From ec54e78b1d278733b3f9fcdc4ca5958369c0c17f Mon Sep 17 00:00:00 2001
From: "Olivier J.N. Bertrand" <olivier.bertrand@uni-bielefeld.de>
Date: Tue, 21 Aug 2018 14:13:34 +0200
Subject: [PATCH] Add output for long calculation
---
navipy/moving/agent.py | 47 +++++++++++++++++++++++++++++++++++-------
1 file changed, 39 insertions(+), 8 deletions(-)
diff --git a/navipy/moving/agent.py b/navipy/moving/agent.py
index 86c1eb1..188a7aa 100644
--- a/navipy/moving/agent.py
+++ b/navipy/moving/agent.py
@@ -29,6 +29,7 @@ from multiprocessing import Queue, JoinableQueue, Process
import inspect
import navipy.moving.maths as navimomath
from navipy.database import DataBaseLoad
+import time
version = float(nx.__version__)
@@ -379,7 +380,9 @@ the agent motion, or
def compute_velocities(self,
ncpu=5,
- timeout=1):
+ timeout=1,
+ filename=None,
+ blocksize=100):
# Create a dataframe to store the velocities
convention = self._brain.renderer.rotation_convention
tuples_posvel = posorient_columns(convention)
@@ -415,14 +418,30 @@ the agent motion, or
# Wait for all of the tasks to finish
# posorients_queue.join()
- for _ in range(nx.number_of_nodes(self._graph)):
+ nline = 0
+ prev_nline = nline
+ t_start = time.time()
+ nbnodes = nx.number_of_nodes(self._graph)
+ for _ in range(nbnodes):
res = results_queue.get(timeout=timeout)
self.velocities.loc[res.name, res.index] = res
+ 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:
+ self.velocities.to_hdf(filename, key='velocities')
+
+ nline += 1
return self.velocities.copy()
def build_graph(self,
ncpu=5,
- timeout=1):
+ timeout=1,
+ filename=None,
+ blocksize=100):
# Build a list of nodes
results_edges = []
posorients_queue = JoinableQueue()
@@ -450,11 +469,23 @@ the agent motion, or
# 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])
self._graph.add_edges_from(results_edges)
self.check_graph()
@@ -510,10 +541,10 @@ the agent motion, or
# [0] because one node of the attractor is enough
# all other node of the attractor are connected to this one
target = list(att['attractor'])[0]
- attractors[att_i]['paths'] = \
- nx.shortest_path(self.graph, target=target)
- attractors[att_i]['sources'] = \
- list(attractors[att_i]['paths'].keys())
+ attractors[att_i]['paths'] = nx.shortest_path(
+ self.graph, target=target)
+ attractors[att_i]['sources'] = list(
+ attractors[att_i]['paths'].keys())
return attractors
def catchment_area(self, attractors=None):
--
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