def setUp(self):
from bayesnet import BNet, BVertex, graph
# create a small BayesNet
G = BNet('Water Sprinkler Bayesian Network')
c,s,r,w = [G.add_v(BVertex(nm,discrete=True,nvalues=nv)) for nm,nv in zip('c s r w'.split(),[2,3,4,2])]
for ep in [(c,r), (c,s), (r,w), (s,w)]:
G.add_e(graph.DirEdge(len(G.e), *ep))
G.InitDistributions()
self.G = G
def __init__(self, url):
"""Loads the data from a XBN file"""
#empty BNet
self.G = BNet()
self.xbn = parse(url)
self.version = ""
node = self.xbn.childNodes
ok=False
#XBN version 1.0
try:
# get basic info on the BN
bnmodel = node[0].childNodes #<BNMODEL>
statdynvar = bnmodel[1].childNodes #children of bnmodel
#<STATICPROPERTIES>,<DYNAMICPROPERTIES>,<VARIABLES>
stat = statdynvar[0].childNodes #<STATICPROPERTIES>
self.version = stat[2].childNodes[0].nodeValue #<VERSION>
ok=True
except:
pass
#XBN version 0.2
try:
bnmodel = node[1].childNodes #<BNMODEL>
statdynvar = bnmodel[1].childNodes #children of bnmodel
#<STATICPROPERTIES>,<DYNAMICPROPERTIES>,<VARIABLES>
stat = statdynvar[1].childNodes #<STATICPROPERTIES>
attrs = stat[3].attributes # ??? but it works, to get the version number
self.version = attrs.get(attrs.keys()[0]).nodeValue #<VERSION>
ok=True
except:
pass
if not ok: raise 'Neither version 1.0 or 0.2, verify your xbn file...'
def setUp(self):
from bayesnet import BNet, BVertex, graph
# create a small BayesNet
self.G = G = BNet('Test')
self.a = a = G.add_v(BVertex('a', discrete=False, nvalues=1))
self.b = b = G.add_v(BVertex('b', discrete=False, nvalues=2))
self.c = c = G.add_v(BVertex('c', discrete=False, nvalues=1))
self.d = d = G.add_v(BVertex('d', discrete=True, nvalues=2))
self.e = e = G.add_v(BVertex('e', discrete=True, nvalues=3))
self.f = f = G.add_v(BVertex('f', discrete=False, nvalues=1))
self.g = g = G.add_v(BVertex('g', discrete=False, nvalues=1))
for ep in [(a, c), (b, c), (d, f), (e, f),
(a, g), (b, g), (d, g), (e, g)]:
G.add_e(graph.DirEdge(len(G.e), *ep))
#a,b : continuous(1,2), no parents
#c : continuous(3), 2 continuous parents (a,b)
#d,e : discrete(2,3), no parents
#f : continuous(1), 2 discrete parents (d,e)
#g : continuous(1), 2 discrete parents (d,e) & 2 continuous parents (a,b)
G.InitDistributions()
self.ad = ad = a.distribution
self.bd = bd = b.distribution
self.cd = cd = c.distribution
self.fd = fd = f.distribution
self.gd = gd = g.distribution
def setUp(self):
from bayesnet import BNet, BVertex, graph
# create a small BayesNet, Water-Sprinkler
G = BNet('Test')
a,b,c,d = [G.add_v(BVertex(nm,discrete=True,nvalues=nv)) for nm,nv in zip('a b c d'.split(),[2,3,4,2])]
ad,bd,cd,dd = a.distribution, b.distribution, c.distribution, d.distribution
# sizes = (2,3,4,2)
# a has 3 parents, b,c and d
for ep in [(b,a), (c,a), (d,a)]:
G.add_e(graph.DirEdge(len(G.e), *ep))
G.InitDistributions()
self.G = G
self.a, self.b, self.c, self.d = a,b,c,d
def _init_BN(self, BNName, BNnodesdef):
BNnodes = {}
BNconnections = []
BN = BNet(BNName)
