code review fix

prune_above_filtration and remove_maximal_simplex in Simplex_tree.h
make_filtration_non_decreasing and rec_make_filtration_non_decreasing in Simplex_tree.h



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@910 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a20c9da65a5a3294e42ad2dd45a399d77fb5ad30

5 files changed, 66 insertions, 25 deletions

diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 2cb37578..1fb8fdee 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -20,6 +20,9 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#ifndef INTRO_ALPHA_COMPLEX_H_
+#define INTRO_ALPHA_COMPLEX_H_
+
 // needs namespace for Doxygen to link on classes
 namespace Gudhi {
 // needs namespace for Doxygen to link on classes
@@ -117,3 +120,5 @@ namespace alphacomplex {
 } // namespace alphacomplex
 
 } // namespace Gudhi
+
+#endif  // INTRO_ALPHA_COMPLEX_H_
diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
index e140fe3d..cd6f5a4b 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
@@ -25,7 +25,7 @@ int main(int argc, char **argv) {
   // ----------------------------------------------------------------------------
   typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
   Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name, alpha_square_max_value);
-
+  
   // ----------------------------------------------------------------------------
   // Display information about the alpha complex
   // ----------------------------------------------------------------------------
@@ -35,14 +35,14 @@ int main(int argc, char **argv) {
 
   std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
   for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
-    if (alpha_complex_from_file.filtration(f_simplex) <= alpha_complex_from_file.filtration()) {
+    //if (alpha_complex_from_file.filtration(f_simplex) <= alpha_complex_from_file.filtration()) {
       std::cout << "   ( ";
       for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) {
         std::cout << vertex << " ";
       }
       std::cout << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] ";
       std::cout << std::endl;
-    }
+    //}
   }
   return 0;
 }
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index 10b87f04..24f3a9dc 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -1,6 +1,8 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHIAlphaShapesExample)
 
+add_executable ( flat flat.cpp )
+
 # need CGAL 4.7
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
 if(CGAL_FOUND)
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index 562b80c3..10b290b5 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -105,6 +105,7 @@ class Alpha_complex : public Simplex_tree<> {
    * the Alpha_complex.
    *
    * @param[in] off_file_name OFF file [path and] name.
+   * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$.
    */
   Alpha_complex(const std::string& off_file_name,
                 Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity())
@@ -115,25 +116,24 @@ class Alpha_complex : public Simplex_tree<> {
       exit(-1);  // ----- >>
     }
     triangulation_ = off_reader.get_complex();
-    set_filtration(max_alpha_square);
-    init();
+    init(max_alpha_square);
   }
 
   /** \brief Alpha_complex constructor from a Delaunay triangulation.
    *
    * @param[in] triangulation_ptr Pointer on a Delaunay triangulation.
+   * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$.
    */
   Alpha_complex(Delaunay_triangulation* triangulation_ptr,
                 Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity())
       : triangulation_(triangulation_ptr) {
-   set_filtration(max_alpha_square);
-   init();
+   init(max_alpha_square);
   }
 
   /** \brief Alpha_complex constructor from a list of points.
    *
-   * @param[in] dimension Dimension of points to be inserted.
    * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d
+   * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$.
    * 
    * The type InputPointRange must be a range for which std::begin and
    * std::end return input iterators on a Kernel::Point_d.
@@ -155,8 +155,7 @@ class Alpha_complex : public Simplex_tree<> {
       std::cerr << "Alpha_complex - insertion failed " << inserted << " != " << (last -first) << std::endl;
       exit(-1);  // ----- >>
     }
-    set_filtration(max_alpha_square);
-    init();
+    init(max_alpha_square);
   }
 
   /** \brief Alpha_complex destructor from a Delaunay triangulation.
@@ -180,12 +179,14 @@ class Alpha_complex : public Simplex_tree<> {
  private:
   /** \brief Initialize the Alpha_complex from the Delaunay triangulation.
    *
+   * @param[in] max_alpha_square maximum for alpha square value.
+   * 
    * @warning Delaunay triangulation must be already constructed with at least one vertex and dimension must be more 
    * than 0.
    * 
    * Initialization can be launched once.
    */
-  void init() {
+  void init(Filtration_value max_alpha_square) {
     if (triangulation_ == nullptr) {
       std::cerr << "Alpha_complex init - Cannot init from a NULL triangulation" << std::endl;
       return;  // ----- >>
@@ -287,6 +288,13 @@ class Alpha_complex : public Simplex_tree<> {
       }
     }
     // --------------------------------------------------------------------------------------------
+
+    // --------------------------------------------------------------------------------------------
+    // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension
+    make_filtration_non_decreasing();
+    // Remove all simplices that have a filtration value greater than max_alpha_square
+    prune_above_filtration(max_alpha_square);
+    // --------------------------------------------------------------------------------------------
   }
 
   template<typename Simplex_handle>
diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
index f64a8ea9..2912019d 100644
--- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -88,20 +88,9 @@ BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file_filtered) {
   std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl;
   BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES);
 
-  const int NUMBER_OF_SIMPLICES = 25;
+  const int NUMBER_OF_SIMPLICES = 23;
   std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
   BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
-
-  int num_filtered_simplices = 0;
-  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
-    if (alpha_complex_from_file.filtration(f_simplex) <= alpha_complex_from_file.filtration()) {
-      num_filtered_simplices++;
-    }
-  }
-  const int NUMBER_OF_FILTERED_SIMPLICES = 23;
-  std::cout << "num_filtered_simplices=" << num_filtered_simplices << std::endl;
-  BOOST_CHECK(num_filtered_simplices == NUMBER_OF_FILTERED_SIMPLICES);
-
 }
 
 bool are_almost_the_same(float a, float b) {
@@ -140,8 +129,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   // ----------------------------------------------------------------------------
   // Init of an alpha complex from the list of points
   // ----------------------------------------------------------------------------
-  double max_alpha_square_value = 1e10;
-  Gudhi::alphacomplex::Alpha_complex<Kernel_s> alpha_complex_from_points(points, max_alpha_square_value);
+  Gudhi::alphacomplex::Alpha_complex<Kernel_s> alpha_complex_from_points(points);
 
   std::cout << "========== Alpha_complex_from_points ==========" << std::endl;
 
@@ -210,4 +198,42 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   BOOST_CHECK_THROW (alpha_complex_from_points.get_point(4), std::out_of_range);
   BOOST_CHECK_THROW (alpha_complex_from_points.get_point(-1), std::out_of_range);
   BOOST_CHECK_THROW (alpha_complex_from_points.get_point(1234), std::out_of_range);
+  
+  // Test after prune_above_filtration
+  alpha_complex_from_points.prune_above_filtration(0.6);
+  // Another way to check num_simplices
+  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  num_simplices = 0;
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    num_simplices++;
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  BOOST_CHECK(num_simplices == 10);
+  std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_simplices() == 10);
+
+  std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.dimension() == 4);
+  std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4);
+
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    switch (alpha_complex_from_points.dimension(f_simplex)) {
+      case 0:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0));
+        break;
+      case 1:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0));
+        break;
+      default:
+        BOOST_CHECK(false);  // Shall not happen
+        break;
+    }
+  }
+
 }