Fix code review

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_doc_fixes@2008 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: d742fb816e1c83a85400d2f0c187e045dcea362f

10 files changed, 39 insertions, 41 deletions

diff --git a/src/Rips_complex/concept/Simplicial_complex_for_rips.h b/src/Rips_complex/concept/Simplicial_complex_for_rips.h
index dc871177..7dab0615 100644
--- a/src/Rips_complex/concept/Simplicial_complex_for_rips.h
+++ b/src/Rips_complex/concept/Simplicial_complex_for_rips.h
@@ -31,11 +31,10 @@ namespace rips_complex {
  * complex, that can be created from a `Rips_complex`. The only available model for the moment is the `Simplex_tree`.
  */
 struct SimplicialComplexForRips {
-  /** \brief Handle to specify the simplex filtration value. */
+  /** \brief Type used to store the filtration values of the simplicial complex. */
   typedef unspecified Filtration_value;
 
-  /** \brief Inserts a given range `Gudhi::rips_complex::Rips_complex::OneSkeletonGraph` in the simplicial
-   * complex. */
+  /** \brief Inserts a given `Gudhi::rips_complex::Rips_complex::OneSkeletonGraph` in the simplicial complex. */
   template<class OneSkeletonGraph>
   void insert_graph(const OneSkeletonGraph& skel_graph);
 
diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index 64fd34bc..ceecfa7b 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -48,7 +48,7 @@ namespace rips_complex {
  * All edges that have a filtration value strictly greater than a given threshold value are not inserted into
  * the complex.
  * 
- * When creating a simplicial complex from this one skeleton graph, rips inserts the one skeleton graph into the data
+ * When creating a simplicial complex from this one skeleton graph, Rips inserts the one skeleton graph into the data
  * structure, and then expands the simplicial when required.
  * 
  * \image html "rips_complex_representation.png" "Rips-complex one skeleton graph representation"
@@ -68,7 +68,7 @@ namespace rips_complex {
  * 
  * \include Rips_complex/example_one_skeleton_rips_from_points.cpp
  * 
- * When launching (rips maximal distance between 2 points is 12.0, is expanded until dimension 1 - one skeleton graph
+ * When launching (Rips maximal distance between 2 points is 12.0, is expanded until dimension 1 - one skeleton graph
  * in other words):
  * 
  * \code $> ./oneskeletonripspoints
@@ -85,7 +85,7 @@ namespace rips_complex {
  * Then it creates a `Simplex_tree` with it.
  * 
  * 
- * Then, it is asked to display information about the rips complex.
+ * Then, it is asked to display information about the Rips complex.
  * 
  * \include Rips_complex/example_rips_complex_from_off_file.cpp
  * 
@@ -111,7 +111,7 @@ namespace rips_complex {
  * 
  * \include Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp
  * 
- * When launching (rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph
+ * When launching (Rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph
  * with other words):
  * 
  * \code $> ./oneskeletonripsdistance
@@ -127,7 +127,7 @@ namespace rips_complex {
  * Then it creates a `Simplex_tree` with it.
  * 
  * 
- * Then, it is asked to display information about the rips complex.
+ * Then, it is asked to display information about the Rips complex.
  * 
  * \include Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp
  * 
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
index 90bd8e38..bbc3c755 100644
--- a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
@@ -29,7 +29,7 @@ int main() {
   distances.push_back({0.11, 0.39, 0.97, 0.30});
 
   // ----------------------------------------------------------------------------
-  // Init of a rips complex from points
+  // Init of a Rips complex from points
   // ----------------------------------------------------------------------------
   double threshold = 1.0;
   Rips_complex rips_complex_from_points(distances, threshold);
@@ -37,13 +37,13 @@ int main() {
   Simplex_tree stree;
   rips_complex_from_points.create_complex(stree, 1);
   // ----------------------------------------------------------------------------
-  // Display information about the one skeleton rips complex
+  // Display information about the one skeleton Rips complex
   // ----------------------------------------------------------------------------
   std::cout << "Rips complex is of dimension " << stree.dimension() <<
                " - " << stree.num_simplices() << " simplices - " <<
                stree.num_vertices() << " vertices." << std::endl;
 
