Merge tag 'tags/gudhi-release-3.2.0' into dfsg/latest

7 files changed, 91 insertions, 69 deletions

diff --git a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
index 46ea8f2e..e5512418 100644
--- a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
+++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
@@ -21,7 +21,7 @@
 int main(int argc, char** argv) {
   srand(time(0));
 
-  std::cout
+  std::clog
       << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical "
       << "complexes. The first parameter of the program is the dimension D of the bitmap. The next D parameters are "
       << "number of top dimensional cubes in each dimension of the bitmap. The program will create random cubical "
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
index 37514dee..aa255ec2 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
@@ -69,7 +69,7 @@ class Bitmap_cubical_complex : public T {
   Bitmap_cubical_complex(const char* perseus_style_file)
       : T(perseus_style_file), key_associated_to_simplex(this->total_number_of_cells + 1) {
     if (globalDbg) {
-      std::cerr << "Bitmap_cubical_complex( const char* perseus_style_file )\n";
+      std::clog << "Bitmap_cubical_complex( const char* perseus_style_file )\n";
     }
     for (std::size_t i = 0; i != this->total_number_of_cells; ++i) {
       this->key_associated_to_simplex[i] = i;
@@ -137,7 +137,7 @@ class Bitmap_cubical_complex : public T {
    **/
   static Simplex_handle null_simplex() {
     if (globalDbg) {
-      std::cerr << "Simplex_handle null_simplex()\n";
+      std::clog << "Simplex_handle null_simplex()\n";
     }
     return std::numeric_limits<Simplex_handle>::max();
   }
@@ -152,7 +152,7 @@ class Bitmap_cubical_complex : public T {
    **/
   inline unsigned dimension(Simplex_handle sh) const {
     if (globalDbg) {
-      std::cerr << "unsigned dimension(const Simplex_handle& sh)\n";
+      std::clog << "unsigned dimension(const Simplex_handle& sh)\n";
     }
     if (sh != null_simplex()) return this->get_dimension_of_a_cell(sh);
     return -1;
@@ -163,7 +163,7 @@ class Bitmap_cubical_complex : public T {
    **/
   Filtration_value filtration(Simplex_handle sh) {
     if (globalDbg) {
-      std::cerr << "Filtration_value filtration(const Simplex_handle& sh)\n";
+      std::clog << "Filtration_value filtration(const Simplex_handle& sh)\n";
     }
     // Returns the filtration value of a simplex.
     if (sh != null_simplex()) return this->data[sh];
@@ -175,7 +175,7 @@ class Bitmap_cubical_complex : public T {
    **/
   static Simplex_key null_key() {
     if (globalDbg) {
-      std::cerr << "Simplex_key null_key()\n";
+      std::clog << "Simplex_key null_key()\n";
     }
     return std::numeric_limits<Simplex_handle>::max();
   }
@@ -185,7 +185,7 @@ class Bitmap_cubical_complex : public T {
    **/
   Simplex_key key(Simplex_handle sh) const {
     if (globalDbg) {
-      std::cerr << "Simplex_key key(const Simplex_handle& sh)\n";
+      std::clog << "Simplex_key key(const Simplex_handle& sh)\n";
     }
     if (sh != null_simplex()) {
       return this->key_associated_to_simplex[sh];
@@ -198,7 +198,7 @@ class Bitmap_cubical_complex : public T {
    **/
   Simplex_handle simplex(Simplex_key key) {
     if (globalDbg) {
-      std::cerr << "Simplex_handle simplex(Simplex_key key)\n";
+      std::clog << "Simplex_handle simplex(Simplex_key key)\n";
     }
     if (key != null_key()) {
       return this->simplex_associated_to_key[key];
@@ -211,7 +211,7 @@ class Bitmap_cubical_complex : public T {
    **/
   void assign_key(Simplex_handle sh, Simplex_key key) {
     if (globalDbg) {
-      std::cerr << "void assign_key(Simplex_handle& sh, Simplex_key key)\n";
+      std::clog << "void assign_key(Simplex_handle& sh, Simplex_key key)\n";
     }
     if (key == null_key()) return;
     this->key_associated_to_simplex[sh] = key;
@@ -251,7 +251,7 @@ class Bitmap_cubical_complex : public T {
 
