Fixing Marc's comments.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/periodic_cubical_complex_fix@2822 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9349d7b76ee2301c2554480f33af0a395451a9a9

2 files changed, 39 insertions, 35 deletions

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 58e5bbbd..6a1ff3ff 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
@@ -1,4 +1,4 @@
-/*    This file is part of the Gudhi Library. The Gudhi 
+/*    This file is part of the Gudhi Library. The Gudhi library
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
@@ -101,7 +101,7 @@ class Bitmap_cubical_complex_base {
    * In the case of functions that compute (co)boundary, the output is a vector if non-negative integers pointing to
    * the positions of (co)boundary element of the input cell.
    * The boundary elements are guaranteed to be returned so that the 
-   * incidence coeficcients are alternating.
+   * incidence coefficients of boundary elements are alternating.
    */
   virtual inline std::vector< size_t > get_boundary_of_a_cell(size_t cell)const;
   /**
@@ -119,38 +119,31 @@ class Bitmap_cubical_complex_base {
    * 
    **/
   virtual inline std::vector< size_t > get_coboundary_of_a_cell(size_t cell)const;
-  /**
-   * In the case of get_dimension_of_a_cell function, the output is a non-negative integer
-   * indicating the dimension of a cell.
-   * Note that unlike in the case of boundary, over here the elements are 
-   * not guaranteed to be returned with alternating incidence numbers.
-   * To compute incidence between cells use compute_incidence_between_cells
-   * procedure
-   **/
    
    /**
-   * This procedure compute incidence numbers between cells. 
-   * Note that first parameter is the address of a cell of dimension n,
-   * and the second parameter is the address of adjusted cell in dimension
-   * n-1. 
+   * This procedure compute incidence numbers between cells. For a cell A of
+   * dimension n and a cell B \subset A of dimension n-1, an incidence
+   * between A and B is the integer with which B appears in the boundary of A.
+   * Note that first parameter is a cell of dimension n,
+   * and the second parameter is an adjusted cell in dimension n-1. 
   **/ 
-  virtual int compute_incidence_between_cells( size_t coBoundary , size_t boundary )
+  virtual int compute_incidence_between_cells( size_t coface , size_t face )
   {	  	  
 	  
 	  //first get the counters for coBoundary and boundary:
-	  std::vector<unsigned> cbd_counter = this->compute_counter_for_given_cell( coBoundary );
-	  std::vector<unsigned> bd_counter = this->compute_counter_for_given_cell( boundary );
+	  std::vector<unsigned> coface_counter = this->compute_counter_for_given_cell( coface );
+	  std::vector<unsigned> face_counter = this->compute_counter_for_given_cell( face );
 	  
 	  //cbd_counter and bd_counter should agree at all positions except from one:
 	  int number_of_position_in_which_counters_do_not_agree = -1;
 	  size_t number_of_full_faces_that_comes_before = 0;
-	  for ( size_t i = 0 ; i != cbd_counter.size() ; ++i )
+	  for ( size_t i = 0 ; i != coface_counter.size() ; ++i )
 	  {
-		  if ( (cbd_counter[i]%2 == 1)&&(number_of_position_in_which_counters_do_not_agree==-1) )
+		  if ( (coface_counter[i]%2 == 1)&&(number_of_position_in_which_counters_do_not_agree==-1) )
 		  {
 			  ++number_of_full_faces_that_comes_before;
 		  }
-		  if ( cbd_counter[i] != bd_counter[i] )
+		  if ( coface_counter[i] != face_counter[i] )
 		  {
 			  if ( number_of_position_in_which_counters_do_not_agree != -1 )
 			  {
@@ -164,8 +157,8 @@ class Bitmap_cubical_complex_base {
 	  int incidence = 1;
 	  if ( number_of_full_faces_that_comes_before%2 )incidence = -1;	 	  
 	  //if the boundary cell is on the right from coboundary cell:
-	  if ( cbd_counter[number_of_position_in_which_counters_do_not_agree]+1 == 
-	       bd_counter[number_of_position_in_which_counters_do_not_agree]
+	  if ( coface_counter[number_of_position_in_which_counters_do_not_agree]+1 == 
+	       face_counter[number_of_position_in_which_counters_do_not_agree]
 	     )
 	     {
 			 incidence *= -1;
@@ -174,7 +167,16 @@ class Bitmap_cubical_complex_base {
 	  return incidence;
   }
    
