def make_graph_dijkstra():
g = Graph(format='png', comment='undirected graph that contains no negative weight path')
g.attr('node', shape='circle')
n = 10
for i in range(n):
g.node(str(i), label=str(i))
edges = ((0, 1),
(2, 0),
(2, 3),
(1, 4),
(4, 5),
(5, 2),
(3, 6),
(4, 7),
(5, 8),
(8, 9))
edge_labels = [5, 6, 2, 2, 3, 4, 1, 7, 1, 1, 1]
for i, e in enumerate(edges):
g.edge(str(e[0]), str(e[1]), label=str(edge_labels[i]))
g.render('graph_dijkstra', view=True, cleanup=True)
def make_bipartite_graph():
g = Graph(format='png', comment='undirected graph that contains no negative weight path', engine='dot')
g.attr('node', shape='circle')
n = 10
with g.subgraph(name='cluster_0') as c:
c.attr(label='process #1')
for i in range(0, n, 2):
c.node(str(i), label=str(i), color='blue')
with g.subgraph(name='cluster_1') as c:
c.attr(label='process #2')
for i in range(1, n, 2):
c.node(str(i), label=str(i), color='red')
edges = ((0, 1),
(1, 2), (1, 4),
(2, 9),
(3, 4),
(4, 5), (4, 9),
(5, 6),
(6, 7), (6, 9),
(8, 9))
for e in edges:
g.edge(str(e[0]), str(e[1]))
g.render('graph_bipartite', view=True, cleanup=True)
def printLinked(self):
dl = Graph('doublylinked', node_attr={'shape': 'record'})
if self.isEmpyty():
pass
else:
self._draw(self.sentinel.next, dl)
dl.render('doublylinked.gv', view=True)
def generate_plot(topology_file):
graph = Graph("topology", filename='topology.gv', engine='neato')
# graph = Graph("topology", filename='topology.gv', engine='neato', outputorder = 'breadthfirst')
delay_re = "[0-9]+.0ms"
server_id = ""
# Add color to server node
# Add color to client node
with open(topology_file) as f:
for line in f.readlines():
if "large" in line:
line = line.replace("tb-set-hardware $node", "")
server_id = line[0]
if line.startswith("set linkClient"):
line = line.replace("set linkClient", "")
node = server(line[0], server_id)
client = "ClientPool-" + line[0]
add_node(graph, node)
add_node(graph, client)
add_edge(graph, node, client, client_edge, str(1))
elif line.startswith("set link"):
line = line.replace("set link", "")
node_one = server(line[0], server_id)
node_two = server(line[1], server_id)
add_node(graph, node_one)
add_node(graph, node_two)
label = re.findall(delay_re, line)[0]
add_edge(graph, node_one, node_two, node_edge, label)
print(graph.source)
graph.save()
graph.render('topology')
return graph
def make_graph_mst():
g = Graph(format='png', comment='undirected graph that contains no negative weight path')
g.attr('node', shape='circle')
n = 9
for i in range(n):
g.node(str(i), label=str(i))
edges = ((0, 1),
(0, 7),
(1, 2),
(1, 7),
(2, 3),
(2, 5),
(2, 8),
(3, 4),
(3, 5),
(4, 5),
(5, 6),
(6, 7),
(6, 8),
(7, 8))
edge_labels = [4, 8, 8, 11, 7, 4, 2, 9, 14, 10, 2, 1, 6, 7]
for i, e in enumerate(edges):
g.edge(str(e[0]), str(e[1]), label=str(edge_labels[i]))
g.render('graph_mst', view=True, cleanup=True)
def reporte_optimizacion():
global listaOpt, listaAsignaciones
cadena = ""
print("------------REPORTE OPTIMIZACION---------------")
SymbolT2 = Graph('g', filename='reporteOptimizacion.gv', format='png',
node_attr={'shape': 'plaintext', 'height': '.1'})
print("ASIGNACIONES -- ")
for i in listaAsignaciones:
print(str(i.izq)+" = "+str(i.der))
for item in listaAsignaciones:
for asi in listaAsignaciones:
if str(item.der) == str(asi.izq) and str(item.izq) == str(asi.der):
print("optimiza 1")
op = str(item.der) + "=" + str(asi.der) + "-"
op += str(item.izq) + "=" + str(asi.izq)
opt = str(item.der) + "=" + str(asi.der) + "- Regla: 1"
o = Optimizacion(op, opt)
listaOpt.append(o)
break;
ope = "goto .R" + "-"+ "Label .R"
opet = "Label .R" + "- Regla: 2"
regla2 = Optimizacion(ope, opet)
listaOpt.append(regla2)
for o in listaOpt:
cadena += '\n <TR><TD>'+o.original+'</TD><TD>'+o.optimizado+'</TD></TR>'
SymbolT2.node('table', '<<TABLE><TR><TD>CODIGO</TD><TD>OPTIMIZACION</TD></TR>' + cadena + '</TABLE>>')
SymbolT2.render('g', format='png', view=True)
def visual_decoding(sent, saveto='tmp'):
"""
Visualize multiple translation from machine translation.
Example:
>>> sentence = ['I have a apple',
'I have a dream',
'H have an egg']
>>> visual_decoding(sent=sentence, saveto='demo')
Args:
sent: a list of str
Multiple translations.
saveto: str
Graph will be saved as 'saveto.png'.
Returns:
None
"""
graph = Graph(format='png',
node_attr={'shape':'box'},
graph_attr={'splines':'polyline'},
edge_attr={'dir':'forward'})
graph.body.extend(['rankdir=LR'])
for i,s in enumerate(sent):
graph = _plot_sent(graph, s, flag=str(i))
graph.render(filename=saveto, view=True)
def show(sql, filename):
# 优化前的树
g = Graph(filename, format='png', node_attr={'shape': 'plaintext'})
etree = parsesql(sql)
showtree(etree, g)
g.render()
img = Image.open(filename + '.gv.png')
plt.figure('before optim')
plt.imshow(img)
plt.axis('off')
# 优化后的树
og = Graph(filename + 'optim',
format='png',
node_attr={'shape': 'plaintext'})
# 两步优化
relation2 = []
otree = down_select(etree, '', relation2)
otree = down_proj(otree, '', relation2, '')
showtree(otree, og)
og.render()
img = Image.open(filename + 'optim' + '.gv.png')
plt.figure('after optim')
plt.imshow(img)
plt.axis('off')
plt.show()
def viz(config: Config, directed: bool, in_index_base: int, out_index_base: int):
from graphviz import Digraph, Graph # type: ignore
firstline = input().split()
G = None
n, m = -1, -1
if (len(firstline) == 1):
# this is tree
G = Graph()
n = int(firstline[0])
m = n - 1
else:
n, m = map(int, firstline)
if directed:
G = Digraph()
else:
G = Graph()
for i in range(n):
G.node(str(i))
for i in range(m):
u, v = map(int, input().split())
if in_index_base == 1:
u -= 1
v -= 1
G.edge(str(u), str(v), cost='1')
output_filepath = os.path.expanduser('~/Dropbox/graph')
G.render(output_filepath, view=True)
def visual_decoding(sent, saveto='tmp'):
"""
Visualize multiple translation from machine translation.
