def __init__(self):
"""
Initializes graph parameters.
"""
self.g = Graph()
self.vertex_id = 0
self.edge_id = 0
class GraphMLExporter():
"""
"""
def __init__(self, lines):
"""
"""
self.lines = lines
self.graph = Graph()
self.i = 0
self.createGraph()
def createGraph(self):
"""
"""
mul = 100
for line in self.lines:
n1 = self.checkNode(str(self.i))
n2 = self.checkNode(str(self.i))
n1['x'] = line.p1.x * mul
n1['y'] = line.p1.y * mul
n1['z'] = line.p1.z * mul
n2['x'] = line.p2.x * mul
n2['y'] = line.p2.y * mul
n2['z'] = line.p2.z * mul
self.graph.add_edge(n1, n2)
def checkNode(self, label):
"""
"""
exist = False
for n in self.graph.nodes():
if label == n['label']:
exist = True
node = n
if exist:
return node
else:
self.i += 1
return self.graph.add_node(label)
def write(self, ):
"""
"""
parser = GraphMLParser()
parser.write(self.graph, "graph.graphml")
class GraphMLExporter():
"""
"""
def __init__(self, lines):
"""
"""
self.lines = lines
self.graph = Graph()
self.i = 0
self.createGraph()
def createGraph(self):
"""
"""
mul = 100
for line in self.lines:
n1 = self.checkNode(str(self.i))
n2 = self.checkNode(str(self.i))
n1['x'] = line.p1.x * mul
n1['y'] = line.p1.y * mul
n1['z'] = line.p1.z * mul
n2['x'] = line.p2.x * mul
n2['y'] = line.p2.y * mul
n2['z'] = line.p2.z * mul
self.graph.add_edge(n1, n2)
def checkNode(self, label):
"""
"""
exist = False
for n in self.graph.nodes():
if label == n['label']:
exist = True
node = n
if exist:
return node
else:
self.i += 1
return self.graph.add_node(label)
def write(self, ):
"""
"""
parser = GraphMLParser()
parser.write(self.graph, "graph.graphml")
def __init__(self, lines):
"""
"""
self.lines = lines
self.graph = Graph()
self.i = 0
self.createGraph()
def loadgraph(addr):
gphml = Graph()
gmatrix = loadmat(addr)["A"].toarray()
for i in range(len(gmatrix)):
n = gphml.add_node()
n.id = str(i)
for i in range(len(gmatrix)):
for j in range(i + 1, len(gmatrix)):
if gmatrix[i, j] == 1:
gphml.add_edge_by_id(str(i), str(j))
return gphml
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 do_harvest(query, iterations):
book_data = {}
currentPosition = 0
query_string = QUERY_FORMAT_STRING.format(query)
graph = Graph()
parser = JSONParser.JSONParser()
# map for collecting nodes
nodes = {}
while (iterations > len(nodes)):
page = requests.get(query_string)
tree = html.fromstring(page.content)
links = tree.xpath('//table[@id="searchresult"]//a/@href')
if (len(links) == 0):
break
for link in links:
book_info_response = requests.get(BASE_URL_DNB + link)
get_data_from_book_info(book_data, book_info_response, "Titel")
get_data_from_book_info(book_data, book_info_response,
"Person(en)")
get_data_from_book_info_link(book_data, book_info_response,
"Schlagwörter")
if (len(book_data['Schlagwörter']) > 0):
for v in book_data.values():
print(v)
for s in book_data['Schlagwörter']:
node = None
node = graph.add_node(s)
nodes[s] = node
s1 = book_data['Schlagwörter'][0]
for s in book_data['Schlagwörter']:
if s != s1:
edge = graph.add_edge(nodes[s1], nodes[s])
edge['label'] = book_data['Titel']
query_string = QUERY_FORMAT_STRING_2.format(query,
str(currentPosition))
currentPosition += len(links)
iterations -= 1
return parser.tostring(graph)
def writeFile(self, filename):
g = Graph()
for i in self.nodes:
node = self.nodes[i]
node.name = str(i)
gnode = g.add_node(i)
gnode['label'] = i
gnode['x'] = node.x
gnode['y'] = node.y
for i in self.edges:
edge = self.edges[i]
edge.name = i
parser = GraphMLParser()
