def __init__(self, F, arg):
"""
If arg is a list:
Generate the core graph corresponding to the group generated by group_gens.
If arg is a graph:
Check for validity and do all folds.
"""
assert is_FreeGroup(F), "F must be a free group"
self.F = F
self.F_rank = F.rank()
self.letter_types = range(1, self.F_rank + 1)
self.letters = list(range(-self.F_rank, 0)) + list(range(1, self.F_rank + 1))
# -r, ..., -1, 1, ..., r
if isinstance(arg, list):
group_gens = arg
assert all([gen in F for gen in group_gens]), "The generators must be elements of F."
self.group_gens = group_gens
G = MultiDiGraph()
G.add_node((0,)) # the marked vertex (id)
for i, gen in enumerate(self.group_gens):
word = gen.Tietze()
word_len = len(word)
# new_nodes = [(i, j) for j in range(1, word_len)]
# G.add_nodes_from(new_nodes)
get_node = lambda j: (0,) if (j % word_len == 0) else (i, j)
for j in range(word_len):
G.add_edge(get_node(j), get_node(j + 1), label=word[j])
G.add_edge(get_node(j + 1), get_node(j), label=-word[j])
elif isinstance(arg, MultiDiGraph):
# We are going to copy the graph, add reverse edges when needed,
# and sort the edges.
# The reason we sort the edges is to get a "canonical" version
# of the object, so subgroup_gens would be the same in different
# objects with the same graph.
G = MultiDiGraph()
G.add_nodes_from(arg.nodes())
edges = arg.edges(data='label')
G_edges = [e for e in edges]
assert len(edges) == len(arg.edges()), "Every edge has to be labelled."
for src, dst, letter in edges:
assert letter in self.letters, \
f"The edge betwen {src} and {dst} has an invalid label"
if (dst, src, -letter) not in G.edges(data='label'):
G_edges.append((dst, src, -letter))
G.add_weighted_edges_from(sorted(G_edges), weight='label')
else:
raise ValueError("arg must be a list of words or a MultiDiGraph.")
self.G = do_all_folds(G)
# The subgraph of positive edges
G_pos = MultiDiGraph()
G_pos.add_edges_from([e for e in self.G.edges(data=True) if e[2]['label'] > 0])
self.G_pos = G_pos
self.subgroup_gens = tuple(sorted(self.get_subgroup()))
def scale_free_graph(n, alpha=0.41, beta=0.54, delta_in=0.2, delta_out=0):
def _choose_node(G, distribution, delta):
cumsum = 0.0
psum = float(sum(
distribution.values())) + float(delta) * len(distribution)
r = random.random()
for i in range(0, len(distribution)):
cumsum += (distribution[i] + delta) / psum
if r < cumsum:
break
return i
G = MultiDiGraph()
G.add_edges_from([(0, 1), (1, 2), (2, 0)])
gamma = 1 - alpha - beta
while len(G) < n:
r = random.random()
if r < alpha:
v = len(G)
w = _choose_node(G, G.in_degree(), delta_in)
elif r < alpha + beta:
v = _choose_node(G, G.out_degree(), delta_out)
w = _choose_node(G, G.in_degree(), delta_in)
else:
v = _choose_node(G, G.out_degree(), delta_out)
w = len(G)
G.add_edge(v, w)
return G
def add_ref_edges(g: nx.MultiDiGraph, node):
"""Add edges with attr `data` for data references of the given node"""
if isinstance(node, clang.graph.StmtInfo):
for ref_rel in node.ref_relations:
g.add_node(ref_rel, attr=(filter_type(ref_rel.type)))
g.add_edge(node, ref_rel, attr="data")
def replace_pattern(self, graph: nx.MultiDiGraph, match: dict):
input = match['input']
lstm = match['lstm']
params = match['params'].value.copy()
hidden_state = match['hidden_state']
cell_state = match['cell_state']
hidden_state_edge_attrs = deepcopy(graph.get_edge_data(hidden_state.id, lstm.id)[0])
cell_state_edge_attrs = deepcopy(graph.get_edge_data(cell_state.id, lstm.id)[0])
graph.remove_edge(match['params'].id, lstm.id)
graph.remove_edge(match['hidden_state'].id, lstm.id)
graph.remove_edge(match['cell_state'].id, lstm.id)
self.repack_weights(graph, input, lstm, params)
reshape = Reshape(graph, dict(dim=[lstm.in_node(0).shape[0], lstm.hidden_size]))
if len(lstm.in_nodes()) > 2:
hidden_state_edge_attrs['in'] = 3
new_init_h = reshape.create_node_with_data([hidden_state], attrs=dict(name=lstm.name + '/HiddenStateResize'))
graph.add_edge(new_init_h.id, lstm.id, **hidden_state_edge_attrs)
if len(lstm.in_nodes()) > 3:
cell_state_edge_attrs['in'] = 4
new_init_c = reshape.create_node_with_data([cell_state], attrs=dict(name=lstm.name + '/CellStateResize'))
graph.add_edge(new_init_c.id, lstm.id, **cell_state_edge_attrs)
def _add_cross_feed_edges(G: nx.MultiDiGraph, sid_lookup: Dict[str, str],
cross_feed_edges: pd.DataFrame,
walk_speed_kmph: float) -> nx.MultiDiGraph:
# Add the cross feed edge connectors to the graph to
# capture transfer points
for i, row in cross_feed_edges.iterrows():
# Extract the row column values as discrete variables
sid = row.stop_id
to = row.to_node
d = row.distance
# Use the lookup table to get converted stop id name
full_sid = sid_lookup[sid]
# Convert to km/hour
kmph = (d / 1000) / walk_speed_kmph
# Convert to seconds
in_seconds = kmph * 60 * 60
# And then add it to the graph
G.add_edge(full_sid, to, length=in_seconds, mode='walk')
# also add reverse edge
G.add_edge(to, full_sid, length=in_seconds, mode='walk')
def _add_entry_point_for_graph(graph: nx.MultiDiGraph, tag=True):
entry_points = []
name = graph.graph["name"]
for node_id in graph.nodes:
if graph.in_degree(node_id) == 0: # 入口节点
entry_points.append(node_id)
if tag is True:
graph.add_node("{}@entry".format(name),
label="ENTRY",
type="ENTRY",
expression="ENTRY")
else:
graph.add_node("entry",
label="ENTRY",
type="ENTRY",
expression="ENTRY")
for entry_point in entry_points:
if tag is True:
graph.add_edge("{}@entry".format(name), entry_point)
else:
graph.add_edge("entry", entry_point)
return graph
def scale_free_graph(n, alpha=0.41,beta=0.54,delta_in=0.2,delta_out=0):
def _choose_node(G,distribution,delta):
cumsum = 0.0
psum = float(sum(distribution.values()))+float(delta)*len(distribution)
r = random.random()
for i in range(0, len(distribution)):
cumsum += (distribution[i]+delta)/psum
if r < cumsum:
break
return i
G = MultiDiGraph()
G.add_edges_from([(0,1),(1,2),(2,0)])
gamma = 1 - alpha - beta
while len(G)<n:
r = random.random()
if r < alpha:
v = len(G)
w = _choose_node(G, G.in_degree(),delta_in)
elif r < alpha+beta:
v = _choose_node(G, G.out_degree(),delta_out)
w = _choose_node(G, G.in_degree(),delta_in)
else:
v = _choose_node(G, G.out_degree(),delta_out)
w = len(G)
G.add_edge(v,w)
return G
def MaybeAddSingleExitBlock(self, g: nx.MultiDiGraph) -> None:
"""Add a magic exit block to unite the exit statements of a CFG.