Example:
>>> sentence = ['I have a apple',
'I have a dream',
'H have an egg']
>>> visual_decoding(sent=sentence, saveto='demo')
Args:
sent: a list of str
Multiple translations.
saveto: str
Graph will be saved as 'saveto.png'.
Returns:
None
"""
graph = Graph(format='png',
node_attr={'shape': 'box'},
graph_attr={'splines': 'polyline'},
edge_attr={'dir': 'forward'})
graph.body.extend(['rankdir=LR'])
for i, s in enumerate(sent):
graph = _plot_sent(graph, s, flag=str(i))
graph.render(filename=saveto, view=True)
def create_interactions_graph(clauses, f):
dot = GGraph(comment='Interactions graph', engine='sfdp')
seen_vars = set()
edges_between_vars = defaultdict(int)
for clause in clauses:
for lit in clause:
var = f(lit)
if var not in seen_vars:
seen_vars.add(var)
dot.node(str(var), label=str(var))
for clause in clauses:
l = len(clause)
for i in xrange(l):
for j in xrange(i+1, l):
edges_between_vars[(str(f(clause[i])), str(f(clause[j])))] += 1
for interacting_vars, weight in edges_between_vars.iteritems():
dot.edge(interacting_vars[0], interacting_vars[1], weight=str(weight))
print edges_between_vars
dot = _apply_styles(dot, styles)
# print dot.source
dot.render(os.path.join('images', 'interactions_graph.gv'), view=True)
def visualize_countries_together_in_item(data, start_time_str=None, end_time_str=None, newspaper_str='*'):
countries_together_dict = _get_countries_together_in_items(data)
# print 'countries_together_dict:', countries_together_dict
dot = Graph(comment='Countries together in item graph', engine='sfdp')
seen_countries = set()
edges_between_countries = defaultdict(int)
## Building the graph
for ID_and_feed, countries in countries_together_dict.iteritems():
countries_list = list(countries)
for country in countries_list:
if country != '' and country not in seen_countries:
dot.node(country, label=country)
seen_countries.add(country)
for i in xrange(len(countries)):
for j in xrange(i+1, len(countries)):
fst = min(countries_list[i], countries_list[j])
snd = max(countries_list[i], countries_list[j])
edges_between_countries[(fst, snd)] += 1
for edge_endpoints, edge_weight in edges_between_countries.iteritems():
dot.edge(edge_endpoints[0], edge_endpoints[1], weight=str(edge_weight))
print 'seen_countries:', seen_countries
print 'edges_between_countries:', edges_between_countries
dot = _apply_styles(dot, styles)
# print dot.source
out_dirname = newspaper_str.replace('*', '').replace('!', '').replace('[', '').replace(']', '')
out_filename = ('countries_together_in_item_%s_%s.gv' % (start_time_str, end_time_str)).replace(':', '-')
dot.render(os.path.join('images', out_dirname, out_filename), view=False)
def draw_pats_tree_colored(pkl, out, col_style='contact', **kwarg):
with open(pkl, 'rb') as f:
var_list = pickle.load(f)
rootnode = var_list[0]
if col_style == 'order':
num_state = dfs(rootnode)
print('num_state ' + str(num_state))
values = np.arange(num_state)
elif col_style == 'rmsd':
values = None
elif col_style == 'contact':
native = kwarg['native']
traj = kwarg['traj']
values = frac_native_contacts(native, traj)
elif col_style == 'f1':
native = kwarg['native']
traj = kwarg['traj']
values = calc_f1(native, traj)
else:
print('Error!: you can not use such color style ' + col_style)
exit(1)
if values is not None:
make_colorbar(min(values), max(values), out + '_colorbar')
else:
make_colorbar(0, rootnode.childNodes[0].rmsd, out + '_colorbar')
# G = Graph(format='pdf')
G = Graph(format='svg')
G.attr("node", shape="circle", style="filled")
G.graph_attr.update(size="30")
make_graph(G, rootnode, values)
G.render(out)
def render_graph(graph, name=None, directory=None, fill_infected='green3'):
""" Render a user graph to an SVG file. Infected nodes are colored
appropriately.
Parameters:
-----------
graph : UserGraph
The graph to render.
name : str
A name for the graph.
directory : str
The directory to render to.
fill_infected : str
The fill color for infected nodes.
