/usr/share/pyshared/Epigrass/manager.py is in epigrass 2.3.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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"""
Model Management and simulation objects.
"""
import cPickle, time
import os, codecs, subprocess
from copy import deepcopy
from simobj import graph, edge, siteobj
from numpy import *
import numpy as np
import spread
from collections import OrderedDict
from numpy.random import uniform, poisson
from data_io import *
from argparse import ArgumentParser
import ConfigParser
import string, sys, getpass
import report as Rp
import epigdal
import json
import __version__
import MySQLdb
from pysqlite2 import dbapi2 as sqlite3
#import pycallgraph
class simulate:
"""
This class takes care of setting up the model, simulating it, and storing the results
"""
def __init__(self, fname=None, host='localhost',port=3306,db='epigrass',user='epigrass', password='epigrass',backend = 'sqlite', silent=False):
#pycallgraph.start_trace()
# self.pool = multiprocessing.Pool()
self.host = host
self.port = port
self.usr = user
self.db = db
self.fname = fname
self.backend = backend
self.passw = password
self.repname = None
self.shapefile = None
self.World = None
self.shpout = True
self.silent = silent
self.dir = os.getcwd()
sys.path.insert(0,self.dir) #add current path to sys.path
self.gui = 0 # True if this object was created by the gui
self.now = time.asctime().replace(' ','_').replace(':','') #current date and time
self.modelName = os.path.split(self.fname)[-1].split('.')[0]
self.config = self.loadModelScript(self.fname)
self.evalConfig(self.config)
if not self.outdir:
self.outdir = outdir = 'outdata-'+self.modelName
if not os.path.exists(self.outdir):
os.mkdir(self.outdir)
if self.shapefile: #create world object if a shapefile is provided
self.World = epigdal.World(*self.shapefile+[self.outdir])
self.chkScript()
self.encoding = 'utf-8'#default encoding for strings in the sites and edges files
self.round = 0 #No replicates
sitios = loadData(self.sites, sep=',', encoding=self.encoding)
ed = loadData(self.edges,sep=',', encoding=self.encoding)
l = self.instSites(sitios)
e = self.instEdges(l,ed)
self.g = self.instGraph(self.modelName,1,l,e)
def loadModelScript(self,fname):
"""
Loads the model specification from the text file.
Returns a dictionary with keys of the form
<section>.<option> and the corresponding values.
"""
config = {}
config = config.copy()
cp =ConfigParser.SafeConfigParser()
cp.read(fname)
for sec in cp.sections():
name = string.lower(sec)
for opt in cp.options(sec):
config[name+"."+string.lower(opt)] = string.strip(cp.get(sec,opt))
return config
def evalConfig(self,config):
"""
Takes in the config dictionary and generates the global variables needed.
"""
try:
#WORLD
#load Shapefile if specified
if config['the world.shapefile']:
self.shapefile = eval(config['the world.shapefile'])
else:
self.shapefile = []
#self.layer = config['the world.vector layer']
self.sites = config['the world.sites'] #file containing site info
self.edges = config['the world.edges'] #file containing edge info
if config['the world.encoding']:
self.encoding = config['the world.encoding']#encoding specification
#Epidemiological model
self.modtype = config['epidemiological model.modtype']
#self.models = eval(config['epidemiological model.models'])
#PARAMETERS
self.beta = config['model parameters.beta']
self.alpha = config['model parameters.alpha']
self.e = config['model parameters.e']
self.r = config['model parameters.r']
self.delta = config['model parameters.delta']
self.B = config['model parameters.b']
self.w = config['model parameters.w']
self.p = config['model parameters.p']
#INITIAL CONDITIONS (inits are string to evaluated inside siteobj.createmodel)
self.S = config['initial conditions.s']
self.E = config['initial conditions.e']
self.I = config['initial conditions.i']
#EPIDEMIC EVENTS
self.seed = eval(config['epidemic events.seed'])
self.vaccinate = eval(config['epidemic events.vaccinate'])
#self.quarantine = eval(config['epidemic events.quarantine'])
#[TRANSPORTATION MODEL]
self.doTransp = eval(config['transportation model.dotransp'])
self.stochTransp = eval(config['transportation model.stochastic'])
self.speed = eval(config['transportation model.speed'])
#SIMULATION AND OUTPUT
self.steps = eval(config['simulation and output.steps'])
self.outdir = config['simulation and output.outdir']
self.MySQLout = eval(config['simulation and output.mysqlout'])
# self.Rep = eval(config['simulation and output.report'])
# self.siteRep = eval(config['simulation and output.siterep'])
self.replicas = eval(config['simulation and output.replicas'])
self.randomize_seeds = eval(config['simulation and output.randseed'])
self.Batch = eval(config['simulation and output.batch'])
except KeyError, v:
V = v.__str__().split('.')
