def test_spiral_layout(self):
G = self.Gs
# a lower value of resolution should result in a more compact layout
# intuitively, the total distance from the start and end nodes
# via each node in between (transiting through each) will be less,
# assuming rescaling does not occur on the computed node positions
pos_standard = np.array(
list(nx.spiral_layout(G, resolution=0.35).values()))
pos_tighter = np.array(
list(nx.spiral_layout(G, resolution=0.34).values()))
distances = np.linalg.norm(pos_standard[:-1] - pos_standard[1:],
axis=1)
distances_tighter = np.linalg.norm(pos_tighter[:-1] - pos_tighter[1:],
axis=1)
assert sum(distances) > sum(distances_tighter)
# return near-equidistant points after the first value if set to true
pos_equidistant = np.array(
list(nx.spiral_layout(G, equidistant=True).values()))
distances_equidistant = np.linalg.norm(pos_equidistant[:-1] -
pos_equidistant[1:],
axis=1)
assert np.allclose(distances_equidistant[1:],
distances_equidistant[-1],
atol=0.01)
def test_smoke_empty_graph(self):
G = []
nx.random_layout(G)
nx.circular_layout(G)
nx.planar_layout(G)
nx.spring_layout(G)
nx.fruchterman_reingold_layout(G)
nx.spectral_layout(G)
nx.shell_layout(G)
nx.bipartite_layout(G, G)
nx.spiral_layout(G)
nx.kamada_kawai_layout(G)
def test_smoke_string(self):
G = self.Gs
nx.random_layout(G)
nx.circular_layout(G)
nx.planar_layout(G)
nx.spring_layout(G)
nx.fruchterman_reingold_layout(G)
nx.spectral_layout(G)
nx.shell_layout(G)
nx.spiral_layout(G)
nx.kamada_kawai_layout(G)
nx.kamada_kawai_layout(G, dim=1)
nx.kamada_kawai_layout(G, dim=3)
def display_pos(G, layout='shortest'):
''' Display Position of the Nodes:
# spiral
# 1. general layout that works well for lots of nodes
# pos = nx.spiral_layout(G)
# "variable-type":
multiplartitle_layout using subsets of (output, intermediatory, input). it works well for small number of nodes, but not for a bigger set of nodes
# "shortest" by default
multiplartitle_layout using shortest distance to the source.
'''
if layout == 'shortest':
var_id = list(G.nodes)[0]
shortest_length = single_source_shortest_path_length(G, var_id)
for node in shortest_length.keys():
G.nodes[node]['shortest'] = shortest_length[node]
pos = nx.multipartite_layout(G,
subset_key="shortest",
align='horizontal')
elif layout == "variable-type":
for node, varType in G.nodes(data=True):
if varType['type'] == 'input':
G.nodes[node]['subset'] = 2
elif varType['type'] == 'output':
G.nodes[node]['subset'] = 0
elif varType['type'] == 'intermediary':
G.nodes[node]['subset'] = 1
else:
G.nodes[node]['subset'] = -1
pos = nx.multipartite_layout(G,
subset_key="subset",
align='horizontal')
elif layout == "planar":
pos = nx.planar_layout(G)
elif layout == "spring":
pos = nx.spring_layout(G)
elif layout == "shell":
pos = nx.shell_layout(G)
elif layout == "spiral":
pos = nx.spiral_layout(G)
else:
pos = nx.spiral_layout(G)
return pos
def show(self, labels='type'):
if labels == 'both' or labels == 'type':
relabel_mapping = {k: v.node_name() for k, v in self.node_reference.items()}
computational_graph = nx.relabel_nodes(self.graph, relabel_mapping, )
options = {'node_size': 2000, 'alpha': 0.7}
if labels == 'both':
plt.figure(figsize=(15, 8))
plt.subplot(121)
pos = nx.spring_layout(computational_graph, iterations=50)
nx.draw(computational_graph, pos, with_labels=True, **options)
plt.subplot(122)
pos = nx.spiral_layout(self.graph, )
nx.draw(self.graph, with_labels=True)
else:
plt.figure(figsize=(15, 8))
plt.subplot()
nx.draw(computational_graph, with_labels=True)