"""
dot = Graph(name=name, format='svg', strict=True)
for user in graph.users():
if user.metadata.get('infected', False):
dot.attr('node', style='filled', fillcolor=fill_infected)
dot.node(unicode(user.tag))
dot.attr('node', style='')
for user in graph.users():
for neighbor in user.neighbors:
dot.edge(unicode(user.tag), unicode(neighbor.tag))
dot.render(directory=directory, cleanup=True)
def draw_pacs_tree_colored(log_file, out):
log = pd.read_csv(log_file, header=None)
log = np.array(log)
n_cycles = log.shape[0]
# G = Graph(format='pdf')
G = Graph(format='svg')
G.attr('node', shape='circle', style='filled')
G.graph_attr.update(size="30")
color_hex = value2hex(0)
G.node('0-0', '0', fillcolor=color_hex)
# G.node('0-0', '', fillcolor=color_hex, color='white', width='12')
color_hex = value2hex(255 / n_cycles * 1)
for i in range(len(log[0])):
state = '1-' + str(i)
G.node(state, str(state), fillcolor=color_hex)
# G.node(state, '', fillcolor=color_hex, color='white', width='12')
G.edge('0-0', state, color='black')
for i in range(1, len(log) + 1):
log_i = log[i - 1]
color_hex = value2hex(255 / n_cycles * (i + 1))
for j, l in enumerate(log_i):
state = str(i + 1) + '-' + str(j)
pstate = str(i) + '-' + str(int(l))
G.node(state, str(state), fillcolor=color_hex)
# G.node(state, '', fillcolor=color_hex, color='white', width='12')
G.edge(pstate, state, color='black')
G.render(out)
make_colorbar(0, n_cycles * 5, out + '_colorbar')
def generate_graph(verbose: bool, file: str):
docker_client = docker.from_env()
networks = get_networks(docker_client, verbose)
containers, links = get_containers(docker_client, verbose)
if file:
base, ext = os.path.splitext(file)
g = Graph(comment="Docker Network Graph",
engine="sfdp",
format=ext[1:],
graph_attr=dict(splines="true"))
else:
g = Graph(comment="Docker Network Graph",
engine="sfdp",
graph_attr=dict(splines="true"))
for _, network in networks.items():
draw_network(g, network)
for container in containers:
draw_container(g, container)
for link in links:
if link.network_name != "none":
draw_link(g, networks, link)
if file:
g.render(base)
else:
print(g.source)
def vis_family_tree(self):
G = Graph(format="png")
num_nodes = len(self.result['states'][0]['node'])
num_relations = len(self.result['relations'])
for i in range(num_nodes):
if i % 2 == 0:
G.node(str(i), str(i), shape='square')
else:
G.node(str(i), str(i), shape='circle')
for i in range(num_relations):
G.node(str(i + num_nodes),
'',
shape='diamond',
style='filled',
height='0.1',
width='0.1')
for i, rel in enumerate(self.result['relations']):
c, f, m = rel
G.edge(str(i + num_nodes), str(c))
G.edge(str(f), str(i + num_nodes))
G.edge(str(m), str(i + num_nodes))
G.render('family-tree')
def change_graph(self, cnt, indices, restore_flg=False):
g = Graph(format='png')
for nnm in self.rc_name:
g.node(nnm)
if restore_flg:
indices = sorted(indices, reverse=True)
self.graph_matrix[indices[0]][indices[1]] = 1
print('Graph Matrix : ', self.graph_matrix)
for i in range(self.graph_matrix.shape[0]):
for j in range(self.graph_matrix.shape[1]):
if i > j and self.graph_matrix[i][j] == 1:
g.edge(self.rc_name[i], self.rc_name[j])
file_name = './graph_restored_' + str(
cnt) # 保存する画像のファイル名を指定(拡張子(.png)を除く)
else:
indices = sorted(indices, reverse=True)
self.graph_matrix[indices[0]][indices[1]] = 0
print('Graph Matrix : ', self.graph_matrix)
for i in range(self.graph_matrix.shape[0]):
for j in range(self.graph_matrix.shape[1]):
if i > j and self.graph_matrix[i][j] == 1:
g.edge(self.rc_name[i], self.rc_name[j])
file_name = './graph_' + str(cnt) # 保存する画像のファイル名を指定(拡張子(.png)を除く)
g.render(filename=file_name,
format='png',
cleanup=True,
directory=None)
im = Image.open(file_name + '.png')
im.show()
def plot(self, render=False, save=False, filename=None):
if filename is None:
filename = "decision_tree.svg"
dot = Graph(name="decision_tree", filename=filename, format="svg")
dot.node(
str(id(self)),
self.splitting_info_to_string()
+ "\nestimate:"
+ str(round(float(self.value), 3)),
)
for i in range(self.depth):
nodes = DecisionTree.get_level_in_list(self, i + 1)
for node in nodes:
if node.left_child is None:
dot.node(
str(id(node)),
"This node is not split"
+ "\nestimate:"
+ str(round(float(node.value), 3)),
)
dot.edge(str(id(node.parent)), str(id(node)))
else:
dot.node(
str(id(node)),
node.splitting_info_to_string()
+ "\nestimate:"
+ str(round(float(node.value), 3)),
)
dot.edge(str(id(node.parent)), str(id(node)))
if render:
dot.render(view=True)
if save:
dot.save()
return dot
def visualize(self, name="graph"):
"""Visualize graph using 'graphviz' library.
To install graphviz you can use 'pip install graphviz'.
Notice that graphviz should also be installed in your system.
For ubuntu, you can install it using 'sudo apt install graphviz'
:param name: Name of the generated file, defaults to "graph"
:type name: str, optional
:raises ImportError: When unable to import graphviz.
