From 050fde353b73da4e93aaee2beab1291cc044be42 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 10 Apr 2020 07:55:30 +0200 Subject: All in a Gudhi::collapse namespace --- src/Collapse/doc/intro_edge_collapse.h | 4 ++-- .../include/gudhi/Flag_complex_sparse_matrix.h | 19 ++++++++++++------- src/Collapse/test/collapse_unit_test.cpp | 2 +- ...distance_matrix_edge_collapse_rips_persistence.cpp | 4 +--- .../point_cloud_edge_collapse_rips_persistence.cpp | 2 +- 5 files changed, 17 insertions(+), 14 deletions(-) diff --git a/src/Collapse/doc/intro_edge_collapse.h b/src/Collapse/doc/intro_edge_collapse.h index b42b5e65..70c816f4 100644 --- a/src/Collapse/doc/intro_edge_collapse.h +++ b/src/Collapse/doc/intro_edge_collapse.h @@ -13,7 +13,7 @@ namespace Gudhi { -namespace edge_collapse { +namespace collapse { /** \defgroup edge_collapse Edge collapse * @@ -91,7 +91,7 @@ namespace edge_collapse { */ /** @} */ // end defgroup strong_collapse -} // namespace edge_collapse +} // namespace collapse } // namespace Gudhi diff --git a/src/Collapse/include/gudhi/Flag_complex_sparse_matrix.h b/src/Collapse/include/gudhi/Flag_complex_sparse_matrix.h index 4862c1b0..0d5f37a4 100644 --- a/src/Collapse/include/gudhi/Flag_complex_sparse_matrix.h +++ b/src/Collapse/include/gudhi/Flag_complex_sparse_matrix.h @@ -35,27 +35,28 @@ #include #include +namespace Gudhi { + +namespace collapse { + + typedef std::size_t Vertex; using Edge = std::pair; // This is an ordered pair, An edge is stored with convention of the first // element being the smaller i.e {2,3} not {3,2}. However this is at the level // of row indices on actual vertex lables using EdgeFilt = std::pair; -using edge_list = std::vector; using MapVertexToIndex = std::unordered_map; -using Map = std::unordered_map; using sparseRowMatrix = Eigen::SparseMatrix; -using rowInnerIterator = sparseRowMatrix::InnerIterator; using doubleVector = std::vector; -using vertexVector = std::vector; using boolVector = std::vector; using EdgeFiltVector = std::vector; -typedef std::vector> Filtered_sorted_edge_list; -typedef std::unordered_map> u_edge_to_idx_map; +using Filtered_sorted_edge_list = std::vector>; +using u_edge_to_idx_map = std::unordered_map>; //! Class SparseMsMatrix /*! @@ -266,7 +267,7 @@ class Flag_complex_sparse_matrix { #endif // DEBUG_TRACES if (not domination_indicator[indx]) { // Iterate over the non-zero columns - for (rowInnerIterator it(sparse_row_adjacency_matrix, indx); it; ++it) { + for (sparseRowMatrix::InnerIterator it(sparse_row_adjacency_matrix, indx); it; ++it) { v = it.index(); // If the vertex v is not dominated and the edge {u,v} is still in the matrix if (not domination_indicator[v] and u_set_removed_redges.find(std::minmax(u, v)) == u_set_removed_redges.end() and @@ -432,4 +433,8 @@ class Flag_complex_sparse_matrix { }; +} // namespace collapse + +} // namespace Gudhi + #endif // FLAG_COMPLEX_SPARSE_MATRIX_H_ diff --git a/src/Collapse/test/collapse_unit_test.cpp b/src/Collapse/test/collapse_unit_test.cpp index 88af53e8..8cfa7d5f 100644 --- a/src/Collapse/test/collapse_unit_test.cpp +++ b/src/Collapse/test/collapse_unit_test.cpp @@ -40,7 +40,7 @@ void trace_and_check_collapse(const Filtered_sorted_edge_list& edges, const Filt } std::cout << "COLLAPSE - keep edges: " << std::endl; - Flag_complex_sparse_matrix flag_complex_sparse_matrix(edges); + Gudhi::collapse::Flag_complex_sparse_matrix flag_complex_sparse_matrix(edges); Filtered_sorted_edge_list collapse_edges; flag_complex_sparse_matrix.filtered_edge_collapse( [&collapse_edges](std::pair edge, double filtration) { diff --git a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp index 98a90892..b937a8ff 100644 --- a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp +++ b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp @@ -78,8 +78,6 @@ int main(int argc, char* argv[]) { program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); - Map map_empty; - Distance_matrix distances; Distance_matrix sparse_distances; @@ -103,7 +101,7 @@ int main(int argc, char* argv[]) { // Now we will perform filtered edge collapse to sparsify the edge list edge_t. std::cout << "Filtered edge collapse begins" << std::endl; - Flag_complex_sparse_matrix mat_filt_edge_coll(edge_t); + Gudhi::collapse::Flag_complex_sparse_matrix mat_filt_edge_coll(edge_t); std::cout << "Matrix instansiated" << std::endl; Simplex_tree stree; diff --git a/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp index 70d8d9c5..5fa24306 100644 --- a/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp +++ b/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp @@ -85,7 +85,7 @@ int main(int argc, char* argv[]) { } std::cout << "Filtered edge collapse begins" << std::endl; - Flag_complex_sparse_matrix mat_filt_edge_coll(proximity_graph); + Gudhi::collapse::Flag_complex_sparse_matrix mat_filt_edge_coll(proximity_graph); std::cout << "Computing the one-skeleton for threshold: " << threshold << std::endl; -- cgit v1.2.3