Merge branch 'master' of https://github.com/GUDHI/gudhi-devel into perslay

8 files changed, 51 insertions, 24 deletions

diff --git a/ext/hera b/ext/hera
-Subproject b528c4067a8aac346eb307d3c23b82d5953cfe2
+Subproject 8bfdd4bd32f005c18b5c75c502b987de552d6e4
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index ef9f8428..4177a0b8 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -24,6 +24,7 @@
 #include <boost/iterator/transform_iterator.hpp>
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/range/adaptor/reversed.hpp>
+#include <boost/range/adaptor/transformed.hpp>
 #include <boost/range/size.hpp>
 #include <boost/container/static_vector.hpp>
 
@@ -1122,16 +1123,12 @@ class Simplex_tree {
       dimension_ = 1;
     }
 
-    root_.members_.reserve(num_vertices(skel_graph));
+    root_.members_.reserve(num_vertices(skel_graph)); // probably useless in most cases
+    auto verts = vertices(skel_graph) | boost::adaptors::transformed([&](auto v){
+        return Dit_value_t(v, Node(&root_, get(vertex_filtration_t(), skel_graph, v))); });
+    root_.members_.insert(boost::begin(verts), boost::end(verts));
+    // This automatically sorts the vertices, the graph concept doesn't guarantee the order in which we iterate.
 
-    typename boost::graph_traits<OneSkeletonGraph>::vertex_iterator v_it,
-        v_it_end;
-    for (std::tie(v_it, v_it_end) = vertices(skel_graph); v_it != v_it_end;
-         ++v_it) {
-      root_.members_.emplace_hint(
-                                  root_.members_.end(), *v_it,
-                                  Node(&root_, get(vertex_filtration_t(), skel_graph, *v_it)));
-    }
     std::pair<typename boost::graph_traits<OneSkeletonGraph>::edge_iterator,
               typename boost::graph_traits<OneSkeletonGraph>::edge_iterator> boost_edges = edges(skel_graph);
     // boost_edges.first is the equivalent to boost_edges.begin()
@@ -1140,7 +1137,7 @@ class Simplex_tree {
       auto edge = *(boost_edges.first);
       auto u = source(edge, skel_graph);
       auto v = target(edge, skel_graph);
-      if (u == v) throw "Self-loops are not simplicial";
+      if (u == v) throw std::invalid_argument("Self-loops are not simplicial");
       // We cannot skip edges with the wrong orientation and expect them to
       // come a second time with the right orientation, that does not always
       // happen in practice. emplace() should be a NOP when an element with the
@@ -1159,6 +1156,21 @@ class Simplex_tree {
     }
   }
 
+  /** \brief Inserts several vertices.
+   * @param[in] vertices A range of Vertex_handle
+   * @param[in] filt filtration value of the new vertices (the same for all)
+   *
+   * This may be faster than inserting the vertices one by one, especially in a random order.
+   * The complex does not need to be empty before calling this function. However, if a vertex is
+   * already present, its filtration value is not modified, unlike with other insertion functions. */
+  template <class VertexRange>
+  void insert_batch_vertices(VertexRange const& vertices, Filtration_value filt = 0) {
+    auto verts = vertices | boost::adaptors::transformed([&](auto v){
+        return Dit_value_t(v, Node(&root_, filt)); });
+    root_.members_.insert(boost::begin(verts), boost::end(verts));
+    if (dimension_ < 0 && !root_.members_.empty()) dimension_ = 0;
+  }
+
   /** \brief Expands the Simplex_tree containing only its one skeleton
    * until dimension max_dim.
    *
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 79bb5a93..ebcc406c 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -1038,3 +1038,17 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_boundaries_and_opposite_vertex_iterat
       BOOST_CHECK(opposite_vertices.size() == 0);
   }
 }
+
+BOOST_AUTO_TEST_CASE(batch_vertices) {
+  typedef Simplex_tree<> typeST;
+  std::clog << "********************************************************************" << std::endl;
+  std::clog << "TEST BATCH VERTEX INSERTION" << std::endl;
+  typeST st;
+  st.insert_simplex_and_subfaces({3}, 1.5);
+  std::vector verts { 2, 3, 5, 6 };
+  st.insert_batch_vertices(verts);
+  BOOST_CHECK(st.num_vertices() == 4);
+  BOOST_CHECK(st.num_simplices() == 4);
+  BOOST_CHECK(st.filtration(st.find({2})) == 0.);
+  BOOST_CHECK(st.filtration(st.find({3})) == 1.5);
+}
diff --git a/src/cmake/modules/GUDHI_submodules.cmake b/src/cmake/modules/GUDHI_submodules.cmake
index 78b045bd..c844386d 100644
--- a/src/cmake/modules/GUDHI_submodules.cmake
+++ b/src/cmake/modules/GUDHI_submodules.cmake
@@ -1,5 +1,3 @@
 # For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
-set(HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include)
-set(HERA_WASSERSTEIN_INCLUDE_DIR ${HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's wasserstein.h")
-set(HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/bottleneck/include)
-set(HERA_BOTTLENECK_INCLUDE_DIR ${HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's bottleneck.h")
\ No newline at end of file
+set(HERA_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/include)
+set(HERA_INCLUDE_DIR ${HERA_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find hera/{wasserstein.h,bottleneck.h}")
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 4487ad86..2144ff6f 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -60,10 +60,9 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
 
