Commited Marc's remarks

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@1017 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: d87eb82f60f4f943f59622f33521bcdce7873091

7 files changed, 23 insertions, 41 deletions

diff --git a/src/Witness_complex/concept/Simplicial_complex.h b/src/Witness_complex/concept/Simplicial_complex.h
index d7f3496d..9e9f2ff8 100644
--- a/src/Witness_complex/concept/Simplicial_complex.h
+++ b/src/Witness_complex/concept/Simplicial_complex.h
@@ -40,16 +40,11 @@ struct Simplicial_complex {
   /** Returns a Simplex_hanlde that is different from all simplex handles 
    * of the simplices. */
   Simplex_handle null_simplex();
-  /** \brief Returns the number of simplices in the complex.
-   *
-   * Does not count the empty simplex. */
-  size_t num_simplices();
 
   /** \brief Iterator over the simplices of the complex,
    * in an arbitrary order.
    *
    * 'value_type' must be 'Simplex_handle'.*/
-  typedef unspecified Complex_simplex_iterator;
   typedef unspecified Complex_simplex_range;
 
   /**
@@ -71,19 +66,17 @@ struct Simplicial_complex {
    */
   typedef unspecified Insertion_result_type;
 
-  /** \brief Input range of vertices.
-   * 'value_type' must be 'Vertex_handle'. */
-  typedef unspecified Input_vertex_range;
-
   /** \brief Inserts a simplex with vertices from a given range
    *  'vertex_range' in the simplicial complex.
    *  */
+  template< typedef Input_vertex_range >
   Insertion_result_type insert_simplex(Input_vertex_range const & vertex_range);
 
   /** \brief Finds a simplex with vertices given by a range
    *
    * If a simplex exists, its Simplex_handle is returned.
    * Otherwise null_simplex() is returned. */
+  template< typedef Input_vertex_range >
   Simplex_handle find(Input_vertex_range const & vertex_range);
 };
 
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
index 77109512..98d1fe9c 100644
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -68,17 +68,6 @@ read_points_cust(std::string file_name, std::vector< std::vector< double > > & p
   in_file.close();
 }
 
-/** Write a gnuplot readable file.
- *  Data range is a random access range of pairs (arg, value)
- */
-template < typename Data_range >
-void write_data(Data_range & data, std::string filename) {
-  std::ofstream ofs(filename, std::ofstream::out);
-  for (auto entry : data)
-    ofs << entry.first << ", " << entry.second << "\n";
-  ofs.close();
-}
-
 int main(int argc, char * const argv[]) {
   if (argc != 3) {
     std::cerr << "Usage: " << argv[0]
@@ -109,7 +98,7 @@ int main(int argc, char * const argv[]) {
 
   // Compute witness complex
   start = clock();
-  WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+  WitnessComplex(knn, nbL, point_vector[0].size(), simplex_tree);
   end = clock();
   std::cout << "Witness complex took "
       << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
index f9d0b5a2..fae80d67 100644
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -60,11 +60,11 @@ void write_data(Data_range & data, std::string filename) {
 int main(int argc, char * const argv[]) {
   if (argc != 2) {
     std::cerr << "Usage: " << argv[0]
-        << " nbL \n";
+        << " number_of_landmarks \n";
     return 0;
   }
 
-  int nbL = atoi(argv[1]);
+  int number_of_landmarks = atoi(argv[1]);
   clock_t start, end;
 
   // Construct the Simplex Tree
@@ -82,13 +82,13 @@ int main(int argc, char * const argv[]) {
     // Choose landmarks
     start = clock();
     std::vector<std::vector< int > > knn;
-    Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, nbL, knn);
+    Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, number_of_landmarks, knn);
 
     // Compute witness complex
-    WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+    WitnessComplex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree);
     end = clock();
     double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
-    std::cout << "Witness complex for " << nbL << " landmarks took "
+    std::cout << "Witness complex for " << number_of_landmarks << " landmarks took "
         << time << " s. \n";
     std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
     l_time.push_back(std::make_pair(nbP, time));
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
index dc364007..617c0258 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
@@ -35,6 +35,12 @@ namespace witness_complex {
   /** \brief Landmark choice strategy by taking random vertices for landmarks.
    *  \details It chooses nbL distinct landmarks from a random access range `points`
    *  and outputs a matrix {witness}*{closest landmarks} in knn.
+   *
+   *  The type KNearestNeighbors can be seen as 
+   *  Witness_range<Closest_landmark_range<Vertex_handle>>, where
+   *  Witness_range and Closest_landmark_range are random access ranges and
+   *  Vertex_handle is the label type of a vertex in a simplicial complex.
+   *  Closest_landmark_range needs to have push_back operation.
    */
 
   template <typename KNearestNeighbours,
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index 34cbc882..3e14a623 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -71,7 +71,6 @@ class Witness_complex {
   typedef std::vector< double > Point_t;
   typedef std::vector< Point_t > Point_Vector;
 
