def get_fbvs_max_size(self, g: MultiGraph, k: int) -> set:
if len(g) <= k + 2:
return set(g.nodes()[:k])
# Construct a trivial FVS of size k + 1 on the first k + 3 vertices of G.
nodes = g.nodes()
# The set of nodes currently under consideration.
node_set = set(nodes[:(k + 2)])
# The current best solution, of size (k + 1) before each compression step,
# and size <= k at the end.
soln = set(nodes[:k])
for i in range(k + 2, len(nodes)):
soln.add(nodes[i])
node_set.add(nodes[i])
if len(soln) < k + 1:
continue
assert (len(soln) == (k + 1))
assert (len(node_set) == (i + 1))
new_soln = self.ic_compression(g.subgraph(node_set), soln, k)
if new_soln is None:
return None
soln = new_soln
assert (len(soln) <= k)
return soln
def test_auto_neb(self):
# Test AutoNEB procedure
graph = MultiGraph()
for idx, minimum in enumerate(self.minima):
graph.add_node(idx + 1, **minimum)
# Set up AutoNEB schedule
spring_constant = float("inf")
eval_config = EvalConfig(128)
optim_config_1 = OptimConfig(10, SGD, {"lr": 0.1}, None, None, eval_config)
optim_config_2 = OptimConfig(10, SGD, {"lr": 0.01}, None, None, eval_config)
weight_decay = 0
subsample_pivot_count = 1
neb_configs = [
NEBConfig(spring_constant, weight_decay, equal, {"count": 2}, subsample_pivot_count, optim_config_1),
NEBConfig(spring_constant, weight_decay, highest, {"count": 3, "key": "dense_train_loss"}, subsample_pivot_count, optim_config_1),
NEBConfig(spring_constant, weight_decay, highest, {"count": 3, "key": "dense_train_loss"}, subsample_pivot_count, optim_config_2),
NEBConfig(spring_constant, weight_decay, highest, {"count": 3, "key": "dense_train_loss"}, subsample_pivot_count, optim_config_2),
]
auto_neb_config = AutoNEBConfig(neb_configs)
self.assertEqual(auto_neb_config.cycle_count, len(neb_configs))
# Run AutoNEB
auto_neb(1, 2, graph, self.model, auto_neb_config)
self.assertEqual(len(graph.edges), auto_neb_config.cycle_count)
def auto_neb(m1,
m2,
graph: MultiGraph,
model: models.ModelWrapper,
config: config.AutoNEBConfig,
callback: callable = None):
# Continue existing cycles or start from scratch
if m2 in graph[m1]:
existing_edges = graph[m1][m2]
previous_cycle_idx = max(existing_edges)
connection_data = graph[m1][m2][previous_cycle_idx]
start_cycle_idx = previous_cycle_idx + 1
else:
connection_data = {
"path_coords":
torch.cat([graph.nodes[m]["coords"].view(1, -1)
for m in (m1, m2)]),
"target_distances":
torch.ones(1)
}
start_cycle_idx = 1
assert start_cycle_idx <= config.cycle_count
# Run NEB and add to graph
for cycle_idx in helper.pbar(
range(start_cycle_idx, config.cycle_count + 1), "AutoNEB"):
cycle_config = config.neb_configs[cycle_idx - 1]
connection_data = neb(connection_data, model, cycle_config)
graph.add_edge(m1,
m2,
key=cycle_idx,
**helper.move_to(connection_data, "cpu"))
if callback is not None:
callback()
def test_relabel_nodes_multigraph():
"""failed after switching to dg.relabel_nodes"""
G = MultiGraph([('a', 'b'), ('a', 'b')])
mapping = {'a': 'aardvark', 'b': 'bear'}
G = relabel_nodes(G, mapping, copy=False)
assert sorted(G.nodes()) == ['aardvark', 'bear']
assert_edges_equal(sorted(G.edges()), [('aardvark', 'bear'),
('aardvark', 'bear')])
def connect_routes(lab, lst, g: nx.MultiGraph):
links = list(lst.linkid)
if len(links) == 0:
return
for i in range(len(links)-1):
conn = g.edges.get((links[i], links[i+1], 0))
if conn is None or conn['label'] != lab.iloc[0]:
g.add_edge(links[i], links[i+1], label=lab.iloc[0])
def initGraph(self):
self.shuttlingGraph = MultiGraph()
for edge in self:
self.shuttlingGraph.add_node(edge.startName)
self.shuttlingGraph.add_node(edge.stopName)
self.shuttlingGraph.add_edge(edge.startName, edge.stopName, key=hash(edge), edge=edge,
weight=abs(edge.stopLine-edge.startLine))
self.nodeLookup[edge.startLine] = edge.startName
self.nodeLookup[edge.stopLine] = edge.stopName
def __make_route_graph(routes):
graph = MultiGraph()
for route in routes:
# assume each segment has weight 1 - we could estimate edge weight via
# distance bewteen stops (we have location information), but we have
# no information to tell us how fast any particular service is.
make_route_segment = lambda src, dst: (src, dst, {'route': route})
segments = zip_with(make_route_segment, route.stops(), tail(route.stops()))
graph.add_edges_from(segments)
return graph
def reduction3(self, g: MultiGraph, k: int) -> (int, List[int], bool):
"""
If there is a vertex v of degree at most 1, delete v.
"""
changed = False
for v in g.nodes():
if g.degree(v) <= 1:
g.remove_node(v)
changed = True
return k, None, changed
def reduction3(self, g: MultiGraph, k: int) -> (int, List[int], bool):
"""
If there is a vertex v of degree at most 1, delete v.