-  std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+  std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
                std::endl;
   for (auto f_simplex : stree.filtration_simplex_range()) {
     std::cout << "   ( ";
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
index 5d1216a0..3fd69ebc 100644
--- a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
@@ -24,7 +24,7 @@ int main() {
   points.push_back({9.0, 17.0});
 
   // ----------------------------------------------------------------------------
-  // Init of a rips complex from points
+  // Init of a Rips complex from points
   // ----------------------------------------------------------------------------
   double threshold = 12.0;
   Rips_complex rips_complex_from_points(points, threshold, Euclidean_distance());
@@ -32,13 +32,13 @@ int main() {
   Simplex_tree stree;
   rips_complex_from_points.create_complex(stree, 1);
   // ----------------------------------------------------------------------------
-  // Display information about the one skeleton rips complex
+  // Display information about the one skeleton Rips complex
   // ----------------------------------------------------------------------------
   std::cout << "Rips complex is of dimension " << stree.dimension() <<
                " - " << stree.num_simplices() << " simplices - " <<
                stree.num_vertices() << " vertices." << std::endl;
 
-  std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+  std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
                std::endl;
   for (auto f_simplex : stree.filtration_simplex_range()) {
     std::cout << "   ( ";
diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
index cc6c3a33..ef3a9d13 100644
--- a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
+++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
@@ -29,7 +29,7 @@ int main(int argc, char **argv) {
   using Distance_matrix = std::vector<std::vector<Filtration_value>>;
 
   // ----------------------------------------------------------------------------
-  // Init of a rips complex from a distance matrix in a csv file
+  // Init of a Rips complex from a distance matrix in a csv file
   // Default separator is ';'
   // ----------------------------------------------------------------------------
   Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
@@ -50,13 +50,13 @@ int main(int argc, char **argv) {
   std::ostream output_stream(streambufffer);
 
   // ----------------------------------------------------------------------------
-  // Display information about the rips complex
+  // Display information about the Rips complex
   // ----------------------------------------------------------------------------
   output_stream << "Rips complex is of dimension " << stree.dimension() <<
                    " - " << stree.num_simplices() << " simplices - " <<
                    stree.num_vertices() << " vertices." << std::endl;
 
-  output_stream << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+  output_stream << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
                    std::endl;
   for (auto f_simplex : stree.filtration_simplex_range()) {
     output_stream << "   ( ";
diff --git a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
index b6c961d0..a1e4e255 100644
--- a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
+++ b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
@@ -29,7 +29,7 @@ int main(int argc, char **argv) {
   using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
 
   // ----------------------------------------------------------------------------
-  // Init of a rips complex from an OFF file
+  // Init of a Rips complex from an OFF file
   // ----------------------------------------------------------------------------
   Gudhi::Points_off_reader<Point> off_reader(off_file_name);
   Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance());
@@ -49,13 +49,13 @@ int main(int argc, char **argv) {
   std::ostream output_stream(streambufffer);
 
   // ----------------------------------------------------------------------------
-  // Display information about the rips complex
+  // Display information about the Rips complex
   // ----------------------------------------------------------------------------
   output_stream << "Rips complex is of dimension " << stree.dimension() <<
                    " - " << stree.num_simplices() << " simplices - " <<
                    stree.num_vertices() << " vertices." << std::endl;
 