else:
plt.figure(figsize=(15, 8))
plt.subplot()
nx.draw(self.graph, with_labels=True)
plt.show()
def create_graph():
repo_name = "progit2"
code_dir = "code"
dir_path = os.path.join(os.getenv("userprofile"), code_dir, repo_name)
repo = Repo(dir_path)
print(dir_path)
graph = nx.DiGraph()
for ref in repo.references:
print(ref.commit, ref)
if graph.has_node(ref.commit.hexsha) and ('refs' in graph.nodes[ref.commit.hexsha]):
refs = graph.nodes[ref.commit.hexsha]['refs']
refs = refs + ", " + ref.name
graph.nodes[ref.commit.hexsha]['refs'] = refs
else:
graph.add_node(ref.commit.hexsha, refs=ref.name)
add_parent_chain_to_graph(graph, ref.commit)
print('graph.nodes list', list(graph.nodes))
pos = nx.spiral_layout(graph)
options = {
'node_color': 'orange',
'node_size': 2,
'width': 1,
'arrow_size': 3,
'with_labels': False,
'pos': pos
}
print('number_of_nodes', graph.number_of_nodes())
print(list(graph.edges(data=True)))
print(list(graph.nodes(data=True)))
nx.draw_networkx(graph, **options)
nx.write_gexf(graph, '{}.gexf'.format(repo_name))
plt.show()
def plot_undirected(reader: MBoxReader,
layout: str = 'shell',
graphml: bool = False):
"""Plot an undirected social network graph from the entire `mbox`, supplied by `MBoxReader`.
`layout` determines the underlying `NetworkX` layout.
Usage:
reader = MboxReader('path-to-mbox.mbox')
plot_undirected(reader)
Args:
reader (MBoxReader): A `MBoxReader` object
layout (str, optional): Can be one of 'shell', 'spring' or 'spiral'. Defaults to 'shell'.
graphml (bool, optional): Determines if a .graphml file is exported to the working directory. Defaults to False.
"""
emails = reader.extract()
G = nx.Graph(name='Email Social Network')
plt.figure(figsize=(12, 12))
counter = Counter()
for email in emails:
ng = PeopleCombination(email)
for combo in ng.combo:
counter[combo] += 1
total_combos = sum(counter.values())
by_freq = {k: v / total_combos for k, v in counter.most_common()}
for rel in counter.keys():
G.add_edge(*rel, weight=by_freq[rel], count=counter[rel])
if graphml:
fileName = f'network-{str(uuid.uuid4().hex)[:8]}.graphml'
nx.write_graphml(G, fileName)
print(f"Graphml exported as {fileName}")
if layout == 'shell':
pos = nx.shell_layout(G)
elif layout == 'spring':
k = 1 / math.sqrt(G.order()) * 2
pos = nx.spring_layout(G, k=k)
else:
pos = nx.spiral_layout(G)
deg = [v * 50 for _, v in G.degree()]
nx.draw_networkx_nodes(G, pos, node_size=deg, linewidths=1.0, alpha=0.60)
nx.draw_networkx_edges(G,
pos,
width=1.0,
style='dashed',
edge_color='cadetblue',
alpha=0.6)
nx.draw_networkx_labels(G,
pos, {n: n.split('@')[0]
for n in G.nodes},
font_size=8,
font_color='darkorchid')
plt.axis('off')
plt.show()
def generateSpectralLayout(layout: Layout):
positions = nx.spectral_layout(layout.G)
print(positions)
nx.draw(layout.G, positions)
plt.show()
positions = nx.planar_layout(layout.G)
print(positions)
nx.draw(layout.G, positions)
plt.show()
positions = nx.circular_layout(layout.G)
print(positions)
nx.draw(layout.G, positions)
plt.show()
positions = nx.bipartite_layout(layout.G, nx.bipartite.sets(layout.G)[0])
print(positions)
nx.draw(layout.G, positions)
plt.show()
positions = nx.shell_layout(layout.G)
print(positions)
nx.draw(layout.G, positions)
plt.show()
positions = nx.random_layout(layout.G)
print(positions)
nx.draw(layout.G, positions)
plt.show()
positions = nx.spiral_layout(layout.G)
print(positions)
nx.draw(layout.G, positions)
plt.show()
def test_smoke_int(self):
G = self.Gi
nx.random_layout(G)
nx.circular_layout(G)
nx.planar_layout(G)
