/usr/share/pyshared/Epigrass/epiplay.py is in epigrass 2.0.4-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#program to play simulations from database
import dgraph, cPickle, glob, os, ogr, time
from math import *
try:
from PyQt4.QtGui import *
except ImportError:
print "Please install PyQT 4"
#
from numpy import *
import sqlobject as SO
from matplotlib import cm
class viewer:
"""
"""
def __init__(self, host='localhost', port=3306, user='epigrass', pw='epigrass', db='epigrass',backend='mysql',encoding='latin-1', gui=None):
self.host = host
self.port = port
self.user = user
self.pw = pw
self.db = db
self.backend = backend
self.encoding = encoding
self.gui = gui
if backend == 'sqlite':
db_filename = os.path.abspath('Epigrass.sqlite')
connection_string = 'sqlite:' + db_filename
elif backend == 'mysql':
connection_string = r'%s://%s:%s@%s/%s'%(backend,user,pw,host,db)
elif backend == 'csv':
pass
else:
sys.exit('Invalid Database Backend specified: %s'%backend)
if not backend == 'csv':
self.connection = SO.connectionForURI(connection_string)
self.dmap = 0#int(input('Draw Map?(0,1) '))
self.tables = self.getTables()
#self.nodes = self.readNodes(self.tables[table])
#self.numbnodes = len(self.nodes)
#self.data = self.readData(self.tables[table])
#self.numbsteps = len(self.data)/self.numbnodes
#self.viewGraph()
def getTables(self):
"""
Returns list of table names from current database connection
"""
if self.backend == 'sqlite':
r = [i[0] for i in self.connection.queryAll("select name from sqlite_master where type='table';")]
elif self.backend == 'mysql':
r = [i[0] for i in self.connection.queryAll('SHOW TABLES')]
elif self.backend =='csv':
r = glob.glob('*.tab')
return r
def getFields(self,table):
"""
Returns a list of fields (column names) for a given table.
table is a string with table name
"""
if self.backend == 'sqlite':
r = [i[1] for i in self.connection.queryAll('PRAGMA table_info(%s)'%table)]
shp =self.connection.queryAll('SELECT the_world$shapefile FROM %s'%(table+'_meta'))
print shp
self.shapefile = eval(shp[0][0])
print self.shapefile
elif self.backend == 'mysql':
r = [i[0] for i in self.connection.queryAll('SHOW FIELDS FROM %s'%table)]
shp =self.connection.queryAll('SELECT the_world$shapefile FROM %s'%(table+'_meta'))
self.shapefile = eval(shp[0][0])
elif self.backend == 'csv':
f = open(table,'r')
r = f.read().strip().split(',')
f.close()
#select only the key names (each element in r is a tuple, containing
# name and field descriptors )
return r
def readNodes(self,name,table):
"""
Reads geocode and coords from database table
for each node and adjacency matrix.
"""
if self.backend =="csv":
# the equivalent of a select for a csv file
f=open(table,"r")
names = f.readline().strip().split(",")#remove header
d = {}
for l in f:
l=l.strip().split(',')
d[l[names.index('geocode')]]=[l[names.index('geocode')],l[names.index('lat')],l[names.index('longit')],l[names.index('name')]]
r= d.values()
f.close()
self.numbnodes = len(r)
else:
r = self.connection.queryAll('SELECT geocode,lat,longit,name FROM %s WHERE time = 0'%table)
self.numbnodes = len(r)
self.nodes_pos = r#[(i[1], i[2], i[0], i[3])for i in r]
self.nodes_gc = [i[0] for i in r]
# get adjacency matrix
# if not os.getcwd() == self.
file = open('adj_'+name)
m = cPickle.load(file)
self.adjacency = m
file.close()
return r,m
def readData(self,table):
"""
read node time series data
"""
if self.backend =="csv":
f=open(table,"r")
f.readline()#remove header
r = []
for l in f:
l=l.strip().split(',')
r.append(l)
f.close()
else:
r = self.connection.queryAll('SELECT * FROM %s'%table)
return r
def readEdges(self,table):
"""
Read edge time series
"""
if self.backend =="csv":
tab = table.split(".")[0]+"_e.tab"
f = open(tab,"r")
f.readline()#remove header
r = [l.strip().split(',') for l in f]
f.close()
self.numbedges = len(r)
else:
tab = table+'e'
r = self.connection.queryAll('SELECT * FROM %s'%tab)
self.numbedges = len(r)
self.elist = [(self.nodes_gc.index(e[0]), self.nodes_gc.index(e[1])) for e in r]
if not self.elist:
self.elist = transpose(self.adjacency.nonzero()).tolist()
return r
def viewGraph(self, nodes, am, var,mapa=''):
"""
Starts the Qt display of the map or graph.
"""
if self.shapefile:
self.gui.openGraphDisplay(mapa,self.shapefile[1],self.shapefile[2], self.nodes_pos, self.elist )
else:
self.gui.openGraphDisplay(mapa,nlist=self.nodes_pos, elist=self.elist )
self.gr = self.gui.graphDisplay
self.gr.qwtPlot.setTitle(var)
def anim(self,data,edata, numbsteps,pos, rate=20):
"""
Starts the animation.
* data: time series from database
* edata: infectious traveling for edge painting
* pos: column number of variable to animate
"""
#FIXME: the animation rate is not working....
self.gr.horizontalSlider.setEnabled(0)
self.gr.horizontalSlider.setMaximum(numbsteps)
for t in xrange(numbsteps):
stepdict = {}
for i in xrange(self.numbnodes):
start = i*numbsteps+t
stepdict[data[start][0]] = data[start][pos] #{geocode: value}
self.gr.drawStep(t, stepdict)
#paint Edges when there are infectious coming or going
if not edata:
continue
elist = []
for i in xrange(self.numbedges):
start = i*numbsteps+t
if edata[start][-1]+edata[start][-2]:
elist.append(edata[start][1])
self.gr.flashBorders(elist)
# time.sleep(1./rate)
self.gr.horizontalSlider.setEnabled(1)
def plotTs(self,ts,name):
"""
Uses gcurve to plot the time-series of a given city object
"""
## try:
## self.gg.display.visible=0
## except:pass
self.gg = VG.gdisplay(title='%s'%name,xtitle='time',ytitle='count')
g=VG.gcurve(color=VG.color.green)
for t,n in enumerate(ts):
g.plot(pos=(t,n))
def keyin(self,data,edata,numbsteps,pos,rate):
"""
Implements keyboard and mouse interactions
"""
while 1:
ob = self.gr.display.mouse.pick
try:
ob.sn(2)
if self.gr.display.mouse.alt and not ob.paren.tsdone:
self.plotTs(ob.paren.ts,ob.paren.name)
ob.paren.tsdone = 1
except:pass
if self.gr.display.mouse.clicked:
m = self.gr.display.mouse.getclick()
#print m.click
loc = m.pos
self.gr.display.center = loc
if self.gr.display.kb.keys: # is there an event waiting to be processed?
s = self.gr.display.kb.getkey() # obtain keyboard information
if s == 'r': #Replay animation
for i in self.gr.nodes:
self.paintNode(0,i,numbsteps,col='g')
i.painted=0
self.anim(data,edata,numbsteps,pos,rate)
else:
pass
if __name__ == "__main__":
Display=viewer(user='root',pw='mysql')
Display.anim()
Display.keyin()
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