Merge pull request #154 from scikit-tda/lowerstar_fix

Lowerstar fix

Author: ctralie

CHANGELOG.md

@@ -1,3 +1,6 @@
+# 0.6.5
+    - Bugfix for lower star filtrations with edges that come in at exactly 0 (courtesy of Riccardo Ceccaroni)
+
 # 0.6.4
     - Add some includes to ripser.cpp for newer Ubuntu/C++ environments
 

ripser/_version.py

@@ -1 +1 @@
-__version__ = "0.6.4"
+__version__ = "0.6.5"

ripser/ripser.cpp

@@ -687,16 +687,14 @@ class ripser
                     v = dset.find(vertices_of_edge[1]);
 
             if (u != v) {
-                if (get_diameter(e) != 0) {
-                    // Elder rule; youngest class (max birth time of u and v)
-                    // dies first
-                    value_t birth =
-                        std::max(dset.get_birth(u), dset.get_birth(v));
-                    value_t death = get_diameter(e);
-                    if (death > birth) {
-                        births_and_deaths_by_dim[0].push_back(birth);
-                        births_and_deaths_by_dim[0].push_back(death);
-                    }
+                // Elder rule; youngest class (max birth time of u and v)
+                // dies first
+                value_t birth =
+                    std::max(dset.get_birth(u), dset.get_birth(v));
+                value_t death = get_diameter(e);
+                if (death > birth) {
+                    births_and_deaths_by_dim[0].push_back(birth);
+                    births_and_deaths_by_dim[0].push_back(death);
                 }
                 dset.link(u, v);
             } else

test/test_lower_star.py

@@ -19,4 +19,10 @@ def test_single_point(self):
         assert dgm.shape[0] == 1
         assert tuple(dgm[0]) == (0,np.inf)
 
-    
+    def test_zero_edge_bug(self):
+        img = np.ones((5, 5))
+        img[1:-1, 1:-1] = 0
+        img[2, 2] = 1
+        r1 = -lower_star_img(-img)
+        r2 = 1-lower_star_img(1-img)
+        assert(np.allclose(r1, r2))