class ZonedNetwork:
def __init__(self,
size: Tuple[int] = (10, 10),
field_size: Tuple[int] = (100, 100)):
self.g = Graph(directed=True)
self.n_zones = size[0] * size[1]
self.fwidth = field_size[0]
self.fheight = field_size[1]
self.n_rows = size[0]
self.n_cols = size[1]
self.row_size: float = self.fheight / self.n_rows
self.col_size: float = self.fwidth / self.n_cols
self.g.add_vertex(self.n_zones)
def get_zone(self, coords: Tuple):
r = int(coords[1] / self.row_size)
c = int(coords[0] / self.col_size)
r = min(self.n_rows - 1, r)
c = min(self.n_cols - 1, c)
return self.g.vertex(r * self.n_cols + c)
def add_passes(self, coords_pairs: List[Tuple]):
pairs = [(self.get_zone((x1, y1)), self.get_zone((x2, y2)))
for x1, y1, x2, y2 in coords_pairs]
return self.g.add_edge_list(pairs)
def save(self, file: str):
self.g.save(file, fmt='graphml')
def vytvořím_graph_tool_graf():
from graph_tool.all import Graph
graf = Graph()
u1 = graf.add_vertex()
u2 = graf.add_vertex()
graf.add_edge(u1, u2)
vprop_double = graf.new_vertex_property("double") # Double-precision floating point
vprop_double[graf.vertex(1)] = 3.1416
vprop_vint = graf.new_vertex_property("vector<int>") # Vector of ints
vprop_vint[graf.vertex(0)] = [1, 3, 42, 54]
eprop_dict = graf.new_edge_property("object") # Arbitrary python object. In this case, a dictionary.
eprop_dict[graf.edges().next()] = {"foo": "bar", "gnu": 42}
gprop_bool = graf.new_graph_property("bool") # Boolean
gprop_bool[graf] = True
graf.save('./data/graph_tool.graphml', fmt='xml')
class Network:
def __init__(self, nodes_info=None, links_info=None, file_name=None):
self.g = Graph()
if nodes_info and links_info:
self.nodes_info = nodes_info
self.links_info = links_info
self.g.vertex_properties["name"] = self.g.new_vertex_property(
'string')
self.g.vertex_properties["id"] = self.g.new_vertex_property(
'int32_t')
self.g.edge_properties["weight"] = self.g.new_edge_property(
'int32_t')
self.create_network()
self.g.vertex_properties["pagerank"] = pagerank(
self.g, weight=self.g.edge_properties["weight"])
self.g.vertex_properties[
"degree_centrality"] = self.degree_centrality()
elif file_name:
self.load_network(file_name)
def create_network(self):
# Add Nodes
for node in self.nodes_info:
self.add_n(node)
# Add Links
for link in self.links_info:
n_loser = 0
n_winner = 0
loser = link['loser']
winner = link['winner']
weight = link['rounds']
for team_id in self.g.vertex_properties.id:
if loser == team_id:
break
n_loser += 1
for team_id in self.g.vertex_properties.id:
if winner == team_id:
break
n_winner += 1
self.add_l(n_loser, n_winner, 16 / weight * 100)
def load_network(self, file_name):
new_file_name = '..' + sep + '..' + sep + 'network-graphs' + sep + file_name
self.g.load(new_file_name, fmt="gt")
def get_normalized_pagerank(self):
max_pgr = 0
for pgr in self.g.vertex_properties.pagerank:
if pgr > max_pgr:
max_pgr = pgr
return [
self.g.vertex_properties.pagerank[v] / max_pgr
for v in self.g.vertices()
]
def add_n(self, node_info):
n = self.g.add_vertex()
self.g.vertex_properties.id[n] = node_info['id']
self.g.vertex_properties.name[n] = node_info['Team_Name']
def add_l(self, loser, winner, weight):
n1 = self.g.vertex(loser)
n2 = self.g.vertex(winner)
l = self.g.add_edge(n1, n2)
self.g.edge_properties.weight[l] = weight
def draw(self, output_file, fmt):
graph_draw(self.g,
vertex_text=self.g.vertex_index,
output=output_file,
fmt=fmt)
def save_network(self, file_name):
try:
new_file_name = '..' + sep + '..' + sep + 'network-graphs' + sep + file_name
self.g.save(new_file_name, fmt="gt")
except:
return False
return True
def vp_pagerank(self):
return self.g.vertex_properties.pagerank
def vp_degree_cent(self):
return self.g.vertex_properties.degree_centrality
def vp_name(self):
return self.g.vertex_properties.name
def vp_id(self):
return self.g.vertex_properties.id
def ep_weight(self):
return self.g.edge_properties.weight
# Calcula as características básicas da rede
def get_basic_info(self):
info = {}
try:
n_vertices = self.g.num_vertices()
n_edges = self.g.num_edges()
density = n_edges / ((n_vertices * (n_vertices - 1)) / 2)