nx.spring_layout(G)
nx.fruchterman_reingold_layout(G)
nx.fruchterman_reingold_layout(self.bigG)
nx.spectral_layout(G)
nx.spectral_layout(G.to_directed())
nx.spectral_layout(self.bigG)
nx.spectral_layout(self.bigG.to_directed())
nx.shell_layout(G)
nx.spiral_layout(G)
nx.kamada_kawai_layout(G)
nx.kamada_kawai_layout(G, dim=1)
nx.kamada_kawai_layout(G, dim=3)
def plot_graph(graph, name, dpi=200, width=0.5, layout='spring'):
plt.figure(figsize=(10, 10))
pos = nx.spiral_layout(graph)
if layout == 'spring':
pos = nx.spring_layout(graph)
elif layout == 'circular':
pos = nx.circular_layout(graph)
nx.draw(graph, pos=pos, node_size=100, width=width)
plt.savefig('figs/graph_view_{}.png'.format(name),
dpi=dpi,
transparent=True)
def draw_MI(M_orig, ax, layout="spring", pos=None):
M = copy(M_orig)
M[np.abs(M) < 1e-5] = 0.0
M[np.abs(M) < np.median(M)] = 0.0
G = nx.from_numpy_matrix(M)
if pos is None:
if layout == "spring":
pos = nx.spring_layout(G, k=0.8 / np.sqrt(len(M)), iterations=74)
elif layout == "bipartite":
pos = nx.bipartite_layout(G, nodes=range(len(M) // 2))
elif layout == "circular":
pos = nx.circular_layout(G)
elif layout == "spectral":
pos = nx.spectral_layout(G)
elif layout == "spiral":
pos = nx.spiral_layout(G)
elif layout == "shell":
pos = nx.shell_layout(G)
elif layout == "planar":
pos = nx.planar_layout(G)
elif layout == "fr":
pos = nx.fruchterman_reingold_layout(G)
elif layout == "kk":
pos = nx.kamada_kawai_layout(G)
if layout == "grid":
Ggrid = nx.grid_2d_graph(*M.shape)
xs = np.linspace(-1, 1, int(np.ceil(np.sqrt(len(M)))))
pos = {}
i = 0
for x in xs:
for y in xs:
if i < len(M):
pos[i] = np.array([x, y])
i += 1
edges, weights = zip(*nx.get_edge_attributes(G, "weight").items())
ws = np.array([w for w in weights])
mx = max(ws)
mn = min(ws)
if mx != mn:
ws = (ws - mn) / (mx - mn)
nx.draw(
G,
pos,
ax=ax,
node_color="k",
node_size=6,
alphs=0.5,
edgelist=edges,
edge_color="k",
width=ws,
)
ax.set_aspect("equal")
def test_default_scale_and_center(self):
sc = self.check_scale_and_center
c = (0, 0)
G = nx.complete_graph(9)
G.add_node(9)
sc(nx.random_layout(G), scale=0.5, center=(0.5, 0.5))
sc(nx.spring_layout(G), scale=1, center=c)
sc(nx.spectral_layout(G), scale=1, center=c)
sc(nx.circular_layout(G), scale=1, center=c)
sc(nx.shell_layout(G), scale=1, center=c)
sc(nx.spiral_layout(G), scale=1, center=c)
sc(nx.kamada_kawai_layout(G), scale=1, center=c)
def test_spiral_layout(self):
G = self.Gs
# a lower value of resolution should result in a more compact layout
# intuitively, the total distance from the start and end nodes
# via each node in between (transiting through each) will be less,
# assuming rescaling does not occur on the computed node positions
pos_standard = nx.spiral_layout(G, resolution=0.35)
pos_tighter = nx.spiral_layout(G, resolution=0.34)
distances = self.collect_node_distances(pos_standard)
distances_tighter = self.collect_node_distances(pos_tighter)
assert sum(distances) > sum(distances_tighter)
# return near-equidistant points after the first value if set to true
pos_equidistant = nx.spiral_layout(G, equidistant=True)
distances_equidistant = self.collect_node_distances(pos_equidistant)
for d in range(1, len(distances_equidistant) - 1):
# test similarity to two decimal places
assert almost_equal(distances_equidistant[d],
distances_equidistant[d + 1], 2)
def plot_directed(reader: MBoxReader,
layout: str = 'shell',
graphml: bool = False) -> None:
"""
Plot a directed social network graph from the entire `mbox`, supplied by `MBoxReader`.
