Backmerge of trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/contiguous_vertices@949 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b20b49bab38fdcbc6571c159200125148e9a1bd6

5 files changed, 30 insertions, 19 deletions

diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h
index 1834903b..e124d524 100644
--- a/src/Persistent_cohomology/concept/FilteredComplex.h
+++ b/src/Persistent_cohomology/concept/FilteredComplex.h
@@ -65,9 +65,9 @@ struct FilteredComplex
   Simplex_key              key      ( Simplex_handle sh );
 /** \brief Returns the simplex associated to a key.
   *
-  * If key is different from null_key(), there must be a unique 
-  * simplex having this key. */  
-  Simplex_handle           simplex  ( Simplex_key key );
+  * If key is different from null_key(), returns the simplex that
+  * has index idx in the filtration. */
+  Simplex_handle           simplex  ( Simplex_key idx );
 /** \brief Assign a key to a simplex. */
   void                     assign_key(Simplex_handle sh, Simplex_key key);
  
diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
index e293e013..0a692717 100644
--- a/src/Persistent_cohomology/example/plain_homology.cpp
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -27,6 +27,10 @@
 
 using namespace Gudhi;
 
+/* We could perfectly well use the default Simplex_tree<> (which uses
+ * Simplex_tree_options_full_featured), the following simply demonstrates
+ * how to save on storage by not storing a filtration value.  */
+
 struct MyOptions : Simplex_tree_options_full_featured {
   // Implicitly use 0 as filtration value for all simplices
   static const bool store_filtration = false;
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index d096792f..643b810c 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -27,7 +27,6 @@
 #include <gudhi/Persistent_cohomology/Field_Zp.h>
 #include <gudhi/Simple_object_pool.h>
 
-#include <boost/tuple/tuple.hpp>
 #include <boost/intrusive/set.hpp>
 #include <boost/pending/disjoint_sets.hpp>
 #include <boost/intrusive/list.hpp>
@@ -223,7 +222,7 @@ class Persistent_cohomology {
 // Sparse column type for the annotation of the boundary of an element.
   typedef std::vector<std::pair<Simplex_key, Arith_element> > A_ds_type;
 // Persistent interval type. The Arith_element field is used for the multi-field framework.
-  typedef boost::tuple<Simplex_handle, Simplex_handle, Arith_element> Persistent_interval;
+  typedef std::tuple<Simplex_handle, Simplex_handle, Arith_element> Persistent_interval;
 
   /** \brief Initializes the Persistent_cohomology class.
    *
@@ -431,9 +430,12 @@ class Persistent_cohomology {
       std::map<Simplex_key, Arith_element> & map_a_ds, Simplex_handle sigma,
       int dim_sigma) {
     // traverses the boundary of sigma, keeps track of the annotation vectors,
-    // with multiplicity, in a map.
-    std::map<Column *, int> annotations_in_boundary;
-    std::pair<typename std::map<Column *, int>::iterator, bool> result_insert_bound;
+    // 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;
+    annotations_in_boundary.clear();
     int sign = 1 - 2 * (dim_sigma % 2);  // \in {-1,1} provides the sign in the
                                          // alternate sum in the boundary.
     Simplex_key key;
@@ -445,22 +447,29 @@ class Persistent_cohomology {
         // Find its annotation vector
         curr_col = ds_repr_[dsets_.find_set(key)];
         if (curr_col != NULL) {  // and insert it in annotations_in_boundary with multyiplicative factor "sign".
-          result_insert_bound = annotations_in_boundary.insert(std::pair<Column *, int>(curr_col, sign));
-          if (!(result_insert_bound.second)) {
-            result_insert_bound.first->second += sign;
-          }
+	  annotations_in_boundary.emplace_back(curr_col, sign);
         }
       }
       sign = -sign;
     }
+    // Place identical annotations consecutively so we can easily sum their multiplicities.
+    std::sort(annotations_in_boundary.begin(), annotations_in_boundary.end(),
+	[](annotation_t const& a, annotation_t const& b) { return a.first < b.first; });
+
     // Sum the annotations with multiplicity, using a map<key,coeff>
     // to represent a sparse vector.
     std::pair<typename std::map<Simplex_key, Arith_element>::iterator, bool> result_insert_a_ds;
 
-    for (auto ann_ref : annotations_in_boundary) {
-      if (ann_ref.second != coeff_field_.additive_identity()) {  // For all columns in the boundary,
-        for (auto cell_ref : ann_ref.first->col_) {  // insert every cell in map_a_ds with multiplicity
-          Arith_element w_y = coeff_field_.times(cell_ref.coefficient_, ann_ref.second);  // coefficient * multiplicity
+    for (auto ann_it = annotations_in_boundary.begin(); ann_it != annotations_in_boundary.end(); /**/) {
+      Column* col = ann_it->first;
+      int mult = ann_it->second;
+      while (++ann_it != annotations_in_boundary.end() && ann_it->first == col) {
+	mult += ann_it->second;
+      }
+      // The following test is just a heuristic, it is not required, and it is fine that is misses p == 0.
+      if (mult != coeff_field_.additive_identity()) {  // For all columns in the boundary,
+        for (auto cell_ref : col->col_) {  // insert every cell in map_a_ds with multiplicity
+          Arith_element w_y = coeff_field_.times(cell_ref.coefficient_, mult);  // coefficient * multiplicity
 
           if (w_y != coeff_field_.additive_identity()) {  // if != 0
             result_insert_a_ds = map_a_ds.insert(std::pair<Simplex_key, Arith_element>(cell_ref.key_, w_y));
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
index 0591fc95..38bc08d1 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
@@ -81,8 +81,7 @@ class Multi_field {
     // set m to primorial(bound_prime)
     prod_characteristics_ = 1;
     for (auto p : primes_) {
-      mpz_mul_ui(prod_characteristics_.get_mpz_t(),
-                 prod_characteristics_.get_mpz_t(), p);
+      prod_characteristics_ *= p;
     }
 
     // Uvect_
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h
index 612658e6..5deb2d88 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h
@@ -23,7 +23,6 @@
 #ifndef PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
 #define PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
 
-#include <boost/tuple/tuple.hpp>
 #include <boost/intrusive/set.hpp>
 #include <boost/intrusive/list.hpp>