sys.exit("Please check the syntax of your '.epg' file.\nVariable %s, from section %s was not specified."%(V[1],V[0]))
if self.replicas:
# self.Rep = 0 #Turns off reports
self.Batch = []#Turns off Batch mode
self.round = 0# Initialize replicate counter
# generate dictionaries for parameters and inits
self.inits = OrderedDict()
self.parms = {}
for k,v in config.items():
if k.startswith('initial conditions'):
self.inits[k.split('.')[-1]] = v
elif k.startswith('model parameters'):
self.parms[k.split('.')[-1]] = v
else:pass
def chkScript(self):
"""
Checks the type of the variables on the script
"""
self.Say("Checking syntax of model script... NOW")
if not os.access(self.sites,os.F_OK):
self.Say('Sites file %s does not exist, please check your script.'%self.sites)
sys.exit()
if not os.access(self.edges,os.F_OK):
self.Say('Egdes file %s does not exist, please check your script.'%self.edges)
sys.exit()
if not self.modtype in ['SIS','SIS_s','SIR','SIR_s','SEIS','SEIS_s','SEIR','SEIR_s','SIpRpS','SIpRpS_s','SIpR,SIpR_s','Influenza','Custom']:
self.Say('Model type %s is invalid, please check your script.'%self.modtype)
self.Say('Script %s passed syntax check NOW.'%self.modelName)
def deg2dec(self,coord):
"""
converts lat/long to decimal
"""
co = coord.split(':')
if int(co[0])<0:
result = float(co[0])-float(co[1])/60-float(co[2])/3600
else:
result = float(co[0])+float(co[1])/60+float(co[2])/3600
return result
def instSites(self,sitelist):
"""
Instantiates and returns a list of siteobj instances, from a list of site specification
as returned by data_io.loadData.
Here the site specific events are passed to each site, and the site models are created.
"""
header = sitelist.pop(0)
ncols = len(header)
objlist=[]
for site in sitelist:
if len(site) != ncols:
raise ValueError("This line in your sites file has a different number elements:\n%s"%str(site))
if ':' in site[0]:
lat = self.deg2dec(site[0])
long = self.deg2dec(site[1])
else:
lat = float(site[0])
long = float(site[1])
objlist.append(siteobj(site[2],site[3],(lat,long),int(strip(site[4])),tuple([float(i.strip()) for i in site[5:]])))
for o in objlist:
if self.stochTransp:
o.stochtransp = 1
else:
o.stochtransp = 0
N = o.totpop #local copy for reference on model creation
values = o.values #local copy for reference on model creation
inits = OrderedDict()
parms = {}
#eval parms and inits
for k,v in self.inits.items():
inits[k] = eval(v)
for k,v in self.parms.items():
parms[k] = eval(v)
#Linhas abaixo estao obsoletas (remover quando tiver tempo para testar)
I = eval(self.I)
E = eval(self.E)
S = eval(self.S)
beta = eval(self.beta)
alpha = eval(self.alpha)
e = eval(self.e)
r = eval(self.r)
delta = eval(self.delta)
B = eval(self.B)
w = eval(self.w)
p = eval(self.p)
#################
if self.vaccinate:
if self.vaccinate[0][0] == 'all':
o.vaccination = [self.vaccinate[0][1],self.vaccinate[0][2]]
else:
for i in self.vaccinate:
if int(o.geocode) == i[0]:
o.vaccination = [i[1],float(i[2])]
# if self.quarantine:
# for i in self.quarantine:
# if int(o.geocode) == i[0]:
# o.quarantine == i[1:]
if self.seed:
#print type(o.geocode), type(self.seed[0])
if self.seed[0][0] == "all":
I += j[2]
inits[self.seed[0][1].lower()] += 1
for j in self.seed:
if int(o.geocode) == j[0]:
#self.Say("%s infected person(s) arrived at %s"%(j[2],o.sitename))
I += j[2]
inits[j[1].lower()] +=j[2]
o.createModel((E,I,S),self.modtype,self.modelName,v=values,bi=inits,bp=parms)
else:
o.createModel((E,I,S),self.modtype,self.modelName,v=values,bi=inits,bp=parms)
else:
o.createModel((E,I,S),self.modtype,self.modelName,v=values,bi=inits,bp=parms)
return objlist
def instEdges(self,sitelist, edgelist):
"""
Instantiates and returns a list of edge objects,
sitelist -- list of siteobj objects.
edgelist -- list of edge specifications as returned by data_io.loadData.
"""
header = edgelist.pop(0)
#print [i.sitename for i in sitelist]
objlist=[]
source = dest = None
for edg in edgelist:
#print edgelist.index(edg)
if edg[5] == edg[6]:
#ignore circular edges
continue
for site in sitelist:
#print site.sitename
if str(site.geocode) == edg[5]:
source = site
#print 'found source = ',source.sitename
elif str(site.geocode) == edg[6]:
dest = site
#print 'found dest = ',dest.sitename
if (source and dest):
#print 'next edge!'
break
if not (source and dest):
#print source ,dest
sys.exit('One of the vertices on edge '+edg[0]+'-'+edg[1]+' could not be found on the site list')
objlist.append(edge(source,dest,edg[2],edg[3],float(edg[4])))
source = dest = None
return objlist
def instGraph(self,name, digraph, siteobjlist, edgeobjlist):
"""
Instantiates and returns a graph object from a list of edge objects.
