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- #!/usr/bin/env python3
- # -*- coding: utf-8 -*-
- """
- Created on Thu Oct 17 18:44:59 2019
-
- @author: ljia
- """
- import numpy as np
- import networkx as nx
- from tqdm import tqdm
- import sys
-
- from gedlibpy import librariesImport, gedlibpy
-
- def GED(g1, g2, lib='gedlibpy', cost='CHEM_1', method='IPFP',
- edit_cost_constant=[], saveGXL='benoit', stabilizer='min', repeat=50):
- """
- Compute GED for 2 graphs.
- """
- if lib == 'gedlibpy':
- def convertGraph(G):
- """Convert a graph to the proper NetworkX format that can be
- recognized by library gedlibpy.
- """
- G_new = nx.Graph()
- for nd, attrs in G.nodes(data=True):
- G_new.add_node(str(nd), chem=attrs['atom'])
- for nd1, nd2, attrs in G.edges(data=True):
- # G_new.add_edge(str(nd1), str(nd2), valence=attrs['bond_type'])
- G_new.add_edge(str(nd1), str(nd2))
-
- return G_new
-
- gedlibpy.restart_env()
- gedlibpy.add_nx_graph(convertGraph(g1), "")
- gedlibpy.add_nx_graph(convertGraph(g2), "")
-
- listID = gedlibpy.get_all_graph_ids()
- gedlibpy.set_edit_cost(cost, edit_cost_constant=edit_cost_constant)
- gedlibpy.init()
- gedlibpy.set_method(method, "")
- gedlibpy.init_method()
-
- g = listID[0]
- h = listID[1]
- if stabilizer == None:
- gedlibpy.run_method(g, h)
- pi_forward = gedlibpy.get_forward_map(g, h)
- pi_backward = gedlibpy.get_backward_map(g, h)
- upper = gedlibpy.get_upper_bound(g, h)
- lower = gedlibpy.get_lower_bound(g, h)
- elif stabilizer == 'min':
- upper = np.inf
- for itr in range(repeat):
- gedlibpy.run_method(g, h)
- upper_tmp = gedlibpy.get_upper_bound(g, h)
- if upper_tmp < upper:
- upper = upper_tmp
- pi_forward = gedlibpy.get_forward_map(g, h)
- pi_backward = gedlibpy.get_backward_map(g, h)
- lower = gedlibpy.get_lower_bound(g, h)
- if upper == 0:
- break
-
- dis = upper
-
- # make the map label correct (label remove map as np.inf)
- nodes1 = [n for n in g1.nodes()]
- nodes2 = [n for n in g2.nodes()]
- nb1 = nx.number_of_nodes(g1)
- nb2 = nx.number_of_nodes(g2)
- pi_forward = [nodes2[pi] if pi < nb2 else np.inf for pi in pi_forward]
- pi_backward = [nodes1[pi] if pi < nb1 else np.inf for pi in pi_backward]
-
- return dis, pi_forward, pi_backward
-
-
- def GED_n(Gn, lib='gedlibpy', cost='CHEM_1', method='IPFP',
- edit_cost_constant=[], stabilizer='min', repeat=50):
- """
- Compute GEDs for a group of graphs.
- """
- if lib == 'gedlibpy':
- def convertGraph(G):
- """Convert a graph to the proper NetworkX format that can be
- recognized by library gedlibpy.