Args:
g: The graph to add the exit block to.
"""
exit_blocks = list(nx_utils.ExitBlockIterator(g))
if not exit_blocks:
raise ValueError("No exit blocks found in graph!")
if (
self.only_add_entry_and_exit_blocks_if_required and len(exit_blocks) == 1
):
exit_block = exit_blocks[0][0]
else:
exit_block = f"{g.name}_exit"
g.add_node(
exit_block, name=exit_block, type="magic", x=self.dictionary["!MAGIC"]
)
# Connect exit blocks.
for node, data in exit_blocks:
g.add_edge(node, exit_block, flow="control")
# Add a dataflow edge out, if there is one.
for src, dst, data in nx_utils.DataFlowEdgeIterator(g):
if dst == node:
g.add_edge(node, exit_block, flow="data")
break
g.exit_block = exit_block
def MaybeAddDataFlowElements(
self, g: nx.MultiDiGraph, tag_hook: typing.Optional[llvm_util.TagHook]
) -> None:
if self.dataflow == "none":
return
prefix = lambda s: f"{g.name}_{s}"
unprefix = lambda s: s[len(f"{g.name}_") :]
# Collect the edges to add so that we don't modify the graph while
# iterating.
edges_to_add: typing.List[typing.Tuple[str, str, str, int]] = []
for statement, data in nx_utils.StatementNodeIterator(g):
# TODO(github.com/ChrisCummins/ProGraML/issues/9): Separate !IDENTIFIER
# and !IMMEDIATE uses.
def_, uses = GetLlvmStatementDefAndUses(
data["text"], store_destination_is_def=self.store_destination_is_def
)
if def_: # Data flow out edge.
def_name = f"{prefix(def_)}_operand"
edges_to_add.append(
(statement, def_name, def_name, 0, def_, data, "def")
)
for position, identifier in enumerate(uses): # Data flow in edge.
identifier_name = f"{prefix(identifier)}_operand"
edges_to_add.append(
(
identifier_name,
statement,
identifier_name,
position,
identifier,
data,
"use",
)
)
for (
src,
dst,
identifier,
position,
name,
original_node,
dtype,
) in edges_to_add:
g.add_edge(src, dst, flow="data", position=position)
node = g.nodes[identifier]
# TODO(github.com/ChrisCummins/ProGraML/issues/9): Separate !IDENTIFIER
# and !IMMEDIATE nodes.
node["type"] = "identifier"
node["name"] = name
node["text"] = name
node["x"] = self.dictionary["!IDENTIFIER"]
if tag_hook is not None:
other_attrs = tag_hook.OnIdentifier(original_node, node, dtype) or {}
for attrname, attrval in other_attrs.items():
node[attrname] = attrval
def get_connection_multigraph(connections):
G = MultiDiGraph()
for c in connections:
dp1 = c.dp1
dp2 = c.dp2
G.add_edge(dp1, dp2, s1=c.s1)
return G
def get_connection_multigraph_weighted(name2dp, connections):
G = MultiDiGraph()
for c in connections:
dp1 = c.dp1
dp2 = c.dp2
if not G.has_edge(dp1, dp2):
already = []
G.add_edge(dp1, dp2)
else:
already = G.edge[dp1][dp2]['spaces']
R = name2dp[c.dp1].get_rtype(c.s1)
already.append(R)
G.edge[dp1][dp2]['spaces'] = already
# cycles = list(simple_cycles(G))
# for cycle in cycles:
# cycle = list(cycle)
# cycle = cycle + [cycle[0]]
#
# for i in range(len(cycle) - 1):
# # XXX
# _val = G.edge[cycle[i]][cycle[i + 1]]['spaces']
# # print('%s -> %s -> %s' % (cycle[i], val, cycle[i + 1]))
return G
def _add_nodes_and_edges(G: nx.MultiDiGraph,
name: str,
stops_df: pd.DataFrame,
summary_edge_costs: pd.DataFrame,
bidirectional: bool = False) -> Dict[str, str]:
# As we convert stop ids to actual nodes, let's keep track of those names
# here so that we can reference them when we add connector edges across
# the various feeds loaded into the graph
sid_lookup = {}
for i, row in stops_df.iterrows():
sid = str(row.stop_id)
full_sid = nameify_stop_id(name, sid)
# Add to the lookup crosswalk dictionary
sid_lookup[sid] = full_sid
G.add_node(full_sid,
boarding_cost=row.avg_cost,
y=row.stop_lat,
x=row.stop_lon)
for i, row in summary_edge_costs.iterrows():
sid_fr = nameify_stop_id(name, row.from_stop_id)
sid_to = nameify_stop_id(name, row.to_stop_id)
G.add_edge(sid_fr, sid_to, length=row.edge_cost, mode='transit')
# If want to add both directions in this step, we can
# by reversing the to/from node order on edge
if bidirectional:
G.add_edge(sid_to, sid_fr, length=row.edge_cost, mode='transit')
return sid_lookup
def EdmondsKarp(layered_network: LayeredGraph,
network: Graph,
s: int,
t: int,
capacity_label: str = 'c') -> int:
# unite_sinks(network=layered_network, t=t)
# united_sink = layered_network.max_node * layered_network.layers
# cut_dead_ends(layered_network, s=s, t=t)
source_net = MultiDiGraph()
for src, dst, key, data in network.edges(data=True, keys=True):
new_key = data[ArcAttrs.arc_type]
source_net.add_edge(src, dst, key=new_key, **data)
source_net[src][dst][new_key][
ArcAttrs.res_capacity] = data[capacity_label]
flow_network = build_flow_network(
layered_network) # create auxiliary network with reversed arcs
while True:
path = search_path(flow_network=flow_network,
source_network=source_net,
s=s,
t=t)
if path:
augment(path, flow_network=flow_network, source_network=source_net)
else:
return gather_in_flows(node=t, flow_network=flow_network)
def get_connection_multigraph(connections):
G = MultiDiGraph()
for c in connections:
dp1 = c.dp1
dp2 = c.dp2
G.add_edge(dp1, dp2, s1=c.s1)
return G
def get_connection_multigraph_weighted(name2dp, connections):
G = MultiDiGraph()
for c in connections:
dp1 = c.dp1
dp2 = c.dp2
if not G.has_edge(dp1, dp2):
already = []
G.add_edge(dp1, dp2)
else:
already = G.edge[dp1][dp2]['spaces']
R = name2dp[c.dp1].get_rtype(c.s1)
already.append(R)
G.edge[dp1][dp2]['spaces'] = already
# cycles = list(simple_cycles(G))
# for cycle in cycles:
# cycle = list(cycle)
# cycle = cycle + [cycle[0]]
#
# for i in range(len(cycle) - 1):
# # XXX
# _val = G.edge[cycle[i]][cycle[i + 1]]['spaces']
# # print('%s -> %s -> %s' % (cycle[i], val, cycle[i + 1]))
return G
def axiom(G: networkx.MultiDiGraph):
axioms = ("(i)nitial", "(w)eakening", "(s)ubstitute")
while command := get_required(f"{'|'.join(axioms)}").lower():
print()
if command == "i":
wffs = get_formulas()
G.add_node(Sequent(wffs, wffs))
return
elif command == "w":
sequent = select(G)
if sequent:
sides = {"(l)eft", "(r)ight"}
while side := get_required(f"{'|'.join(sides)}") in sides:
if side == "l":
print("<<weakening left side>>")
wffs = get_formulas()
weakened = sequent
for wff in wffs:
weakened = InferenceRules.l_weakening(
weakened, wff)
G.add_node(weakened)
G.add_edge(sequent, weakened, label="(l_weakening)")
return
elif side == "r":
print("<<weakening right side>>")
wffs = get_formulas()
weakened = sequent
for wff in wffs:
weakened = InferenceRules.r_weakening(
weakened, wff)
G.add_node(weakened)
G.add_edge(sequent, weakened, label="(r_weakening)")
return
def pad_op_transform(graph: nx.MultiDiGraph, match: dict):
op = match['op']
pad_op = match['pad_op']
input_data = pad_op.in_node(0)
pads = pad_op.in_node(1).value if len(
pad_op.in_nodes()) == 2 else pad_op.pads
if pad_op.mode != 'constant':
log.info(
'The pad node "{}" with pad mode "{}" cannot be fused.'.format(
pad_op.soft_get('name'), pad_op.mode))
return
if pad_op.mode == 'constant' and pad_op.fill_value != 0.0:
log.info('The pad node "{}" with non-zero fill value cannot be fused.'.
format(pad_op.soft_get('name')))
return
input_tensor_dims = len(match['pad_output'].shape)
if np.any(pads[get_features_dim(op.graph.graph['layout'],input_tensor_dims)] != 0) or \
np.any(pads[get_batch_dim(op.graph.graph['layout'], input_tensor_dims)] != 0):
log.info(
'The pad node "{}" with padding over feature/batch dimension cannot be fused.'
.format(pad_op.soft_get('name')))
return
op.pad += pads
op.pad_spatial_shape = op.pad[op.spatial_dims]
op['auto_pad'] = None
assert (graph[match['pad_output'].node][match['op'].node][0]['in'] == 0)
edge_attrs = graph.get_edge_data(match['pad_output'].id, match['op'].id)[0]
graph.remove_edge(match['pad_output'].id, match['op'].id)
graph.add_edge(input_data.id, match['op'].id, **{'in': 0, **edge_attrs})
def add_all_edges(g1: nx.MultiDiGraph, g2: nx.MultiDiGraph, preserve: bool = True) -> int:
"""
Add all edges from source graph (``g2``) to target graph (``g1``).