# Save the nodesdef for future use (saving)
self._BNDef = BNnodesdef
for node in BNnodesdef:
(nodename, isdiscrete, numstates, leafnode) = node
BNnodes[nodename] = BN.add_v(BVertex(nodename, isdiscrete, numstates))
# TODO: Find a way to improve this and avoid to have to loop a
# second time
# reason is because BNnodes[leafnode] is not sure to be there when
# going through the first loop
for node in BNnodesdef:
(nodename, isdiscrete, numstates, leafnode) = node
if type(leafnode) == type([]):
for r in leafnode:
if r != None:
BNconnections.append((BNnodes[nodename], BNnodes[r]))
elif leafnode != None:
BNconnections.append((BNnodes[nodename], BNnodes[leafnode]))
else:
#do nothing
pass
for ep in BNconnections:
BN.add_e(DirEdge(len(BN.e), *ep))
# Ok our Bnet has been created, let's save it in the controller
self._BN = BN
# Let's not forget to initialize the distribution
self._BN.InitDistributions()
def setUp(self):
from bayesnet import BNet, BVertex, graph
# create a small BayesNet
G = BNet('Water Sprinkler Bayesian Network')
c,s,r,w = [G.add_v(BVertex(nm, discrete=True, nvalues=nv)) for nm, nv \
in zip('c s r w'.split(), [2, 3, 4, 2])]
for ep in [(c, r), (c, s), (r, w), (s, w)]:
G.add_e(graph.DirEdge(len(G.e), *ep))
G.InitDistributions()
self.G = G
def setUp(self):
from bayesnet import BNet, BVertex, graph
# create a small BayesNet, Water-Sprinkler
G = BNet('Test')
a, b, c, d = [G.add_v(BVertex(nm, discrete=True, nvalues=nv)) for \
nm, nv in zip('a b c d'.split(), [2, 3, 4, 2])]
ad, bd, cd, dd = a.distribution, b.distribution, \
c.distribution, d.distribution
# sizes = (2,3,4,2)
# a has 3 parents, b,c and d
for ep in [(b, a), (c, a), (d, a)]:
G.add_e(graph.DirEdge(len(G.e), *ep))
G.InitDistributions()
self.G = G
self.a, self.b, self.c, self.d = a, b, c, d
class LoadXBN:
""" Loads the data from a XBN file
>>> xbn = LoadXBN('WetGrass.xbn')
>>> BNet = xbn.Load()
BNet is a openbayes.bayesnet.BNet class
"""
variablesList = []
structureList = []
distributionList = []
def __init__(self, url):
"""Loads the data from a XBN file"""
#empty BNet
self.G = BNet()
self.xbn = parse(url)
self.version = ""
node = self.xbn.childNodes
ok=False
#XBN version 1.0
try:
# get basic info on the BN
bnmodel = node[0].childNodes #<BNMODEL>
statdynvar = bnmodel[1].childNodes #children of bnmodel
#<STATICPROPERTIES>,<DYNAMICPROPERTIES>,<VARIABLES>
stat = statdynvar[0].childNodes #<STATICPROPERTIES>
self.version = stat[2].childNodes[0].nodeValue #<VERSION>
ok=True
except:
pass
#XBN version 0.2
try:
bnmodel = node[1].childNodes #<BNMODEL>
statdynvar = bnmodel[1].childNodes #children of bnmodel
#<STATICPROPERTIES>,<DYNAMICPROPERTIES>,<VARIABLES>
stat = statdynvar[1].childNodes #<STATICPROPERTIES>
attrs = stat[3].attributes # ??? but it works, to get the version number
self.version = attrs.get(attrs.keys()[0]).nodeValue #<VERSION>
ok=True
except:
pass
if not ok: raise 'Neither version 1.0 or 0.2, verify your xbn file...'