"""
changed = False
for v in g.nodes():
if g.degree(v) <= 1:
g.remove_node(v)
changed = True
return k, None, changed
def rem(g: nx.MultiGraph) -> None:
node_attributes = nx.get_node_attributes(G, 'elderly')
nodes = list(g.nodes)
for node in nodes:
neigh = list(g.neighbors(node))
if len(neigh) == 2 and (g.degree(node) % 2) == 0:
try:
set1 = {
edge['label']
for edge in g.get_edge_data(node, neigh[0]).values()
}
except:
print(g.get_edge_data(node, neigh[0]))
set2 = {
edge['label']
for edge in g.get_edge_data(node, neigh[1]).values()
}
if set1 == set2:
#prec=node_attributes[neigh[0]]+0.001
succ = node_attributes[neigh[1]] + 0.001
node_attr = node_attributes[node] + 0.001
# if (abs((node_attr-prec))<1000) and (abs((node_attr-succ))<1000):
if (abs((node_attr - succ)) < 1000):
g.remove_node(node)
for edge_label in set1:
g.add_edge(neigh[0], neigh[1], label=edge_label)
def add_drugs_in_graph(graph: nwx.MultiGraph, drugs_list_graph: list):
'''
Add graph node in a graph
@parameter : graph
@parameter : drugs_list_graph
@return : drugs_list_graph
'''
for item in drugs_list_graph:
graph.add_node(item["drug"], atccode=item["atccode"])
return graph
def add_edge_journal_in_graph(graph: nwx.MultiGraph, journal_edge):
for item in journal_edge:
if item['edge_list']:
for edge in item['edge_list']:
graph.add_edge(edge[0],
edge[1],
journal=item['journal'],
date=item['date'])
return graph
def reduction1(self, g: MultiGraph, k: int) -> (int, List[int], bool):
"""
If there is a loop at a vertex v, delete v from the graph and decrease k by 1.
"""
changed = False
vs = g.nodes_with_selfloops()
for v in vs:
g.remove_node(v)
k -= 1
changed = True
return k, vs, changed
def reduction1(self, g: MultiGraph, k: int) -> (int, List[int], bool):
"""
If there is a loop at a vertex v, delete v from the graph and decrease k by 1.
"""
changed = False
vs = g.nodes_with_selfloops()
for v in vs:
g.remove_node(v)
k -= 1
changed = True
return k, vs, changed
def get_fbvs(graph):
if is_acyclic(graph):
return set()
if type(graph) is not MultiGraph:
graph = MultiGraph(graph)
for i in range(1, graph.number_of_nodes()):
result = get_fbvs_max_size(graph, i)
if result is not None:
return result # in the worst case, result is n-2 nodes
def test_diamond():
multigraph = MultiGraph()
multigraph.add_nodes_from(range(4))
breakpoint_graph = BreakpointGraph(multigraph)
first_color = ['A', 'C']
second_color = ['B', 'D']
topology = (first_color, second_color)
breakpoint_graph.add_edge(0, 1, Multicolor(*[A]))
breakpoint_graph.add_edge(2, 3, Multicolor(*[B]))
breakpoint_graph.add_edge(1, 2, Multicolor(*[C]))
breakpoint_graph.add_edge(0, 3, Multicolor(*[D]))
assert (len(find_diamond_patterns(breakpoint_graph)) == 1)
def add_edge_pubmed_in_graph(graph: nwx.MultiGraph, pubmed_edge):
for item in pubmed_edge:
if item['edge_list']:
for edge in item['edge_list']:
graph.add_edge(edge[0],
edge[1],
id_pubmed=item['id_pubmed'],
title_pubmed=item['title_pubmed'],
date=item['date'])
return graph
def test_paths():
multigraph = MultiGraph()
multigraph.add_nodes_from(range(4))
breakpoint_graph = BreakpointGraph(multigraph)
first_color = ['A', 'C']
second_color = ['B', 'D']
topology = (first_color, second_color)
breakpoint_graph.add_edge(0, 1, Multicolor(*first_color))
breakpoint_graph.add_edge(2, 3, Multicolor(*first_color))
breakpoint_graph.add_edge(1, 2, Multicolor(*second_color))
breakpoint_graph.add_edge(0, 3, Multicolor(*second_color))
assert (get_size_of_alternating_structures(breakpoint_graph, topology) == 3)
def add_edge_clinical_in_graph(graph: nwx.MultiGraph, clinical_edge):
for item in clinical_edge:
if item['edge_list']:
for edge in item['edge_list']:
graph.add_edge(edge[0],
edge[1],
id_clinical=item['id_clinical'],
title_clinical=item['title_clinical'],
date=item['date'])
return graph
def generate_snapshots_over_time(G: nx.MultiGraph,
minutes=0,
hours=0,
days=0,
max_snapshots=None,
interval=None,
include_final=False,
cummulative=True):
"""
:param G: MultiGraph you want to watch over time, with "created_at" edge attribute
:param minutes: Number of minutes between two snapshots (Default 0)
:param hours: Number of hours between two snapshots (Default 0)
:param days: Number of days between two snapshots (Default 0)
:param max_snapshots: Maximum number of generated snapshots (Default None - all snapshots are created)
:param interval: Tuple (start, end) specifying in which interval to generate snapshots (Default None - takes min, max created_at date of G)
:param include_final: If True, set G as value for max_date (Default False)
:return: A dict with timestamps
"""
if nx.get_edge_attributes(G, "created_at") == {}:
raise Exception("Graph needs 'created_at' edge attribute")
if minutes < 0 or hours < 0 or days < 0 or minutes + hours + days <= 0:
raise Exception("Illegal minutes, hours or days values")
edges = G.edges(data=True)
created_ats = [attr["created_at"] for (_, _, attr) in edges]
if interval is None:
date = str_to_datetime(min(created_ats))
max_date = str_to_datetime(max(created_ats))
else:
date = str_to_datetime(interval[0])
max_date = str_to_datetime(interval[1])
snapshots = {}
while date <= max_date and (max_snapshots is None
or len(snapshots) < max_snapshots):
if cummulative:
edges_snapshot = [(a, b) for (a, b, attr) in edges
if str_to_datetime(attr["created_at"]) <= date]
else:
edges_snapshot = [
(a, b) for (a, b, attr) in edges
if (date <= str_to_datetime(attr["created_at"]) <= date +
timedelta(minutes=minutes, hours=hours, days=days))
]
nodes_snapshot = list(sum(edges_snapshot, ()))
G_snapshot = G.subgraph(nodes_snapshot)
snapshots[date] = reduce_multi_graph(G_snapshot)
date += timedelta(minutes=minutes, hours=hours, days=days)
if include_final:
snapshots[max_date] = reduce_multi_graph(G)
return snapshots
def __init__(self, nodes=None, edges=None):
self.graph = MultiGraph()
# Nodes
nodes = nodes or {}
for node_id, (lon, lat) in nodes.items():
self.add_node(node_id, lon, lat)
# Edges
edges = edges or {}
for (n1, n2), (edge_type, dict_attrs) in edges.items():
self.add_edge(n1, n2, edge_type, **dict_attrs)
def generalized_degree(self, g: MultiGraph, f: set, active_node, node) -> (int, set):
assert g.has_node(node), "Calculating gd for node which is not in g!"