     Filtration_simplex_iterator operator++() {
       if (globalDbg) {
-        std::cerr << "Filtration_simplex_iterator operator++\n";
+        std::clog << "Filtration_simplex_iterator operator++\n";
       }
       ++this->position;
       return (*this);
@@ -265,7 +265,7 @@ class Bitmap_cubical_complex : public T {
 
     Filtration_simplex_iterator& operator=(const Filtration_simplex_iterator& rhs) {
       if (globalDbg) {
-        std::cerr << "Filtration_simplex_iterator operator =\n";
+        std::clog << "Filtration_simplex_iterator operator =\n";
       }
       this->b = rhs.b;
       this->position = rhs.position;
@@ -274,21 +274,21 @@ class Bitmap_cubical_complex : public T {
 
     bool operator==(const Filtration_simplex_iterator& rhs) const {
       if (globalDbg) {
-        std::cerr << "bool operator == ( const Filtration_simplex_iterator& rhs )\n";
+        std::clog << "bool operator == ( const Filtration_simplex_iterator& rhs )\n";
       }
       return (this->position == rhs.position);
     }
 
     bool operator!=(const Filtration_simplex_iterator& rhs) const {
       if (globalDbg) {
-        std::cerr << "bool operator != ( const Filtration_simplex_iterator& rhs )\n";
+        std::clog << "bool operator != ( const Filtration_simplex_iterator& rhs )\n";
       }
       return !(*this == rhs);
     }
 
     Simplex_handle operator*() {
       if (globalDbg) {
-        std::cerr << "Simplex_handle operator*()\n";
+        std::clog << "Simplex_handle operator*()\n";
       }
       return this->b->simplex_associated_to_key[this->position];
     }
@@ -314,14 +314,14 @@ class Bitmap_cubical_complex : public T {
 
     Filtration_simplex_iterator begin() {
       if (globalDbg) {
-        std::cerr << "Filtration_simplex_iterator begin() \n";
+        std::clog << "Filtration_simplex_iterator begin() \n";
       }
       return Filtration_simplex_iterator(this->b);
     }
 
     Filtration_simplex_iterator end() {
       if (globalDbg) {
-        std::cerr << "Filtration_simplex_iterator end()\n";
+        std::clog << "Filtration_simplex_iterator end()\n";
       }
       Filtration_simplex_iterator it(this->b);
       it.position = this->b->simplex_associated_to_key.size();
@@ -347,7 +347,7 @@ class Bitmap_cubical_complex : public T {
    **/
   Filtration_simplex_range filtration_simplex_range() {
     if (globalDbg) {
-      std::cerr << "Filtration_simplex_range filtration_simplex_range()\n";
+      std::clog << "Filtration_simplex_range filtration_simplex_range()\n";
     }
     // Returns a range over the simplices of the complex in the order of the filtration
     return Filtration_simplex_range(this);
@@ -370,8 +370,8 @@ class Bitmap_cubical_complex : public T {
   std::pair<Simplex_handle, Simplex_handle> endpoints(Simplex_handle sh) {
     std::vector<std::size_t> bdry = this->get_boundary_of_a_cell(sh);
     if (globalDbg) {
-      std::cerr << "std::pair<Simplex_handle, Simplex_handle> endpoints( Simplex_handle sh )\n";
-      std::cerr << "bdry.size() : " << bdry.size() << "\n";
+      std::clog << "std::pair<Simplex_handle, Simplex_handle> endpoints( Simplex_handle sh )\n";
+      std::clog << "bdry.size() : " << bdry.size() << "\n";
     }
     // this method returns two first elements from the boundary of sh.
     if (bdry.size() < 2)
@@ -392,7 +392,7 @@ class Bitmap_cubical_complex : public T {
    public:
     Skeleton_simplex_iterator(Bitmap_cubical_complex* b, std::size_t d) : b(b), dimension(d) {
       if (globalDbg) {
-        std::cerr << "Skeleton_simplex_iterator ( Bitmap_cubical_complex* b , std::size_t d )\n";
+        std::clog << "Skeleton_simplex_iterator ( Bitmap_cubical_complex* b , std::size_t d )\n";
       }
       // find the position of the first simplex of a dimension d
       this->position = 0;
@@ -406,7 +406,7 @@ class Bitmap_cubical_complex : public T {
 
