToVoxelMesh")
      // constructors
      .def(py::init(&SmartPointer<ToVoxelMesh<T, D>>::template New<>))
      .def(py::init(&SmartPointer<ToVoxelMesh<T, D>>::template New<
                    SmartPointer<Mesh<T>> &>))
      .def(py::init(&SmartPointer<ToVoxelMesh<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, SmartPointer<Mesh<T>> &>))
      .def(py::init(&SmartPointer<ToVoxelMesh<T, D>>::template New<
                    std::vector<SmartPointer<Domain<T, D>>> &,
                    SmartPointer<Mesh<T>> &>))
      // methods
      .def("insertNextLevelSet", &ToVoxelMesh<T, D>::insertNextLevelSet,
           "Insert next level set to output in the mesh.")
      .def("setMesh", &ToVoxelMesh<T, D>::setMesh, "Set the mesh to generate.")
      .def("apply", &ToVoxelMesh<T, D>::apply,
           "Convert the levelset to a surface mesh.");
 
  // Writer
  py::class_<Writer<T, D>, SmartPointer<Writer<T, D>>>(module, "Writer")
      // constructors
      .def(py::init(&SmartPointer<Writer<T, D>>::template New<>))
      .def(py::init(&SmartPointer<Writer<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      .def(py::init(&SmartPointer<Writer<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &, std::string>))
      // methods
      .def("setLevelSet", &Writer<T, D>::setLevelSet,
           "Set levelset to write to file.")
      .def("setFileName", &Writer<T, D>::setFileName,
           "Set the filename for the output file.")
      .def("apply", &Writer<T, D>::apply, "Write to file.");
 
// WriteVisualizationMesh
#ifdef VIENNALS_USE_VTK
  py::class_<WriteVisualizationMesh<T, D>,
             SmartPointer<WriteVisualizationMesh<T, D>>>(
      module, "WriteVisualizationMesh")
      // constructors
      .def(
          py::init(&SmartPointer<WriteVisualizationMesh<T, D>>::template New<>))
      .def(py::init(&SmartPointer<WriteVisualizationMesh<T, D>>::template New<
                    SmartPointer<Domain<T, D>> &>))
      // methods
      .def("insertNextLevelSet",
           &WriteVisualizationMesh<T, D>::insertNextLevelSet,
           "Insert next level set to convert. Bigger level sets wrapping "
           "smaller ones, should be inserted last.")
      .def("setFileName", &WriteVisualizationMesh<T, D>::setFileName,
           "Set Name of File to write.")
      .def("setExtractHullMesh",
           &WriteVisualizationMesh<T, D>::setExtractHullMesh,
           "Whether to extract a hull mesh. Defaults to false.")
      .def("setExtractVolumeMesh",
           &WriteVisualizationMesh<T, D>::setExtractVolumeMesh,
           " Whether to extract a tetra volume mesh. Defaults to true.")
      .def("setMetaData", &WriteVisualizationMesh<T, D>::setMetaData,
           "Set the metadata to be written to the file.")
      .def("addMetaData",
           py::overload_cast<const std::string &, T>(
               &WriteVisualizationMesh<T, D>::addMetaData),
           "Add a single metadata entry to the file.")
      .def("addMetaData",
           py::overload_cast<const std::string &, const std::vector<T> &>(
               &WriteVisualizationMesh<T, D>::addMetaData),
           "Add a single metadata entry to the file.")
      .def("addMetaData",
           py::overload_cast<
               const std::unordered_map<std::string, std::vector<T>> &>(
               &WriteVisualizationMesh<T, D>::addMetaData),
           "Add metadata to the file.")
      .def("apply", &WriteVisualizationMesh<T, D>::apply,
           "Make and write mesh.");
#endif
 
  if constexpr (D == 2) {
    // CompareArea
    py::class_<CompareArea<T, D>, SmartPointer<CompareArea<T, D>>>(
        module, "CompareArea")
        // constructors
        .def(py::init(&SmartPointer<CompareArea<T, D>>::template New<>))
        .def(py::init(
            &SmartPointer<CompareArea<T, D>>::template New<
                SmartPointer<Domain<T, D>> &, SmartPointer<Domain<T, D>> &>))
        // methods
        .def("setLevelSetTarget", &CompareArea<T, D>::setLevelSetTarget,
             "Sets the target level set.")
        .def("setLevelSetSample", &CompareArea<T, D>::setLevelSetSample,
             "Sets the sample level set.")
        .def("setDefaultIncrement", &CompareArea<T, D>::setDefaultIncrement,
             "Set default increment value")
        .def("setXRangeAndIncrement", &CompareArea<T, D>::setXRangeAndIncrement,
             "Sets the x-range and custom increment value")
        .def("setYRangeAndIncrement", &CompareArea<T, D>::setYRangeAndIncrement,
             "Sets the y-range and custom increment value")
        .def("setOutputMesh", &CompareArea<T, D>::setOutputMesh,
             "Set the output mesh where difference areas will be stored")
        .def("getAreaMismatch", &CompareArea<T, D>::getAreaMismatch,
             "Returns the computed area mismatch.")
        .def("getCustomAreaMismatch", &CompareArea<T, D>::getCustomAreaMismatch,
             "Returns the computed area mismatch, with custom increments "
             "applied.")
        .def("getCellCount", &CompareArea<T, D>::getCellCount,
             "Returns the number of cells where the level sets differ.")
        .def("getCustomCellCount", &CompareArea<T, D>::getCustomCellCount,
             "Returns the number of cells where the level sets differ, with "
             "custom increments applied.")
        .def("apply", &CompareArea<T, D>::apply,
             "Computes the area difference between the two level sets.");
 