k = set(g.neighbors(node))
k.remove(active_node)
k = k.intersection(f)
gx = self.compress(g, k, node)
neighbors = list(gx.neighbors(node))
neighbors.remove(active_node)
return len(neighbors), neighbors
def generalized_degree(g: MultiGraph, f: set, active_node, node) -> (int, set): assert g.has_node(node), "Calculating gd for node which is not in g!" k = set(g.neighbors(node)) k.remove(active_node) k = k.intersection(f) gx = compress(g, k, node) neighbors = gx.neighbors(node) neighbors.remove(active_node) return (len(neighbors), neighbors)
def add_weak_gene(gene: EdgeGene, graph: nx.MultiGraph) -> bool:
key = gene.A1 + gene.A2
edge = (gene.P1, gene.P2, key)
if any(starmap(
lambda p, a: p in graph and not any(x == a for x in get_node_space(graph, p)),
[(gene.P1, gene.A1), (gene.P2, gene.A2)])):
return False
if graph.has_edge(gene.P1, gene.P2):
keys = graph[gene.P1][gene.P2]
if len(keys) > 1:
return False
graph.remove_edge(gene.P1, gene.P2, next(iter(keys)))
graph.add_edge(*edge, gene=gene)
return True
def _transact(graph: nx.MultiGraph, src: int, tgt: int, amount: int, new_node: int, info: dict):
from more_itertools import pairwise
path, weights, fees = find_route(graph, src, tgt, amount)
# no path found
if path is None:
info['no_path'] += 1
return
for (node, neighbour) in pairwise(path):
channel_trans_amt = weights[neighbour]
channel_policy = graph.get_policy(node, neighbour)
# channel cannot handle transaction
if channel_policy.balance < channel_trans_amt:
info['channel_imbalance'] += 1
if node == new_node or neighbour == new_node:
info['failure'][node, neighbour] += 1
raise Exception('Adversary channel imbalance')
return
# record successful transaction
info['total_success'] += 1
total_amt = 0
# move amount between nodes in path
for (node, neighbour) in pairwise(path):
if neighbour is None:
# remove total amount from src
graph.nodes[path[0]]['data'].capacity -= total_amt
# add amount to tgt
graph.nodes[node]['data'].capacity += weights[node]
break
channel_trans_amt = weights[neighbour]
channel_policy = graph.get_policy(node, neighbour)
# pay channel fees to node
graph.nodes[node]['data'].capacity += fees[node]
total_amt += fees[node]
# shift channel balance
channel_policy.balance -= channel_trans_amt
graph.get_policy(neighbour, node).balance += channel_trans_amt
# record profit for adversary
if node == new_node or neighbour == new_node:
info['success'][node, neighbour] += 1
info['profit'][node, neighbour] += fees[node]
def main():
parser = ArgumentParser()
parser.add_argument("project_directory", nargs=1)
parser.add_argument("config_file", nargs=1)
parser.add_argument("--no-backup", default=False, action="store_true")
args = parser.parse_args()
project_directory = args.project_directory[0]
config_file = args.config_file[0]
graph_path, project_config_path = setup_project(config_file,
project_directory)
model, minima_count, min_config, lex_config = read_config_file(
project_config_path)
# Setup Logger
root_logger = getLogger()
root_logger.setLevel(INFO)
root_logger.addHandler(StreamHandler(sys.stdout))
root_logger.addHandler(
FileHandler(join(project_directory, "exploration.log")))
# === Create/load graph ===
if isfile(graph_path):
if not args.no_backup:
root_logger.info("Copying current 'graph.p' to backup file.")
copyfile(
graph_path,
graph_path.replace(".p", f"_bak{strftime('%Y%m%d-%H%M')}.p"))
else:
root_logger.info(
"Not creating a backup of 'graph.p' because of user request.")
graph = repair_graph(load_pickle_graph(graph_path), model)
else:
graph = MultiGraph()
# Call this after every optmisiation
def save_callback():
store_pickle_graph(graph, graph_path)
# === Ensure the specified number of minima ===
for _ in pbar(range(len(graph.nodes), minima_count), "Finding minima"):
minimum_data = find_minimum(model, min_config)
graph.add_node(
max(graph.nodes) + 1 if len(graph.nodes) > 0 else 1,
**move_to(minimum_data, "cpu"))
save_callback()
# === Connect minima ===
landscape_exploration(graph, model, lex_config, callback=save_callback)
def subgraph_by_timestamp(mg: nx.MultiGraph, start: int, end: int) -> nx.Graph:
edges = filter(
lambda edge: start <= edge[2]["timestamp"] and edge[2]["timestamp"] <
end,
mg.edges(data=True),
)
g = nx.Graph()
for node in mg.nodes():
g.add_node(node)
for u, v, data in edges:
if g.has_edge(u, v):
g[u][v]["weight"] += data["weight"]
else:
g.add_edge(u, v, weight=data["weight"])
return g
def get_graph_extents(
networkX_multigraph: nx.MultiGraph
) -> Tuple[float, float, float, float]:
"""
Parameters
----------
networkX_multigraph
A `NetworkX` `MultiGraph` with `x` and `y` node parameters.
Returns
-------
Tuple
A tuple of `min_x`, `min_y`, `max_x`, `max_y` values.
