Review all cout and cerr. cerr is reserved for warnings/error and cout for traces

3 files changed, 51 insertions, 54 deletions

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..2f95dff3 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::cout << "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::cout << "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::cout << "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::cout << "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::cout << "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::cout << "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::cout << "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::cout << "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::cout << "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::cout << "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::cout << "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::cout << "bool operator != ( const Filtration_simplex_iterator& rhs )\n";
       }
       return !(*this == rhs);
     }
 
     Simplex_handle operator*() {
       if (globalDbg) {
-        std::cerr << "Simplex_handle operator*()\n";
+        std::cout << "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::cout << "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::cout << "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::cout << "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::cout << "std::pair<Simplex_handle, Simplex_handle> endpoints( Simplex_handle sh )\n";
+      std::cout << "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::cout << "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::cout << "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::cout << "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::cout << "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::cout << "bool operator != ( const Skeleton_simplex_iterator& rhs )\n";
       }
       return !(*this == rhs);
     }
 
     Simplex_handle operator*() {
       if (globalDbg) {
-        std::cerr << "Simplex_handle operator*() \n";
+        std::cout << "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::cout << "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::cout << "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::cout << "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::cout << "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..96036fd4 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
@@ -142,7 +142,7 @@ 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.");
         }
@@ -521,11 +521,11 @@ 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::cout << "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::cout << "After binning : " << this->data[i] << std::endl;
     }
   }
 }
@@ -539,11 +539,11 @@ 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::cout << "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::cout << "After binning : " << this->data[i] << std::endl;
     }
   }
 }
@@ -617,7 +617,7 @@ void Bitmap_cubical_complex_base<T>::read_perseus_style_file(const char* perseus
   inFiltration >> dimensionOfData;
 
   if (dbg) {
-    std::cerr << "dimensionOfData : " << dimensionOfData << std::endl;
+    std::cout << "dimensionOfData : " << dimensionOfData << std::endl;
   }
 
   std::vector<unsigned> sizes;
@@ -630,7 +630,7 @@ 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::cout << "size_in_this_dimension : " << size_in_this_dimension << std::endl;
     }
   }
   this->set_up_containers(sizes);
@@ -651,7 +651,7 @@ 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::cout << "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 +754,20 @@ 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::cout << "\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::cout << "i-1 :" << i - 1 << std::endl;
+      std::cout << "cell : " << cell << std::endl;
+      std::cout << "position : " << position << std::endl;
+      std::cout << "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::cout << "Nonzero length in this direction \n";
       dimension++;
     }
     cell = cell % this->multipliers[i - 1];
@@ -803,7 +803,7 @@ 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::cout << "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] << "  ";
       }
@@ -813,14 +813,14 @@ 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::cout << "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::cout << "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..3942dc34 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::cout << "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::cout << "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::cout << 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::cout << 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::cout << cell - this->multipliers[i - 1] << " "
                       << cell - (2 * this->sizes[i - 1] - 1) * this->multipliers[i - 1] << " ";
           }
         }