     Skeleton_simplex_iterator operator++() {
       if (globalDbg) {
-        std::cerr << "Skeleton_simplex_iterator operator++()\n";
+        std::clog << "Skeleton_simplex_iterator operator++()\n";
       }
       // increment the position as long as you did not get to the next element of the dimension dimension.
       ++this->position;
@@ -425,7 +425,7 @@ class Bitmap_cubical_complex : public T {
 
     Skeleton_simplex_iterator& operator=(const Skeleton_simplex_iterator& rhs) {
       if (globalDbg) {
-        std::cerr << "Skeleton_simplex_iterator operator =\n";
+        std::clog << "Skeleton_simplex_iterator operator =\n";
       }
       this->b = rhs.b;
       this->position = rhs.position;
@@ -435,21 +435,21 @@ class Bitmap_cubical_complex : public T {
 
     bool operator==(const Skeleton_simplex_iterator& rhs) const {
       if (globalDbg) {
-        std::cerr << "bool operator ==\n";
+        std::clog << "bool operator ==\n";
       }
       return (this->position == rhs.position);
     }
 
     bool operator!=(const Skeleton_simplex_iterator& rhs) const {
       if (globalDbg) {
-        std::cerr << "bool operator != ( const Skeleton_simplex_iterator& rhs )\n";
+        std::clog << "bool operator != ( const Skeleton_simplex_iterator& rhs )\n";
       }
       return !(*this == rhs);
     }
 
     Simplex_handle operator*() {
       if (globalDbg) {
-        std::cerr << "Simplex_handle operator*() \n";
+        std::clog << "Simplex_handle operator*() \n";
       }
       return this->position;
     }
@@ -476,14 +476,14 @@ class Bitmap_cubical_complex : public T {
 
     Skeleton_simplex_iterator begin() {
       if (globalDbg) {
-        std::cerr << "Skeleton_simplex_iterator begin()\n";
+        std::clog << "Skeleton_simplex_iterator begin()\n";
       }
       return Skeleton_simplex_iterator(this->b, this->dimension);
     }
 
     Skeleton_simplex_iterator end() {
       if (globalDbg) {
-        std::cerr << "Skeleton_simplex_iterator end()\n";
+        std::clog << "Skeleton_simplex_iterator end()\n";
       }
       Skeleton_simplex_iterator it(this->b, this->dimension);
       it.position = this->b->data.size();
@@ -500,7 +500,7 @@ class Bitmap_cubical_complex : public T {
    **/
   Skeleton_simplex_range skeleton_simplex_range(unsigned dimension) {
     if (globalDbg) {
-      std::cerr << "Skeleton_simplex_range skeleton_simplex_range( unsigned dimension )\n";
+      std::clog << "Skeleton_simplex_range skeleton_simplex_range( unsigned dimension )\n";
     }
     return Skeleton_simplex_range(this, dimension);
   }
@@ -515,7 +515,7 @@ class Bitmap_cubical_complex : public T {
 template <typename T>
 void Bitmap_cubical_complex<T>::initialize_simplex_associated_to_key() {
   if (globalDbg) {
-    std::cerr << "void Bitmap_cubical_complex<T>::initialize_elements_ordered_according_to_filtration() \n";
+    std::clog << "void Bitmap_cubical_complex<T>::initialize_elements_ordered_according_to_filtration() \n";
   }
   this->simplex_associated_to_key = std::vector<std::size_t>(this->data.size());
   std::iota(std::begin(simplex_associated_to_key), std::end(simplex_associated_to_key), 0);
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
index 0d6299d2..f8f80ded 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
@@ -13,6 +13,8 @@
 
