Merge from Doxygen_for_GUDHI_1.3.0.

Doxygen fixes for Gudhi version 1.3.0


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1111 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3f5c37263f802621ba818fdb4ab73eba1fec29c8

9 files changed, 765 insertions, 31 deletions

diff --git a/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.ipe b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.ipe
new file mode 100644
index 00000000..bec245e7
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diff --git a/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png
new file mode 100644
index 00000000..afb2a75e
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png
diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
index cde0b2fc..83921427 100644
--- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -76,7 +76,7 @@ namespace Cubical_complex {
  * directions, allows to determine, dimension, neighborhood, boundary and coboundary of every cube \f$C \in

  * \mathcal{K}\f$.

  *

- * \image html "bitmapAllCubes.png" "Cubical complex.

+ * \image html "Cubical_complex_representation.png" Cubical complex.

  *

  * Note that the cubical complex in the figure above is, in a natural way, a product of one dimensional cubical

  * complexes in \f$\mathbb{R}\f$. The number of all cubes in each direction is equal \f$2n+1\f$, where \f$n\f$ is the

@@ -145,7 +145,8 @@ namespace Cubical_complex {
 

  * \section BitmapExamples Examples

  * End user programs are available in example/Bitmap_cubical_complex folder.

-

+ * 

+ * \copyright GNU General Public License v3.

  */

 /** @} */  // end defgroup cubical_complex

 

diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index 8f9cfa80..ad86b763 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -2,16 +2,25 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHIBitmap)
 
 add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
-target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt)
 add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
 
 add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
-target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Random_bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100)
 
 add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp )
-target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt)
 add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt)
 
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 67e1fed3..56fa297c 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
@@ -46,18 +46,14 @@ const bool globalDbg = false;
 template <typename T> class is_before_in_filtration;
 
 /**
- * This is a Bitmap_cubical_complex class. It joints a functionalities of Bitmap_cubical_complex_base and
+ * @brief Cubical complex represented as a bitmap.
+ * @ingroup cubical_complex
+ * @details This is a Bitmap_cubical_complex class. It joints a functionalities of Bitmap_cubical_complex_base and
  * Bitmap_cubical_complex_periodic_boundary_conditions_base classes into
  * Gudhi persistent homology engine. It is a template class that inherit from its template parameter. The template
  * parameter is supposed to be either Bitmap_cubical_complex_base or
  * Bitmap_cubical_complex_periodic_boundary_conditions_base class.
  **/
-
-/**
- *@class Bitmap_cubical_complex
- *@brief Cubical complex represented as a bitmap.
- *@ingroup cubical_complex
- */
 template <typename T>
 class Bitmap_cubical_complex : public T {
  public:
@@ -321,7 +317,7 @@ class Bitmap_cubical_complex : public T {
   };
 
   /**
-   * Filtration_simplex_range provides the ranges for Filtration_simplex_iterator.
+   * @brief Filtration_simplex_range provides the ranges for Filtration_simplex_iterator.
    **/
   class Filtration_simplex_range {
     // Range over the simplices of the complex in the order of the filtration.
@@ -492,7 +488,7 @@ class Bitmap_cubical_complex : public T {
   };
 
   /**
-   * Class needed for compatibility with Gudhi. Not useful for other purposes.
+   * @brief Class needed for compatibility with Gudhi. Not useful for other purposes.
    **/
   class Skeleton_simplex_range {
     // Range over the simplices of the complex in the order of the filtration.
@@ -549,7 +545,8 @@ void Bitmap_cubical_complex<T>::initialize_simplex_associated_to_key() {
   this->simplex_associated_to_key = std::vector<size_t>(this->data.size());
   std::iota(std::begin(simplex_associated_to_key), std::end(simplex_associated_to_key), 0);
 #ifdef GUDHI_USE_TBB
-  tbb::parallel_sort(simplex_associated_to_key, is_before_in_filtration<T>(this));
+  tbb::parallel_sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(),
+                     is_before_in_filtration<T>(this));
 #else
   std::sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(), is_before_in_filtration<T>(this));
 #endif
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
index 266ce051..3a8c3988 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
@@ -31,8 +31,8 @@ namespace Gudhi {
 namespace Cubical_complex {
 
