def shortTest():
gedlibpy.restart_env()
print("Here is the mini Python function !")
gedlibpy.load_GXL_graphs(
"include/gedlib-master/data/datasets/Mutagenicity/data/",
"include/gedlib-master/data/collections/Mutagenicity.xml")
listID = gedlibpy.get_all_graph_ids()
gedlibpy.set_edit_cost("CHEM_1")
gedlibpy.init()
gedlibpy.set_method("BIPARTITE", "")
gedlibpy.init_method()
g = listID[0]
h = listID[1]
gedlibpy.run_method(g, h)
print("Node Map : ", gedlibpy.get_node_map(g, h))
print("Assignment Matrix : ")
afficheMatrix(gedlibpy.get_assignment_matrix(g, h))
print("Upper Bound = " + str(gedlibpy.get_upper_bound(g, h)) +
", Lower Bound = " + str(gedlibpy.get_lower_bound(g, h)) +
", Runtime = " + str(gedlibpy.get_runtime(g, h)))
def classiqueTest():
gedlibpy.restart_env()
gedlibpy.load_GXL_graphs(
'include/gedlib-master/data/datasets/Mutagenicity/data/',
'collections/MUTA_10.xml')
listID = gedlibpy.get_all_graph_ids()
afficheId = ""
for i in listID:
afficheId += str(i) + " "
print("Number of graphs = " + str(len(listID)) + ", list of Ids = " +
afficheId)
gedlibpy.set_edit_cost("CHEM_1")
gedlibpy.init()
gedlibpy.set_method("IPFP", "")
gedlibpy.init_method()
g = listID[0]
h = listID[0]
gedlibpy.run_method(g, h)
liste = gedlibpy.get_all_map(g, h)
print("Forward map : ", gedlibpy.get_forward_map(g, h),
", Backward map : ", gedlibpy.get_backward_map(g, h))
print("Node Map : ", gedlibpy.get_node_map(g, h))
print("Upper Bound = " + str(gedlibpy.get_upper_bound(g, h)) +
", Lower Bound = " + str(gedlibpy.get_lower_bound(g, h)) +
", Runtime = " + str(gedlibpy.get_runtime(g, h)))
def nxTest(dataset):
gedlibpy.restart_env()
for graph in dataset:
gedlibpy.add_nx_graph(graph, "")
listID = gedlibpy.get_all_graph_ids()
gedlibpy.set_edit_cost("CHEM_1")
gedlibpy.init()
gedlibpy.set_method("IPFP", "")
gedlibpy.init_method()
print(listID)
g = listID[0]
h = listID[1]
gedlibpy.run_method(g, h)
print("Node Map : ", gedlibpy.get_node_map(g, h))
print("Upper Bound = " + str(gedlibpy.get_upper_bound(g, h)) +
", Lower Bound = " + str(gedlibpy.get_lower_bound(g, h)) +
", Runtime = " + str(gedlibpy.get_runtime(g, h)))
def GED(g1, g2, lib='gedlibpy', cost='CHEM_1', method='IPFP',
edit_cost_constant=[], 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_symbol'])
# G_new.add_node(str(nd), x=str(attrs['attributes'][0]),
# y=str(attrs['attributes'][1]))
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 == 'mean':
# @todo: to be finished...
upper_list = [np.inf] * repeat
for itr in range(repeat):
gedlibpy.run_method(g, h)
upper_list[itr] = gedlibpy.get_upper_bound(g, h)
pi_forward = gedlibpy.get_forward_map(g, h)
pi_backward = gedlibpy.get_backward_map(g, h)
lower = gedlibpy.get_lower_bound(g, h)
upper = np.mean(upper_list)
elif stabilizer == 'median':
if repeat % 2 == 0:
repeat += 1
upper_list = [np.inf] * repeat
pi_forward_list = [0] * repeat
pi_backward_list = [0] * repeat
for itr in range(repeat):
gedlibpy.run_method(g, h)
upper_list[itr] = gedlibpy.get_upper_bound(g, h)
pi_forward_list[itr] = gedlibpy.get_forward_map(g, h)
pi_backward_list[itr] = gedlibpy.get_backward_map(g, h)
lower = gedlibpy.get_lower_bound(g, h)
upper = np.median(upper_list)
idx_median = upper_list.index(upper)
pi_forward = pi_forward_list[idx_median]
pi_backward = pi_backward_list[idx_median]
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
elif stabilizer == 'max':
upper = 0
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)
elif stabilizer == 'gaussian':
pass
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_symbol'])
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