 #include <gudhi/Bitmap_cubical_complex/counter.h>
 
+#include <boost/config.hpp>
+
 #include <iostream>
 #include <vector>
 #include <string>
@@ -110,6 +112,16 @@ class Bitmap_cubical_complex_base {
   virtual inline std::vector<std::size_t> get_coboundary_of_a_cell(std::size_t cell) const;
 
   /**
+   * This function finds a top-dimensional cell that is incident to the input cell and has
+   * the same filtration value. In case several cells are suitable, an arbitrary one is
+   * returned. Note that the input parameter can be a cell of any dimension (vertex, edge, etc).
+   * On the other hand, the output is always indicating the position of
+   * a top-dimensional cube in the data structure.
+   * \pre The filtration values are assigned as per `impose_lower_star_filtration()`.
+   **/
+  inline size_t get_top_dimensional_coface_of_a_cell(size_t splx);
+
+  /**
   * This procedure compute incidence numbers between cubes. For a cube \f$A\f$ of
   * dimension n and a cube \f$B \subset A\f$ of dimension n-1, an incidence
   * between \f$A\f$ and \f$B\f$ is the integer with which \f$B\f$ appears in the boundary of \f$A\f$.
@@ -142,7 +154,7 @@ class Bitmap_cubical_complex_base {
       }
       if (coface_counter[i] != face_counter[i]) {
         if (number_of_position_in_which_counters_do_not_agree != -1) {
-          std::cout << "Cells given to compute_incidence_between_cells procedure do not form a pair of coface-face.\n";
+          std::cerr << "Cells given to compute_incidence_between_cells procedure do not form a pair of coface-face.\n";
           throw std::logic_error(
               "Cells given to compute_incidence_between_cells procedure do not form a pair of coface-face.");
         }
@@ -197,7 +209,7 @@ class Bitmap_cubical_complex_base {
   /**
    * Returns number of all cubes in the data structure.
    **/
-  inline unsigned size() const { return this->data.size(); }
+  inline std::size_t size() const { return this->data.size(); }
 
   /**
    * Writing to stream operator. By using it we get the values T of cells in order in which they are stored in the
@@ -408,7 +420,7 @@ class Bitmap_cubical_complex_base {
 
     void print_counter() const {
       for (std::size_t i = 0; i != this->counter.size(); ++i) {
-        std::cout << this->counter[i] << " ";
+        std::clog << this->counter[i] << " ";
       }
     }
     friend class Bitmap_cubical_complex_base;
@@ -521,11 +533,11 @@ void Bitmap_cubical_complex_base<T>::put_data_to_bins(std::size_t number_of_bins
   // now put the data into the appropriate bins:
   for (std::size_t i = 0; i != this->data.size(); ++i) {
     if (dbg) {
-      std::cerr << "Before binning : " << this->data[i] << std::endl;
+      std::clog << "Before binning : " << this->data[i] << std::endl;
     }
     this->data[i] = min_max.first + dx * (this->data[i] - min_max.first) / number_of_bins;
     if (dbg) {
-      std::cerr << "After binning : " << this->data[i] << std::endl;
+      std::clog << "After binning : " << this->data[i] << std::endl;
     }
   }
 }
@@ -539,11 +551,11 @@ void Bitmap_cubical_complex_base<T>::put_data_to_bins(T diameter_of_bin) {
   // now put the data into the appropriate bins:
   for (std::size_t i = 0; i != this->data.size(); ++i) {
     if (dbg) {
-      std::cerr << "Before binning : " << this->data[i] << std::endl;
+      std::clog << "Before binning : " << this->data[i] << std::endl;
     }
     this->data[i] = min_max.first + diameter_of_bin * (this->data[i] - min_max.first) / number_of_bins;
     if (dbg) {
-      std::cerr << "After binning : " << this->data[i] << std::endl;
+      std::clog << "After binning : " << this->data[i] << std::endl;
     }
   }
 }
@@ -603,6 +615,19 @@ void Bitmap_cubical_complex_base<T>::setup_bitmap_based_on_top_dimensional_cells
 }
 
