def plot_MRF(adj_mat, thresh=0.01, ax=None):
# Filter out subthreshold values in adj_mat
adj_mat = np.where(
np.abs(adj_mat) > thresh, adj_mat, np.zeros(adj_mat.shape))
# Create graph object
G = nx.Graph(adj_mat)
pos = nx.layout.circular_layout(G, scale=0.5)
node_colors = [palette[n] for n in G.nodes]
edge_colors = [v['weight'] for _, _, v, in G.edges(data=True)]
vmin, vmax = min(edge_colors), max(edge_colors)
cmap = plt.get_cmap()
nx.draw_networkx_nodes(G,
pos,
ax=ax,
node_color=node_colors,
node_size=700)
nx.draw_networkx_edges(G,
pos,
ax=ax,
edge_color=edge_colors,
edge_cmap=cmap,
edge_vmin=vmin,
edge_vmax=vmax,
width=2.5)
# Colourbar
sm = plt.cm.ScalarMappable(cmap=cmap,
norm=plt.Normalize(vmin=vmax, vmax=vmin))
fig.colorbar(sm, orientation="horizontal", pad=0.01, ax=ax)
nx.draw_networkx_labels(G, pos, ax=ax)
def draw_graph(relationships):
G = nx.Graph()
add_edges(relationships, G)
elarge = [(u, v) for (u, v, d) in G.edges(data=True)]
# positions for all nodes
pos = nx.spring_layout(G, k=1, seed=1)
# nodes
nx.draw_networkx_nodes(G, pos, node_size=90, node_color="k")
# edges
nx.draw_networkx_edges(G, pos, edgelist=elarge, width=0.1, edge_color="b")
# labels
nx.draw_networkx_labels(G,
pos,
font_size=0.3,
font_family="sans-serif",
font_color="w")
# no_overwrite("output\\graph", ".pdf")
no_overwrite("output\\graph", ".png")
def draw_graph_labels(graph, nodes=[], colors=[]):
# Draw the graph
pos = graphviz_layout(graph, prog='neato')
nx.draw_networkx_nodes(graph,
pos,
nodelist=graph.nodes(),
node_color="blue")
for i, x in enumerate(nodes):
nx.draw_networkx_nodes(graph, pos, nodelist=x, node_color=colors[i])
nx.draw_networkx_edges(graph, pos, graph.edges(), edge_color="black")
plt.axis('off')
plt.show()
def save_graph(graph, n, p):
#initialze Figure
plt.figure(num=None, figsize=(20, 20), dpi=80)
plt.axis('off')
fig = plt.figure(figsize=(50, 40))
pos = nx.circular_layout(graph)
nx.draw_networkx_nodes(graph, pos)
nx.draw_networkx_edges(graph, pos)
nx.draw_networkx_labels(graph, pos)
file_name = 'Q8_Assets/SmallWorld_N_' + str(n) + '_P_' + str(p) + '.pdf'
plt.savefig(file_name, bbox_inches="tight")
plt.close(fig)
del fig
def save_graph(graph, n, p):
#initialze Figure
plt.figure(num=None, figsize=(20, 20), dpi=80)
plt.axis('off')
fig = plt.figure(figsize=(20, 15))
pos = nx.spring_layout(graph)
nx.draw_networkx_nodes(graph, pos)
nx.draw_networkx_edges(graph, pos)
nx.draw_networkx_labels(graph, pos)
file_name = 'Q7_Assets/ErdosRenyi_N_' + str(n) + '_P_' + str(p) + '.pdf'
plt.savefig(file_name, bbox_inches="tight")
plt.close(fig)
del fig
def drawGraph(filename):
location = latlong('latlong_us.txt')
g = nx.Graph()
with open(filename) as f:
for line in f:
src, dst = line.split('->')
tmp = src.split(':')[1].split(',')
src = tmp[0].replace(' ', '') + ',' + tmp[1].strip()
tmp = dst.split(':')[1].split(',')
dst = tmp[0].strip().replace(' ', '') + ',' + tmp[1].strip().split()[0]
g.add_edge(src, dst)
print len(g.nodes())
print len(g.edges())
pos = {}
cnt = 0
for node in g.nodes():
cnt += 1
inx = None
if location.has_key(node):
