1 files changed, 0 insertions, 214 deletions
diff --git a/example/Persistent_cohomology/performance_rips_persistence.cpp b/example/Persistent_cohomology/performance_rips_persistence.cpp
deleted file mode 100644
index b4d282ac..00000000
--- a/example/Persistent_cohomology/performance_rips_persistence.cpp
+++ /dev/null
@@ -1,214 +0,0 @@
-/*    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):       Clément Maria
- *
- *    Copyright (C) 2014  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/reader_utils.h>
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/distance_functions.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Persistent_cohomology/Multi_field.h>
-#include <gudhi/Hasse_complex.h>
-
-#include <chrono>
-#include <string>
-#include <vector>
-
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
-/* Compute the persistent homology of the complex cpx with coefficients in Z/pZ. */
-template< typename FilteredComplex>
-void timing_persistence(FilteredComplex & cpx
-                        , int p);
-
-/* Compute multi-field persistent homology of the complex cpx with coefficients in
- * Z/rZ for all prime number r in [p;q].*/
-template< typename FilteredComplex>
-void timing_persistence(FilteredComplex & cpx
-                        , int p
-                        , int q);
-
-/* Timings for the computation of persistent homology with different 
- * representations of a Rips complex and different coefficient fields. The 
- * Rips complex is built on a set of 10000 points sampling a Klein bottle embedded 
- * in dimension 5.
- * We represent complexes with a simplex tree and 
- * with a Hasse diagram. The Hasse diagram represents explicitly all 
- * codimension 1 incidence relations in the complex, and hence leads to 
- * a faster computation of persistence because boundaries are precomputed. 
- * Hovewer, the simplex tree may be constructed directly from a point cloud and
- * is more compact.
- * We compute persistent homology with coefficient fields Z/2Z and Z/1223Z.
- * We present also timings for the computation of multi-field persistent 
- * homology in all fields Z/rZ for r prime between 2 and 1223.
- */
-int main(int argc, char * argv[]) {
-  std::chrono::time_point<std::chrono::system_clock> start, end;
-  int elapsed_sec;
-  {
-
-  std::string filepoints = "../../../data/points/Kl.txt";
-  Filtration_value threshold = 0.27;
-  int dim_max = 3;
-  int p = 2;
-  int q = 1223;
-
-  // Extract the points from the file filepoints
-  typedef std::vector<double> Point_t;
-  std::vector< Point_t > points;
-  read_points(filepoints, points);
-
-  // Compute the proximity graph of the points
-  start = std::chrono::system_clock::now();
-  Graph_t prox_graph = compute_proximity_graph(points, threshold
-                                               , euclidean_distance<Point_t>);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n";
-
-  // Construct the Rips complex in a Simplex Tree
-  Simplex_tree<Simplex_tree_options_fast_persistence> st;
-  start = std::chrono::system_clock::now();
-
-  // insert the proximity graph in the simplex tree
-  st.insert_graph(prox_graph);
-  // expand the graph until dimension dim_max
-  st.expansion(dim_max);
-
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Compute Rips complex in " << elapsed_sec << " ms.\n";
-  std::cout << "  - dimension           = " << st.dimension() << std::endl;
-  std::cout << "  - number of simplices = " << st.num_simplices() << std::endl;
-
-  // Sort the simplices in the order of the filtration
-  start = std::chrono::system_clock::now();
-  st.initialize_filtration();
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Order the simplices of the filtration in " << elapsed_sec << " ms.\n";
-
-  // Copy the keys inside the simplices
-  start = std::chrono::system_clock::now();
-  {
-    int count = 0;
-    for (auto sh : st.filtration_simplex_range())
-      st.assign_key(sh, count++);
-  }
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Copied the keys inside the simplices in " << elapsed_sec << " ms.\n";
-
-  // Convert the simplex tree into a hasse diagram
-  start = std::chrono::system_clock::now();
-  Hasse_complex<> hcpx(st);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n";
-
-
-  std::cout << "Timings when using a simplex tree: \n";
-  timing_persistence(st, p);
-  timing_persistence(st, q);
-  timing_persistence(st, p, q);
-
-  std::cout << "Timings when using a Hasse complex: \n";
-  timing_persistence(hcpx, p);
-  timing_persistence(hcpx, q);
-  timing_persistence(hcpx, p, q);
-
-  start = std::chrono::system_clock::now();
-  }
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "Running the complex destructors in " << elapsed_sec << " ms.\n";
-  return 0;
-}
-
-template< typename FilteredComplex>
-void
-timing_persistence(FilteredComplex & cpx
-                   , int p) {
-  std::chrono::time_point<std::chrono::system_clock> start, end;
-  int elapsed_sec;
-  {
-  start = std::chrono::system_clock::now();
-  Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Initialize pcoh in " << elapsed_sec << " ms.\n";
-  // initializes the coefficient field for homology
-  start = std::chrono::system_clock::now();
-  pcoh.init_coefficients(p);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Initialize the coefficient field in " << elapsed_sec << " ms.\n";
-
-  start = std::chrono::system_clock::now();
-
-  pcoh.compute_persistent_cohomology(INFINITY);
-
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Compute persistent homology in Z/" << p << "Z in " << elapsed_sec << " ms.\n";
-  start = std::chrono::system_clock::now();
-  }
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Run the persistence destructors in " << elapsed_sec << " ms.\n";
-}
-
-template< typename FilteredComplex>
-void
-timing_persistence(FilteredComplex & cpx
-                   , int p
-                   , int q) {
-  std::chrono::time_point<std::chrono::system_clock> start, end;
-  int elapsed_sec;
-  {
-  start = std::chrono::system_clock::now();
-  Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Initialize pcoh in " << elapsed_sec << " ms.\n";
-  // initializes the coefficient field for homology
-  start = std::chrono::system_clock::now();
-  pcoh.init_coefficients(p, q);
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Initialize the coefficient field in " << elapsed_sec << " ms.\n";
-  // compute persistent homology, disgarding persistent features of life shorter than min_persistence
-
-  start = std::chrono::system_clock::now();
-
-  pcoh.compute_persistent_cohomology(INFINITY);
-
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Compute multi-field persistent homology in all coefficient fields Z/pZ "
-      << "with p in [" << p << ";" << q << "] in " << elapsed_sec << " ms.\n";
-  start = std::chrono::system_clock::now();
-  }
-  end = std::chrono::system_clock::now();
-  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
-  std::cout << "  Run the persistence destructors in " << elapsed_sec << " ms.\n";
-}