Factory to build python alpha complex. 3d version of alpha complex. Needs change in doc as alphacomplexdoc.off is a fake 3d off data file

1 files changed, 144 insertions, 0 deletions

diff --git a/src/python/include/Alpha_complex_factory.h b/src/python/include/Alpha_complex_factory.h
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+++ b/src/python/include/Alpha_complex_factory.h
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+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2020 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#ifndef INCLUDE_ALPHA_COMPLEX_FACTORY_H_
+#define INCLUDE_ALPHA_COMPLEX_FACTORY_H_
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Alpha_complex.h>
+#include <gudhi/Alpha_complex_3d.h>
+#include <gudhi/Alpha_complex_options.h>
+#include <CGAL/Epeck_d.h>
+#include <CGAL/Epick_d.h>
+
+#include <boost/range/adaptor/transformed.hpp>
+
+#include "Simplex_tree_interface.h"
+
+#include <iostream>
+#include <vector>
+#include <string>
+#include <memory>  // for std::unique_ptr
+
+namespace Gudhi {
+
+namespace alpha_complex {
+
+template <typename CgalPointType>
+std::vector<double> pt_cgal_to_cython(CgalPointType& point) {
+  std::vector<double> vd;
+  for (auto coord = point.cartesian_begin(); coord != point.cartesian_end(); coord++)
+    vd.push_back(CGAL::to_double(*coord));
+  return vd;
+}
+
+template <typename CgalPointType>
+static CgalPointType pt_cython_to_cgal(std::vector<double> const& vec) {
+  return CgalPointType(vec.size(), vec.begin(), vec.end());
+}
+
+class Abstract_alpha_complex {
+ public:
+  virtual std::vector<double> get_point(int vh) = 0;
+  virtual void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square,
+                                   bool default_filtration_value) = 0;
+};
+
+class Exact_Alphacomplex_dD : public Abstract_alpha_complex {
+ private:
+  using Exact_kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
+  using Point_exact_kernel = typename Exact_kernel::Point_d;
+
+ public:
+  Exact_Alphacomplex_dD(const std::vector<std::vector<double>>& points, bool exact_version)
+      : exact_version_(exact_version) {
+    ac_exact_ptr_ = std::make_unique<Alpha_complex<Exact_kernel>>(
+      boost::adaptors::transform(points, pt_cython_to_cgal<Point_exact_kernel>));
+  }
+
+  std::vector<double> get_point(int vh) {
+    Point_exact_kernel const& point = ac_exact_ptr_->get_point(vh);
+    return pt_cgal_to_cython(point);
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square,
+                           bool default_filtration_value){
+    ac_exact_ptr_->create_complex(*simplex_tree, max_alpha_square, exact_version_, default_filtration_value);
+  }
+
+ private:
+  bool exact_version_;
+  std::unique_ptr<Alpha_complex<Exact_kernel>> ac_exact_ptr_;
+};
+
+class Inexact_Alphacomplex_dD : public Abstract_alpha_complex {
+ private:
+  using Inexact_kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+  using Point_inexact_kernel = typename Inexact_kernel::Point_d;
+
+ public:
+  Inexact_Alphacomplex_dD(const std::vector<std::vector<double>>& points, bool exact_version)
+      : exact_version_(exact_version) {
+    ac_inexact_ptr_ = std::make_unique<Alpha_complex<Inexact_kernel>>(
+      boost::adaptors::transform(points, pt_cython_to_cgal<Point_inexact_kernel>));
+  }
+
+  std::vector<double> get_point(int vh) {
+    Point_inexact_kernel const& point = ac_inexact_ptr_->get_point(vh);
+    return pt_cgal_to_cython(point);
+  }
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square,
+                           bool default_filtration_value){
+    ac_inexact_ptr_->create_complex(*simplex_tree, max_alpha_square, exact_version_, default_filtration_value);
+  }
+
+ private:
+  bool exact_version_;
+  std::unique_ptr<Alpha_complex<Inexact_kernel>> ac_inexact_ptr_;
+};
+
+template <complexity Complexity>
+class Alphacomplex_3D : public Abstract_alpha_complex {
+ private:
+  using Point_3 = typename Alpha_complex_3d<Complexity, false, false>::Bare_point_3;
+
+  static Point_3 pt_cython_to_cgal_3(std::vector<double> const& vec) {
+    return Point_3(vec[0], vec[1], vec[2]);
+  }
+
+ public:
+  Alphacomplex_3D(const std::vector<std::vector<double>>& points) {
+    alpha3d_ptr_ = std::make_unique<Alpha_complex_3d<Complexity, false, false>>(
+      boost::adaptors::transform(points, pt_cython_to_cgal_3));
+  }
+
+  std::vector<double> get_point(int vh) {
+    Point_3 const& point = alpha3d_ptr_->get_point(vh);
+    return pt_cgal_to_cython(point);
+  }
+
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square,
+                           bool default_filtration_value){
+    alpha3d_ptr_->create_complex(*simplex_tree, max_alpha_square);
+    if (default_filtration_value) {
+      // TODO
+    }
+  }
+
+ private:
+  std::unique_ptr<Alpha_complex_3d<Complexity, false, false>> alpha3d_ptr_;
+};
+
+
+}  // namespace alpha_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_ALPHA_COMPLEX_FACTORY_H_