- """
- G_new = nx.Graph()
- for nd, attrs in G.nodes(data=True):
- G_new.add_node(str(nd), chem=attrs['atom'])
- for nd1, nd2, attrs in G.edges(data=True):
- # G_new.add_edge(str(nd1), str(nd2), valence=attrs['bond_type'])
- G_new.add_edge(str(nd1), str(nd2))
-
- return G_new
-
- gedlibpy.restart_env()
- gedlibpy.add_nx_graph(convertGraph(g1), "")
- gedlibpy.add_nx_graph(convertGraph(g2), "")
-
- listID = gedlibpy.get_all_graph_ids()
- gedlibpy.set_edit_cost(cost, edit_cost_constant=edit_cost_constant)
- gedlibpy.init()
- gedlibpy.set_method(method, "")
- gedlibpy.init_method()
-
- g = listID[0]
- h = listID[1]
- if stabilizer == None:
- gedlibpy.run_method(g, h)
- pi_forward = gedlibpy.get_forward_map(g, h)
- pi_backward = gedlibpy.get_backward_map(g, h)
- upper = gedlibpy.get_upper_bound(g, h)
- lower = gedlibpy.get_lower_bound(g, h)
- elif stabilizer == 'min':
- upper = np.inf
- for itr in range(repeat):
- gedlibpy.run_method(g, h)
- upper_tmp = gedlibpy.get_upper_bound(g, h)
- if upper_tmp < upper:
- upper = upper_tmp
- pi_forward = gedlibpy.get_forward_map(g, h)
- pi_backward = gedlibpy.get_backward_map(g, h)
- lower = gedlibpy.get_lower_bound(g, h)
- if upper == 0:
- break
-
- dis = upper
-
- # make the map label correct (label remove map as np.inf)
- nodes1 = [n for n in g1.nodes()]
- nodes2 = [n for n in g2.nodes()]
- nb1 = nx.number_of_nodes(g1)
- nb2 = nx.number_of_nodes(g2)
- pi_forward = [nodes2[pi] if pi < nb2 else np.inf for pi in pi_forward]
- pi_backward = [nodes1[pi] if pi < nb1 else np.inf for pi in pi_backward]
-
- return dis, pi_forward, pi_backward
-
-
- def ged_median(Gn, Gn_median, measure='ged', verbose=False,
- ged_cost='CHEM_1', ged_method='IPFP', saveGXL='benoit'):
- dis_list = []
- pi_forward_list = []
- for idx, G in tqdm(enumerate(Gn), desc='computing median distances',
- file=sys.stdout) if verbose else enumerate(Gn):
- dis_sum = 0
- pi_forward_list.append([])
- for G_p in Gn_median:
- dis_tmp, pi_tmp_forward, pi_tmp_backward = GED(G, G_p,
- cost=ged_cost, method=ged_method, saveGXL=saveGXL)
- pi_forward_list[idx].append(pi_tmp_forward)
- dis_sum += dis_tmp
- dis_list.append(dis_sum)
- return dis_list, pi_forward_list
-
-
- def get_nb_edit_operations(g1, g2, forward_map, backward_map):
- """Compute the number of each edit operations.
- """
- n_vi = 0
- n_vr = 0
- n_vs = 0
- n_ei = 0
- n_er = 0
- n_es = 0
-
- nodes1 = [n for n in g1.nodes()]
- for i, map_i in enumerate(forward_map):
- if map_i == np.inf:
- n_vr += 1
- elif g1.node[nodes1[i]]['atom'] != g2.node[map_i]['atom']:
- n_vs += 1
- for map_i in backward_map:
- if map_i == np.inf:
- n_vi += 1
-
- # idx_nodes1 = range(0, len(node1))
-
- edges1 = [e for e in g1.edges()]
- nb_edges2_cnted = 0
- for n1, n2 in edges1:
- idx1 = nodes1.index(n1)
- idx2 = nodes1.index(n2)
- # one of the nodes is removed, thus the edge is removed.
- if forward_map[idx1] == np.inf or forward_map[idx2] == np.inf:
- n_er += 1
- # corresponding edge is in g2. Edge label is not considered.
- elif (forward_map[idx1], forward_map[idx2]) in g2.edges() or \
- (forward_map[idx2], forward_map[idx1]) in g2.edges():
- nb_edges2_cnted += 1
- # corresponding nodes are in g2, however the edge is removed.
- else:
- n_er += 1
- n_ei = nx.number_of_edges(g2) - nb_edges2_cnted
-
- return n_vi, n_vr, n_vs, n_ei, n_er, n_es
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