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 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 __init__(self):
self._graph = Graph('equation')
self._subgraph_terms = Graph('terms')
self._terms = {}
self._graph.attr(rankdir='BT', ordering='out') #, splines='false')
self._subgraph_terms.attr(rank='same', rankdir='LR')
def compartment_to_dot(compartment):
g = Graph(name=compartment.id,cluster=True,subgraph=True)
for subsystem in compartment.subsystems:
gsub = subsystem_to_dot(subsystem)
gsub.subgraph = True
gsub.tag('::'+subsystem.id)
g.add(gsub)
for comp in compartment.compartments:
gcomp = compartment_to_dot(comp)
gcomp.subgraph = True
gcomp.tag('::'+comp.id)
g.add(gcomp)
label = AttrStmt('graph',label=compartment.name,
fontsize=compartment.get_param('COMPARTMENT_FONTSIZE'))
g.add(label)
SHOW_EXCHANGES = compartment.get_param('SHOW_EXCHANGES')
if SHOW_EXCHANGES and compartment.local_exchanges:
gex = Graph(name=compartment.id+"::EX",cluster=True)
gex.add(g)
gex.add(AttrStmt('graph',style="dotted"))
for ex in compartment.local_exchanges:
gex.add(exchange_to_dot(ex))
return gex
else:
return g
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(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 __init__(self, filename=None, name=None, start_graph=True):
if name is None:
self.graph = Graph(name=self.create_name())
else:
self.graph = Graph(name=name)
if filename is None:
self.filename = "grafy_startowe\\" + self.graph.name + ".dot"
else:
self.filename = filename
self.create_nodes()
self.create_edges()
self.finish_creating(self.filename, start_graph)
def init_graph():
dot = Graph(comment='Topology')
dot.node('A')
dot.node('B')
dot.node('C')
dot.node('D')
dot.node('E')
dot.node('F')
dot.node('G')
dot.node('H')
dot.node('I')
dot.edge('A', 'B', label='2')
dot.edge('A', 'D', label='5')
dot.edge('B', 'C', label='7')
dot.edge('B', 'E', label='1')
dot.edge('C', 'F', label='9')
dot.edge('D', 'E', label='3')
dot.edge('D', 'G', label='3')
dot.edge('E', 'H', label='30')
dot.edge('E', 'F', label='2')
dot.edge('H', 'G', label='5')
dot.edge('H', 'I', label='8')
dot.edge('F', 'I', label='6')
dot.view()
def newBlock(self, value, dataObj=None):
'''
### Function Description
Create new block diagram. This is the main function to create a new block diagram object.
This module use Graph for visualiztion. There's no direction edge in this method.
### Parameters Description
* value:
* type: str, int
* description: text for block diagram. Identifier for user to name the node
* id:
* type: int
* description: serial number for each node
* dataObj:
* type: object
* description: store object item in node for advanced application
'''
if self.rootNode == None:
self.rootNode = Node(value, self.nodeIDCount, dataObj)
self.nodeIDCount += 1
self.rootNode.isRootNode = True
self.currNodePtr = self.rootNode
self.newNodePtr = self.rootNode
self.add2NodeListPtr(self.rootNode)
print('*Block Diagram is created. The root node ID is %d' %
self.currNodePtr.id)
self.graph = Graph(name='BlockDiagram',
filename='BlockDiagram.gv',
engine='dot')
self.addGraphvizNode()
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 gen_graph_from_nodes(nodes, type_fail=None):
graph = Graph(format='png', strict=True)
graph.node_attr['fontname'] = 'Courier New'
graph.edge_attr['fontname'] = 'Courier New'
for node in nodes:
graph.node(
_type_str(node.type),
'{type: %s|ast_node: %s|parent\'s type: %s}' %
(_type_str(node.type), node.ast_node.as_string().replace(
'<', '\\<').replace('>', '\\>') if node.ast_node else 'None',
_type_str(node.parent.type) if node.parent else 'NA'),
shape='record',
style='rounded')
for neighb, ctx_node in node.adj_list:
graph.edge(_type_str(node.type),
_type_str(neighb.type),
label=(f' {ctx_node.as_string()}' if ctx_node else ''))
if type_fail:
graph.node('tf',
'{TypeFail|src_node: %s}' %
(type_fail.src_node.as_string().replace('<', '\\<').replace(
'>', '\\>') if type_fail.src_node else 'None'),
shape='record')
graph.edge('tf', _type_str(type_fail.tnode1.type), style='dashed')
graph.edge('tf', _type_str(type_fail.tnode2.type), style='dashed')
graph.view('tnode_graph')
def _topology_graph():
g = Graph(engine='dot',
graph_attr={
'ratio': '0.41',
'pad': '0.7 ',
'newrank': 'false',
'splines': 'compound'
})
for isd in ISD.objects.iterator():
g_isd = _make_isd_graph(isd)
