def testGetIterator(self):
generator = CitationIterGenerator()
iterator = generator.getIterator()
lastW = iterator.next()
for W in iterator:
self.assertTrue((W-W.T).getnnz() == 0)
self.assertTrue((lastW - W[0:lastW.shape[0], 0:lastW.shape[0]]).getnnz() ==0 )
lastW = W
numVertices = W.shape[0]
#Now compute the vertexIds manually:
dataDir = PathDefaults.getDataDir() + "cluster/"
edgesFilename = dataDir + "Cit-HepTh.txt"
dateFilename = dataDir + "Cit-HepTh-dates.txt"
#We can't load in numbers using numpy since some may start with zero
edges = []
file = open(edgesFilename, 'r')
file.readline()
file.readline()
file.readline()
file.readline()
for line in file:
(vertex1, sep, vertex2) = line.partition("\t")
vertex1 = vertex1.strip()
vertex2 = vertex2.strip()
edges.append([int("1" + vertex1), int("1" + vertex2)])
edges = numpy.array(edges, numpy.int)
#Check file read correctly
self.assertTrue((edges[0, :] == numpy.array([11001, 19304045])).all())
self.assertTrue((edges[1, :] == numpy.array([11001, 19308122])).all())
self.assertTrue((edges[9, :] == numpy.array([11001, 19503124])).all())
vertexIds1 = numpy.unique(edges)
logging.info("Number of graph vertices: " + str(vertexIds1.shape[0]))
file = open(dateFilename, 'r')
file.readline()
vertexIds2 = []
for line in file:
(id, sep, date) = line.partition("\t")
id = id.strip()
date = date.strip()
vertexIds2.append(int("1" + id))
#Check file read correctly
vertexIds2 = numpy.array(vertexIds2, numpy.int)
self.assertTrue((vertexIds2[0:10] == numpy.array([19203201, 19203202, 19203203, 19203204, 19203205, 19203206, 19203207, 19203208, 19203209, 19203210], numpy.int)).all())
vertexIds2 = numpy.unique(numpy.array(vertexIds2, numpy.int))
graph = DictGraph(False)
graph.addEdges(edges)
#Find the set of vertices with known citation
vertices = []
vertexId2Set = set(vertexIds2.tolist())
for i in graph.getAllVertexIds():
Util.printIteration(i, 50000, edges.shape[0])
if i in vertexId2Set:
vertices.append(i)
vertices.extend(graph.neighbours(i))
logging.debug("Number of final vertices: " + str(numVertices))
numVertices2 = numpy.unique(numpy.array(vertices)).shape[0]
self.assertEquals(numVertices, numVertices2)
#Now compare the weight matrices using the undirected graph
#Note the order of vertices is different from the iterator
graph = DictGraph()
graph.addEdges(edges)
subgraph = graph.subgraph(numpy.unique(numpy.array(vertices)))
W2 = subgraph.getSparseWeightMatrix()
self.assertEquals(W.getnnz(), W2.getnnz())
def getIterator():
maxGraphSize = None
generator = CitationIterGenerator(maxGraphSize=maxGraphSize)
return generator.getIterator()