-  // typedef typename Simplicial_complex::Filtration_value Filtration_value;
   typedef std::vector< Vertex_handle > typeVectorVertex;
   typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex;
   typedef std::pair< Simplex_handle, bool > typePairSimplexBool;
@@ -109,9 +108,9 @@ class Witness_complex {
    */
   template< typename KNearestNeighbors >
   Witness_complex(KNearestNeighbors const & knn,
-                  Simplicial_complex & sc_,
                   int nbL_,
-                  int dim) : nbL(nbL_), sc(sc_) {
+                  int dim,
+                  Simplicial_complex & sc_) : nbL(nbL_), sc(sc_) {
     // Construction of the active witness list
     int nbW = knn.size();
     typeVectorVertex vv;
@@ -120,7 +119,7 @@ class Witness_complex {
      * it will diminuish in the course of iterations
      */
     ActiveWitnessList active_w;  // = new ActiveWitnessList();
-    for (int i = 0; i != nbL; ++i) {
+    for (Vertex_handle i = 0; i != nbL; ++i) {
       // initial fill of 0-dimensional simplices
       // by doing it we don't assume that landmarks are necessarily witnesses themselves anymore
       counter++;
@@ -131,9 +130,7 @@ class Witness_complex {
     int k = 1; /* current dimension in iterative construction */
     for (int i = 0; i != nbW; ++i)
       active_w.push_back(i);
-    // std::cout << "Successfully added edges" << std::endl;
     while (!active_w.empty() && k < dim) {
-      // std::cout << "Started the step k=" << k << std::endl;
       typename ActiveWitnessList::iterator it = active_w.begin();
       while (it != active_w.end()) {
         typeVectorVertex simplex_vector;
@@ -142,7 +139,7 @@ class Witness_complex {
         if (ok) {
           for (int i = 0; i != k + 1; ++i)
             simplex_vector.push_back(knn[*it][i]);
-          sc.insert_simplex(simplex_vector, 0.0);
+          sc.insert_simplex(simplex_vector);
           // TODO(SK) Error if not inserted : normally no need here though
           it++;
         } else {
@@ -162,9 +159,7 @@ class Witness_complex {
    */
   template <typename KNearestNeighbors>
   bool all_faces_in(KNearestNeighbors const &knn, int witness_id, int k) {
-    // std::cout << "All face in with the landmark " << inserted_vertex << std::endl;
     std::vector< Vertex_handle > facet;
-    // Vertex_handle curr_vh = curr_sh->first;
     // CHECK ALL THE FACETS
     for (int i = 0; i != k + 1; ++i) {
       facet = {};
@@ -175,7 +170,6 @@ class Witness_complex {
       }  // endfor
       if (sc.find(facet) == sc.null_simplex())
         return false;
-      // std::cout << "++++ finished loop safely\n";
     }  // endfor
     return true;
   }
@@ -206,12 +200,12 @@ class Witness_complex {
       bool is_witnessed = false;
       typeVectorVertex simplex;
       int nbV = 0;  // number of verticed in the simplex
-      for (int v : sc.simplex_vertex_range(sh))
+      for (Vertex_handle v : sc.simplex_vertex_range(sh))
         simplex.push_back(v);
       nbV = simplex.size();
       for (typeVectorVertex w : knn) {
         bool has_vertices = true;
-        for (int v : simplex)
+        for (Vertex_handle v : simplex)
           if (std::find(w.begin(), w.begin() + nbV, v) == w.begin() + nbV) {
             has_vertices = false;
             // break;
diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp
index 7d44b90c..03df78ee 100644
--- a/src/Witness_complex/test/simple_witness_complex.cpp
+++ b/src/Witness_complex/test/simple_witness_complex.cpp
@@ -53,7 +53,7 @@ BOOST_AUTO_TEST_CASE(simple_witness_complex) {
   knn.push_back({5, 0, 1, 3, 6, 2, 4});
   knn.push_back({5, 6, 1, 0, 2, 3, 4});
   knn.push_back({1, 6, 0, 5, 2, 3, 4});
-  WitnessComplex witnessComplex(knn, complex, 7, 7);
+  WitnessComplex witnessComplex(knn, 7, 7, complex);
 
   BOOST_CHECK(witnessComplex.is_witness_complex(knn, false));
 }
diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp
index cb1639e1..bd3df604 100644
--- a/src/Witness_complex/test/witness_complex_points.cpp
+++ b/src/Witness_complex/test/witness_complex_points.cpp
@@ -52,13 +52,13 @@ BOOST_AUTO_TEST_CASE(witness_complex_points) {
   Simplex_tree complex1;
   Gudhi::witness_complex::landmark_choice_by_random_point(points, 100, knn);
   assert(!knn.empty());
-  WitnessComplex witnessComplex1(knn, complex1, 100, 3);
+  WitnessComplex witnessComplex1(knn, 100, 3, complex1);
   BOOST_CHECK(witnessComplex1.is_witness_complex(knn, b_print_output));
 
   // Second test: furthest choice
   knn.clear();
   Simplex_tree complex2;
   Gudhi::witness_complex::landmark_choice_by_furthest_point(points, 100, knn);
-  WitnessComplex witnessComplex2(knn, complex2, 100, 3);
+  WitnessComplex witnessComplex2(knn, 100, 3, complex2);
   BOOST_CHECK(witnessComplex2.is_witness_complex(knn, b_print_output));
 }