 template <typename T>
+size_t Bitmap_cubical_complex_base<T>::get_top_dimensional_coface_of_a_cell(size_t splx) {
+  if (this->get_dimension_of_a_cell(splx) == this->dimension()){return splx;}
+  else{
+    for (auto v : this->get_coboundary_of_a_cell(splx)){
+      if(this->get_cell_data(v) == this->get_cell_data(splx)){
+        return this->get_top_dimensional_coface_of_a_cell(v);
+      }
+    }
+  }
+  BOOST_UNREACHABLE_RETURN(-2);
+}
+
+template <typename T>
 Bitmap_cubical_complex_base<T>::Bitmap_cubical_complex_base(const std::vector<unsigned>& sizes_in_following_directions,
                                                             const std::vector<T>& top_dimensional_cells) {
   this->setup_bitmap_based_on_top_dimensional_cells_list(sizes_in_following_directions, top_dimensional_cells);
@@ -617,7 +642,7 @@ void Bitmap_cubical_complex_base<T>::read_perseus_style_file(const char* perseus
   inFiltration >> dimensionOfData;
 
   if (dbg) {
-    std::cerr << "dimensionOfData : " << dimensionOfData << std::endl;
+    std::clog << "dimensionOfData : " << dimensionOfData << std::endl;
   }
 
   std::vector<unsigned> sizes;
@@ -630,7 +655,7 @@ void Bitmap_cubical_complex_base<T>::read_perseus_style_file(const char* perseus
     sizes.push_back(size_in_this_dimension);
     dimensions *= size_in_this_dimension;
     if (dbg) {
-      std::cerr << "size_in_this_dimension : " << size_in_this_dimension << std::endl;
+      std::clog << "size_in_this_dimension : " << size_in_this_dimension << std::endl;
     }
   }
   this->set_up_containers(sizes);
@@ -651,7 +676,7 @@ void Bitmap_cubical_complex_base<T>::read_perseus_style_file(const char* perseus
       }
 
       if (dbg) {
-        std::cerr << "Cell of an index : " << it.compute_index_in_bitmap()
+        std::clog << "Cell of an index : " << it.compute_index_in_bitmap()
                   << " and dimension: " << this->get_dimension_of_a_cell(it.compute_index_in_bitmap())
                   << " get the value : " << filtrationLevel << std::endl;
       }
@@ -754,20 +779,20 @@ std::vector<std::size_t> Bitmap_cubical_complex_base<T>::get_coboundary_of_a_cel
 template <typename T>
 unsigned Bitmap_cubical_complex_base<T>::get_dimension_of_a_cell(std::size_t cell) const {
   bool dbg = false;
-  if (dbg) std::cerr << "\n\n\n Computing position o a cell of an index : " << cell << std::endl;
+  if (dbg) std::clog << "\n\n\n Computing position o a cell of an index : " << cell << std::endl;
   unsigned dimension = 0;
   for (std::size_t i = this->multipliers.size(); i != 0; --i) {
     unsigned position = cell / this->multipliers[i - 1];
 
     if (dbg) {
-      std::cerr << "i-1 :" << i - 1 << std::endl;
-      std::cerr << "cell : " << cell << std::endl;
-      std::cerr << "position : " << position << std::endl;
-      std::cerr << "multipliers[" << i - 1 << "] = " << this->multipliers[i - 1] << std::endl;
+      std::clog << "i-1 :" << i - 1 << std::endl;
+      std::clog << "cell : " << cell << std::endl;
+      std::clog << "position : " << position << std::endl;
+      std::clog << "multipliers[" << i - 1 << "] = " << this->multipliers[i - 1] << std::endl;
     }
 
