diff options
Diffstat (limited to 'src/Alpha_complex')
-rw-r--r-- | src/Alpha_complex/example/Alpha_complex_from_off.cpp | 14 | ||||
-rw-r--r-- | src/Alpha_complex/example/alphaoffreader_for_doc.txt | 38 | ||||
-rw-r--r-- | src/Alpha_complex/include/gudhi/Alpha_complex.h | 202 | ||||
-rw-r--r-- | src/Alpha_complex/test/Alpha_complex_unit_test.cpp | 145 | ||||
-rw-r--r-- | src/Alpha_complex/test/S4_100.off | 102 | ||||
-rw-r--r-- | src/Alpha_complex/test/S8_10.off | 12 |
6 files changed, 131 insertions, 382 deletions
diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp index 3ce4c7f4..b698d6d7 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -10,7 +10,7 @@ void usage(char * const progName) { std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value" << std::endl; std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0" << std::endl; - exit(-1); // ----- >> + exit(-1); // ----- >> } int main(int argc, char **argv) { @@ -37,12 +37,14 @@ 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()) { - std::cout << " ( "; - for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) { - std::cout << vertex << " "; + 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; } - std::cout << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] "; - std::cout << std::endl; } return 0; } diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc.txt b/src/Alpha_complex/example/alphaoffreader_for_doc.txt index 1153f097..71f29a00 100644 --- a/src/Alpha_complex/example/alphaoffreader_for_doc.txt +++ b/src/Alpha_complex/example/alphaoffreader_for_doc.txt @@ -1,27 +1,27 @@ Alpha complex is of dimension 2 - 25 simplices - 7 vertices. Iterator on alpha complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] ( 1 ) -> [0] ( 2 ) -> [0] ( 3 ) -> [0] ( 4 ) -> [0] ( 5 ) -> [0] ( 6 ) -> [0] - ( 7 ) -> [0] - ( 4 3 ) -> [6.25] - ( 6 5 ) -> [7.25] - ( 3 1 ) -> [8.5] - ( 2 1 ) -> [9.25] - ( 4 2 ) -> [10] - ( 3 2 ) -> [11.25] - ( 4 3 2 ) -> [12.5] - ( 3 2 1 ) -> [12.9959] - ( 7 6 ) -> [13.25] - ( 5 3 ) -> [20] - ( 7 5 ) -> [22.7367] - ( 7 6 5 ) -> [22.7367] - ( 7 4 ) -> [30.25] - ( 7 3 ) -> [36.5] - ( 7 4 3 ) -> [36.5] - ( 7 5 3 ) -> [37.2449] - ( 5 1 ) -> [59.7107] - ( 5 3 1 ) -> [59.7107] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] + ( 6 2 ) -> [36.5] + ( 6 3 2 ) -> [36.5] + ( 6 4 2 ) -> [37.2449] + ( 4 0 ) -> [59.7107] + ( 4 2 0 ) -> [59.7107] diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 213436e0..518d1792 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -99,8 +99,6 @@ class Alpha_complex : public Simplex_tree<> { Delaunay_triangulation* triangulation_; /** \brief Kernel for triangulation_ functions access.*/ Kernel kernel_; - /** \brief Maximum value for alpha square.*/ - Filtration_value max_alpha_square_; public: /** \brief Alpha_complex constructor from an OFF file name. @@ -110,14 +108,14 @@ class Alpha_complex : public Simplex_tree<> { * @param[in] off_file_name OFF file [path and] name. */ Alpha_complex(const std::string& off_file_name, Filtration_value max_alpha_square) - : triangulation_(nullptr), - max_alpha_square_(max_alpha_square) { + : triangulation_(nullptr) { Gudhi::Delaunay_triangulation_off_reader<Delaunay_triangulation> off_reader(off_file_name); if (!off_reader.is_valid()) { std::cerr << "Alpha_complex - Unable to read file " << off_file_name << std::endl; exit(-1); // ----- >> } triangulation_ = off_reader.get_complex(); + set_filtration(max_alpha_square); init(); } @@ -126,9 +124,9 @@ class Alpha_complex : public Simplex_tree<> { * @param[in] triangulation_ptr Pointer on a Delaunay triangulation. */ Alpha_complex(Delaunay_triangulation* triangulation_ptr, Filtration_value max_alpha_square) - : triangulation_(triangulation_ptr), - max_alpha_square_(max_alpha_square) { - init(); + : triangulation_(triangulation_ptr) { + set_filtration(max_alpha_square); + init(); } /** \brief