"""
# get min and maxes for x and y
min_x = np.inf
max_x = -np.inf
min_y = np.inf
max_y = -np.inf
for n, d in networkX_multigraph.nodes(data=True):
if d['x'] < min_x:
min_x = d['x']
if d['x'] > max_x:
max_x = d['x']
if d['y'] < min_y:
min_y = d['y']
if d['y'] > max_y:
max_y = d['y']
return min_x, min_y, max_x, max_y
def _get_fbvs_max_size(self, g: MultiGraph, k: int) -> set:
# Exhaustively apply reductions
k, x0 = self.apply_reductions(g, k)
# Originally reduction 5: if k < 0, terminate the algorithm and conclude that
# (G, k) is a no-instance.
if k < 0:
return None
# If G is an empty graph, then we return soln_redux
if len(g) == 0:
return x0
# Pick a random edge, then a random end node of that edge
rand_edge = choice(g.edges())
v = choice(rand_edge)
# We recurse on (G - v, k − 1).
xn = self._get_fbvs_max_size(graph_minus(g, {v}), k - 1)
if xn is None:
# If the recursive step returns a failure, then we return a failure as well.
return None
else:
# If the recursive step returns a feedback vertex set Xn, then we return X = Xn ∪ {v} ∪ X0.
return xn.union({v}).union(x0)
def setUp(self):
# Create digraph with negative resource costs with unreachable node 'E'
self.G = DiGraph(directed=True, n_res=2)
self.G.add_edge('Source', 'A', res_cost=array([1, 2]), weight=0)
self.G.add_edge('A', 'C', res_cost=array([-1, 0.3]), weight=0)
self.G.add_edge('A', 'B', res_cost=array([-1, 3]), weight=0)
self.G.add_edge('B', 'D', res_cost=array([-1, 2]), weight=0)
# Unreachable node E
self.G.add_edge('B', 'E', res_cost=array([10, 1]), weight=0)
self.G.add_edge('C', 'D', res_cost=array([1, 0.1]), weight=0)
self.G.add_edge('D', 'Sink', res_cost=array([1, 0.1]), weight=0)
# Create digraph with a resource infeasible minimum cost path
self.H = MultiGraph(directed=True)
self.H.add_edge('Source', 'A', res_cost=array([1, 1]), weight=-1)
self.H.add_edge('A', 'B', res_cost=array([1, 1]), weight=-1)
self.H.add_edge('B', 'Sink', res_cost=array([1, 1]), weight=-1)
self.H.add_edge('Sink', 'Source', weight=-1)
self.max_res, self.min_res = ["foo"], ["bar"]
# Create digraph to test issue 72
self.F = DiGraph(n_res=1)
self.F.add_edge('Source', 'A', res_cost=array([1]), weight=1)
self.F.add_edge('A', 'B', res_cost=array([10]), weight=1)
self.F.add_edge('A', 'Sink', res_cost=array([1]), weight=1)
def _get_fbvs_max_size(self, g: MultiGraph, k: int) -> set:
# Exhaustively apply reductions
k, x0 = self.apply_reductions(g, k)
# Originally reduction 5: if k < 0, terminate the algorithm and conclude that
# (G, k) is a no-instance.
if k < 0:
return None
# If G is an empty graph, then we return soln_redux
if len(g) == 0:
return x0
# Pick a random edge, then a random end node of that edge
rand_edge = choice(g.edges())
v = choice(rand_edge)
# We recurse on (G - v, k − 1).
xn = self._get_fbvs_max_size(graph_minus(g, {v}), k - 1)
if xn is None:
# If the recursive step returns a failure, then we return a failure as well.
return None
else:
# If the recursive step returns a feedback vertex set Xn, then we return X = Xn ∪ {v} ∪ X0.
return xn.union({v}).union(x0)
def compress(g: MultiGraph, t: set, compressed_node, mutate=False) -> MultiGraph: if not t: return g if mutate: gx = g else: gx = g.copy() tx = t if compressed_node in tx: tx = t.copy() tx.remove(compressed_node) gx.add_node(compressed_node) for node in tx: for edge in gx.edges(node): if edge[0] == node: node_2 = edge[1] else: node_2 = edge[0] if not (node_2 in t or node_2 == compressed_node): gx.add_edge(compressed_node, node_2) gx.remove_node(node) remove = set() for node in gx.adj[compressed_node]: if len(gx.adj[compressed_node][node]) >= 2: # Using a set to remove to avoid messing up iteration of adj remove.add(node) for node in remove: gx.remove_node(node) return gx
def test_run_walks():
mg = MultiGraph()
mg.add_edge('a', 'b')
mg.add_edge('b', 'c')
dw = DeepWalk(mg, 10, 100)
dw.get_walks(workers=1)
# Number of neighbors for all nodes together is 4, times niter: 400
assert len(dw.walks) == 400, len(dw.walks)
assert len([w for w in dw.walks if w[0] == 'a']) == 100
assert len([w for w in dw.walks if w[0] == 'b']) == 200
dw.get_walks(workers=2)
# Number of neighbors for all nodes together is 4, times niter: 400
assert len(dw.walks) == 400, len(dw.walks)
assert len([w for w in dw.walks if w[0] == 'a']) == 100
assert len([w for w in dw.walks if w[0] == 'b']) == 200
def multiple_edges(self, new):
"""
Get/set whether or not self allows multiple edges.
