extened Makefile, added ./tools/removeiso.py, added option --graphviz, readme Makefile

tools/removeiso.py

@@ -0,0 +1,77 @@
+#!/usr/bin/python3
+"""
+SPDX-FileCopyrightText: 2023 Ämin Baumeler <amin@indyfac.ch> and Eleftherios-Ermis Tselentis <eleftheriosermis.tselentis@oeaw.ac.at>
+
+SPDX-License-Identifier: GPL-3.0-or-later
+"""
+import sys
+import getopt
+import numpy as np
+import networkx as nx
+
+"""Parse command line arguments first."""
+helpstr = """Usage: """+sys.argv[0]+""" -f <filename>
+
+Filters out the isomorphic graphs in `filename'."""
+
+FILENAME = False
+
+try:
+    opts, args = getopt.getopt(sys.argv[1:], "hf:")
+except getopt.GetoptError:
+    print(helpstr, file=sys.stderr)
+    sys.exit(2)
+for opt, arg in opts:
+    if opt == '-h':
+        print(helpstr)
+        sys.exit()
+    elif opt == '-f':
+        FILENAME = arg
+
+if not FILENAME:
+    print(helpstr, file=sys.stderr)
+    sys.exit(2)
+
+
+with open(FILENAME, 'rb') as f:
+    num_lines = sum(1 for _ in f)
+print(f"Total number of digraphs is {num_lines}", file=sys.stderr)
+
+
+nonisodigraphs = set()
+
+cnt = 0
+fnd = 0
+with open(FILENAME, 'r') as f:
+    while 1:
+        cnt = cnt + 1
+        print("\r{:.2f}%".format(100*cnt/num_lines), end='', file=sys.stderr)
+        line = f.readline().strip('{}\n')
+        if not line:
+            break
+        G = nx.from_numpy_matrix(np.vectorize(int)(np.matrix([x.split(',') for x in line.split('},{')])), create_using=nx.DiGraph)
+
+        couldbeold = False
+        for H in nonisodigraphs:
+            # Returns False if graphs are definitely not isomorphic.
+            # True does NOT guarantee isomorphism.
+            if nx.faster_could_be_isomorphic(G, H):
+                couldbeold = True
+                break
+
+        if not couldbeold:
+            nonisodigraphs.add(G)
+            fnd = fnd + 1
+            print(f"{{{{{line}}}}}")
+            continue
+
+        new = True
+        for H in nonisodigraphs:
+            if nx.is_isomorphic(G, H):
+                new = False
+                break
+        if new:
+            nonisodigraphs.add(G)
+            fnd = fnd + 1
+            print(f"{{{{{line}}}}}")
+    print(f"\r100%  Found {fnd} non-isomoric graphs", file=sys.stderr)