From 1fb56392a467e805457b5aad3edf74d65020676e Mon Sep 17 00:00:00 2001
From: Dimitri Lozeve <dimitri.lozeve@gmail.com>
Date: Thu, 14 Jun 2018 12:19:39 +0100
Subject: [PATCH] Implement weight rank clique filtration

---
 filtration.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 filtration.py

diff --git a/filtration.py b/filtration.py
new file mode 100644
index 0000000..99d7c3f
--- /dev/null
+++ b/filtration.py
@@ -0,0 +1,21 @@
+import numpy as np
+import igraph as ig
+import dionysus as d
+
+
+def wrcf(G, weight="weight"):
+    # 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)