def test_graph_io():
g = create_graph()
fname = tempfile.mktemp()
parser = GraphMLParser()
parser.write(g, fname)
with open(fname) as f:
print(f.read())
parser = GraphMLParser()
g = parser.parse(fname)
assert len(g.nodes()) == 5
assert len(g.edges()) == 4
def leeGraphML(file):
'''
Lee un grafo en formato graphML usando la libreria pygraphMl,
y lo devuelve como lista con pesos
'''
parser = GraphMLParser()
g = parser.parse(file)
V = []
E = []
for node in g.nodes():
V.append(node['label'])
for e in g.edges():
source = e.node1
target = e.node2
try:
peso = float(e['d1'])
except:
peso = None
E.append((source['label'], target['label'], peso))
return (V, E)
def createGraphML():
global g
g = Graph()
c.execute('select uid from userdata')
dataList = c.fetchall()
gnodes = []
edges = []
for i in dataList:
i = str(i)
i = i.replace("(", "").replace(",)", "").replace("L", "")
i = int(i)
c.execute('select distinct low from graphdata where high=?', (i, ))
relate = c.fetchall()
if not i in gnodes:
g.add_node(i)
gnodes.append(i)
for e in relate:
e = str(e)
e = e.replace("(", "").replace(",)", "").replace("L", "")
e = int(e)
if not e in gnodes:
g.add_node(e)
gnodes.append(e)
# edges.append(i)
# edges.append(e)
#1 if edges2.count(e) > 1:
g.add_edge_by_label(str(i), str(e))
parser = GraphMLParser()
parser.write(g, "myGraph.graphml")
def __write_graphML(self):
"""Writes the .graphml file.
Uses class Graph from pygraphml library to create the graph.
Also it uses class GraphMLParser from pygraphml library to write the file.
"""
gr = Graph()
# Adding nodes in the graph with properties.
for sub in self.nodes_prop.keys():
n = gr.add_node(sub)
for pair_prop in self.nodes_prop[sub]:
n[pair_prop[0]] = pair_prop[1]
# Adding nodes in the graph without properties.
for node in self.nodes.values():
if node not in self.nodes_prop.keys():
gr.add_node(node)
# Checking the relations between nodes and creating respective edges.
for relation in self.relations:
source = self.nodes[relation[0]]
target = self.nodes[relation[2]]
edge = gr.add_edge_by_label(source, target)
edge.set_directed(True)
edge['model'] = relation[1]
# Writting the file.
parser = GraphMLParser()
file_name = self.file_name.split(".")
file_name = file_name[0]
parser.write(gr, file_name + ".graphml")
print("File " + file_name + ".graphml is succesfully written")
def fromGraph(cls, rs, args):
session = Session()
file, cpu = args
parser = GraphMLParser()
g = parser.parse(os.path.join(DATA_FOLDER, file))
nodes = [Node(name=str(n.id), cpu_capacity=cpu) for n in g.nodes()]
nodes_from_g = {str(n.id): n for n in g.nodes()}
session.add_all(nodes)
session.flush()
edges = [Edge
(node_1=session.query(Node).filter(Node.name == str(e.node1.id)).one(),
node_2=session.query(Node).filter(Node.name == str(e.node2.id)).one(),
bandwidth=float(e.attributes()["d42"].value),
delay=get_delay(nodes_from_g[str(e.node1.id)], nodes_from_g[str(e.node2.id)])
)
for e in g.edges() if
"d42" in e.attributes()
and isOK(nodes_from_g[str(e.node1.id)], nodes_from_g[str(e.node2.id)])
]
session.add_all(edges)
session.flush()
# filter out nodes for which we have edges
valid_nodes = list(set([e.node_1.name for e in edges] + [e.node_2.name for e in edges]))