-  output_stream << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+  output_stream << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
                    std::endl;
   for (auto f_simplex : stree.filtration_simplex_range()) {
     output_stream << "   ( ";
diff --git a/src/Rips_complex/example/full_skeleton_rips_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt
index 319931e0..55de4ab8 100644
--- a/src/Rips_complex/example/full_skeleton_rips_for_doc.txt
+++ b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt
@@ -1,5 +1,5 @@
 Rips complex is of dimension 3 - 24 simplices - 7 vertices.
-Iterator on rips complex simplices in the filtration order, with [filtration value]:
+Iterator on Rips complex simplices in the filtration order, with [filtration value]:
    ( 0 ) -> [0] 
    ( 1 ) -> [0] 
    ( 2 ) -> [0] 
diff --git a/src/Rips_complex/example/one_skeleton_rips_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt
index b0e25cc5..706512a5 100644
--- a/src/Rips_complex/example/one_skeleton_rips_for_doc.txt
+++ b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt
@@ -1,5 +1,5 @@
 Rips complex is of dimension 1 - 18 simplices - 7 vertices.
-Iterator on rips complex simplices in the filtration order, with [filtration value]:
+Iterator on Rips complex simplices in the filtration order, with [filtration value]:
    ( 0 ) -> [0] 
    ( 1 ) -> [0] 
    ( 2 ) -> [0] 
diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h
index f0f39db8..65e742ce 100644
--- a/src/Rips_complex/include/gudhi/Rips_complex.h
+++ b/src/Rips_complex/include/gudhi/Rips_complex.h
@@ -51,7 +51,7 @@ namespace rips_complex {
  * to a given threshold. Edge length is computed from a user given point cloud with a given distance function, or a
  * distance matrix.
  * 
- * \tparam Filtration_value must meet `SimplicialComplexForRips` concept.
+ * \tparam Filtration_value  is the type used to store the filtration values of the simplicial complex.
  */
 template<typename Filtration_value>
 class Rips_complex {
@@ -70,7 +70,7 @@ class Rips_complex {
   /** \brief Rips_complex constructor from a list of points.
    *
    * @param[in] points Range of points.
-   * @param[in] threshold rips value.
+   * @param[in] threshold Rips value.
    * @param[in] distance distance function that returns a `Filtration_value` from 2 given points.
    * 
    * \tparam InputPointRange must be a range for which `std::begin` and `std::end` return input iterators on a
@@ -81,20 +81,20 @@ class Rips_complex {
    */
   template<typename InputPointRange, typename Distance >
   Rips_complex(const InputPointRange& points, Filtration_value threshold, Distance distance) {
-    compute_proximity_graph<InputPointRange, Distance >(points, threshold, distance);
+    compute_proximity_graph(points, threshold, distance);
   }
 
   /** \brief Rips_complex constructor from a distance matrix.
    *
    * @param[in] distance_matrix Range of distances.
-   * @param[in] threshold rips value.
+   * @param[in] threshold Rips value.
    * 
-   * \tparam InputDistanceRange must have a `size()` method and on which `distance_matrix[i][j]` returns
-   * the distance between points \f$i\f$ and \f$j\f$ as long as \f$ 0 \leqslant i \leqslant j \leqslant
+   * \tparam DistanceMatrix must have a `size()` method and on which `distance_matrix[i][j]` returns
+   * the distance between points \f$i\f$ and \f$j\f$ as long as \f$ 0 \leqslant i < j \leqslant
    * distance\_matrix.size().\f$
    */
-  template<typename InputDistanceRange>
-  Rips_complex(const InputDistanceRange& distance_matrix, Filtration_value threshold) {
+  template<typename DistanceMatrix>
+  Rips_complex(const DistanceMatrix& distance_matrix, Filtration_value threshold) {
     compute_proximity_graph(boost::irange((size_t)0, distance_matrix.size()), threshold,
                             [&](size_t i, size_t j){return distance_matrix[j][i];});
   }
@@ -105,7 +105,7 @@ class Rips_complex {
    * \tparam SimplicialComplexForRips must meet `SimplicialComplexForRips` concept.
    * 
    * @param[in] complex SimplicialComplexForRips to be created.
-   * @param[in] dim_max graph expansion for rips until this given maximal dimension.
+   * @param[in] dim_max graph expansion for Rips until this given maximal dimension.
    * @exception std::invalid_argument In debug mode, if `complex.num_vertices()` does not return 0.
    *
    */
@@ -144,7 +144,7 @@ class Rips_complex {
     // --------------------------------------------------------------------------------------------
     // Creates the vector of edges and its filtration values (returned by distance function)
     Vertex_handle idx_u = 0;
-    for (auto it_u = std::begin(points); it_u != std::end(points); ++it_u) {
+    for (auto it_u = std::begin(points); it_u != std::end(points); ++it_u, ++idx_u) {
       Vertex_handle idx_v = idx_u + 1;
       for (auto it_v = it_u + 1; it_v != std::end(points); ++it_v, ++idx_v) {
         Filtration_value fil = distance(*it_u, *it_v);
@@ -153,7 +153,6 @@ class Rips_complex {
           edges_fil.push_back(fil);
         }
       }
-      ++idx_u;
     }
 
