diff options
author | skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-02-11 16:05:15 +0000 |
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committer | skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-02-11 16:05:15 +0000 |
commit | b7796215d4eac6b4c43ad70998c3737a6527eebb (patch) | |
tree | ef35441548725cb5aa1266fb93f9bf344fb2798f /src | |
parent | 2d8cc490a799d991fee29d923c15368c83d24f85 (diff) |
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
Diffstat (limited to 'src')
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)); } |