`layout` determines the underlying `NetworkX` layout.
Usage:
reader = MboxReader('path-to-mbox.mbox')
plot_directed(reader)
Args:
reader (MBoxReader): A `MBoxReader` object
layout (str, optional): Can be one of 'shell', 'spring' or 'spiral'. Defaults to 'shell'.
graphml (bool, optional): Determines if a .graphml file is exported to the working directory. Defaults to False.
"""
emails = reader.extract()
plt.figure(figsize=(12, 12))
G = nx.MultiDiGraph(name='Email Social Network')
for email in emails:
sender = email.sender.name
source_addr = sender if sender != '' else email.sender.email.split(
'@')[0]
all_recipients = [
em.name if em.name != '' or None else em.email.split('@')[0]
for em in email.recipients + email.cc
]
for recipient in all_recipients:
G.add_edge(source_addr, recipient, message=email.subject)
if graphml:
fileName = f'network-{str(uuid.uuid4().hex)[:8]}.graphml'
nx.write_graphml(G, fileName)
if layout == 'shell':
pos = nx.shell_layout(G)
elif layout == 'spring':
pos = nx.spring_layout(G)
else:
pos = nx.spiral_layout(G)
nx.draw(G,
pos,
node_size=0,
alpha=0.4,
edge_color='cadetblue',
font_size=7,
with_labels=True)
ax = plt.gca()
ax.margins(0.08)
plt.show()
def test_scale_and_center_arg(self):
sc = self.check_scale_and_center
c = (4, 5)
G = nx.complete_graph(9)
G.add_node(9)
sc(nx.random_layout(G, center=c), scale=0.5, center=(4.5, 5.5))
# rest can have 2*scale length: [-scale, scale]
sc(nx.spring_layout(G, scale=2, center=c), scale=2, center=c)
sc(nx.spectral_layout(G, scale=2, center=c), scale=2, center=c)
sc(nx.circular_layout(G, scale=2, center=c), scale=2, center=c)
sc(nx.shell_layout(G, scale=2, center=c), scale=2, center=c)
sc(nx.spiral_layout(G, scale=2, center=c), scale=2, center=c)
sc(nx.kamada_kawai_layout(G, scale=2, center=c), scale=2, center=c)
def test_smoke_string(self):
G = self.Gs
vpos = nx.random_layout(G)
vpos = nx.circular_layout(G)
vpos = nx.planar_layout(G)
vpos = nx.spring_layout(G)
vpos = nx.fruchterman_reingold_layout(G)
vpos = nx.spectral_layout(G)
vpos = nx.shell_layout(G)
vpos = nx.spiral_layout(G)
if self.scipy is not None:
vpos = nx.kamada_kawai_layout(G)
vpos = nx.kamada_kawai_layout(G, dim=1)
def demo():
nodes_dict = {
'node1': {
'node2': 1.3,
'node3': 2
},
'node2': {
'node1': 1.3,
'node4': 3,
'node5': 0.5
},
'node3': {
'node2': 1,
'node4': 2
}
}
cng = create_nx_graph(nodes_dict)
# if no nodes want to be emphasised, if node_colorlist is None, each node has a random color
cng.plot(figsize=(8, 8),
node_sizelist=[1000],
font_size=20,
edge_color='blue')
cng.plot(figsize=(8, 8),
node_colorlist=['blue'],
font_size=20,
edge_color='blue')
# we want to emphasis node1, we give size and color for it and others
cng.plot(nodelist=['node1'],
node_colorlist=['red', 'blue'],
node_sizelist=[1000, 100],
figsize=(8, 8),
font_size=20)
# we want to emphasis node1 and node2, we give size and color for it and others
cng.plot(nodelist=['node1', 'node2'],
node_colorlist=['red', 'blue', 'green'],
node_sizelist=[1000, 500, 100],
figsize=(8, 8),
font_size=20)
# other layout
pos = nx.spiral_layout(cng.networkG)
cng.plot(figsize=(8, 8),
node_sizelist=[1000],
font_size=20,
edge_color='blue',
pos=pos)
def layout_network(self, order_by_ip=True, rectangular_grid=False):
"""Determine node locations/coordinates to allow visualization/plotting of the network.