nodes = list(set([n for n in nodes if str(n.name) in valid_nodes]))
session.add_all(nodes)
session.flush()
session.add_all(edges)
session.flush()
return cls(edges, nodes)
def save_graph(self, file_name):
"""
Save graph to .graphml file
@param file_name : name of the file to which graph will be saved
"""
parser = GraphMLParser()
parser.write(self.g, file_name)
def readGraphMLFile(graphMLFile):
graphMLParser = GraphMLParser()
try:
graphNet = graphMLParser.parse(graphMLFile)
except xml.parsers.expat.ExpatError as e:
print("%s is not a GraphML file\n" % graphMLFile)
print("Error message is %s" % str(e))
sys.exit(-1)
return graphNet
def from_graphml(fname: str) -> Graph:
parser = GraphMLParser()
gml = parser.parse(fname)
g = Graph()
for node in gml._nodes:
g.adj[Node(id=node.id)]
for edge in gml._edges:
g.adj[Node(id=edge.node1.id)].append(Node(id=edge.node2.id))
return g
def generate_chain(screen_name, store_graph):
fh = open("downloaded/%s/tweets.txt" % screen_name, "r")
chain = {}
g = Graph()
nodes = {}
def generate_trigram(words):
if len(words) < 3:
return
for i in range(len(words) - 2):
yield (words[i], words[i + 1], words[i + 2])
if ((words[i], words[i + 1]) in nodes):
if ((words[i + 2]) in nodes):
g.add_edge(nodes[(words[i], words[i + 1])],
nodes[(words[i + 2])])
else:
nodes[(words[i + 2])] = g.add_node(words[i + 2])
g.add_edge(nodes[(words[i], words[i + 1])],
nodes[(words[i + 2])])
else:
nodes[(words[i],
words[i + 1])] = g.add_node(words[i] + words[i + 1])
if ((words[i + 2]) in nodes):
g.add_edge(nodes[(words[i], words[i + 1])],
nodes[(words[i + 2])])
else:
nodes[(words[i + 2])] = g.add_node(words[i + 2])
g.add_edge(nodes[(words[i], words[i + 1])],
nodes[(words[i + 2])])
for line in fh.readlines():
words = line.split()
for word1, word2, word3 in generate_trigram(words):
key = (word1, word2)
if key in chain:
chain[key].append(word3)
else:
chain[key] = [word3]
if (store_graph):
parser = GraphMLParser()
parser.write(g, "downloaded/%s/graph.graphml" % screen_name)
pickle.dump(chain, open("downloaded/%s/chain.p" % screen_name, "wb"))
def writeToGraphml(pages, fileName):
graph = Graph()
nodes = []
# creating nodes
for page in pages:
node = graph.add_node(page.id)
node['title'] = page.title
node['url'] = page.url
if not page.mainCategory is None:
node['main_category'] = page.mainCategory.title
nodes.append(node)
# creating edges
for page in pages:
# if there are edges
if page.linksTo:
for pageId in page.linksTo:
e = graph.add_edge(nodes[page.id], nodes[pageId])
e.set_directed(True)
parser = GraphMLParser()
parser.write(graph, fileName)
from pygraphml.GraphMLParser import *
from pygraphml.Graph import *
from pygraphml.Node import *
from pygraphml.Edge import *
import sys
# parser = GraphMLParser()
# g = parser.parse(sys.argv[1])
# root = g.set_root_by_attribute("RootNode")
# #print g.root()
# for n in g.DFS_prefix():
# print n
# #g.show(True)
g = Graph()
n1 = g.add_node("salut")
n2 = g.add_node("coucou")
n1['positionX'] = 555
g.add_edge(n1, n2)
parser = GraphMLParser()
parser.write(g, "ttest.graphml")
#g.show()
def write(self, ):
"""
"""
parser = GraphMLParser()
parser.write(self.graph, "graph.graphml")
