def relayout_graph(self, name: str):
"""Расположить вершины графа по какому-то алгоритму.
Алгоритмы:
* circular - по кругу
* kamada_kawai - Kamada-Kawai Algorithm
* planar - без пересечений ребер
* random - рандом
* shell - пока то же, что circular
* spring - Fruchterman-Reingold Algorithm
:param name:
:type name: str
"""
def kamada_kawai(G):
return nx.kamada_kawai_layout(G, weight=1)
# def spectral(G):
# return nx.spectral_layout(G, scale=20)
func_dict = {
'circular': nx.circular_layout,
'kamada_kawai': kamada_kawai,
'planar': nx.planar_layout,
'random': nx.random_layout,
'shell': nx.shell_layout, # TODO
'spring': nx.spring_layout,
# 'spectral': spectral
}
scale_dict = {
'circular': 0.5,
'random': 0.3
}
self.calculate_matrix()
matrix = np.array(self.matrix)
G = nx.from_numpy_matrix(matrix) # Получить networkx-граф из матрицы
try:
pos = func_dict[name](G)
except nx.exception.NetworkXException:
self.box = QMessageBox.critical(self.widget,
'Ошибка', 'Граф не планарен')
return
# Расчехлить позиции
pos = np.array([pos[i] for i in range(len(pos))])
# Масштабировать
scale = SupremeSettings()['graphmodule_graph_scale']
try:
pos = nx.rescale_layout(pos, scale=scale * scale_dict[name])
except KeyError:
pos = nx.rescale_layout(pos, scale=scale)
# Применить позиции
for index, position in enumerate(pos):
x, y = position
node = self._nodes[self.head[index]]
if node != self.widget.scene().mouseGrabberItem():
node.setX(x)
node.setY(y)
self._adjust_scene()
def rescale_coords(pos, scale=1, center=0):
node_list = pos.keys()
# dict to array
npos = np.row_stack((pos[x] for x in node_list))
npos = npos.astype(np.float64)
npos = nx.rescale_layout(npos, scale=scale) + center
# array to dict
return dict(zip(node_list, npos))
def show(G: nx.DiGraph):
scale = 1000
pos = graphviz_layout(G, prog='dot')
new_pos = nx.rescale_layout(pos=np.array(list(pos.values())), scale=scale).tolist()
for idx,key in enumerate(pos.keys()):
pos[key] = new_pos[idx]
nx.set_edge_attributes(G, 'color', 'r')
labels = nx.get_node_attributes(G, 'fancy_label')
nx.draw_networkx(G, pos=pos, arrows=True, labels=labels, edge_color='r' )
# plt.savefig(f"plot_{uuid.uuid4()}.png", dpi=1000)
plt.show()
def layout(self):
"""Initialize the CausalModel object by reading the information from the dot file with the passed path.
The file should be a `dot` file and if it contains multiple graphs, only the first such graph is returned. All graphs _except_ the first are silently ignored.
Parameters
----------
path : str or file
Filename or file handle.
Returns
-------
None
Examples
--------
>>> G = CausalModel()
>>> G.load_model('temp.dot')
Notes
-----
The heavy lifting is done by `networkx.drawing.nx_pydot.read_dot`
"""
pos = graphviz_layout(self.dag, 'dot')
keys = list(pos.keys())
coords = np.array([pos[key] for key in keys])
coords = nx.rescale_layout(coords, 1)
pos = dict(zip(keys, coords))
xs = []
ys = []
for key, value in pos.items():
xs.append(value[0])
ys.append(value[1])
# All xx coordinates are the same, switch x and y
# To make it horizontal instead of vertical
if len(set(xs)) == 1:
pos = {key: [-value[1], value[0]] for key, value in pos.items()}
return pos
def rescaleCoordinate(self, X, Y, scale):
coordinates = np.array([[X, Y]])
return (nx.rescale_layout(coordinates, scale))
degrees = dict()
for node, val in g.degree():
degrees[node] = val
ids = list(g.nodes())
x = []
y = []
degree = []
for elem in ids:
degree.append(degrees[elem])
x.append(pos[elem][0])
y.append(pos[elem][1])
p = empty(shape=(len(x), 2))
p[:, 0] = asarray(x)
p[:, 1] = asarray(y)
scale = canvas_size // 2 - padding
pos_new = nx.rescale_layout(p, scale=scale)
pos = dict()
for i in range(len(ids)):
pos[ids[i]] = (pos_new[i][0], pos_new[i][1])
x[i] = pos_new[i][0] + scale + padding
y[i] = pos_new[i][1] + scale + padding
conf_list_n = {Id: (X, Y, Degree) for Id, X, Y, Degree in zip(ids, x, y, degree)}
max_weight = 4
time_desease = dict()
for i in ids:
time_desease[i] = 2
def fruchterman_reingold_layout(
G,
k=None,
pos=None,
fixed=None,
iterations=50,
threshold=1e-4,
weight="weight",
scale=1,
center=None,
dim=2,
seed=None,
min_dist=0.01,
):
"""Position nodes using Fruchterman-Reingold force-directed algorithm.
Parameters
----------
G : NetworkX graph or list of nodes
A position will be assigned to every node in G.
k : float (default=None)
Optimal distance between nodes. If None the distance is set to
1/sqrt(n) where n is the number of nodes. Increase this value
to move nodes farther apart.
pos : dict or None optional (default=None)
Initial positions for nodes as a dictionary with node as keys
and values as a coordinate list or tuple. If None, then use
random initial positions.
fixed : list or None optional (default=None)
Nodes to keep fixed at initial position.
iterations : int optional (default=50)
Maximum number of iterations taken
threshold: float optional (default = 1e-4)
Threshold for relative error in node position changes.