INPUT:
new: boolean or None
DOCTEST:
sage: G = sage.graphs.base.graph_backends.NetworkXGraphBackend()
sage: G.multiple_edges(True)
sage: G.multiple_edges(None)
True
"""
try:
assert(not isinstance(self._nxg, (NetworkXGraphDeprecated, NetworkXDiGraphDeprecated)))
except AssertionError:
self._nxg = self._nxg.mutate()
from networkx import Graph,MultiGraph,DiGraph,MultiDiGraph
if new is None:
return self._nxg.is_multigraph()
if new == self._nxg.is_multigraph():
return
if new:
if self._nxg.is_directed():
self._nxg = MultiDiGraph(self._nxg)
else:
self._nxg = MultiGraph(self._nxg)
else:
if self._nxg.is_directed():
self._nxg = DiGraph(self._nxg)
else:
self._nxg = Graph(self._nxg)
def compress(self, g: MultiGraph, t: set, compressed_node, mutate=False) -> MultiGraph:
if not t:
return g
if mutate:
gx = g
else:
gx = g.copy()
tx = t
if compressed_node in tx:
tx = t.copy()
tx.remove(compressed_node)
gx.add_node(compressed_node)
for node in tx:
for edge in gx.edges(node):
if edge[0] == node:
node_2 = edge[1]
else:
node_2 = edge[0]
if not (node_2 in t or node_2 == compressed_node):
gx.add_edge(compressed_node, node_2)
gx.remove_node(node)
remove = set()
for node in gx.adj[compressed_node]:
if len(gx.adj[compressed_node][node]) >= 2:
# Using a set to remove to avoid messing up iteration of adj
remove.add(node)
for node in remove:
gx.remove_node(node)
return gx
def __init__(self,
symbols=None,
positions=None,
numbers=None,
tags=None,
momenta=None,
masses=None,
magmoms=None,
charges=None,
scaled_positions=None,
cell=None,
pbc=None,
celldisp=None,
constraint=None,
calculator=None,
info=None,
edges=None):
super().__init__(symbols, positions, numbers, tags, momenta, masses,
magmoms, charges, scaled_positions, cell, pbc,
celldisp, constraint, calculator, info)
if self.pbc.any():
self._graph = MultiGraph()
else:
self._graph = Graph()
nodes = [[i, {
'number': n
}] for i, n in enumerate(self.arrays['numbers'])]
self._graph.add_nodes_from(nodes)
if edges:
self._graph.add_edges_from(edges, bonds=1)
self._surface_atoms = None
def simplify(streckennetz: nx.MultiGraph) -> nx.MultiGraph:
print('simplifying...')
# Remove the shorter edge of two parallel edges
edges_to_remove = []
for edges_index in streckennetz.edges():
edges = streckennetz[edges_index[0]][edges_index[1]]
if len(edges) > 1:
min_length = edges[0]['length']
min_length_index = 0
for i in edges:
if edges[i]['length'] < min_length:
min_length = edges[i]['length']
min_length_index = i
edges_to_remove.append(list(edges_index) + [min_length_index])
print('found', len(edges_to_remove), 'parallel edges')
streckennetz.remove_edges_from(edges_to_remove)
# Remove nodes, that only have a single edge
while True:
nodes_to_remove = []
for node in streckennetz.nodes():
if streckennetz.degree(
node) < 2 and 'type' not in streckennetz.nodes[node]:
nodes_to_remove.append(node)
if nodes_to_remove:
print('found', len(nodes_to_remove), 'deadend nodes')
streckennetz.remove_nodes_from(nodes_to_remove)
nodes_to_remove = []
else:
break
return streckennetz
def reward(g: nx.MultiGraph, edge: Tuple[int, int], const_amt: int, fee_type: str, fee: int = None) -> int:
# debugging
# print_flag = fee is not None
u, v = edge
if fee is not None:
g.update_fee(u, v, fee, fee_type)
else:
fee = getattr(g.get_policy(u, v), fee_type)
ebc = edge_betweenness(g, const_amt)[edge]
# debugging
# if print_flag:
# print('({:>3d}, {:>3d}) fee {:>9d} ebc {:>9f} '.format(
# u, v, fee, ebc), end='')
return fee * ebc
def get_fbvs_max_size(self, g: MultiGraph, k: int) -> set:
# we will run the algorithm 4^k times
n = 4 ** k
for _ in range (1, n):
# pass a copy of g, since we need a fresh copy of g for every run
sol = self._get_fbvs_max_size(g.copy(), k)
if sol is not None:
# we found a fbvs for (g,k), so we can return it right away
return sol
return None
def graph_minus(g: MultiGraph, w: set) -> MultiGraph: gx = MultiGraph() for (n1, n2) in g.edges(): if n1 not in w and n2 not in w: gx.add_edge(n1, n2) for n in g.nodes(): if n not in w: gx.add_node(n) return gx
def fvs_disjoint(self, g: MultiGraph, w: set, k: int) -> set:
"""
Given an undirected graph G and a fbvs W in G of size at least (k + 1), is it possible to construct
a fbvs X of size at most k using only the nodes of G - W?
:return: The set X, or `None` if it's not possible to construct X
"""
# If G[W] isn't a forest, then a solution X not using W can't remove W's cycles.
if not is_acyclic(g.subgraph(w)):
return None
# Apply reductions exhaustively.
k, soln_redux = self.apply_reductions(g, w, k)
# If k becomes negative, it indicates that the reductions included
# more than k nodes. In other word, reduction 2 shows that there are more than k nodes
# in G - W that will create cycle in W. Hence, no solution of size <= k exists.
if k < 0:
return None
# From now onwards we assume that k >= 0
# If G has been reduced to nothing and k is >= 0 then the solution generated by the reductions
# is already optimal.
if len(g) == 0:
return soln_redux
# Recall that H is a forest as W is a feedback vertex set. Thus H has a node x of degree at most 1.
# Find an x in H of degree at most 1.
h = graph_minus(g, w)
x = None
for v in h.nodes():
if h.degree(v) <= 1:
x = v
break
assert x is not None, "There must be at least one node x of degree at most 1"
# Branch on (G - {x}, W, k−1) and (G, W ∪ {x}, k)
# G is copied in the left branch (as it is modified), but passed directly in the right.
soln_left = self.fvs_disjoint(graph_minus(g, {x}), w, k - 1)
if soln_left is not None:
return soln_redux.union(soln_left).union({x})
soln_right = self.fvs_disjoint(g, w.union({x}), k)
if soln_right is not None:
return soln_redux.union(soln_right)
return None
def reduction1(g: MultiGraph, w: set, h: MultiGraph, k: int) -> (int, int, bool): changed = False for v in g.nodes(): if g.degree(v) <= 1: g.remove_node(v) h.remove_nodes_from([v]) changed = True return (k, None, changed)
def reduction2(g: MultiGraph, w: set, h: MultiGraph, k: int) -> (int, int, bool):
for v in h.nodes():
# Check if G[W ∪ {v}] contains a cycle.
if not is_forest(g.subgraph(w.union({v}))):
g.remove_node(v)
h.remove_nodes_from([v])
return (k - 1, v, True)
return (k, None, False)
def mif_preprocess_2(g: MultiGraph, f: set, active_v, k: int) -> set: mif_set = set() while not is_independent_set(g, f): mif_set = mif_set.union(f) for component in nxc.connected_components(g.subgraph(f)): if len(component) > 1: if active_v in component: active_v = component.pop() compressed_node = active_v else: compressed_node = component.pop() g = compress(g, component, compressed_node, True) f = f.intersection(g.nodes()) # Maybe faster with # f = f.difference(component) # f.add(compressed_node) mif_set = mif_set.union(component) break mif_set2 = mif_main(g, f, active_v, k) if mif_set2: mif_set = mif_set2.union(mif_set) if k == None or len(mif_set) >= k: return mif_set return None
def reduction1(self, g: MultiGraph, w: set, h: MultiGraph, k: int) -> (int, int, bool):
"""
Delete all nodes of degree 0 or 1 as they can't be part of any cycles.
