def labeling_to_root(self, graph, vertex):
labeled_graph = nx.Graph(graph)
source_path_lengths = nx.single_source_dijkstra_path_length(
graph, vertex)
nx.set_node_attributes(labeled_graph, source_path_lengths, 'labeling')
return labeled_graph
def create_graph_rendrer(threshold, df, graph_df):
plot_new = Plot(plot_width=1100,
plot_height=800,
x_range=Range1d(-1.1, 1.1),
y_range=Range1d(-1.1, 1.1))
plot_new.title.text = "Dash-Graph"
color_dict = {}
for i in range(1, df['UserID'].max() + 1):
color_dict[i] = df.groupby('UserID').groups[i].size * 1.9
pal_hex_lst = bokeh.palettes.viridis(21)
mapper = LinearColorMapper(palette=pal_hex_lst, low=0, high=21)
G = create_graph(graph_df, threshold, True)
# add graph's attributes
node_size = {k: ((5 * v) + 5) for k, v in G.degree()}
nx.set_node_attributes(G, color_dict, 'node_color')
nx.set_node_attributes(G, node_size, 'node_size')
graph_renderer = from_networkx(G, nx.spring_layout)
graph_renderer.node_renderer.glyph = Circle(size='node_size',
fill_color={
'field': 'node_color',
'transform': mapper
})
graph_renderer.edge_renderer.glyph = MultiLine(line_color="black",
line_alpha=0.8,
line_width=0.5)
graph_renderer.selection_policy = NodesAndLinkedEdges()
plot.renderers.append(graph_renderer)
def canonicalizes(self, subgraph):
st = time.time()
#wl_subgraph_normalized=self.wl_normalization(subgraph)['labeled_graph']
#g_relabel=convert_node_labels_to_integers(wl_subgraph_normalized)
g_relabel = convert_node_labels_to_integers(subgraph)
labeled_graph = nx.Graph(g_relabel)
nauty_graph = Graph(len(g_relabel.nodes()), directed=False)
nauty_graph.set_adjacency_dict(
{n: list(nbrdict)
for n, nbrdict in g_relabel.adjacency()})
labels_dict = nx.get_node_attributes(g_relabel, 'labeling')
canonical_labeling_dict = {
k: canonical_labeling(nauty_graph)[k]
for k in range(len(g_relabel.nodes()))
}
new_ordered_dict = self.rank_label_wrt_dict(g_relabel, labels_dict,
canonical_labeling_dict)
nx.set_node_attributes(labeled_graph, new_ordered_dict, 'labeling')
ed = time.time()
self.all_times['canonicalizes'].append(ed - st)
return labeled_graph
def zeroReceptiveField(self):
graph = nx.star_graph(self.k - 1) #random graph peu importe sa tete
nx.set_node_attributes(graph, self.dummy_value, 'attr_name')
nx.set_node_attributes(graph,
{k: k
for k, v in dict(graph.nodes()).items()},
'labeling')
return graph
def __init__(self,
nx_graph,
w,
s=1,
k=10,
labeling_procedure_name='betweeness',
use_node_deg=False,
one_hot=False,
dummy_value=-1):
self.nx_graph = nx_graph
self.use_node_deg = use_node_deg
if self.use_node_deg:
node_degree_dict = dict(self.nx_graph.degree())
normalized_node_degree_dict = {
k: v / len(self.nx_graph.nodes())
for k, v in node_degree_dict.items()
}
nx.set_node_attributes(self.nx_graph, normalized_node_degree_dict,
'attr_name')
self.all_times = {}
self.all_times['neigh_assembly'] = []
self.all_times['normalized_subgraph'] = []
self.all_times['canonicalizes'] = []
self.all_times['compute_subgraph_ranking'] = []
self.all_times['labeling_procedure'] = []
self.all_times['first_labeling_procedure'] = []
self.w = w
self.s = s
self.k = k
self.dummy_value = dummy_value
self.exists_dummies = False
self.one_hot = one_hot
self.labeling_procedure_name = labeling_procedure_name
if self.labeling_procedure_name == 'approx_betweeness':
st = time.time()
self.dict_first_labeling = self.betweenness_centrality_labeling(
self.nx_graph, approx=int(len(self.nx_graph.nodes()) / 5) + 1)
self.labeling_procedure_name = 'betweeness'
end = time.time()
self.all_times['first_labeling_procedure'].append(end - st)
elif self.labeling_procedure_name == 'betweeness':
st = time.time()
self.dict_first_labeling = self.betweenness_centrality_labeling(
self.nx_graph)
end = time.time()
self.all_times['first_labeling_procedure'].append(end - st)