mean_degree = (2 * n_edges) / n_vertices
# Cálculo do coeficiente de clusterização "na mão", usando a média dos
# coeficientes locais calculados pela Graph Tools
local_cc = local_clustering(self.g)
clustering_coef = fsum(
[local_cc[x] for x in self.g.vertices() if local_cc[x] != 0.0])
clustering_coef /= n_vertices
info["Número de times"] = n_vertices
info["Número de confrontos"] = n_edges
info["Densidade"] = density
info["Grau médio"] = mean_degree
info["Coeficiente de Clusterização"] = clustering_coef
except:
info.clear()
return info
def degree_centrality(self):
degree_centrality = self.g.new_vertex_property('float')
for v in self.g.vertices():
degree_centrality[v] = v.in_degree() / (self.g.num_vertices() - 1)
return degree_centrality
# Calcula a distribuição de graus da rede
def degree_distribution(self):
degree_dist = {}
try:
for v in self.g.vertices():
if v.in_degree() not in degree_dist.keys():
degree_dist[v.in_degree()] = 1
else:
degree_dist[v.in_degree()] += 1
for k in degree_dist.keys():
degree_dist[k] /= self.g.num_vertices()
except:
degree_dist.clear()
return degree_dist
class GeneralGraph():
"""
General wrapper for graph-tool or networkx graphs to add edges and nodes
according to constraints
"""
def __init__(self, directed=True, verbose=1):
self.graphtool = GRAPH_TOOL
# Initialize graph
if self.graphtool:
self.graph = Graph(directed=directed)
self.weight = self.graph.new_edge_property("float")
else:
if directed:
print("directed graph")
self.graph = nx.DiGraph()
else:
self.graph = nx.Graph()
# set metaparameter
self.time_logs = {}
self.verbose = verbose
def set_edge_costs(self,
layer_classes=["resistance"],
class_weights=[1],
**kwargs):
"""
Initialize edge cost variables
:param classes: list of cost categories
:param weights: list of weights for cost categories - must be of same
shape as classes (if None, then equal weighting)
"""
class_weights = np.array(class_weights)
# set different costs:
self.cost_classes = layer_classes
if self.graphtool:
self.cost_props = [
self.graph.new_edge_property("float")
for _ in range(len(layer_classes))
]
self.cost_weights = class_weights / np.sum(class_weights)
if self.verbose:
print(self.cost_classes, self.cost_weights)
# save weighted instance for plotting
self.instance = np.sum(
np.moveaxis(self.cost_instance, 0, -1) * self.cost_weights,
axis=2) * self.hard_constraints
def set_shift(self,
start,
dest,
pylon_dist_min=3,
pylon_dist_max=5,
max_angle=np.pi / 2,
**kwargs):
"""
Initialize shift variable by getting the donut values
:param lower, upper: min and max distance of pylons
:param vec: vector of diretion of edges
:param max_angle: Maximum angle of edges to vec
"""
vec = dest - start
if self.verbose:
print("SHIFT:", pylon_dist_min, pylon_dist_max, vec, max_angle)
self.shifts = get_half_donut(pylon_dist_min,
pylon_dist_max,
vec,
angle_max=max_angle)
self.shift_tuples = self.shifts
def set_corridor(self,
dist_surface,
start_inds,
dest_inds,
sample_func="mean",
sample_method="simple",
factor_or_n_edges=1):
# set new corridor
corridor = (dist_surface > 0).astype(int)
self.factor = factor_or_n_edges
self.cost_rest = self.cost_instance * (self.hard_constraints >
0).astype(int) * corridor
# downsample
tic = time.time()
if self.factor > 1:
self.cost_rest = CostUtils.downsample(self.cost_rest,
self.factor,
mode=sample_method,
func=sample_func)
self.time_logs["downsample"] = round(time.time() - tic, 3)
# repeat because edge artifacts
self.cost_rest = self.cost_rest * (self.hard_constraints >
0).astype(int) * corridor
# add start and end TODO ugly
self.cost_rest[:, dest_inds[0],
dest_inds[1]] = self.cost_instance[:, dest_inds[0],
dest_inds[1]]
self.cost_rest[:, start_inds[0],
start_inds[1]] = self.cost_instance[:, start_inds[0],
start_inds[1]]
def add_nodes(self, nodes):
"""
Add vertices to the graph
param nodes: list of node names if networkx, integer if graphtool
"""
tic = time.time()
# add nodes to graph
if self.graphtool:
_ = self.graph.add_vertex(nodes)
self.n_nodes = len(list(self.graph.vertices()))
else:
self.graph.add_nodes_from(np.arange(nodes))
self.n_nodes = len(self.graph.nodes())
