Some doxygen improvements with a cell complex construction basic example

5 files changed, 101 insertions, 4 deletions

diff --git a/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h b/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h
index 5eb0cb22..3316bd81 100644
--- a/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h
+++ b/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h
@@ -196,20 +196,31 @@ the vertex cells in the cell complex to their Cartesian coordinates.
 
 \section example Examples
 
+\subsection examplewithoutboundaries Basic example without boundaries
+\include Coxeter_triangulation/cell_complex_from_basic_circle_manifold.cpp
+
+The program output is:
+
+\include Coxeter_triangulation/cell_complex_from_basic_circle_manifold_for_doc.txt
+
+\subsection exampleswithboundaries Example with boundaries
+
 Here is an example of constructing a piecewise-linear approximation of a flat torus embedded in \f$\mathbb{R}^4\f$,
 rotated by a random rotation in \f$\mathbb{R}^4\f$ and cut by a hyperplane.
 
 \include Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp
 
-The output in medit is:
+The output in <a target="_blank" href="https://www.ljll.math.upmc.fr/frey/software.html">medit</a> is:
 
 \image html "flat_torus_with_boundary.png" "Output from the example of a flat torus with boundary"
 
+\subsection exampleswithcustomfunction Example with a custom function
+
 In the following more complex example, we define a custom function for the implicit manifold.
 
 \include Coxeter_triangulation/manifold_tracing_custom_function.cpp
 
-The output in medit looks as follows:
+The output in <a target="_blank" href="https://www.ljll.math.upmc.fr/frey/software.html">medit</a> looks as follows:
 
 \image html "custom_function.png" "Output from the example with a custom function"
 
