Merge pull request #89 from MunchLab/drawing_improvements

Drawing improvements

Author: lizliz

cereeberus/cereeberus/draw/layout.py

@@ -105,6 +105,14 @@ def reeb_x_layout(G, f, seed=None, repulsion=0.5):
     Returns:
         dict: Mapping node -> x-position.
     """
+
+    def _normalize_to_unit_interval(x):
+        """Normalize coordinates to [-1, 1] if there is nonzero spread."""
+        x_range = x.max() - x.min()
+        if x_range > 1e-9:
+            return 2 * (x - x.min()) / x_range - 1
+        return x
+
     nodes = list(G.nodes)
     n = len(nodes)
     if n == 0:
@@ -135,9 +143,23 @@ def reeb_x_layout(G, f, seed=None, repulsion=0.5):
 
     # Initialise with barycenter ordering, then add tiny jitter to break ties
     x0 = _barycenter_init(n, f_vals, edges, level_nodes)
+
+    # With no edges, the spring term is absent and repulsion alone can drive
+    # points apart indefinitely. In this case, return the barycenter layout
+    # directly (normalised), which is deterministic and finite.
+    if len(edges) == 0:
+        x0 = _normalize_to_unit_interval(x0)
+        return {v: float(x0[idx[v]]) for v in nodes}
+
     rng = np.random.default_rng(seed)
     x0 = x0 + rng.standard_normal(n) * 1e-3
 
+    # Keep the optimizer in a compact region and add a tiny centering term so
+    # the objective remains well-conditioned.
+    bounds = [(-2.0, 2.0)] * n
+    center_weight = 1e-6
+    x0 = np.clip(x0, -2.0, 2.0)
+
     def energy(x):
         e = 0.0
         for i, j in edges:
@@ -146,6 +168,7 @@ def energy(x):
             for i, j in same_height_pairs:
                 diff = x[i] - x[j]
                 e += repulsion / (diff**2 + 1e-6)
+        e += center_weight * np.dot(x, x)
         return e
 
     def gradient(x):
@@ -161,14 +184,13 @@ def gradient(x):
                 grad_val = -2 * repulsion * diff / denom
                 g[i] += grad_val
                 g[j] -= grad_val
+        g += 2 * center_weight * x
         return g
 
-    result = minimize(energy, x0, jac=gradient, method="L-BFGS-B")
+    result = minimize(energy, x0, jac=gradient, method="L-BFGS-B", bounds=bounds)
     x_opt = result.x
 
     # Normalise to [-1, 1]
-    x_range = x_opt.max() - x_opt.min()
-    if x_range > 1e-9:
-        x_opt = 2 * (x_opt - x_opt.min()) / x_range - 1
+    x_opt = _normalize_to_unit_interval(x_opt)
 
     return {v: float(x_opt[idx[v]]) for v in nodes}

doc_source/images/line.png

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cereeberus"
-version = "0.1.13"
+version = "0.1.14"
 authors = [
   { name="Liz Munch", email="muncheli@msu.edu" },
 ]

