From 94b40f8045085a1573b80102bdd5f5b43b9db16c Mon Sep 17 00:00:00 2001
From: "Olivier J.N. Bertrand" <olivier.bertrand@uni-bielefeld.de>
Date: Thu, 30 Aug 2018 18:06:51 +0200
Subject: [PATCH] Simply build graph by using velocities
---
navipy/moving/agent.py | 83 +++++++++++++++++-------------------------
1 file changed, 33 insertions(+), 50 deletions(-)
diff --git a/navipy/moving/agent.py b/navipy/moving/agent.py
index f7ad52a..4672b94 100644
--- a/navipy/moving/agent.py
+++ b/navipy/moving/agent.py
@@ -439,56 +439,39 @@ the agent motion, or
nline += 1
return self.velocities.copy()
- def build_graph(self,
- ncpu=5,
- timeout=1,
- filename=None,
- blocksize=100):
- # Build a list of nodes
- results_edges = []
- posorients_queue = JoinableQueue()
- results_queue = Queue()
- if version < 2:
- graph_nodes = list(self._graph.nodes())
- else:
- graph_nodes = list(self._graph.nodes)
- for node in graph_nodes:
- posorients_queue.put(self._graph.nodes[node]['posorient'])
-
- # Start ndatabase loader
- num_agents = ncpu
- agents = [GridAgent(copy.copy(self._brain),
- posorients_queue=posorients_queue,
- results_queue=results_queue)
- for _ in range(num_agents)]
- for w in agents:
- w.mode_of_motion = self.mode_of_motion
- w.start()
-
- # Add a poison pill for each agent
- for _ in range(num_agents):
- posorients_queue.put(None)
-
- # Wait for all of the tasks to finish
- # posorients_queue.join()
- nline = 0
- prev_nline = nline
- t_start = time.time()
- nbnodes = nx.number_of_nodes(self._graph)
- for _ in range(nx.number_of_nodes(self._graph)):
- result = results_queue.get(timeout=timeout)
- results_edges.append((result[0].name,
- result[1].name))
- if (nline-prev_nline) > blocksize:
- t_elapse = time.time()-t_start
- t_peritem = t_elapse/nline
- remain = nbnodes-nline
- print('Computed {} in {}'.format(nline, t_elapse))
- print('Remain {}, done in {}'.format(remain, remain*t_peritem))
- if filename is not None:
- np.save(filename, np.array(results_edges))
- nline += 1
- # print(results_edges[-1])
+ def build_graph(self, movemode, moveparam):
+ """
+ Connect edges with a given velocity
+ """
+ if self.velocities.dropna().shape[0] == 0:
+ raise NameError('compute_velocities should be called first')
+ edges = pd.Series(data=np.nan, index=self.velocities.index)
+ # Make sure that the velocity start at the correct location
+ posorients = self._brain.posorients
+ myvelocities = self.velocities.copy()
+ myvelocities = myvelocities.swaplevel(axis=1)
+ myvelocities.x = posorients.x
+ myvelocities.y = posorients.y
+ myvelocities.z = posorients.z
+ myvelocities.alpha_0 = posorients.alpha_0
+ myvelocities.alpha_1 = posorients.alpha_1
+ myvelocities.alpha_2 = posorients.alpha_2
+ myvelocities = myvelocities.swaplevel(axis=1)
+ for ii, row in myvelocities.iterrows():
+ if np.any(np.isnan(row)):
+ continue
+ # Move according to user mode of motion
+ nposorient = navimomath.next_pos(row, movemode, moveparam)
+ # Snap to the closest point
+ nextpos_index = navimomath.closest_pos(
+ nposorient, myvelocities)
+ edges[ii] = nextpos_index.name
+ # Format for graph
+ validedges = edges.dropna()
+ results_edges = np.vstack(
+ [validedges.index,
+ validedges.values]).transpose()
+ # Add to graph
self._graph.add_edges_from(results_edges)
self.check_graph()
--
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