diff --git a/src/Coxeter_triangulation/example/CMakeLists.txt b/src/Coxeter_triangulation/example/CMakeLists.txt
index cbab2024..e7822ff7 100644
--- a/src/Coxeter_triangulation/example/CMakeLists.txt
+++ b/src/Coxeter_triangulation/example/CMakeLists.txt
@@ -13,3 +13,10 @@ if (TBB_FOUND)
 endif()
 add_test(NAME Coxeter_triangulation_manifold_tracing_custom_function_example
          COMMAND $<TARGET_FILE:Coxeter_triangulation_manifold_tracing_custom_function_example>)
+
+add_executable ( Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example cell_complex_from_basic_circle_manifold.cpp )
+if (TBB_FOUND)
+   target_link_libraries(Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example ${TBB_LIBRARIES})
+endif()
+add_test(NAME Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example
+         COMMAND $<TARGET_FILE:Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example>)
diff --git a/src/Coxeter_triangulation/example/cell_complex_from_basic_circle_manifold.cpp b/src/Coxeter_triangulation/example/cell_complex_from_basic_circle_manifold.cpp
new file mode 100644
index 00000000..0d32f916
--- /dev/null
+++ b/src/Coxeter_triangulation/example/cell_complex_from_basic_circle_manifold.cpp
@@ -0,0 +1,55 @@
+#include <iostream>
+
+#include <gudhi/Coxeter_triangulation.h>
+#include <gudhi/Implicit_manifold_intersection_oracle.h>  // for Gudhi::coxeter_triangulation::make_oracle
+#include <gudhi/Manifold_tracing.h>
+#include <gudhi/Cell_complex.h>
+#include <gudhi/Functions/Function_Sm_in_Rd.h>
+
+using namespace Gudhi::coxeter_triangulation;
+
+int main(int argc, char** argv) {
+  // Oracle is a circle of radius 1
+  double radius = 1.;
+  auto oracle = make_oracle(Function_Sm_in_Rd(radius, 1)); 
+
+  // Define a Coxeter triangulation.
+  Coxeter_triangulation<> cox_tr(oracle.amb_d());
+  // Theory forbids that a vertex of the triangulation lies exactly on the circle.
+  // Add some offset to avoid algorithm degeneracies.
+  cox_tr.change_offset(-Eigen::VectorXd::Random(oracle.amb_d()));
+  // For a better manifold approximation, one can change the circle radius value or change the linear transformation
+  // matrix.
+  // The number of points and edges will increase with a better resolution.
+  //cox_tr.change_matrix(0.5 * cox_tr.matrix());
+
+  // Manifold tracing algorithm
+  using Out_simplex_map = typename Manifold_tracing<Coxeter_triangulation<> >::Out_simplex_map;
+
+  std::vector<Eigen::VectorXd> seed_points(1, oracle.seed());
+  Out_simplex_map interior_simplex_map;
+  manifold_tracing_algorithm(seed_points, cox_tr, oracle, interior_simplex_map);
+
+  // Constructing the cell complex
+  std::size_t intr_d = oracle.amb_d() - oracle.cod_d();
+  Cell_complex<Out_simplex_map> cell_complex(intr_d);
+  cell_complex.construct_complex(interior_simplex_map);
+
+  // List of Hasse_cell pointers to retrieve vertices values from edges
+  std::map<Cell_complex<Out_simplex_map>::Hasse_cell*, std::size_t> vi_map;
+  std::size_t index = 0;
+
+  std::clog << "Vertices:" << std::endl;
+  for (const auto& cp_pair : cell_complex.cell_point_map()) {
+    std::clog << index << " : (" << cp_pair.second(0) << ", " << cp_pair.second(1) << ")" << std::endl;
+    vi_map.emplace(std::make_pair(cp_pair.first, index++));
+  }
+
+  std::clog << "Edges:" << std::endl;
+  for (const auto& sc_pair : cell_complex.interior_simplex_cell_map(1)) {
+    Cell_complex<Out_simplex_map>::Hasse_cell* edge_cell = sc_pair.second;
+    for (const auto& vi_pair : edge_cell->get_boundary()) std::clog << vi_map[vi_pair.first] << " ";
+    std::clog << std::endl;
+  }
+  return 0;
+}
diff --git a/src/Coxeter_triangulation/example/cell_complex_from_basic_circle_manifold_for_doc.txt b/src/Coxeter_triangulation/example/cell_complex_from_basic_circle_manifold_for_doc.txt
new file mode 100644
index 00000000..b323cca3
--- /dev/null
+++ b/src/Coxeter_triangulation/example/cell_complex_from_basic_circle_manifold_for_doc.txt
@@ -0,0 +1,26 @@
+Vertices:
+0 : (-0.680375, 0.523483)
+1 : (0.147642, 0.887879)
+2 : (-0.847996, 0.30801)
+3 : (-0.881369, 0.0951903)
+4 : (0.638494, -0.550215)
+5 : (0.415344, 0.843848)
+6 : (0.812453, -0.0815816)
+7 : (0.319625, -0.7709)
+8 : (0.319625, 0.889605)
+9 : (0.579487, 0.638553)
+10 : (-0.680375, -0.461325)
+11 : (-0.364269, -0.760962)
+Edges:
+3 2 
+3 10 
+10 11 
+11 7 
+7 4 
+2 0 
+0 1 
+6 9 
+6 4 
+1 8 
+8 5 
+5 9 
diff --git a/src/Coxeter_triangulation/include/gudhi/Cell_complex/Hasse_diagram_cell.h b/src/Coxeter_triangulation/include/gudhi/Cell_complex/Hasse_diagram_cell.h
index 24045c0c..04d50784 100644
--- a/src/Coxeter_triangulation/include/gudhi/Cell_complex/Hasse_diagram_cell.h
+++ b/src/Coxeter_triangulation/include/gudhi/Cell_complex/Hasse_diagram_cell.h
@@ -36,8 +36,6 @@ class Hasse_diagram;
  * It also allow to store any additional information of a type Additional_information which is a template parameter of
  * the class (set by default to void).
  *
- * Please refer to \ref Hasse_diagram for examples.
- *
  * The complex is a template class requiring the following parameters:
  * Incidence_type_ - determine the type of incidence coefficients. Use integers in most general case.
  * Filtration_type_ - type of filtration of cells.