Alpha_complex constructor from a list of points. @@ -143,14 +141,14 @@ class Alpha_complex : public Simplex_tree<> { template<typename ForwardIterator > Alpha_complex(int dimension, size_type size, ForwardIterator firstPoint, ForwardIterator lastPoint, Filtration_value max_alpha_square) - : triangulation_(nullptr), - max_alpha_square_(max_alpha_square) { + : triangulation_(nullptr) { triangulation_ = new Delaunay_triangulation(dimension); size_type inserted = triangulation_->insert(firstPoint, lastPoint); if (inserted != size) { std::cerr << "Alpha_complex - insertion failed " << inserted << " != " << size << std::endl; exit(-1); // ----- >> } + set_filtration(max_alpha_square); init(); } @@ -169,8 +167,9 @@ class Alpha_complex : public Simplex_tree<> { * @warning Exception std::out_of_range is thrown in case vertex is not in the map vertex_handle_to_iterator_. */ Point_d get_point(Vertex_handle vertex) { - if (vertex_handle_to_iterator_[vertex] != nullptr) { - return vertex_handle_to_iterator_[vertex]->point(); + auto found_it = vertex_handle_to_iterator_.find(vertex); + if (found_it != vertex_handle_to_iterator_.end()) { + return found_it->second->point(); } else { throw std::out_of_range("Vertex out of vector range"); } @@ -210,20 +209,21 @@ class Alpha_complex : public Simplex_tree<> { Vertex_handle vertex_handle = Vertex_handle(); // Loop on triangulation vertices list for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) { + if (!triangulation_->is_infinite(*vit)) { #ifdef DEBUG_TRACES - std::cout << "Vertex insertion - " << vertex_handle << " -> " << vit->point() << std::endl; + std::cout << "Vertex insertion - " << vertex_handle << " -> " << vit->point() << std::endl; #endif // DEBUG_TRACES - vertex_iterator_to_handle_[vit] = vertex_handle; - vertex_handle_to_iterator_[vertex_handle] = vit; - vertex_handle++; + vertex_iterator_to_handle_.emplace(vit, vertex_handle); + vertex_handle_to_iterator_.emplace(vertex_handle, vit); + vertex_handle++; + } } // -------------------------------------------------------------------------------------------- - Filtration_value filtration_max = 0.0; // -------------------------------------------------------------------------------------------- // Simplex_tree construction from loop on triangulation finite full cells list for (auto cit = triangulation_->finite_full_cells_begin(); cit != triangulation_->finite_full_cells_end(); ++cit) { - Vector_vertex vertex_full_cell; + Vector_vertex vertexVector; #ifdef DEBUG_TRACES std::cout << "Simplex_tree insertion "; #endif // DEBUG_TRACES @@ -233,149 +233,98 @@ class Alpha_complex : public Simplex_tree<> { std::cout << " " << vertex_iterator_to_handle_[*vit]; #endif // DEBUG_TRACES // Vector of vertex construction for simplex_tree structure - vertex_full_cell.push_back(vertex_iterator_to_handle_[*vit]); + vertexVector.push_back(vertex_iterator_to_handle_[*vit]); } } #ifdef DEBUG_TRACES std::cout << std::endl; #endif // DEBUG_TRACES - - Simplex_tree<> full_cell; - full_cell.set_dimension(triangulation_->maximal_dimension()); - // Create a simplex tree containing only one of the full cells - Simplex_result insert_result = full_cell.insert_simplex_and_subfaces(vertex_full_cell); + // Insert each simplex and its subfaces in the simplex tree - filtration is NaN + Simplex_result insert_result = insert_simplex_and_subfaces(vertexVector, + std::numeric_limits<double>::quiet_NaN()); if (!insert_result.second) { std::cerr << "Alpha_complex::init insert_simplex_and_subfaces failed" << std::endl; exit(-1); // ----->> } - // +++ For i : d -> 0 - for (int fc_decr_dim = full_cell.dimension(); (fc_decr_dim >= 0); fc_decr_dim--) { - // +++ Foreach Sigma of dim i - // No