Merge pull request #193 from higra/increasing_altitudes

Increasing altitudes asserts

doc/requirements.txt

@@ -1,4 +1,4 @@
-sphinx==2.1.0
+sphinx==3.0.3
 sphinx-tabs
 breathe
 higra==0.5.1

doc/source/python/tree_algorithm.rst

@@ -14,6 +14,7 @@ Algorithm for trees
     labelisation_hierarchy_supervertices
     reconstruct_leaf_data
     sort_hierarchy_with_altitudes
+    test_altitudes_increasingness
     test_tree_isomorphism
     tree_fusion_depth_map
 
@@ -31,6 +32,8 @@ Algorithm for trees
 
 .. autofunction:: higra.sort_hierarchy_with_altitudes
 
+.. autofunction:: higra.test_altitudes_increasingness
+
 .. autofunction:: higra.test_tree_isomorphism
 
 .. autofunction:: higra.tree_fusion_depth_map

higra/algo/horizontal_cuts.py

@@ -77,20 +77,23 @@ def __labelisation_leaves(self, tree, leaf_graph, handle_rag=True):
     return labels
 
 
-# @hg.extend_class(hg.HorizontalCutExplorer, method_name="__new__")
-# def __make_HorizontalCutExplorer(cls, tree, altitudes):
-#     """
-#     Creates an horizontal cut explorer for th given valued hierarchy.
-#
-#     Altitudes must be increasing
-#
-#     :param tree: input tree
-#     :param altitudes: tree nodes altitudes
-#     :return: an ``HorizontalCutExplorer``
-#     """
-#     return cls._make_HorizontalCutExplorer(tree, altitudes)
-#
-#
-# @hg.extend_class(hg.HorizontalCutExplorer, method_name="__init__")
-# def __dummy_init_HorizontalCutExplorer(*_):
-#     pass
+@hg.extend_class(hg.HorizontalCutExplorer, method_name="__new__")
+def __make_HorizontalCutExplorer(cls, tree, altitudes):
+    """
+    Creates an horizontal cut explorer for the given valued hierarchy.
+
+    Altitudes must be increasing
+
+    :param tree: input tree
+    :param altitudes: tree nodes altitudes
+    :return: an ``HorizontalCutExplorer``
+    """
+    if not hg.test_altitudes_increasingness(tree, altitudes):
+        raise ValueError("'altitudes' must be increasing for 'tree'.")
+
+    return cls._make_HorizontalCutExplorer(tree, altitudes)
+
+
+@hg.extend_class(hg.HorizontalCutExplorer, method_name="__init__")
+def __dummy_init_HorizontalCutExplorer(*_):
+    pass

higra/algo/py_horizontal_cuts.cpp

@@ -67,10 +67,10 @@ struct def_horizontal_cut_explorer_ctr {
     template<typename type, typename C>
     static
     void def(C &c, const char *doc) {
-        c.def(py::init(
+        c.def_static("_make_HorizontalCutExplorer",
                 [](const typename c_t::tree_type &tree, const xt::pyarray<type> &altitudes) {
                     return c_t(tree, altitudes);
-                }),
+                },
               doc,
               py::arg("tree"),
               py::arg("altitudes"));
@@ -92,15 +92,7 @@ Each cut of the hierarchy can be accessed through:
   - the altitude of the cut. This operations runs in :math:`\mathcal{O}(k*\log(n))`, with :math:`k` the number of regions in the retrieved cut.)"""
     );
     add_type_overloads<def_horizontal_cut_explorer_ctr<class_t>, HG_TEMPLATE_NUMERIC_TYPES>
-            (c,
-             R"(Create an horizontal cut explorer for the provided valued hierarchy.
-
-Altitudes must be increasing
-
-:param tree: input tree
-:param altitudes: tree nodes altitudes
-:return: an ``HorizontalCutExplorer``
-)");
+            (c,"");
     c.def("num_cuts", &class_t::num_cuts, "Number of horizontal cuts in the hierarchy.");
     c.def("num_regions_cut",
           &class_t::num_regions_cut,

higra/algo/tree.py

@@ -287,7 +287,6 @@ def binary_labelisation_from_markers(tree, object_marker, background_marker, lea
     return labels
 
 
-@hg.argument_helper(hg.CptHierarchy)
 def sort_hierarchy_with_altitudes(tree, altitudes):
     """
     Sort the nodes of a tree according to their altitudes.
@@ -303,11 +302,30 @@ def sort_hierarchy_with_altitudes(tree, altitudes):
     The returned "node_map" is an array that maps any node index :math:`i` of the new tree,
     to the index of this node in the original tree.
 
