def readFile(self, filename):
self.reset()
try:
parser = GraphMLParser()
g = parser.parse(filename)
except Exception:
box.showerror("Chyba při zpracování vstupního souboru", "Chybný formát souboru.")
return
nodeMap = {}
try:
for gnode in g.nodes():
nodeMap[gnode.id] = self.__add_node(int(gnode['x']), int(gnode['y']))
except KeyError:
box.showerror("Chyba při zpracování vstupního souboru", "Uzlum chybi udaje o pozici (atributy x a y).")
self.reset()
return
try:
for gedge in g.edges():
start = nodeMap[gedge.node1.id]
end = nodeMap[gedge.node2.id]
isCurve = gedge.node1.id == gedge.node2.id
self.__add_edge(start, end, isCurve)
self.label.configure(text=os.path.basename(filename))
except KeyError:
box.showerror("Chyba při zpracování vstupního souboru",
"Soubor obsahuje hrany spojujici neexistujici hrany")
self.reset()
return
self.repaint()
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 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 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 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 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 _graphml2nx(fname):
g=nx.DiGraph()
def _attrdict(node):
attrs=node.attributes()
return {key:attrs[key].value for key in attrs if key not in attr_blacklist}
parser=GraphMLParser()
imported_graph=parser.parse(fname)
edges=[(edge.node1.id, edge.node2.id) for edge in imported_graph.edges()]
nodes=[(node.id, _attrdict(node)) for node in imported_graph.nodes()]
g.add_edges_from(edges)
g.add_nodes_from(nodes)
assert(nx.is_tree(g))
assert(nx.is_directed(g))
return g
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
from pygraphml import Graph
from pygraphml import GraphMLParser
# data sets are from http://www.graphdrawing.org/data.html
parser = GraphMLParser()
g = parser.parse('./random-dag/g.400.12.graphml')
with open('example.lgf', 'w') as fp:
fp.write('@nodes\nlabel\n')
for n in g.nodes():
fp.write(n['label'][1:] + '\n')
fp.write('@arcs\n\t\tlabel\n')
counter = 0
for n in g.nodes():
for nn in g.children(n):
fp.write(n['label'][1:] + '\t' + nn['label'][1:] + '\t' +
str(counter) + '\n')
counter += 1
fp.write('@end\n')
'Mehadia': 241,
'Neamt': 234,
'Oradea': 380,
'Pitesti': 100,
'Rimnicu Vilcea': 193,
'Sibiu': 253,
'Timisoara': 329,
'Urziceni': 80,
'Vaslui': 199,
'Zerind': 374
}
def romania_heuristic(problem, node):
return romania_sld_table[ node['label'] ]
romania_graph = parser.parse("test-graphs/romania.graphml")
romania_start_node = "Arad"
romania_problem = Problem(romania_graph, romania_start_node, romania_goal_test)
romania_sln = Informed.a_star(romania_problem, romania_heuristic)
# romania_sln = Uninformed.ucs(romania_problem)
print("A* solution for the Romania problem: \n %s \n" % romania_sln)
####### Radiation problem from the HW1 #######
def radiation_goal_test(node):
return node['label'] == '4'
# TODO: come up with a good heuristic for this problem
def open_file(file):
parser = GraphMLParser()
graph = parser.parse(file)
#graph.show()
return graph
from pygraphml import GraphMLParser
import sys
reload(sys)
sys.setdefaultencoding("latin-1")
file = "mln.graphml"
parser = GraphMLParser()
g = parser.parse(file)
friends = []
friends_with_no_count = []
nodes = g.nodes()
count = 0
for node in nodes:
uid = node['uid']
friend_count = node.attr.get('friend_count', None)
if friend_count is not None:
friends.append(int(friend_count.value))
else:
friends_with_no_count.append(node['Label'])
count += 1
friends.append(len(friends))
facebook = open("facebook_friends_count.csv", "w")
facebook.write("NUM,COUNT\n")
num=1
ALSlm = []
allpms = []
alllms = []
#alllsPn = []
#lllsPm = []
#allpmlengths = []
#allpmdiverse = []
#alllsPnOnPm = []
#alltermWithoutConst = []
ginfos = ["nodes", "paths", "edges"]
#alllinks = []
#get the graph
parser = GraphMLParser()
gname = "bridge2" #"Bics"#"BeyondTheNetwork"#"Cogentco"#"bridge2"#"BeyondTheNetwork"#"Getnet"
g = parser.parse("./archive/{}.graphml".format(gname))
"""
#pmlengths = ["top 1 traversal", "avg"]
gname="AS20965"#"AS8717"#"AS20965"#"AS8717"
g = ipM.loadgraph("./MatlabData/CAIDA_{}.mat".format(gname))
"""
expinfo["init"] = init
expinfo["t"] = t
expinfo["tmax"] = tmax
expinfo["numberMonitors"] = numberMonitors
expinfo["loops"] = loops
expinfo["cond"] = cond
#expinfo["numberPathsBtw2M"]=numberPathsBtw2M
expinfo["gname"] = gname
expinfo["budgets"] = budgets
expinfo["# of nodes with {} degree".format(degreeLimit)] = paH.getnNodes(
from pygraphml import Graph
from pygraphml import GraphMLParser
parser = GraphMLParser()
g = parser.parse(
'rendered_55days_inconsistency_graph_with_AggregationAndLabel.graphml')
nodes = g.BFS()
for node in nodes:
node['r'] = node['r']
node['g'] = node['g']
node['b'] = node['b']
parser.write(g, "myGraph.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)
from pygraphml import Graph
from pygraphml import GraphMLParser
import numpy
import sys
reload(sys)
sys.setdefaultencoding('utf-8')
parser=GraphMLParser()
g=parser.parse("mln.graphml")
#g.show()
datafile=open("facebook.data","w")
dropfile=open("facebook_dropped.data","w")
nodes = g.nodes()
friendCounts=[]
for node in nodes:
try:
count=node['friend_count']
friendCounts.append(int(count))
except Exception, e:
dropfile.write(str(node)+"\n")
friendCounts.append(len(nodes))
friendCounts=sorted(friendCounts)
datafile.write("Friend_count\t"+str(len(nodes))+"\n")
datafile.write("std\t"+str(numpy.std(friendCounts))+"\n")
datafile.write("mean\t"+str(numpy.mean(friendCounts))+"\n")
datafile.write("median\t"+str(numpy.median(friendCounts))+"\n")
for fcount in friendCounts:
datafile.write(str(fcount)+"\n")
datafile.close()
dropfile.close()
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)