     // --------------------------------------------------------------------------------------------
diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp
index 1bdd0512..ae68ba0d 100644
--- a/src/Rips_complex/test/test_rips_complex.cpp
+++ b/src/Rips_complex/test/test_rips_complex.cpp
@@ -51,12 +51,12 @@ bool are_almost_the_same(float a, float b) {
 BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) {
   // ----------------------------------------------------------------------------
   //
-  // Init of a rips complex from a OFF file
+  // Init of a Rips complex from a OFF file
   //
   // ----------------------------------------------------------------------------
   std::string off_file_name("alphacomplexdoc.off");
   double rips_threshold = 12.0;
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " - rips threshold=" <<
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - Rips threshold=" <<
       rips_threshold << "==========" << std::endl;
 
   Gudhi::Points_off_reader<Point> off_reader(off_file_name);
@@ -185,7 +185,7 @@ BOOST_AUTO_TEST_CASE(Rips_complex_from_points) {
   points.push_back(Point(coords.begin(), coords.end()));
 
   // ----------------------------------------------------------------------------
-  // Init of a rips complex from the list of points
+  // Init of a Rips complex from the list of points
   // ----------------------------------------------------------------------------
   Rips_complex rips_complex_from_points(points, 2.0, Custom_square_euclidean_distance());
 
@@ -195,7 +195,7 @@ BOOST_AUTO_TEST_CASE(Rips_complex_from_points) {
   rips_complex_from_points.create_complex(st, DIMENSION);
 
   // Another way to check num_simplices
-  std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  std::cout << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" << std::endl;
   int num_simplices = 0;
   for (auto f_simplex : st.filtration_simplex_range()) {
     num_simplices++;
@@ -236,12 +236,12 @@ BOOST_AUTO_TEST_CASE(Rips_complex_from_points) {
 BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
   // ----------------------------------------------------------------------------
   //
-  // Init of a rips complex from a OFF file
+  // Init of a Rips complex from a OFF file
   //
   // ----------------------------------------------------------------------------
   std::string csv_file_name("full_square_distance_matrix.csv");
   double rips_threshold = 12.0;
-  std::cout << "========== CSV FILE NAME = " << csv_file_name << " - rips threshold=" <<
+  std::cout << "========== CSV FILE NAME = " << csv_file_name << " - Rips threshold=" <<
       rips_threshold << "==========" << std::endl;
 
   Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
@@ -332,12 +332,12 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
 BOOST_AUTO_TEST_CASE(Rips_create_complex_throw) {
   // ----------------------------------------------------------------------------
   //
-  // Init of a rips complex from a OFF file
+  // Init of a Rips complex from a OFF file
   //
   // ----------------------------------------------------------------------------
   std::string off_file_name("alphacomplexdoc.off");
   double rips_threshold = 12.0;
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " - rips threshold=" <<
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - Rips threshold=" <<
       rips_threshold << "==========" << std::endl;
 
   Gudhi::Points_off_reader<Point> off_reader(off_file_name);