     if (position % 2 == 1) {
-      if (dbg) std::cerr << "Nonzero length in this direction \n";
+      if (dbg) std::clog << "Nonzero length in this direction \n";
       dimension++;
     }
     cell = cell % this->multipliers[i - 1];
@@ -803,9 +828,9 @@ void Bitmap_cubical_complex_base<T>::impose_lower_star_filtration() {
 
   while (indices_to_consider.size()) {
     if (dbg) {
-      std::cerr << "indices_to_consider in this iteration \n";
+      std::clog << "indices_to_consider in this iteration \n";
       for (std::size_t i = 0; i != indices_to_consider.size(); ++i) {
-        std::cout << indices_to_consider[i] << "  ";
+        std::clog << indices_to_consider[i] << "  ";
       }
     }
     std::vector<std::size_t> new_indices_to_consider;
@@ -813,14 +838,14 @@ void Bitmap_cubical_complex_base<T>::impose_lower_star_filtration() {
       std::vector<std::size_t> bd = this->get_boundary_of_a_cell(indices_to_consider[i]);
       for (std::size_t boundaryIt = 0; boundaryIt != bd.size(); ++boundaryIt) {
         if (dbg) {
-          std::cerr << "filtration of a cell : " << bd[boundaryIt] << " is : " << this->data[bd[boundaryIt]]
+          std::clog << "filtration of a cell : " << bd[boundaryIt] << " is : " << this->data[bd[boundaryIt]]
                     << " while of a cell: " << indices_to_consider[i] << " is: " << this->data[indices_to_consider[i]]
                     << std::endl;
         }
         if (this->data[bd[boundaryIt]] > this->data[indices_to_consider[i]]) {
           this->data[bd[boundaryIt]] = this->data[indices_to_consider[i]];
           if (dbg) {
-            std::cerr << "Setting the value of a cell : " << bd[boundaryIt]
+            std::clog << "Setting the value of a cell : " << bd[boundaryIt]
                       << " to : " << this->data[indices_to_consider[i]] << std::endl;
           }
         }
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
index edd794fe..18901469 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
@@ -128,7 +128,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c
       }
       if (coface_counter[i] != face_counter[i]) {
         if (number_of_position_in_which_counters_do_not_agree != -1) {
-          std::cout << "Cells given to compute_incidence_between_cells procedure do not form a pair of coface-face.\n";
+          std::cerr << "Cells given to compute_incidence_between_cells procedure do not form a pair of coface-face.\n";
           throw std::logic_error(
               "Cells given to compute_incidence_between_cells procedure do not form a pair of coface-face.");
         }
@@ -237,7 +237,7 @@ Bitmap_cubical_complex_periodic_boundary_conditions_base<T>::Bitmap_cubical_comp
     if (inFiltration.eof()) break;
 
     if (dbg) {
-      std::cerr << "Cell of an index : " << it.compute_index_in_bitmap()
+      std::clog << "Cell of an index : " << it.compute_index_in_bitmap()
                 << " and dimension: " << this->get_dimension_of_a_cell(it.compute_index_in_bitmap())
                 << " get the value : " << filtrationLevel << std::endl;
     }
@@ -278,7 +278,7 @@ std::vector<std::size_t> Bitmap_cubical_complex_periodic_boundary_conditions_bas
     std::size_t cell) const {
   bool dbg = false;
   if (dbg) {
-    std::cerr << "Computations of boundary of a cell : " << cell << std::endl;
+    std::clog << "Computations of boundary of a cell : " << cell << std::endl;
   }
 