else:
st = time.time()
self.dict_first_labeling = self.labeling_procedure(self.nx_graph)
end = time.time()
self.all_times['first_labeling_procedure'].append(end - st)
self.original_labeled_graph = self.dict_first_labeling['labeled_graph']
def create_empty_receptive_field(self):
"""
Method that creates a dummy receptive field for padding purposes
:return: a receptive field of dummy nodes
"""
graph = nx.star_graph(self.rf_size - 1)
nx.set_node_attributes(graph, self.dummy_value, 'attr_name')
nx.set_node_attributes(graph, {element: element for element, v in dict(graph.nodes()).items()}, 'labeling')
return graph
def compute_subgraph_ranking(self,subgraph,vertex,original_order_to_respect):
st=time.time()
labeled_graph=nx.Graph(subgraph)
ordered_subgraph_from_centrality=self.labeling_to_root(subgraph,vertex)
all_labels_in_subgraph_dict=nx.get_node_attributes(ordered_subgraph_from_centrality,'labeling')
new_ordered_dict=self.rank_label_wrt_dict(ordered_subgraph_from_centrality,all_labels_in_subgraph_dict,original_order_to_respect)
nx.set_node_attributes(labeled_graph,new_ordered_dict,'labeling')
ed=time.time()
self.all_times['compute_subgraph_ranking'].append(ed-st)
return labeled_graph
def betweenness_centrality_labeling(self,graph,approx=None):
result={}
labeled_graph=nx.Graph(graph)
if approx is None:
centrality=list(nx.betweenness_centrality(graph).items())
else:
centrality=list(nx.betweenness_centrality(graph,k=approx).items())
sorted_centrality=sorted(centrality,key=lambda n:n[1],reverse=True)
dict_={}
label=0
for t in sorted_centrality:
dict_[t[0]]=label
label+=1
nx.set_node_attributes(labeled_graph,dict_,'labeling')
ordered_nodes=list(zip(*sorted_centrality))[0]
result['labeled_graph']=labeled_graph
result['sorted_centrality']=sorted_centrality
result['ordered_nodes']=ordered_nodes
return result
def compute_graph_ranking(graph: nx.Graph,
vertex: int,
original_node_order: dict):
"""
Method that relabels a graph w.r.t. nodes distances to given root
:param graph: subgraph to rank
:param vertex: landmark vertex for the ranking
:param original_node_order: original ranking
:return: graph labeled by the new ranking
"""
labeled_graph = nx.Graph(graph)
ordered_graph = compute_ranking_distance(graph, vertex)
labels = nx.get_node_attributes(ordered_graph, 'labeling')
new_order = relabel_graph(graph=ordered_graph,
original_labeling=labels,
new_labeling=original_node_order)
nx.set_node_attributes(labeled_graph, new_order, 'labeling')
return labeled_graph
def nauty_graph_automorphism(graph: nx.Graph):
"""
Graph canonicalization funtion, meant to break timebreakers of the non-injective ranking function
:param graph: subgraph to be canonicalized
:return: canonicalized subgraph
"""
# convert labels to integers to give nauty the node partitions required
graph_int_labeled = convert_node_labels_to_integers(graph)
canonicalized_graph = nx.Graph(graph_int_labeled)
# get canonicalized graph using nauty
nauty = Graph(len(graph_int_labeled.nodes()), directed=False)
nauty.set_adjacency_dict({node: list(nbr) for node, nbr in graph_int_labeled.adjacency()})
labels_dict = nx.get_node_attributes(graph_int_labeled, 'labeling')
canonical_labeling_order = {k: canonical_labeling(nauty)[k] for k in
range(len(graph_int_labeled.nodes()))}
canonical_order = relabel_graph(graph_int_labeled, labels_dict, canonical_labeling_order)
nx.set_node_attributes(canonicalized_graph, canonical_order, 'labeling')
return canonicalized_graph
def activate_nodes(fileN, p, beginRange, endRange, outFileName):
# READ GRAPH FROM FILE
g = nx.read_edgelist(fileN)
#g = nx.read_weighted_edgelist(fileN)
# SORT BY DEGREE
sorted(g.degree, key=lambda x: x[1], reverse=True)
# SET ATTRIBUTE 0 TO ALL NODES
attr = 0
nx.set_node_attributes(g, attr, 'attr')
att = nx.get_node_attributes(g, 'attr')