def Load(self):
self.getBnInfos()
self.getStaticProperties()
self.getDynamicProperties()
self.getVariablesXbn()
self.getStructureXbn()
self.getDistribution()
return self.G
def getBnInfos(self):
bn = BnInfos()
node = self.xbn.childNodes
if self.version == "1.0":
attrs = node[0].attributes
else: #version 0.2
attrs = node[1].attributes
for attrName in attrs.keys():
attrNode = attrs.get(attrName)
attrValue = attrNode.nodeValue
if attrName == "NAME":
bn.name = attrValue
# not used in BNet class
elif attrName == "ROOT":
bn.root = attrValue
self.G.name = attrValue
return bn
def getStaticProperties(self):
prop = StaticProperties()
node = self.xbn.childNodes
if self.version == "1.0":
bnmodel = node[0].childNodes
statdynvar = bnmodel[1].childNodes
stat = statdynvar[0].childNodes
for elem in stat:
if elem.nodeType == Node.ELEMENT_NODE:
if elem.nodeName == "FORMAT":
info = elem.childNodes
prop.format = info[0].nodeValue
elif elem.nodeName == "VERSION":
info = elem.childNodes
prop.version = info[0].nodeValue
elif elem.nodeName == "CREATOR":
info = elem.childNodes
prop.creator = info[0].nodeValue
else: #version 0.2
bnmodel = node[1].childNodes
statdynvar = bnmodel[1].childNodes
stat = statdynvar[1].childNodes
for elem in stat:
if elem.nodeType == Node.ELEMENT_NODE:
if elem.nodeName == "FORMAT":
attrs = elem.attributes
prop.format = attrs.get(attrs.keys()[0]).nodeValue
elif elem.nodeName == "VERSION":
attrs = elem.attributes
prop.version = attrs.get(attrs.keys()[0]).nodeValue
elif elem.nodeName == "CREATOR":
attrs = elem.attributes
prop.creator = attrs.get(attrs.keys()[0]).nodeValue
return prop
def getDynamicProperties(self):
prop = DynamicProperties()
try:
del prop.dynPropType [:]
prop.dynProperty.clear()
prop.dynPropXml.clear()
except:
pass
node = self.xbn.childNodes
if self.version == "1.0":
bnmodel = node[0].childNodes
statdynvar = bnmodel[1].childNodes
dyn = statdynvar[2].childNodes
else:
bnmodel = node[1].childNodes
statdynvar = bnmodel[1].childNodes
dyn = statdynvar[3].childNodes
for elem in dyn:
if elem.nodeType == Node.ELEMENT_NODE:
if elem.nodeName == "PROPERTYTYPE":
dictDyn = {}
attrs = elem.attributes
for attrName in attrs.keys():
attrNode = attrs.get(attrName)
attrValue = attrNode.nodeValue
if attrName == "NAME":
dictDyn["NAME"] = attrValue
elif attrName == "TYPE":
dictDyn["TYPE"] = attrValue
elif attrName == "ENUMSET":
dictDyn["ENUMSET"] = attrValue
if self.version == "1.0":
for info in elem.childNodes:
if info.nodeName == "COMMENT":
dictDyn["COMMENT"] = info.childNodes[0].nodeValue
else:
comment = elem.childNodes
comText = comment[1].childNodes
dictDyn["COMMENT"] = comText[0].nodeValue
prop.dynPropType.append(dictDyn)
elif elem.nodeName == "PROPERTY":
if self.version == "1.0":
attrs = elem.attributes
attrValue = attrs.get(attrs.keys()[0]).nodeValue
prop.dynProperty[attrValue] = elem.childNodes[0].childNodes[0].nodeValue
else:
attrs = elem.attributes
value = elem.childNodes
valueText = value[1].childNodes
prop.dynProperty[attrs.get(attrs.keys()[0]).nodeValue] = valueText[0].nodeValue
elif elem.nodeName == "PROPXML":
if self.version == "1.0":
attrs = elem.attributes
attrValue = attrs.get(attrs.keys()[0]).nodeValue