"""
g = graph(name,digraph)
g.speed = self.speed
for j in siteobjlist:
g.addSite(j)
for i in edgeobjlist:
g.addEdge(i)
return g
def randomizeSeed(self, option):
"""
Generate and return a list of randomized seed sites
to be used in a repeated runs scenario.
Seed sites are sampled with a probability proportional to the
log of their population size.
option: if 1 randomize; if 2, return unrundomized sequence
"""
if option==1:
poplist = [log10(site.totpop) for site in self.g.site_dict.itervalues()]
lpl = len(poplist)
popprob = array(poplist)/sum(poplist) #acceptance probability
u = floor(uniform(0,lpl, self.replicas))
sites=[]
i=0
site_list = self.g.site_list
while i < self.replicas:
p = uniform(0,1)
if p <= popprob[int(u[i])]:
sites.append(site_list[int(u[i])])
i += 1
elif option ==2:
sites = self.g.site_list
return sites
def setSeed(self,seed,n=1):
'''
Resets the number of infected to zero in all nodes but seed,
which get n infected cases.
seed must be a siteobj object.
'''
#inits[self.seed[0][1].lower()] += 1
seedvar = self.seed[0][1].lower() #retrieve the name of the variable containing the seeds
self.Say('seedvar= %s'%seedvar)
site_list = self.g.site_list
self.seed =[(seed.geocode, seedvar,n)]
for site in site_list:
if site.geocode == seed.geocode:
site.bi[seedvar] = n
# site.ts[0][seedpos] = n
self.Say("%s infected case(s) arrived at %s"%(n,seed.sitename))
else:
site.bi[seedvar] = 0
# site.ts[0][seedpos] = 0
def start(self):
"""
Start the simulation
"""
if '/' in self.modelName:
self.modelName = os.path.split(self.modelName)[-1]
# print "====>", self.gui
time.sleep(10)
self.Say('Simulation starting.')
start = time.time()
self.runGraph(self.g,self.steps,transp=self.doTransp)
elapsed = time.time()-start
self.Say('Simulation lasted %s seconds.'%elapsed)
if self.MySQLout:
if self.backend == 'csv':
self.outToCsv(self.modelName)
else:
self.outToDb(self.modelName)
if self.shpout:
self.outToShp()
self.dumpData()
spread.Spread(self.g, self.outdir, self.encoding)
#self.saveModel(self.modelName)
#pycallgraph.make_dot_graph(self.modelName+'_callgraph.png')
def createDataFrame(self,site):
"""
Saves the time series *site.ts* to outfile as specified on the
model script.
"""
data = array(site.ts, Float)
inc = site.incidence
f = open(self.outdir+self.outfile,'w')
f.write('time,E,I,S,incidence\n')
try:
for t,i in enumerate(data):
j = [str(k) for k in i]
line = str(t)+','.join(j) + str(inc[t])+'\n'
f.write(line)
finally:
f.close()
return 'E,I,S\n'+tss
def grassVect2ascii(self,layer):
"""
Convert Grass vector layer to an ascii file epigrass can read
Deprecated!
"""
com = 'v.out.ascii input=%s output=map.txt format=standard'%layer
os.system(com)
def outToShp(self):
"""
Creates Data Layers in shapefile format
"""
if not self.World:
return
#Initialize world output layers
self.Say("REading Nodes from shapefile...")
self.World.get_node_list(self.World.ds.GetLayerByName(self.World.layerlist[0]))
self.Say("Done reading nodes!")
self.Say("Creating Nodes shapefile...")
self.World.create_node_layer()
self.Say("Done creating Nodes shapefile!")
elist = [(gcs[0],gcs[1],sum(e.ftheta),sum(e.btheta)) for gcs,e in self.g.edge_dict.iteritems()]
self.Say("Creating Edges shapefile...")
self.World.create_edge_layer(elist)
self.Say("Done creating Edges shapefile!")
#Generate site epidemic stats
varlist = ["prevalence","totalcases", "arrivals","population"]
sitestats = [(site.geocode,float(site.totalcases)/site.totpop,site.totalcases,sum(site.thetahist),float(site.totpop)) for site in self.g.site_dict.itervalues()]
names = {k: v.sitename for k,v in self.g.site_dict.iteritems()}
self.Say("Creating Data shapefile...")
self.World.create_data_layer(varlist,sitestats)
self.Say("Done creating Data shapefile!")
#Generate the kml too.
self.out_to_kml(names)
self.Say("Done creating KML files!")
