Added example stuff

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@968 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a769b41f7d2d784a2740c149da08dac8124e3df9

6 files changed, 271 insertions, 16 deletions

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 4473078a..b5770ba6 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -4,9 +4,6 @@ project(GUDHIWitnessComplex)
 # A simple example
    add_executable( witness_complex_from_file witness_complex_from_file.cpp )
    add_test( witness_complex_from_bunny &{CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)   
-   
-   add_executable( witness_complex_bench witness_complex_bench.cpp )
-   add_test( witness_complex_bench_from_bunny &{CMAKE_CURRENT_BINARY_DIR}/witness_complex_bench ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)   
 
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
@@ -21,12 +18,12 @@ if(CGAL_FOUND)
       message(STATUS "Eigen3 use file: ${EIGEN3_USE_FILE}.")
       include_directories (BEFORE "../../include")
 
-      add_executable ( witness_complex_bench2 witness_complex_bench2.cpp )
-      target_link_libraries(witness_complex_bench2 ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_executable ( witness_complex_sphere witness_complex_sphere.cpp )
+      target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
     else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")      
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for witness_complex_sphere example.")      
     endif()
   else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile witness_complex_sphere example. Version 4.6.0 is required.")
   endif ()
 endif()
diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h
new file mode 100644
index 00000000..0d42cda2
--- /dev/null
+++ b/src/Witness_complex/example/generators.h
@@ -0,0 +1,134 @@
+#ifndef GENERATORS_H
+#define GENERATORS_H
+
+#include <fstream>
+
+#include <CGAL/Epick_d.h>
+#include <CGAL/point_generators_d.h>
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef K::FT FT;
+typedef K::Point_d Point_d;
+typedef std::vector<Point_d> Point_Vector;
+typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
+typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
+
+/**
+ * \brief Rock age method of reading off file
+ *
+ */
+inline void
+off_reader_cust ( std::string file_name , std::vector<Point_d> & points)
+{  
+  std::ifstream in_file (file_name.c_str(),std::ios::in);
+  if(!in_file.is_open())
+    {
+      std::cerr << "Unable to open file " << file_name << std::endl;
+      return;
+    }
+  std::string line;
+  double x;
+  // Line OFF. No need in it
+  if (!getline(in_file, line))
+    {
+      std::cerr << "No line OFF\n";
+      return;
+    }
+  // Line with 3 numbers. No need
+  if (!getline(in_file, line))
+    {
+      std::cerr << "No line with 3 numbers\n";
+      return;
+    }
+  // Reading points
+  while( getline ( in_file , line ) )
+    {
+      std::vector< double > point;
+      std::istringstream iss( line );
+      while(iss >> x) { point.push_back(x); }
+      points.push_back(Point_d(point));
+    }
+  in_file.close();
+}
+
+/**
+ * \brief Customized version of read_points
+ * which takes into account a possible nbP first line
+ *
+ */
+inline void
+read_points_cust ( std::string file_name , Point_Vector & points)
+{  
+  std::ifstream in_file (file_name.c_str(),std::ios::in);
+  if(!in_file.is_open())
+    {
+      std::cerr << "Unable to open file " << file_name << std::endl;
+      return;
+    }
+  std::string line;
+  double x;
+  while( getline ( in_file , line ) )
+    {
+      std::vector< double > point;
+      std::istringstream iss( line );
+      while(iss >> x) { point.push_back(x); }
+      Point_d p(point.begin(), point.end());
+      if (point.size() != 1)
+        points.push_back(p);
+    }
+  in_file.close();
+}
+
+/** \brief Generate points on a grid in a cube of side 2
+ * having {+-1}^D as vertices and insert them in W.
+ * The grid has "width" points on each side. 
+ * If torus is true then it is supposed that the cube represents
+ * a flat torus, hence the opposite borders are associated.
+ * The points on border in this case are not placed twice.
+ */
+void generate_points_grid(Point_Vector& W, int width, int D, bool torus)
+{
+  int nb_points = 1;
+  for (int i = 0; i < D; ++i)
+    nb_points *= width;
+  for (int i = 0; i < nb_points; ++i)
+    {
+      std::vector<double> point;
+      int cell_i = i;
+      for (int l = 0; l < D; ++l)
+        {
+          if (torus)
+            point.push_back(-1+(2.0/(width-1))*(cell_i%width));
+          else
+            point.push_back(-1+(2.0/width)*(cell_i%width));
+          //attention: the bottom and the right are covered too!
+          cell_i /= width;
+        }
+      W.push_back(point);
+    }