"""
changed = False
for v in g.nodes():
if g.degree(v) <= 1:
g.remove_node(v)
h.remove_nodes_from([v])
changed = True
return k, None, changed
def mif_preprocess_1(g: MultiGraph, f: set, active_v, k: int) -> set: if nxc.number_connected_components(g) >= 2: mif_set = set() for component in nxc.connected_components(g): f_i = component.intersection(f) gx = g.subgraph(component) component_mif_set = mif_preprocess_2(gx, f_i, active_v, None) if component_mif_set: mif_set = mif_set.union(component_mif_set) if k != None: k -= (len(component_mif_set) - len(f_i)) if k <= 0: return mif_set if k == None or len(mif_set) >= k: return mif_set return None return mif_preprocess_2(g, f, active_v, k)
def fvs_disjoint(g: MultiGraph, w: set, k: int) -> set:
# Check that G[W] is a forest.
# If it isn't, then a solution X not using W can't remove W's cycles.
if not is_forest(g.subgraph(w)):
return None
# Apply reductions exhaustively.
k, soln_redux = apply_reductions(g, w, k)
# If k becomes negative, it indicates that the reductions included
# more than k vertices, hence no solution of size <= k exists.
if k < 0:
return None
# If G has been reduced to nothing and k is >= 0 then the solution generated by the reductions
# is already optimal.
if len(g) == 0:
return soln_redux
# Find an x in H of degree at most 1.
h = graph_minus(g, w)
x = None
for v in h.nodes():
if h.degree(v) <= 1:
x = v
break
assert x is not None
# Branch.
# G is copied in the left branch (as it is modified), but passed directly in the right.
soln_left = fvs_disjoint(graph_minus(g, {x}), w, k - 1)
if soln_left is not None:
return soln_redux.union(soln_left).union({x})
soln_right = fvs_disjoint(g, w.union({x}), k)
if soln_right is not None:
return soln_redux.union(soln_right)
return None
def reduction2(self, g: MultiGraph, w: set, h: MultiGraph, k: int) -> (int, int, bool):
"""
If there exists a node v in H such that G[W ∪ {v}]
contains a cycle, then include v in the solution, delete v and decrease the
parameter by 1. That is, the new instance is (G - {v}, W, k - 1).
If v introduces a cycle, it must be part of X as none of the vertices in W
will be available to neutralise this cycle.
"""
for v in h.nodes():
# Check if G[W ∪ {v}] contains a cycle.
if not is_acyclic(g.subgraph(w.union({v}))):
g.remove_node(v)
h.remove_nodes_from([v])
return k - 1, v, True
return k, None, False
def test_bag():
multigraph1 = MultiGraph()
multigraph1.add_nodes_from(range(4))
breakpoint_graph1 = BreakpointGraph(multigraph1)
double_color = ['A', 'B']
breakpoint_graph1.add_edge(0, 1, Multicolor(*double_color))
breakpoint_graph1.add_edge(2, 3, Multicolor('A'))
breakpoint_graph1.add_edge(1, 2, Multicolor('C'))
breakpoint_graph1.add_edge(0, 3, Multicolor('D'))
assert (len(find_bag_patterns(breakpoint_graph1)) == 1)
multigraph2 = MultiGraph()
multigraph2.add_nodes_from(range(4))
breakpoint_graph2 = BreakpointGraph(multigraph2)
double_color = ['A', 'B']
breakpoint_graph2.add_edge(0, 1, Multicolor(*double_color))
breakpoint_graph2.add_edge(2, 3, Multicolor('B'))
breakpoint_graph2.add_edge(1, 2, Multicolor('C'))
breakpoint_graph2.add_edge(0, 3, Multicolor('C'))
assert (len(find_bag_patterns(breakpoint_graph2)) == 0)
def reduction4(self, g: MultiGraph, k: int) -> (int, List[int], bool):
"""
If there is a vertex v of degree 2, delete v and connect its two neighbors by a new edge.
"""
for v in g.nodes():
if g.degree(v) == 2:
# Delete v and make its neighbors adjacent.
ne = g.neighbors(v)
# We must check whether v has 2 neighbors, or just one but connected to v by multiple edges
if len(ne) == 2:
[n1, n2] = ne
else:
[n1] = ne
n2 = n1
g.remove_node(v)
# Only add the edge if there are currently less than 2 edges between these two nodes
es = g[n1].get(n2, {})
if len(es) < 2:
g.add_edge(n1, n2)
return k, None, True
return k, None, False
def graph_minus_slow(g: MultiGraph, w: set) -> MultiGraph: gx = g.copy() gx.remove_nodes_from(w) return gx
class ShuttlingGraph(list):
def __init__(self, shuttlingEdges=list() ):
super(ShuttlingGraph, self).__init__(shuttlingEdges)
self.currentPosition = None
self.currentPositionName = None
self.nodeLookup = dict()
self.currentPositionObservable = Observable()
self.graphChangedObservable = Observable()
self.initGraph()
self._hasChanged = True
def initGraph(self):
self.shuttlingGraph = MultiGraph()
for edge in self:
self.shuttlingGraph.add_node(edge.startName)
self.shuttlingGraph.add_node(edge.stopName)
self.shuttlingGraph.add_edge(edge.startName, edge.stopName, key=hash(edge), edge=edge,
weight=abs(edge.stopLine-edge.startLine))
self.nodeLookup[edge.startLine] = edge.startName
self.nodeLookup[edge.stopLine] = edge.stopName
def rgenerateNodeLookup(self):
self.nodeLookup.clear()
for edge in self:
self.nodeLookup[edge.startLine] = edge.startName
self.nodeLookup[edge.stopLine] = edge.stopName
@property
def hasChanged(self):
return self._hasChanged
@hasChanged.setter
def hasChanged(self, value):
self._hasChanged = value
def position(self, line):
return self.nodeLookup.get(line)
def setPosition(self, line):
if self.currentPosition!=line:
self.currentPosition = line
self.currentPositionName = self.position(line)
self.currentPositionObservable.fire( line=line, text=firstNotNone(self.currentPositionName, "") )
def getMatchingPosition(self,graph):
"""Try to match node name/position to the current settings in the provided ShuttlingGraph."""