Parameters
----------
order_by_ip : bool
Set to true if you want node positions lists ordered by ip address.
rectangular_grid : bool
Set to true for a grid placement that is roughly rectangular.
It will not be exactly rectangular because noise is added to avoid edge line overlap.
Notes
-------
1) Various networkx options are listed in layout_types below. Pick any compatible layout.
2) networkx layouts return dictionaries that can't be sorted.
The order_by_ip option re-orders node locations based on how the layout
dictionary is iterated, which may or may not improve plot readability.
See: https://networkx.github.io/documentation/stable/reference/drawing.html"""
# networkx routines to find node layout
# Each returns a dictionary of positions keyed by node. The positions are [x, y].
layout_types = [
nx.bipartite_layout, nx.circular_layout, nx.kamada_kawai_layout,
nx.planar_layout, nx.random_layout, nx.rescale_layout,
nx.rescale_layout_dict, nx.shell_layout, nx.spring_layout,
nx.spectral_layout, nx.spiral_layout, nx.multipartite_layout
]
if rectangular_grid:
# Custom square layout with noise created to best spread network sorted by IP address
self.node_positions = self.square_layout(self.send_graph,
noise=0.15)
else:
# Choose any of the layout_types for line below
self.node_positions = nx.spiral_layout(self.send_graph)
# Sort node locations by ip address if the user requests.
# It is not clear the order of the nx layouts since they are dictionaries that can't be sorted
# Re-ordering may/may not improve plot readability, but it won't corrupt the node coordinates
if order_by_ip:
# Extract nodes from position dictionary then sort them in a list
tmp = {}
node = (i for i in sorted(self.node_positions.keys(),
key=ipaddress.IPv4Address))
for k, v in self.node_positions.items():
tmp[next(node)] = v
self.node_positions = tmp
def test_center_parameter(self):
G = nx.path_graph(1)
vpos = nx.random_layout(G, center=(1, 1))
vpos = nx.circular_layout(G, center=(1, 1))
assert tuple(vpos[0]) == (1, 1)
vpos = nx.planar_layout(G, center=(1, 1))
assert tuple(vpos[0]) == (1, 1)
vpos = nx.spring_layout(G, center=(1, 1))
assert tuple(vpos[0]) == (1, 1)
vpos = nx.fruchterman_reingold_layout(G, center=(1, 1))
assert tuple(vpos[0]) == (1, 1)
vpos = nx.spectral_layout(G, center=(1, 1))
assert tuple(vpos[0]) == (1, 1)
vpos = nx.shell_layout(G, center=(1, 1))
assert tuple(vpos[0]) == (1, 1)
vpos = nx.spiral_layout(G, center=(1, 1))
assert tuple(vpos[0]) == (1, 1)
def test_smoke_int(self):
G = self.Gi
vpos = nx.random_layout(G)
vpos = nx.circular_layout(G)
vpos = nx.planar_layout(G)
vpos = nx.spring_layout(G)
vpos = nx.fruchterman_reingold_layout(G)
vpos = nx.fruchterman_reingold_layout(self.bigG)
vpos = nx.spectral_layout(G)
vpos = nx.spectral_layout(G.to_directed())
vpos = nx.spectral_layout(self.bigG)
vpos = nx.spectral_layout(self.bigG.to_directed())
vpos = nx.shell_layout(G)
vpos = nx.spiral_layout(G)
if self.scipy is not None:
vpos = nx.kamada_kawai_layout(G)
vpos = nx.kamada_kawai_layout(G, dim=1)
def createLayout(G, layout=None):
pos = nx.spring_layout(G, seed=36)
if layout == 'Planar' and nx.check_planarity(G)[0]:
print(nx.check_planarity(G))
pos = nx.planar_layout(G)
elif layout == 'Circular':
pos = nx.circular_layout(G)