   std::vector<std::size_t> boundary_elements;
@@ -292,7 +292,6 @@ std::vector<std::size_t> Bitmap_cubical_complex_periodic_boundary_conditions_bas
     if (position % 2 == 1) {
       // if there are no periodic boundary conditions in this direction, we do not have to do anything.
       if (!directions_in_which_periodic_b_cond_are_to_be_imposed[i - 1]) {
-        // std::cerr << "A\n";
         if (sum_of_dimensions % 2) {
           boundary_elements.push_back(cell - this->multipliers[i - 1]);
           boundary_elements.push_back(cell + this->multipliers[i - 1]);
@@ -301,12 +300,11 @@ std::vector<std::size_t> Bitmap_cubical_complex_periodic_boundary_conditions_bas
           boundary_elements.push_back(cell - this->multipliers[i - 1]);
         }
         if (dbg) {
-          std::cerr << cell - this->multipliers[i - 1] << " " << cell + this->multipliers[i - 1] << " ";
+          std::clog << cell - this->multipliers[i - 1] << " " << cell + this->multipliers[i - 1] << " ";
         }
       } else {
         // in this direction we have to do boundary conditions. Therefore, we need to check if we are not at the end.
         if (position != 2 * this->sizes[i - 1] - 1) {
-          // std::cerr << "B\n";
           if (sum_of_dimensions % 2) {
             boundary_elements.push_back(cell - this->multipliers[i - 1]);
             boundary_elements.push_back(cell + this->multipliers[i - 1]);
@@ -315,10 +313,9 @@ std::vector<std::size_t> Bitmap_cubical_complex_periodic_boundary_conditions_bas
             boundary_elements.push_back(cell - this->multipliers[i - 1]);
           }
           if (dbg) {
-            std::cerr << cell - this->multipliers[i - 1] << " " << cell + this->multipliers[i - 1] << " ";
+            std::clog << cell - this->multipliers[i - 1] << " " << cell + this->multipliers[i - 1] << " ";
           }
         } else {
-          // std::cerr << "C\n";
           if (sum_of_dimensions % 2) {
             boundary_elements.push_back(cell - this->multipliers[i - 1]);
             boundary_elements.push_back(cell - (2 * this->sizes[i - 1] - 1) * this->multipliers[i - 1]);
@@ -327,7 +324,7 @@ std::vector<std::size_t> Bitmap_cubical_complex_periodic_boundary_conditions_bas
             boundary_elements.push_back(cell - this->multipliers[i - 1]);
           }
           if (dbg) {
-            std::cerr << cell - this->multipliers[i - 1] << " "
+            std::clog << cell - this->multipliers[i - 1] << " "
                       << cell - (2 * this->sizes[i - 1] - 1) * this->multipliers[i - 1] << " ";
           }
         }
diff --git a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
index f18adb36..6f35b6da 100644
--- a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
+++ b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
@@ -1402,12 +1402,12 @@ BOOST_AUTO_TEST_CASE(check_if_boundary_of_boundary_is_zero_periodic_case_2d) {
        it != ba.all_cells_iterator_end(); ++it) {    
     int i = 1;
 
-    // std::cout << "Element : " << *it << std::endl;
+    // std::clog << "Element : " << *it << std::endl;
 
     Bitmap_cubical_complex_periodic_boundary_conditions_base::Boundary_range bdrange = ba.boundary_range(*it);
     for (Bitmap_cubical_complex_periodic_boundary_conditions::Boundary_iterator bd = bdrange.begin();
          bd != bdrange.end(); ++bd) {
-      // std::cout <<  *bd << " ";
+      // std::clog <<  *bd << " ";
       Bitmap_cubical_complex_periodic_boundary_conditions::Boundary_range second_bdrange = ba.boundary_range(*bd);
       int j = 1;
       for (Bitmap_cubical_complex_periodic_boundary_conditions::Boundary_iterator bd2 = second_bdrange.begin();
@@ -1441,7 +1441,7 @@ BOOST_AUTO_TEST_CASE(check_if_boundary_of_boundary_is_zero_periodic_case_3d) {
   std::vector<int> elems_in_boundary(number_of_all_elements, 0);
   for (Bitmap_cubical_complex_periodic_boundary_conditions::All_cells_iterator it = ba.all_cells_iterator_begin();
        it != ba.all_cells_iterator_end(); ++it) {
-    // std::cout << "Element : " << *it << std::endl;
+    // std::clog << "Element : " << *it << std::endl;
     
     int i = 1;
 