Parameters
----------
g1: networkx.MultiDiGraph
Target graph
g2: networkx.MultiDiGraph
Source graph
preserve: bool
Whether or not to preserve conflicting properties
Returns
-------
int
Number of edges merged during this operation
"""
logging.info(f"Adding {g2.number_of_edges()} edges from {g2} to {g1}")
merge_count = 0
for u, v, key, data in g2.edges(keys=True, data=True):
if g1.has_edge(u, v, key):
merge_edge(g1, u, v, key, data, preserve)
merge_count += 1
else:
g1.add_edge(u, v, key, **data)
return merge_count
def get_graphs():
g1 = MultiDiGraph()
g1.name = 'Graph 1'
g1.add_node('A', id='A', name='Node A', category=['biolink:NamedThing'])
g1.add_node('B', id='B', name='Node B', category=['biolink:NamedThing'])
g1.add_node('C', id='C', name='Node C', category=['biolink:NamedThing'])
g1.add_edge('C', 'B', key='C-biolink:subclass_of-B', edge_label='biolink:sub_class_of', relation='rdfs:subClassOf')
g1.add_edge('B', 'A', key='B-biolink:subclass_of-A', edge_label='biolink:sub_class_of', relation='rdfs:subClassOf', provided_by='Graph 1')
g2 = MultiDiGraph()
g2.name = 'Graph 2'
g2.add_node('A', id='A', name='Node A', description='Node A in Graph 2', category=['biolink:NamedThing'])
g2.add_node('B', id='B', name='Node B', description='Node B in Graph 2', category=['biolink:NamedThing'])
g2.add_node('C', id='C', name='Node C', description='Node C in Graph 2', category=['biolink:NamedThing'])
g2.add_node('D', id='D', name='Node D', description='Node D in Graph 2', category=['biolink:NamedThing'])
g2.add_node('E', id='E', name='Node E', description='Node E in Graph 2', category=['biolink:NamedThing'])
g2.add_edge('B', 'A', key='B-biolink:related_to-A', edge_label='biolink:related_to', relation='biolink:related_to')
g2.add_edge('D', 'A', key='D-biolink:related_to-A', edge_label='biolink:related_to', relation='biolink:related_to')
g2.add_edge('E', 'A', key='E-biolink:related_to-A', edge_label='biolink:related_to', relation='biolink:related_to')
g3 = MultiDiGraph()
g3.name = 'Graph 3'
g3.add_edge('F', 'E', key='F-biolink:same_as-E', edge_label='biolink:same_as', relation='OWL:same_as')
return [g1, g2, g3]
def add_path_step(line_code: int, current_node, from_node_label: str,
step_count: int, line_graph: nx.DiGraph,
graph: nx.MultiDiGraph, taboo_list: Set[int]):
if step_count == 5:
return
for neighbour in nx.neighbors(line_graph, current_node):
if neighbour in taboo_list:
continue
edge = line_graph.get_edge_data(current_node, neighbour)
cluster_number = edge['cluster']
to_node_label = str(step_count + 1) + '_' + str(cluster_number)
existing_edges = graph.get_edge_data(from_node_label,
to_node_label,
default=None)
if not edge_exists(existing_edges, line_code, current_node, neighbour):
graph.add_edge(from_node_label,
to_node_label,
line_code=line_code,
from_node=current_node,
to_node=neighbour,
cluster=cluster_number)
taboo_list.add(neighbour)
add_path_step(line_code, neighbour, to_node_label, step_count + 1,
line_graph, graph, taboo_list)
def relationship_edges(schema_graph_nx: nx.MultiDiGraph, class_add_mod: dict,
**kwargs) -> nx.MultiDiGraph:
"""
Notes:
=====
# pass the below dictionary as the third argument (kwargs) to relationship_edges().
# "in" indicates that the relationship has an in-edges behaviour.
# "out" indicates that the relationship has an out-edges behaviour.
rel_dict = {
"rdfs:subClassOf": {
"parentOf": "in"
},
"schema:domainIncludes": {
"domainValue": "in"
},
"sms:requiresDependency": {
"requiresDependency": "out"
},
"sms:requiresComponent": {
"requiresComponent": "out"
},
"schema:rangeIncludes": {
"rangeValue": "out"
}
}
"""
for rel, rel_lab_node_type in kwargs.items():
for rel_label, node_type in rel_lab_node_type.items():
if rel in class_add_mod:
parents = class_add_mod[rel]
if type(parents) == list:
for _parent in parents:
if node_type == "in":
n1 = extract_name_from_uri_or_curie(_parent["@id"])
n2 = class_add_mod["rdfs:label"]
if node_type == "out":
n1 = class_add_mod["rdfs:label"]
n2 = extract_name_from_uri_or_curie(_parent["@id"])
# do not allow self-loops
if n1 != n2:
schema_graph_nx.add_edge(n1, n2, key=rel_label)
elif type(parents) == dict:
if node_type == "in":
n1 = extract_name_from_uri_or_curie(parents["@id"])
n2 = class_add_mod["rdfs:label"]
if node_type == "out":
n1 = class_add_mod["rdfs:label"]
n2 = extract_name_from_uri_or_curie(parents["@id"])
# do not allow self-loops
if n1 != n2:
schema_graph_nx.add_edge(n1, n2, key=rel_label)
return schema_graph_nx
def convert_grandalf_graph_to_networkx_graph(G):
from networkx import MultiDiGraph
nxg = MultiDiGraph()
for v in G.V():
nxg.add_node(v.data)
for e in G.E():
nxg.add_edge(e.v[0].data, e.v[1].data)
return nxg
def add_edge(mygraph: MultiDiGraph, edge: str, origincolor: str,
colormap: dict) -> MultiDiGraph:
edge = reduce(str.removesuffix, [" bags", " bag"], edge)
origincolornum = colormap.get(origincolor)
num, tcolor = edge.split(" ", 1)
for _ in range(int(num)):
mygraph.add_edge(origincolornum, colormap.get(tcolor))
return mygraph
def convert_grandalf_graph_to_networkx_graph(G):
from networkx import MultiDiGraph
nxg = MultiDiGraph()
for v in G.V():
nxg.add_node(v.data)
for e in G.E():
nxg.add_edge(e.v[0].data, e.v[1].data)
return nxg
def get_meausurements_graph(po: PlacedObject) -> MultiDiGraph:
G = MultiDiGraph()
for name, sr in iterate_measurements_relations((), po):
a = sr.a
b = sr.b
attr_dict = dict(sr=sr)
G.add_edge(a, b, attr_dict=attr_dict)
return G
def simplify_twoways(n, g: nx.MultiDiGraph, check_lanes: bool):
edge_u1 = list(g.out_edges(n, data=True))[0][:2]
edge_u2 = list(g.out_edges(n, data=True))[1][:2]
temp1 = reversed(edge_u1)
edge_u1 = tuple(temp1)
temp2 = reversed(edge_u2)
edge_u2 = tuple(temp2)
new_id_out = list(g.out_edges(n, data=True))[0][2]['id']
new_id_in = list(g.in_edges(n, data=True))[0][2]['id']
coords_out = list(
filter(
None,
list(g.in_edges(n, data=True))[1][2]['others'] + [[n[1], n[0]]] +
