def remove_node_presence(self,node,time):
"""
Remove node and its interactions over the period
:param node: node to remove
:param time: a period, couple (start, stop) or an interval
"""
if not isinstance(time,Intervals):
time= Intervals(time)
if self._graph.has_node(node):
self._graph.nodes()[node]["t"]= self._graph.nodes()[node]["t"]-time
if self._graph.nodes()[node]["t"].duration()==0:
self._graph.remove_node(node)
if self._start in time or self._end in time or time.end()==self._end:
new_max = -math.inf
new_min = math.inf
for k,v in self.node_presence().items():
new_max = max(new_max,v.end())
new_min = min(new_min,v.start())
self._start = new_min
self._end = new_max
def cumulated_graph(self, times=None):
"""
Compute the cumulated graph.
Return a networkx graph corresponding to the cumulated graph of the given period (whole graph by default)
:param times: Intervals object or list of pairs (start, end)
:return: a networkx (weighted) graph
"""
if times == None:
times = Intervals([(self._start, self._end)])
elif not isinstance(times, Intervals):
times = Intervals(times)
to_return = nx.Graph()
for n, t in nx.get_node_attributes(self._graph, "t").items():
intersect = t.intersection(times)
to_return.add_node(n, weight=intersect.duration())
for (u, v), t in nx.get_edge_attributes(self._graph, "t").items():
intersect = t.intersection(times)
to_return.add_edge(u, v, weight=intersect.duration())
return to_return
def local_format_to_dyn_graph(self):
to_return = dn.DynGraphIG()
for n in self._dyn_graph_nodes:
intv = Intervals(self._dyn_graph_nodes[n])
to_return.add_node_presence(n,intv)
for e in self._dyn_graph_edges:
[n1,n2] = list(e)
intv = Intervals(self._dyn_graph_edges[e])
to_return._add_interaction_safe(n1,n2,intv)
return to_return
def local_format_to_dyn_graph(self):
to_return = dn.DynGraphIG()
print(self._dyn_graph_nodes)
for n in self._dyn_graph_nodes:
intv = Intervals(self._dyn_graph_nodes[n])
print(n, intv)
to_return.add_node_presence(n, intv)
print(nx.get_node_attributes(to_return._graph, "t"))
for e in self._dyn_graph_edges:
[n1, n2] = list(e)
intv = Intervals(self._dyn_graph_edges[e])
to_return._add_interaction_safe(n1, n2, intv)
print(to_return.node_presence())
return to_return
def _to_DynCommunitiesIG_fast(self):
"""
Work only in the standard represntation: all sn have duration 1, no missing snapshot
:return:
"""
dyn_com_local = {}
for t, part in self.snapshot_communities().items():
for id, nodes in part.items():
for n in nodes:
name = id
dyn_com_local.setdefault(name, {}).setdefault(n, [])
if len(dyn_com_local[name]
[n]) > 0 and dyn_com_local[name][n][-1][-1] == t:
dyn_com_local[name][n][-1] = (
dyn_com_local[name][n][-1][0], t + 1)
else:
dyn_com_local[name][n].append((t, t + 1))
to_return_com = tn.DynCommunitiesIG()
for c in dyn_com_local:
for n in dyn_com_local[c]:
dyn_com_local[c][n] = Intervals(dyn_com_local[c][n])
to_return_com._fast_set_affiliations(dyn_com_local)
return to_return_com
def cumulated_graph(self, times=None, weighted=True):
"""
Compute the cumulated graph.
Return a networkx graph corresponding to the cumulated graph of the given period (whole graph by default)
:param times: a pair (start,end)
:return: a networkx (weighted) graph
"""
if times == None:
times = (self._start, self._end)
times_interval = Intervals(times)
to_return = nx.Graph()
for n, t in nx.get_node_attributes(self._graph, "t").items():
intersect = t.intersection(times_interval)
if weighted:
to_return.add_node(n, weight=intersect.duration())
else:
to_return.add_node(n)
for (u, v), t in nx.get_edge_attributes(self._graph, "t").items():
intersect = list(
t.irange(times[0], times[1], inclusive=(True, False)))
if len(intersect) > 0:
if weighted:
to_return.add_edge(u, v, weight=len(intersect))
else:
to_return.add_edge(u, v)
return to_return
def test_inf(self):
print("--------------------")
anInt = Intervals()
anInt.add_interval((10, np.inf))
anInt.add_interval((20, np.inf))
self.assertEqual([(10, np.inf)], anInt.periods())
anInt._substract_one_period((20, np.inf))
self.assertEqual([(10, 20)], anInt.periods())
def slice(self, start, end):
"""
Keep only the selected period
:param start: time of the beginning of the slice
:param end: time of the end of the slice
"""
to_return = tn.DynGraphIG()
slice_time = Intervals((start, end))
for n, presence in self.node_presence().items():
to_return.add_node_presence(n, slice_time.intersection(presence))
for e, presence in self.interactions().items():
to_return.add_interaction(e[0], e[1],
slice_time.intersection(presence))
return to_return
def add_node_presence(self, n, time):
"""
Add presence for a node for a period
:param n: node
:param time: a period, couple (start, stop) or an interval
"""
if not isinstance(time, Intervals):
time = Intervals(time)
if not self._graph.has_node(n):
self._graph.add_node(n, t=time)
else:
self._graph.nodes[n]["t"] += time
self._start = min(self._start, time.start())
self._end = max(self._end, time.end())
def _local_formats_to_dyn_structures(self):
to_return_graph = dn.DynGraphIG()
for n in self._dyn_graph_local_nodes:
intv = Intervals(self._dyn_graph_local_nodes[n])
to_return_graph.add_node_presence(n, intv)
for e in self._dyn_graph_local_edges:
[n1, n2] = list(e)
intv = Intervals(self._dyn_graph_local_edges[e])
to_return_graph._add_interaction_safe(n1, n2, intv)
for c in self._dyn_com_local:
for n in self._dyn_com_local[c]:
self._dyn_com_local[c][n] = Intervals(
self._dyn_com_local[c][n])
to_return_com = dn.DynCommunitiesIG()
to_return_com._fast_set_affiliations(self._dyn_com_local)
return to_return_graph, to_return_com
def to_DynGraphSN(self, slices=None):
"""
Convert to a snapshot representation.