need to skip this loop in case alpha²(Sigma) > max_alpha_square_ because of - // if (fc_decr_dim == f_simplex_dim) which means "only for a full cell" - for (auto fc_simplex : full_cell.skeleton_simplex_range(fc_decr_dim)) { - int f_simplex_dim = full_cell.dimension(fc_simplex); - if (fc_decr_dim == f_simplex_dim) { - Vector_of_CGAL_points pointVector; - Vector_vertex current_vertex; -#ifdef DEBUG_TRACES - std::cout << "Sigma of dim " << fc_decr_dim << " is"; -#endif // DEBUG_TRACES - for (auto vertex : full_cell.simplex_vertex_range(fc_simplex)) { - pointVector.push_back(get_point(vertex)); - current_vertex.push_back(vertex); -#ifdef DEBUG_TRACES - std::cout << " " << vertex; -#endif // DEBUG_TRACES - } + } + // -------------------------------------------------------------------------------------------- + + // -------------------------------------------------------------------------------------------- + // ### For i : d -> 0 + for (int decr_dim = dimension(); decr_dim >= 0; decr_dim--) { + // ### Foreach Sigma of dim i + for (auto f_simplex : skeleton_simplex_range(decr_dim)) { + int f_simplex_dim = dimension(f_simplex); + if (decr_dim == f_simplex_dim) { + Vector_of_CGAL_points pointVector; #ifdef DEBUG_TRACES - std::cout << std::endl; + std::cout << "Sigma of dim " << decr_dim << " is"; #endif // DEBUG_TRACES - Simplex_handle sigma_handle = find(current_vertex); - bool skip_propagation = false; - // +++ If filt(Sigma) is NaN : filt(Sigma) = alpha²(Sigma) - if ((sigma_handle == null_simplex()) || isnan(filtration(sigma_handle))) { - Filtration_value alpha_complex_filtration = compute_alpha_square(pointVector.begin(), pointVector.end(), - f_simplex_dim); - if (alpha_complex_filtration <= max_alpha_square_) { - // Only insert Sigma in Simplex tree if alpha²(Sigma) <= max_alpha_square_ - if (sigma_handle == null_simplex()) { + for (auto vertex : simplex_vertex_range(f_simplex)) { + pointVector.push_back(get_point(vertex)); #ifdef DEBUG_TRACES - std::cout << "Alpha_complex::init Sigma not found" << std::endl; + std::cout << " " << vertex; #endif // DEBUG_TRACES - insert_result = insert_simplex(current_vertex, std::numeric_limits<double>::quiet_NaN()); - if (!insert_result.second) { - std::cerr << "Alpha_complex::init insert_simplex failed" << std::endl; - exit(-1); // ----->> - } - // Sigma is the new inserted simplex handle - sigma_handle = insert_result.first; - } + } #ifdef DEBUG_TRACES - std::cout << "Alpha_complex::init filtration = " << alpha_complex_filtration << std::endl; + std::cout << std::endl; #endif // DEBUG_TRACES - assign_filtration(sigma_handle, alpha_complex_filtration); - filtration_max = fmax(filtration_max, alpha_complex_filtration); - } else { - // if alpha²(Sigma) > max_alpha_square_ skip propagation - skip_propagation = true; + // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma) + if (isnan(filtration(f_simplex))) { + Filtration_value alpha_complex_filtration = 0.0; + // No need to compute squared_radius on a single point - alpha is 0.0 + if (f_simplex_dim > 0) { + // squared_radius function initialization + Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object(); + + alpha_complex_filtration = squared_radius(pointVector.begin(), pointVector.end()); + } + assign_filtration(f_simplex, alpha_complex_filtration); #ifdef DEBUG_TRACES - std::cout << "Alpha_complex::init skip propagation on this full cell" << std::endl; + std::cout << "filt(Sigma) is NaN : filt(Sigma) =" << filtration(f_simplex) << std::endl; #endif // DEBUG_TRACES - } - } // --- If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma) - if ((filtration(sigma_handle) <= max_alpha_square_) && !skip_propagation) { - // Propagate alpha filtration value in Simplex tree if alpha²(Sigma) <= max_alpha_square_ - // in case Sigma is not