Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1938 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8af39a00b9134dbcc77883412c29d7184479979b

2 files changed, 75 insertions, 3 deletions

diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index b31df6a4..b3339b7d 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -110,7 +110,7 @@ class Persistent_cohomology {
         cell_pool_() {
     if (cpx_->num_simplices() > std::numeric_limits<Simplex_key>::max()) {
       // num_simplices must be strictly lower than the limit, because a value is reserved for null_key.
-      throw std::out_of_range ("The number of simplices is more than Simplex_key type numeric limit.");
+      throw std::out_of_range("The number of simplices is more than Simplex_key type numeric limit.");
     }
     Simplex_key idx_fil = 0;
     for (auto sh : cpx_->filtration_simplex_range()) {
@@ -300,8 +300,7 @@ class Persistent_cohomology {
     // with multiplicity. We used to sum the coefficients directly in
     // annotations_in_boundary by using a map, we now do it later.
     typedef std::pair<Column *, int> annotation_t;
-    // Danger: not thread-safe!
-    static std::vector<annotation_t> annotations_in_boundary;
+    thread_local std::vector<annotation_t> annotations_in_boundary;
     annotations_in_boundary.clear();
     int sign = 1 - 2 * (dim_sigma % 2);  // \in {-1,1} provides the sign in the
                                          // alternate sum in the boundary.
@@ -690,6 +689,22 @@ class Persistent_cohomology {
     return persistent_pairs_;
   }
 
+  /** @brief Returns persistence intervals for a given dimension.
+   * @param[in] dimension Dimension to get the birth and death pairs from.
+   * @return A vector of persistence intervals (birth and death) on a fixed dimension.
+   */
+  std::vector< std::pair< Filtration_value , Filtration_value > >
+  intervals_in_dimension(int dimension) {
+    std::vector< std::pair< Filtration_value , Filtration_value > > result;
+    // auto && pair, to avoid unnecessary copying
+    for (auto && pair : persistent_pairs_) {
+      if (cpx_->dimension(get<0>(pair)) == dimension) {
+        result.emplace_back(cpx_->filtration(get<0>(pair)), cpx_->filtration(get<1>(pair)));
+      }
+    }
+    return result;
+  }
+
  private:
   /*
    * Structure representing a cocycle.
diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
index 40221005..0ed3fddf 100644
--- a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
+++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
@@ -84,6 +84,8 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers )
   // 2  1 0 inf 
   // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1.
   
+  std::cout << "BETTI NUMBERS" << std::endl;
+
   BOOST_CHECK(pcoh.betti_number(0) == 2);
   BOOST_CHECK(pcoh.betti_number(1) == 1);
   BOOST_CHECK(pcoh.betti_number(2) == 0);
@@ -93,6 +95,8 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers )
   BOOST_CHECK(bns[0] == 2);
   BOOST_CHECK(bns[1] == 1);
   BOOST_CHECK(bns[2] == 0);
+
+  std::cout << "GET PERSISTENT PAIRS" << std::endl;
   
   // Custom sort and output persistence
   cmp_intervals_by_dim_then_length<Mini_simplex_tree> cmp(&st);
@@ -115,6 +119,33 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers )
   BOOST_CHECK(st.dimension(get<0>(persistent_pairs[2])) == 0);
   BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 0);
   BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex());
+
+  std::cout << "INTERVALS IN DIMENSION" << std::endl;
+
+  auto intervals_in_dimension_0 = pcoh.intervals_in_dimension(0);
+  std::cout << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl;
+  for (std::size_t i = 0; i < intervals_in_dimension_0.size(); i++)
+    std::cout << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," <<
+                 intervals_in_dimension_0[i].second << "]" << std::endl;
+  BOOST_CHECK(intervals_in_dimension_0.size() == 2);
+  BOOST_CHECK(intervals_in_dimension_0[0].first == 0);
+  BOOST_CHECK(intervals_in_dimension_0[0].second == std::numeric_limits<Mini_simplex_tree::Filtration_value>::infinity());
+  BOOST_CHECK(intervals_in_dimension_0[1].first == 0);
+  BOOST_CHECK(intervals_in_dimension_0[1].second == std::numeric_limits<Mini_simplex_tree::Filtration_value>::infinity());
+
+
+  auto intervals_in_dimension_1 = pcoh.intervals_in_dimension(1);
+  std::cout << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl;
+  for (std::size_t i = 0; i < intervals_in_dimension_1.size(); i++)
+    std::cout << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," <<
+                 intervals_in_dimension_1[i].second << "]" << std::endl;
+  BOOST_CHECK(intervals_in_dimension_1.size() == 1);
+  BOOST_CHECK(intervals_in_dimension_1[0].first == 0);
+  BOOST_CHECK(intervals_in_dimension_1[0].second == std::numeric_limits<Mini_simplex_tree::Filtration_value>::infinity());
+
+  auto intervals_in_dimension_2 = pcoh.intervals_in_dimension(2);
+  std::cout << "intervals_in_dimension_2.size() = " << intervals_in_dimension_2.size() << std::endl;
+  BOOST_CHECK(intervals_in_dimension_2.size() == 0);
 }
 
 using Simplex_tree = Gudhi::Simplex_tree<>;
@@ -231,4 +262,30 @@ BOOST_AUTO_TEST_CASE( betti_numbers )
   BOOST_CHECK(st.dimension(get<0>(persistent_pairs[2])) == 0);
   BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 1);
   BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex());
+
+  std::cout << "INTERVALS IN DIMENSION" << std::endl;
+
+  auto intervals_in_dimension_0 = pcoh.intervals_in_dimension(0);
+  std::cout << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl;
+  for (std::size_t i = 0; i < intervals_in_dimension_0.size(); i++)
+    std::cout << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," <<
+                 intervals_in_dimension_0[i].second << "]" << std::endl;
+  BOOST_CHECK(intervals_in_dimension_0.size() == 2);
+  BOOST_CHECK(intervals_in_dimension_0[0].first == 2);
+  BOOST_CHECK(intervals_in_dimension_0[0].second == std::numeric_limits<Mini_simplex_tree::Filtration_value>::infinity());
+  BOOST_CHECK(intervals_in_dimension_0[1].first == 1);
+  BOOST_CHECK(intervals_in_dimension_0[1].second == std::numeric_limits<Mini_simplex_tree::Filtration_value>::infinity());
+
+  auto intervals_in_dimension_1 = pcoh.intervals_in_dimension(1);
+  std::cout << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl;
+  for (std::size_t i = 0; i < intervals_in_dimension_1.size(); i++)
+    std::cout << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," <<
+                 intervals_in_dimension_1[i].second << "]" << std::endl;
+  BOOST_CHECK(intervals_in_dimension_1.size() == 1);
+  BOOST_CHECK(intervals_in_dimension_1[0].first == 4);
+  BOOST_CHECK(intervals_in_dimension_1[0].second == std::numeric_limits<Mini_simplex_tree::Filtration_value>::infinity());
+
+  auto intervals_in_dimension_2 = pcoh.intervals_in_dimension(2);
+  std::cout << "intervals_in_dimension_2.size() = " << intervals_in_dimension_2.size() << std::endl;
+  BOOST_CHECK(intervals_in_dimension_2.size() == 0);
 }