elif layout == 'Kamada-Kawai':
pos = nx.kamada_kawai_layout(G)
elif layout == 'Random':
pos = nx.random_layout(G)
elif layout == 'Spectral':
pos = nx.spectral_layout(G)
elif layout == 'Spiral':
pos = nx.spiral_layout(G, resolution=1.0)
return pos
def save_graph(G, filename):
plt.figure(num=None, figsize=(100, 100), dpi=100)
plt.axis('off')
fig = plt.figure(1)
pos = nx.spiral_layout(G, center=[0,0])
pos = nx.spring_layout(G, k=2, iterations=0)
plt.figtext(.5, .85, 'PARKOUR THEORY', fontsize=130, fontweight='bold', ha='center')
nx.draw_networkx_nodes(G, pos, alpha=0.25)
nx.draw_networkx_edges(G, pos, alpha=0.1)
nx.draw_networkx_labels(G, pos, font_color='r', font_size=11)
plt.savefig(filename, bbox_inches="tight")
pylab.close()
del fig
def CreateGraph():
G = nx.Graph()
f = open('input.txt')
titulo = f.readline() # Título da janela
plt.gcf().canvas.set_window_title(titulo)
num = int(f.readline()) # Lê a segunda linha do .txt
n = int(f.readline()) # n = Número de arestas
for i in range(n):
graph_edge_list = f.readline().split(",")
graph_edge_list[1] = graph_edge_list[1].rstrip('\n')
#print(graph_edge_list)
#print("\n\n")
G.add_edge(graph_edge_list[0], graph_edge_list[1])
# Define o layout com base no input
if num == 1:
layout = nx.circular_layout(G)
elif num == 2:
layout = nx.random_layout(G)
elif num == 3:
layout = nx.shell_layout(G)
elif num == 4:
layout = nx.spring_layout(G)
elif num == 5:
layout = nx.spectral_layout(G)
elif num == 6:
layout = nx.spiral_layout(G)
else:
print(f"{num}")
layout = nx.circular_layout(G)
return G, layout
def draw_graph(self, node_type='', layout=''):
if layout == 'spring':
pos = nx.spring_layout(self.scgraph.code_graph)
if layout == 'spectral':
pos = nx.spectral_layout(self.scgraph.code_graph)
if layout == 'planar':
pos = nx.planar_layout(self.scgraph.code_graph)
if layout == 'shell':
pos = nx.shell_layout(self.scgraph.code_graph)
if layout == 'circular':
pos = nx.circular_layout(self.scgraph.code_graph)
if layout == 'spiral':
pos = nx.spiral_layout(self.scgraph.code_graph)
if layout == 'random':
pos = nx.random_layout(self.scgraph.code_graph)
if node_type == 'cycles':
self.scgraph.draw('cycles', layout)
if node_type == 'dict':
self.scgraph.draw('dict', layout)
def selectLayout(G, layout_selected):
if layout_selected == 'circular_layout':
pos = nx.circular_layout(G)
if layout_selected == 'spring_layout':
pos = nx.spring_layout(G)
if layout_selected == 'kamada_kawai_layout':
pos = nx.kamada_kawai_layout(G)
if layout_selected == 'random_layout':
pos = nx.random_layout(G)
if layout_selected == 'shell_layout':
pos = nx.shell_layout(G)
if layout_selected == 'spectral_layout':
pos = nx.spectral_layout(G)
if layout_selected == 'planar_layout':
pos = nx.planar_layout(G)
if layout_selected == 'fruchterman_reingold_layout':
pos = nx.fruchterman_reingold_layout(G)
if layout_selected == 'spiral_layout':
pos = nx.spiral_layout(G)
return pos
def test_empty_graph(self):
G = nx.empty_graph()
vpos = nx.random_layout(G, center=(1, 1))
assert vpos == {}
vpos = nx.circular_layout(G, center=(1, 1))
assert vpos == {}
vpos = nx.planar_layout(G, center=(1, 1))
assert vpos == {}
vpos = nx.bipartite_layout(G, G)
assert vpos == {}
vpos = nx.spring_layout(G, center=(1, 1))
assert vpos == {}