def open_file(file):
parser = GraphMLParser()
graph = parser.parse(file)
#graph.show()
return graph
def displayGroundTruth(self,agent=WORLD,x0=0,y0=0,maxRows=10,recursive=False,selfCycle=False):
if agent == WORLD:
self.clear()
if __graph__:
self.xml = Graph()
else:
self.xml = None
x = x0
y = y0
if agent == WORLD:
if not self.graph:
self.graph = graph.DependencyGraph(self.world)
self.graph.computeGraph()
g = self.graph
state = self.world.state
else:
g = self.graph = graph.DependencyGraph(self.world)
state = self.world.agents[agent].getBelief()
assert len(state) == 1
g.computeGraph(state=next(iter(state.values())),belief=True)
layout = getLayout(g)
if agent == WORLD:
# Lay out the action nodes
x = self.drawActionNodes(layout['action'],x,y,maxRows)
xPostAction = x
believer = None
xkey = 'xpost'
ykey = 'ypost'
else:
believer = agent
xkey = beliefKey(believer,'xpost')
ykey = beliefKey(believer,'ypost')
# Lay out the post variable nodes
x = self.drawStateNodes(layout['state post'],g,x,y,xkey,ykey,believer,maxRows)
# Lay out the observation nodes
if agent == WORLD:
x = self.drawObservationNodes(x,0,self.graph,xkey,ykey)
# Lay out the utility nodes
if agent == WORLD:
if recursive:
uNodes = [a.name for a in self.world.agents.values() \
if a.getAttribute('beliefs','%s0' % (a.name)) is True]
else:
uNodes = self.world.agents.keys()
else:
uNodes = [agent]
x = self.drawUtilityNodes(x,y,g,uNodes)
if agent == WORLD:
# Draw links from utility back to actions
for name in self.world.agents:
if recursive and \
self.world.agents[name].getAttribute('beliefs','%s0' % (name)) is not True:
y += (maxRows+1) * self.rowHeight
self.displayGroundTruth(name,xPostAction,y,maxRows=maxRows,recursive=recursive)
if name in g:
actions = self.world.agents[name].actions
for action in actions:
if action in g:
if gtnodes and str(action) not in gtnodes:
continue
self.drawEdge(name,action,g)
self.colorNodes()
# Draw links, reusing post nodes as pre nodes
for key,entry in g.items():
if isStateKey(key) or isBinaryKey(key):
if not isFuture(key):
key = makeFuture(key)
if agent != WORLD:
key = beliefKey(agent,key)
elif agent != WORLD:
continue
if gtnodes:
if (isFuture(key) and makePresent(key) not in gtnodes) or (not isFuture(key) and str(key) not in gtnodes):
if not isBeliefKey(key):
continue
for child in entry['children']:
if agent != WORLD and child in self.world.agents and not child in uNodes:
continue
if (isStateKey(child) or isBinaryKey(child)) and agent != WORLD:
if isBinaryKey(child) or state2agent(child) == WORLD or \
state2feature(child) not in self.world.agents[state2agent(child)].omega:
child = beliefKey(agent,child)
elif agent != WORLD and not child in uNodes:
continue
if child in self.world.agents and not child in uNodes:
continue
if gtnodes and makePresent(child) not in gtnodes:
continue
if selfCycle or key != child:
self.drawEdge(key,child,g)
x += self.colWidth
if recursive:
rect = QRectF(-self.colWidth/2,y0-self.rowHeight/2,
x,(float(maxRows)+.5)*self.rowHeight)
self.agents[agent] = {'box': QGraphicsRectItem(rect)}
self.agents[agent]['box'].setPen(QPen(QBrush(QColor('black')),3))
self.agents[agent]['box'].setZValue(0.)