+     /**
+   * In the case of get_dimension_of_a_cell function, the output is a non-negative integer
+   * indicating the dimension of a cell.
+   * Note that unlike in the case of boundary, over here the elements are 
+   * not guaranteed to be returned with alternating incidence numbers.
+   * To compute incidence between cells use compute_incidence_between_cells
+   * procedure
+   **/
   inline unsigned get_dimension_of_a_cell(size_t cell)const;
+  
   /**
    * In the case of get_cell_data, the output parameter is a reference to the value of a cube in a given position.
    * This allows reading and changing the value of filtration. Note that if the value of a filtration is changed, the
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 9411f4b2..176d64ad 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
@@ -105,27 +105,29 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c
   
   
   /**
-   * This procedure compute incidence numbers between cells. 
-   * Note that first parameter is the address of a cell of dimension n,
-   * and the second parameter is the address of adjusted cell in dimension
+   * This procedure compute incidence numbers between cells. For a cell A of
+   * dimension n and a cell B \subset A of dimension n-1, an incidence
+   * between A and B is the integer with which B appears in the boundary of A. 
+   * Note that first parameter is a cell of dimension n,
+   * and the second parameter is an adjusted cell in dimension
    * n-1. 
   **/ 
-  virtual int compute_incidence_between_cells( size_t coBoundary , size_t boundary )
+  virtual int compute_incidence_between_cells( size_t coface , size_t face )
   {	  	  
 	  //first get the counters for coBoundary and boundary:
-	  std::vector<unsigned> cbd_counter = this->compute_counter_for_given_cell( coBoundary );
-	  std::vector<unsigned> bd_counter = this->compute_counter_for_given_cell( boundary );
+	  std::vector<unsigned> coface_counter = this->compute_counter_for_given_cell( coface );
+	  std::vector<unsigned> face_counter = this->compute_counter_for_given_cell( face );
 	  
 	  //cbd_counter and bd_counter should agree at all positions except from one:
 	  int number_of_position_in_which_counters_do_not_agree = -1;
 	  size_t number_of_full_faces_that_comes_before = 0;
-	  for ( size_t i = 0 ; i != cbd_counter.size() ; ++i )
+	  for ( size_t i = 0 ; i != coface_counter.size() ; ++i )
 	  {
-		  if ( (cbd_counter[i]%2 == 1)&&(number_of_position_in_which_counters_do_not_agree==-1) )
+		  if ( (coface_counter[i]%2 == 1)&&(number_of_position_in_which_counters_do_not_agree==-1) )
 		  {
 			  ++number_of_full_faces_that_comes_before;
 		  }
-		  if ( cbd_counter[i] != bd_counter[i] )
+		  if ( coface_counter[i] != face_counter[i] )
 		  {
 			  if ( number_of_position_in_which_counters_do_not_agree != -1 )
 			  {
@@ -139,13 +141,13 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c
 	  int incidence = 1;
 	  if ( number_of_full_faces_that_comes_before%2 )incidence = -1;	 	  
 	  //if the boundary cell is on the right from coboundary cell:
-	  if ( (cbd_counter[number_of_position_in_which_counters_do_not_agree]+1 == 
-	       bd_counter[number_of_position_in_which_counters_do_not_agree])
+	  if ( (coface_counter[number_of_position_in_which_counters_do_not_agree]+1 == 
+	       face_counter[number_of_position_in_which_counters_do_not_agree])
 	       ||
 	       (  
-	       (cbd_counter[number_of_position_in_which_counters_do_not_agree] != 1) 
+	       (coface_counter[number_of_position_in_which_counters_do_not_agree] != 1) 
 	       &&
-	       (bd_counter[number_of_position_in_which_counters_do_not_agree]==0)
+	       (face_counter[number_of_position_in_which_counters_do_not_agree]==0)
 	       )
 	     )
 	     {