-if(HERA_WASSERSTEIN_INCLUDE_DIR STREQUAL HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR OR
-    HERA_BOTTLENECK_INCLUDE_DIR STREQUAL HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR)
+if(HERA_INCLUDE_DIR STREQUAL HERA_INTERNAL_INCLUDE_DIR)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                     copy_directory ${CMAKE_SOURCE_DIR}/ext/hera ${GUDHI_USER_VERSION_DIR}/ext/hera)
+                     copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/include ${GUDHI_USER_VERSION_DIR}/ext/hera/include)
 endif()
 
 set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
diff --git a/src/python/gudhi/hera/bottleneck.cc b/src/python/gudhi/hera/bottleneck.cc
index 0cb562ce..ec461f7c 100644
--- a/src/python/gudhi/hera/bottleneck.cc
+++ b/src/python/gudhi/hera/bottleneck.cc
@@ -16,7 +16,7 @@
 using py::ssize_t;
 #endif
 
-#include <bottleneck.h> // Hera
+#include <hera/bottleneck.h> // Hera
 
 double bottleneck_distance(Dgm d1, Dgm d2, double delta)
 {
diff --git a/src/python/gudhi/hera/wasserstein.cc b/src/python/gudhi/hera/wasserstein.cc
index fa0cf8aa..3516352e 100644
--- a/src/python/gudhi/hera/wasserstein.cc
+++ b/src/python/gudhi/hera/wasserstein.cc
@@ -8,10 +8,16 @@
  *      - YYYY/MM Author: Description of the modification
  */
 
-#include <wasserstein.h> // Hera
-
 #include <pybind11_diagram_utils.h>
 
+#ifdef _MSC_VER
+// https://github.com/grey-narn/hera/issues/3
+// ssize_t is a non-standard type (well, posix)
+using py::ssize_t;
+#endif
+
+#include <hera/wasserstein.h> // Hera
+
 double wasserstein_distance(
     Dgm d1, Dgm d2,
     double wasserstein_power, double internal_p,
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 2c67c2c5..1ecbe985 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -48,10 +48,8 @@ ext_modules = cythonize(ext_modules, compiler_directives={'language_level': '3'}
 
 for module in pybind11_modules:
     my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)]
-    if module == 'hera/wasserstein':
-        my_include_dirs = ['@HERA_WASSERSTEIN_INCLUDE_DIR@'] + my_include_dirs
-    elif module == 'hera/bottleneck':
-        my_include_dirs = ['@HERA_BOTTLENECK_INCLUDE_DIR@'] + my_include_dirs
+    if module.startswith('hera/'):
+        my_include_dirs = ['@HERA_INCLUDE_DIR@'] + my_include_dirs
     ext_modules.append(Extension(
         'gudhi.' + module.replace('/', '.'),
         sources = [source_dir + module + '.cc'],