+}
+
+/** \brief Generate nbP points uniformly in a cube of side 2
+ * having {+-1}^dim as its vertices and insert them in W.
+ */
+void generate_points_random_box(Point_Vector& W, int nbP, int dim)
+{
+  Random_cube_iterator rp(dim, 1.0);
+  for (int i = 0; i < nbP; i++)
+    {
+      W.push_back(*rp++);
+    }
+}
+
+/** \brief Generate nbP points uniformly on a (dim-1)-sphere
+ *  and insert them in W.
+ */
+void generate_points_sphere(Point_Vector& W, int nbP, int dim)
+{
+  CGAL::Random_points_on_sphere_d<Point_d> rp(dim,1);
+  for (int i = 0; i < nbP; i++)
+    W.push_back(*rp++);
+}
+
+
+#endif
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
new file mode 100644
index 00000000..1fa0fc42
--- /dev/null
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -0,0 +1,126 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ *    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/>.
+ */
+#define BOOST_PARAMETER_MAX_ARITY 12
+
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <utility> 
+
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/reader_utils.h>
+
+#include "generators.h"
+
+using namespace Gudhi;
+
+typedef std::vector< Vertex_handle > typeVectorVertex;
+//typedef std::vector< std::vector <double> > Point_Vector;
+
+typedef Witness_complex< Simplex_tree<> > WitnessComplex;
+
+/**
+ * \brief Customized version of read_points
+ * which takes into account a possible nbP first line
+ *
+ */
+inline void
+read_points_cust ( std::string file_name , std::vector< std::vector< double > > & points)
+{  
+  std::ifstream in_file (file_name.c_str(),std::ios::in);
+  if(!in_file.is_open())
+    {
+      std::cerr << "Unable to open file " << file_name << std::endl;
+      return;
+    }
+  std::string line;
+  double x;
+  while( getline ( in_file , line ) )
+    {
+      std::vector< double > point;
+      std::istringstream iss( line );
+      while(iss >> x) { point.push_back(x); }
+      if (point.size() != 1)
+        points.push_back(point);
+    }
+  in_file.close();
+}
+
+/** Write a gnuplot readable file.
+ *  Data range is a random access range of pairs (arg, value)
+ */
+template < typename Data_range >
+void write_data( Data_range & data, std::string filename )
+{
+  std::ofstream ofs(filename, std::ofstream::out);
+  for (auto entry: data)
+    ofs << entry.first << ", " << entry.second << "\n";
+  ofs.close();
+}
+
+int main (int argc, char * const argv[])
+{
+  if (argc != 3)
+    {
+      std::cerr << "Usage: " << argv[0]
+                << " path_to_point_file nbL \n";
+      return 0;
+    }
+
+  std::string file_name   = argv[1];
+  int nbL       = atoi(argv[2]);
+  clock_t start, end;
+
+  // Construct the Simplex Tree
+  Simplex_tree<> simplex_tree;
+
+  std::vector< std::pair<int, double> > l_time;      
+  
+  // Read the point file
+  for (int nbP = 500; nbP < 10000; nbP += 500)
+    {
+      Point_Vector point_vector;
+      generate_points_sphere(point_vector, nbP, 4);
+      std::cout << "Successfully generated " << point_vector.size() << " points.\n";
+      std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
+            
+      // Choose landmarks
+      start = clock();
+      std::vector<std::vector< int > > knn;
+      Landmark_choice_by_random_point(point_vector, nbL, knn);
+      
+      // Compute witness complex
+      WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+      end = clock();
+      double time = (double)(end-start)/CLOCKS_PER_SEC;
+      std::cout << "Witness complex for " << nbL << " landmarks took "
+       << time << " s. \n";
+      l_time.push_back(std::make_pair(nbP,time));
+    }
+  write_data(l_time, "w_time.dat");
+}
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 791d0e45..915e445c 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -27,7 +27,7 @@
 #include <boost/iterator/transform_iterator.hpp>
 #include <algorithm>
 #include <utility>
-#include "gudhi/distance_functions.h"
+#include <gudhi/distance_functions.h>
 #include <vector>
 #include <list>
 #include <set>
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
index c7d85a4d..ea38b5c0 100644
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -22,9 +22,8 @@
 
 #include <iostream>
 #include <ctime>
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Witness_complex.h"
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
 
 using namespace Gudhi;
 
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index a86bf493..0a50101d 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -22,11 +22,10 @@
 
 #include <iostream>
 #include <ctime>
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/Landmark_choice_by_random_point.h"
-#include "gudhi/Landmark_choice_by_furthest_point.h"
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/Landmark_choice_by_furthest_point.h>
 
 
 using namespace Gudhi;