All in a Gudhi::collapse namespace

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 <ctime>
 #include <fstream>
 
+namespace Gudhi {
+
+namespace collapse {
+
+
 typedef std::size_t Vertex;
 using Edge = std::pair<Vertex, Vertex>;  // 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<Edge, double>;
-using edge_list = std::vector<Edge>;
 
 using MapVertexToIndex = std::unordered_map<Vertex, std::size_t>;
-using Map = std::unordered_map<Vertex, Vertex>;
 
 using sparseRowMatrix = Eigen::SparseMatrix<double, Eigen::RowMajor>;
-using rowInnerIterator = sparseRowMatrix::InnerIterator;
 
 using doubleVector = std::vector<double>;
-using vertexVector = std::vector<Vertex>;
 using boolVector = std::vector<bool>;
 
 using EdgeFiltVector = std::vector<EdgeFilt>;
 
-typedef std::vector<std::tuple<double, Vertex, Vertex>> Filtered_sorted_edge_list;
-typedef std::unordered_map<Edge, std::size_t, boost::hash<Edge>> u_edge_to_idx_map;
+using Filtered_sorted_edge_list = std::vector<std::tuple<double, Vertex, Vertex>>;
+using u_edge_to_idx_map = std::unordered_map<Edge, std::size_t, boost::hash<Edge>>;
 
 //!  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<std::size_t, std::size_t> 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;