Merge pull request #194 from higra/attribute_topological_height

Attribute topological height
higra · Apr 29, 2020 · 3ac5f3b · 3ac5f3b
2 parents 7e0303d + 4606e35
commit 3ac5f3b
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diff --git a/.travis.yml b/.travis.yml
@@ -6,6 +6,36 @@ branches:
   - /^\d+\.\d+\.\d+(-\S*)?$/
 matrix:
   include:
+  - os: linux
+    if: tag IS present
+    services:
+      - docker
+    env: BUILD_WHEEL=1 CIBW_BUILD="cp35-*" CIBW_SKIP=*-manylinux1_i686
+  - os: linux
+    if: tag IS present
+    services:
+      - docker
+    env: BUILD_WHEEL=1 CIBW_BUILD="cp36-*" CIBW_SKIP=*-manylinux1_i686
+  - os: linux
+    if: tag IS present
+    services:
+      - docker
+    env: BUILD_WHEEL=1 CIBW_BUILD="cp37-*" CIBW_SKIP=*-manylinux1_i686
+  - os: linux
+    services:
+    - docker
+    env: BUILD_WHEEL=1 CIBW_BUILD="cp38-*" CIBW_SKIP=*-manylinux1_i686
+  - os: osx
+    if: tag IS present
+    env: BUILD_WHEEL=1 CIBW_BUILD="cp35-*"
+  - os: osx
+    if: tag IS present
+    env: BUILD_WHEEL=1 CIBW_BUILD="cp36-*"
+  - os: osx
+    if: tag IS present
+    env: BUILD_WHEEL=1 CIBW_BUILD="cp37-*"
+  - os: osx
+    env: BUILD_WHEEL=1 CIBW_BUILD="cp38-*"
   - os: linux
     addons:
       apt:
@@ -38,37 +68,6 @@ matrix:
     osx_image: xcode8
     compiler: clang
     env: HG_USE_TBB=On
-  - sudo: required
-    if: tag IS present
-    services:
-      - docker
-    env: BUILD_WHEEL=1 CIBW_BUILD="cp35-*" CIBW_SKIP=*-manylinux1_i686
-  - sudo: required
-    if: tag IS present
-    services:
-      - docker
-    env: BUILD_WHEEL=1 CIBW_BUILD="cp36-*" CIBW_SKIP=*-manylinux1_i686
-  - sudo: required
-    if: tag IS present
-    services:
-      - docker
-    env: BUILD_WHEEL=1 CIBW_BUILD="cp37-*" CIBW_SKIP=*-manylinux1_i686
-  - sudo: required
-    services:
-    - docker
-    env: BUILD_WHEEL=1 CIBW_BUILD="cp38-*" CIBW_SKIP=*-manylinux1_i686
-  - os: osx
-    if: tag IS present
-    env: BUILD_WHEEL=1 CIBW_BUILD="cp35-*"
-  - os: osx
-    if: tag IS present
-    env: BUILD_WHEEL=1 CIBW_BUILD="cp36-*"
-  - os: osx
-    if: tag IS present
-    env: BUILD_WHEEL=1 CIBW_BUILD="cp37-*"
-  - os: osx
-    env: BUILD_WHEEL=1 CIBW_BUILD="cp38-*"
-
 env:
   global:
   - MINCONDA_VERSION="latest"

diff --git a/doc/source/python/tree_attributes.rst b/doc/source/python/tree_attributes.rst
@@ -26,6 +26,7 @@ Tree attributes
     attribute_piecewise_constant_Mumford_Shah_energy
     attribute_regular_altitudes
     attribute_sibling
+    attribute_topological_height
     attribute_tree_sampling_probability
     attribute_volume
 
@@ -67,6 +68,8 @@ Tree attributes
 
 .. autofunction:: higra.attribute_sibling
 
+.. autofunction:: higra.attribute_topological_height
+
 .. autofunction:: higra.attribute_tree_sampling_probability
 
 .. autofunction:: higra.attribute_volume
diff --git a/higra/attribute/tree_attributes.py b/higra/attribute/tree_attributes.py
@@ -655,3 +655,23 @@ def attribute_tree_sampling_probability(tree, leaf_graph, leaf_graph_edge_weight
         leaf_graph_vertex_weights = leaf_graph_vertex_weights / np.sum(leaf_graph_edge_weights)
         tree_node_weights = hg.accumulate_sequential(tree, leaf_graph_vertex_weights, hg.Accumulators.sum)
         return hg.attribute_children_pair_sum_product(tree, tree_node_weights)
+
+
+@hg.auto_cache
+def attribute_topological_height(tree):
+    """
+    Given a node :math:`n` of :attr:`tree`, the topological height of :math:`n` is the number of edges on the longest
+    path from the node :math:`n` to a leaf of :attr:`tree`.
+
+    The topological height of the leaves is equal to 0.
+
+    :param tree: Input tree
+    :return: a 1d array
+    """
+
+    res = hg.accumulate_and_add_sequential(tree,
+                                           np.ones(tree.num_vertices(), dtype=np.int64),
+                                           np.zeros(tree.num_leaves(), dtype=np.int64),
+                                           hg.Accumulators.max)
+
+    return res
diff --git a/test/python/test_attribute/test_attributes.py b/test/python/test_attribute/test_attributes.py
@@ -624,6 +624,12 @@ def test_attribute_tree_sampling_probability_null_model(self):
               (Z * Z)
         self.assertTrue(np.allclose(ref, res))
 
+    def test_topological_height(self):
+        tree = hg.Tree((6, 6, 9, 9, 7, 8, 10, 8, 10, 10, 10))
+        res = hg.attribute_topological_height(tree)
+        ref = (0, 0, 0, 0, 0, 0, 1, 1, 2, 1, 3)
+        self.assertTrue(np.array_equal(res, ref))
+
 
 if __name__ == '__main__':
     unittest.main()