parser.write(g, filename)
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)
g.add_edge_by_label(str(i), str(e))
parser = GraphMLParser()
parser.write(g, "myGraph.graphml")
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 __init__(self, lines):
"""
"""
self.lines = lines
self.graph = Graph()
self.i = 0
self.createGraph()
def create_graph():
Item.ID = 0
g = Graph()
n1 = g.add_node("A")
n2 = g.add_node("B")
n3 = g.add_node("C")
n4 = g.add_node("D")
n5 = g.add_node("E")
g.add_edge(n1, n3)
g.add_edge(n2, n3)
g.add_edge(n3, n4)
g.add_edge(n3, n5)
return g
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)
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 generate_graph_with_clusters(summary, attr): from pygraphml import Graph items = summary.items() labels = np.array([artist for artist, obj in items]) g = Graph() for artist in labels: g.add_node(artist) if attr == "emotion": for category in EMOTION_CATEGORIES: g.add_node(category) elif attr == "topic": for category in TOPIC_CATEGORIES: g.add_node(category) for artist_id, x in enumerate(items): arist, obj = x if attr == "emotion": for idx, score in enumerate(obj["emotions"]): edge = g.add_edge_by_label(EMOTION_CATEGORIES[idx], labels[artist_id]) if score == 0: edge["weight"] = 0.001 # Set to very small value else: edge["weight"] = score elif attr == "topic": for idx, score in enumerate(obj["topics"]): edge = g.add_edge_by_label(TOPIC_CATEGORIES[idx], labels[artist_id]) if score == 0: edge["weight"] = 0.001 # Set to very small value else: edge["weight"] = score 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 generate_graph(similarity, attr): from pygraphml import Graph items = similarity.items() labels = np.array([artist for artist, obj in items]) network = np.zeros((labels.size, labels.size)) g = Graph() for artist in labels: g.add_node(artist) for artist_id, x in enumerate(items): network[artist_id, artist_id] = 1 artist, obj = x if attr == "emotion": for idx, score in enumerate(obj["emotion_sim"]): if network[artist_id, idx] == 0 and network[idx, artist_id] == 0: edge = g.add_edge_by_label(labels[artist_id], labels[idx]) if score == 0: edge["weight"] = 0.001 else: edge["weight"] = score network[artist_id, idx] = 1 network[idx, artist_id] = 1 elif attr == "topic": for idx, score in enumerate(obj["topic_sim"]): if network[artist_id, idx] == 0 and network[idx, artist_id] == 0: edge = g.add_edge_by_label(labels[artist_id], labels[idx]) if score == 0: edge["weight"] = 0.001 else: edge["weight"] = score network[artist_id, idx] = 1 network[idx, artist_id] = 1 return g
class DirectedEdge(Edge):
def __init__(self, src, dst, weight):
Edge.__init__(self, src, dst, weight)
def add_to_graph(self, g, nodes):
g.add_edge(nodes[self.src], nodes[self.dst], directed=True)
Nodes = {}
Values = {}
Allocations = {}
args = sys.argv[1:]
g = Graph()
# Find all allocations and values
with open(args[0], 'r') as f:
for line in f:
j = json.loads(line)
if "allocation" in j:
alloc = j["allocation"]
Id = int(alloc["id"])
pos = int(alloc["pos"])
size = int(alloc["size"])
AS = json.loads(alloc["addrsp"])
AM = json.loads(alloc["mem"])
pagetype = alloc["type"]
as_type = AS["type"]
newAlloc = Allocation(Id, pos, size, pagetype, as_type)
def get_data_from_book_info (book_data, response, field_name):
tree = html.fromstring(response.content)
field_data = tree.xpath('//td/strong[text() = "{}"]/../../td/text()'.format(field_name))
field_string = ""