inx = node
else:
for key in location.keys():
addr = node.split(',')
if (addr[0] in key and addr[1] in key):
inx = key
if not inx:
print node
print "%d/%d" % (cnt, len(g.nodes()))
raise
pos[node] = (180-location[inx][1], location[inx][0])
#pos=nx.graphviz_layout(g,prog="fdp")
#pos=nx.spring_layout(g)
plt.figure(figsize=(10,8))
#plt.axis('off')
plt.xticks([]), plt.yticks([])
nx.draw_networkx_nodes(g, pos = pos, node_color = 'red', node_size = 30, with_labels=False)
nx.draw_networkx_edges(g,pos,alpha=0.4)
plt.axis('equal')
plt.show()
def draw_graph_with_labels_training(GraphGenerationObject):
# Draw the graph
pos = graphviz_layout(GraphGenerationObject.Graph, prog='neato')
nx.draw_networkx_nodes(GraphGenerationObject.Graph,
pos,
nodelist=GraphGenerationObject.learning_green_nodes,
node_color="green")
nx.draw_networkx_nodes(GraphGenerationObject.Graph,
pos,
nodelist=GraphGenerationObject.learning_red_nodes,
node_color="red")
nx.draw_networkx_nodes(GraphGenerationObject.Graph,
pos,
nodelist=GraphGenerationObject.blue_nodes,
node_color="blue")
nx.draw_networkx_labels(GraphGenerationObject.Graph,
pos,
nodelist=GraphGenerationObject.Graph.nodes())
nx.draw_networkx_edges(GraphGenerationObject.Graph,
pos,
GraphGenerationObject.Graph.edges(),
edge_color="black")
plt.axis('off')
plt.show()
def demo_pytorch_computational_graph(
t,
init_gradient=None,
figsize=(12, 6),
padding=40
):
import torch
import networkx as nx
import numpy as np
import matplotlib.pyplot as plt
if init_gradient is None:
init_gradient = torch.tensor(1.0)
G_forward = nx.DiGraph() # for layout
G = nx.MultiDiGraph()
stack = [(t.grad_fn, t.grad_fn(init_gradient))]
node_labels = {}
while stack:
node, outer_gradient = stack.pop()
node_id = str(id(node)) + node.name()
node_labels[node_id] = node.name()
for n, n_outer_gradient in zip(node.next_functions, outer_gradient):
if n[0] is not None:
n_id = str(id(n[0])) + n[0].name()
node_labels[n_id] = n[0].name()
G_forward.add_edge(n_id, node_id)
G.add_edge(node_id, n_id, label=n_outer_gradient.item())
stack.append((n[0], n[0](n_outer_gradient)))
# place nodes left-to-right
# "regular" top-to-bottom layout
nodes_layout = nx.nx_pydot.graphviz_layout(G_forward, prog='dot')
# make right-to-left from top-to-bottom
nodes_layout = {k: (-v[1], v[0]) for k, v in nodes_layout.items()}
# visualize
x_min = min([c[0] for c in nodes_layout.values()])
x_max = max([c[0] for c in nodes_layout.values()])
y_min = min([c[1] for c in nodes_layout.values()])
y_max = max([c[1] for c in nodes_layout.values()])
plt.figure(figsize=figsize)
plt.xlim(x_min - padding, x_max + padding)
plt.ylim(y_min - padding, y_max + padding)
# draw nodes
nx.draw_networkx_nodes(G, node_color="#a2c4fc", pos=nodes_layout)
nx.draw_networkx_labels(G, pos=nodes_layout, labels=node_labels)
# draw edges
for e in G.edges:
l = G.edges[e]["label"]
current_multiplicity = e[2]
coords = tuple(0.5 * (np.array(nodes_layout[e[0]]) + np.array(nodes_layout[e[1]])) - 10 * current_multiplicity)
plt.annotate(l, coords, color="r", ha='center')
# hacky arrows
plt.annotate(
