def testInsertion(self):
mn = gum.MarkovNet()
self._fill(mn)
with self.assertRaises(gum.InvalidArgument):
mn.addFactor(gum.Potential()) # no empty factor
with self.assertRaises(gum.InvalidArgument):
mn.addFactor({"11", "31"}) # already exist
mn1 = gum.MarkovNet()
self._fill(mn1)
pot = gum.Potential().add(mn1.variable("11")).add(mn1.variable("21"))
pot.randomDistribution()
mn1.addFactor(pot)
self.assertEqual(pot.__str__(), mn1.factor({"11", "21"}).__str__())
mn1 = gum.MarkovNet()
self._fill(mn1)
pot = gum.Potential().add(mn1.variable("21")).add(mn1.variable("11"))
pot.randomDistribution()
mn1.addFactor(pot)
# should be equal : does not depend of the order of vars in the MarkonNet
self.assertEqual(pot.__str__(), mn1.factor({"11", "21"}).__str__())
# but the data should be the same
I = gum.Instantiation(pot)
factor = mn1.factor({"21", "11"})
I.setFirst()
while not I.end():
self.assertAlmostEqual(pot.get(I), factor.get(I), places=7)
I.inc()
def testEqualityOperators(self):
mn1 = gum.MarkovNet()
self._fill(mn1)
mn2 = gum.MarkovNet()
self.assertNotEqual(mn1, mn2)
self._fill(mn2)
self.assertEqual(mn1, mn2)
mn2.generateFactors()
self.assertNotEqual(mn1, mn2)
def testCopyOperator(self):
mn = gum.MarkovNet()
mn2 = gum.MarkovNet()
self._fill(mn)
mn2 = mn
self.assertEqual(mn2.__str__(),
"MN{nodes: 5, edges: 6, domainSize: 567, dim: 102}")
for n in mn.nodes():
self.assertEqual(mn.variable(n).name(), mn2.variable(n).name())
self.assertEqual(mn.neighbours(n), mn2.neighbours(n))
def undiGraphToMarkovNetwork(graph, variables=dict(), domainSize=2):
"""
Build a markov network from an UndiGraph
Variables can be either given in parameters or can be created if they are not defined
Parameters
----------
graph : pyAgrum.UndiGraph
the graph
variables : dict<str:pyAgrum.DiscreteVariable>
already defined variables, keys are variables name
domainSize : int
the domain of variables that are not defined
Returns
-------
pyAgrum.MarkovNet
the resulting Markov network
"""
nodes = graph.nodes()
cliques = getAllMaximalCliquesUndiGraph(graph)
definedVariables = variables.keys()
mn = gum.MarkovNet()
for node in nodes:
if node in definedVariables:
mn.add(variables[node])
else:
mn.add(gum.LabelizedVariable(str(node), "", domainSize))
for clique in cliques:
mn.addFactor(clique)
return mn
def createRandomMNTree(nodeNumber, minDomainSize=2, maxDomainSize=2):
"""
Build a random markov network and return it, the returned markov network is a tree
Examples
--------
>>> import markovNetworkLearning as mnl
>>> mn=mnl.createRandomMNTree(15,2,4)
Parameters
----------
nodeNumber : int
the number of variables of the markov network
minDomainSize : int
2 or above, default value : 2, each variable will have a random domain size randomly selected between minDomainSize and maxDomainSize
maxDomainSize : int
2 or above, and more than minDomainSize, default value : 2, each variable will have a random domain size randomly selected between minDomainSize and maxDomainSize
Returns
-------
pyAgrum.MarkovNet
the resulting Markov network
"""
variablesDomainSize = np.random.randint(minDomainSize,
maxDomainSize + 1,
size=nodeNumber)
tree = gum.MarkovNet()
if nodeNumber > 0:
tree.add(gum.LabelizedVariable("0", "", int(variablesDomainSize[0])))
for i in range(1, nodeNumber):