# hard-coding backbone ISDs to be at the top
if isd.isd_id in [16, 26]:
g_isd.attr(rank='source')
# putting core ASes into a subgraph, laid out at the top
with g_isd.subgraph() as s:
s.attr(rank='min')
for as_ in isd.ases.filter(owner=None, is_core=True):
_add_as_node(s, as_)
# putting non-core ASes into a subgraph, without rank
with g_isd.subgraph() as s:
s.attr(rank='none')
for as_ in isd.ases.filter(owner=None, is_core=False):
_add_as_node(s, as_)
g.subgraph(g_isd)
for link in Link.objects.filter(interfaceA__AS__owner=None,
interfaceB__AS__owner=None):
_add_link(g, link)
return g
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 main():
SIZE = 20
PLOIDY = 2
MUTATIONS = 2
indices = range(SIZE)
# Build fake data
seqA = list("0" * SIZE)
allseqs = [seqA[:] for x in range(PLOIDY)] # Hexaploid
for s in allseqs:
for i in [choice(indices) for x in range(MUTATIONS)]:
s[i] = "1"
allseqs = [make_sequence(s, name=name) for (s, name) in \
zip(allseqs, [str(x) for x in range(PLOIDY)])]
# Build graph structure
G = Graph("Assembly graph", filename="graph")
G.attr(rankdir="LR", fontname="Arial", splines="true")
G.attr(ranksep=".2", nodesep="0.02")
G.attr('node', shape='point')
G.attr('edge', dir='none', penwidth='4')
colorset = get_map('Set2', 'qualitative', 8).mpl_colors
colorset = [to_hex(x) for x in colorset]
colors = sample(colorset, PLOIDY)
for s, color in zip(allseqs, colors):
sequence_to_graph(G, s, color=color)
zip_sequences(G, allseqs)
# Output graph
G.view()
def display_nodes(nodes):
graph = Graph()
for node in nodes:
graph.node(node.identifier, node.name)
for child in node.children:
graph.edge(node.identifier, child.identifier)
return graph
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 build_graph():
g = Graph(format='png')
node_id = 0
def build_edge_with_id(context, char, node):
nonlocal node_id
for key, child in node._children.items():
label = key
number = str(ord(key) + 1)
if key == '\0':
label = 'null'
if child._value is None:
g.node(context + number,
label=label,
style='filled',
fillcolor='white',
fontcolor='black')
else:
g.node(context + number,
label=label,
style='filled',
fillcolor='blue',
fontcolor='black')
g.edge(context, context + number, color='black')
return g, build_edge_with_id
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 plot(overlapping_policies):
g = Graph("G", filename="Overlapping_policies", engine="sfdp")
for key in overlapping_policies.keys():
for value in overlapping_policies[key]:
g.edge(key, value)
overlapping_policies[value].remove(key)
g.view()
def get_topologie_data(self):
node_data = {}
for node in self.nodes:
node_data[str(node.id)] = {
"neighbors": node.neighbors
}
from graphviz import Graph
graph = Graph("PLC-Topologie", filename="topologie.gv")
# graph.edge(str(Node.id), str(alt_id))
tmp = []
del_list = []
for node in self.nodes:
for neighbor in node.neighbors:
if str(node.id) == neighbor:
del_list.append(node.id)
elif str(node.id) + ":" + str(neighbor) not in tmp and str(neighbor) + ":" + str(node.id) not in tmp:
tmp.append(str(node.id) + ":" + str(neighbor))
graph.edge(str(node.id), str(neighbor))
for node in self.nodes:
if node.id in del_list:
del node.neighbors[str(node.id)]
graph.view()
return node_data
def BFSGetDist(self,v0=0): #搜索无权图其他点到 v0 的最短路径
Q = Queue()
v = v0
path = [[v] for i in range(self.vexnum)]
self.visited[v] = True
Q.enqueue(v)
while not Q.empty():
v = Q.dequeue()
for w in self.arc[v]:
if self.visited[w] == False:
self.visited[w] = True
path[w] = path[v] + [w]
Q.enqueue(w)
for v in range(self.vexnum):
if v != v0:
print(len(path[v]) - 1,end=' ')
print("->".join(str(i) for i in path[v]))
vg = Graph('图及其应用')
with open('case1.txt') as case:
n = int(case.readline()) #n 表示图中的顶点数
for i in range(n):
vg.node(name=str(i),color='red')
vexs = [str(i) for i in range(n)]
matrix = [[0] * n for i in range(n)]
edges = case.readlines()
arcnum = len(edges)
for edge in edges:
v1,v2 = map(int, edge.split())
matrix[v1][v2] = 1
matrix[v2][v1] = 1 #无向图
vg.edge(str(v1),str(v2),color='blue') g = MGraph(vexs,matrix,arcnum)
alg = ALGraph(vexs,matrix,arcnum)
g.findArticul()
alg.BFSGetDist(0)
vg.view()
def draw_graph(graph, edges):
g = Graph()
for node in graph.get_nodes():
g.node(node)
for edge in edges:
g.edge(edge[0], edge[1], minlen='2')
g.view("./grafiPDF/grafo")
def update_root(self, position, board, is_my_move):
'''