for field in field_data:
field_string = field_string + field.replace("\n","").replace("\r","").replace("\t","")
book_data[field_name] = field_string
if __name__ == "__main__":
book_data = {}
currentPosition = 0;
query_string = QUERY_FORMAT_STRING.format(QUERY);
file_handles = {};
graph = Graph();
parser = GraphMLParser()
filename = "book_data_" + QUERY + ".graphml"
# map for collecting nodes
nodes = {}
while(True):
page = requests.get(query_string)
tree = html.fromstring(page.content)
links = tree.xpath('//table[@id="searchresult"]//a/@href')
if(len(links) == 0):
break;
for link in links:
book_info_response = requests.get(BASE_URL_DNB + link)
from pygraphml import Graph
# Create graph
g = Graph()
n1 = g.add_node("A")
n2 = g.add_node("B")
n3 = g.add_node("C")
n4 = g.add_node("D")
n5 = g.add_node("E")
g.add_edge(n1, n3)
g.add_edge(n2, n3)
g.add_edge(n3, n4)
g.add_edge(n3, n5)
g.show()
# binary tree with a "deep and cheap" left half and an expensive but shallow right half
from pygraphml import Graph, GraphMLParser
test2 = Graph()
a = test2.add_node("A")
b = test2.add_node("B")
c = test2.add_node("C")
d = test2.add_node("D")
e = test2.add_node("E")
f = test2.add_node("F")
g = test2.add_node("G")
h = test2.add_node("H")
i = test2.add_node("I")
j = test2.add_node("J")
k = test2.add_node("K")
l = test2.add_node("L")
m = test2.add_node("M")
n = test2.add_node("N")
o = test2.add_node("O")
p = test2.add_node("P")
q = test2.add_node("Q")
r = test2.add_node("R")
s = test2.add_node("S")
test2.add_edge(a, b, directed=True)
test2.add_edge(b, c, directed=True)
test2.add_edge(b, d, directed=True)
test2.add_edge(c, e, directed=True)
test2.add_edge(c, f, directed=True)
# Toy problem from the textbook: Romanian road map
from pygraphml import Graph, GraphMLParser
romania = Graph()
oradea = romania.add_node("Oradea")
zerind = romania.add_node("Zerind")
arad = romania.add_node("Arad")
sibiu = romania.add_node("Sibiu")
fagaras = romania.add_node("Fagaras")
timisoara = romania.add_node("Timisoara")
rv = romania.add_node("Rimnicu Vilcea")
lugoj = romania.add_node("Lugoj")
pitesti = romania.add_node("Pitesti")
mehadia = romania.add_node("Mehadia")
drobeta = romania.add_node("Drobeta")
craiova = romania.add_node("Craiova")
bucharest = romania.add_node("Bucharest")
giurgiu = romania.add_node("Giurgiu")
urziceni = romania.add_node("Urziceni")
neamt = romania.add_node("Neamt")
iasi = romania.add_node("Iasi")
vaslui = romania.add_node("Vaslui")
hirsova = romania.add_node("Hirsova")
eforie = romania.add_node("Eforie")
o2z = romania.add_edge(oradea, zerind, directed=False)
o2z['weight'] = 71
z2a = romania.add_edge(zerind, arad, directed=False)
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')
class WorldView(QGraphicsScene):
rowHeight = 100
colWidth = 150
def __init__(self,parent = None):
super(WorldView,self).__init__(parent)
self.setBackgroundBrush(QColor('white'))
self.nodes = {'state pre': {},
'state post': {},
'action': {},
'utility': {},
'observation': {}}
self.edgesOut = {}
self.edgesIn = {}
self.agents = {}
self.world = None
self.graph = {}
self.dirty = False
self.center = None
self.xml = None
def clear(self):
super(WorldView,self).clear()
for table in self.nodes.values():
table.clear()
self.edgesOut.clear()
self.edgesIn.clear()
self.center = None
def displayWorld(self,agents=None):
self.clear()
self.graph = graph.DependencyGraph(self.world)
self.graph.computeGraph(agents)
layout = getLayout(self.graph)