list(g.out_edges(n, data=True))[0][2]['others']))
coords_in = list(reversed(coords_out))
edge_v1 = list(g.in_edges(n, data=True))[0][:2]
edge_v2 = list(g.in_edges(n, data=True))[1][:2]
edges_u = (edge_u1, edge_u2)
edges_v = (edge_v1, edge_v2)
lanes_u1 = list(g.out_edges(n, data=True))[0][2]['lanes']
lanes_u2 = list(g.out_edges(n, data=True))[1][2]['lanes']
lanes_v1 = list(g.in_edges(n, data=True))[0][2]['lanes']
lanes_v2 = list(g.in_edges(n, data=True))[1][2]['lanes']
if edges_u == edges_v:
# remove edges and node
is_deleted = [False, False]
is_loop = False # finding oneway loop (from_id == to_id)
for i in edges_u:
if check_oneway_loop(i):
is_loop = True
for i in edges_v:
if check_oneway_loop(i):
is_loop = True
if is_loop:
return
if lanes_u1 == lanes_v2 or lanes_u1 is None or lanes_v2 is None or check_lanes: # merge only edges with same number of lanes
g.remove_edge(edge_u1[1], edge_u1[0])
g.remove_edge(edge_u2[0], edge_u2[1])
g.add_edge(edge_v2[0],
edge_v1[0],
id=new_id_out,
others=coords_out,
lanes=lanes_u1)
is_deleted[0] = True
if lanes_u2 == lanes_v1 or lanes_u2 is None or lanes_v1 is None or check_lanes: # merge only edges with same number of lanes
if edge_u1[1] != edge_u1[0] or edge_u2[0] != edge_u2[
1]: # check loops
g.remove_edge(edge_u1[0], edge_u1[1])
g.remove_edge(edge_u2[1], edge_u2[0])
g.add_edge(edge_v1[0],
edge_v2[0],
id=new_id_in,
others=coords_in,
lanes=lanes_v1)
is_deleted[1] = True
if is_deleted[0] and is_deleted[1] or check_lanes:
g.remove_node(n)
def read_cref_table(
inmap,
strip_paths=["/usr", "lib/STM32Cube_FW_F4_V1.16.0"],
simplify_paths=["libgcc.a", "libc_nano.a", "libnosys.a"],
hide_aeabi_symbols=True
):
# Helper function to simplify filenames in order to increase graph clarity
def process_filename(last_module):
# Strip certain file paths
for key in strip_paths:
if last_module.find(key) > -1:
s = last_module.split("/")
print(last_module + " - " + s[len(s)-1])
last_module = s[len(s)-1]
# Remove symbol names (in round brackets) from certain libraries
for key in simplify_paths:
if last_module.find(key) > -1:
s = last_module.split("(")
print(last_module + " - " + s[0])
last_module = s[0]
return last_module
# Create new graph
modules = MultiDiGraph()
# Parse all table lines
redundant_associations = []
while True:
l = inmap.readline()
words = l.split()
if len(words) == 2:
# New symbol A, which is defined in file B
last_symbol = words[0]
last_module = process_filename(words[1])
elif len(words) == 1:
# One more file uses the previous symbol
filename = process_filename(words[0])
# References of a file to itself are not particularly interesting
if filename != last_module:
if last_symbol.find("__aeabi") > -1 and hide_aeabi_symbols:
t = (filename, last_module)
if not (t in redundant_associations):
redundant_associations.append(t)
modules.add_edge(filename, last_module);
else:
modules.add_edge(filename, last_module, label=last_symbol);
elif len(l) == 0:
# End of table
break
# Return the generated graph
return modules
def find_and_replace_pattern(self, graph: nx.MultiDiGraph):
data_nodes = [
Node(graph, node) for node in graph.node
if Node(graph, node).kind == 'data'
]
for node in data_nodes:
# Get all requested shapes for current node
# This mapping will contain pairs like {shape:[list of consumers nodes]}
mapping = {}
for consumer in node.out_nodes():
edge_attrs = graph.get_edge_data(node.id, consumer.id)[0]
if 'new_shape' in edge_attrs:
if np.array_equal(edge_attrs['new_shape'], node.shape):
continue
new_shape = tuple([x for x in edge_attrs['new_shape']])
if not new_shape in mapping:
mapping.update({new_shape: [consumer]})
else:
mapping[new_shape].append(consumer)
if node.has_valid('value'):
# Check that requested shape are the same
# In case if they are different, we duplicate them
for shape_key in mapping.keys():
shape = list(shape_key)
new_value = np.reshape(node.value, shape)
node_copy = Op.create_input_data_node(
graph, node.id + '/copy', value=np.array(new_value))
for consumer in mapping[shape_key]:
edge_attrs = graph.get_edge_data(node.id,
consumer.id)[0]
del edge_attrs['new_shape']
# Remove edge from previous data node and connect new data node with its consumer
graph.remove_edge(node.id, consumer.id)
graph.add_edge(node_copy.id, consumer.id, **edge_attrs)
else:
# Insert Reshape layer between data node and consumer
for shape_key in mapping.keys():
shape = list(shape_key)
reshape = Reshape(graph,
attrs={
'dim': shape,
'name': 'EltwiseReshapeNormalization'
})
reshape_data = reshape.create_node_with_data(inputs=[node])
# Iterate over consumers and reconnect them to Reshape layer output
for consumer in mapping[shape_key]:
edge_attrs = graph.get_edge_data(node.id,
consumer.id)[0]
del edge_attrs['new_shape']
# Reconnect edge from original data node to Reshape output datanode
graph.remove_edge(node.id, consumer.id)
graph.add_edge(reshape_data.id, consumer.id,
**edge_attrs)
def get_graphs():
g1 = MultiDiGraph()
g1.name = 'Graph 1'
g1.add_node('HGNC:12345', id='HGNC:12345', name='Test Gene', category=['biolink:Gene'])
g1.add_node('B', id='B', name='Node B', category=['biolink:NamedThing'])
g1.add_node('C', id='C', name='Node C', category=['biolink:NamedThing'])
g1.add_edge('C', 'B', key='C-biolink:subclass_of-B', edge_label='biolink:sub_class_of', relation='rdfs:subClassOf')
g1.add_edge('B', 'A', key='B-biolink:subclass_of-A', edge_label='biolink:sub_class_of', relation='rdfs:subClassOf', provided_by='Graph 1')
return [g1]
def FullConnection(group1: Group, group2: Group, graph: nx.MultiDiGraph):
for node in group1.get_nodes():
graph.add_node(node)
for node in group2.get_nodes():
graph.add_node(node)
for i in group1.get_nodes():
for j in group2.get_nodes():
graph.add_edge(i, j)
def construct_multi_di_graph(edges: List[Tuple[str, str, Any]]) -> MultiDiGraph:
"""Constructs a multi directed graph from a list of edges.
Arguments:
edges: A list of tuples with entries: start, end and identifier.