otherNode = random.choice(list(tree.nodes()))
tree.add(gum.LabelizedVariable(str(i), "",
int(variablesDomainSize[i])))
tree.addFactor({otherNode, str(i)})
return tree
def testEraseWithNames(self):
mn = gum.MarkovNet()
self._fill(mn)
with self.assertRaises(gum.NotFound):
mn.erase("36")
mn.erase("41")
self.assertEqual(mn.size(), 4)
self.assertEqual(mn.sizeEdges(), 3)
self.assertEqual(mn.dim(), (3 * 3 + 3 * 7 + 3 * 7))
self.assertEqual(mn.__str__(),
"MN{nodes: 4, edges: 3, domainSize: 189, dim: 51}")
def testErase(self):
mn = gum.MarkovNet()
self._fill(mn)
with self.assertRaises(gum.InvalidArgument):
mn.erase(36)
mn.erase(3)
self.assertEqual(mn.size(), 4)
self.assertEqual(mn.sizeEdges(), 3)
self.assertEqual(mn.dim(), (3 * 3 + 3 * 7 + 3 * 7))
self.assertEqual(mn.__str__(),
"MN{nodes: 4, edges: 3, domainSize: 189, dim: 51}")
def testEraseFactorWithNames(self):
mn = gum.MarkovNet()
self._fill(mn)
with self.assertRaises(gum.InvalidArgument):
mn.eraseFactor({"31", "21"})
mn.eraseFactor({"31", "51"})
self.assertEqual(mn.size(), 5)
self.assertEqual(mn.sizeEdges(), 5)
self.assertEqual(mn.dim(), (3 * 3 + 3 * 3 + 3 * 3 * 7))
self.assertEqual(mn.__str__(),
"MN{nodes: 5, edges: 5, domainSize: 567, dim: 81}")
def testIterations(self):
mn = gum.MarkovNet()
self._fill(mn)
cpt = 0
for node in mn.nodes():
cpt += 1
self.assertEqual(cpt, mn.size())
cpt = 0
for edg in mn.edges():
cpt += 1
self.assertEqual(cpt, mn.sizeEdges())
def testConstructor(self):
mn = gum.MarkovNet()
self._fill(mn)
self.assertEqual(mn.size(), 5)
self.assertEqual(mn.sizeEdges(), 6)
self.assertEqual(mn.dim(), (3 * 3 + 3 * 3 + 3 * 7 + 3 * 3 * 7))
self.assertEqual(mn.__str__(),
"MN{nodes: 5, edges: 6, domainSize: 567, dim: 102}")
self.assertEqual(mn.neighbours("41"), {0, 1, 4})
self.assertEqual(mn.neighbours(3), {0, 1, 4})
self.assertEqual(mn.variable(1).name(), "21")
self.assertEqual(mn.nodeId(mn.variable(2)), 2)
self.assertEqual(mn.idFromName("31"), 2)
self.assertEqual(mn.variableFromName("41").name(), "41")
self.assertEqual(mn.maxVarDomainSize(), 7)
self.assertEqual(mn.minParam(), 0.0)
self.assertEqual(mn.minNonZeroParam(), 0.03)
self.assertEqual(mn.maxParam(), 1.0)
self.assertEqual(mn.maxNonOneParam(), 0.97)
def dictToMarkovNetwork(graph, variables=dict(), domainSize=2):
"""
Build a markov network from an adjacency list
Variables can be either given in parameters or can be created if they are not defined
Parameters
----------
graph : dict
the graph, as an adjacency list
variables : dict<str:pyAgrum.DiscreteVariable>
already defined variables, keys are variables name
domainSize : int
the domain of variables that are not defined
Returns
-------
pyAgrum.MarkovNet
the resulting Markov network
"""
for var1 in graph.keys():
for var2 in graph[var1]:
if var1 not in graph[var2]:
raise ValueError(
'Can only convert an adjacency list into a markov network : as "'
+ str(var2) + '" is a neighbor of "' + str(var1) +
'", then "' + str(var1) + '" must be a neighbor of "' +
str(var2) + '".')
nodes = graph.keys()
cliques = getAllMaximalCliquesDict(graph)
definedVariables = variables.keys()
mn = gum.MarkovNet()
for node in nodes:
if node in definedVariables:
mn.add(variables[node])
else:
mn.add(gum.LabelizedVariable(str(node), "", domainSize))
for clique in cliques:
mn.addFactor(clique)
return mn