vpos = nx.fruchterman_reingold_layout(G, center=(1, 1))
assert vpos == {}
vpos = nx.spectral_layout(G, center=(1, 1))
assert vpos == {}
vpos = nx.shell_layout(G, center=(1, 1))
assert vpos == {}
vpos = nx.spiral_layout(G, center=(1, 1))
assert vpos == {}
def set_nx_layout(self, layout='random', **kwargs):
"""Configura el layout para dibujar el grafo con networkx"""
g = self.g
if layout == 'random':
self.pos = nx.random_layout(g)
elif layout == 'shell':
self.pos = nx.shell_layout(g, **kwargs)
elif layout == 'spring':
self.pos = nx.spring_layout(g, **kwargs)
elif layout == 'circular':
self.pos = nx.circular_layout(g, **kwargs)
elif layout == 'kamada_kawai':
self.pos = nx.kamada_kawai_layout(g, **kwargs)
elif layout == 'bipartite':
self.pos = nx.bipartite_layout(g, **kwargs)
elif layout == 'spectral':
self.pos = nx.spectral_layout(g, **kwargs)
elif layout == 'spiral':
self.pos = nx.spiral_layout(g, **kwargs)
elif layout == 'planar':
self.pos = nx.planar_layout(g, **kwargs)
def generateGraph(NG, NH, NR, typeGraph, setScale, layoutMethod):
nmbOutputs = len(NG)
nmbOutputs2 = len(NG[0])
#below function will read through the mat file and try to find how many modules their are
#using the network functions create a direction graph (nodes with a connection with a direction so connection 1 to 2 has a direction and is not the same as 2 to 1)
plot = nx.DiGraph()
plot.add_nodes_from(range(nmbOutputs))
for x in range(nmbOutputs):
for y in range(nmbOutputs2):
if (NG[x][y] == 1):
plot.add_edge(y, x)
print("number of nodes: ", plot.number_of_nodes(), " number of edges: ",
plot.number_of_edges())
pos = []
typeGraph = layoutMethod.get()
#creating coordinates
#the below functions can be chosen and generate position for the network and return them
if (typeGraph == "circular"):
pos = nx.circular_layout(plot, scale=setScale, center=(500, 500))
print("circular layout")
if (typeGraph == "kamada_kawai"):
pos = nx.kamada_kawai_layout(plot, scale=setScale, center=(500, 500))
print("kamada_kawai layout")
if (typeGraph == "spring"):
pos = nx.spring_layout(plot, scale=setScale, center=(500, 500))
print("spring layout")
if (typeGraph == "spectral"):
pos = nx.spectral_layout(plot, scale=setScale, center=(500, 500))
print("spectral layout")
if (typeGraph == "spiral"):
pos = nx.spiral_layout(plot, scale=setScale, center=(500, 500))
print("spiral layout")
return pos
def plot_graph(
self,
save_file: bool = False,
output_filename: str = f"test.jpg",
filtered_graph: nx.Graph = None,
):
"""
Args:
graph_type:
save_file:
output_filename:
filtered_graph:
Returns:
"""
graph = filtered_graph if filtered_graph is not None else self.graph
labels = {}
for node in list(graph.nodes):
labels[node] = node.key_name
node_colors = self.generate_node_color_list(graph)
# pos = nx.bipartite_layout(graph, graph.nodes, align='horizontal')
pos = nx.spiral_layout(graph)
# pos = nx.spring_layout(graph)
nx.draw(
graph,
pos=pos,
arrowsize=20,
verticalalignment='bottom',
labels=labels,
with_labels=True,
node_color=node_colors,
)
if not save_file:
plt.show()
else:
plt.savefig(output_filename)
def extract_dynamic_ca(str1):
htap = '/Users/apple/Documents/gs_result/'
global cur
global edges
res = 0
alters = []
if str1 == 'ego':
Chen = 'O6tge4UAAAAJ.parse'