# verbose
if self.verbose:
print("Added nodes:", nodes, "in time:", time.time() - tic)
self.time_logs["add_nodes"] = round(time.time() - tic, 3)
def add_edges(self):
tic_function = time.time()
n_edges = 0
# kernels, posneg = ConstraintUtils.get_kernel(self.shifts,
# self.shift_vals)
# edge_array = []
times_edge_list = []
times_add_edges = []
if self.verbose:
print("n_neighbors:", len(self.shift_tuples))
for i in range(len(self.shift_tuples)):
tic_edges = time.time()
# set cost rest if necessary (random graph)
self.set_cost_rest()
# compute shift and weights
out = self._compute_edges(self.shift_tuples[i])
# Error if -1 entries because graph-tool crashes with -1 nodes
if np.any(out[:, :2].flatten() < 0):
print(np.where(out[:, :2] < 0))
raise RuntimeError
n_edges += len(out)
times_edge_list.append(round(time.time() - tic_edges, 3))
# add edges to graph
tic_graph = time.time()
if self.graphtool:
self.graph.add_edge_list(out, eprops=self.cost_props)
else:
nx_edge_list = [(e[0], e[1], {
"weight": np.sum(e[2:] * self.cost_weights)
}) for e in out]
self.graph.add_edges_from(nx_edge_list)
times_add_edges.append(round(time.time() - tic_graph, 3))
# alternative: collect edges here and add alltogether
# edge_array.append(out)
# # alternative: add edges all in one go
# tic_concat = time.time()
# edge_lists_concat = np.concatenate(edge_array, axis=0)
# self.time_logs["concatenate"] = round(time.time() - tic_concat, 3)
# print("time for concatenate:", self.time_logs["concatenate"])
# tic_graph = time.time()
# self.graph.add_edge_list(edge_lists_concat, eprops=[self.weight])
# self.time_logs["add_edges"] = round(
# (time.time() - tic_graph) / len(shifts), 3
# )
self.n_edges = len(list(self.graph.edges()))
self._update_time_logs(times_add_edges, times_edge_list, tic_function)
if self.verbose:
print("DONE adding", n_edges, "edges:", time.time() - tic_function)
def _update_time_logs(self, times_add_edges, times_edge_list,
tic_function):
self.time_logs["add_edges"] = round(np.mean(times_add_edges), 3)
self.time_logs["add_edges_times"] = times_add_edges
self.time_logs["edge_list"] = round(np.mean(times_edge_list), 3)
self.time_logs["edge_list_times"] = times_edge_list
self.time_logs["add_all_edges"] = round(time.time() - tic_function, 3)
if self.verbose:
print("Done adding edges:", len(list(self.graph.edges())))
def sum_costs(self):
"""
Additive weighting of costs
Take the individual edge costs, compute weighted sum --> self.weight
"""
# add sum of all costs
if not self.graphtool:
return
tic = time.time()
summed_costs_arr = np.zeros(self.cost_props[0].get_array().shape)
for i in range(len(self.cost_props)):
prop = self.cost_props[i].get_array()
summed_costs_arr += prop * self.cost_weights[i]
self.weight.a = summed_costs_arr
self.time_logs["sum_of_costs"] = round(time.time() - tic, 3)
def remove_vertices(self, dist_surface, delete_padding=0):
"""
Remove edges in a certain corridor (or all) to replace them by
a refined surface
@param dist_surface: a surface where each pixel value corresponds to
the distance of the pixel to the shortest path
@param delete_padding: define padding in which part of the corridor to
delete vertices (cannot delete all because then graph unconnected)
"""
tic = time.time()
self.graph.clear_edges()
self.graph.shrink_to_fit()
self.time_logs["remove_edges"] = round(time.time() - tic, 3)
def get_pareto(self,
vary,
source,
dest,
out_path=None,
compare=[0, 1],
plot=1):
"""
Arguments:
vary: how many weights to explore
e.g 3 --> each cost class can have weight 0, 0.5 or 1
source, dest: as always the source and destination vertex
out_path: where to save the pareto figure(s)
compare: indices of cost classes to compare
Returns:
paths: All found paths
pareto: The costs for each combination of weights
"""
tic = time.time()
# initialize lists
pareto = list()
paths = list()
cost_sum = list()
# get the edge costs
cost_arrs = [cost.get_array() for cost in self.cost_props]
# [self.cost_props[comp].get_array() for comp in compare]
# get vary weights between 0 and 1
var_weights = np.around(np.linspace(0, 1, vary), 2)
# construct weights array
if len(compare) == 2:
weights = [[v, 1 - v] for v in var_weights]
elif len(compare) == 3:
weights = list()
for w0 in var_weights:
for w1 in var_weights[var_weights <= 1 - w0]:
weights.append([w0, w1, 1 - w0 - w1])
else:
raise ValueError("argument compare can only have length 2 or 3")
# w_avail: keep weights of non-compare classes, get leftover amount
w_avail = np.sum(np.asarray(self.cost_weights)[compare])
# compute paths for each combination of weights
for j in range(len(weights)):
# option 2: np.zeros(len(cost_arrs)) + non_compare_weight
w = self.cost_weights.copy()
# replace the ones we want to compare
w[compare] = np.array(weights[j]) * w_avail
# weighted sum of edge costs
self.weight.a = np.sum(
[cost_arrs[i] * w[i] for i in range(len(cost_arrs))], axis=0)
# get shortest path
path, path_costs, _ = self.get_shortest_path(source, dest)
# don't take cost_sum bc this is sum of original weighting
pareto.append(np.sum(path_costs, axis=0)[compare])
paths.append(path)
# take overall sum of costs (unweighted) that this w leads to
cost_sum.append(np.sum(path_costs))
# print best weighting
best_weight = np.argmin(cost_sum)
w = self.cost_weights.copy()
w[compare] = np.array(weights[best_weight]) * w_avail
print("Best weights:", w, "with (unweighted) costs:", np.min(cost_sum))
self.time_logs["pareto"] = round(time.time() - tic, 3)
pareto = np.array(pareto)
classes = [self.cost_classes[comp] for comp in compare]
# Plotting
if plot:
if len(compare) == 2:
plot_pareto_scatter_2d(pareto,
weights,
classes,
cost_sum=cost_sum,
out_path=out_path)
elif len(compare) == 3:
# plot_pareto_3d(pareto, weights, classes)
plot_pareto_scatter_3d(pareto,
weights,
classes,
cost_sum=cost_sum,
out_path=out_path)
return paths, weights, cost_sum
def get_shortest_path(self, source, target):
"""
Compute shortest path from source vertex to target vertex
"""
tic = (time.time())
# #if source and target are given as indices:
if self.graphtool:
vertices_path, _ = shortest_path(self.graph,
source,
target,
weights=self.weight,
negative_weights=True)
else:
try:
vertices_path = nx.dijkstra_path(self.graph, source, target)
except nx.exception.NetworkXNoPath:
return []
self.time_logs["shortest_path"] = round(time.time() - tic, 3)
return vertices_path
def save_graph(self, OUT_PATH):
"""
Save the graph in OUT_PATH
"""
if self.graphtool:
for i, cost_class in enumerate(self.cost_classes):
self.graph.edge_properties[cost_class] = self.cost_props[i]
self.graph.edge_properties["weight"] = self.weight
self.graph.save(OUT_PATH + ".xml.gz")
else:
nx.write_weighted_edgelist(self.graph,
OUT_PATH + '.weighted.edgelist')
def load_graph(self, IN_PATH):
"""
Retrieve graph from IN_PATH
"""
if self.graphtool:
self.g_prev = load_graph(IN_PATH + ".xml.gz")
self.weight_prev = self.g_prev.ep.weight
# weight = G2.ep.weight[G2.edge(66, 69)]
else:
self.g_prev = nx.read_edgelist(IN_PATH + '.weighted.edgelist',
nodetype=int,
data=(('weight', float), ))
# -----------------------------------------------------------------------
# INTERFACE
def single_sp(self, **kwargs):
"""
Function for full processing until shortest path
"""
self.start_inds = kwargs["start_inds"]
self.dest_inds = kwargs["dest_inds"]
self.set_shift(self.start_inds, self.dest_inds, **kwargs)
# self.set_corridor(
# np.ones(self.hard_constraints.shape) * 0.5,
# self.start_inds,
# self.dest_inds,
# factor_or_n_edges=1
# )
if self.verbose:
print("1) Initialize shifts and instance (corridor)")
self.set_edge_costs(**kwargs)
# add vertices
self.add_nodes()
if self.verbose:
print("2) Initialize distances to inf and predecessors")
self.add_edges()
if self.verbose:
print("3) Compute source shortest path tree")
print("number of vertices and edges:", self.n_nodes, self.n_edges)
# weighted sum of all costs
self.sum_costs()
source_v, target_v = self.add_start_and_dest(self.start_inds,
self.dest_inds)
# get actual best path
path, path_costs, cost_sum = self.get_shortest_path(source_v, target_v)
if self.verbose:
print("4) shortest path", cost_sum)
return path, path_costs, cost_sum
class PointerProvenancePlot(Plot):
"""
Base class for plots using the pointer provenance graph.