#close files
self.World.close_sources()
def out_to_kml(self, names):
"""
Generates output to kml files
"""
self.Say("Creating KML output files...")
lr = self.World.datasource.GetLayer(0)
k = epigdal.KmlGenerator()
k.addNodes(lr,names)
k.writeToFile(self.outdir)
site_list = self.g.site_list
site_dict = self.g.site_dict
# Temporarily disabled animation output due to the sheer size of the kmz files
# if len(site_dict)*len(site_dict.values()[0].ts)<10000: #Only reasonably sized animations
# for i, v in enumerate(site_dict.values()[0].vnames):
# ka = epigdal.AnimatedKML(os.path.join(self.outdir, 'Data.kml'), extrude = True)
# data = [(str(site.geocode), t, p[i]) for site in site_dict.itervalues() for t, p in enumerate(site.ts)]
# ka.add_data(data)
# ka.save(v+'_animation')
# self.Say(v+'_animation')
# del ka
# else:
# self.Say("Simulation too large to export as kml.")
self.Say("Done creating KML files!")
def series_to_JSON(self):
"""
Saves timeseries to JSON for uploading to epigrass web
"""
self.Say('Saving series to JSON')
series = {}
for gc,s in self.g.site_dict.iteritems():
ts = np.array(s.ts)
sdict = {}
for i,vn in enumerate(s.vnames):
sdict[vn] = ts[:,i].tolist()
series[gc] = sdict
with open('series.json','w') as f:
json.dump(series,f)
def writeMetaCSV(self, table):
"""
Writes a meta CSV table
"""
if not self.outdir == os.getcwd():
os.chdir(self.outdir)
f = open(table+'_meta', 'w')
cfgitems = self.config.items()
h = ';'.join([k.strip().replace(' ','_').replace('.', '$') for k,v in cfgitems])
l = ';'.join([v.split('#')[0] for k, v in cfgitems])
f.write(h+'\n')
f.write(l+'\n')
f.close()
os.chdir(self.dir)
def outToCsv(self,table):
"""
Save simulation results in csv file.
"""
if not self.outdir == os.getcwd():
os.chdir(self.outdir)
tablee = table+"_"+self.now+"_e.tab" #edgetable name
table += "_"+self.now+".tab"#sitetable name
f = open(table,"w")
head = ['geocode','time','totpop','name',
'lat','longit']
headerwritten = False
for site in self.g.site_dict.itervalues():
t = 0
regb = [str(site.geocode),str(t),str(site.totpop),
site.sitename.replace('"','').encode('ascii','replace'),
str(site.pos[0]),str(site.pos[1])
]
if site.values:
for n,v in enumerate(site.values):
head.append('values%s'%n)
regb.append(str(v))
#print site.sitename, site.ts
ts = array(site.ts[1:]) #remove init conds so that ts and inc are the same size
head.extend(['incidence','arrivals'])
for n,v in enumerate(site.vnames):
head.append(str(v))
for i in ts:
reg = deepcopy(regb)
reg.extend([str(site.incidence[t]),str(site.thetahist[t])])
reg[1] = str(t)
for n,v in enumerate(site.vnames):
reg.append(str(i[n]))
if not headerwritten:
h =",".join(head)
f.write(h+'\n')
headerwritten = True
f.write(','.join(reg)+'\n')
t += 1
f.close()
#inserting data in edges file
g = open(tablee,'w')
t=0
head = ['source_code','dest_code','time','ftheta','btheta']
ehw = False
for e in self.g.edge_list:
for f,b in zip(e.ftheta,e.btheta):
if not ehw:
g.write(','.join(head)+'\n')
ehw = True
ereg = [e.source.geocode,e.dest.geocode,t,f,b]
ereg = [str(i) for i in ereg]
g.write(','.join(ereg)+'\n')
t += 1
g.close()
os.chdir(self.dir)