if self.world.diagram is None:
self.world.diagram = diagram.Diagram()
# Lay out the pre variable nodes
x = self.drawStateNodes(layout['state pre'],self.graph,0,0,'xpre','ypre')
# Lay out the action nodes
x = self.drawActionNodes(layout['action'],x,0)
# Lay out the post variable nodes
x = self.drawStateNodes(layout['state post'],self.graph,x,0,'xpost','ypost')
# Lay out the utility nodes
x = self.drawUtilityNodes(x,0,self.graph,sorted(self.world.agents.keys()))
self.colorNodes()
# Lay out edges
for key,entry in self.graph.items():
if key in self.nodes[entry['type']]:
node = self.nodes[entry['type']][key]
for child in entry['children']:
if child in self.nodes[self.graph[child]['type']]:
self.drawEdge(key,child)
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')
def getGraphNode(self,label):
for node in self.xml.nodes():
if node['label'] == label:
return node
else:
return(self.xml.add_node(label))
def drawStateNodes(self,nodes,graph,x0,y0,xkey,ykey,believer=None,maxRows=10):
x = x0
even = True
for layer in nodes:
y = y0
for key in sorted(layer):
if believer:
label = beliefKey(believer,key)
if self.xml:
self.xml.add_node('%sBeliefOf%s' % (believer,makePresent(key)))
else:
if gtnodes and makePresent(key) not in gtnodes:
continue
label = key
if self.xml:
self.xml.add_node(makePresent(key))
variable = self.world.variables[makePresent(key)]
if y >= y0+maxRows*self.rowHeight:
even = not even
if even:
y = y0
else:
y = y0+50
x += int(0.75*self.colWidth)
if not xkey in variable:
variable[xkey] = x
variable[ykey] = y
# Move on to next Y
y += self.rowHeight
if graph[key]['agent'] != WORLD and graph[key]['agent']:
agent = self.world.agents[graph[key]['agent']]
if isBinaryKey(key):
node = VariableNode(agent,key[len(agent.name)+1:],label,
variable[xkey],variable[ykey],
100,50,scene=self)
else:
node = VariableNode(agent,key[len(agent.name)+3:],label,
variable[xkey],variable[ykey],
100,50,scene=self)
else:
node = VariableNode(None,state2feature(key),key,
variable[xkey],variable[ykey],
100,50,scene=self)
self.nodes[graph[key]['type']][label] = node
x += self.colWidth
return x
def drawActionNodes(self,nodes,x0,y0,maxRows=10):
x = x0
y = y0
for action in sorted(nodes):
if gtnodes and str(action) not in gtnodes:
continue
if self.world.diagram.getX(action) is None:
self.setDirty()
self.world.diagram.x[action] = x
self.world.diagram.y[action] = y
# Move on to next Y
y += self.rowHeight
if y >= maxRows*self.rowHeight:
y = y0
x += self.colWidth
else:
x = max(x,self.world.diagram.getX(action))
y = max(y,self.world.diagram.getY(action))
node = ActionNode(self.world.agents[self.graph[action]['agent']],action,scene=self)
self.nodes[self.graph[action]['type']][action] = node
if self.xml:
self.xml.add_node(str(action))
x += self.colWidth
return x
def drawUtilityNodes(self,x0,y0,graph,agents):
x = x0
y = y0 - self.rowHeight/2
for name in agents:
if name in graph:
agent = self.world.agents[name]
if self.world.diagram.getX(agent.name) is None:
self.setDirty()
y += self.rowHeight
self.world.diagram.x[agent.name] = x
self.world.diagram.y[agent.name] = y
else:
x = self.world.diagram.getX(agent.name)
y = self.world.diagram.getY(agent.name)
node = UtilityNode(agent,x,y,scene=self)
self.nodes[graph[name]['type']][name] = node
if self.xml:
self.xml.add_node(name)
if self.xml:
self.xml.add_edge(self.getGraphNode(stateKey(name,'horizon')),
self.getGraphNode(name),True)
x += self.colWidth
return x
def drawObservationNodes(self,x0,y0,graph,xkey,ykey,believer=None,maxRows=10):
