def testEvaluate(self):
numVertices = 6
numFeatures = 1
vList = VertexList(numVertices, numFeatures)
g1 = DenseGraph(vList)
g1.addEdge(0, 1)
g1.addEdge(2, 1)
g1.addEdge(3, 1)
g1.addEdge(4, 1)
g1.addEdge(5, 2)
g2 = DenseGraph(vList)
g2.addEdge(0, 2)
g2.addEdge(1, 2)
g2.addEdge(3, 2)
g2.addEdge(4, 2)
g2.addEdge(5, 1)
g3 = DenseGraph(vList)
g3.addEdge(0, 1)
g4 = SparseGraph(vList)
g4.addEdge(0, 1)
g4.addEdge(2, 1)
g4.addEdge(3, 1)
g4.addEdge(4, 1)
g4.addEdge(5, 2)
lmbda = 0.01
pgk = RandWalkGraphKernel(lmbda)
logging.debug((pgk.evaluate(g1, g1)))
logging.debug((pgk.evaluate(g1, g2)))
logging.debug((pgk.evaluate(g2, g1)))
logging.debug((pgk.evaluate(g2, g2)))
logging.debug((pgk.evaluate(g1, g3)))
logging.debug((pgk.evaluate(g3, g3)))
#Tests - graph kernel is symmetric, permutations of indices are identical
self.assertAlmostEquals(pgk.evaluate(g1, g2),
pgk.evaluate(g2, g1),
places=6)
self.assertAlmostEquals(pgk.evaluate(g1, g3),
pgk.evaluate(g3, g1),
places=6)
self.assertAlmostEquals(pgk.evaluate(g1, g1),
pgk.evaluate(g1, g2),
places=6)
self.assertAlmostEquals(pgk.evaluate(g2, g4),
pgk.evaluate(g1, g2),
places=6)
#All evaluation of themselves are above zero
self.assertTrue(pgk.evaluate(g1, g1) >= 0)
self.assertTrue(pgk.evaluate(g2, g2) >= 0)
self.assertTrue(pgk.evaluate(g3, g3) >= 0)
class PajekWriterTest(unittest.TestCase):
def setUp(self):
#Let's set up a very simple graph
numVertices = 5
numFeatures = 1
edges = []
vList = VertexList(numVertices, numFeatures)
#An undirected dense graph
self.dGraph1 = DenseGraph(vList, True)
self.dGraph1.addEdge(0, 1, 1)
self.dGraph1.addEdge(0, 2, 1)
self.dGraph1.addEdge(2, 4, 1)
self.dGraph1.addEdge(2, 3, 1)
self.dGraph1.addEdge(3, 4, 1)
#A directed sparse graph
self.dGraph2 = DenseGraph(vList, False)
self.dGraph2.addEdge(0, 1, 1)
self.dGraph2.addEdge(0, 2, 1)
self.dGraph2.addEdge(2, 4, 1)
self.dGraph2.addEdge(2, 3, 1)
self.dGraph2.addEdge(3, 4, 1)
#Now try sparse graphs
vList = VertexList(numVertices, numFeatures)
self.sGraph1 = SparseGraph(vList, True)
self.sGraph1.addEdge(0, 1, 1)
self.sGraph1.addEdge(0, 2, 1)
self.sGraph1.addEdge(2, 4, 1)
self.sGraph1.addEdge(2, 3, 1)
self.sGraph1.addEdge(3, 4, 1)
self.sGraph2 = SparseGraph(vList, False)
self.sGraph2.addEdge(0, 1, 1)
self.sGraph2.addEdge(0, 2, 1)
self.sGraph2.addEdge(2, 4, 1)
self.sGraph2.addEdge(2, 3, 1)
self.sGraph2.addEdge(3, 4, 1)
#Finally, try DictGraphs
self.dctGraph1 = DictGraph(True)
self.dctGraph1.addEdge(0, 1, 1)
self.dctGraph1.addEdge(0, 2, 2)
self.dctGraph1.addEdge(2, 4, 8)
self.dctGraph1.addEdge(2, 3, 1)
self.dctGraph1.addEdge(12, 4, 1)
self.dctGraph2 = DictGraph(False)
self.dctGraph2.addEdge(0, 1, 1)
self.dctGraph2.addEdge(0, 2, 1)
self.dctGraph2.addEdge(2, 4, 1)
self.dctGraph2.addEdge(2, 3, 1)
self.dctGraph2.addEdge(12, 4, 1)
def tearDown(self):
pass
def testInit(self):
pass
def testWriteToFile(self):
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
#Have to check the files
fileName1 = directory + "denseTestUndirected"
pw.writeToFile(fileName1, self.dGraph1)
fileName2 = directory + "denseTestDirected"
pw.writeToFile(fileName2, self.dGraph2)
fileName3 = directory + "sparseTestUndirected"
pw.writeToFile(fileName3, self.sGraph1)
fileName4 = directory + "sparseTestDirected"
pw.writeToFile(fileName4, self.sGraph2)
fileName5 = directory + "dictTestUndirected"
pw.writeToFile(fileName5, self.dctGraph1)
fileName6 = directory + "dictTestDirected"
pw.writeToFile(fileName6, self.dctGraph2)
def testWriteToFile2(self):
