def to_DynGraphIG(self):
"""
Convert the graph into a DynGraph_IG.
##Can be optimized !
:return:
"""
sn_duration = self.frequency()
by_edges = dict()
by_nodes = dict()
for t, g in self.snapshots().items():
for e in g.edges():
by_edges.setdefault(frozenset(e), []).append(t)
for n in g.nodes():
by_nodes.setdefault(n, []).append(t)
by_edges = {
tuple(e): tn.Intervals.from_time_list(v, sn_duration)
for e, v in by_edges.items()
}
by_nodes = {
n: tn.Intervals.from_time_list(v, sn_duration)
for n, v in by_nodes.items()
}
return tn.DynGraphIG(start=min(self.snapshots_timesteps()),
end=max(self.snapshots_timesteps()) + sn_duration,
edges=by_edges,
nodes=by_nodes,
frequency=sn_duration)
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 test_add_nodes_ig(self):
dg = tn.DynGraphIG()
dg.add_node_presence(1,(1,2))
dg.add_node_presence(2,(1,2))
dg.add_nodes_presence_from(3,(1,7))
dg.add_nodes_presence_from([4,5],(1,2))
dg.add_nodes_presence_from([6, 7], (1,3))
dg.remove_node_presence(2,(1,2))
dg.remove_node_presence(3, (2,3))
self.assertEqual(set(dg.graph_at_time(1).nodes()),set([1,3,4,5,6,7]))
self.assertEqual(set(dg.graph_at_time(2).nodes()),set([6,7]))
self.assertEqual(set(dg.graph_at_time(3).nodes()),set([3]))
self.assertEqual(set(dg.graph_at_time(4).nodes()),set([3]))
self.assertEqual(set(dg.graph_at_time(6).nodes()),set([3]))
def to_DynGraphIG(self, sn_duration, convert_time_to_integer=False):
"""
Convert the graph into a DynGraph_IG.
By default, snapshot_affiliations last from their time ID to the time ID of the next snapshot.
Be careful, for the last snaphsot, we cannot know his duration, therefore, if sn_duration is not provided, it has a default duration equal to the min
of all durations
:param sn_duration: duration of sns, None for automatic behavior
:param convert_time_to_integer: if True, use the snapshot order in the list of SN rather than its time step
:return:
"""
toReturn = tn.DynGraphIG()
for i in range(len(self._snapshots)):
if convert_time_to_integer:
current_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 = self.snapshots_timesteps()
minDuration = min([
dates[i + 1] - dates[i]
for i in range(len(dates) - 1)
])
tNext = current_t + minDuration
if (len(self._snapshots.peekitem(i)[1].nodes())) > 0:
toReturn.add_nodes_presence_from(
self._snapshots.peekitem(i)[1].nodes(), (current_t, tNext))
if len(list(self._snapshots.peekitem(i)[1].edges())) > 0:
toReturn.add_interactions_from(
list(self._snapshots.peekitem(i)[1].edges()),
(current_t, tNext))
return toReturn
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 _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 from_pandas_interaction_list(interactions,
format,
frequency=1,
source="n1",
target="n2",
time="time"):
interactions = two_columns2unidrected_edge(interactions,
source="n1",
target="n2")
if format == tn.DynGraphSN:
all_times = set(interactions[time])
all_graphs = {}
for t in all_times:
this_t = interactions[interactions["time"] == t]
all_graphs[t] = nx.from_pandas_edgelist(this_t,
source=source,
target=target)
return tn.DynGraphSN(all_graphs, frequency=frequency)
if format == tn.DynGraphLS:
#all_edges = set(interactions["e"])
#print(len(all_edges))
edges_time = {}
for i, row in interactions.iterrows():
edges_time.setdefault(row["e"], []).append(row[time])
#for e in all_edges:
# edges_time[e]= list(interactions[interactions["e"]==e][time])
to_return = tn.DynGraphLS(edges=edges_time, frequency=frequency)
return to_return
if format == tn.DynGraphIG:
#all_edges = set(interactions["e"])
edges_time = {}
for i, row in interactions.iterrows():
edges_time.setdefault(row["e"], []).append(row[time])
for e, v in edges_time.items():
edges_time[e] = tn.Intervals.from_time_list(v, frequency)
#for e in all_edges:
# edges_time[e]= list(interactions[interactions["e"]==e][time])
# edges_time[e]=tn.Intervals.from_time_list(edges_time)
to_return = tn.DynGraphIG(edges_time)
return to_return
def read_IG(file_address: str):
"""
Read as list of periods
Read an interval graph as a list of periods, for the graph, the nodes, and the edges