omega = sorted(sum([[stateKey(name,omega) for omega in self.world.agents[name].omega]
for name in self.world.agents],[]))
x = x0
y = y0
even = True
oNodes = {}
for key in omega:
if gtnodes and makePresent(key) not in gtnodes:
continue
if believer:
label = beliefKey(believer,key)
if self.xml:
self.xml.add_node('%sBeliefOf%s' % (believer,makePresent(key)))
else:
label = key
if self.xml:
oNodes[key] = self.xml.add_node(key)
variable = self.world.variables[makePresent(key)]
if y >= y0+maxRows*self.rowHeight:
even = not even
if even:
y = y0
else:
y = y0+50
x += int(0.75*self.colWidth)
if not xkey in variable:
variable[xkey] = x
variable[ykey] = y
# Move on to next Y
y += self.rowHeight
agent = self.world.agents[state2agent(key)]
if isBinaryKey(key):
node = VariableNode(agent,key[len(agent.name)+1:],key,
variable[xkey],variable[ykey],
100,50,scene=self)
else:
node = VariableNode(agent,key[len(agent.name)+3:],key,
variable[xkey],variable[ykey],
100,50,scene=self)
self.nodes['observation'][label] = node
x += self.colWidth
return x
def drawEdge(self,parent,child,graph=None,rect0=None,rect1=None):
if self.xml:
if isinstance(parent,str):
parentVal = makePresent(parent)
else:
parentVal = str(parent)
if isBeliefKey(parentVal):
parentVal = '%sBeliefOf%s' % (belief2believer(parentVal),
makePresent(belief2key(parentVal)))
if isinstance(child,str):
childVal = makePresent(child)
else:
childVal = str(child)
if isBeliefKey(childVal):
childVal = '%sBeliefOf%s' % (belief2believer(childVal),
makePresent(belief2key(childVal)))
for nP in self.xml.nodes():
if nP['label'] == str(parentVal):
break
else:
raise RuntimeError('Unable to find GraphML node %s' % (parentVal))
for nC in self.xml.nodes():
if nC['label'] == str(childVal):
break
else:
raise RuntimeError('Unable to find GraphML node %s (link from %s)' % \
(childVal,parentVal))
self.xml.add_edge(nP,nC,True)
if graph is None:
graph = self.graph
if isBeliefKey(parent):
node0 = self.nodes[graph[belief2key(parent)]['type']][parent]
else:
node0 = self.nodes[graph[parent]['type']][parent]
if isBeliefKey(child):
node1 = self.nodes[graph[belief2key(child)]['type']][child]
else:
node1 = self.nodes[graph[child]['type']][child]
if rect0 is None:
rect0 = node0.boundingRect()
if rect1 is None:
rect1 = node1.boundingRect()
if parent == child:
# Loop back to self
x0 = rect0.x()+rect0.width()/15
y0 = rect0.y()+2*rect0.height()/3
path = QPainterPath(QPointF(x0,y0))
path.arcTo(rect0.x(),rect0.y()+rect0.height()/2,rect0.width(),rect0.height(),145,250)
edge = QGraphicsPathItem(path,node0)
arrow = drawArrow(QLineF(x0-5,y0+25,x0,y0),edge)
elif rect0.y() == rect1.y():
# Same row, so arc
x0 = rect0.x()+rect0.width()/2
x1 = rect1.x()+rect1.width()/2
path = QPainterPath(QPointF(x1,rect1.y()+rect1.height()/2))
path.arcTo(x1,rect1.y()+rect1.height()/2,x0-x1,rect1.height(),180,180)
edge = QGraphicsPathItem(path)
node0.scene().addItem(edge)
if x1 < x0:
arrow = drawArrow(QLineF(x1+25,rect1.y()+rect1.height()+15,
x1-5,rect1.y()+rect1.height()),edge)
else:
arrow = drawArrow(QLineF(x1-25,rect1.y()+rect1.height()+15,
x1+5,rect1.y()+rect1.height()),edge)
else:
# straight-line link
if rect0.x() < rect1.x():
x0 = rect0.right()
x1 = rect1.left()
else:
x0 = rect0.left()
x1 = rect1.right()
y0 = rect0.y()+rect0.height()/2
y1 = rect1.y()+rect1.height()/2
edge = QGraphicsLineItem(x0,y0,x1,y1)
node0.scene().addItem(edge)
arrow = drawArrow(edge.line(),edge)
edge.setZValue(1.)