prop.dynPropXml[attrValue] = elem.childNodes[0].childNodes[0].nodeValue
else:
attrs = elem.attributes
value = elem.childNodes
valueText = value[1].childNodes
prop.dynPropXml[attrs.get(attrs.keys()[0]).nodeValue] = valueText[0].nodeValue
return prop
def getVariablesXbn(self):
self.variablesList = []
node = self.xbn.childNodes
if self.version == "1.0":
bnmodel = node[0].childNodes
statdynvar = bnmodel[1].childNodes
variables = statdynvar[4].childNodes
else:
bnmodel = node[1].childNodes
statdynvar = bnmodel[1].childNodes
variables = statdynvar[5].childNodes
for var in variables:
if var.nodeType == Node.ELEMENT_NODE:
v = Variables()
v.stateName = []
v.propertyNameValue = {}
attrs = var.attributes
for attrName in attrs.keys():
attrNode = attrs.get(attrName)
attrValue = attrNode.nodeValue
if attrName == "NAME":
v.name = attrValue
elif attrName == "TYPE":
v.type = attrValue
elif attrName == "XPOS":
v.xpos = attrValue
elif attrName == "YPOS":
v.ypos = attrValue
for info in var.childNodes:
if info.nodeType == Node.ELEMENT_NODE:
if (info.nodeName == "DESCRIPTION") or (info.nodeName == "FULLNAME"):
try:
v.description = info.childNodes[0].nodeValue
except:
v.description = ""
elif info.nodeName == "STATENAME":
v.stateName.append(info.childNodes[0].nodeValue)
elif (info.nodeName == "PROPERTY"):
attrsb = info.attributes
attrValueb = attrsb.get(attrsb.keys()[0]).nodeValue
if self.version == "1.0":
v.propertyNameValue[attrValueb] = info.childNodes[0].childNodes[0].nodeValue
else:
v.propertyNameValue[attrValueb] = info.childNodes[1].childNodes[0].nodeValue
self.variablesList.append(v)
# create the corresponding nodes into the BNet class
for v in self.variablesList:
#---TODO: Discrete or Continuous. Here True means always discrete
bv = BVertex(v.name,True,len(v.stateName))
bv.state_names = v.stateName
self.G.add_v(bv)
#---TODO: add the names of the states into the vertex
return self.variablesList
def getStructureXbn(self):
self.structureList = []
node = self.xbn.childNodes
if self.version == "1.0":
bnmodel = node[0].childNodes
statdynstruct = bnmodel[1].childNodes
structure = statdynstruct[6].childNodes
else:
bnmodel = node[1].childNodes
statdynstruct = bnmodel[1].childNodes
structure = statdynstruct[7].childNodes
for arc in structure:
if arc.nodeType == Node.ELEMENT_NODE:
attrs = arc.attributes
for attrName in attrs.keys():
attrNode = attrs.get(attrName)
attrValue = attrNode.nodeValue
if attrName == "PARENT":
self.structureList.append(attrValue)
elif attrName == "CHILD":
self.structureList.append(attrValue)
for ind in range(0,len(self.structureList),2):
par = self.G.v[self.structureList[ind]]
child = self.G.v[self.structureList[ind+1]]
self.G.add_e(DirEdge(len(self.G.e),par,child))
# initialize the distributions
self.G.InitDistributions()
return self.structureList
def getDistribution(self):
self.distributionList = []
node = self.xbn.childNodes
if self.version == "1.0":
bnmodel = node[0].childNodes
statdyndist = bnmodel[1].childNodes
distribution = statdyndist[8].childNodes
else:
bnmodel = node[1].childNodes
statdyndist = bnmodel[1].childNodes
distribution = statdyndist[9].childNodes
for dist in distribution:
d = Distribution()