# def outToODb(self,table,mode='b'):
# """
# Insert simulation results in a database using sqlobject.
# if mode = b, do batch inserts
# if mode = p, do parallel inserts
# """
# #set connection parameters
# try:
# DO.Connect(self.backend.lower(),self.usr,self.passw,self.host,self.port,self.db)
# self.Say('Saving data on %s database...'%self.backend)
# except:
# self.Say('Database Connection Failed')
# #basic connection variables
# name = table+'_'+self.now
# self.outtable = name
#
# DO.Site.sqlmeta.table = name
# DO.Edge.sqlmeta.table = name+'e'
# if self.backend.lower()=='sqlite':
# DO.Site.sqlmeta.createSQL = {'sqlite':['PRAGMA synchronous=OFF;','PRAGMA default_cache_size=12000000;']}
# DO.Site._connection.commit()
# DO.Edge.sqlmeta.createSQL = {'sqlite':['PRAGMA synchronous=OFF;','PRAGMA default_cache_size=12000000;']}
# DO.Edge._connection.commit()
# #adding columns to sites table
# try: #Only add if they don't exist. On Batch runs this will catch the add error
# DO.Site.sqlmeta.addColumn(StringCol('incidence'))
# DO.Site.sqlmeta.addColumn(StringCol('arrivals'))
# except: pass
# if self.g.site_list[0].values:#add columns for 'values' variables
# for i in xrange(len(self.g.site_list[0].values)):
# try:
# DO.Site.sqlmeta.addColumn(StringCol('values%s'%i))
# except: pass
# for s in self.g.site_list[0].vnames: #add columns for state variables
# try:
# DO.Site.sqlmeta.addColumn(StringCol(s))
# except: pass
# #creating tables
# DO.Site.createTable()
# DO.Edge.createTable()
# #saving pickle of adjacency matrix
# matname = 'adj_'+self.modelName # table
# adjfile = open(matname,'w')
# cPickle.dump(self.g.getConnMatrix(),adjfile)
# adjfile.close()
# #calling insert function
# if mode == 'b':
# self.batchInsert()
# elif mode == 'p':
# self.parInsert()
#
# def batchInsert(self):
# """
# Do the inserts all at once. After the simulation is done
# """
# #inserting data in sites table
# for site in self.g.site_list:
# dicin={
# 'geocode':site.geocode,
# 'lat':float(site.pos[0]),
# 'longit':float(site.pos[1]),
# 'name':site.sitename.replace('"','').encode('ascii','replace'),
# 'totpop':int(site.totpop)}
# if site.values:
# for n,v in enumerate(site.values):
# #print v,type(v)
# dicin['values%s'%n] = str(v)
# ts = array(site.ts[1:]) #remove init conds so that ts and inc are the same size
# t = 0
# for i in ts:
# dicin['incidence']= str(site.incidence[t])
# dicin['arrivals'] = str(site.thetahist[t])
# dicin['time'] = t
# for n,v in enumerate(site.vnames):
# #print i[n],type( i[n])
# dicin[v] = str(i[n])
# DO.Site(**dicin)
# t += 1
# #DO.Site._connection.commit()
# #inserting data in edges table
# for e in self.g.edge_list:
# rlist = []
# edicin={
# 'source_code':e.source.geocode,
# 'dest_code':e.dest.geocode}
# t=0
# for f,b in zip(e.ftheta,e.btheta):
# edicin['time'] = t
# edicin['ftheta'] = f
# edicin['btheta'] = b
# rlist.append(edicin)
# t += 1
# insobj = DO.sqlbuilder.Insert(DO.Edge.sqlmeta.table,valueList=rlist)
# DO.Edge._connection.queryAll(DO.Edge._connection.sqlrepr(insobj))
# #DO.Edge._connection.commit()
#
# def parInsert(self):
# """
# do the insertions in a separate process.
# """
# pid = os.fork()
# if pid:
# #parent process get on with the simulation
# return
# else:
# #child process inserts data in sites table
# time.sleep(1+self.g.simstep)
# for site in self.g.site_list:
# dicin={
# 'geocode':site.geocode,
# 'lat':float(site.pos[0]),
# 'longit':float(site.pos[1]),
# 'name':site.sitename.replace('"','').encode('ascii','replace'),
# 'totpop':int(site.totpop)}
# if site.values:
# for n,v in enumerate(site.values):
# #print v,type(v)
# dicin['values%s'%n] = str(v)
# ts = array(site.ts[1:]) #remove init conds so that ts and inc are the same size
# t = self.g.simstep
# dicin['incidence']= str(site.incidence[t])
# dicin['arrivals'] = str(site.thetahist[t])
# dicin['time'] = t
# for n,v in enumerate(site.vnames):
# #print i[n],type( i[n])
# dicin[v] = str(i[n])
# DO.Site(**dicin)
# DO.Site._connection.commit()
# #inserting data in edges table
# for e in self.g.edge_list:
# edicin={
# 'source_code':e.source.geocode,
# 'dest_code':e.dest.geocode}
# edicin['time'] = t
# edicin['ftheta'] = e.ftheta[t]
# edicin['btheta'] = e.btheta[t]
# DO.Edge(**edicin)
# DO.Edge._connection.commit()
# sys.exit("commit successful")
def writeMetaTable(self, table):
"""
Creates a Meta-Info Table on the database with the contents of the .epg file
"""
try:
table = table+'_meta'
if self.backend.lower() == "mysql":
con = MySQLdb.connect(host=self.host, port=self.port,
user=self.usr,passwd=self.passw, db=self.db)
elif self.backend.lower() == "sqlite":
if not self.outdir == os.getcwd():
os.chdir(self.outdir)
con = sqlite3.connect("Epigrass.sqlite")
os.chdir(self.dir)
# Create table
sqlstr1 = "CREATE TABLE %s("%table
vars = []
cfgitems = self.config.items()
for k, v in cfgitems:
vars.append(k.strip().replace(' ','_').replace('.', '$'))
sqlstr2 = ', '.join(["%s text"%i for i in vars])
Cursor = con.cursor()
Cursor.execute(sqlstr1+sqlstr2+');')
#doing inserts
values = [v.split('#')[0] for k, v in cfgitems]
# for k, v in cfgitems:
# v = v.split('#')[0]
# if not v:
# v = ' '
# values.append()
str3 = ','.join(['"%s"'%i for i in values])+')'
sqlstr3 = '''INSERT INTO %s VALUES(%s''' % (table, str3)
#print sqlstr3
Cursor.execute(sqlstr3)
finally:
if con:
con.commit()
con.close()
def outToDb(self,table):
"""
Insert simulation results on a mysql or SQLite table
"""
if self.backend.lower() == "mysql":
self.Say('Saving data on MySQL...')
