Add get_simplices method - contrary to get_filtration method, sort is not performed

6 files changed, 62 insertions, 3 deletions

diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp
index 4353939f..47ea7e36 100644
--- a/src/Simplex_tree/example/simple_simplex_tree.cpp
+++ b/src/Simplex_tree/example/simple_simplex_tree.cpp
@@ -166,10 +166,19 @@ int main(int argc, char* const argv[]) {
   // ++ GENERAL VARIABLE SET
 
   std::cout << "********************************************************************\n";
-  // Display the Simplex_tree - Can not be done in the middle of 2 inserts
   std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices\n";
   std::cout << "   - dimension " << simplexTree.dimension() << "\n";
-  std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
+  std::cout << "* Iterator on simplices, with [filtration value]:\n";
+  for (Simplex_tree::Simplex_handle f_simplex : simplexTree.complex_simplex_range()) {
+    std::cout << "   "
+              << "[" << simplexTree.filtration(f_simplex) << "] ";
+    for (auto vertex : simplexTree.simplex_vertex_range(f_simplex)) std::cout << "(" << vertex << ")";
+    std::cout << std::endl;
+  }
+
+  std::cout << "********************************************************************\n";
+  // Can not be done in the middle of 2 inserts
+  std::cout << "* Iterator on simplices sorted by filtration values, with [filtration value]:\n";
   for (auto f_simplex : simplexTree.filtration_simplex_range()) {
     std::cout << "   "
               << "[" << simplexTree.filtration(f_simplex) << "] ";
diff --git a/src/python/example/simplex_tree_example.py b/src/python/example/simplex_tree_example.py
index 7f20c389..34833899 100755
--- a/src/python/example/simplex_tree_example.py
+++ b/src/python/example/simplex_tree_example.py
@@ -38,6 +38,10 @@ else:
 
 print("dimension=", st.dimension())
 
+print("simplices=")
+for simplex_with_filtration in st.get_simplices():
+    print("(%s, %.2f)" % tuple(simplex_with_filtration))
+
 st.initialize_filtration()
 print("filtration=")
 for simplex_with_filtration in st.get_filtration():
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index 66c173a6..82f155de 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -24,6 +24,12 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
     cdef cppclass Simplex_tree_simplex_handle "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Simplex_handle":
         pass
 
+    cdef cppclass Simplex_tree_simplices_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Complex_simplex_iterator":
+        Simplex_tree_simplices_iterator()
+        Simplex_tree_simplex_handle& operator*()
+        Simplex_tree_simplices_iterator operator++()
+        bint operator!=(Simplex_tree_simplices_iterator)
+
     cdef cppclass Simplex_tree_skeleton_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>::Skeleton_simplex_iterator":
         Simplex_tree_skeleton_iterator()
         Simplex_tree_simplex_handle& operator*()
@@ -53,6 +59,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         bool make_filtration_non_decreasing()
         # Iterators over Simplex tree
         pair[vector[int], double] get_simplex_and_filtration(Simplex_tree_simplex_handle f_simplex)
+        Simplex_tree_simplices_iterator get_simplices_iterator_begin()
+        Simplex_tree_simplices_iterator get_simplices_iterator_end()
         vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_begin()
         vector[Simplex_tree_simplex_handle].const_iterator get_filtration_iterator_end()
         Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension)
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index efac2d80..c01cc905 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -208,10 +208,25 @@ cdef class SimplexTree:
         return self.get_ptr().insert_simplex_and_subfaces(csimplex,
                                                         <double>filtration)
 
-    def get_filtration(self):
+    def get_simplices(self):
         """This function returns a generator with simplices and their given
         filtration values.
 
+        :returns:  The simplices.
+        :rtype:  generator with tuples(simplex, filtration)
+        """
+        cdef Simplex_tree_simplices_iterator it = self.get_ptr().get_simplices_iterator_begin()
+        cdef Simplex_tree_simplices_iterator end = self.get_ptr().get_simplices_iterator_end()
+        cdef Simplex_tree_simplex_handle sh = dereference(it)
+
+        while it != end:
+            yield self.get_ptr().get_simplex_and_filtration(dereference(it))
+            preincrement(it)
+
+    def get_filtration(self):
+        """This function returns a generator with simplices and their given
+        filtration values sorted by increasing filtration values.
+
         :returns:  The simplices sorted by increasing filtration values.
         :rtype:  generator with tuples(simplex, filtration)
         """
diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h
index 66ce5afd..4a7062d6 100644
--- a/src/python/include/Simplex_tree_interface.h
+++ b/src/python/include/Simplex_tree_interface.h
@@ -36,6 +36,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   using Simplex_and_filtration = std::pair<Simplex, Filtration_value>;
   using Filtered_simplices = std::vector<Simplex_and_filtration>;
   using Skeleton_simplex_iterator = typename Base::Skeleton_simplex_iterator;
+  using Complex_simplex_iterator = typename Base::Complex_simplex_iterator;
 
  public:
   bool find_simplex(const Simplex& vh) {
@@ -122,6 +123,16 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   }
 
   // Iterator over the simplex tree
+  Complex_simplex_iterator get_simplices_iterator_begin() {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::complex_simplex_range().begin();
+  }
+
+  Complex_simplex_iterator get_simplices_iterator_end() {
+    // this specific case works because the range is just a pair of iterators - won't work if range was a vector
+    return Base::complex_simplex_range().end();
+  }
+
   typename std::vector<Simplex_handle>::const_iterator get_filtration_iterator_begin() {
     // Base::initialize_filtration(); already performed in filtration_simplex_range
     // this specific case works because the range is just a pair of iterators - won't work if range was a vector
diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py
index 04b26e92..f7848379 100755
--- a/src/python/test/test_simplex_tree.py
+++ b/src/python/test/test_simplex_tree.py
@@ -249,3 +249,15 @@ def test_make_filtration_non_decreasing():
     assert st.filtration([3, 4, 5]) == 2.0
     assert st.filtration([3, 4]) == 2.0
     assert st.filtration([4, 5]) == 2.0
+
+def test_simplices_iterator():
+    st = SimplexTree()
+    
+    assert st.insert([0, 1, 2], filtration=4.0) == True
+    assert st.insert([2, 3, 4], filtration=2.0) == True
+
+    for simplex in st.get_simplices():
+        print("simplex is: ", simplex[0])
+        assert st.find(simplex[0]) == True
+        print("filtration is: ", simplex[1])
+        assert st.filtration(simplex[0]) == simplex[1]