"",
xy=nodes_layout[e[1]], xycoords='data',
xytext=nodes_layout[e[0]], textcoords='data',
arrowprops=dict(
arrowstyle="simple",
color="r",
alpha=0.5,
shrinkA=10, shrinkB=10,
connectionstyle="arc3,rad={}".format(-0.1*(1 + current_multiplicity))
),
)
def visualize(forward_idx=0, backward_idx=0):
plt.figure(figsize=figsize)
plt.xlim(x_min - padding, x_max + padding)
plt.ylim(y_min - padding, y_max + padding)
plt.axis('equal')
if title:
plt.title(r"Computational graph for " + title, fontsize=font_size)
# draw nodes
nx.draw_networkx_nodes(G_forward, node_color="#a2c4fc", pos=nodes_layout, node_size=node_size)
nx.draw_networkx_labels(G_forward, pos=nodes_layout, labels=node_labels, font_size=font_size)
edges_kwargs = dict(pos=nodes_layout, connectionstyle="arc3,rad=-0.1", width=2)
# draw forward edges
nx.draw_networkx_edges(G_forward, edge_color=forward_color, alpha=0.5, **edges_kwargs)
# draw backward edges
nx.draw_networkx_edges(G_backward, edge_color=backward_color, alpha=0.5, **edges_kwargs)
# draw labels
def label_coordinates(v1, v2, norm_fraction=0.15, backward=False):
v1 = np.array(v1)
v2 = np.array(v2)
center = 0.5 * (v1 + v2)
if backward:
d = v1 - v2
else:
d = v2 - v1
norm = np.sqrt(d @ d)
d /= norm
shift = np.array([-d[1], d[0]]) * norm_fraction * norm
if backward:
shift = -shift
angle = math.degrees(math.atan2(d[1], d[0]))
if angle > 90:
angle -= 180
elif angle < -90:
angle += 180
return tuple(center + shift), angle
active_forward_edges = []
for e, l in forward_edge_label[:forward_idx]:
active_forward_edges.append(e)
norm_fraction = 0.1 + 0.05 * len(l.split("\n")) # larger shift for multiline labels
coords, angle = label_coordinates(nodes_layout[e[0]], nodes_layout[e[1]], norm_fraction=norm_fraction)
plt.annotate(l, coords, color=forward_color, size=font_size, ha='center', rotation=angle,
rotation_mode='anchor')
# highlight forward edges
nx.draw_networkx_edges(G_forward, edgelist=active_forward_edges, edge_color=forward_color, alpha=1,
**edges_kwargs)
active_backward_edges = []
for e, l in backward_edge_label[:backward_idx]:
active_backward_edges.append(e)
norm_fraction = 0.1 + 0.05 * len(l.split("\n")) # larger shift for multiline labels
coords, angle = label_coordinates(nodes_layout[e[0]], nodes_layout[e[1]], norm_fraction=norm_fraction,
backward=True)
plt.annotate(l, coords, color=backward_color, size=font_size, ha='center', rotation=angle,
rotation_mode='anchor')
# highlight backward edges
nx.draw_networkx_edges(G_backward, edgelist=active_backward_edges, edge_color=backward_color, alpha=1,
**edges_kwargs)
plt.show()
def solve(a, p, b):
nitems = len(p)
items = range(nitems)
vertices = [[i, j] for i in range(b)
for j in items] # Vertices are named (i,j), see lecture
k = 0
for vertice in vertices:
vertice.append(k)
k += 1
G = nx.DiGraph()
arcs = [] # List of tuples, i.e. [((i,j), (k,l),w), ((k,l), (u,v),0)]
for i, j, x_1 in vertices:
for k, l, x_2 in vertices:
if (i == k and j == l):
continue
elif (i == k and l - j == 1):
arcs.append((x_1, x_2, 0))
G.add_edge(x_1, x_2, weight=0)
elif (i - k == -1 and j == l):