"""
g = MultiDiGraph()
for start, end, key in edges:
g.add_edge(start, end, key=key)
return g
def inserir_nodo_grafo(grafo: MultiDiGraph, chave: int, nodo: dict,
nodo_novo: dict):
grafo.add_node(chave,\
posicao_labirinto=nodo_novo["posicao_labirinto"],\
chave=chave,\
acao=nodo_novo["acao"],\
custo_caminho=nodo_novo["custo_caminho"])
if nodo is not None:
grafo.add_edge(nodo["chave"], chave)
def add_cfg_edges(g: nx.MultiDiGraph, node):
"""Add edges with attr `cfg` or `in` for control flow for the given node"""
if isinstance(node, clang.graph.FunctionInfo):
for cfg_b in node.cfgBlocks:
g.add_node(cfg_b, attr="cfg")
for succ in cfg_b.successors:
g.add_edge(cfg_b, succ, attr="cfg")
g.add_node(succ, attr="cfg")
for stmt in cfg_b.statements:
g.add_edge(stmt, cfg_b, attr="in")
g.add_node(stmt, attr=(stmt.name))
def add_data_from_single_image_graph_to_cluster_graph(line_graph: nx.DiGraph,
graph: nx.MultiDiGraph):
for node in line_graph.adj:
for neighbour in nx.neighbors(line_graph, node):
edge = line_graph.get_edge_data(node, neighbour)
for neighbour2 in nx.neighbors(line_graph, neighbour):
edge2 = line_graph.get_edge_data(neighbour, neighbour2)
graph.add_edge(edge['cluster'],
edge2['cluster'],
key=None,
nodes_from=str(node) + "_" + str(neighbour),
nodes_to=str(neighbour) + "_" + str(neighbour2))
def AddInterproceduralCallEdges(
graph: nx.MultiDiGraph,
call_multigraph: nx.MultiDiGraph,
function_entry_exit_nodes: typing.Dict[str, typing.Tuple[int, int]],
) -> None:
"""Add call edges between procedures to match the call graph.
Args:
graph: The disconnected per-function graphs.
call_multigraph: A call graph with parallel edges to indicate multiple calls
from the same function.
function_entry_exit_nodes: A mapping from function name to a tuple of entry
and exit statements.
"""
# Drop the parallel edges by converting the call graph back to a regular
# directed graph. Iterating over the edges in this graph then provides the
# functions that need connecting, while the multigraph tells us how many
# connections to expect.
call_graph = nx.DiGraph(call_multigraph)
for src, dst in call_graph.edges:
# Ignore connections to the root node, we have already processed them.
if src == "external node":
continue
call_sites = llvm_statements.FindCallSites(graph, src, dst)
if not call_sites:
continue
# Check that the number of call sounds we found matches the expected number
# from the call graph.
# multigraph_call_count = call_multigraph.number_of_edges(src, dst)
# if len(call_sites) != multigraph_call_count:
# raise ValueError("Call graph contains "
# f"{humanize.Plural(multigraph_call_count, 'call')} from "
# f"function `{src}` to `{dst}`, but found "
# f"{len(call_sites)} call sites in the graph")
for call_site in call_sites:
if dst not in function_entry_exit_nodes:
continue
# Lookup the nodes to connect.
call_entry, call_exit = function_entry_exit_nodes[dst]
# Connect the nodes.
graph.add_edge(call_site,
call_entry,
flow=programl_pb2.Edge.CALL,
position=0)
graph.add_edge(call_exit,
call_site,
flow=programl_pb2.Edge.CALL,
position=0)
def read_cref(inmap):
modules = MultiDiGraph()
while True:
l = inmap.readline()
words = l.split()
if len(words) == 2:
last_symbol = words[0]
last_module = words[1]
elif len(words) == 1:
modules.add_edge(words[0], last_module, label=last_symbol);
elif len(l) == 0:
break
return modules
def InjectConnection(group1: Group, group2: Group, graph: nx.MultiDiGraph):
neuron_group_1 = group1.get_nodes()
neuron_group_2 = group2.get_nodes()
if len(neuron_group_1) != len(neuron_group_2):
raise Exception('Size of group do not match for inject connection')
for node in neuron_group_1:
graph.add_node(node)
for node in neuron_group_2:
graph.add_node(node)
for i in range(len(neuron_group_1)):
graph.add_edge(neuron_group_1[i], neuron_group_2[i])
def selector(request):
request.session['viewer'] = request.path_info
if request.method == 'POST':
form = Neo4jQueryForm(request.POST)
if form.is_valid():
host = request.session.get('host', None)
if host:
gdb = GraphDatabase(host)
node = gdb.node[form.cleaned_data['node']]
depth = form.cleaned_data['depth']
new_nodes = []
graph = MultiDiGraph()
node_id = str(node.id)
graph.add_node(node_id, **node.properties)
new_nodes.append(node_id)
for i in range(depth):
added_nodes = []
for node_id in new_nodes:
node = gdb.node[node_id]
for relation in node.relationships.all():
start = relation.start
end = relation.end
if start not in new_nodes:
start_id = str(start.id)
graph.add_node(start_id, **start.properties)
added_nodes.append(start_id)
if end not in new_nodes:
end_id = str(end.id)
graph.add_node(end_id, **end.properties)
added_nodes.append(end_id)
graph.add_edge(start_id, end_id, **relation.properties)
new_nodes += added_nodes
interactor = NetworkxInteractor(graph)
request.session['interactor'] = interactor
request.session['layout'] = None
response_dictionary = set_response_dictionary(request)
else:
form = Neo4jConnectionForm()
return render_to_response('neo4j/index.html', {
'form': form,
})
return render_to_response('neo4j/explorer.html',
response_dictionary)
else:
interactor = request.session.get('interactor')
return render_to_response('neo4j/explorer.html',
set_response_dictionary(request))
def scale_free_graph(n, G=None,
alpha=0.41,
beta=0.54,
gamma=0.05,
delta_in=0.2,
delta_out=0,
seed=None):
"""Return a scale free directed graph
Parameters
----------
n : integer
Number of nodes in graph
G : NetworkX graph (optional)
Use as starting graph in algorithm
alpha : float
Probability for adding a new node conecgted to an existing node
chosen randomly according to the in-degree distribution.
beta : float
Probability for adding an edge between two existing nodes.