@@ -1449,7 +1449,7 @@ BOOST_AUTO_TEST_CASE(check_if_boundary_of_boundary_is_zero_periodic_case_3d) {
     for (Bitmap_cubical_complex_periodic_boundary_conditions::Boundary_iterator bd = bdrange.begin();
          bd != bdrange.end(); ++bd) {
       Bitmap_cubical_complex_periodic_boundary_conditions::Boundary_range second_bdrange = ba.boundary_range(*bd);
-      // std::cout << *bd << " ";
+      // std::clog << *bd << " ";
       int j = 1;
       for (Bitmap_cubical_complex_periodic_boundary_conditions::Boundary_iterator bd2 = second_bdrange.begin();
            bd2 != second_bdrange.end(); ++bd2) {
@@ -1551,7 +1551,7 @@ BOOST_AUTO_TEST_CASE(compute_incidence_between_cells_test_periodic_boundary_cond
     Bitmap_cubical_complex_periodic_boundary_conditions_base::Boundary_range bdrange = ba.boundary_range(*it);
     for (Bitmap_cubical_complex_periodic_boundary_conditions::Boundary_iterator bd = bdrange.begin();
          bd != bdrange.end(); ++bd) {
-      // std::cout <<  *bd << " ";
+      // std::clog <<  *bd << " ";
       Bitmap_cubical_complex_periodic_boundary_conditions::Boundary_range second_bdrange = ba.boundary_range(*bd);
       for (Bitmap_cubical_complex_periodic_boundary_conditions::Boundary_iterator bd2 = second_bdrange.begin();
            bd2 != second_bdrange.end(); ++bd2) {
@@ -1571,11 +1571,11 @@ BOOST_AUTO_TEST_CASE(perseus_file_read) {
 
   auto it = increasing.top_dimensional_cells_iterator_begin();
   double value = increasing.get_cell_data(*it);
-  std::cout << "First value of sinusoid.txt is " << value << std::endl;
+  std::clog << "First value of sinusoid.txt is " << value << std::endl;
   BOOST_CHECK(value == 10.);
   // Next value
   ++it;
   value = increasing.get_cell_data(*it);
-  std::cout << "Second value of sinusoid.txt is " << value << std::endl;
+  std::clog << "Second value of sinusoid.txt is " << value << std::endl;
   BOOST_CHECK(value == std::numeric_limits<double>::infinity());
 }
diff --git a/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp
index a9792c2d..510861cd 100644
--- a/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp
+++ b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp
@@ -19,7 +19,7 @@
 #include <cstddef>
 
 int main(int argc, char** argv) {
-  std::cout
+  std::clog
       << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical "
       << "complexes provided in text files in Perseus style (the only numbered in the first line is a dimension D of a"
       << "bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let "
@@ -62,7 +62,7 @@ int main(int argc, char** argv) {
   pcoh.output_diagram(out);
   out.close();
 
-  std::cout << "Result in file: " << output_file_name << "\n";
+  std::clog << "Result in file: " << output_file_name << "\n";
 
   return 0;
 }
diff --git a/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp
index fa97bac0..86816417 100644
--- a/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp
+++ b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp
@@ -20,7 +20,7 @@
 #include <string>
 
 int main(int argc, char** argv) {
-  std::cout
+  std::clog
       << "This program computes persistent homology, by using "
       << "Bitmap_cubical_complex_periodic_boundary_conditions class, of cubical complexes provided in text files in "
       << "Perseus style (the only numbered in the first line is a dimension D of a bitmap. In the lines I between 2 "
@@ -64,7 +64,7 @@ int main(int argc, char** argv) {
   pcoh.output_diagram(out);
   out.close();
 
-  std::cout << "Result in file: " << output_file_name << "\n";
+  std::clog << "Result in file: " << output_file_name << "\n";
 
   return 0;
 }