From e7c6a8ae371de46469f0509697572c9f30071281 Mon Sep 17 00:00:00 2001
From: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 11 Feb 2016 14:18:49 +0000
Subject: Added relaxed witness complex + persistence example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1016 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 06f7fec6464e35a6ca0aa18f7a25cbb7a7f68ad5
---
 src/Witness_complex/example/CMakeLists.txt         |   3 +
 .../example/relaxed_witness_persistence.cpp        | 108 +++++++++++++++++++++
 2 files changed, 111 insertions(+)
 create mode 100644 src/Witness_complex/example/relaxed_witness_persistence.cpp

(limited to 'src/Witness_complex/example')

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index b304479e..9b874261 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -35,6 +35,9 @@ if(CGAL_FOUND)
       add_executable ( witness_complex_sphere witness_complex_sphere.cpp )
       target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
       add_test( witness_complex_sphere_10 ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_sphere 10)   
+      add_executable ( relaxed_witness_persistence relaxed_witness_persistence.cpp )
+      target_link_libraries(relaxed_witness_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test( relaxed_witness_persistence_10 ${CMAKE_CURRENT_BINARY_DIR}/relaxed_witness_persistence 10)   
     else()
       message(WARNING "Eigen3 not found. Version 3.1.0 is required for witness_complex_sphere example.")      
     endif()
diff --git a/src/Witness_complex/example/relaxed_witness_persistence.cpp b/src/Witness_complex/example/relaxed_witness_persistence.cpp
new file mode 100644
index 00000000..09fe0d31
--- /dev/null
+++ b/src/Witness_complex/example/relaxed_witness_persistence.cpp
@@ -0,0 +1,108 @@
+/*    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/>.
+ */
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Relaxed_witness_complex.h>
+#include <gudhi/reader_utils.h>
+#include <gudhi/Persistent_cohomology.h>
+#include "Landmark_choice_random_knn.h"
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <utility>
+#include <algorithm>
+#include <set>
+#include <queue>
+#include <iterator>
+
+#include <boost/tuple/tuple.hpp>
+#include <boost/iterator/zip_iterator.hpp>
+#include <boost/iterator/counting_iterator.hpp>
+#include <boost/range/iterator_range.hpp>
+
+#include "generators.h"
+#include "output.h"
+
+using namespace Gudhi;
+using namespace Gudhi::witness_complex;
+using namespace Gudhi::persistent_cohomology;
+
+typedef std::vector<Point_d> Point_Vector;
+typedef Relaxed_witness_complex< Simplex_tree<> > RelaxedWitnessComplex;
+
+int main (int argc, char * const argv[])
+{
+  if (argc != 6) {
+      std::cerr << "Usage: " << argv[0]
+                << " nbP nbL dim alpha limD\n";
+      return 0;
+    }
+  /*
+  boost::filesystem::path p;
+  for (; argc > 2; --argc, ++argv)
+    p /= argv[1];
+  */
+  
+  int nbP       = atoi(argv[1]);
+  int nbL       = atoi(argv[2]);
+  int dim       = atoi(argv[3]);
+  double alpha  = atof(argv[4]);
+  int limD      = atoi(argv[5]);
+  //Construct the Simplex Tree
+  clock_t start, end;
+
+  // Construct the Simplex Tree
+  Simplex_tree<> simplex_tree;
+
+  // Read the point file
+  Point_Vector point_vector;
+  generate_points_sphere(point_vector, nbP, dim);
+  std::cout << "Successfully generated " << point_vector.size() << " points.\n";
+  std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
+
+  // Choose landmarks
+  std::vector<std::vector< int > > knn;
+  std::vector<std::vector< FT > > distances;
+  Gudhi::witness_complex::landmark_choice_by_random_knn(point_vector, nbL, alpha, limD, knn, distances);
+  
+  // Compute witness complex
+  start = clock();
+  RelaxedWitnessComplex(distances,
+                        knn,
+                        simplex_tree,
+                        nbL,
+                        alpha,
+                        limD);
+  end = clock();
+  double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
+  std::cout << "Witness complex for " << nbL << " landmarks took "
+            << time << " s. \n";
+  // std::cout << simplex_tree << "\n";
+  
+  // Compute the persistence diagram of the complex
+  persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree, false);
+  int p = 3;
+  pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
+  pcoh.compute_persistent_cohomology( alpha/10 );
+  pcoh.output_diagram();
+}
-- 
cgit v1.2.3