found AND not inserted (alpha_complex_filtration > max_alpha_square_), - // filtration(null_simplex()) returns INFINITY => no propagation - propagate_alpha_filtration(full_cell, fc_simplex, fc_decr_dim, sigma_handle); - } } - } // --- Foreach Sigma of dim i - } // --- For i : d -> 0 + propagate_alpha_filtration(f_simplex, decr_dim); + } + } } // -------------------------------------------------------------------------------------------- - -#ifdef DEBUG_TRACES - std::cout << "filtration_max=" << filtration_max << std::endl; -#endif // DEBUG_TRACES - set_filtration(filtration_max); - } - - template<typename ForwardIterator > - Filtration_value compute_alpha_square(ForwardIterator firstPoint, ForwardIterator lastPoint, int f_simplex_dim) { - Filtration_value alpha_square_value = 0.0; - // No need to compute squared_radius on a single point - alpha is 0.0 - if (f_simplex_dim > 0) { - // squared_radius function initialization - Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object(); - - alpha_square_value = squared_radius(firstPoint, lastPoint); - } - return alpha_square_value; } - void propagate_alpha_filtration(Simplex_tree& full_cell, Simplex_handle fc_simplex, int fc_decr_dim, - Simplex_handle sigma_handle) { + template<typename Simplex_handle> + void propagate_alpha_filtration(Simplex_handle f_simplex, int decr_dim) { // ### Foreach Tau face of Sigma - for (auto f_boundary : full_cell.boundary_simplex_range(fc_simplex)) { + for (auto f_boundary : boundary_simplex_range(f_simplex)) { #ifdef DEBUG_TRACES std::cout << " | --------------------------------------------------" << std::endl; std::cout << " | Tau "; -#endif // DEBUG_TRACES - Vector_vertex tau_vertex; - for (auto vertex : full_cell.simplex_vertex_range(f_boundary)) { - tau_vertex.push_back(vertex); -#ifdef DEBUG_TRACES + for (auto vertex : simplex_vertex_range(f_boundary)) { std::cout << vertex << " "; -#endif // DEBUG_TRACES } -#ifdef DEBUG_TRACES std::cout << "is a face of Sigma" << std::endl; + std::cout << " | isnan(filtration(Tau)=" << isnan(filtration(f_boundary)) << std::endl; #endif // DEBUG_TRACES - Simplex_handle tau_handle = find(tau_vertex); // ### If filt(Tau) is not NaN - - if ((tau_handle != null_simplex()) && (!isnan(filtration(tau_handle)))) { + if (!isnan(filtration(f_boundary))) { // ### filt(Tau) = fmin(filt(Tau), filt(Sigma)) - Filtration_value alpha_complex_filtration = fmin(filtration(tau_handle), filtration(sigma_handle)); - assign_filtration(tau_handle, alpha_complex_filtration); - // No need to check for filtration_max, alpha_complex_filtration is a min of an existing filtration value + Filtration_value alpha_complex_filtration = fmin(filtration(f_boundary), filtration(f_simplex)); + assign_filtration(f_boundary, alpha_complex_filtration); #ifdef DEBUG_TRACES - std::cout << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << alpha_complex_filtration << std::endl; + std::cout << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << filtration(f_boundary) << std::endl; #endif // DEBUG_TRACES + // ### Else } else { // No need to compute is_gabriel for dimension <= 2 // i.e. : Sigma = (3,1) => Tau = 1 - if (fc_decr_dim > 1) { + if (decr_dim > 1) { // insert the Tau points in a vector for is_gabriel function Vector_of_CGAL_points pointVector; Vertex_handle vertexForGabriel = Vertex_handle(); - for (auto vertex : full_cell.simplex_vertex_range(f_boundary)) { + for (auto vertex : simplex_vertex_range(f_boundary)) { pointVector.push_back(get_point(vertex)); } // Retrieve the Sigma point that is not part of Tau - parameter for is_gabriel function - for (auto vertex : simplex_vertex_range(sigma_handle)) { + for (auto vertex : simplex_vertex_range(f_simplex)) { if (std::find(pointVector.begin(), pointVector.end(), get_point(vertex)) == pointVector.end()) { // vertex