4 files changed, 213 insertions, 34 deletions

diff --git a/src/python/include/Alpha_complex_factory.h b/src/python/include/Alpha_complex_factory.h
new file mode 100644
index 00000000..d699ad9b
--- /dev/null
+++ b/src/python/include/Alpha_complex_factory.h
@@ -0,0 +1,139 @@
+/*    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 const& point) {
+  std::vector<double> vd;
+  vd.reserve(point.dimension());
+  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 bool 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 Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
+  using Point = typename Kernel::Point_d;
+
+ public:
+  Exact_Alphacomplex_dD(const std::vector<std::vector<double>>& points, bool exact_version)
+    : exact_version_(exact_version),
+      alpha_complex_(boost::adaptors::transform(points, pt_cython_to_cgal<Point>)) {
+  }
+
+  virtual std::vector<double> get_point(int vh) override {
+    Point const& point = alpha_complex_.get_point(vh);
+    return pt_cgal_to_cython(point);
+  }
+
+  virtual bool create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square,
+                                   bool default_filtration_value) override {
+    return alpha_complex_.create_complex(*simplex_tree, max_alpha_square, exact_version_, default_filtration_value);
+  }
+
+ private:
+  bool exact_version_;
+  Alpha_complex<Kernel> alpha_complex_;
+};
+
+class Inexact_Alphacomplex_dD : public Abstract_alpha_complex {
+ private:
+  using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+  using Point = typename Kernel::Point_d;
+
+ public:
+  Inexact_Alphacomplex_dD(const std::vector<std::vector<double>>& points, bool exact_version)
+    : exact_version_(exact_version),
+      alpha_complex_(boost::adaptors::transform(points, pt_cython_to_cgal<Point>)) {
+  }
+
+  virtual std::vector<double> get_point(int vh) override {
+    Point const& point = alpha_complex_.get_point(vh);
+    return pt_cgal_to_cython(point);
+  }
+  virtual bool create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square,
+                                   bool default_filtration_value) override {
+    return alpha_complex_.create_complex(*simplex_tree, max_alpha_square, exact_version_, default_filtration_value);
+  }
+
+ private:
+  bool exact_version_;
+  Alpha_complex<Kernel> alpha_complex_;
+};
+
+template <complexity Complexity>
+class Alphacomplex_3D : public Abstract_alpha_complex {
+ private:
+  using Point = typename Alpha_complex_3d<Complexity, false, false>::Bare_point_3;
+
+  static Point pt_cython_to_cgal_3(std::vector<double> const& vec) {
+    return Point(vec[0], vec[1], vec[2]);
+  }
+
+ public:
+  Alphacomplex_3D(const std::vector<std::vector<double>>& points)
+    : alpha_complex_(boost::adaptors::transform(points, pt_cython_to_cgal_3)) {
+  }
+
+  virtual std::vector<double> get_point(int vh) override {
+    Point const& point = alpha_complex_.get_point(vh);
+    return pt_cgal_to_cython(point);
+  }
+
+  virtual bool create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square,
+                           bool default_filtration_value) override {
+    return alpha_complex_.create_complex(*simplex_tree, max_alpha_square);
+  }
+
+ private:
+  Alpha_complex_3d<Complexity, false, false> alpha_complex_;
+};
+
+
+}  // namespace alpha_complex
+
+}  // namespace Gudhi
+
+#endif  // INCLUDE_ALPHA_COMPLEX_FACTORY_H_
diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h
index 40de88f3..23be194d 100644
--- a/src/python/include/Alpha_complex_interface.h
+++ b/src/python/include/Alpha_complex_interface.h
@@ -11,57 +11,66 @@
 #ifndef INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
 #define INCLUDE_ALPHA_COMPLEX_INTERFACE_H_
 
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Alpha_complex.h>
-#include <CGAL/Epeck_d.h>
-#include <CGAL/Epick_d.h>
-
-#include <boost/range/adaptor/transformed.hpp>
+#include "Alpha_complex_factory.h"
+#include <gudhi/Alpha_complex_options.h>
 
 #include "Simplex_tree_interface.h"
 
 #include <iostream>
 #include <vector>
 #include <string>
+#include <memory>  // for std::unique_ptr
 
 namespace Gudhi {
 
 namespace alpha_complex {
 
 class Alpha_complex_interface {
-  using Dynamic_kernel = CGAL::Epeck_d< CGAL::Dynamic_dimension_tag >;
-  using Point_d = Dynamic_kernel::Point_d;
-
  public:
-  Alpha_complex_interface(const std::vector<std::vector<double>>& points) {
-    auto mkpt = [](std::vector<double> const& vec){
-      return Point_d(vec.size(), vec.begin(), vec.end());
-    };
-    alpha_complex_ = new Alpha_complex<Dynamic_kernel>(boost::adaptors::transform(points, mkpt));
-  }
-
-  Alpha_complex_interface(const std::string& off_file_name, bool from_file = true) {
-    alpha_complex_ = new Alpha_complex<Dynamic_kernel>(off_file_name);
-  }
-
-  ~Alpha_complex_interface() {
-    delete alpha_complex_;
+  Alpha_complex_interface(const std::vector<std::vector<double>>& points, bool fast_version, bool exact_version)
+  : points_(points),
+    fast_version_(fast_version),
+    exact_version_(exact_version) {
   }
 
   std::vector<double> get_point(int vh) {
-    std::vector<double> vd;
-    Point_d const& ph = alpha_complex_->get_point(vh);
-    for (auto coord = ph.cartesian_begin(); coord != ph.cartesian_end(); coord++)
-      vd.push_back(CGAL::to_double(*coord));
-    return vd;
+    return alpha_ptr_->get_point(vh);
   }
 
