class GraphAdapter(AdapterBase):
def __init__(
self,
seed_str,
name,
file_extension='gml',
vertex_schema={
'gene': 'vector<bool>',
'gen': 'int',
'fitness': 'vector<long>',
'score': 'long'
},
edge_schema={
'label': 'string',
'gen': 'int'
}):
self.seed = seed_str
self.name = name
self.file_extension = file_extension
self.graph = Graph()
# Create graph properties
self.graph.gp.labels = self.graph.new_gp('vector<string>')
self.graph.gp.labels = [seed_str]
self.graph.gp.name = self.graph.new_gp('string')
self.graph.gp.name = self.name
# Create vertex properties
for key in vertex_schema:
self.graph.vp[key] = self.graph.new_vp(vertex_schema[key])
# Create edge properties
for key in edge_schema:
self.graph.ep[key] = self.graph.new_ep(edge_schema[key])
def add_node(self, gene, gen=0, attrs={}):
v = self.graph.add_vertex()
self.graph.vp.gene[v] = gene
self.graph.vp.gen[v] = gen
self.set_props(v, attrs)
return self.graph.vertex_index[v]
def add_edge(self, TAG, srcID, destID, attrs={}):
e = self.graph.add_edge(srcID, destID)
self.graph.ep.label[e] = TAG
for key in attrs:
self.graph.ep[key][e] = attrs[key]
return self.graph.edge_index[e]
def getNode(self, nodeID):
return self.graph.vertex(nodeID)
def getEdge(self, edgeID):
return self.graph.edge(edgeID)
def fetchIndividual(self, individual):
targets = graph_tool.util.find_vertex(self.graph, self.graph.vp.gene,
individual)
# find the last node, the one with highest `gen`
if targets:
# guaranteed to be in order!!
return self.graph.vertex_index[targets[-1]]
else:
return None
def walk_edge(self, TAG, startID):
pass
def update_fitness(self, nodeID, fitness):
v = self.graph.vertex(nodeID)
self.set_props(v, {'fitness': fitness})
def update_score(self, nodeID, score):
v = self.graph.vertex(nodeID)
self.set_props(v, {'score': score})
def set_props(self, v, attrs):
for key in attrs:
self.graph.vp[key][v] = attrs[key]
def save(self):
filename = os.path.join('graphs',
self.name) + '.' + self.file_extension
self.graph.save(filename)
return filename
def numNodes(self):
return self.graph.num_vertices()