is not found in Tau vertexForGabriel = vertex; @@ -392,24 +341,11 @@ class Alpha_complex : public Simplex_tree<> { #endif // DEBUG_TRACES // ### If Tau is not Gabriel of Sigma if (false == is_gab) { - if (tau_handle == null_simplex()) { -#ifdef DEBUG_TRACES - std::cout << " | Tau not found" << std::endl; -#endif // DEBUG_TRACES - // in case Tau is not yet created - Simplex_result insert_result = insert_simplex(tau_vertex, std::numeric_limits<double>::quiet_NaN()); - if (!insert_result.second) { - std::cerr << "Alpha_complex::propagate_alpha_filtration insert_simplex failed" << std::endl; - exit(-1); // ----->> - } - // Sigma is the new inserted simplex handle - tau_handle = insert_result.first; - } // ### filt(Tau) = filt(Sigma) - assign_filtration(tau_handle, filtration(sigma_handle)); - // No need to check for filtration_max, alpha_complex_filtration is an existing filtration value + Filtration_value alpha_complex_filtration = filtration(f_simplex); + assign_filtration(f_boundary, alpha_complex_filtration); #ifdef DEBUG_TRACES - std::cout << " | filt(Tau) = filt(Sigma) = " << filtration(sigma_handle) << std::endl; + std::cout << " | filt(Tau) = filt(Sigma) = " << filtration(f_boundary) << std::endl; #endif // DEBUG_TRACES } } diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp index c15f07e1..b2597eff 100644 --- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -40,144 +40,68 @@ typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d; // The triangulation uses the default instantiation of the TriangulationDataStructure template parameter -BOOST_AUTO_TEST_CASE(S4_100_OFF_file) { +BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file) { // ---------------------------------------------------------------------------- // // Init of an alpha-complex from a OFF file // // ---------------------------------------------------------------------------- - std::string off_file_name("S4_100.off"); - double max_alpha_square_value = 1e10; - std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" << - max_alpha_square_value << "==========" << std::endl; - - Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value); - - const int DIMENSION = 4; - std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl; - BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION); - - const int NUMBER_OF_VERTICES = 100; - 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 = 6879; - std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl; - // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES); - - // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [ - int num_simplices = 0; - for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) { - num_simplices++; - } - std::cout << "num_simplices=" << num_simplices << std::endl; - BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES); - // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ] -} - -BOOST_AUTO_TEST_CASE(S4_100_OFF_file_filtered) { - // ---------------------------------------------------------------------------- - // - // Init of an alpha-complex from a OFF file - // - // ---------------------------------------------------------------------------- - std::string off_file_name("S4_100.off"); - double max_alpha_square_value = 0.999; + std::string off_file_name("../../../data/points/alphacomplexdoc.off"); + double max_alpha_square_value = 60.0; std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" << max_alpha_square_value << "==========" << std::endl; Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value); - const int DIMENSION = 4; + const int DIMENSION = 2; std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl; BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION); - const int NUMBER_OF_VERTICES = 100; + const int