One existing node is chosen randomly according the in-degree
distribution and the other chosen randomly according to the out-degree
distribution.
gamma : float
Probability for adding a new node conecgted to an existing node
chosen randomly according to the out-degree distribution.
delta_in : float
Bias for choosing ndoes from in-degree distribution.
delta_out : float
Bias for choosing ndoes from out-degree distribution.
delta_out : float
Bias for choosing ndoes from out-degree distribution.
seed : integer (optional)
Seed for random number generator
Examples
--------
>>> G=nx.scale_free_graph(100)
Notes
-----
The sum of alpha, beta, and gamma must be 1.
Algorithm from
@article{bollobas2003dsf,
title={{Directed scale-free graphs}},
author={Bollob{\'a}s, B. and Borgs, C. and Chayes, J. and Riordan, O.},
journal={Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms},
pages={132--139},
year={2003},
publisher={Society for Industrial and Applied Mathematics Philadelphia, PA, USA}
}
"""
def _choose_node(G,distribution,delta):
cumsum=0.0
# normalization
psum=float(sum(distribution.values()))+float(delta)*len(distribution)
r=random.random()
for i in range(0,len(distribution)):
cumsum+=(distribution[i]+delta)/psum
if r < cumsum:
break
return i
if G is None:
# start with 3-cycle
G=MultiDiGraph()
G.add_edges_from([(0,1),(1,2),(2,0)])
if alpha <= 0:
raise ValueError('alpha must be >= 0.')
if beta <= 0:
raise ValueError('beta must be >= 0.')
if gamma <= 0:
raise ValueError('beta must be >= 0.')
if alpha+beta+gamma !=1.0:
raise ValueError('alpha+beta+gamma must equal 1.')
G.name="directed_scale_free_graph(%s,alpha=%s,beta=%s,gamma=%s,delta_in=%s,delta_out=%s)"%(n,alpha,beta,gamma,delta_in,delta_out)
# seed random number generated (uses None as default)
random.seed(seed)
while len(G)<n:
r = random.random()
# random choice in alpha,beta,gamma ranges
if r<alpha:
# alpha
# add new node v
v = len(G)
# choose w according to in-degree and delta_in
w = _choose_node(G, G.in_degree(with_labels=True),delta_in)
elif r < alpha+beta:
# beta
# choose v according to out-degree and delta_out
v = _choose_node(G, G.out_degree(with_labels=True),delta_out)
# choose w according to in-degree and delta_in
w = _choose_node(G, G.in_degree(with_labels=True),delta_in)
else:
# gamma
# choose v according to out-degree and delta_out
v = _choose_node(G, G.out_degree(with_labels=True),delta_out)
# add new node w
w = len(G)
G.add_edge(v,w)
return G
def add_edge(self,node1,node2,**kwargs):# inefficient but nobody cares and it's convenient
e=Edge(node1,node2,self.keycounter,kwargs)
MultiDiGraph.add_edge(self,node1,node2,object = e,key = self.keycounter)
self.InverseLookUp[kwargs["morphism"]] = e
self.keycounter+=1
return e
def parseArnetminerDataset():
"""
Parse the four area dataset, and use only barebones structures to keep everything efficient.
Skips papers that:
(1)
The final parsed network
"""
inputFile = open(os.path.join(projectRoot, 'data','DBLP-citation-Feb21.txt'))
graph = MultiDiGraph()
# Sets for authors, papers, conferences, and terms found so far
indexToPaperIdMap = {}
citationCountMap = {}
indexSet = set()
beginning = inputFile.tell()
print "Parsing nodes for graph..."
# Counts for statistics
VALID_PAPERS = 1566322 # 99.62% of total papers in DBLP dataset
papersProcessed = 0
skippedPaperIndices = set()
invalidPaperIndices = set()
# Add each paper to graph (adding missing associated terms, authors, and conferences)
for title, authors, conference, terms, citationCount, index in __papersFromFile(inputFile, skippedPaperIndices, invalidPaperIndices):
# Check that index is unique, and record it
assert index not in indexSet
indexSet.add(index)
# Create unique identifier with paper index & title
paperId = '%d----%s' % (index, title)
citationCountMap[paperId] = citationCount
indexToPaperIdMap[index] = paperId
# Add symmetric edges & nodes (if they don't already exist in the network)
for author in authors:
graph.add_edges_from([(author, paperId), (paperId, author)])
graph.add_edges_from([(conference, paperId), (paperId, conference)])
for term in terms:
graph.add_edges_from([(term, paperId), (paperId, term)])
# Output progress
papersProcessed += 1
sys.stdout.write("\r Processed %d / %d papers..." % (papersProcessed, VALID_PAPERS))
# Rewind file
inputFile.seek(beginning)
print "Parsing citations for graph..."