arcs.append((x_1, x_2, 1))
G.add_edge(x_1, x_2, weight=1)
# print(arcs)
# G.add_nodes_from([0, 1, 2, 3, 4])
# G.add_weighted_edges_from([(1,2,3),(1,3,2)])
# G.add_edge('a', 'b', weight=0.6)
# G.add_edge('a', 'c', weight=0.2)
# G.add_edge('c', 'd', weight=0.1)
# G.add_edge('c', 'e', weight=0.7)
# G.add_edge('c', 'f', weight=0.9)
# G.add_edge('a', 'd', weight=0.3)
elarge = [(u, v) for (u, v, d) in G.edges(data=True) if d['weight'] > 0.5]
esmall = [(u, v) for (u, v, d) in G.edges(data=True) if d['weight'] <= 0.5]
# pos = nx.spring_layout(G) # positions for all nodes
pos = nx.random_layout(G)
# nodes
nx.draw_networkx_nodes(G, pos, node_size=200)
# edges
nx.draw_networkx_edges(G, pos, edgelist=elarge, width=1)
nx.draw_networkx_edges(G,
pos,
edgelist=esmall,
width=1,
alpha=0.5,
edge_color='b',
style='dashed')
# labels
nx.draw_networkx_labels(G, pos, font_size=3, font_family='sans-serif')
# G.add_nodes_from(vertices)
# print(G.number_of_nodes())
# G.add_edge(1, 2)
# print the adjacency list
# for line in nx.generate_adjlist(G):
# print(line)
# write edgelist to grid.edgelist
# nx.write_edgelist(G, path="grid.edgelist", delimiter=":")
# read edgelist from grid.edgelist
# H = nx.read_edgelist(path="grid.edgelist", delimiter=":")
# print(H)
plt.axis('off')
plt.show()
def sistemaColoniaFormiga(grafo, mapa, origem, destino, lista_vertice,
coeficiente_evaporacao, iteracao, vel_iteracao,
formiga):
rota_total = [('AP', 'PA'), ('AC', 'RO'), ('RO', 'AM'), ('AM', 'AC'),
('RR', 'AM'), ('RR', 'PA'), ('PA', 'AM'), ('PA', 'TO'),
('RS', 'SC'), ('SC', 'PR'), ('PR', 'MS'), ('PR', 'SP'),
('SP', 'RJ'), ('RJ', 'MG'), ('MG', 'SP'), ('MS', 'MT'),
('MT', 'RO'), ('MT', 'PA'), ('MT', 'GO'), ('GO', 'DF'),
('DF', 'MG'), ('MG', 'GO'), ('GO', 'BA'), ('BA', 'TO'),
('TO', 'GO'), ('TO', 'MA'), ('MA', 'PI'), ('PI', 'TO'),
('BA', 'MG'), ('BA', 'ES'), ('BA', 'SE'), ('SE', 'AL'),
('AL', 'PE'), ('PE', 'PI'), ('PE', 'PB'), ('PI', 'CE'),
('CE', 'RN'), ('RN', 'PB'), ('PB', 'CE'), ('PB', 'PE'),
('PA', 'MA'), ('PI', 'BA'), ('MG', 'MS'), ('MS', 'GO'),
('MS', 'SP'), ('MG', 'ES'), ('RJ', 'ES')]
pos = {
'AC': (53.71, 229.51),
'AL': (579.10, 233.28),
'AM': (133.96, 158.04),
'AP': (340.86, 60.23),
'BA': (505.12, 274.66),
'CE': (531.45, 160.55),
'DF': (387.83, 351.83),
'ES': (513.90, 390.02),
'GO': (382.24, 306.00),
'MA': (444.93, 161.80),
'MG': (453.71, 369.95),
'MT': (281.92, 283.47),
'MS': (293.21, 392.52),
'PA': (314.53, 163.06),
'PE': (551.52, 208.20),
'PB': (587.88, 198.17),
'PI': (488.82, 200.67),
'PR': (342.11, 467.76),
'RN': (577.85, 168.07),
'RO': (174.09, 262.12),
'RR': (194.15, 53.97),
'RS': (315.78, 544.25),
'RJ': (473.77, 437.66),
'SC': (374.71, 512.90),
'SE': (567.82, 249.58),
'SP': (383.49, 423.87),
'TO': (397.29, 237.04)
}
lista_formigas = []
for i in range(formiga):
lista_formigas.append(str(i + 1))
im = Image.open('back.png')
fig1 = plt.figure()
fig1.set_facecolor('#CCCCCC')
# ax3 = fig1.add_subplot(2,2,2) # plot do gráfico1
# ax3.set_title('Gráfico 2 das Formigas')
# ax3.set_facecolor('#CCCCCC')
# ax3.grid()
# ax3.plot()
ax2 = fig1.add_subplot(1, 2, 2) # plot do gráfico1