-  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square) {
-    alpha_complex_->create_complex(*simplex_tree, max_alpha_square);
+  void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square,
+                           bool default_filtration_value) {
+    if (points_.size() > 0) {
+      std::size_t dimension = points_[0].size();
+      if (dimension == 3 && !default_filtration_value) {
+        if (fast_version_)
+          alpha_ptr_ = std::make_unique<Alphacomplex_3D<Gudhi::alpha_complex::complexity::FAST>>(points_);
+        else if (exact_version_)
+          alpha_ptr_ = std::make_unique<Alphacomplex_3D<Gudhi::alpha_complex::complexity::EXACT>>(points_);
+        else
+          alpha_ptr_ = std::make_unique<Alphacomplex_3D<Gudhi::alpha_complex::complexity::SAFE>>(points_);
+        if (!alpha_ptr_->create_simplex_tree(simplex_tree, max_alpha_square, default_filtration_value)) {
+          // create_simplex_tree will fail if all points are on a plane - Retry with dD by setting dimension to 2
+          dimension--;
+          alpha_ptr_.reset();
+        }
+      }
+      // Not ** else ** because we have to take into account if 3d fails
+      if (dimension != 3 || default_filtration_value) {
+        if (fast_version_) {
+          alpha_ptr_ = std::make_unique<Inexact_Alphacomplex_dD>(points_, exact_version_);
+        } else {
+          alpha_ptr_ = std::make_unique<Exact_Alphacomplex_dD>(points_, exact_version_);
+        }
+        alpha_ptr_->create_simplex_tree(simplex_tree, max_alpha_square, default_filtration_value);
+      }
+    }
   }
 
  private:
-  Alpha_complex<Dynamic_kernel>* alpha_complex_;
+  std::unique_ptr<Abstract_alpha_complex> alpha_ptr_;
+  std::vector<std::vector<double>> points_;
+  bool fast_version_;
+  bool exact_version_;
 };
 
 }  // namespace alpha_complex
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index 56d7c41d..e288a8cf 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -15,10 +15,13 @@
 #include <gudhi/distance_functions.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Points_off_io.h>
+#include <gudhi/Flag_complex_edge_collapser.h>
 
 #include <iostream>
 #include <vector>
 #include <utility>  // std::pair
+#include <tuple>
+#include <iterator>  // for std::distance
 
 namespace Gudhi {
 
@@ -157,6 +160,34 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     return new_dgm;
   }
 
+  Simplex_tree_interface* collapse_edges(int nb_collapse_iteration) {
+    using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>;
+    std::vector<Filtered_edge> edges;
+    for (Simplex_handle sh : Base::skeleton_simplex_range(1)) {
+      if (Base::dimension(sh) == 1) {
+        typename Base::Simplex_vertex_range rg = Base::simplex_vertex_range(sh);
+        auto vit = rg.begin();
+        Vertex_handle v = *vit;
+        Vertex_handle w = *++vit;
+        edges.emplace_back(v, w, Base::filtration(sh));
+      }
+    }
+
+    for (int iteration = 0; iteration < nb_collapse_iteration; iteration++) {
+      edges = Gudhi::collapse::flag_complex_collapse_edges(edges);
+    }
+    Simplex_tree_interface* collapsed_stree_ptr = new Simplex_tree_interface();
+    // Copy the original 0-skeleton
+    for (Simplex_handle sh : Base::skeleton_simplex_range(0)) {
+      collapsed_stree_ptr->insert({*(Base::simplex_vertex_range(sh).begin())}, Base::filtration(sh));
+    }
+    // Insert remaining edges
+    for (auto remaining_edge : edges) {
+      collapsed_stree_ptr->insert({std::get<0>(remaining_edge), std::get<1>(remaining_edge)}, std::get<2>(remaining_edge));
+    }
+    return collapsed_stree_ptr;
+  }
+
   // Iterator over the simplex tree
   Complex_simplex_iterator get_simplices_iterator_begin() {
     // this specific case works because the range is just a pair of iterators - won't work if range was a vector
diff --git a/src/python/include/pybind11_diagram_utils.h b/src/python/include/pybind11_diagram_utils.h
index d9627258..2d5194f4 100644
--- a/src/python/include/pybind11_diagram_utils.h
+++ b/src/python/include/pybind11_diagram_utils.h
@@ -18,8 +18,8 @@ namespace py = pybind11;
 typedef py::array_t<double> Dgm;
 
 // Get m[i,0] and m[i,1] as a pair
-static auto pairify(void* p, ssize_t h, ssize_t w) {
-  return [=](ssize_t i){
+static auto pairify(void* p, py::ssize_t h, py::ssize_t w) {
+  return [=](py::ssize_t i){
     char* birth = (char*)p + i * h;
     char* death = birth + w;
     return std::make_pair(*(double*)birth, *(double*)death);
@@ -32,8 +32,8 @@ inline auto numpy_to_range_of_pairs(py::array_t<double> dgm) {
   if((buf.ndim!=2 || buf.shape[1]!=2) && (buf.ndim!=1 || buf.shape[0]!=0))
     throw std::runtime_error("Diagram must be an array of size n x 2");
   // In the case of shape (0), avoid reading non-existing strides[1] even if we won't use it.
-  ssize_t stride1 = buf.ndim == 2 ? buf.strides[1] : 0;
-  auto cnt = boost::counting_range<ssize_t>(0, buf.shape[0]);
+  py::ssize_t stride1 = buf.ndim == 2 ? buf.strides[1] : 0;
+  auto cnt = boost::counting_range<py::ssize_t>(0, buf.shape[0]);
   return boost::adaptors::transform(cnt, pairify(buf.ptr, buf.strides[0], stride1));
   // Be careful that the returned range cannot contain references to dead temporaries.
 }