:param slices: can be one of
- None, snapshot_affiliations are created such as a new snapshot is created at every node/edge change,
- an integer, snapshot_affiliations are created using a sliding window
- a list of periods, represented as pairs (start, end), each period yielding a snapshot
:return: a dynamic graph represented as snapshot_affiliations, the weight of nodes/edges correspond to their presence time during the snapshot
"""
dgSN = tn.DynGraphSN()
if slices == None:
times = self.change_times()
slices = [(times[i], times[i + 1]) for i in range(len(times) - 1)]
if isinstance(slices, int):
duration = slices
slices = []
start = self.start
end = start + duration
while (end <= self.end):
end = start + duration
slices.append((start, end))
start = end
end = end + duration
for ts in slices:
dgSN.add_snapshot(t=ts[0], graphSN=nx.Graph())
for n, interv in self.node_presence().items():
for ts in slices:
presence = interv.intersection(Intervals([ts])).duration()
if presence > 0:
dgSN.snapshots(ts[0]).add_node(n, weight=presence)
for e, interv in self.interactions().items():
for ts in slices:
presence = interv.intersection(Intervals([ts])).duration()
if presence > 0:
dgSN.snapshots(ts[0]).add_edge(e[0], e[1], weight=presence)
return dgSN
def add_interaction(self, u, v, time):
"""
Add an interaction between nodes u and v at time time
:param u: first node
:param b: second node
:param time: pair (start,end) or Intervals
:return:
"""
if not isinstance(time, Intervals):
time = Intervals(time)
self.add_node_presence(u, time)
self.add_node_presence(v, time)
self._add_interaction_safe(u, v, time)
start = time.start()
end = time.end()
self._start = min(self._start, start)
self._end = max(self._end, end)
def slice(self, start, end):
"""
Keep only the selected period
:param start: time of the beginning of the slice (inclusive)
:param end: time of the end of the slice (exclusive)
"""
to_return = tn.DynGraphLS()
slice_time = Intervals((start, end))
for n, presence in self.node_presence().items():
duration = slice_time.intersection(presence)
if duration.duration() > 0:
to_return.add_node_presence(n, duration)
for e, presence in self.interactions_intervals().items():
to_return.add_interaction(e[0], e[1], presence.islice(start, end))
to_return.add_interaction(e[0], e[1],
slice_time.intersection(presence))
return to_return
def slice(self,start,end):
"""
Keep only the selected period
:param start: time of the beginning of the slice
:param end: time of the end of the slice
"""
to_return = tn.DynGraphIG()
slice_time = Intervals((start,end))
for n,presence in self.node_presence().items():
duration = slice_time.intersection(presence)
if duration.duration()>0:
to_return.add_node_presence(n,duration)
for e,presence in self.interactions_intervals().items():
el = list(e)
duration = slice_time.intersection(presence)
if duration.duration()>0:
to_return.add_interaction(el[0],el[1],duration)
return to_return
def to_DynCommunitiesIG(self, sn_duration, convertTimeToInteger=False):
"""
Convert to SG communities
:param sn_duration: time of a snapshot, or None for automatic: each snapshot last until start of the next
:param convertTimeToInteger: if True, communities IDs will be forgottent and replaced by consecutive integers
:return: DynamicCommunitiesIG
"""
dynComTN = tn.DynCommunitiesIG()
for i in range(len(self.snapshots)):
if convertTimeToInteger:
t = i
tNext = i + 1
else:
current_t = self.snapshots.peekitem(i)[0]
if sn_duration != None:
tNext = current_t + sn_duration
else:
if i < len(self.snapshots) - 1:
tNext = self.snapshots.peekitem(i + 1)[0]
else:
# computing the min duration to choose as duration of the last period
dates = list(self.snapshots.keys())
minDuration = min([
dates[i + 1] - dates[i]
for i in range(len(dates) - 1)
])
tNext = current_t + minDuration
for (cID, nodes) in self.snapshots.peekitem(
i)[1].items(): #for each community for this timestep
dynComTN.add_affiliation(nodes, cID,
Intervals((current_t, tNext)))
#convert also events
for (u, v, d) in self.events.edges(data=True):
if d["type"] != "continue": #if communities have different IDs