NUMBER_OF_VERTICES = 7; 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 = 5966; // Versus 6879, because of filtered alpha value + const int NUMBER_OF_SIMPLICES = 25; std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl; - // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES); + BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES); - // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [ - int num_simplices = 0; - for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) { - num_simplices++; - } - std::cout << "num_simplices=" << num_simplices << std::endl; - BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES); - // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ] } -BOOST_AUTO_TEST_CASE(S8_10_OFF_file) { +BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file_filtered) { // ---------------------------------------------------------------------------- // // Init of an alpha-complex from a OFF file // // ---------------------------------------------------------------------------- - std::string off_file_name("S8_10.off"); - double max_alpha_square_value = 1e10; + std::string off_file_name("../../../data/points/alphacomplexdoc.off"); + double max_alpha_square_value = 59.0; std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" << max_alpha_square_value << "==========" << std::endl; Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value); - const int DIMENSION = 8; + const int DIMENSION = 2; std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl; BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION); - const int NUMBER_OF_VERTICES = 10; + const int NUMBER_OF_VERTICES = 7; 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 = 1007; + const int NUMBER_OF_SIMPLICES = 25; std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl; - // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES); + BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES); - // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [ - int num_simplices = 0; + int num_filtered_simplices = 0; for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) { - num_simplices++; + if (alpha_complex_from_file.filtration(f_simplex) <= alpha_complex_from_file.filtration()) { + num_filtered_simplices++; + } } - std::cout << "num_simplices=" << num_simplices << std::endl; - BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES); - // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ] -} - -BOOST_AUTO_TEST_CASE(S8_10_OFF_file_filtered) { - // ---------------------------------------------------------------------------- - // - // Init of an alpha-complex from a OFF file - // - // ---------------------------------------------------------------------------- - std::string off_file_name("S8_10.off"); - double max_alpha_square_value = 1.0; - std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" << - max_alpha_square_value << "==========" << std::endl; - - Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value); - - const int DIMENSION = 8; - std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl; - BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION); - - const int NUMBER_OF_VERTICES = 10; - 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 = 1004; // Versus 1007, because of filtered alpha value - std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl; - // TODO(VR) : BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_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); - // + TODO(VR) : in wait of num_simplices fix in Simplex_tree [ - int num_simplices = 0; - for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) { - num_simplices++; - } - std::cout << "num_simplices=" << num_simplices << std::endl; - BOOST_CHECK(num_simplices == NUMBER_OF_SIMPLICES); - // - TODO(VR) : in wait of num_simplices fix