if agent != WORLD:
self.agents[agent]['text'] = QGraphicsTextItem(self.agents[agent]['box'])
doc = QTextDocument(agent,self.agents[agent]['text'])
self.agents[agent]['text'].setPos(rect.x(),rect.y())
self.agents[agent]['text'].setTextWidth(rect.width())
self.agents[agent]['text'].setDocument(doc)
if agent != WORLD:
color = self.world.diagram.getColor(agent)
color.setAlpha(128)
self.agents[agent]['box'].setBrush(QBrush(QColor(color)))
self.addItem(self.agents[agent]['box'])
if agent == WORLD:
for observer in self.world.agents.values():
if observer.O is not True:
for omega,table in observer.O.items():
if gtnodes and omega not in gtnodes:
continue
if self.xml:
for oNode in self.xml.nodes():
if oNode['label'] == omega:
break
else:
raise ValueError('Unable to find node for %s' % (omega))
for action,tree in table.items():
if action is not None:
if self.xml and (len(gtnodes) == 0 or str(action) in gtnodes):
for aNode in self.xml.nodes():
if aNode['label'] == str(action):
break
else:
raise ValueError('Unable to find node for %s' % (action))
self.xml.add_edge(aNode,oNode,True)
for key in tree.getKeysIn():
if key != CONSTANT:
if self.xml:
for sNode in self.xml.nodes():
if sNode['label'] == key:
break
else:
raise ValueError('Unable to find node for %s' % (key))
self.xml.add_edge(sNode,oNode,True)
label = '%sBeliefOf%s' % (observer.name,key)
bNode = self.getGraphNode(label)
self.xml.add_edge(oNode,bNode,True)
if recursive:
belief = beliefKey(observer.name,makeFuture(key))
self.drawEdge(omega,belief)
for name in self.world.agents:
# Draw links from non-belief reward components
model = '%s0' % (name)
R = self.world.agents[name].getReward(model)
if R:
for parent in R.getKeysIn() - set([CONSTANT]):
if beliefKey(name,makeFuture(parent) not in self.nodes['state post']):
# Use real variable
self.drawEdge(makeFuture(parent),name,g)
parser = GraphMLParser()
parser.write(self.xml,'/tmp/GroundTruth-USC.graphml')
from pygraphml import GraphMLParser
from lxml import etree
if (__name__ == "__main__"):
gp = GraphMLParser()
g = gp.parse("weather.graphml")
node0 = g.get_node("in the middle", "NodeLabel")
group = node0.container_node[0]
g.set_root(node0)
nodes = g.BFS(direction="contained_nodes")
for node in nodes:
print(node.attr.get("NodeLabel"))
node1 = g.get_node("n0", "id")
test = etree.tostring(g.xml, encoding=str)
gp.write(g)
def read_graphml(filename, color_map=[]):
parser = GraphMLParser()
g = parser.parse(filename)
g.set_root('n0')
print dir(g)
id = '%s_%s'%(filename.split('.')[0],filename.split('.')[1])
net = Network(id=id)
net.notes = "NeuroMLlite conversion of %s from https://www.neurodata.io/project/connectomes/"%filename
#net.parameters = {}
dummy_cell = Cell(id='testcell', pynn_cell='IF_cond_alpha')
dummy_cell.parameters = { "tau_refrac":5, "i_offset":0 }
net.cells.append(dummy_cell)
net.synapses.append(Synapse(id='ampa',
pynn_receptor_type='excitatory',
pynn_synapse_type='cond_alpha',
parameters={'e_rev':0, 'tau_syn':2}))
for node in g.nodes():
info = ''
for a in node.attributes():
info+=node.attr[a].value+'; '
if len(info)>2: info = info[:-4]
color = '%s %s %s'%(random.random(),random.random(),random.random()) \
if not info in color_map else color_map[info]
print('> Node: %s (%s), color: %s'%(node.id, info, color))
p0 = Population(id=node.id,
size=1,
component=dummy_cell.id,
properties={'color':color})
net.populations.append(p0)
for edge in g.edges():
#print dir(edge)
#print edge.attributes()
src = edge.node1.id
tgt = edge.node2.id
weight = float(str(edge.attr['e_weight'].value)) if 'e_weight' in edge.attr else 1
#print('>> Edge from %s -> %s, weight %s'%(src, tgt, weight))
net.projections.append(Projection(id='proj_%s_%s'%(src,tgt),
presynaptic=src,
postsynaptic=tgt,
synapse='ampa',
weight=weight,
random_connectivity=RandomConnectivity(probability=1)))
#g.show()
#print(net)
#print(net.to_json())
new_file = net.to_json_file('%s.json'%net.id)
duration=1000
dt = 0.1
sim = Simulation(id='Sim%s'%net.id,
network=new_file,
duration=duration,
dt=dt,
recordRates={'all':'*'})
check_to_generate_or_run(sys.argv, sim)