"""
def __init__(self, *args, **kwargs):
super(PointerProvenancePlot, self).__init__(*args, **kwargs)
self._cached_dataset_valid = False
"""Tells whether we need to rebuild the dataset when caching."""
def init_parser(self, dataset, tracefile):
if self.caching and os.path.exists(self._get_cache_file()):
# if caching we will nevere use this
return None
return PointerProvenanceParser(dataset, tracefile)
def init_dataset(self):
logger.debug("Init provenance graph for %s", self.tracefile)
self.dataset = Graph(directed=True)
vdata = self.dataset.new_vertex_property("object")
self.dataset.vp["data"] = vdata
return self.dataset
def _get_cache_file(self):
return self.tracefile + "_provenance_plot.gt"
def build_dataset(self):
"""
Build the provenance tree
"""
if self.caching:
try:
logger.debug("Load cached provenance graph")
self.dataset = load_graph(self._get_cache_file())
except IOError:
self.parser.parse()
self.dataset.save(self._get_cache_file())
else:
self.parser.parse()
num_nodes = self.dataset.num_vertices()
logger.debug("Total nodes %d", num_nodes)
vertex_mask = self.dataset.new_vertex_property("bool")
progress = ProgressPrinter(num_nodes, desc="Search kernel nodes")
for node in self.dataset.vertices():
# remove null capabilities
# remove operations in kernel mode
vertex_data = self.dataset.vp.data
node_data = vertex_data[node]
if ((node_data.pc != 0 and node_data.is_kernel) or
(node_data.cap.length == 0 and node_data.cap.base == 0)):
vertex_mask[node] = True
progress.advance()
progress.finish()
self.dataset.set_vertex_filter(vertex_mask, inverted=True)
vertex_mask = self.dataset.copy_property(vertex_mask)
num_nodes = self.dataset.num_vertices()
logger.debug("Filtered kernel nodes, remaining %d", num_nodes)
progress = ProgressPrinter(
num_nodes, desc="Merge (cfromptr + csetbounds) sequences")
for node in self.dataset.vertices():
progress.advance()
# merge cfromptr -> csetbounds subtrees
num_parents = node.in_degree()
if num_parents == 0:
# root node
continue
elif num_parents > 1:
logger.error("Found node with more than a single parent %s", node)
raise RuntimeError("Too many parents for a node")
parent = next(node.in_neighbours())
parent_data = self.dataset.vp.data[parent]
node_data = self.dataset.vp.data[node]
if (parent_data.origin == CheriNodeOrigin.FROMPTR and
node_data.origin == CheriNodeOrigin.SETBOUNDS):
# the child must be unique to avoid complex logic
# when merging, it may be desirable to do so with
# more complex traces
node_data.origin = CheriNodeOrigin.PTR_SETBOUNDS
if parent.in_degree() == 1:
next_parent = next(parent.in_neighbours())
vertex_mask[parent] = True
self.dataset.add_edge(next_parent, node)
elif parent.in_degree() == 0:
vertex_mask[parent] = True
else:
logger.error("Found node with more than a single parent %s",
parent)
raise RuntimeError("Too many parents for a node")
progress.finish()
self.dataset.set_vertex_filter(vertex_mask, inverted=True)
vertex_mask = self.dataset.copy_property(vertex_mask)
num_nodes = self.dataset.num_vertices()
logger.debug("Merged (cfromptr + csetbounds), remaining %d", num_nodes)
progress = ProgressPrinter(num_nodes, desc="Find short-lived cfromptr")
for node in self.dataset.vertices():
progress.advance()
node_data = self.dataset.vp.data[node]
if node_data.origin == CheriNodeOrigin.FROMPTR:
vertex_mask[node] = True