"""
try:
from graphviz import Graph
except ImportError:
msg = ("Could not import 'graphviz' module. "
"Make shure 'graphviz' is installed "
"or install it typing 'pip install graphviz'")
raise ImportError(msg)
# Create graph
dot = Graph()
# Create nodes
for n in range(1, self.n_nodes + 1):
dot.node(str(n))
# Create edges
for n1, n2 in self.edges:
dot.edge(str(n1), str(n2))
# Visualize
dot.render(name, view=True, cleanup=True)
def main():
p = argparse.ArgumentParser(
description='This script is for generate graph figure')
p.add_argument('-g', '--graph', type=str,
help='path to graph csv file', required=True)
p.add_argument('-o', '--out', type=str,
help='output_file', required=True)
option_args = p.parse_known_args()[0]
path = option_args.graph
out_file = option_args.out
if not os.path.exists(path):
print("File not found")
sys.exit(1)
adj_matrix = read_graph(path)
g = Graph(format='png')
for i in range(len(adj_matrix)):
for j in range(i + 1, len(adj_matrix)):
g.edge(str(i), str(j), label=str(adj_matrix[i][j]))
g.render(out_file)
def visualize(self):
l = len(self.top_result)
connections = dict()
tags = dict()
for i in range(l - 1):
for j in range(1, l):
if i != j:
key = (i, j)
message_list = self.get_message_list_between(self.top_result[i], self.top_result[j])
tag_cloud = self.subject.calculate_tag_cloud(message_list)
tags[key] = self.get_top_tag_cloud(tag_cloud, 5)
# DOT language
dot = GraphV(comment = "Information Flow - Enron")
for i in range(l):
dot.node(str(i), self.top_result[i] + " - " + self.company.get_role(self.top_result[i]))
for (edge, tag) in tags.iteritems():
node_1 = edge[0]
node_2 = edge[1]
note = ", ".join(tag)
print note
dot.edge(str(node_1), str(node_2), label=note)
dot.render('test-output/round-table.gv', view=False)
def graph_data(pkg_name):
if not pkg_name:
abort(404)
filepath = os.path.join(cache_dir, pkg_name.lower())
if not os.path.exists(filepath + '.png'):
nodes, edges = reqs_graph(pkg_name)
if not nodes:
return redirect(url_for('static', filename='img/blank.png'))
dot = Graph()
dot.format = 'png'
dot.node('0', nodes[0], fillcolor='#fbb4ae', style='filled', shape='box')
for i, pkg_name in enumerate(nodes[1:]):
dot.node(str(i+1), pkg_name, fillcolor='#ccebc5', style='filled')
dot.edges([
[str(i[0]), str(i[1])]
for i in edges
])
dot.render(filepath)
return send_file(filepath + '.png')
def printQueue(self):
sl = Graph('singlylinked', node_attr={'shape': 'record'})
if self.stack_empty():
pass
else:
self._draw(self.sentinel.next, 0, sl)
sl.render('singlylinked.gv', view=True)
def generateCompDiagram(comp):
tempDirPath = state.get('tempDirPath')
filepath = join(tempDirPath, uuid.uuid4().hex + '.gv')
indexTracker = {}
g = Graph('G', filename=filepath)
g.format = 'png'
with g.subgraph(name='clusterComponent') as c:
for group in comp.groups:
with c.subgraph(name='cluster' + uuid.uuid4().hex) as a:
a.attr(color='blue')
for port in group.ports:
name = port.portType
idx = 0
if not (name in indexTracker):
indexTracker[name] = 1
else:
idx = indexTracker[name]
indexTracker[name] += 1
if (port.direction == 'in'):
a.node_attr.update(color='green', style='filled')
elif (port.direction == 'out'):
a.node_attr.update(color='red', style='filled')
else:
a.node_attr.update(color='orange')
a.node(name + '_' + str(idx), label=name, style='filled')
g.render()
Popen(["xdg-open", filepath + '.png'])
def gen_img(graph: Graph,
node_num,
rm_ratio: float = 0.2,
root_folder='train',
source_folder='',
source_file='train.txt'):
"""
在graph上，以rm_ratio的概率随机删除一些链路，然后用随机选取的一对节点作为源宿点，判断其是否联通。并将生成的图像放到root_folder目录中，
对应的文件名称和标签放到source_folder目录下的train.txt文件中。
"""
# 生成原始数据
rds = rand_edges(graph, rm_ratio)
graph.remove_edges_from(rds)
src, dst = gen_src_dst(0, node_num)
label = get_label(src, dst, graph)
# 构造graphviz对象
name = str(time.time())
g = Graph(format='jpeg', engine='neato')
g.attr('node', shape='circle')
g.attr('edge')
for node in graph.nodes():
g.node(name=str(node))
g.node(name=str(src), shape='triangle')
g.node(name=str(dst), shape='triangle')
for edge in graph.edges():
g.edge(str(edge[0]), str(edge[1]))
for edge in rds:
g.edge(str(edge[0]), str(edge[1]), color='white')
g.render(filename=name, directory=root_folder, view=False, cleanup=True)
# 存储到文件中去
file = open(os.path.join(source_folder, source_file), 'a')
file.write(name + '.jpeg ' + str(label) + '\n')
file.flush()
file.close()
def display(ref, filename='temp'):
"""Render a tree to SVG format.
*Warning:* Made for use within IPython/Jupyter only.
Args:
ref (Tree).
filename (str): Temporary filename to store SVG output.
Returns:
SVG: IPython SVG wrapper object for tree.
"""
# Ensure all modules are available
try:
from graphviz import Graph
from IPython.display import SVG
except:
raise Exception("Missing module: graphviz and/or IPython.")
# Traverse tree and generate temporary Graph object
output_format = 'svg'
graph = Graph(filename, format=output_format)
q = Queue()
q.enqueue(ref)
while not q.isempty():
ref = q.dequeue()
graph.node(str(id(ref)), label=str(ref.key))
for child in ref.children:
graph.edge(str(id(ref)), str(id(child)))
q.enqueue(child)
# Render to temporary file and SVG object
graph.render(filename=filename, cleanup=True)
return SVG(filename + '.' + output_format)
def createGraph(mi, names, graph_name):
"""Given dict of mutual information, print the Minimum Spanning Tree as per Chow Liu Algorithm"""
milist = sorted(mi.items(), key=lambda f: np.fabs(f[1]))
size = len(names)
parents = -1 * np.ones(size, dtype=int)
edges = []
count = 0
i = 0
while count < size - 1:
verts, val = milist[i]
if detect_cycle(parents, verts) == False:
temp1 = verts[0]
while (temp1 != -1):
temp2 = parents[temp1]
parents[temp1] = verts[1]
temp1 = temp2
count += 1
edges.append(verts)
i += 1
graph = Graph(comment='minimum spanning tree', format='png')
for i in range(size):
graph.node(names[i])
for j in edges:
graph.edge(names[j[0]], names[j[1]])
graph.render(graph_name, view=True)
