1 files changed, 50 insertions, 45 deletions

diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
index 13634ff7..5321bb0a 100644
--- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
@@ -3,6 +3,7 @@
  *    library for computational topology.
  *
  *    Author(s):       Vincent Rouvreau
+ *                     Pawel Dlotko - 2017 - Swansea University, UK
  *
  *    Copyright (C) 2014  INRIA
  *
@@ -38,7 +39,6 @@
 #include <tuple>
 #include <map>
 #include <utility>
-#include <list>
 #include <vector>
 #include <cstdlib>
 
@@ -50,14 +50,14 @@ using PK = CGAL::Periodic_3_regular_triangulation_traits_3<Kernel>;
 
 // Vertex type
 using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
-using Vb = CGAL::Regular_triangulation_vertex_base_3<PK,DsVb>;
-using AsVb = CGAL::Alpha_shape_vertex_base_3<PK,Vb>;
+using Vb = CGAL::Regular_triangulation_vertex_base_3<PK, DsVb>;
+using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>;
 // Cell type
 using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>;
-using Cb = CGAL::Regular_triangulation_cell_base_3<PK,DsCb>;
-using AsCb = CGAL::Alpha_shape_cell_base_3<PK,Cb>;
-using Tds = CGAL::Triangulation_data_structure_3<AsVb,AsCb>;
-using P3RT3 = CGAL::Periodic_3_regular_triangulation_3<PK,Tds>;
+using Cb = CGAL::Regular_triangulation_cell_base_3<PK, DsCb>;
+using AsCb = CGAL::Alpha_shape_cell_base_3<PK, Cb>;
+using Tds = CGAL::Triangulation_data_structure_3<AsVb, AsCb>;
+using P3RT3 = CGAL::Periodic_3_regular_triangulation_3<PK, Tds>;
 using Alpha_shape_3 = CGAL::Alpha_shape_3<P3RT3>;
 
 using Point_3 = P3RT3::Bare_point;
@@ -74,14 +74,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
 using Facet = Alpha_shape_3::Facet;
 using Edge_3 = Alpha_shape_3::Edge;
 using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
 
 // gudhi type definition
 using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
 using Filtration_value = ST::Filtration_value;
 using Simplex_tree_vertex = ST::Vertex_handle;
 using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
 using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
 using Persistent_cohomology =
     Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -112,18 +111,46 @@ int main(int argc, char* const argv[]) {
     usage(argv[0]);
   }
 
-  // Retrieve the triangulation
+  // Retrieve the points
   std::vector<Point_3> lp = off_reader.get_point_cloud();
 
+  // Read iso_cuboid_3 information from file
+  std::ifstream iso_cuboid_str(argv[3]);
+  double x_min, y_min, z_min, x_max, y_max, z_max;
+  if (iso_cuboid_str.is_open()) {
+    if (!(iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max)) {
+      std::cerr << argv[3] << " - Bad file format." << std::endl;
+      usage(argv[0]);
+    }
+
+  } else {
+    std::cerr << "Unable to read file " << argv[3] << std::endl;
+    usage(argv[0]);
+  }
+  // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
+  if ((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min)) {
+    std::cerr << "The size of the cuboid in every directions is not the same." << std::endl;
+    exit(-1);
+  }
+
+  double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min);
+
   // Read weights information from file
   std::ifstream weights_ifstr(argv[2]);
   std::vector<Weighted_point_3> wp;
-  if (weights_ifstr.good()) {
+  if (weights_ifstr.is_open()) {
     double weight = 0.0;
     std::size_t index = 0;
     wp.reserve(lp.size());
     // Attempt read the weight in a double format, return false if it fails
     while ((weights_ifstr >> weight) && (index < lp.size())) {
+      if ((weight >= maximal_possible_weight) || (weight < 0)) {
+        std::cerr << "At line " << (index + 1) << ", the weight (" << weight
+                  << ") is negative or more than or equal to maximal possible weight (" << maximal_possible_weight
+                  << ") = 1/64*cuboid length squared, which is not an acceptable input." << std::endl;
+        exit(-1);
+      }
+
       wp.push_back(Weighted_point_3(lp[index], weight));
       index++;
     }
@@ -136,23 +163,18 @@ int main(int argc, char* const argv[]) {
     usage(argv[0]);
   }
 
-  // Read iso_cuboid_3 information from file
-  std::ifstream iso_cuboid_str(argv[3]);
-  double x_min, y_min, z_min, x_max, y_max, z_max;
-  if (iso_cuboid_str.good()) {
-    iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max;
-  } else {
-    std::cerr << "Unable to read file " << argv[3] << std::endl;
-    usage(argv[0]);
-  }
-
   // Define the periodic cube
   P3RT3 prt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
   // Heuristic for inserting large point sets (if pts is reasonably large)
   prt.insert(wp.begin(), wp.end(), true);
   // As prt won't be modified anymore switch to 1-sheeted cover if possible
-  if (prt.is_triangulation_in_1_sheet()) prt.convert_to_1_sheeted_covering();
-  std::cout << "Periodic Delaunay computed." << std::endl;
+  if (prt.is_triangulation_in_1_sheet()) {
+    prt.convert_to_1_sheeted_covering();
+  } else {
+    std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl;
+    exit(-1);
+  }
+  std::cout << "Weighted Periodic Delaunay computed." << std::endl;
 
   // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
   // Maybe need to set it to GENERAL mode
@@ -180,37 +202,23 @@ int main(int argc, char* const argv[]) {
   ST simplex_tree;
   Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-  int dim_max = 0;
-  Filtration_value filtration_max = 0.0;
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
     if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
-      if (dim_max < 3) {
-        // Cell is of dim 3
-        dim_max = 3;
-      }
     } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
-      if (dim_max < 2) {
-        // Facet is of dim 2
-        dim_max = 2;
-      }
     } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
-      if (dim_max < 1) {
-        // Edge_3 is of dim 1
-        dim_max = 1;
-      }
     } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
     // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
-    Simplex_tree_vector_vertex the_simplex_tree;
+    Simplex_tree_vector_vertex the_simplex;
     for (auto the_alpha_shape_vertex : vertex_list) {
       Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
       if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -219,15 +227,15 @@ int main(int argc, char* const argv[]) {
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
-        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+        the_simplex.push_back(vertex);
+        map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
       } else {
         // alpha shape found
         Simplex_tree_vertex vertex = the_map_iterator->second;
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
 #endif  // DEBUG_TRACES
-        the_simplex_tree.push_back(vertex);
+        the_simplex.push_back(vertex);
       }
     }
     // Construction of the simplex_tree
@@ -235,10 +243,7 @@ int main(int argc, char* const argv[]) {
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
-    if (filtr > filtration_max) {
-      filtration_max = filtr;
-    }
-    simplex_tree.insert_simplex(the_simplex_tree, filtr);
+    simplex_tree.insert_simplex(the_simplex, filtr);
     if (the_alpha_value_iterator != the_alpha_values.end())
       ++the_alpha_value_iterator;
     else