elif self.backend.lower() == "sqlite":
self.Say('Saving data on SQLite...')
con=None
try:
table = table+'_'+self.now
self.writeMetaTable(table)
self.outtable = table
if self.backend.lower() == "mysql":
con = MySQLdb.connect(host=self.host, port=self.port,
user=self.usr,passwd=self.passw, db=self.db)
elif self.backend.lower() == "sqlite":
if not self.outdir == os.getcwd():
os.chdir(self.outdir)
con = sqlite3.connect("Epigrass.sqlite")
os.chdir(self.dir)
# Define number of variables to be stored
nvar = len(self.g.site_dict.values()[0].ts[-1]) +4 #state variables, plus coords, plus incidence, plus infected arrivals.
str1 = '`%s` FLOAT(9),'*nvar #nvar variables in the table
str1lite = '%s REAL,'*nvar #nvar variables in the SQLite table
varnames = ['lat','longit']+list(self.g.site_dict.values()[0].vnames)+['incidence']+['Arrivals']
# print nvar, varnames, str1
str1 = str1[:-1] % tuple(varnames) #insert variable names (MySQL)
str1lite = str1lite[:len(str1lite)-1] % tuple(varnames) #insert variable names (SQLITE)
Cursor = con.cursor()
str2 = """CREATE TABLE %s(
`geocode` INT( 9 ) ,
`time` INT( 9 ) ,
`name` varchar(128) ,
""" % table
str2lite = """CREATE TABLE %s(
geocode INTEGER ,
time INTEGER ,
name TEXT ,
""" % table
sql = str2+str1+');'
sqlite = str2lite+str1lite+');'
if self.backend.lower() == "mysql":
Cursor.execute(sql)
str3 = (nvar+3)*'%s,'
str3 = str3[:-1]+')'
elif self.backend.lower() == "sqlite":
Cursor.execute(sqlite)
str3 = (nvar+3)*'?,'
str3 = str3[:-1]+')'
sql2 = 'INSERT INTO %s' % table + ' VALUES('+str3
nvalues = []
for site in self.g.site_dict.itervalues():
geoc = site.geocode
lat = site.pos[0]
long = site.pos[1]
name = site.sitename
ts = array(site.ts[1:]) #remove init conds so that ts and inc are the same size
inc = site.incidence
thist = site.thetahist
t = 0
for i in ts:
tstep = str(t)
nvalues.append(tuple([geoc,tstep,name]+[lat,long]+list(i)+[inc[t]]+[float(thist[t])]))
t += 1
Cursor.executemany(sql2,nvalues)
#Creating a table for edge data
self.etable = etable = table+'e'
esql = """CREATE TABLE %s(
`source_code` INT( 9 ) ,
`dest_code` INT( 9 ) ,
`time` INT( 9 ) ,
`ftheta` FLOAT(9) ,
`btheta` FLOAT(9) );"""%etable
esqlite = """CREATE TABLE %s(
source_code INTEGER ,
dest_code INTEGER ,
time INTEGER ,
ftheta REAL ,
btheta REAL );"""%etable
if self.backend.lower() == "mysql":
Cursor.execute(esql)
esql2 = 'INSERT INTO %s' % etable + ' VALUES(%s,%s,%s,%s,%s)'
elif self.backend.lower() == "sqlite":
Cursor.execute(esqlite)
esql2 = 'INSERT INTO %s' % etable + ' VALUES(?,?,?,?,?)'
values = []
for gcs,e in self.g.edge_dict.iteritems():
s = gcs[0]
d = gcs[1]
t=0
for f,b in zip(e.ftheta,e.btheta):
values.append((s,d,t,f,b))
t += 1
Cursor.executemany(esql2,values)
finally:
if con:
con.close()
#saving pickle of adjacency matrix
matname = 'adj_'+self.modelName # table
fname = os.path.join(self.outdir,matname)
adjfile = open(fname,'w')
cPickle.dump(self.g.getConnMatrix(),adjfile)
adjfile.close()
def criaAdjMatrix(self):
# saving the adjacency matrix
codeslist = [str(i.geocode) for i in self.g.site_dict.itervalues()]
if not os.path.exists('adjmat.csv'):
self.Say('Saving the adjacency matrix...')
am = self.g.getConnMatrix()
amf = open ('adjmat.csv','w')
amf.write(','.join(codeslist)+'\n')
for row in am:
row = [str(i) for i in row]
amf.write(','.join(row)+'\n')
amf.close()
self.Say('Done!')