doc_source/images/torus-extraverts.png

@@ -0,0 +1,53 @@
+import unittest
+
+import networkx as nx
+import numpy as np
+from cereeberus.data import ex_reebgraphs as ex_rg
+from cereeberus.draw.layout import reeb_x_layout
+
+
+class TestDrawLayout(unittest.TestCase):
+    def test_reeb_x_layout_returns_finite_x_for_all_nodes(self):
+        R = ex_rg.torus(multigraph=False, seed=0)
+
+        x_positions = reeb_x_layout(R, R.f, seed=17, repulsion=0.8)
+
+        self.assertEqual(set(x_positions.keys()), set(R.nodes))
+        for v in R.nodes:
+            self.assertTrue(np.isfinite(x_positions[v]))
+            self.assertLessEqual(x_positions[v], 1.0 + 1e-9)
+            self.assertGreaterEqual(x_positions[v], -1.0 - 1e-9)
+
+    def test_reeb_x_layout_is_reproducible_with_seed(self):
+        R = ex_rg.torus(multigraph=False, seed=0)
+
+        x_a = reeb_x_layout(R, R.f, seed=123, repulsion=0.8)
+        x_b = reeb_x_layout(R, R.f, seed=123, repulsion=0.8)
+
+        for v in R.nodes:
+            self.assertAlmostEqual(x_a[v], x_b[v])
+
+    def test_reeb_x_layout_empty_graph(self):
+        G = nx.Graph()
+        x_positions = reeb_x_layout(G, {}, seed=1, repulsion=0.5)
+        self.assertEqual(x_positions, {})
+
+    def test_reeb_x_layout_same_height_isolated_nodes(self):
+        # Regression test: no edges + same-height nodes should not trigger
+        # unbounded optimisation drift.
+        G = nx.Graph()
+        nodes = ["u", "v", "w", "z"]
+        G.add_nodes_from(nodes)
+        f = {node: 0.0 for node in nodes}
+
+        x_positions = reeb_x_layout(G, f, seed=9, repulsion=1.0)
+
+        self.assertEqual(set(x_positions.keys()), set(nodes))
+        for node in nodes:
+            self.assertTrue(np.isfinite(x_positions[node]))
+            self.assertLessEqual(x_positions[node], 1.0 + 1e-9)
+            self.assertGreaterEqual(x_positions[node], -1.0 - 1e-9)
+
+
+if __name__ == "__main__":
+    unittest.main()

pyproject.toml

@@ -1,9 +1,12 @@
 import unittest
-from cereeberus import ReebGraph, MapperGraph
+
+import numpy as np
 from cereeberus.data import ex_graphs as ex_g
-from cereeberus.data import ex_reebgraphs as ex_rg
 from cereeberus.data import ex_mappergraphs as ex_mg
-import numpy as np
+from cereeberus.data import ex_reebgraphs as ex_rg
+
+from cereeberus import MapperGraph, ReebGraph
+
 
 class TestMapperClass(unittest.TestCase):
 
@@ -129,8 +132,19 @@ def test_dist_matrix(self):
         # Check the whole put together matrix
         M = R.thickening_distance_matrix()
         self.assertEqual(M[5][3,10], np.inf)
+
+    def test_set_pos_from_f_preserves_delta_scaled_y_values(self):
+        # Mapper layout should keep y = delta * f(v), with repulsion only affecting x.
+        MG = ex_mg.torus(delta=0.2, seed=11)
+        MG.set_pos_from_f(seed=5, repulsion=0.9)
+
+        self.assertEqual(set(MG.nodes), set(MG.pos_f.keys()))
+        for v in MG.nodes:
+            self.assertEqual(MG.pos_f[v][1], MG.delta * MG.f[v])
 
 
 
+if __name__ == '__main__':
+    unittest.main()
 if __name__ == '__main__':
     unittest.main()

tests/test_draw_layout.py

@@ -1,8 +1,11 @@
 import unittest
-from cereeberus import ReebGraph
+
 from cereeberus.data import ex_graphs as ex_g
 from cereeberus.data import ex_reebgraphs as ex_rg
 
+from cereeberus import ReebGraph
+
+
 class TestReebClass(unittest.TestCase):
 
     def check_reeb(self, R):
@@ -227,11 +230,22 @@ def test_matrices(self):
         B = R.boundary_matrix()
         self.assertEqual(B.shape, (len(R.nodes), len(R.edges)))
 
+    def test_set_pos_from_f_preserves_y_function_values(self):
+        # The constrained layout updates x-coordinates only; y should remain f(v).
+        R = ex_rg.torus(multigraph=False)
+        R.set_pos_from_f(seed=3, repulsion=1.2)
+
+        self.assertEqual(set(R.nodes), set(R.pos_f.keys()))
+        for v in R.nodes:
+            self.assertEqual(R.pos_f[v][1], R.f[v])
+
 
 
 
 
 
 
+if __name__ == '__main__':
+    unittest.main()
 if __name__ == '__main__':
     unittest.main()