if not parent in self.edgesOut:
self.edgesOut[parent] = {}
if child in self.edgesOut[parent]:
node0.scene().removeItem(self.edgesOut[parent][child][0])
self.edgesOut[parent][child] = (edge,arrow)
if not child in self.edgesIn:
self.edgesIn[child] = {}
if parent != child:
self.edgesIn[child][parent] = (edge,arrow)
return edge
def highlightEdges(self,center):
"""
Hide any edges *not* originating or ending at the named node
:type center: {str}
"""
self.center = center
for key,table in list(self.edgesOut.items())+list(self.edgesIn.items()):
if center is None or key in center:
# All edges are important!
for edge,arrow in table.values():
edge.show()
else:
for subkey,(edge,arrow) in table.items():
if center is None or subkey in center:
# This edge is important
edge.show()
else:
# This edge is unimportant
edge.hide()
def boldEdges(self,center):
"""
Highlight any edges originating or ending at the named node
:type center: {str}
"""
for key,table in self.edgesOut.items()+self.edgesIn.items():
if key in center:
# All edges are important!
for edge,arrow in table.values():
edge.setPen(QPen(QBrush(QColor('black')),5))
edge.setZValue(2.0)
else:
for subkey,(edge,arrow) in table.items():
if subkey in center:
# This edge is important
edge.setPen(QPen(QBrush(QColor('black')),5))
edge.setZValue(2.0)
else:
# This edge is unimportant
edge.setPen(QPen(QColor('black')))
edge.setZValue(1.0)
def updateEdges(self,key,rect):
self.setDirty()
if key in self.edgesOut:
for subkey,(edge,arrow) in self.edgesOut[key].items():
if self.center is None or key in self.center or subkey in self.center:
if isinstance(edge,QGraphicsLineItem):
line = edge.line()
line.setP1(QPointF(rect.x()+rect.width(),rect.y()+rect.height()/2))
edge.setLine(line)
drawArrow(line,arrow=arrow)
elif key != subkey:
edge.scene().removeItem(edge)
del self.edgesOut[key][subkey]
del self.edgesIn[subkey][key]
self.drawEdge(key,subkey,rect0=rect)
if key in self.edgesIn:
for subkey,(edge,arrow) in self.edgesIn[key].items():
if self.center is None or key in self.center or subkey in self.center:
if isinstance(edge,QGraphicsLineItem):
line = edge.line()
line.setP2(QPointF(rect.x(),rect.y()+rect.height()/2))
edge.setLine(line)
drawArrow(line,arrow=arrow)
elif key != subkey:
edge.scene().removeItem(edge)
del self.edgesIn[key][subkey]
del self.edgesOut[subkey][key]
self.drawEdge(subkey,key,rect1=rect)
def step(self):
self.world.step()
self.world.printState()
self.colorNodes('likelihood')
def colorNodes(self,mode='agent'):
cache = None
for category,nodes in self.nodes.items():
for node in nodes.values():
color = node.defaultColor
if mode == 'agent':
if node.agent:
color = self.world.diagram.getColor(node.agent.name)
elif node.agent is None:
color = self.world.diagram.getColor(None)
elif mode == 'likelihood':
if cache is None:
# Pre-compute some outcomes
cache = {}
outcomes = self.world.step(real=False)
for outcome in outcomes:
# Update action probabilities
for name,distribution in outcome['actions'].items():
if name not in cache:
cache[name] = Distribution()
for action in distribution.domain():
cache[name].addProb(action,outcome['probability']*distribution[action])
# Update state probabilities
for vector in outcome['new'].domain():
for key,value in vector.items():
if key not in cache:
cache[key] = Distribution()
cache[key].addProb(value,outcome['probability']*outcome['new'][vector])
if category == 'state pre':
if node.agent:
key = stateKey(node.agent.name,node.feature)
else:
key = stateKey(None,node.feature)
variable = self.world.variables[key]
marginal = self.world.getFeature(key)
if variable['domain'] is bool:
color = dist2color(marginal)
else:
raise RuntimeError('Unable to display color of %s over domain %s' % (key,variable['domain']))
elif category == 'action':
uniform = 1./float(len(cache[node.agent.name]))
prob = cache[node.agent.name].getProb(node.action)
if prob < uniform:
prob = 0.5*prob/uniform
else:
prob = 0.5*(prob-uniform)/(1.-uniform) + 0.5
distribution = Distribution({True: prob})
distribution[False] = 1.-distribution[True]
color = dist2color(distribution)
elif category == 'state post':
if node.agent:
key = stateKey(node.agent.name,node.feature)
else:
key = stateKey(None,node.feature)
key = makePresent(key)
if self.world.variables[key]['domain'] is bool:
dist = self.world.float2value(key,cache[key])
color = dist2color(dist)
node.setBrush(QBrush(color))
def setDirty(self):
self.parent().parent().parent().actionSave.setEnabled(True)
self.dirty = True
def unsetDirty(self):
self.parent().parent().parent().actionSave.setEnabled(False)
self.dirty = False
def minRect(self):
"""
@return: a rectangle cropped to show only object space
"""
rect = None
for nodes in self.nodes.values():