# if (node_data.origin == CheriNodeOrigin.FROMPTR and
# len(node_data.address) == 0 and
# len(node_data.deref["load"]) == 0 and
# len(node_data.deref["load"]) == 0):
# # remove cfromptr that are never stored or used in
# # a dereference
# remove_list.append(node)
progress.finish()
self.dataset.set_vertex_filter(vertex_mask, inverted=True)
class Network:
def __init__(self):
self.g = Graph(directed=True)
self.player_id_to_vertex = {}
self.pairs = {} # player pair: edge
# property maps for additional information
self.g.vertex_properties['player_id'] = self.g.new_vertex_property(
"string")
self.g.vertex_properties['player_coords'] = self.g.new_vertex_property(
"vector<float>")
self.g.vertex_properties[
'average_player_coords'] = self.g.new_vertex_property(
"vector<float>")
self.g.vertex_properties[
'player_n_coords'] = self.g.new_vertex_property("int")
self.g.edge_properties['weight'] = self.g.new_edge_property("float")
@property
def edge_weights(self):
return self.g.edge_properties['weight']
@property
def player_id_pmap(self):
return self.g.vertex_properties['player_id']
@property
def player_coords_pmap(self):
return self.g.vertex_properties['player_coords']
@property
def player_n_coords_pmap(self):
return self.g.vertex_properties['player_n_coords']
@property
def average_player_coords_pmap(self):
# lazy evaluation of means
for v in self.g.vertices():
self.g.vertex_properties['average_player_coords'][v] = np.asarray(
self.player_coords_pmap[v]) / self.player_n_coords_pmap[v]
return self.g.vertex_properties['average_player_coords']
def add_players(self, pids: List[str]):
n = len(pids)
vs = list(self.g.add_vertex(n))
self.player_id_to_vertex.update({pids[i]: vs[i] for i in range(n)})
for i in range(n):
self.player_id_pmap[vs[i]] = pids[i]
return vs
def add_passes(self,
id_pairs: List[Tuple],
coords_pairs: List[Tuple],
pass_scores=None):
pairs = [(self.player_id_to_vertex[i1], self.player_id_to_vertex[i2])
for i1, i2 in id_pairs]
# append player coordinates
n = len(coords_pairs)
if pass_scores is None:
pass_scores = [1 for _ in range(n)]
for i in range(n):
# remember orig and dest location
# orig player
coords = self.player_coords_pmap[pairs[i][0]]
if len(coords) == 0:
coords = np.asarray([coords_pairs[i][0], coords_pairs[i][1]])
else:
# accumulate
coords += np.asarray([coords_pairs[i][0], coords_pairs[i][1]])
self.player_coords_pmap[pairs[i][0]] = coords
self.player_n_coords_pmap[pairs[i][0]] += 1
# dest player
coords = self.player_coords_pmap[pairs[i][1]]
if len(coords) == 0:
coords = np.asarray([coords_pairs[i][2], coords_pairs[i][3]])
else:
# accumulate
coords += np.asarray([coords_pairs[i][2], coords_pairs[i][3]])
self.player_coords_pmap[pairs[i][1]] = coords
self.player_n_coords_pmap[pairs[i][1]] += 1
# if the edge exists, increment its weight instead of creating a new edge
e = self.pairs.get(pairs[i])
if e is not None:
self.edge_weights[e] += pass_scores[i]
else:
e = self.g.add_edge(*pairs[i])
self.pairs[pairs[i]] = e
self.edge_weights[e] = pass_scores[i]
def cleanup(self):
"""remove isolated vertices"""
to_remove = []
for v in self.g.vertices():
if v.in_degree() + v.out_degree() == 0:
to_remove.append(v)
n = len(to_remove)
self.g.remove_vertex(to_remove, fast=True)
print("Removed {0} isolated vertices".format(n))
def save(self, file: str):
self.g.save(file, fmt='graphml')