dynComTN.events.add_event(u[1], v[1], d["time"][0],
d["time"][1], d["type"])
return dynComTN
def _add_interaction_safe(self, u, v, time):
"""
Same as add_interaction but do not modify nodes presences to save time. To use only if nodes
have been added manually first
:param u:
:param v:
:param time: pair or directly an Intervals object
:return:
"""
if not self._graph.has_edge(u, v):
self._graph.add_edge(u, v, t=Intervals())
if isinstance(time, Intervals):
self._graph.add_edge(u, v, t=time)
else:
start = time[0]
end = time[1]
self._graph[u][v]["t"].add_interval((start, end))
def add_node_presence(self, n, time):
"""
Add presence for a node for a period
:param n: node
:param time: a period, couple (start, stop)
"""
if not self._graph.has_node(n):
self._graph.add_node(n, t=Intervals())
if isinstance(time, Intervals):
self._graph.node[n]["t"] = time
else:
start = time[0]
stop = time[1]
self._graph.node[n]["t"].add_interval((start, stop))
start = time[0]
end = time[1]
self.start = min(self.start, start)
self.end = max(self.end, end)
def test_union(self):
anInt = Intervals()
anInt.add_interval((5, 10))
another = Intervals()
another.add_interval((3, 105))
test1 = another.union(anInt)
test2 = anInt.union(another)
print(test1)
print(test2)
self.assertEqual(test1, test2)
self.assertEqual(test1, another)
anInt = Intervals()
anInt.add_interval((5, 10))
another = Intervals()
another.add_interval((30, 105))
test1 = another.union(anInt)
test2 = anInt.union(another)
self.assertEqual(test1, test2)
self.assertEqual(test1, Intervals([(5, 10), (30, 105)]))
def test_addingIntervals(self):
anInt = Intervals()
anInt.add_interval((2, 3))
anInt.add_interval((5, 7))
results = anInt.periods()
self.assertEqual(results, [(2, 3), (5, 7)])
def test_addingIntervalsComplex(self):
anInt = Intervals()
anInt.add_interval((2, 3))
anInt.add_interval((5, 6))
self.assertEqual(anInt.periods(), [(2, 3), (5, 6)])
anInt.add_interval((6, 10))
self.assertEqual(anInt.periods(), [(2, 3), (5, 10)])
anInt.add_interval((20, 100))
self.assertEqual(anInt.periods(), [(2, 3), (5, 10), (20, 100)])
anInt.add_interval((101, 201))
self.assertEqual(anInt.periods(), [(2, 3), (5, 10), (20, 100),
(101, 201)])
anInt.add_interval((100, 101))
self.assertEqual(anInt.periods(), [(2, 3), (5, 10), (20, 201)])
anInt.add_interval((3, 300))
self.assertEqual(anInt.periods(), [(2, 300)])
def test_addingOverlappingIntervals2(self):
anInt = Intervals()
anInt.add_interval((2, 3))
anInt.add_interval((0, 5))
results = anInt.periods()
self.assertEqual(results, [(0, 5)])
def test_intersect(self):
anInt = Intervals()
anInt.add_interval((5, 10))
anInt.add_interval((12, 20))
anInt.add_interval((50, 100))
another = Intervals()
another.add_interval((3, 105))
test1 = another.intersection(anInt)
test2 = anInt.intersection(another)
self.assertEqual(test1, test2)
self.assertEqual(test1, anInt)
another = Intervals()
another.add_interval((3, 18))
test1 = another.intersection(anInt)
self.assertEqual(test1.periods(), [(5, 10), (12, 18)])
another = Intervals()
another.add_interval((19, 55))
test1 = anInt.intersection(another)
self.assertEqual(test1.periods(), [(19, 20), (50, 55)])
def test_delete(self):
anInt = Intervals()
anInt.add_interval((10, 100))
anInt._substract_one_period((20, 30))
self.assertEqual(anInt.periods(), [(10, 20), (30, 100)])
def test_deleteComplete(self):
anInt = Intervals()
anInt.add_interval((10, 100))
anInt.add_interval((200, 300))
anInt._substract_one_period((5, 15))
self.assertEqual([(15, 100), (200, 300)], anInt.periods())
anInt._substract_one_period((20, 30))
self.assertEqual([(15, 20), (30, 100), (200, 300)], anInt.periods())
anInt._substract_one_period((0, 300))
self.assertEqual([], anInt.periods())
def test_oneInterval(self):
anInt = Intervals()
anInt.add_interval((2, 3))
results = anInt.periods()
self.assertEqual(results, [(2, 3)])
def test_delete2(self):
anInt = Intervals()
anInt.add_interval((10, 100))
anInt.add_interval((200, 300))
anInt._substract_one_period((0, 5))
anInt._substract_one_period((150, 160))
anInt._substract_one_period((350, 450))
self.assertEqual(anInt.periods(), [(10, 100), (200, 300)])