#print att
numNodes = 0
for k, v in att.items():
numNodes = numNodes + 1
#print("Key : {0}, Value : {1}".format(k, v))
#numNodes = number_of_nodes(g)
if (p == 0.3):
# RANGE ADJUST
a = 100 - beginRange
b = 100 - endRange
beginAtt = (a * numNodes) / 100
endAtt = (b * numNodes) / 100
# FINAL POSITIONS OF RANGE ON DICTIONARY
beginAtt = numNodes - beginAtt
endAtt = numNodes - endAtt
while (beginAtt <= endAtt):
att[att.keys()[beginAtt]] = 1
beginAtt = beginAtt + 1
#for k, v in att.items():
#print("Key : {0}, Value : {1}".format(k, v))
if (p == 0.2):
# RANGE ADJUST
a = 100 - beginRange
b = 100 - (endRange - 10)
beginAtt = (a * numNodes) / 100
endAtt = (b * numNodes) / 100
# FINAL POSITIONS OF RANGE ON DICTIONARY
beginAtt = numNodes - beginAtt
endAtt = numNodes - endAtt
while (beginAtt <= endAtt):
att[att.keys()[beginAtt]] = 1
beginAtt = beginAtt + 1
#for k, v in att.items():
#print("Key : {0}, Value : {1}".format(k, v))
if (p == 0.1):
# RANGE ADJUST
a = 100 - beginRange
b = 100 - (endRange - 20)
beginAtt = (a * numNodes) / 100
endAtt = (b * numNodes) / 100
# FINAL POSITIONS OF RANGE ON DICTIONARY
beginAtt = numNodes - beginAtt
endAtt = numNodes - endAtt
while (beginAtt <= endAtt):
att[att.keys()[beginAtt]] = 1
beginAtt = beginAtt + 1
#for k, v in att.items():
#print("Key : {0}, Value : {1}".format(k, v))
if (p == 0.05):
# RANGE ADJUST
a = 100 - beginRange
b = 100 - (endRange - 25)
beginAtt = (a * numNodes) / 100
endAtt = (b * numNodes) / 100
# FINAL POSITIONS OF RANGE ON DICTIONARY
beginAtt = numNodes - beginAtt
endAtt = numNodes - endAtt
while (beginAtt <= endAtt):
att[att.keys()[beginAtt]] = 1
beginAtt = beginAtt + 1
#for k, v in att.items():
#print("Key : {0}, Value : {1}".format(k, v))
nx.set_node_attributes(g, att, 'attr')
nx.write_edgelist(g, outFileName+".elist.txt", data=['attr'])
#att = nx.get_node_attributes(g, 'attr')
#for k, v in att.items():
# print("Key : {0}, Value : {1}".format(k, v))
measure_MI(g)
def wl_normalization(self, graph):
result = {}
labeled_graph = nx.Graph(graph)
relabel_dict_ = {}
graph_node_list = list(graph.nodes())
for i in range(len(graph_node_list)):
relabel_dict_[graph_node_list[i]] = i
i += 1
inv_relabel_dict_ = {v: k for k, v in relabel_dict_.items()}
graph_relabel = nx.relabel_nodes(graph, relabel_dict_)
label_lookup = {}
label_counter = 0
l_aux = list(
nx.get_node_attributes(graph_relabel, 'attr_name').values())
labels = np.zeros(len(l_aux), dtype=np.int32)
adjency_list = list([
list(x[1].keys()) for x in graph_relabel.adjacency()
]) #adjency list à l'ancienne comme version 1.0 de networkx
for j in range(len(l_aux)):
if not (l_aux[j] in label_lookup):
label_lookup[l_aux[j]] = label_counter
labels[j] = label_counter
label_counter += 1
else:
labels[j] = label_lookup[l_aux[j]]
# labels are associated to a natural number
# starting with 0.
new_labels = copy.deepcopy(labels)
# create an empty lookup table
label_lookup = {}
label_counter = 0
for v in range(len(adjency_list)):
# form a multiset label of the node v of the i'th graph
# and convert it to a string
long_label = np.concatenate(
(np.array([labels[v]]), np.sort(labels[adjency_list[v]])))
long_label_string = str(long_label)
# if the multiset label has not yet occurred, add it to the
# lookup table and assign a number to it
if not (long_label_string in label_lookup):
label_lookup[long_label_string] = label_counter
new_labels[v] = label_counter
label_counter += 1
else:
new_labels[v] = label_lookup[long_label_string]
# fill the column for i'th graph in phi
labels = copy.deepcopy(new_labels)
dict_ = {inv_relabel_dict_[i]: labels[i] for i in range(len(labels))}
nx.set_node_attributes(labeled_graph, dict_, 'labeling')
result['labeled_graph'] = labeled_graph
result['ordered_nodes'] = [
x[0] for x in sorted(dict_.items(), key=lambda x: x[1])
]
return result