 /**
- * This is an implementation of a counter being a vector of integers. 
- * The constructor of the class takes as an input two vectors W and V. 
+ * @brief This is an implementation of a counter being a vector of integers. 
+ * @details The constructor of the class takes as an input two vectors W and V. 
  * It assumes that W < V coordinatewise.
  * If the initial counter W is not specified, it is assumed to be vector of zeros. 
  * The class allows to iterate between W and V by using increment() function.
@@ -40,7 +40,6 @@ namespace Cubical_complex {
  * The current counter reach the end counter V if the value returned by the increment function is FALSE.
  * This class is needed for the implementation of a bitmapCubicalComplex.
  **/
-
 class counter {
  public:
   /**
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 7294da98..2f74ba9e 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
@@ -39,13 +39,9 @@ namespace Gudhi {
 namespace Cubical_complex {
 
 /**
- * @class Bitmap_cubical_complex_base
  * @brief Cubical complex represented as a bitmap, class with basic implementation.
  * @ingroup cubical_complex
- */
-
-/**
- * This is a class implementing a basic bitmap data structure to store cubical complexes.
+ * @details This is a class implementing a basic bitmap data structure to store cubical complexes.
  * It implements only the most basic subroutines.
  * The idea of the bitmap is the following. Our aim is to have a memory efficient
  * data structure to store d-dimensional cubical complex
@@ -193,7 +189,7 @@ class Bitmap_cubical_complex_base {
   // ITERATORS
 
   /**
-   * Iterator through all cells in the complex (in order they appear in the structure -- i.e.
+   * @brief Iterator through all cells in the complex (in order they appear in the structure -- i.e.
    * in lexicographical order).
    **/
   class All_cells_iterator : std::iterator< std::input_iterator_tag, T > {
@@ -261,7 +257,7 @@ class Bitmap_cubical_complex_base {
   }
 
   /**
-   * All_cells_range class provides ranges for All_cells_iterator
+   * @brief All_cells_range class provides ranges for All_cells_iterator
    **/
   class All_cells_range {
    public:
@@ -312,7 +308,7 @@ class Bitmap_cubical_complex_base {
   }
 
   /**
-   * Iterator through top dimensional cells of the complex. The cells appear in order they are stored
+   * @brief Iterator through top dimensional cells of the complex. The cells appear in order they are stored
    * in the structure (i.e. in lexicographical order)
    **/
   class Top_dimensional_cells_iterator : std::iterator< std::input_iterator_tag, T > {
@@ -414,7 +410,7 @@ class Bitmap_cubical_complex_base {
   }
 
   /**
-   * Top_dimensional_cells_iterator_range class provides ranges for Top_dimensional_cells_iterator_range
+   * @brief Top_dimensional_cells_iterator_range class provides ranges for Top_dimensional_cells_iterator_range
    **/
   class Top_dimensional_cells_range {
    public:
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 a446c0e8..0d0f2f84 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
@@ -39,12 +39,9 @@ namespace Cubical_complex {
 // the cells on the right / top are not in the Bitmap_cubical_complex_periodic_boundary_conditions_base
 
 /**
- * @class Bitmap_cubical_complex_periodic_boundary_conditions_base
  * @brief Cubical complex with periodic boundary conditions represented as a bitmap.
  * @ingroup cubical_complex
- */
-/**
- * This is a class implementing a bitmap data structure with periodic boundary conditions. Most of the functions are
+ * @details This is a class implementing a bitmap data structure with periodic boundary conditions. Most of the functions are
  * identical to the functions from Bitmap_cubical_complex_base.
  * The ones that needed to be updated are the constructors and get_boundary_of_a_cell and get_coboundary_of_a_cell.
  */
diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index b6fc8a3b..0e5340c7 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -12,6 +12,9 @@ endif()
 
 add_executable ( BitmapCCUT Bitmap_test.cpp )
 target_link_libraries(BitmapCCUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(BitmapCCUT ${TBB_RELEASE_LIBRARY})
+endif()
 
 # Unitary tests
 add_test(NAME BitmapCCUT