def render_dungeon(dungeon: Dungeon, session_id: str, rogue_position: int):
filename = f'./dungeons/d-{session_id}.gv'
g = Graph('Dungeon_graph', filename=filename, format='png', engine='fdp')
for room in dungeon.rooms:
contains_key = any(key.room_id == room.id for key in dungeon.keys)
shape = 'circle'
if rogue_position == room.id:
shape = 'triangle'
elif contains_key:
shape = 'doublecircle'
elif room.id == dungeon.finish_room_id:
shape = 'star'
g.attr('node', color=str(room.color), shape=shape)
g.node(str(room.id))
for door in dungeon.doors:
if door.is_closed:
style = 'dashed'
else:
style = 'solid'
g.attr('edge', color=str(door.color), style=style)
g.edge(str(door.first_room_id), str(door.second_room_id))
g.render()
return f'{filename}.png'
def graph_label(data, renewable):
num_all_rows_of_state = 19
g = Graph("all_years_clustering", engine="fdp",
format="svg", edge_attr={"penwidth": "4"}, node_attr={"style": "filled"})
for lab in data:
if len(data[lab]) == 1:
g.node(next(iter(data[lab])))
continue
complete_node = []
incomplete_node = []
for state in data[lab]:
dist = data[lab][state]
if dist == num_all_rows_of_state:
complete_node += [state]
else:
incomplete_node += [(state, dist)]
node_color = colors.to_hex([0, 1, 0, renewable[lab]], keep_alpha=True)
if len(complete_node) > 0:
g.node(str(lab), label=",".join(complete_node), fillcolor=node_color)
else:
g.node(str(lab), label="", width=str(0.2), height=str(0.2), fillcolor=node_color)
for state, dist in incomplete_node:
edge_color = [0, 0, 0, dist / num_all_rows_of_state]
g.edge(str(lab), state, weight=str(dist),
color=colors.to_hex(edge_color, keep_alpha=True))
g.render("output/all_years_clustering", view=True, cleanup=True)
def viz(self):
""" Build a dotmap for graphviz
but also constructs the connected_stitch structures
"""
flatmap = flatten(self.stitch_map())
if self.pattern_type == 'round':
dot = Graph(engine="twopi",
graph_attr={
'root': 'a1',
'overlap': 'false'
},
node_attr={
'shape': 'circle',
'margin': '0.00001 0.0001'
},
format="png",
name=self.name)
else:
dot = Graph(format="png", name=self.name)
# first pass nodes
for stitch in flatmap:
dot.node("a" + str(stitch.id), str(stitch.stitch))
# second pass edges
for stitch in flatmap:
if (stitch.prev):
dot.edge("a" + str(stitch.id), "a" + str(stitch.prev.id))
if (stitch.bottom):
dot.edge("a" + str(stitch.id), "a" + str(stitch.bottom.id))
dot.render(view=True)
def llenarCeldas(self, var):
eFila = self.eFilas.primero
concatenar = '<<TABLE>'
#print("\n**************recorrido por filas*************************")
while eFila != None:
concatenar = concatenar + '\n<TR>'
actual = eFila.accesoNodo
#print("\nfila"+str(actual.fila))
#print("columna valor ")
while actual != None:
#print(str(actual.columna)+" "+ actual.valor)
if (actual.valor == '*'):
concatenar = concatenar + '<TD bgcolor="black">'
if (actual.valor == '-'):
concatenar = concatenar + '<TD>'
concatenar = concatenar + '</TD>'
actual = actual.derecha
concatenar = concatenar + '\n</TR>'
eFila = eFila.siguiente
concatenar = concatenar + '\n</TABLE>>'
#print(concatenar)
h = Graph(var, format='png')
h.node('tab', label=concatenar)
concatenar = ""
h.render()
class DrawGraphviz:
"""
Draw a tree with Graphviz
"""
m_start: int
m_end: int
dot: Graph
def __init__(self, save_name, start, end):
self.args = args
self.m_end = end
self.m_start = start
self.dot = Graph(name='diagram-' + save_name, strict=True)
self.dot.graph_attr['rankdir'] = 'LR'
self.dot.node_attr['shape'] = 'box'
def __draw_func(self, node: GraphNode, parent: GraphNode or None):
if node.step > self.m_end:
return
if node.step >= self.m_start:
self.dot.node(str(id(node)), node.name)
if parent is not None and node.step >= self.m_start + 1:
self.dot.edge(str(id(parent)), str(id(node)))
for child_node in node.child:
self.__draw_func(child_node, node)
def draw(self, root: GraphNode):
self.__draw_func(root, None)
self.dot.render(view=True, format='pdf')
def imagen(gateway):
#nodos redes activas
temporal = sorted(nodos.items())
nodos.clear()
for i in temporal:
nodos[i[0]] = i[1]
#layouts interfaces reportadas en tabla route
temp2 = sorted(layouts.items())
layouts.clear()
for interfaz in temp2:
layouts[interfaz[0]] = interfaz[1]
#FastEth interfaces activas incompletas
temp2 = sorted(FastEth.items())
FastEth.clear()
for fa in temp2:
FastEth[fa[0]] = fa[1]
#Activas interfaces activas completas
name = layouts.keys()
for uno in name:
for i in FastEth[uno]:
fa = i[:i.index(' ')]
for r in layouts[uno]:
if fa in r:
i = i + r[r.index(' '):]
activas[uno].append(i) #
temp2 = sorted(activas.items())
activas.clear()
for fa in temp2:
activas[fa[0]] = fa[1]
dicredes = {}
cad = ''
grafica = Graph('red')
grafica.node('linux mint', shape='rectangle', label='MV' + '\n' + gateway)
grafica.node('switch', shape='rectangle')
grafica.edge('linux mint', 'switch')
for x in nodos:
aux4 = activas[x]
for y in aux4:
cad = cad + y + '\n'
grafica.node(x, label=x + '\n' + cad, shape='rectangle')
cad = ''
redes = nodos[x]
for red in redes:
if red not in dicredes.keys():
dicredes[red] = []
dicredes[red].append(x)
else:
dicredes[red].append(x)
for d in dicredes:
print(d + ':' + str(dicredes[d]))
if d.find('56') >= 0:
for each in dicredes[d]:
grafica.edge('switch', each, label=d)
if len(dicredes[d]) == 2 and d.find('8') == 0:
grafica.edge(dicredes[d][0], dicredes[d][1], label=d)
grafica.format = 'png'
grafica.render('static/red')
def render_graph(graph, edge_list, filename="graph", fmt="pdf"): g = Graph(format=fmt) for src in graph: g.node(name=str(src)) for src in graph: for dst in graph[src]: g.edge(str(src), str(dst), color="red" if is_edge_in_list((src, dst), edge_list) else "black") g.render(filename=filename)
def render(self):
graph = Graph(comment='All trees')
for i in range(len(self.chromosomes)):
tree = self.chromosomes[i].tree
graph.subgraph(graph=tree.render(f'{i+1} [Original]'))
graph.render('test-output/round-table.gv')