for node in nodes.values():
if rect is None:
rect = node.boundingRect()
else:
rect = rect.united(node.boundingRect())
return rect
def saveImage(self,fname):
rect = self.minRect() #self.sceneRect()
pix = QImage(rect.width(), rect.height(),QImage.Format_ARGB32)
painter = QPainter(pix)
self.render(painter,rect)
painter.end()
pix.save(fname)
def saveSubgraphs(self,dirName,onlyConnected=True):
previous = self.center
for nodeType,nodes in self.nodes.items():
for key,node in nodes.items():
if not onlyConnected or key in self.edgesOut or key in self.edgesIn:
center = {key}
if nodeType == 'state post':
for agent in self.world.agents:
subkey = beliefKey(agent,key)
if subkey in nodes:
center.add(subkey)
self.highlightEdges(center)
if isinstance(key,ActionSet):
self.saveImage(os.path.join(dirName,'%s.png' % (str(key))))
else:
self.saveImage(os.path.join(dirName,'%s.png' % (escapeKey(key))))
self.highlightEdges(previous)
class Property_Graph:
def __init__(self):
"""
Initializes graph parameters.
"""
self.g = Graph()
self.vertex_id = 0
self.edge_id = 0
def add_vertex(self, label, value, property=None):
"""
Adds a vertex to the graph.
@param label: default label or key by which vertex is to be
added (vertex will be uniquely by this label and its value) e.g. "name"
@param value: value of above label e.g. "product0012"
@param property: list of length 2 containing key name of property as first element
and value of property as second element
"""
# check if node with same label already exists, if it does then return that node instance
for n in self.g._nodes:
if n[label] == value:
return n
# add new node to graph
node = self.g.add_node(str(self.vertex_id))
# add default label and its value
node[label] = value
# add additional properties if provided
if property != None:
node[property[0]] = property[1]
self.vertex_id += 1
return node
def add_edge(self,
label,
label_value1,
label_value2,
default_property,
property=None):
"""
Adds edge between two vertices.
@param label: label or key value by which vertex will be searched e.g. "name" or "URI"
@param label_value1 : value of above label or key of source vertex
@param label_value2 : value of above label or key of target vertex
@param default_property : default_property of edge (predicate in RDF terms)
@param property : additional property, list of length 2 containing key name of property
as first element and value of property as second element
"""
n1 = None
n2 = None
# Search source and target nodes
for n in self.g._nodes:
if n[label] == label_value1:
n1 = n
if n[label] == label_value2:
n2 = n
# If source or target doesn't exists, then return
if n1 == None or n2 == None:
return
# Add edge
edge = self.g.add_edge(n1, n2, directed=True)
# Add edge default property
edge['property'] = default_property
edge['id'] = str(self.edge_id)
# Add additional property if provided
if property != None:
edge[property[0]] = edge[property[1]]
self.edge_id += 1
def add_vertices_and_edge(self, label, label_value1, label_value2, default_edge_property,\
edge_property=None, vertex1_property=None, vertex2_property=None):
"""
Adds two vertices and edge connecting them
@param label: default label or key by which vertex is to be
added (vertex will be uniquely by this label and its value) e.g. "name"
@param label_value1 : value of above label or key of source vertex
@param label_value2 : value of above label or key of target vertex
@param default_edge_property : default_property of edge (predicate in RDF terms)
@param edge_property : additional property, list of length 2 containing key name of property
as first element and value of property as second element
@param vertex1_property: list of length 2 containing key name of property as first element
and value of property as second element
@param vertex2_property: list of length 2 containing key name of property as first element
and value of property as second element
"""
n1 = self.add_vertex(label, label_value1, vertex1_property)
n2 = self.add_vertex(label, label_value2, vertex2_property)
edge = self.g.add_edge(n1, n2, directed=True)
edge['label'] = default_edge_property
edge['id'] = str(self.edge_id)
self.edge_id += 1
if edge_property != None:
edge[edge_property[0]] = edge[edge_property[1]]
def add_property(self, label, label_value, property, to_edge=False):
"""
Adds property to a edge or vertex
@param label : label or key by which desired edge or vertex will be searched
@param label_value : value of above label or key
@param property : property to be added, list of length 2 containing key name of
property as first element and value of property as second element
@param to_edge : If set True, property will be added to edge, default value is False.
