Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4088 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 422db01787f7c105092e7f12b023a7a8e1f7d316

4 files changed, 156 insertions, 3 deletions

diff --git a/src/common/benchmark/CMakeLists.txt b/src/common/benchmark/CMakeLists.txt
new file mode 100644
index 00000000..a3787d6e
--- /dev/null
+++ b/src/common/benchmark/CMakeLists.txt
@@ -0,0 +1,3 @@
+project(common_benchmark)
+
+add_executable(Graph_simplicial_complex_benchmark Graph_simplicial_complex_benchmark.cpp)
diff --git a/src/common/benchmark/Graph_simplicial_complex_benchmark.cpp b/src/common/benchmark/Graph_simplicial_complex_benchmark.cpp
new file mode 100644
index 00000000..825d6cb5
--- /dev/null
+++ b/src/common/benchmark/Graph_simplicial_complex_benchmark.cpp
@@ -0,0 +1,150 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2018 Inria
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Clock.h>
+#include <gudhi/Points_off_io.h>
+
+#include <boost/graph/adjacency_list.hpp>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits>  // for numeric limits
+#include <fstream>
+#include <cassert>
+
+
+std::ofstream results_csv("results.csv");
+
+template< typename Adjacency_list, typename ForwardPointRange, typename Distance >
+Adjacency_list proximity_graph_computation(const ForwardPointRange& points, double threshold, Distance distance) {
+  std::vector<std::pair< int, int >> edges;
+  std::vector< double > edges_fil;
+  std::map< int, double > vertices;
+
+  int idx_u, idx_v;
+  double fil;
+  idx_u = 0;
+  for (auto it_u = points.begin(); it_u != points.end(); ++it_u) {
+    idx_v = idx_u + 1;
+    for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) {
+      fil = distance(*it_u, *it_v);
+      if (fil <= threshold) {
+        edges.emplace_back(idx_u, idx_v);
+        edges_fil.push_back(fil);
+      }
+    }
+    ++idx_u;
+  }
+
+  // Points are labeled from 0 to idx_u-1
+  Adjacency_list skel_graph(edges.begin(), edges.end(), edges_fil.begin(), idx_u);
+
+  auto vertex_prop = boost::get(Gudhi::vertex_filtration_t(), skel_graph);
+
+  typename boost::graph_traits<Adjacency_list>::vertex_iterator vi, vi_end;
+  for (std::tie(vi, vi_end) = boost::vertices(skel_graph);
+       vi != vi_end; ++vi) {
+    boost::put(vertex_prop, *vi, 0.);
+  }
+
+  return skel_graph;
+}
+
+template <typename Adjacency_list>
+void benchmark_proximity_graph(const std::string& msg, const std::string& off_file_name) {
+  Gudhi::Points_off_reader<std::vector<double>> off_reader(off_file_name);
+  assert(off_reader.is_valid());
+
+  std::cout << "+ " << msg << std::endl;
+
+  results_csv << "\"nb_points\";"
+              << "\"nb_simplices\";"
+              << "\"compute proximity graph(sec.)\";"
+              << "\"complex_creation_time(sec.)\";"
+              << "\"" << msg << "\";" << std::endl;
+
+  Gudhi::Clock pg_compute_proximity_graph("    benchmark_proximity_graph - compute proximity graph");
+  pg_compute_proximity_graph.begin();
+  // benchmark begin
+  Adjacency_list proximity_graph = proximity_graph_computation<Adjacency_list>(off_reader.get_point_cloud(),
+                                                                               std::numeric_limits<double>::infinity(),
+                                                                               Gudhi::Euclidean_distance());
+  // benchmark end
+  pg_compute_proximity_graph.end();
+  std::cout << pg_compute_proximity_graph;
+
+  Gudhi::Simplex_tree<> complex;
+  Gudhi::Clock st_create_clock("    benchmark_proximity_graph - complex creation");
+  st_create_clock.begin();
+  // benchmark begin
+  complex.insert_graph(proximity_graph);
+  // benchmark end
+  st_create_clock.end();
+  std::cout << st_create_clock;
+
+  results_csv << off_reader.get_point_cloud().size() << ";" << complex.num_simplices() << ";"
+              << pg_compute_proximity_graph.num_seconds() << ";"
+              << st_create_clock.num_seconds() << ";" << std::endl;
+
+  std::cout << "    benchmark_proximity_graph - nb simplices = " << complex.num_simplices() << std::endl;
+}
+
+int main(int argc, char * const argv[]) {
+  std::string off_file_name(argv[1]);
+
+  // The fastest, the less memory used
+  using vecSdirectedS = boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS,
+                                              boost::property<Gudhi::vertex_filtration_t, double>,
+                                              boost::property<Gudhi::edge_filtration_t, double>>;
+  benchmark_proximity_graph<vecSdirectedS>("vecSdirectedS", off_file_name);
+
+  using vecSundirectedS = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
+                                                boost::property<Gudhi::vertex_filtration_t, double>,
+                                                boost::property<Gudhi::edge_filtration_t, double>>;
+  benchmark_proximity_graph<vecSundirectedS>("vecSundirectedS", off_file_name);
+
+  using vecSbidirectionalS = boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS,
+                                                   boost::property<Gudhi::vertex_filtration_t, double>,
+                                                   boost::property<Gudhi::edge_filtration_t, double>>;
+  benchmark_proximity_graph<vecSbidirectionalS>("vecSbidirectionalS", off_file_name);
+
+  using setSdirectedS = boost::adjacency_list<boost::setS, boost::vecS, boost::directedS,
+                                              boost::property<Gudhi::vertex_filtration_t, double>,
+                                              boost::property<Gudhi::edge_filtration_t, double>>;
+  benchmark_proximity_graph<setSdirectedS>("setSdirectedS", off_file_name);
+
+  using setSundirectedS = boost::adjacency_list<boost::setS, boost::vecS, boost::undirectedS,
+                                                boost::property<Gudhi::vertex_filtration_t, double>,
+                                                boost::property<Gudhi::edge_filtration_t, double>>;
+  benchmark_proximity_graph<setSundirectedS>("setSundirectedS", off_file_name);
+
+  using setSbidirectionalS = boost::adjacency_list<boost::setS, boost::vecS, boost::bidirectionalS,
+                                                   boost::property<Gudhi::vertex_filtration_t, double>,
+                                                   boost::property<Gudhi::edge_filtration_t, double>>;
+  benchmark_proximity_graph<setSbidirectionalS>("setSbidirectionalS", off_file_name);
+
+  return 0;
+}
diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h
index 49fe56cc..0d81ca71 100644
--- a/src/common/include/gudhi/graph_simplicial_complex.h
+++ b/src/common/include/gudhi/graph_simplicial_complex.h
@@ -49,7 +49,7 @@ struct vertex_filtration_t {
  *
  */
 template <typename SimplicialComplexForProximityGraph>
-using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
+using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::directedS
 , boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >
 , boost::property < edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >>;
 
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 26eeb76d..0ee7649d 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -172,10 +172,10 @@ bool read_simplex(std::istream& in_, std::vector<Vertex_handle>& simplex, Filtra
   if (!(in_ >> dim)) return false;
   Vertex_handle v;
   for (int i = 0; i < dim + 1; ++i) {
-    in_ >> v;
+    if (!(in_ >> v)) return false;
     simplex.push_back(v);
   }
-  in_ >> fil;
+  if (!(in_ >> fil)) return false;
   in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n');  // ignore until the carriage return
   return true;
 }