Commit: 25efd5dac9a6ae0aa4cd8cc4260b23ca11d6619a - myprojects-hg-reborn (hg)

Commit MetaInfo

• Révision: 25efd5dac9a6ae0aa4cd8cc4260b23ca11d6619a (tree)
• l'heure: 2010-04-22 01:19:02
• Auteur: lorenzo
• Commiter: lorenzo

Message de Log

Now the code can also define the number of susceptible individuals as the
number of individuals in the seed's CC (instead of simply the number of
individuals entering the museum after the seed). The code is still being
developed, hence be careful!

Change Summary

• modified: Python-codes/iterate_deterministic_infection_also_on_days.py

Modification

diff -r b6ad982fc39c -r 25efd5dac9a6 Python-codes/iterate_deterministic_infection_also_on_days.py
--- a/Python-codes/iterate_deterministic_infection_also_on_days.py	Wed Apr 21 15:57:19 2010 +0000
+++ b/Python-codes/iterate_deterministic_infection_also_on_days.py	Wed Apr 21 16:19:02 2010 +0000
@@ -4,6 +4,12 @@
 import numpy as n
 import sys
 import string
+import igraph as ig
+
+def array_to_dict_iter(array):
+    for row in array:
+        yield dict(source=row[0], target=row[1])
+
 
 
 
@@ -23,6 +29,8 @@
 def time_infection(data_no_loops, infected):
     before_and_after=\
         network_after_infection_introduction(infected,data_no_loops)
+
+    seed=infected
     
     net_infected=before_and_after[0]
 
@@ -30,6 +38,22 @@
     #number of people the seed can infect (not the number of visitors since
     #the seed cannot infect a priori those who left before he entered)
 
+    g = ig.Graph.DictList(vertices=None, edges=array_to_dict_iter(net_infected[:,1:3]))
+
+    g=g.simplify()
+    clustering=g.clusters()
+    c_sizes=s.asarray(clustering.sizes())
+
+    name_list=g.vs["name"]
+
+    name_list=s.asarray(name_list)
+
+    sel=s.where(name_list==seed)[0]
+    seed_membership=clustering.membership[sel]
+
+    susceptible_improved=c_sizes[seed_membership]
+
+
     infected_list_overall=s.zeros(0).astype("int64")
     infected_times_overall=s.zeros(0).astype("int64")
 
@@ -93,7 +117,7 @@
         cumulative_new_infected[i]=len(set_infected)
                     
     return [infected_list_overall,infected_times_overall,\
-            cumulative_new_infected, time_unique, susceptible]
+            cumulative_new_infected, time_unique, susceptible,susceptible_improved ]
 
 
 
@@ -250,6 +274,7 @@
 
     total_infected_distr=s.zeros(len(visitor_list)).astype("int64")
     total_susceptible_distr=s.zeros(len(visitor_list)).astype("int64")
+    total_susceptible_distr_improved=s.zeros(len(visitor_list)).astype("int64")
 
 
     for visitor_iter in xrange(len(visitor_list)):
@@ -268,10 +293,11 @@
 
         total_infected_distr[visitor_iter]=count_infections[-1]
         total_susceptible_distr[visitor_iter]=dynamic_infection[4]
+        total_susceptible_distr_improved[visitor_iter]=dynamic_infection[5]
 
 
 
-    return [total_infected_distr.astype("int64"),len(visitor_list)*s.ones(len(visitor_list)).astype("int64"),total_susceptible_distr.astype("int64")]
+    return [total_infected_distr.astype("int64"),len(visitor_list)*s.ones(len(visitor_list)).astype("int64"),total_susceptible_distr.astype("int64"),total_susceptible_distr_improved.astype("int64")]
 
 
 def iterate_calculation_number_infected_on_time_periods(period_list,data_laundry):
@@ -279,6 +305,7 @@
     number_infected_overall=s.zeros(0).astype("int64")
     number_non_isolated_overall=s.zeros(0).astype("int64")
     number_susceptible_overall=s.zeros(0).astype("int64")
+    number_susceptible_overall_improved=s.zeros(0).astype("int64")
 
     #change period_list into an array of strings
     
@@ -305,10 +332,11 @@
         number_non_isolated_overall=s.hstack((number_non_isolated_overall,number_non_isolated_and_infected[1]))
         
         number_susceptible_overall=s.hstack((number_susceptible_overall,number_non_isolated_and_infected[2]))
+        number_susceptible_overall_improved=s.hstack((number_susceptible_overall_improved,number_non_isolated_and_infected[3]))
 
 
     return [number_infected_overall,number_non_isolated_overall,\
-            number_susceptible_overall]
+            number_susceptible_overall, number_susceptible_overall_improved]
 
 
 
@@ -356,12 +384,13 @@
 
 period_list=n.loadtxt('periods_with_min_number_visitors.dat').astype('int64')
 
-data_laundry=0
+data_laundry=1
 number_and_number_infected=iterate_calculation_number_infected_on_time_periods(period_list,data_laundry)
 
 n.savetxt("number_distr_infected_overall.dat", number_and_number_infected[0], fmt="%d")
 n.savetxt("number_distr_non_isolated_overall.dat", number_and_number_infected[1], fmt="%d")
 n.savetxt("number_distr_susceptible_overall.dat", number_and_number_infected[2], fmt="%d")
+n.savetxt("number_distr_susceptible_overall_improved.dat", number_and_number_infected[3], fmt="%d")