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
def setVertexColour(vertexIndex, graph):
colours = ["grey05", "grey10", "grey15", "grey20", "grey25"]
return colours[vertexIndex]
def setVertexSize(vertexIndex, graph):
return vertexIndex
def setEdgeColour(vertexIndex1, vertexIndex2, graph):
colours = ["grey05", "grey10", "grey15", "grey20", "grey25"]
return colours[vertexIndex1]
def setEdgeSize(vertexIndex1, vertexIndex2, graph):
return vertexIndex1 + vertexIndex2
pw.setVertexColourFunction(setVertexColour)
fileName1 = directory + "vertexColourTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setVertexColourFunction(None)
pw.setVertexSizeFunction(setVertexSize)
fileName1 = directory + "vertexSizeTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setVertexSizeFunction(None)
pw.setEdgeColourFunction(setEdgeColour)
fileName1 = directory + "edgeColourTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setEdgeColourFunction(None)
pw.setEdgeSizeFunction(setEdgeSize)
fileName1 = directory + "edgeSizeTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setEdgeColourFunction(None)
def testWriteToFile3(self):
"""
We will test out writing out some random graphs to Pajek
"""
numVertices = 20
numFeatures = 0
vList = VertexList(numVertices, numFeatures)
graph = SparseGraph(vList)
p = 0.1
generator = ErdosRenyiGenerator(p)
graph = generator.generate(graph)
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
pw.writeToFile(directory + "erdosRenyi20", graph)
#Now write a small world graph
p = 0.2
k = 3
graph.removeAllEdges()
generator = SmallWorldGenerator(p, k)
graph = generator.generate(graph)
pw.writeToFile(directory + "smallWorld20", graph)
def testVertexLabelPairs(self):
numVertices = 6
numFeatures = 1
vList = VertexList(numVertices, numFeatures)
vList.setVertices(numpy.array([numpy.arange(0, 6)]).T)
graph = DenseGraph(vList, True)
graph.addEdge(0, 1, 0.1)
graph.addEdge(1, 3, 0.1)
graph.addEdge(0, 2, 0.2)
graph.addEdge(2, 3, 0.5)
graph.addEdge(0, 4, 0.1)
graph.addEdge(3, 4, 0.1)
tol = 10**-6
edges = graph.getAllEdges()
X = GraphUtils.vertexLabelPairs(graph, edges)
self.assertTrue(numpy.linalg.norm(X - edges) < tol)
X = GraphUtils.vertexLabelPairs(graph, edges[[5, 2, 1], :])
self.assertTrue(numpy.linalg.norm(X - edges[[5, 2, 1], :]) < tol)
#Try a bigger graph
numVertices = 6
numFeatures = 2
vList = VertexList(numVertices, numFeatures)
vList.setVertices(numpy.random.randn(numVertices, numFeatures))
graph = DenseGraph(vList, True)
graph.addEdge(0, 1, 0.1)
graph.addEdge(1, 3, 0.1)
edges = graph.getAllEdges()
X = GraphUtils.vertexLabelPairs(graph, edges)
self.assertTrue(
numpy.linalg.norm(X[0, 0:numFeatures] - vList.getVertex(1)) < tol)
self.assertTrue(
numpy.linalg.norm(X[0, numFeatures:numFeatures * 2] -
vList.getVertex(0)) < tol)
self.assertTrue(
numpy.linalg.norm(X[1, 0:numFeatures] - vList.getVertex(3)) < tol)
self.assertTrue(
numpy.linalg.norm(X[1, numFeatures:numFeatures * 2] -
vList.getVertex(1)) < tol)
#Try directed graphs
graph = DenseGraph(vList, False)
graph.addEdge(0, 1, 0.1)
graph.addEdge(1, 3, 0.1)
edges = graph.getAllEdges()
X = GraphUtils.vertexLabelPairs(graph, edges)
self.assertTrue(
numpy.linalg.norm(X[0, 0:numFeatures] - vList.getVertex(0)) < tol)
self.assertTrue(
numpy.linalg.norm(X[0, numFeatures:numFeatures * 2] -
vList.getVertex(1)) < tol)
self.assertTrue(
numpy.linalg.norm(X[1, 0:numFeatures] - vList.getVertex(1)) < tol)
self.assertTrue(
numpy.linalg.norm(X[1, numFeatures:numFeatures * 2] -
vList.getVertex(3)) < tol)