d.condelem = []
d.dpiIndex = []
d.dpiData = []
if dist.nodeType == Node.ELEMENT_NODE:
attrs = dist.attributes
for attrName in attrs.keys():
attrNode = attrs.get(attrName)
attrValue = attrNode.nodeValue
if attrName == "TYPE":
d.type = attrValue
for distInfos in dist.childNodes:
if distInfos.nodeType == Node.ELEMENT_NODE:
if distInfos.nodeName == "CONDSET":
for elem in distInfos.childNodes:
if elem.nodeType == Node.ELEMENT_NODE:
attrsb = elem.attributes
d.condelem.append(attrsb.get(attrsb.keys()[0]).nodeValue)
elif distInfos.nodeName == "PRIVATE":
if distInfos.nodeType == Node.ELEMENT_NODE:
attrsb = distInfos.attributes
d.name = attrsb.get(attrsb.keys()[0]).nodeValue
elif distInfos.nodeName == "DPIS":
for dpi in distInfos.childNodes:
if dpi.nodeName == "DPI":
d.dpiData.append(dpi.childNodes[0].nodeValue)
attrs = dpi.attributes
for attrName in attrs.keys():
attrNode = attrs.get(attrName)
attrValue = attrNode.nodeValue
if attrName == "INDEXES":
d.dpiIndex.append(attrValue)
if dist.nodeType == Node.ELEMENT_NODE:
self.distributionList.append(d)
for d in self.distributionList:
dist = self.G.v[d.name].distribution # the distribution class into the BNet
#---TODO: what about gaussians ???
dist.distribution_type = 'Multinomial'
if d.type == 'ci':
# conditionally independant values are defined
# fill the matrix with the conditionally independant term
new = array([float(da) for da in d.dpiData[0].split()],type='Float32') # transform a string into a numarray
for pa in dist.family[1:]:
new = new[...,NewAxis]
n_states = pa.nvalues # number of states for each parent
new = concatenate([new]*n_states, axis=-1)
# replace all values in the distribution with the ci values
dist[:]=new
if len(d.dpiIndex):
# when multiple elements (nodes with parents)
for data,index in zip(d.dpiData,d.dpiIndex):
# data, index are strings containing the data and index
ii = tuple([int(i) for i in index.split()]) # transform the string into a tuple of integers
# create a dictionnary with the name of the dimension and the value it takes
dictin = {} # e.g. dictin = {'Alternator':1,'FanBelt':0}
for pa,iii in zip(d.condelem,ii):
dictin[pa] = iii
dd = array([float(da) for da in data.split()],type='Float32') # transform a string into a numarray
dist[dictin] = dd
else:
# for nodes with no parents
# simply insert the data into the matrix
dd = array([float(da) for da in d.dpiData[0].split()],type='Float32')
dist[:] = dd
return self.distributionList
if __name__ == '__main__':
from bayesnet import *
suite = unittest.makeSuite(DistributionTestCase, 'test')
runner = unittest.TextTestRunner()
runner.run(suite)
##
suite = unittest.makeSuite(MultinomialTestCase, 'test')
runner = unittest.TextTestRunner()
runner.run(suite)
# create a small BayesNet
G = BNet('Water Sprinkler Bayesian Network')
c,s,r,w = [G.add_v(BVertex(nm,discrete=True,nvalues=nv)) for nm,nv in zip('c s r w'.split(),[2,2,2,0])]
w.discrete = False
w.nvalues = 0
for ep in [(c,r), (c,s), (r,w), (s,w)]:
G.add_e(graph.DirEdge(len(G.e), *ep))
print G
G.InitDistributions()
c.setDistributionParameters([0.5, 0.5])
s.distribution.setParameters([0.5, 0.9, 0.5, 0.1])
r.distribution.cpt=na.array([0.8, 0.2, 0.2, 0.8])