if not graph:
return self.currentPosition # no change
# Matching node name. Need to set the corresponding position
for edge in self:
if edge.startName == graph.currentPositionName:
return edge.startLine
if edge.stopName == graph.currentPositionName:
return edge.stopLine
#if graph.currentPosition:
# return graph.currentPosition #just use the graph's position
return self.currentPosition
def addEdge(self, edge):
self._hasChanged = True
self.append(edge)
self.shuttlingGraph.add_edge(edge.startName, edge.stopName, key=hash(edge), edge=edge, weight=abs(edge.stopLine-edge.startLine))
self.nodeLookup[edge.startLine] = edge.startName
self.nodeLookup[edge.stopLine] = edge.stopName
self.graphChangedObservable.firebare()
self.setPosition(self.currentPosition)
def isValidEdge(self, edge):
return ((edge.startLine not in self.nodeLookup or self.nodeLookup[edge.startLine] == edge.startName)
and (edge.stopLine not in self.nodeLookup or self.nodeLookup[edge.stopLine] == edge.stopName))
def getValidEdge(self):
index = 0
while self.shuttlingGraph.has_node("Start_{0}".format(index)):
index += 1
startName = "Start_{0}".format(index)
index = 0
while self.shuttlingGraph.has_node("Stop_{0}".format(index)):
index += 1
stopName = "Stop_{0}".format(index)
index = 0
startLine = (max( self.nodeLookup.keys() )+1) if self.nodeLookup else 1
stopLine = startLine + 1
return ShuttleEdge(startName, stopName, startLine, stopLine, 0, 0, 0, 0)
def removeEdge(self, edgeno):
self._hasChanged = True
edge = self.pop(edgeno)
self.shuttlingGraph.remove_edge(edge.startName, edge.stopName, hash(edge))
if self.shuttlingGraph.degree(edge.startName) == 0:
self.shuttlingGraph.remove_node(edge.startName)
if self.shuttlingGraph.degree(edge.stopName) == 0:
self.shuttlingGraph.remove_node(edge.stopName)
self.graphChangedObservable.firebare()
self.rgenerateNodeLookup()
self.setPosition(self.currentPosition)
def setStartName(self, edgeno, startName):
self._hasChanged = True
startName = str(startName)
edge = self[edgeno]
if edge.startName != startName:
self.shuttlingGraph.remove_edge(edge.startName, edge.stopName, key=hash(edge))
if self.shuttlingGraph.degree(edge.startName) == 0:
self.shuttlingGraph.remove_node(edge.startName)
edge.startName = startName
self.shuttlingGraph.add_edge(edge.startName, edge.stopName, key=hash(edge), edge=edge,
weight=abs(edge.stopLine-edge.startLine) )
self.graphChangedObservable.firebare()
self.setPosition(self.currentPosition)
self.rgenerateNodeLookup()
return True
def setStopName(self, edgeno, stopName):
self._hasChanged = True
stopName = str(stopName)
edge = self[edgeno]
if edge.stopName != stopName:
self.shuttlingGraph.remove_edge(edge.startName, edge.stopName, key=hash(edge))
if self.shuttlingGraph.degree(edge.stopName) == 0:
self.shuttlingGraph.remove_node(edge.stopName)
edge.stopName = stopName
self.shuttlingGraph.add_edge(edge.startName, edge.stopName, key=hash(edge), edge=edge,
weight=abs(edge.stopLine-edge.startLine) )
self.graphChangedObservable.firebare()
self.rgenerateNodeLookup()
self.setPosition(self.currentPosition)
return True
def setStartLine(self, edgeno, startLine):
self._hasChanged = True
edge = self[edgeno]
if startLine != edge.startLine and (startLine not in self.nodeLookup or self.nodeLookup[startLine] == edge.startName):
self.nodeLookup.pop(edge.startLine)
edge.startLine = startLine
self.shuttlingGraph.edge[edge.startName][edge.stopName][hash(edge)]['weight'] = abs(edge.stopLine-edge.startLine)
self.rgenerateNodeLookup()
self.graphChangedObservable.firebare()
self.setPosition(self.currentPosition)
return True
return False
def setStopLine(self, edgeno, stopLine):
self._hasChanged = True
edge = self[edgeno]
if stopLine != edge.stopLine and (stopLine not in self.nodeLookup or self.nodeLookup[stopLine] == edge.stopName):
self.nodeLookup.pop(edge.stopLine)
edge.stopLine = stopLine
self.shuttlingGraph.edge[edge.startName][edge.stopName][hash(edge)]['weight'] = abs(edge.stopLine-edge.startLine)
self.rgenerateNodeLookup()
self.graphChangedObservable.firebare()
self.setPosition(self.currentPosition)
return True
return False
def setIdleCount(self, edgeno, idleCount):
self._hasChanged = True
self[edgeno].idleCount = idleCount
return True
def setSteps(self, edgeno, steps):
self._hasChanged = True
self[edgeno].steps = steps
return True
def shuttlePath(self, fromName, toName ):
fromName = firstNotNone(fromName, self.currentPositionName)
fromName = fromName if fromName else self.position(float(self.currentPosition))
if fromName not in self.shuttlingGraph:
raise ShuttlingGraphException("Shuttling failed, origin '{0}' is not a valid shuttling node".format(fromName))
if toName not in self.shuttlingGraph:
raise ShuttlingGraphException("Shuttling failed, target '{0}' is not a valid shuttling node".format(toName))
sp = shortest_path(self.shuttlingGraph, fromName, toName)
path = list()
for a, b in pairs_iter(sp):