def plot(graph, engine='dot', filename='output/test'):
"""Possible engines: dot, neato, fdp, sfdp, twopi, circo"""
g = Graph(format='png', engine=engine)
for v in graph:
g.node(str(index(v)))
for v, w in graph.edges:
g.edge(str(index(v)), str(index(w)))
g.render(filename)
def generateGraph():
G = Graph(
engine = 'dot',
filename = 'Btrfs-Graph.dot',
name = 'BRTFS-Browser',
comment = 'https://github.com/Zo0MER/BRTFS-Browser.git',
graph_attr = {'rankdir': 'RL',
'charset':'utf-8',
'bgcolor':'#eeeeee',
'labelloc':'t',
'splines':'compound',
'nodesep':'0.7',
'ranksep':'5'
},
node_attr = {'fontsize': '18.0',
'shape':'box'
}
)
#node with title and hyperlink on github
G.node('meta',
label = 'Btrfs-debug-tree \nhttps://github.com/Zo0MER/BRTFS-Browser.git',
href = 'https://github.com/Zo0MER/BRTFS-Browser.git',
fontcolor = '#4d2600',
fontsize = '30.0'
)
first = inode[0]
inode.remove(inode[0])
if (inode):
#link first item ROOT_TREE_DIR INODE_ITEM, INODE_REF with all INODE_ITEM EXTEND_DATA
for pair in inode:
G.edge(''.join([str(x) for x in first]), ''.join([str(x) for x in pair]))
else:
G.node(first)
#save *.dot and others
pathout = enterPath.get()
filenameout = enterFilename.get()
if (filenameout):
filenameout = filenameout + '.gv.dot'
else:
filenameout = "btrfs-graph"
G.filename = filenameout + '.gv.dot'
G.directory = pathout
G.save()
for t in types:
G.format = t
G.render()
def rev_del(G,weights,count,Y,N):
for i in range(m):
gv = Graph('G', filename='rev_del',format='png')
gv.node_attr.update(color='lightblue2', style='filled')
gv.body.extend(['rankdir=LR'])
for j in range(i+1,m):
gv.edge(str(B[j][1]),str(B[j][2]),label=str(B[j][0]))
for n in N:
gv.edge(str(B[n[3]][1]),str(B[n[3]][2]),label=str(B[n[3]][0]),color="red")
for y in Y:
gv.edge(str(B[y[3]][1]),str(B[y[3]][2]),label=str(B[y[3]][0]),color="blue")
gv.edge(str(B[i][1]),str(B[i][2]),label=str(B[i][0]),color="green")
gv.render(str(count))
count+=1
count=Connectivity(G,weights[i],A,count,Y,N)
return count
def plot(graph, engine='dot', filename='output/test', vertex_names={}):
"""
Possible engines: dot, neato, fdp, sfdp, twopi, circo
Vertex_names is an optional dict from vertices to strings.
"""
g = Graph(format='png', engine=engine)
def vertex_to_string(v):
return (vertex_names[v] if v in vertex_names else '') + ' ({})'.format(str(index(v)))
for v in graph:
g.node(vertex_to_string(v))
for v, w in graph.edges:
g.edge(vertex_to_string(v), vertex_to_string(w))
g.render(filename)
def create_conflicts_graph(clauses):
dot = GGraph(comment='Conflicts graph', engine='sfdp')
for i in xrange(len(clauses)):
dot.node(str(i), label=str(i))
for i in xrange(len(clauses)):
for j in xrange(i+1, len(clauses)):
clause_i = clauses[i]
clause_j = clauses[j]
edge_labels = []
for lit in clause_i:
if -lit in clause_j:
var = abs(lit)
edge_labels.append(str(var))
if len(edge_labels) > 0:
dot.edge(str(i), str(j), label=','.join(edge_labels))
dot = _apply_styles(dot, styles)
dot.render(os.path.join('images', 'conflicts_graph.gv'), view=True)
def render(self, filename):
""" Renders the graph to a file.
Args:
filename (str): Filename of the map file.
"""
dot = Graph(comment='ISTravel graph', engine='fdp')
for city in self.cities:
dot.node(str(city))
ploted = []
for node in self.connections:
for edge in self.connections[node]:
if edge not in ploted:
ploted.append(edge)
dot.edge(
str(edge.nodes[0]),
str(edge.nodes[1]),
label=edge.transport[:2]
)
dot.render(filename[:filename.rfind('.')]+".gv")
def visualize_topics(quora_data):
dot = Graph(comment='Topics graph', engine='sfdp')
seen_topics = set()
for document in quora_data:
question = _get_question(document)
topics = document[question]['topics']
# Iterating over topics and adding nodes for topics if necessary
for topic in topics:
if topic not in seen_topics:
dot.node(topic, label=topic)
seen_topics.add(topic)
# Iterating over topics and adding edges between topics belonging to the same question
for i in xrange(len(topics)):
for j in xrange(i+1, len(topics)):
dot.edge(topics[i], topics[j])
# topic1, topic2 in product(topics, topics):
# dot.edge(topic1, topic2)
dot = _apply_styles(dot, styles)
# print dot.source
dot.render(os.path.join('images', 'topics.gv'), view=True)
def main():
source = sys.argv[1]
with open(source, 'r') as infile:
regions = json.load(infile)
g = Graph('chroma', filename='chroma.graphview', format='png')
for region in regions:
name = region['name']
style = {"style": "filled"}
if "owner" in region:
owner = region["owner"]
if owner == 0:
style["color"] = "orange"
else:
style["color"] = "blue"
style["fontcolor"] = "white"
g.node(name, **style)
for conn in region['connections']:
g.edge(name, conn)
g.render()
def Connectivity(G,e,A,count,Y,N): #checks connectivity of graph on removing edge e
if A[0][0]==e:
u=A[0][1]
v=A[0][2]
tup=A.pop(0)
index=len(B)-len(A)-1
tup.append(index)
G[u-1][v-1]=G[v-1][u-1]=0
L=[]
if path(G,u,v,u,L):
N.append(tup)
gv = Graph('G', filename='rev_del',format='png')
gv.node_attr.update(color='lightblue2', style='filled')
gv.body.extend(['rankdir=LR'])
index=len(B)-len(A)-1
for z in range(index+1,m):
gv.edge(str(B[z][1]),str(B[z][2]),label=str(B[z][0]))
for n in N:
gv.edge(str(B[n[3]][1]),str(B[n[3]][2]),label=str(B[n[3]][0]),color="red")
for y in Y:
gv.edge(str(B[y[3]][1]),str(B[y[3]][2]),label=str(B[y[3]][0]),color="blue")
gv.render(str(count))
count+=1
return count
else:
G[u-1][v-1]=G[v-1][u-1]=e
Y.append(tup)
gv = Graph('G', filename='rev_del',format='png')
gv.node_attr.update(color='lightblue2', style='filled')
gv.body.extend(['rankdir=LR'])
index=len(B)-len(A)-1
for z in range(index+1,m):
gv.edge(str(B[z][1]),str(B[z][2]),label=str(B[z][0]))
for n in N:
gv.edge(str(B[n[3]][1]),str(B[n[3]][2]),label=str(B[n[3]][0]),color="red")
for y in Y:
gv.edge(str(B[y[3]][1]),str(B[y[3]][2]),label=str(B[y[3]][0]),color="blue")
gv.render(str(count))
count+=1
return count
def save_nodes(self, filename="graph", nodes = None):
print "Saving graph..."