The iteration stops if the error is below this threshold.
weight : string or None optional (default='weight')
The edge attribute that holds the numerical value used for
the edge weight. If None, then all edge weights are 1.
scale : number (default: 1)
Scale factor for positions. Not used unless `fixed is None`.
center : array-like or None
Coordinate pair around which to center the layout.
Not used unless `fixed is None`.
dim : int
Dimension of layout.
seed : int, RandomState instance or None optional (default=None)
Set the random state for deterministic node layouts.
If int, `seed` is the seed used by the random number generator,
if numpy.random.RandomState instance, `seed` is the random
number generator,
if None, the random number generator is the RandomState instance used
by numpy.random.
Returns
-------
pos : dict
A dictionary of positions keyed by node
Examples
--------
>>> G = nx.path_graph(4)
>>> pos = nx.spring_layout(G)
# The same using longer but equivalent function name
>>> pos = nx.fruchterman_reingold_layout(G)
"""
if center is None:
center = np.zeros(dim)
lg = len(G)
if not lg:
return {}
if lg == 1:
return {nx.utils.arbitrary_element(G.nodes()): center}
nfixed = dict(zip(G, range(len(G))))
if fixed is not None:
fixed = np.asarray([nfixed[v] for v in fixed])
if pos is not None:
# Determine size of existing domain to adjust initial positions
dom_size = max(coord for pos_tup in pos.values() for coord in pos_tup)
if dom_size == 0:
dom_size = 1
pos_arr = seed.rand(len(G), dim) * dom_size + center
for i, n in enumerate(G):
if n in pos:
pos_arr[i] = np.asarray(pos[n])
else:
pos_arr = None
A = nx.to_numpy_array(G, weight=weight)
if k is None and fixed is not None:
# We must adjust k by domain size for layouts not near 1x1
nnodes, _ = A.shape
k = dom_size / np.sqrt(nnodes)
# Cycles
cycles = [[nfixed[x] for x in c] for c in nx.cycle_basis(G)]
#
pos = _fruchterman_reingold(
A, k, pos_arr, fixed, iterations, threshold, dim, seed, min_dist, cycles
)
if fixed is None:
pos = nx.rescale_layout(pos, scale=scale) + center
pos = dict(zip(G, pos))
return pos
def rescale_nx_pos(self):
"""Devuelve una nueva escala para las coordenadas de los nodos en el dibujo del grafo"""
self.pos = nx.rescale_layout(g, pos = self.pos)
def draw_graph(graph, labels=None, graph_layout='reingold', #please don't change this
node_size=500, #size of data dots
node_color='#2c8ca4', #hex code or word like 'yellow'
node_alpha=0.5, #opacity of dots
node_text_size=5, #size of text.
edge_color='#fcd454', edge_alpha=0.2, edge_tickness=1,
edge_text_pos=0.3,
text_font='sans-serif'):
# create networkx graph
G=nx.Graph()
# add edges
for edge in graph:
G.add_edge(edge[0], edge[1]) #takes edge from edge list G (see below)
# these are different layouts for the network you may try
# use reingold!!
if graph_layout == 'spring':
graph_pos=nx.spring_layout(G)
elif graph_layout == 'spectral':
graph_pos=nx.spectral_layout(G)
elif graph_layout == 'random':
graph_pos=nx.random_layout(G)
elif graph_layout == 'bipartite':
graph_pos = nx.bipartite_layout(G, nodes=effortlist,
align='vertical')
elif graph_layout == 'circular':
graph_pos=nx.circular_layout(G)
elif graph_layout == 'kawai':
graph_pos=nx.kamada_kawai_layout(G)
elif graph_layout == 'rescale':
graph_pos=nx.rescale_layout(G)
elif graph_layout == 'reingold': #USE THIS ONE
graph_pos=nx.fruchterman_reingold_layout(G, pos=GraphPositions, fixed=all_node_list)
else:
graph_pos=nx.shell_layout(G)
# draw graph
#modified to assigned colors/sizes on nodes of each information category (bias, effort, tech)
nx.draw_networkx_nodes(G,graph_pos,nodelist=effortlist,node_size=node_size,
alpha=node_alpha, node_color='black') #assign color/size/opacity to 'effort' nodes
nx.draw_networkx_nodes(G, graph_pos, nodelist=techlist, node_size=300,
alpha=node_alpha, node_color='#545454') #assign color/size/opacity to 'tech' nodes
nx.draw_networkx_nodes(G, graph_pos, nodelist=biaslist, node_size=200,
alpha=node_alpha, node_color=node_color) #assign color/size/opacity to 'bias' nodes
nx.draw_networkx_edges(G,graph_pos,width=edge_tickness,
alpha=edge_alpha,edge_color=edge_color)
nx.draw_networkx_labels(G, graph_pos,font_size=node_text_size,
font_family=text_font)
#below is for edge labels, which I removed from the edges
#if labels is None:
# labels = range(len(graph))
#edge_labels = dict(zip(graph, labels))
#nx.draw_networkx_edge_labels(G, graph_pos, edge_labels=edge_labels,
# label_pos=edge_text_pos)
# show graph
plt.show()