Added persistence examples

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1670 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c7762be9b79ba70cca84a378915c2deef13211fd

4 files changed, 351 insertions, 3 deletions

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 469c9aac..38cfa821 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -7,7 +7,12 @@ if(CGAL_FOUND)
     if (EIGEN3_FOUND)
       add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
       add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
-      #add_executable ( relaxed_witness_persistence relaxed_witness_persistence.cpp )
+      add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp )
+      target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+      add_test(Witness_complex_test_torus_persistence src/Witness_complex/example/Witness_complex_example_witncess_complex_persistence ../data/points/tore3D_1307.off -l 20 -a 0.5)
+      add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
+      target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+      add_test(Witness_complex_test_torus_persistence src/Witness_complex/example/Witness_complex_example_strong_witness_persistence ../data/points/tore3D_1307.off -l 20 -a 0.5)
     endif(EIGEN3_FOUND)
   endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
 endif()
diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp
new file mode 100644
index 00000000..bf6b4011
--- /dev/null
+++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp
@@ -0,0 +1,172 @@
+/*    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) 2016  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/>.
+ */
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Strong_witness_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/pick_n_random_points.h>
+
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+
+using namespace Gudhi;
+using namespace Gudhi::persistent_cohomology;
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef typename K::Point_d Point_d;
+
+typedef typename std::vector<Point_d> Point_vector;
+typedef typename Gudhi::witness_complex::Strong_witness_complex<K> Strong_witness_complex;
+typedef Gudhi::Simplex_tree<> SimplexTree;
+
+typedef int Vertex_handle;
+typedef double Filtration_value;
+
+void program_options(int argc, char * argv[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string file_name;
+  std::string filediag;
+  Filtration_value max_squared_alpha;
+  int p, nbL;
+  Filtration_value min_persistence;
+  SimplexTree simplex_tree;
+
+  program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, min_persistence);
+
+  // Extract the points from the file file_name
+  Point_vector witnesses, landmarks;
+  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+  if (!off_reader.is_valid()) {
+      std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+      exit(-1);  // ----- >>
+  }
+  witnesses = Point_vector(off_reader.get_point_cloud());
+  std::cout << "Successfully read " << witnesses.size() << " points.\n";
+  std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
+
+  // Choose landmarks from witnesses
+  Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+
+  // Compute witness complex
+  Strong_witness_complex strong_witness_complex(landmarks.begin(),
+                                                landmarks.end(),
+                                                witnesses.begin(),
+                                                witnesses.end());
+  
+  strong_witness_complex.create_complex(simplex_tree, max_squared_alpha);
+  
+  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+  std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp > pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(p);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (filediag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(filediag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
+
+  return 0;
+}
+
+
+void program_options(int argc, char * argv[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , Filtration_value & min_persistence) {
+  
+  namespace po = boost::program_options;
+  
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&file_name),
+      "Name of file containing a point set in off format.");
+  
+
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("landmarks,l", po::value<int>(&nbL),
+       "Number of landmarks to choose from the point cloud.")
+      ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+       "Maximal length of an edge for the Rips complex construction.")
+      ("field-charac,p", po::value<int>(&p)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+ 
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+  po::variables_map vm;
+
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+  
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of a Strong witness complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
+
diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp
index 6b0060d9..849a0a40 100644
--- a/src/Witness_complex/example/example_witness_complex_off.cpp
+++ b/src/Witness_complex/example/example_witness_complex_off.cpp
@@ -53,8 +53,6 @@ int main(int argc, char * const argv[]) {
   int nbL = atoi(argv[2]);
   double alpha2 = atof(argv[3]);
   clock_t start, end;
-
-  // Construct the Simplex Tree
   Gudhi::Simplex_tree<> simplex_tree;
 
   // Read the point file
@@ -78,6 +76,7 @@ int main(int argc, char * const argv[]) {
                                   landmarks.end(),
                                   point_vector.begin(),
                                   point_vector.end());
+
   witness_complex.create_complex(simplex_tree, alpha2);
   end = clock();
   std::cout << "Witness complex took "
diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp
new file mode 100644
index 00000000..9b06b504
--- /dev/null
+++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp
@@ -0,0 +1,172 @@
+/*    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) 2016  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/>.
+ */
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/pick_n_random_points.h>
+
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+
+using namespace Gudhi;
+using namespace Gudhi::persistent_cohomology;
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef typename K::Point_d Point_d;
+
+typedef typename std::vector<Point_d> Point_vector;
+typedef typename Gudhi::witness_complex::Witness_complex<K> Witness_complex;
+typedef Gudhi::Simplex_tree<> SimplexTree;
+
+typedef int Vertex_handle;
+typedef double Filtration_value;
+
+void program_options(int argc, char * argv[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string file_name;
+  std::string filediag;
+  Filtration_value max_squared_alpha;
+  int p, nbL;
+  Filtration_value min_persistence;
+  SimplexTree simplex_tree;
+
+  program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, min_persistence);
+
+  // Extract the points from the file file_name
+  Point_vector witnesses, landmarks;
+  Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+  if (!off_reader.is_valid()) {
+      std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+      exit(-1);  // ----- >>
+  }
+  witnesses = Point_vector(off_reader.get_point_cloud());
+  std::cout << "Successfully read " << witnesses.size() << " points.\n";
+  std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
+
+  // Choose landmarks from witnesses
+  Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+
+  // Compute witness complex
+  Witness_complex witness_complex(landmarks.begin(),
+                                  landmarks.end(),
+                                  witnesses.begin(),
+                                  witnesses.end());
+  
+  witness_complex.create_complex(simplex_tree, max_squared_alpha);
+  
+  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+  std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp > pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(p);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (filediag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(filediag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
+
+  return 0;
+}
+
+
+void program_options(int argc, char * argv[]
+                     , int & nbL
+                     , std::string & file_name
+                     , std::string & filediag
+                     , Filtration_value & max_squared_alpha
+                     , int & p
+                     , Filtration_value & min_persistence) {
+  
+  namespace po = boost::program_options;
+  
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&file_name),
+      "Name of file containing a point set in off format.");
+  
+
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("landmarks,l", po::value<int>(&nbL),
+       "Number of landmarks to choose from the point cloud.")
+      ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+       "Maximal length of an edge for the Rips complex construction.")
+      ("field-charac,p", po::value<int>(&p)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+ 
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+  po::variables_map vm;
+
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+  
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of a Weak witness complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
+