from graphviz import Graph
dot = Graph(comment='Dungeon Example')
if nodes == None:
nodes = self.linear_nodes(self.nodes)
#else:
#max_appeared = appeared.values()
#if max_appeared == []: start = 0
#else: start = max(max_appeared) + 1
#print start
#for node in nodes:
# if node.id not in appeared:
# appeared[node.id] = start
for node in nodes:
name = node.name
if hasattr(node, "replace_on_room_clear"):
replace = node.replace_on_room_clear[0]
name += "\n"
try:
name += replace.name
except AttributeError:
name += replace
amount = 255 #60+(appeared[node.id]*64)
fill = "#%02x%02xFF"%(amount, amount)
#print fill
shape = "oval"
if node is self.entrance:
shape = "box"
dot.node(str(node.id), name, style="filled", fillcolor=fill, shape=shape)
done_edges = []
for node in nodes:
for edge in node.connections:
if sorted([node.id, edge.id]) in done_edges: continue
dot.edge(str(node.id), str(edge.id))
done_edges.append(sorted([node.id, edge.id]))
dot.render(filename)
print "Graph saved"
def graph(node, fname):
from graphviz import Graph
g = Graph('G')
add_edges(node, g)
g.render(fname, view=True)
from slideshow import slideshow
from graphviz import Graph
count=1
gv = Graph('G', filename='heading',format="png")
gv.node_attr.update(color='white', style='filled',fontsize="50")
gv.node("Reverse Delete Algorithm")
gv.render(str(count))
count+=1
gv = Graph('G', filename='Description',format="png")
gv.node_attr.update(color='white', style='filled',fontsize="25")
gv.edge("Start with graph G, which contains a list of edges E.","Go through E in decreasing order of edge weights.",color="white")
gv.edge("Go through E in decreasing order of edge weights.","For each edge, check if deleting the edge will further disconnect the graph.",color="white")
gv.edge("For each edge, check if deleting the edge will further disconnect the graph.","Perform any deletion that does not lead to additional disconnection.",color="white")
gv.render(str(count))
count+=1
gv = Graph('G', filename='Legend',format="png")
gv.node_attr.update(color='white', style='filled',fontsize="30")
gv.body.extend(['rankdir=LR', 'size="8,5"'])
gv.node("green",color="green")
gv.node("red",color="red")
gv.node("blue",color="blue")
gv.edge("Current edge:","green",color="green")
gv.edge("Deleted edge/Edge not in Spanning Tree:","red",color="red")
gv.edge("Edge present in Spanning Tree:","blue",color="blue")
gv.node('Legend:', shape='Mdiamond',color="yellow")
gv.render(str(count))
count+=1
class SNAnalyzer(object):
def __init__(self,inPath,outPath,engine,analyzeType):
self.network = {}
self.nameIndex = {}
self.inPath = inPath
self.outPath = outPath
self.engine = engine
self.aType = analyzeType
self.networkFileParse(self.inPath)
def random_id(self,len):
alpha = 'abcdefghijklmnopqrstuvwxyz'
id = ''
for i in range(0,len):
id += random.choice(alpha)
return id
def networkFileParse(self,path):
f = open(path, 'r')
for line in f:
line = line.replace("\n","")
self.nameIndex.update({line.split(":")[0]:self.random_id(3)})
self.network.update({line.split(":")[0]:e.split(",") for e in line.split(":")[1:]})
f.close()
def graphUpdate(self):
if self.aType == "tw":
self.graph = Digraph()
elif self.aType == "fb":
self.graph = Graph()
else:
exit("Invalid Analyze Type")
for key in self.nameIndex.keys():
self.graph.node(self.nameIndex[key], key)
for key in self.network.keys():
for friend in self.network[key]:
if friend != "":
self.graph.edge(self.nameIndex[key],self.nameIndex[friend])
def generateGraphCode(self):
self.graphUpdate()
return self.graph.source
def renderGraph(self):
self.graphUpdate()
self.graph.engine = self.engine
self.graph.render(self.outPath, view=True)
def addNode(self,newNode):
if newNode not in self.nameIndex.keys():
self.nameIndex[newNode] = self.random_id(3)
self.network[newNode] = []
else:
print("Error: Network already has that {} named Node !".format(newNode))
def removeNode(self,targetNode):
if targetNode in self.nameIndex.keys():
del self.nameIndex[targetNode]
del self.network[targetNode]
for key in self.network.keys():
if targetNode in self.network[key]:
self.network[key].remove(targetNode)
else:
print("Error: Network not has that {} named Node !".format(targetNode))
def hasRelation(self,sourceNode,targetNode):
friends = self.network[sourceNode]
if targetNode in friends:
return True
else:
return False
def addRelation(self,sourceNode,targetNode):
if not self.hasRelation(sourceNode,targetNode):
self.network[sourceNode].append(targetNode)
else:
print("Error: The Node {} is already related to {} !".format(sourceNode, targetNode))
def removeRelation(self,sourceNode,targetNode):
if self.hasRelation(sourceNode,targetNode):
self.network[sourceNode].remove(targetNode)
else:
print("Error: The Node {} is not related with {} !".format(sourceNode, targetNode))
from graphviz import Graph #these are undirected
import sqlite3
#open up the db, pull everything
conn = sqlite3.connect('../db/prot.db')
c = conn.cursor()
c.execute('SELECT * from protein')
proids = {x[0]:x[1] for x in c.fetchall()}
c.execute('SELECT * from tags')
tagids = {x[0]:x[1] for x in c.fetchall()}
c.execute('SELECT * from ptag')
matches = c.fetchall()
graph = Graph('All protein tags', engine='neato')
for key in proids:
graph.node(proids[key])
for key in tagids:
graph.node(tagids[key])
for x,y in matches:
graph.edge(proids[x],tagids[y],len="10.0")
graph.render('tag.gv')
conn.close()
def main(restricted = False):
global styles
#gc.set_debug(gc.DEBUG_LEAK)
site = input("What site to crawl?")