in Simplex_tree ] } bool are_almost_the_same(float a, float b) { @@ -222,10 +146,11 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { std::cout << "========== Alpha_complex_from_points ==========" << std::endl; + // Another way to check num_simplices std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; - int num_simplices = 0; // TODO(VR) : in wait of num_simplices fix in Simplex_tree + int num_simplices = 0; for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) { - num_simplices++; // TODO(VR) : in wait of num_simplices fix in Simplex_tree + num_simplices++; std::cout << " ( "; for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) { std::cout << vertex << " "; @@ -233,13 +158,12 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] "; std::cout << std::endl; } + BOOST_CHECK(num_simplices == 15); + std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl; + BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15); std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl; BOOST_CHECK(alpha_complex_from_points.dimension() == 4); - // TODO(VR) : std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() - // << std::endl; - // TODO(VR) : BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15); - BOOST_CHECK(num_simplices == 15); // TODO(VR) : in wait of num_simplices fix in Simplex_tree 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); @@ -263,6 +187,11 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { } } + Point p0 = alpha_complex_from_points.get_point(0); + std::cout << "alpha_complex_from_points.get_point(0)=" << p0 << std::endl; + BOOST_CHECK(4 == p0.dimension()); + BOOST_CHECK(is_point_in_list(points, p0)); + Point p1 = alpha_complex_from_points.get_point(1); std::cout << "alpha_complex_from_points.get_point(1)=" << p1 << std::endl; BOOST_CHECK(4 == p1.dimension()); @@ -278,12 +207,8 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { BOOST_CHECK(4 == p3.dimension()); BOOST_CHECK(is_point_in_list(points, p3)); - Point p4 = alpha_complex_from_points.get_point(4); - std::cout << "alpha_complex_from_points.get_point(4)=" << p4 << std::endl; - BOOST_CHECK(4 == p4.dimension()); - BOOST_CHECK(is_point_in_list(points, p4)); - - BOOST_CHECK_THROW (alpha_complex_from_points.get_point(5), std::out_of_range); - BOOST_CHECK_THROW (alpha_complex_from_points.get_point(0), std::out_of_range); + // Test to the limit + 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); } diff --git a/src/Alpha_complex/test/S4_100.off b/src/Alpha_complex/test/S4_100.off deleted file mode 100644 index cd017e12..00000000 --- a/src/Alpha_complex/test/S4_100.off +++ /dev/null @@ -1,102 +0,0 @@ -nOFF -4 100 0 0 -0.562921 -0.735261 -0.256472 0.277007 --0.803733 -0.0527915 -0.315125 0.501918 --0.24946 -0.354982 -0.410773 -0.801887 -0.916381 -0.0512295 0.371049 0.141223 -0.182222 0.940836 -0.171362 -0.228599 --0.787145 -0.129213 0.568102 -0.202402 -0.0187866 -0.22093 -0.832882 -0.507095 --0.4702 -0.533814 0.353776 0.607286 --0.159798 -0.504771 0.263586 0.806346 -0.295546 0.162541 0.452931 0.825279 -0.242043 -0.107437 -0.913612 -0.308521 -0.875759 -0.113035 -0.469189 -0.0114505 -0.547877 -0.762247 -0.256972 -0.229729 --0.172302 0.521057 0.412013 -0.727363 --0.724729 -0.0574074 -0.0290602 0.686023 -0.700434 -0.102636 0.687285 0.162779 --0.681386 0.0946893 0.610047 0.393178 --0.847553 -0.357132 0.383743 0.0827718 -0.72297 -0.161631 -0.608517 0.284424 -0.757394 0.141549 0.196065 -0.606528 -0.78094 0.00901997 0.434536 0.448586 -0.14166 -0.619339 0.614589 -0.467582 -0.473105 -0.537832 -0.0103746 0.697711 --0.208004 0.536218 0.818027 0.00605288 -0.743694 -0.628926 0.188072 0.126488 --0.462228 -0.278147 0.35514 -0.76345 --0.17361 0.249211 0.758567 -0.57648 -0.416958 -0.254924 -0.576373 -0.654946 --0.590751 -0.286089 -0.424896 