def setUp(self):
self.numVertices = 10
self.numFeatures = 3
self.maxEdgeTypes = 3
self.vList = VertexList(self.numVertices, self.numFeatures)
self.sMultiGraph = SparseMultiGraph(self.vList, self.maxEdgeTypes)
def testGetAllEdges(self):
sMultiGraph = SparseMultiGraph(self.vList, self.maxEdgeTypes, False)
self.assertEquals(sMultiGraph.getAllEdges().shape[0], 0)
self.assertEquals(sMultiGraph.getAllEdges().shape[1], 3)
sMultiGraph.addEdge(0, 1, 0)
sMultiGraph.addEdge(0, 1, 1)
sMultiGraph.addEdge(0, 2, 0)
allEdges = numpy.array([[0, 1, 0], [0, 2, 0], [0, 1, 1]])
self.assertTrue((sMultiGraph.getAllEdges() == allEdges).all())
def testGetNeighboursByEdgeType(self):
sMultiGraph = SparseMultiGraph(self.vList, self.maxEdgeTypes, True)
sMultiGraph.addEdge(0, 1, 2)
sMultiGraph.addEdge(0, 3, 1)
sMultiGraph.addEdge(2, 1, 0)
sMultiGraph.addEdge(1, 4, 0)
sMultiGraph.addEdge(9, 4, 0)
sMultiGraph.addEdge(9, 4, 1)
self.assertEquals(sMultiGraph.getNeighboursByEdgeType(0, 1), [3])
self.assertEquals(sMultiGraph.getNeighboursByEdgeType(0, 2), [1])
self.assertEquals(sMultiGraph.getNeighboursByEdgeType(0, 0), [])
self.assertEquals(set(sMultiGraph.getNeighboursByEdgeType(4, 0)),
set([1, 9]))
def testGetNeighbours(self):
sMultiGraph = SparseMultiGraph(self.vList, self.maxEdgeTypes, True)
sMultiGraph.addEdge(0, 1, 2)
sMultiGraph.addEdge(0, 3, 1)
sMultiGraph.addEdge(2, 1, 0)
sMultiGraph.addEdge(1, 4, 0)
sMultiGraph.addEdge(9, 4, 0)
sMultiGraph.addEdge(9, 4, 1)
self.assertEquals(set(sMultiGraph.neighbours(0)), set([1, 3]))
self.assertEquals(set(sMultiGraph.neighbours(1)), set([0, 2, 4]))
self.assertEquals(sMultiGraph.neighbours(3), [0])
self.assertEquals(set(sMultiGraph.neighbours(4)), set([9, 1]))
self.assertEquals(sMultiGraph.neighbours(9), [4])
def readGraph(self,
vertexFileName,
edgeFileNames,
undirected=True,
delimiter=None):
"""
Read a MultiGraph from at least 2 files: one is the information about
vertices and the other(s) are lists of edges. For the list of vertices
the first column must be the ID of the vertex.
"""
X = numpy.loadtxt(vertexFileName,
skiprows=1,
converters=self.converters,
usecols=self.vertexIndices,
delimiter=delimiter)
numVertices = X.shape[0]
numFeatures = X.shape[1] - 1
vertexIds = X[:, 0]
vertexIdsDict = {}
for i in range(0, numVertices):
vertexIdsDict[vertexIds[i]] = i
if self.nanProcessor != None:
X[:, 1:numFeatures + 1] = self.nanProcessor(X[:,
1:numFeatures + 1])
vertexList = VertexList(numVertices, numFeatures)
vertexList.setVertices(X[:, 1:numFeatures + 1])
maxEdgeTypes = len(edgeFileNames)
sparseMultiGraph = SparseMultiGraph(vertexList, maxEdgeTypes,
undirected)
for i in range(0, maxEdgeTypes):
self.__readEdgeFile(vertexIdsDict, edgeFileNames[i],
sparseMultiGraph, i)
logging.info("MultiGraph read with " +
str(sparseMultiGraph.getNumVertices()) +
" vertices and " + str(sparseMultiGraph.getNumEdges()) +
" edges")
return sparseMultiGraph
def testGetNumEdges(self):
sMultiGraph = SparseMultiGraph(self.vList, self.maxEdgeTypes)
self.assertEquals(sMultiGraph.getNumEdges(), 0)
for i in range(self.maxEdgeTypes):
self.assertEquals(sMultiGraph.getNumEdges(i), 0)
sMultiGraph.addEdge(0, 1, 2)
sMultiGraph.addEdge(0, 1, 1)
self.assertEquals(sMultiGraph.getNumEdges(), 2)
self.assertEquals(sMultiGraph.getNumEdges(1), 1)
self.assertEquals(sMultiGraph.getNumEdges(2), 1)
sMultiGraph.addEdge(0, 1, 0)
sMultiGraph.addEdge(0, 2, 0)
self.assertEquals(sMultiGraph.getNumEdges(), 4)
self.assertEquals(sMultiGraph.getNumEdges(0), 2)
def testInit(self):
sMultiGraph = SparseMultiGraph(self.vList, self.maxEdgeTypes)
sMultiGraph = SparseMultiGraph(self.vList, self.maxEdgeTypes, False)
self.assertRaises(ValueError, SparseMultiGraph, self.vList, 0)
self.assertRaises(ValueError, SparseMultiGraph, self.vList, -1)
def testIsUndirected(self):
self.assertEquals(self.sMultiGraph.isUndirected(), True)
sMultiGraph = SparseMultiGraph(self.vList, self.maxEdgeTypes, False)
self.assertEquals(sMultiGraph.isUndirected(), False)