-    :param tree: input tree (Concept :class:`~higra.CptHierarchy`)
+    :param tree: input tree
     :param altitudes: node altitudes of the input tree
     :return: the sorted tree (Concept :class:`~higra.CptHierarchy`), its node altitudes, and the node map
     """
+    if not test_altitudes_increasingness(tree, altitudes):
+        raise ValueError("'altitudes' must be increasing for 'tree'.")
+
     new_tree, node_map = hg.cpp._sort_hierarchy_with_altitudes(tree, altitudes)
     new_altitudes = altitudes[node_map]
 
     return new_tree, new_altitudes, node_map
+
+
+def test_altitudes_increasingness(tree, altitudes):
+    """
+    Test if the altitudes of the given tree are increasing; i.e. if for any nodes :math:`i, j` such that :math:`j`
+    is an ancestor of :math:`i`, then :math:`altitudes[i] \leq altitudes[j]`.
+
+
+    :param tree: input tree
+    :param altitudes: node altitudes of the input tree
+    :return: ``True`` if :attr:`altitudes` are increasing for :attr:`tree`, ``False`` otherwise.
+    """
+    if altitudes.ndim != 1 or altitudes.size != tree.num_vertices():
+        raise ValueError("'altitudes' must be a 1d array of size 'tree.num_vertices()'.")
+
+    return np.all(altitudes <= altitudes[tree.parents()])

test/python/test_algo/test_horizontal_cuts.py

@@ -35,6 +35,12 @@ def test_horizontal_cut_explorer_indexed(self):
             self.assertTrue(np.all(np.sort(c.nodes()) == np.sort(cut_nodes[i])))
             self.assertTrue(c.altitude() == alt_cuts[i])
 
+    def test_horizontal_cut_explorer_assert(self):
+        tree = hg.Tree(np.asarray((5, 5, 6, 6, 7, 7, 7, 7)))
+        altitudes = np.asarray((0, 0, 1, 0, 0, 2, 1, 1))
+        with self.assertRaises(ValueError):
+            hch = hg.HorizontalCutExplorer(tree, altitudes)
+
     def test_horizontal_cut_explorer_altitudes(self):
         tree = hg.Tree((11, 11, 11, 12, 12, 16, 13, 13, 13, 14, 14, 17, 16, 15, 15, 18, 17, 18, 18))
         altitudes = np.asarray((0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 3, 1, 2, 3))

test/python/test_algo/test_tree.py

@@ -179,7 +179,6 @@ def functor(tree, altitudes):
         sm_ref = np.asarray((0, 0, 0, 0, 1, 0, 0))
         self.assertTrue(np.all(sm == sm_ref))
 
-
     def test_filter_non_relevant_node_from_tree(self):
         g = hg.get_4_adjacency_graph((1, 8))
         edge_weights = np.asarray((0, 2, 0, 0, 1, 0, 0))
@@ -225,6 +224,32 @@ def test_sort_hierarchy_with_altitudes(self):
         ref_altitudes = np.asarray((0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 7))
         self.assertTrue(np.all(ref_altitudes == naltitudes))
 
+        tree = hg.Tree(np.asarray((5, 5, 6, 6, 7, 7, 7, 7)))
+        altitudes = np.asarray((0, 0, 1, 0, 0, 2, 1, 1))
+        with self.assertRaises(ValueError):
+            hg.sort_hierarchy_with_altitudes(tree, altitudes)
+
+    def test_test_altitudes_increasingness(self):
+        tree = hg.Tree(np.asarray((5, 5, 6, 6, 7, 7, 7, 7)))
+
+        altitudes = np.asarray((0, 0, 0, 0, 0, 2, 1, 3))
+        self.assertTrue(hg.test_altitudes_increasingness(tree, altitudes))
+
+        altitudes = np.asarray((0, 0, 0, 0, 0, 1, 2, 2))
+        self.assertTrue(hg.test_altitudes_increasingness(tree, altitudes))
+
+        altitudes = np.asarray((2, 0, 0, 1, 2, 2, 1, 3))
+        self.assertTrue(hg.test_altitudes_increasingness(tree, altitudes))
+
+        altitudes = np.asarray((0, 0, 0, 0, 0, 0, 0, 0))
+        self.assertTrue(hg.test_altitudes_increasingness(tree, altitudes))
+
+        altitudes = np.asarray((0, 0, 2, 0, 0, 2, 1, 3))
+        self.assertFalse(hg.test_altitudes_increasingness(tree, altitudes))
+
+        altitudes = np.asarray((0, 0, 1, 0, 0, 2, 1, 1))
+        self.assertFalse(hg.test_altitudes_increasingness(tree, altitudes))
+
 
 if __name__ == '__main__':
     unittest.main()