0.623402 --0.639538 -0.739693 -0.203745 0.0482932 -0.0731787 0.132121 0.864022 0.480266 --0.149644 -0.164724 -0.249746 -0.94239 --0.348592 0.0120379 -0.928656 -0.126239 -0.395328 -0.54513 0.149976 -0.723917 --0.974164 0.14707 0.157191 0.068302 --0.166425 0.119943 -0.627304 -0.751269 -0.031947 -0.358518 -0.708301 -0.607251 -0.93781 -0.155368 -0.30951 0.0240237 -0.276094 -0.753155 -0.597088 -0.00387459 --0.642876 -0.200551 -0.263517 -0.690687 -0.178711 0.604987 -0.262989 0.729993 --0.520347 0.497922 -0.676144 0.155374 --0.703999 0.500219 -0.484381 0.139789 --0.131013 0.835735 0.506779 0.166004 --0.536116 -0.566557 0.229226 0.582279 --0.334105 0.158252 0.926091 0.0754059 --0.0362677 0.296076 0.897108 0.325915 --0.57486 0.798575 0.15324 -0.0912754 -0.498602 0.0186805 0.72824 0.469801 --0.960329 0.0473356 0.261005 -0.0860505 -0.899134 -0.381392 -0.214508 0.00921711 -0.570576 0.567224 0.393019 -0.445237 --0.761763 -0.614589 -0.0546476 -0.197513 -0.188584 0.289531 0.174031 0.922129 --0.458506 -0.583876 0.639297 -0.2004 -0.785343 -0.21571 0.0794082 -0.574804 -0.0819036 0.65961 -0.247426 0.704973 -0.573125 0.49706 0.373026 0.534145 --0.513286 -0.626226 0.208535 -0.548536 -0.460558 0.468686 0.507832 -0.55707 -0.716158 -0.488201 0.388209 -0.313164 -0.881074 0.152441 0.380128 -0.236589 -0.885793 0.0386389 0.161009 -0.433537 --0.365162 0.298384 0.292846 0.831784 -0.364934 0.632269 -0.197205 -0.654346 --0.31469 -0.429991 0.665304 -0.522923 --0.734198 0.462914 -0.135691 -0.477756 --0.422885 0.674444 -0.364143 -0.483419 -0.829218 -0.154622 -0.381147 0.378439 -0.887881 0.310479 -0.109528 0.321363 --0.354398 -0.693974 0.456019 -0.429941 --0.492045 -0.160008 0.044387 0.854587 -0.0595532 0.158421 0.412577 -0.895062 --0.211441 0.491794 -0.153521 0.83058 --0.33558 -0.504711 0.353831 -0.71236 --0.735211 -0.197714 0.525626 0.379593 -0.465818 -0.424245 0.769469 -0.104627 --0.641071 -0.286339 -0.704442 -0.103923 --0.00446569 0.0249849 -0.194417 -0.980591 --0.610081 -0.252448 0.176698 -0.729966 --0.0859217 -0.154471 0.715027 0.676382 -0.091315 0.0723382 -0.855023 -0.505337 -0.165362 0.200983 -0.428242 -0.865373 --0.587465 0.303019 -0.152442 0.734729 -0.454946 -0.319828 0.437063 -0.706902 --0.384368 0.277509 0.879225 -0.0470385 -0.523335 -0.330233 -0.208592 0.757335 -0.895086 0.0448492 0.268089 -0.353466 --0.0272491 -0.567336 -0.72254 -0.39411 --0.0745014 -0.121818 -0.882466 0.448179 -0.382304 -0.240135 0.851109 -0.267941 --0.418057 -0.852847 -0.3128 0.00606452 --0.554046 0.304237 0.272381 -0.725453 -0.155115 -0.0894732 -0.245017 -0.952838 -0.114459 -0.130722 0.953669 0.245614 -0.0913002 -0.462466 0.244433 0.847374 --0.198849 0.0785111 0.131441 -0.967997 --0.303154 -0.686484 0.639333 0.167604 -0.521455 0.256835 -0.0584503 -0.811606 --0.109787 0.870544 0.161523 0.451676 diff --git a/src/Alpha_complex/test/S8_10.off b/src/Alpha_complex/test/S8_10.off deleted file mode 100644 index 4e147c44..00000000 --- a/src/Alpha_complex/test/S8_10.off +++ /dev/null @@ -1,12 +0,0 @@ -nOFF -8 10 0 0 -0.440036 -0.574754 -0.200485 0.216537 -0.501251 -0.0329236 -0.196529 0.313023 --0.129367 -0.184089 -0.213021 -0.415848 0.783529 -0.0438025 0.317256 0.120749 -0.132429 0.683748 -0.124536 -0.166133 -0.540695 -0.0887576 0.390234 -0.139031 -0.0137399 -0.161581 -0.609142 -0.370872 -0.320669 -0.364053 0.24127 0.41416 --0.115313 -0.36425 0.190208 0.581871 0.204605 0.112527 0.313562 0.571337 -0.168272 -0.0746917 -0.635156 -0.214488 0.629498 -0.0812499 -0.337255 -0.00823068 -0.369896 -0.514626 -0.173493 -0.1551 -0.127105 0.384377 0.303936 -0.536566 --0.49013 -0.0388242 -0.0196532 0.463953 0.515962 -0.0756047 0.506276 0.119908 --0.434258 0.060347 0.388793 0.250579 -0.653127 -0.275207 0.295714 0.0637842 -0.596172 -0.133284 -0.501793 0.234541 0.428452 0.0800735 0.110912 -0.343109 |