"""
if to_edge:
# Yet to be implemented
pass
else:
for n in self.g._nodes:
if n[label] == label_value:
n[property[0]] = property[1]
break
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)
# Radiation grid from CSCI 6550 HW 1
from pygraphml import Graph, GraphMLParser
radiation = Graph()
two = radiation.add_node("2")
three = radiation.add_node("3")
four = radiation.add_node("4")
six = radiation.add_node("6")
seven = radiation.add_node("7")
nine = radiation.add_node("9")
ten = radiation.add_node("10")
eleven = radiation.add_node("11")
twelve = radiation.add_node("12")
thirteen = radiation.add_node("13")
fourteen = radiation.add_node("14")
fifteen = radiation.add_node("15")
edge = radiation.add_edge(two, three, directed=True)
edge['weight'] = 9
edge = radiation.add_edge(two, six, directed=True)
edge['weight'] = 11
edge = radiation.add_edge(three, two, directed=True)
edge['weight'] = 9
edge = radiation.add_edge(three, four, directed=True)
edge['weight'] = 10
edge = radiation.add_edge(three, seven, directed=True)
edge['weight'] = 11
# basic binary tree with all edge weights = 1
from pygraphml import Graph, GraphMLParser
test1 = Graph()
a = test1.add_node("A")
b = test1.add_node("B")
c = test1.add_node("C")
d = test1.add_node("D")
e = test1.add_node("E")
f = test1.add_node("F")
g = test1.add_node("G")
h = test1.add_node("H")
i = test1.add_node("I")
j = test1.add_node("J")
k = test1.add_node("K")
l = test1.add_node("L")
m = test1.add_node("M")
n = test1.add_node("N")
o = test1.add_node("O")
test1.add_edge(a, b, directed=True)
test1.add_edge(a, c, directed=True)
test1.add_edge(b, d, directed=True)
test1.add_edge(b, e, directed=True)
test1.add_edge(c, f, directed=True)
test1.add_edge(c, g, directed=True)
test1.add_edge(d, h, directed=True)
test1.add_edge(d, i, directed=True)
test1.add_edge(e, j, directed=True)
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()
super().__init__(graph)
self.W = W
self._process()
if __name__ == '__main__':
parser = argparse.ArgumentParser('A small graph vizualization tool')
parser.add_argument(
'--input',
help='input file (currently works only with graphml format)',
required=True)
parser.add_argument('--output',
help='result (given FNAME, creates files '
'"FNAME" with graph representation in dot format and '
'"FNAME.png" with a picture',
default='graph')
parser.add_argument('--alg', help='vizualization algorithm', required=True)
parser.add_argument('--params', help='algo parameters', default='{}')
args = parser.parse_args()
algo_params = json.loads(args.params)
graph = Graph.from_graphml(args.input)
if args.alg == 'layered-tree':
drawer = LayeredTreeDrawer(RootedTree(graph))
elif args.alg == 'coffman-graham':
drawer = CoffmanGrahamDrawer(
DAG(graph),
W=0 if 'W' not in algo_params else algo_params['W'],
)
drawer.dot_draw(args.output)