# Counts for statistics
papersProcessed = 0
successfulCitations = 0
omittedPaperCitations = 0
invalidPaperCitations = 0
invalidCitations = 0
# Add citations to the graph
for title, index, citations in __citationsFromFile(inputFile):
citingId = '%d----%s' % (index, title)
for citationIndex in citations:
# Add citation edge if it was found
if citationIndex in indexToPaperIdMap:
successfulCitations += 1
graph.add_edge(citingId, indexToPaperIdMap[citationIndex])
# Tally missing citation appropriately
elif citationIndex in skippedPaperIndices:
omittedPaperCitations += 1
elif citationIndex in invalidPaperIndices:
invalidPaperCitations += 1
else:
print "\nCitation '%d' not found for '%s'" % (citationIndex, title)
invalidCitations += 1
# Output progress
papersProcessed += 1
sys.stdout.write("\r Processed Citations for %d / %d papers..." % (papersProcessed, VALID_PAPERS))
# Basic statistics about cleanliness of citations
totalCitations = invalidCitations + successfulCitations
successfulCitationsPercent = 100 * float(successfulCitations) / totalCitations
omittedPaperCitationsPercent = 100 * float(omittedPaperCitations) / totalCitations
invalidPaperCitationsPercent = 100 * float(invalidPaperCitations) / totalCitations
invalidCitationsPercent = 100 * float(invalidCitations) / totalCitations
print "\n\nTotal Citations: %d" % totalCitations
print " Citations Added (Successful): %d (%2.2f%%)" % (successfulCitations, successfulCitationsPercent)
print " Citations Skipped (Skipped Paper): %d (%2.2f%%)" % (omittedPaperCitations, omittedPaperCitationsPercent)
print " Citations Skipped (Invalid Paper): %d (%2.2f%%)" % (invalidPaperCitations, invalidPaperCitationsPercent)
print " Citations Invalid (Unknown): %d (%2.2f%%)" % (invalidCitations, invalidCitationsPercent)
return graph
class Grafatality(object):
def __init__(self, filename='graph.json'):
self.filename=filename
self.graph = MultiDiGraph()
self.typed_nodes = {}
self.typed_nodes[None] = []
try:
self.load_file(filename)
except IOError as e:
print 'file "%s" does not exist, creating' % filename
def handle(self, line):
obj = ujson.loads(line)
action = obj['action']
if action == 'add_node':
self.load_node(obj)
elif action == 'add_edge':
self.load_edge(obj)
elif action == 'remove_edge':
self.load_remove_edge(obj)
def load_file(self, filename):
f = open(filename)
for line in f:
self.handle(line)
f.close()
def listify_typed_node(self, node):
if type(node) == list:
node = tuple(node)
if len(node) == 2:
node = tuple(node)
return node
def load_edge(self, obj):
data = obj.get('data', None)
key = obj.get('key', None)
src_node = obj['src_node']
dst_node = obj['dst_node']
src_node = self.listify_typed_node(src_node)
dst_node = self.listify_typed_node(dst_node)
if data:
self.graph.add_edge(src_node, dst_node, key=key, **data)
else:
self.graph.add_edge(src_node, dst_node, key=key)
def load_remove_edge(self, obj):
key = obj.get('key', None)
self.graph.remove_edge(obj['src_node'], obj['dst_node'], key=key)
def load_node(self, obj):
data = obj.get('data', None)
node = obj['node']
node_type = None
node = self.listify_typed_node(node)
if data:
self.graph.add_node(node, node_type=node_type, **data)
else:
self.graph.add_node(node, node_type=node_type)
def add_node(self, node, node_type=None, **attr):
if node_type:
if not node_type in self.typed_nodes:
self.typed_nodes[node_type] = []
node = (node, node_type)
self.typed_nodes[node_type].append(node)
else:
self.typed_nodes[None].append(node)
data = {"action": "add_node",
"node": node}
if len(attr):
data['data'] = attr
self.append_log(data)
return self.graph.add_node(node, **attr)
def nodes_of_type(self, node_type=None, full=True):
if full:
return self.typed_nodes[node_type]
else:
return self.typed_nodes[node_type][0]
def add_edge(self, src_node, dst_node, key=None, **attr):
data = {"action": "add_edge",
"src_node": src_node,
"dst_node": dst_node}
if len(attr):
data['data'] = attr
if key:
data['key'] = key
self.append_log(data)
return self.graph.add_edge(src_node, dst_node, key=key, **attr)
def remove_edge(self, src_node, dst_node, key):
data = {"action": "remove_edge",
"src_node": src_node,
"dst_node": dst_node,
"key": key}
self.append_log(data)
return self.graph.remove_edge(src_node, dst_node, key)
def append_log(self,data):
"""
This persists the data and while it may be true that
the logfile could be kept open indefinitely, for some reason
this causes dataloss when running multiprocess files.
"""
self.log = open(self.filename, 'a')
self.log.write(ujson.encode(data))
self.log.write("\n")
self.log.close()
def shutdown(self):
self.log.close()
class AbstractGame:
def __init__(self, player1, player2, initial_gamestate):
self.game_graph = MultiDiGraph()
self.player1 = player1
self.player2 = player2
self.initial_gamestate = self.canonicalize(initial_gamestate)
def canonicalize(self, gamestate):
raise NotImplementedError
def possible_moves(self, gamestate, player):
raise NotImplementedError
def other_player(self, player):
if player == self.player1:
return self.player2
elif player == self.player2:
return self.player1
else:
raise ValueError("%s is neither %s nor %s" % (player, self.player1, self.player2))
def is_winning_position(self, gamestate, player):
raise NotImplementedError
def is_losing_position(self, gamestate, player):
raise NotImplementedError
def good_moves(self, gamestate, player, lookahead_depth):
if lookahead_depth == 0:
yield from self.possible_moves(gamestate, player)
else:
lookahead_depth -= 1
sign = {self.player1: 1, self.player2: -1}
def is_game_over(gamestate):
return evaluate_gamestate(gamestate, 0) != 0
def evaluate_gamestate(gamestate, depth):
"""
Returns 1 if this gamestate favors the first player, -1 if it favors the second player,
and 0 if it is neutral.
"""
if self.is_winning_position(gamestate, self.player1):
return 1000 - depth
elif self.is_winning_position(gamestate, self.player2):
return -1000 + depth
else:
return 0
def negamax(gamestate, current_depth, current_player):
if is_game_over(gamestate) or current_depth > lookahead_depth:
return sign[current_player] * evaluate_gamestate(gamestate, current_depth)
max_score = -1000
for possible_gamestate in self.possible_moves(gamestate, current_player):
max_score = max(max_score,
-negamax(possible_gamestate, current_depth + 1, self.other_player(current_player)))
return max_score
moves_and_lookaheads = {move: -negamax(move, 1, self.other_player(player)) for move in self.possible_moves(gamestate, player)}
if len(moves_and_lookaheads) == 0:
return
best_lookahead = max(moves_and_lookaheads.values())
good_moves = {self.canonicalize(move) for move, lookahead in moves_and_lookaheads.items() if lookahead == best_lookahead}
for move in good_moves:
yield move
def play(self, lookahead=0):
new_moves = set() # A set of node, player tuples containing all new moves that can be played in this graph.
def play_new_moves():
new_new_moves = set() # The moves that will be new after current new moves have been played.
for gamestate, player in new_moves:
next_player = self.other_player(player)
for move_result in self.good_moves(gamestate, player, lookahead):
move_result = self.canonicalize(move_result)
if move_result not in self.game_graph: # Add the result to the graph if it's not there.
self.game_graph.add_node(move_result, players=set())
self.game_graph.add_edge(gamestate, move_result, key=player) # Add this move to the graph
if next_player not in self.game_graph.node[move_result]['players']:
self.game_graph.node[move_result]['players'].add(next_player)
new_new_moves.add((move_result, next_player))
new_moves.clear()
new_moves.update(new_new_moves)
new_moves.add((self.initial_gamestate, self.player1))
self.game_graph.add_node(self.initial_gamestate, players=set())
while len(new_moves) != 0:
play_new_moves()
self.game_graph