# addr[8] is the list of co-authors; starting from addr[12] can cal the papers.
addr = extract_info(htap, Chen)
ego_papers = []
set_papers = set()
print('total papers: ', len(addr) - 12)
if len(addr) > 8:
new_dict = literal_eval(addr[8])
print('total co-authors:', len(new_dict))
# print(new_dict)
nodes = [new_dict[key] for key in new_dict]
if len(addr) > 12:
# print(addr[12])
for paper in addr[12:]:
new_list = literal_eval(paper)
ego_papers.append(new_list)
# print(new_list)
if re.match('\d{4}', new_list[-1]):
cur += 1
# print(new_list[1], new_list[-1])
set_papers.add(new_list[1])
# print(new_list)
print('papers with year:', cur)
ego = addr[1]
nodes.append(ego)
print(ego)
alters = []
for key in new_dict:
# print(key, new_dict[key])
addr = extract_info(htap, key + '.parse')
year = find_earliest_year(set_papers, addr)
if year != 2021:
res += 1
# print(ego,'and',new_dict[key], key, "'s co-authorship begin from",year)
edges.append([ego, new_dict[key], year])
alters.append(key)
print('co-author with first year:', res)
print('co-author with gs_result files:', good)
print(alters)
else:
# filename = 'thu_net.json'
# with open(filename, 'r') as f:
alters = preparation.preparation()
#print(alters)
for i in range(len(alters)):
key1 = alters[i]
addr = extract_info(htap, key1 + '.parse')
name1 = addr[1]
alter1_papers = set()
if len(addr) > 12:
# print(addr[12])
for paper in addr[12:]:
new_list = literal_eval(paper)
# print(new_list)
if re.match('\d{4}', new_list[-1]):
cur += 1
# print(new_list[1], new_list[-1])
alter1_papers.add(new_list[1])
for j in range(i + 1, len(alters)):
key = alters[j]
addr = extract_info(htap, key + '.parse')
name2 = addr[1]
year = find_earliest_year(alter1_papers, addr)
if year != 2021:
res += 1
# print(new_dict[key1],'and',new_dict[key], key, "'s co-authorship begin from",year)
edges.append([name1, name2, year])
# edges.append([new_dict[key1], new_dict[key], year])
print('# of eges in ego network:', res)
edges = sorted(edges, key=lambda x: x[2])
print(len(edges))
# print(len(nodes))
# print(nodes)
for edge in edges:
print(edge)
# networkx visualization is a total piece of shit...
G = nx.Graph()
graph_cur = 0
# G.add_nodes_from([(node,{'name': node}) for node in nodes])
year = edges[0][2]
for edge in edges:
cur_year = edge[2]
if cur_year != year:
year = cur_year
edge_labels = nx.get_edge_attributes(G, 'year')
# edge_labels = nx.get_edge_attributes(G, 'year')
# nx.write_gexf(G, "test"+str(graph_cur)+".gexf")
graph_cur += 1
pos = nx.spiral_layout(G)
nx.draw(G,
pos,
node_color='yellow',
edge_color='brown',
with_labels=True,
font_size=8,
node_size=10)
nx.draw_networkx_edge_labels(G,
pos,
edge_labels=edge_labels,
font_size=8)
plt.show()
G.add_edge(edge[0], edge[1], year=str(edge[2]))