maxDepth = int(input("Max depth?"))
http = httplib2.Http()
links = set()
pages = set()
#dot = Digraph(comment = site, format="png")
dot = Graph(comment = site, format="png", engine="sfdp")
dot.overlap = "true"
#dot.graph_attr.update(size = "10000000,10000000")
try:
soup = BeautifulSoup(urllib2.urlopen(site), "html.parser")
pageTitle = soup.title.string
pages.add(pageTitle)
titles[site] = pageTitle
soup.decompose()
except Exception as e:
pageTitle = site
print("Error: {0}".format(e))
siteBase = ""
try:
pos1 = site.find(".")
pos2 = site.find(".", pos1 + 1)
siteBase = site[pos1+1:pos2]
except Exception as e:
print("Error: {0}".format(e))
print (siteBase)
crawlPage(site, pageTitle, maxDepth, pages, links, restricted, siteBase)
#print(pages)
#print(links)
#for p in pages:
#print("Adding node: " + p)
#dot.node(p)
for l in links:
try:
#print("Adding edge: " + l[0] + " -> " + l[1])
dot.edge(l[0], l[1])
except Exception as e:
print("Error: {0}".format(e))
#print(dot)
#dot = apply_styles(dot, styles)
loc = str(dot).find("{")+1
dot = Source(str(dot)[0:loc] + "\n\tgraph [overlap = prism]\n" + str(dot)[loc:], format="png", engine="sfdp")
#print("-------------------")
filename = r'C:\Users\Gabe\Miniconda3\MyScripts\test-crawler15'
dot.save()
try:
os.remove(filename)
except Exception as e:
print("Error: {0}".format(e))
try:
outFile = open(filename + ".txt", "w")
outFile.write(str(dot))
outFile.close()
except Exception as e:
print("Error: {0}".format(e))
dot.render(filename, view=True)
class VisitorGraph(Visitor):
"""this class implement a tree visitor for our form"""
def __init__(self):
self.handler_dict = {Form.OperatorForm:(self.func_op_fo,{Form.D: (self.diff, {})\
, Form.Wedge: (self.wed, {}), Form.Add: (self.add,{}), \
Form.Hodge: (self.hod, {}),Form.Pullback: (self.pull, {}) }),\
Form.TerminalForm:(self.func_term_fo,{})}
self.dot = Graph(comment='Tree of our form')#Digraph(comment='Tree of our form') #to store the dot for vizgraph
self.edges = [] #to store the edge for the graph
self.post = [] #to store the post order traversal
self.pre = [] # to store the pre order traversal
self.comp = 0 #to differentiate the edge
#D form
def diff(self, form, children=None):
"""function when a diff operation is made"""
if form.scalar == 1:
return( 'd')
elif form.scalar == -1:
return( "-d" )
else:
return( "{}d ".format(form.scalar) )
#Wedge
def wed(self, form, children=None):
"""function when a wedge operation is made"""
if form.scalar == 1:
return( '^')
elif form.scalar == -1:
return( "-^" )
else:
return( "{}^ ".format(form.scalar) )
#Add
def add(self, form, children=None):
"""function when a add operation is made"""
if form.scalar == 1:
return( '+')
elif form.scalar == -1:
return( "-+" )
else:
return( "{}+ ".format(form.scalar) )
#Hodge
def hod(self, form, children=None):
"""function when a hodge star operation is made"""
if form.scalar == 1:
return( '*')
elif form.scalar == -1:
return( "-*" )
else:
return( "{}* ".format(form.scalar) )
#Pullback
def pull(self, form, children=None):
"""function when a hodge star operation is made"""
if form.scalar == 1:
return("phi")
else:
return( "{}phi ".format(form.scalar) )
#TerminalForm
def func_term_fo(self, form):
"""function that print a terminal Form"""
if form.scalar == 1:
return( form.name)
elif form.scalar == -1:
return( "-{} ".format(form.name) )
else:
return( "{}{} ".format(form.scalar, form.name) )
def _visit_preorder(self, form):
"""the intern preorder method for visiting the tree"""
if not isinstance(form,Form.TerminalForm):
children=form.forms
inter = self.find_method(form)(form)
self.pre.append(inter)
for fo in children:
self._visit_preorder(fo)
#in post order the find_method will be there
else:
inter = self.find_method(form)(form)
self.pre.append(inter)
def visit_preorder(self, form):
"""the preorder method for visiting the tree"""
self.pre=[]
self._visit_preorder(form)
return self.pre
def _visit_postorder(self, form):
"""the intern postorder method for visiting the tree"""
if not isinstance(form,Form.TerminalForm):
children=form.forms
for fo in children:
self._visit_postorder(fo)
inter = self.find_method(form)(form)
self.post.append(inter)
else:
inter = self.find_method(form)(form)
self.post.append(inter)
def visit_postorder(self, form):
"""the postorder method for visiting the tree"""
self.post=[]
self._visit_postorder(form)
return self.post
def _create_graph(self, form, parent_name=""):
"""the method for creating a graph of the tree, the edges are store inside the edges attribute"""
if not isinstance(form,Form.TerminalForm):
children = form.forms
node = (self.find_method(form)(form))
nbr1 = str(self.comp)
self.comp+=1
name = nbr1
self.dot.node(name, node)
if parent_name is not "":
inter=parent_name+name
self.edges.append(inter)
self.dot.edge(parent_name, name)
parent_name=name
for fo in children:
self._create_graph(fo,parent_name)
else:
node = (self.find_method(form)(form))
nbr1 = str(self.comp)
self.comp+=1
name = nbr1
#~ print(name)
self.dot.node(name,node)
if parent_name is not "":
inter = parent_name+name
self.edges.append(inter)
self.dot.edge(parent_name, name)
def draw_graph(self, form, name='sample'):
"""the method for drawing a graph of the tree, name is the file
name under which we want to save it"""
self.dot = Graph(comment='Tree of our form')#Digraph(comment='Tree of our form')
self.edges = []
self.comp = 0
self._create_graph(form)
namefile='drawing/'+name+'.gv'
self.dot.render(namefile, view=True)