edge = sorted(self.shuttlingGraph.edge[a][b].values(), key=itemgetter('weight'))[0]['edge']
path.append((a, b, edge, self.index(edge)))
return path
def nodes(self):
return self.shuttlingGraph.nodes()
def toXmlElement(self, root):
mydict = dict( ( (key, str(getattr(self, key))) for key in ('currentPosition', 'currentPositionName') if getattr(self, key) is not None ) )
myElement = ElementTree.SubElement(root, "ShuttlingGraph", attrib=mydict )
for edge in self:
edge.toXmlElement( myElement )
return myElement
def setStartType(self, edgeno, Type):
self._hasChanged = True
self[edgeno].startType = str(Type)
return True
def setStopType(self, edgeno, Type):
self._hasChanged = True
self[edgeno].stopType = str(Type)
return True
def setStartLength(self, edgeno, length):
edge = self[edgeno]
if length!=edge.startLength:
if length+edge.stopLength<edge.sampleCount:
self._hasChanged = True
edge.startLength = int(length)
else:
return False
return True
def setStopLength(self, edgeno, length):
edge = self[edgeno]
if length!=edge.stopLength:
if edge.startLength+length<edge.sampleCount:
self._hasChanged = True
edge.stopLength = int(length)
else:
return False
return True
@staticmethod
def fromXmlElement( element ):
edgeElementList = element.findall("ShuttleEdge")
edgeList = [ ShuttleEdge.fromXmlElement(e) for e in edgeElementList ]
return ShuttlingGraph(edgeList)
def fvs_via_mif(g: MultiGraph, k: int) -> set: mif_set = mif(g, g.order()-k) if mif_set: nodes = set(g.nodes()) mif_set = nodes.difference(mif_set) return mif_set
for n in N:
f.write(str(round(my_data[n][0])) + " ")
f.write(str(round(my_data[n][1])) + " ")
f.write(str(round(my_data[n][2])))
f.write("\n")
f.close()
fh = open("trash","w")
call(["./blossom4","-3", "-x","data.dat", "-w", "output.dat"], stdout=fh)
fh.close()
result = genfromtxt('output.dat', delimiter=' ', usecols = (0, 1))
result = result[1:]
#MINMAXMATCHING END
H = MultiGraph()
H.add_nodes_from(T.nodes())
H.add_edges_from(T.edges())
for (key, value) in a.items():
if N < N:
H.add_edge(N, N)
t = Set()
for (i, j) in eulerian_circuit(H):
if i in t:
continue
t.add(i)
print i
#the result is t
#t_e = zip(t[:-1], t[1:])
def is_independent_set(g: MultiGraph, f: set) -> bool: for edge in itertools.combinations(f, 2): if g.has_edge(edge[0], edge[1]): return False return True
def reduction3(self, g: MultiGraph, w: set, h: MultiGraph, k: int) -> (int, int, bool):
"""
If there is a node v ∈ V(H) of degree 2 in G such
that at least one neighbor of v in G is from V (H), then delete this node
and make its neighbors adjacent (even if they were adjacent before; the graph
could become a multigraph now).
"""
for v in h.nodes():
if g.degree(v) == 2:
# If v has a neighbour in H, short-curcuit it.
if len(h[v]) >= 1:
# Delete v and make its neighbors adjacent.
[n1, n2] = g.neighbors(v)
g.remove_node(v)
g.add_edge(n1, n2)
# Update H accordingly.
h.remove_nodes_from([v])
if n1 not in w and n2 not in w:
h.add_edge(n1, n2)
return k, None, True
return k, None, False
basename = splitext(basename(sys.argv[1]))[0]
random.seed(1)
print "Reading {}, writing {}".format(sys.argv[1], outname)
graph = read_gml(sys.argv[1])
hsubspec = "flowsize=exponential(1/10000.0) flowstart=exponential(100) ipproto=randomchoice(6) sport=randomchoice(22,80,443) dport=randomunifint(1025,65535) lossrate=randomchoice(0.001)"
mnodes = add_measurement(graph)
newgraph = MultiGraph(name=basename,
counterexportfile=basename+"_counters",
flowexport="text",
flowsampling=1.0,
pktsampling=1.0,
exportcycle=60,
counterexport=True,
counterexportinterval=1,
longflowtmo=60,
flowinactivetmo=60,
harpoonsubspec=hsubspec,
measurementnodes=mnodes)
def get_cap(label):
if 'OC192/STM64' in label:
return '10Gb'
elif 'OC3' in label:
return '155Mb'
elif 'OC12' in label:
return '622Mb'
elif 'OC48' in label:
return '2.4Gb'
for n in N:
f.write(str(round(my_data[n][0])) + " ")
f.write(str(round(my_data[n][1])) + " ")
f.write(str(round(my_data[n][2])))
f.write("\n")
f.close()
fh = open("trash.dat","w")
call(["./blossom4","-3", "-x","data.dat", "-w", "output.dat"], stdout=fh)
fh.close()
result = genfromtxt('output.dat', delimiter=' ', usecols = (0, 1))
result = result[1:]
#MINMAXMATCHING END
H = MultiGraph()
H.add_nodes_from(T.nodes())
H.add_edges_from(T.edges())
for (key, value) in result:
H.add_edge(N[int(key)], N[int(value)])
f = open("data.dat", "wb")
t = Set()
for (i, j) in eulerian_circuit(H):
if i in t:
continue
t.add(i)
f.write(str(i) + " ")
f.close()
fh = open("trash.dat", "w")
def reduction3(g: MultiGraph, w: set, h: MultiGraph, k: int) -> (int, int, bool): for v in h.nodes(): if g.degree(v) == 2: # If v has a neighbour in H, short-curcuit it. if len(h[v]) >= 1: # Delete v and make its neighbors adjacent. [n1, n2] = g.neighbors(v) g.remove_node(v) g.add_edge(n1, n2) # Update H accordingly. h.remove_nodes_from([v]) if n1 not in w and n2 not in w: h.add_edge(n1, n2) return (k, None, True) return (k, None, False)
