Dissertation: final update

dissertation/wrcf.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+import numpy as np
+import igraph as ig
+import dionysus as d
+
+
+def wrcf(G, weight="weight"):
+    """Compute the weight-rank clique filtration (WRCF) of a graph.
+
+    :param G: igraph Graph
+    :param weight: name of the weight attribute
+
+    :return: a Dionysus filtration.
+    """
+    # Define filtration step 0 as the set of all nodes
+    filt = d.Filtration()
+    for v in G.vs:
+        filt.append(d.Simplex([v.index], 0))
+    # Rank all edge weights
+    distinct_weights = np.unique(G.es[weight])[::-1]
+    for t, w in enumerate(distinct_weights):
+        # At filtration step t, threshold the graph at weight[t]
+        subg = G.subgraph_edges(G.es(lambda e: e[weight] >= w))
+        # Find all maximal cliques and define them to be simplices
+        for clique in subg.maximal_cliques():
+            for s in d.closure([d.Simplex(clique)], len(clique)):
+                filt.append(d.Simplex(s, t+1))
+    filt.sort()
+    return(filt)
+
+
+def wrcf_diagram(graph, weight="weight"):
+    """Compute persistence diagrams of a graph using WRCF.
+
+    :param graph: igraph Graph
+    :param weight: name of the weight attribute
+
+    :return: a list of persistence diagrams.
+    """
+    filt = wrcf(graph, weight=weight)
+    pers = d.homology_persistence(filt)
+    dgms = d.init_diagrams(pers, filt)
+    return dgms