Update performance_rips_persistence, which hasn't been working for a long time. We might want to run it in the testsuite with a smaller parameter so it doesn't take too long.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@863 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1fd91395f855297cf4815d64e94b06a8c400c99b

1 files changed, 62 insertions, 19 deletions

diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/example/performance_rips_persistence.cpp
index 0e912d57..fc48d6b1 100644
--- a/src/Persistent_cohomology/example/performance_rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/performance_rips_persistence.cpp
@@ -63,10 +63,11 @@ void timing_persistence(FilteredComplex & cpx
  */
 int main(int argc, char * argv[]) {
   std::chrono::time_point<std::chrono::system_clock> start, end;
-  int enlapsed_sec;
+  int elapsed_sec;
+  {
 
-  std::string filepoints = "../examples/Kl.txt";
-  Filtration_value threshold = 0.3;
+  std::string filepoints = "../../../data/points/Kl.txt";
+  Filtration_value threshold = 0.27;
   int dim_max = 3;
   int p = 2;
   int q = 1223;
@@ -81,8 +82,8 @@ int main(int argc, char * argv[]) {
   Graph_t prox_graph = compute_proximity_graph(points, threshold
                                                , euclidean_distance<Point_t>);
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
-  std::cout << "Compute Rips graph in " << enlapsed_sec << " sec.\n";
+  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<> st;
@@ -94,8 +95,8 @@ int main(int argc, char * argv[]) {
   st.expansion(dim_max);
 
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
-  std::cout << "Compute Rips complex in " << enlapsed_sec << " sec.\n";
+  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;
 
@@ -103,15 +104,26 @@ int main(int argc, char * argv[]) {
   start = std::chrono::system_clock::now();
   st.initialize_filtration();
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
-  std::cout << "Order the simplices of the filtration in " << enlapsed_sec << " sec.\n";
+  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();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
-  std::cout << "Convert the simplex tree into a Hasse diagram in " << enlapsed_sec << " sec.\n";
+  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";
@@ -124,6 +136,11 @@ int main(int argc, char * argv[]) {
   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;
 }
 
@@ -132,19 +149,32 @@ void
 timing_persistence(FilteredComplex & cpx
                    , int p) {
   std::chrono::time_point<std::chrono::system_clock> start, end;
-  int enlapsed_sec;
-
+  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();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
-  std::cout << "  Compute persistent homology in Z/" << p << "Z in " << enlapsed_sec << " sec.\n";
+  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>
@@ -153,11 +183,19 @@ timing_persistence(FilteredComplex & cpx
                    , int p
                    , int q) {
   std::chrono::time_point<std::chrono::system_clock> start, end;
-  int enlapsed_sec;
-
+  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();
@@ -165,7 +203,12 @@ timing_persistence(FilteredComplex & cpx
   pcoh.compute_persistent_cohomology(INFINITY);
 
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
+  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 " << enlapsed_sec << " sec.\n";
+      << "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";
 }