ax2.set_title('Gráfico 1 das Formigas ')
ax2.set_facecolor('#CCCCCC')
ax2.grid()
ax2.plot()
ax1 = fig1.add_subplot(1, 2, 1) # plot do mapa
ax1.set_title('Mapa de Colônia')
ax1.set_xticklabels([])
ax1.set_xlabel('Latitude')
ax1.set_yticklabels([])
ax1.set_ylabel('Longitude')
ax1.set_facecolor('#CCCCCC')
ax1.plot()
nx.draw_networkx_nodes(mapa,
pos,
node_color='#6986a3',
alpha=0.8,
node_size=100)
nx.draw_networkx_nodes(mapa,
pos,
nodelist=[origem],
node_color='green',
node_size=150,
alpha=0.9,
label='Origem')
nx.draw_networkx_nodes(mapa,
pos,
nodelist=[destino],
node_color='red',
node_size=150,
alpha=0.9,
label='Destino')
nx.draw_networkx_edges(mapa, pos, width=1.5, alpha=0.9, edge_color='white')
nx.draw_networkx_labels(mapa, pos, font_size=6, font_color='white')
# nx.draw_networkx_edge_labels(mapa, pos, font_size=5) # EXIBE OS PESOS DAS ARESTAS
def refresh(x):
for i in range(1):
lista_caminho_formiga = []
rota = []
for j in range(formiga):
list_caminho = []
caminho(grafo, origem, destino, list_caminho)
removeCiclo(list_caminho)
lista_caminho_formiga.append(list_caminho)
distanciaTotal = atualizaTaxaFeromonio(grafo,
lista_caminho_formiga,
coeficiente_evaporacao,
lista_vertice)
ax2.plot_date(lista_formigas, distanciaTotal)
ax2.bar(lista_formigas,
distanciaTotal,
color='white',
label='teste')
ax2.plot(distanciaTotal, lw=0.02)
# ax2.hist(distanciaTotal)
print(distanciaTotal)
for j in range(formiga):
for k in range(len(lista_caminho_formiga[j]) - 1):
rota.append((lista_caminho_formiga[j][k],
lista_caminho_formiga[j][k + 1]))
nx.draw_networkx_edges(mapa,
pos,
edgelist=rota,
width=2,
alpha=0.01,
edge_color='black')
nx.draw_networkx_edges(mapa,
pos,
edgelist=rota_total,
width=2.7,
alpha=0.0095,
edge_color='w')
ax2.set_title('Comportamento das Formigas')
ax2.set_ylabel('Distância (KM)')
ax2.set_xticks(lista_formigas)
ax2.set_xticklabels(distanciaTotal)
ax2.set_xlabel('Distância Percorrida até o destino (KM)')
plt.legend(loc='lower left')
plt.imshow(im)
ani1 = gif.FuncAnimation(fig1,
refresh,
iteracao,
interval=vel_iteracao,
repeat=False)
plt.tight_layout()
plt.show()
def draw(self, node_type='', layout=''):
"""
Draw graph with vertices, edges, and faces labeled by colored nodes and their integer indices
corresponding to the qubit indices for the surface code
"""
if not node_type in ['cycles', 'dict']:
raise ValueError('node_type can be "cycles" or "dict"')
if layout == 'spring':
pos = nx.spring_layout(self.code_graph)
if layout == 'spectral':
pos = nx.spectral_layout(self.code_graph)
if layout == 'planar':
pos = nx.planar_layout(self.code_graph)
if layout == 'shell':
pos = nx.shell_layout(self.code_graph)
if layout == 'circular':
pos = nx.circular_layout(self.code_graph)
if layout == 'spiral':
pos = nx.spiral_layout(self.code_graph)
if layout == 'random':
pos = nx.random_layout(self.code_graph)
# white nodes
nx.draw_networkx_nodes(self.code_graph,
pos,
nodelist=list(self.alpha),
node_color='c',
node_size=500,
alpha=0.3)
# vertex nodes
nx.draw_networkx_nodes(self.code_graph,