    // CompareNarrowBand
    py::class_<CompareNarrowBand<T, D>, SmartPointer<CompareNarrowBand<T, D>>>(
        module, "CompareNarrowBand")
        // constructors
        .def(py::init(&SmartPointer<CompareNarrowBand<T, D>>::template New<>))
        .def(py::init(
            &SmartPointer<CompareNarrowBand<T, D>>::template New<
                SmartPointer<Domain<T, D>> &, SmartPointer<Domain<T, D>> &>))
        // methods
        .def("setLevelSetTarget", &CompareNarrowBand<T, D>::setLevelSetTarget,
             "Sets the target level set.")
        .def("setLevelSetSample", &CompareNarrowBand<T, D>::setLevelSetSample,
             "Sets the sample level set.")
        .def("setXRange", &CompareNarrowBand<T, D>::setXRange,
             "Set the x-coordinate range to restrict the comparison area")
        .def("setYRange", &CompareNarrowBand<T, D>::setYRange,
             "Set the y-coordinate range to restrict the comparison area")
        .def("clearXRange", &CompareNarrowBand<T, D>::clearXRange,
             "Clear the x-range restriction")
        .def("clearYRange", &CompareNarrowBand<T, D>::clearYRange,
             "Clear the y-range restriction")
        .def("setOutputMesh", &CompareNarrowBand<T, D>::setOutputMesh,
             "Set the output mesh where difference values will be stored")
        .def("setOutputMeshSquaredDifferences",
             &CompareNarrowBand<T, D>::setOutputMeshSquaredDifferences,
             "Set whether to output squared differences (true) or absolute "
             "differences (false)")
        .def("apply", &CompareNarrowBand<T, D>::apply,
             "Apply the comparison and calculate the sum of squared "
             "differences.")
        .def("getSumSquaredDifferences",
             &CompareNarrowBand<T, D>::getSumSquaredDifferences,
             "Return the sum of squared differences calculated by apply().")
        .def("getSumDifferences", &CompareNarrowBand<T, D>::getSumDifferences,
             "Return the sum of absolute differences calculated by apply().")
        .def("getNumPoints", &CompareNarrowBand<T, D>::getNumPoints,
             "Return the number of points used in the comparison.")
        .def("getRMSE", &CompareNarrowBand<T, D>::getRMSE,
             "Calculate the root mean square error from previously computed "
             "values.");
 
    // CompareSparseField
    py::class_<CompareSparseField<T, D>,
               SmartPointer<CompareSparseField<T, D>>>(module,
                                                       "CompareSparseField")
        // constructors
        .def(py::init(&SmartPointer<CompareSparseField<T, D>>::template New<>))
        .def(py::init(
            &SmartPointer<CompareSparseField<T, D>>::template New<
                SmartPointer<Domain<T, D>> &, SmartPointer<Domain<T, D>> &>))
        // methods
        .def("setLevelSetExpanded",
             &CompareSparseField<T, D>::setLevelSetExpanded,
             "Sets the expanded level set for comparison.")
        .def("setLevelSetIterated",
             &CompareSparseField<T, D>::setLevelSetIterated,
             "Sets the iterated level set to compare against the expanded one.")
        .def("setXRange", &CompareSparseField<T, D>::setXRange,
             "Set the x-coordinate range to restrict the comparison area")
        .def("setYRange", &CompareSparseField<T, D>::setYRange,
             "Set the y-coordinate range to restrict the comparison area")
        .def("clearXRange", &CompareSparseField<T, D>::clearXRange,
             "Clear the x-range restriction")
        .def("clearYRange", &CompareSparseField<T, D>::clearYRange,
             "Clear the y-range restriction")
        .def("setOutputMesh", &CompareSparseField<T, D>::setOutputMesh,
             "Set the output mesh where difference values will be stored")
        .def("setFillIteratedWithDistances",
             &CompareSparseField<T, D>::setFillIteratedWithDistances,
             "Set whether to fill the iterated level set with distance values")
        .def("apply", &CompareSparseField<T, D>::apply,
             "Apply the comparison and calculate the sum of squared "
             "differences.")
        .def("getSumSquaredDifferences",
             &CompareSparseField<T, D>::getSumSquaredDifferences,
             "Return the sum of squared differences calculated by apply().")
        .def("getSumDifferences", &CompareSparseField<T, D>::getSumDifferences,
             "Return the sum of absolute differences calculated by apply().")
        .def("getNumPoints", &CompareSparseField<T, D>::getNumPoints,
             "Return the number of points used in the comparison.")
        .def("getNumSkippedPoints",
             &CompareSparseField<T, D>::getNumSkippedPoints,
             "Return the number of points skipped during comparison.")
        .def("getRMSE", &CompareSparseField<T, D>::getRMSE,
             "Calculate the root mean square error from previously computed "
             "values.");
  }
}