Update the root as the selected child node
'''
del self.g
self.g = Graph(format='png',
graph_attr={'fixed_size': 'false'},
node_attr={'fontsize': '13'})
if self.root.child[position] is None or self.root.child[
position].is_my_move != is_my_move:
self.root = self.build_node(board)
else:
self.root = self.root.child[position]
del self.root.parent
self.root.parent = None
# change name in graph
self.root.node = self.root.node.split("label=" + str(self.root.position))[0] + "label=" + str('root') + \
self.root.node.split("label=" + str(self.root.position))[1]
self.root.edge = None
for c in self.root.child:
if c is not None:
c.node = c.node.split("label=\"\"")[0] + "label=" + str(
c.position) + c.node.split("label=\"\"")[1]
self.recycle_tree(self.root)
def color(self):
# Dict to save color
color = defaultdict(list)
for node in self.graph:
if (len(color) == 0):
color[0].append(node)
continue
else:
for i in range(len(color)):
temp = 0
for colored_node in color[i]:
if (node in self.graph[colored_node]):
temp = 1
break
if (temp == 1):
continue
else:
color[i].append(node)
break
if (node not in color[i]):
color[len(color)].append(node)
# Out put file
output_file = Graph('Coloring graph', filename='Greedy Coloring Graph.gv',strict="True")
output_file.attr( shape="circle", size='1')
list_color=["red","blue", "yellow","green","gray","snow","DarkOrange1","MediumPurple1","khaki4","orchid", "cyan2", "blue violet", "GreenYellow",
"HotPink", "LightGoldenrod4","DarkSeaGreen", "sienna","brown"]
for i in range (len(color)):
for node in color[i]:
output_file.node(str(node),fillcolor=list_color[i],style="filled")
for opp_node in self.graph[node]:
output_file.edge(str(node),str(opp_node))
output_file.view()
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 navigate(self, node: Node):
chds = node.childrens
for n in chds:
self.graph.edge(str(node.ev_id), str(n.ev_id), None, dir='forward')
if n.validity == Validity.INVALID:
self.graph.node(str(n.ev_id),
self.name_for_node(n),
fillcolor=self.INVALID_COLOR,
style='filled')
elif n.validity == Validity.VALID:
self.graph.node(str(n.ev_id),
self.name_for_node(n),
fillcolor=self.VALID_COLOR,
style='filled')
elif n.validity == Validity.UNKNOWN:
self.graph.node(str(n.ev_id), self.name_for_node(n))
elif n.validity is Validity.NOT_IN_PROV:
self.graph.node(str(n.ev_id),
self.name_for_node(n),
fillcolor=self.PROV_PRUNED_NODE_COLOR,
style='filled')
if len(chds) > 0:
g = Graph()
for c in chds:
g.node(str(c.ev_id))
g.graph_attr['rank'] = 'same'
self.graph.subgraph(g)
for n in chds:
self.navigate(n)
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 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 concrete_bipartite_as_graph(self, subjects, patterns) -> Graph: # pragma: no cover
"""Returns a :class:`graphviz.Graph` representation of this bipartite graph."""
if Graph is None:
raise ImportError('The graphviz package is required to draw the graph.')
bipartite = self._build_bipartite(subjects, patterns)
graph = Graph()
nodes_left = {} # type: Dict[TLeft, str]
nodes_right = {} # type: Dict[TRight, str]
node_id = 0
for (left, right), value in bipartite._edges.items():
if left not in nodes_left:
subject_id, i = left
name = 'node{:d}'.format(node_id)
nodes_left[left] = name
label = '{}, {}'.format(i, self.subjects_by_id[subject_id])
graph.node(name, label=label)
node_id += 1
if right not in nodes_right:
pattern, i = right
name = 'node{:d}'.format(node_id)
nodes_right[right] = name
label = '{}, {}'.format(i, self.automaton.patterns[pattern][0])
graph.node(name, label=label)
node_id += 1
edge_label = value is not True and str(value) or ''
graph.edge(nodes_left[left], nodes_right[right], edge_label)
return graph
def draw(self, filename='test.gv'):
"""
Отрисовывает граф используя библиотеку Graphviz. Больше примеров:
https://graphviz.readthedocs.io/en/stable/examples.html
"""
g = Graph('G', filename=filename, engine='sfdp')
for v, attr in enumerate(self.attributes):
if 'color' in '':
g.attr('node', style='filled', fillcolor=attr['color'])
if attr['color'] == 'black':
g.attr('node', fontcolor='white')
else:
g.attr('node', style='', color='', fontcolor='', fillcolor='')
if 'name' in '':
g.node(str(v), label='{} ({})'.format(attr['name'], v))
else:
g.node(str(v))
for i in range(self.number_of_vertices()):
for j in self.adj[i]:
if i < j:
g.edge(str(i), str(j))
g.view()