See write_IG for an explanation of the format
:param file_address:
"""
aDynGraph = tn.DynGraphIG()
file = open(file_address)
for line in file:
parts = line.split("\t")
if parts[0] == "SG":
for period in parts[1:]:
times = period.split(":")
aDynGraph.start = int(times[0])
aDynGraph.end = int(times[1])
if parts[0] == "N":
nodeName = parts[1]
parts = parts[2:]
for period in parts:
times = period.split(":")
start = int(times[0])
end = int(times[1])
aDynGraph.add_node_presence(nodeName, (start, end))
if parts[0] == "E":
n1 = parts[1]
n2 = parts[2]
parts = parts[3:]
for period in parts:
times = period.split(":")
start = int(times[0])
end = int(times[1])
aDynGraph.add_interaction(n1, n2, (start, end))
return aDynGraph
def test_add_interactions_ig(self):
dg = tn.DynGraphIG()
dg.add_interaction(1,2,(4,5))
self.assertEqual(set(dg.graph_at_time(4).edges()),set([(1,2)]))
dg.add_interaction(1, 2, (6,7))
self.assertEqual(dg.edge_presence((1,2),as_intervals=True),tn.Intervals([(4,5),(6,7)]))
dg.add_interactions_from({2, 3}, (6,7,9))
self.assertEqual(list(dg.graph_at_time(6).edges()),[(1,2),(2,3)])
dg.add_interactions_from([(5, 6),(6,7)], (9,10))
self.assertEqual(list(dg.graph_at_time(9).edges()),[(5,6),(6,7)])
dg.add_interactions_from([(1, 2),(1,3)], (10,12))
self.assertEqual(list(dg.graph_at_time(10).edges()),[(1,2),(1,3)])
self.assertEqual(list(dg.graph_at_time(11).edges()),[(1,2),(1,3)])
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 plot_longitudinal(dynamic_graph=None,communities=None, sn_duration=None,to_datetime=False, nodes=None,width=800,height=600,bokeh=False,auto_show=False):
"""
A longitudinal view of nodes/snapshot_communities
Plot snapshot_affiliations such as each node corresponds to a horizontal line and time corresponds to the horizontal axis
:param dynamic_graph: DynGraphSN or DynGraphIG
:param communities: dynamic snapshot_affiliations, DynCommunitiesSN or DynCommunitiesIG
:param sn_duration: the duration of a snapshot, as int or timedelta. If none, inferred automatically as lasting until next snpashot
:param to_datetime: one of True/False/function. If True, step IDs are converted to dates using datetime.utcfromtimestamp. If a function, should take a step ID and return a datetime object.
:param nodes: If none, plot all nodes in lexicographic order. If a list of nodes, plot only those nodes, in that order
:param width: width of the figure
:param height: height of the figure
"""
if dynamic_graph==None:
if isinstance(communities,tn.DynCommunitiesSN):
dynamic_graph = tn.DynGraphSN()
else:
dynamic_graph = tn.DynGraphIG()
if to_datetime==True:
to_datetime=datetime.utcfromtimestamp
if sn_duration!=None and not isinstance(sn_duration,timedelta):
sn_duration=timedelta(seconds=sn_duration)
if isinstance(dynamic_graph,tn.DynGraphSN):
if communities == None:
communities = tn.DynCommunitiesSN()
t = list(dynamic_graph.snapshots_timesteps())
if communities != None and isinstance(communities,tn.DynCommunitiesSN):
t = t + list(communities.snapshots.keys())
t = sorted(list(set(t)))
CDS = _sn_graph2CDS(dynamic_graph, communities, to_datetime=to_datetime,ts=t)
else:
if communities == None:
communities = tn.DynCommunitiesIG()
CDS = _ig_graph2CDS(dynamic_graph, communities, to_datetime=to_datetime)
if isinstance(dynamic_graph,tn.DynGraphSN) and sn_duration!=None:
CDS.data["duration"] = [sn_duration]*len(CDS.data["time"])
if to_datetime!=False:
CDS.data["duration_display"] = [x/1000 for x in CDS.data["duration"]]
else:
CDS.data["duration_display"]=CDS.data["duration"]
#CDS.data["duration"] = [v+0.1 for v in CDS.data["duration"]]
#should work for timedelta and integers
CDS.data["time_shift"] = [CDS.data["time"][i] + CDS.data["duration"][i] / 2 for i in range(len(CDS.data["duration"]))]
if nodes==None:
nodes = sorted(list(set(CDS.data["node"])))
nodes = [str(x) for x in nodes]
#return _plot_longitudinal_bokeh(CDS,nodes,to_datetime,width,height,auto_show)
if bokeh:
return _plot_longitudinal_bokeh(CDS,nodes,to_datetime,width,height, auto_show)
else:
return _plot_longitudinal_pyplot(CDS,nodes,to_datetime,width,height)