pos,
nodelist=list(self.sigma),
node_color='b',
node_size=500,
alpha=0.6)
# face nodes
nx.draw_networkx_nodes(self.code_graph,
pos,
nodelist=list(self.phi),
node_color='r',
node_size=500,
alpha=0.6)
# edges
nx.draw_networkx_edges(self.code_graph, pos, width=1.0, alpha=0.5)
labels = {}
if node_type == 'cycles':
'''
label nodes the cycles of sigma, alpha, and phi
'''
for node in self.alpha_dict:
# stuff = self.alpha_dict[node]
labels[node] = f'$e$({node})'
for node in self.sigma_dict:
# something = self.sigma_dict[node]
labels[node] = f'$v$({node})'
for node in self.phi_dict:
# something2 = self.phi_dict[node]
labels[node] = f'$f$({node})'
nx.draw_networkx_labels(self.code_graph, pos, labels, font_size=12)
if node_type == 'dict':
'''
label nodes with v, e, f and indices given by node_dict corresponding to
qubit indices of surface code
'''
for node in self.alpha_dict:
# stuff = self.alpha_dict[node]
labels[node] = f'$e$({self.alpha_dict[node]})'
for node in self.sigma_dict:
# something = self.sigma_dict[node]
labels[node] = f'$v$({self.sigma_dict[node]})'
for node in self.phi_dict:
# something2 = self.phi_dict[node]
labels[node] = f'$f$({self.phi_dict[node]})'
nx.draw_networkx_labels(self.code_graph, pos, labels, font_size=12)
# plt.axis('off')
# plt.savefig("labels_and_colors.png") # save as png
plt.show() # display
distances = [[0 for i in range(no_of_cities)] for j in range(no_of_cities)]
pheromone = [[0 for i in range(no_of_cities)] for j in range(no_of_cities)]
ants = [Ant(randint(0, no_of_cities - 1), [], 0) for i in range(no_of_ants)]
for i in range(no_of_cities):
for j in range(no_of_cities):
if i != j and distances[i][j] == 0:
distances[i][j] = randint(1, 20)
distances[j][i] = distances[i][j]
# plot graph
graph = networkx.from_numpy_matrix(numpy.array(distances))
print(distances)
pos = nx.shell_layout(graph)
nx.draw_networkx_nodes(graph, pos, node_size=80)
nx.draw_networkx_labels(graph, pos, font_size=13, font_family='sans-serif')
labels = nx.get_edge_attributes(graph, 'weight')
nx.draw_networkx_edge_labels(graph, pos, edge_labels=labels, label_pos=0.61)
nx.draw(graph, pos)
plt.axis('off')
plt.show()
print()
# assign ants to cities
for i in range(no_of_ants):
ants[i].visitedCitiesSet.append(ants[i].currentCity)
# start process
# if p in dist:
# dist[p] += 1
# else:
# dist[p] = 1
# print('')
# print("length #paths")
# verts = dist.keys()
# for d in sorted(verts):
# print('%s %d' % (d, dist[d]))
# print("radius: %d" % nx.radius(G))
# print("diameter: %d" % nx.diameter(G))
# print("eccentricity: %s" % nx.eccentricity(G))
# print("center: %s" % nx.center(G))
# print("periphery: %s" % nx.periphery(G))
# print("density: %s" % nx.density(G))
# #nx.draw(G, with_labels=True)
plt.figure(3, figsize=(13, 7))
# nx.draw_networkx(DG, pos, with_labels=True, node_size = 80)
nx.draw_networkx_nodes(DG, pos, node_size=20, node_color="blue")
nx.draw_networkx_edges(DG, pos, alpha=0.4, width=0.5)
nx.draw_networkx_labels(DG, pos, alpha=0.7, font_size=8)
plt.axis('off')
plt.show()
# print(DG.nodes())
# print(len(DG.nodes()))