def dumpData(self):
"""
Dumps data as csv (comma-separated-values)
"""
self.Say("Starting simulation Analysis")
curdir = os.getcwd()
if not self.outdir == curdir:
os.chdir(self.outdir)
codeslist = self.g.site_dict.keys()
self.criaAdjMatrix()
#saving the shortest path matrices
# if not os.path.exists('spmat.csv'):
# self.Say('Calculating the shortest path matrices...')
# ap = self.g.getAllPairs()
# f = open('ap','w')
# cPickle.dump(ap,f)
# f.close()
# spd = self.g.shortDistMatrix
# apf = open ('spmat.csv','w')
# apf.write(','.join(codeslist)+'\n')
# spdf = open ('spdmat.csv','w')
# spdf.write(','.join(codeslist)+'\n')
# for row in ap:
# row = [str(i) for i in row]
# apf.write(','.join(row)+'\n')
# apf.close()
# for row in spd:
# row = [str(i) for i in row]
# spdf.write(','.join(row)+'\n')
# spdf.close()
# print 'Done!'
#Saving epidemic path
self.Say('Saving Epidemic path...')
if self.round:
epp = codecs.open('epipath%s.csv'%str(self.round),'w',self.encoding)
else:
epp = codecs.open('epipath.csv','w',self.encoding)
epp.write('time,site,infector\n')
for i in self.g.epipath:
#print i
site = self.g.site_dict[i[1]]
infectors = i[-1]
# sorting infectors by number of infective contributed
if len(infectors):
reverse_infectors = infectors.items()
reverse_infectors.sort(key=lambda t:t[1])
mli = reverse_infectors[-1][0].sitename#Most likely infector
else:
mli = 'NA'
#print i[1].sitename, type(i[1].sitename), mli
epp.write(str(i[0])+','+site.sitename+','+mli+'\n')
epp.close()
self.Say('Done!')
self.g.save_topology('network.graphml')
#saving Epistats
self.Say('Saving Epidemiological results...')
stats = [str(i) for i in self.g.getEpistats()]
seed = [s for s in self.g.site_dict.itervalues() if s.geocode == self.seed[0][0]][0]
stats.pop(1) #Remove epispeed which is a vector
if os.path.exists('epistats.csv'):
stf = codecs.open('epistats.csv','a',self.encoding)#append to file
else:
stf = codecs.open('epistats.csv','w',self.encoding)#create a new file
stf.write('seed,name,size,infected_sites,spreadtime,median_survival,totvaccinated,totquarantined,seeddeg,seedpop\n')
## stf.write('seed,name,size,infected_sites,spreadtime,median_survival,totvaccinated,totquarantined,seeddeg,seedpop\n')
#scent = str(seed.getCentrality())
#sbetw = str(seed.getBetweeness())
#sthidx = str(seed.getThetaindex())
sdeg = str(seed.getDegree())
spop = str(seed.totpop)
sname =seed.sitename
sstats = '%s,%s'%(sdeg,spop)
# sstats = '%s,%s,%s,%s,%s'%(scent,sbetw,sthidx,sdeg,spop)
stf.write(str(self.seed[0][0])+','+sname+','+','.join(stats)+','+sstats+'\n')
stf.close()
self.Say('Done!')
#Saving site stats
self.Say('Saving site statistics...')
#self.g.getAllPairs()
if os.path.exists('sitestats.csv'):
sitef = codecs.open('sitestats.csv','a',self.encoding) #append to file
else:
sitef = codecs.open('sitestats.csv','w',self.encoding)
#sitef.write('round,geocode,name,infection_time,degree,centrality,betweeness,theta_index,distance,seed,seedname\n')
sitef.write('round,geocode,name,infection_time,degree,seed,seedname\n')
for s in self.g.site_dict.itervalues():
degree = str(s.getDegree())
#central = str(s.getCentrality())
#bet = str(s.getBetweeness())
#thidx = str(s.getThetaindex())
seedgc = str(self.seed[0][0])
seedname = seed.sitename
# f = open('ap','r')
# ap = cPickle.load(f)
# f.close()
# distseed = str(ap[codeslist.index(str(s.geocode)),codeslist.index(str(self.seed[0][0]))])
it = str(s.infected) #infection time
if it == 'FALSE':
it = 'NA'
# sitef.write(str(self.round)+','+str(s.geocode)+','+s.sitename+','+it+','+degree+','+central+','+bet+','+thidx+','+distseed+','+seedgc+','+seedname+'\n')
sitef.write(str(self.round)+','+str(s.geocode)+','+s.sitename+','+it+','+degree+','+seedgc+','+seedname+'\n')
# Saving series to JSON
self.series_to_JSON()
os.chdir(curdir)
self.Say('Done saving data!')
def saveModel(self,fname):
"""
Save the fully specified graph.
"""
f = open(fname,'w')
cPickle.dump(self.g,f)
f.close()
def loadModel(self,fname):
"""
Loads a pre-saved graph.
