Fix Cech with radius distance

Add a meta generation script for off_file_generator


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cechcomplex_vincent@3256 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fb13baa124ddc97c0dc61835ab0c72595d666155

2 files changed, 25 insertions, 50 deletions

diff --git a/src/Cech_complex/example/cech_complex_example_from_points.cpp b/src/Cech_complex/example/cech_complex_example_from_points.cpp
index 882849c3..97327e69 100644
--- a/src/Cech_complex/example/cech_complex_example_from_points.cpp
+++ b/src/Cech_complex/example/cech_complex_example_from_points.cpp
@@ -1,25 +1,3 @@
-/*    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/Cech_complex.h>
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/distance_functions.h>
@@ -37,23 +15,22 @@ int main() {
   using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>;
 
   Point_cloud points;
-  points.push_back({1.0, 1.0});
-  points.push_back({7.0, 0.0});
-  points.push_back({4.0, 6.0});
-  points.push_back({9.0, 6.0});
-  points.push_back({0.0, 14.0});
-  points.push_back({2.0, 19.0});
-  points.push_back({9.0, 17.0});
+  points.push_back({0., 0.});
+  points.push_back({0., 2.});
+  points.push_back({std::sqrt(3.), 1.});
+  points.push_back({1., 0.});
+  points.push_back({1., 2.});
+  points.push_back({1. - std::sqrt(3.), 1.});
 
   // ----------------------------------------------------------------------------
   // Init of a Cech complex from points
   // ----------------------------------------------------------------------------
-  // 7.1 is a magic number to force one blocker, and one non-blocker
-  Filtration_value threshold = 7.1;
-  Cech_complex cech_complex_from_points(points, threshold, Gudhi::Euclidean_distance());
+  // 5. is a magic number to force one blocker, and one non-blocker
+  Filtration_value max_radius = 12.;
+  Cech_complex cech_complex_from_points(points, max_radius);
 
   Simplex_tree stree;
-  cech_complex_from_points.create_complex(stree, 2);
+  cech_complex_from_points.create_complex(stree, -1);
   // ----------------------------------------------------------------------------
   // Display information about the one skeleton Cech complex
   // ----------------------------------------------------------------------------
diff --git a/src/Cech_complex/example/cech_complex_step_by_step.cpp b/src/Cech_complex/example/cech_complex_step_by_step.cpp
index e71086b6..8705a3e5 100644
--- a/src/Cech_complex/example/cech_complex_step_by_step.cpp
+++ b/src/Cech_complex/example/cech_complex_step_by_step.cpp
@@ -65,23 +65,22 @@ class Cech_blocker {
       std::cout << "#(" << vertex << ")#";
 #endif  // DEBUG_TRACES
     }
-    Min_sphere ms(dimension_, points.begin(),points.end());
-    Filtration_value radius = std::sqrt(ms.squared_radius());
+    Filtration_value radius = Gudhi::Radius_distance()(points);
 #ifdef DEBUG_TRACES
-    std::cout << "radius = " << radius << " - " << (radius > threshold_) << std::endl;
+    std::cout << "radius = " << radius << " - " << (radius > max_radius_) << std::endl;
 #endif  // DEBUG_TRACES
     simplex_tree_.assign_filtration(sh, radius);
-    return (radius > threshold_);
+    return (radius > max_radius_);
   }
-  Cech_blocker(Simplex_tree& simplex_tree, Filtration_value threshold, const std::vector<Point>& point_cloud)
+  Cech_blocker(Simplex_tree& simplex_tree, Filtration_value max_radius, const std::vector<Point>& point_cloud)
     : simplex_tree_(simplex_tree),
-      threshold_(threshold),
+      max_radius_(max_radius),
       point_cloud_(point_cloud) {
     dimension_ = point_cloud_[0].size();
   }
  private:
   Simplex_tree simplex_tree_;
-  Filtration_value threshold_;
+  Filtration_value max_radius_;
   std::vector<Point> point_cloud_;
   int dimension_;
 };
@@ -89,31 +88,31 @@ class Cech_blocker {
 
 void program_options(int argc, char * argv[]
                      , std::string & off_file_points
-                     , Filtration_value & threshold
+                     , Filtration_value & max_radius
                      , int & dim_max);
 
 
 int main(int argc, char * argv[]) {
   std::string off_file_points;
-  Filtration_value threshold;
+  Filtration_value max_radius;
   int dim_max;
 
-  program_options(argc, argv, off_file_points, threshold, dim_max);
+  program_options(argc, argv, off_file_points, max_radius, dim_max);
 
   // Extract the points from the file filepoints
   Points_off_reader off_reader(off_file_points);
 
   // Compute the proximity graph of the points
   Proximity_graph prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(off_reader.get_point_cloud(),
-                                                                            threshold,
-                                                                            Gudhi::Euclidean_distance());
+                                                                            max_radius,
+                                                                            Gudhi::Radius_distance());
 
   // Construct the Rips complex in a Simplex Tree
   Simplex_tree st;
   // insert the proximity graph in the simplex tree
   st.insert_graph(prox_graph);
   // expand the graph until dimension dim_max
-  st.expansion_with_blockers(dim_max, Cech_blocker(st, threshold, off_reader.get_point_cloud()));
+  st.expansion_with_blockers(dim_max, Cech_blocker(st, max_radius, off_reader.get_point_cloud()));
 
   std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
   std::cout << "   and has dimension " << st.dimension() << " \n";
@@ -123,7 +122,6 @@ int main(int argc, char * argv[]) {
 
 #if DEBUG_TRACES
   std::cout << "********************************************************************\n";
-  // Display the Simplex_tree - Can not be done in the middle of 2 inserts
   std::cout << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n";
   std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
   for (auto f_simplex : st.filtration_simplex_range()) {
@@ -140,7 +138,7 @@ int main(int argc, char * argv[]) {
 
 void program_options(int argc, char * argv[]
                      , std::string & off_file_points
-                     , Filtration_value & threshold
+                     , Filtration_value & max_radius
                      , int & dim_max) {
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
@@ -151,8 +149,8 @@ void program_options(int argc, char * argv[]
   po::options_description visible("Allowed options", 100);
   visible.add_options()
       ("help,h", "produce help message")
-      ("max-edge-length,r",
-       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+      ("max-radius,r",
+       po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()),
        "Maximal length of an edge for the Rips complex construction.")
       ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
        "Maximal dimension of the Rips complex we want to compute.");