"""
g = cPickle.load(fname)
return g
def runGraph(self,graphobj,iterations=1, transp=0):
"""
Starts the simulation on a graph.
"""
g = graphobj
g.maxstep = iterations
sites = graphobj.site_dict.values()
edges = graphobj.edge_dict.values()
# g.sites_done = 0
if transp:
for n in xrange(iterations):
print "==> {}\r".format(g.simstep),
results=[i.runModel(self.parallel) for i in sites]
if self.parallel:
[r.wait() for r in results]
for j in edges:
j.migrate()
if self.gui:
self.gui.stepLCD.display(g.simstep)
self.gui.app.processEvents()
g.simstep += 1
g.sites_done = 0
else:
for n in xrange(iterations):
for i in sites:
i.runModel(self.parallel)
if self.gui:
self.gui.stepLCD.display(g.simstep)
self.gui.app.processEvents()
self.gui.RT.mutex.lock()
self.gui.RT.emit(self.gui.QtCore.SIGNAL("drawStep"), g.simstep, dict([(s.geocode, s.incidence[-1]) for s in sites]))
self.gui.RT.mutex.unlock()
g.simstep += 1
def Say(self, string):
"""
Exits outputs messages to the console or the gui accordingly
"""
if self.gui:
self.gui.textEdit1.insertPlainText(string+'\n''')
else:
if self.silent:
return
print string+'\n'
def storeSimulation(s,db='epigrass', host='localhost',port=3306):
"""
store the Simulate object *s* in the epigrass database
to allow distributed runs. Currently not working.
"""
now = time.asctime().replace(' ','_').replace(':','')
table = 'Model_'+S.modelName+now
con = MySQLdb.connect(host=host, port=port, user=usr,passwd=passw, db=db)
Cursor = con.cursor()
sql = """CREATE TABLE %s(
`simulation` BLOB);""" % table
Cursor.execute(sql)
blob = cPickle.dumps(s)
sql2 = 'INSERT INTO %s' % table + ' VALUES(%s)'
Cursor.execute(sql2,blob)
con.close()
def onStraightRun(args):
"""
Runs the model from the commandline
"""
if args.backend =="mysql":
S = simulate(fname=args.epg[0],host=args.dbhost, user=args.dbuser, password=args.dbpass, backend=args.backend)
else:
S = simulate(fname=args.epg[0],backend=args.backend)
S.parallel = args.parallel
if not S.replicas:
S.start()
spread.Spread(S.g)
else:
repRuns(S)
if S.Batch:
self.Say('Simulation Started.')
# run the batch list
for i in S.Batch:
#Makes sure it comes back to original directory before opening models in the batch list
os.chdir(S.dir)
#delete the old graph object to save memory
S.graph = None
# Generates the simulation object
T = simulate(fname=i,host=S.host, user=S.usr, password=S.passw, backend=S.backend)
self.Say('starting model %s'%i)
T.start() # Start the simulation
# spread.Spread(T.g)
def repRuns(S):
"""
Do repeated runs
"""
randseed=S.randomize_seeds
fname=S.fname
host=S.host
user=S.usr
password=S.passw
backend=S.backend
nseeds= S.seed[0][2] #number o individual to be used as seeds
self.Say("Replication type: ", randseed)
if randseed:
seeds = S.randomizeSeed(randseed)
reps = S.replicas
for i in xrange(reps):
self.Say("Starting replicate number %s"%i)
S = simulate(fname=fname,host=host, user=user, password=password, backend=backend)
if randseed:
S.setSeed(seeds[i],nseeds)
S.round = i
S.shpout = False
S.start()
del S
def main():
# Options and Argument parsing for running model from the command line, without the GUI.
usage = "usage: PROG [options] your_model.epg"
# parser = OptionParser(usage=usage, version="%prog "+__version__.version)
parser = ArgumentParser(usage=usage, description="Run epigrass models from the console",prog="PROG "+__version__.version)
parser.add_argument("-b", "--backend", dest="backend",
help="Define which datastorage backend to use", metavar="<mysql|sqlite|csv>", default="sqlite")
parser.add_argument("-u", "--dbusername",
dest="dbuser", help="MySQL user name")
parser.add_argument("-p", "--password",
dest="dbpass", help="MySQL password for user")
parser.add_argument("-H", "--dbhost",
dest="dbhost",default="localhost", help="MySQL hostname or IP address")
parser.add_argument("-P", "--parallel", action="store_true", default=False,
dest="parallel", help="use multiprocessing to run the simulation")
parser.add_argument("epg", metavar='EPG', nargs=1,
help='Epigrass model definition file (.epg).')
args = parser.parse_args()
if args.backend == "mysql" and not (options.dbuser and options.dbpass):
parser.error("You must specify a user and password when using MySQL.")
if args.backend not in ['mysql', 'sqlite', 'csv']:
parser.error('"%s" is an invalid backend type.'%options.backend)
print '==> ',args.epg
onStraightRun(args)
if __name__ == '__main__':
main()
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