Python DictGraph.subgraph方法代码示例

# 需要导入模块: from apgl.graph.DictGraph import DictGraph [as 别名]
# 或者: from apgl.graph.DictGraph.DictGraph import subgraph [as 别名]
    def testSubgraph(self):
        graph = DictGraph()

        graph.addEdge(0, 1)
        graph.addEdge(0, 2)
        graph.addEdge(0, 3)
        graph.addEdge(1, 2)
        graph.addEdge(2, 3)
        graph.setVertex(0, "abc")
        graph.setVertex(3, "cde")

        self.assertEquals(graph.getNumEdges(), 5)

        subgraph = graph.subgraph([0, 1, 2])
        self.assertEquals(subgraph.getNumVertices(), 3)
        self.assertEquals(subgraph.getNumEdges(), 3)
        self.assertEquals(subgraph.isUndirected(), True)
        self.assertEquals(subgraph.getEdge(0, 1), 1)
        self.assertEquals(subgraph.getEdge(0, 2), 1)
        self.assertEquals(subgraph.getEdge(1, 2), 1)
        self.assertEquals(subgraph.getVertex(0), "abc")

        #Check the original graph is fine
        self.assertEquals(graph.getNumVertices(), 4)
        self.assertEquals(graph.getNumEdges(), 5)
        self.assertEquals(graph.getVertex(0), "abc")
        self.assertEquals(graph.getVertex(3), "cde")

        #Now a quick test for directed graphs
        graph = DictGraph(False)

        graph.addEdge(0, 1)
        graph.addEdge(0, 2)
        graph.addEdge(0, 3)
        graph.addEdge(1, 2)
        graph.addEdge(2, 3)

        subgraph = graph.subgraph([0, 1, 2])
        self.assertEquals(subgraph.getNumEdges(), 3)
        self.assertEquals(subgraph.isUndirected(), False)
        self.assertEquals(subgraph.getEdge(0, 1), 1)
        self.assertEquals(subgraph.getEdge(0, 2), 1)
        self.assertEquals(subgraph.getEdge(1, 2), 1)

# 需要导入模块: from apgl.graph.DictGraph import DictGraph [as 别名]
# 或者: from apgl.graph.DictGraph.DictGraph import subgraph [as 别名]
    def __init__(self, minGraphSize=500, maxGraphSize=None, dayStep=30):
        
        dataDir = PathDefaults.getDataDir() + "cluster/"
        edgesFilename = dataDir + "Cit-HepTh.txt"
        dateFilename = dataDir + "Cit-HepTh-dates.txt"

        #Note the IDs are integers but can start with zero so we prefix "1" to each ID 
        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([vertex1, vertex2])
            
            #if vertex1 == vertex2: 
            #    print(vertex1)

        file.close()

        logging.info("Loaded edge file " + str(edgesFilename) + " with " + str(len(edges)) + " edges")

        #Keep an edge graph 
        graph = DictGraph(False)
        graph.addEdges(edges)
        logging.info("Created directed citation graph with " + str(graph.getNumEdges()) + " edges and " + str(graph.getNumVertices()) + " vertices")

        #Read in the dates articles appear in a dict which used the year and month
        #as the key and the value is a list of vertex ids. For each month we include
        #all papers uploaded that month and those directed cited by those uploads. 
        startDate = datetime.date(1990, 1, 1)

        file = open(dateFilename, 'r')
        file.readline()
        numLines = 0 
        subgraphIds = []

        for line in file:
            (id, sep, date) = line.partition("\t")
            id = id.strip()
            date = date.strip()
            

            inputDate = datetime.datetime.strptime(date.strip(), "%Y-%m-%d")
            inputDate = inputDate.date()

            if graph.vertexExists(id):
                tDelta = inputDate - startDate
                            
                graph.vertices[id] = tDelta.days 
                subgraphIds.append(id)
                
                #If a paper cites another, it must have been written before 
                #the citing paper - enforce this rule. 
                for neighbour in graph.neighbours(id): 
                    if graph.getVertex(neighbour) == None: 
                        graph.setVertex(neighbour, tDelta.days) 
                        subgraphIds.append(neighbour)
                    elif tDelta.days < graph.getVertex(neighbour): 
                        graph.setVertex(neighbour, tDelta.days) 
                        
            numLines += 1 
            
        file.close()
        
        subgraphIds = set(subgraphIds)
        graph = graph.subgraph(list(subgraphIds))
        logging.debug(graph)
        logging.info("Loaded date file " + str(dateFilename) + " with " + str(len(subgraphIds)) + " dates and " + str(numLines) + " lines")

        W = graph.getSparseWeightMatrix()
        W = W + W.T
        
        vList = VertexList(W.shape[0], 1)
        vList.setVertices(numpy.array([graph.getVertices(graph.getAllVertexIds())]).T)
        
        #Note: we have 16 self edges and some two-way citations so this graph has fewer edges than the directed one 
        self.graph = SparseGraph(vList, W=W)
        logging.debug(self.graph)
        
        #Now pick the max component 
        components = self.graph.findConnectedComponents()
        self.graph = self.graph.subgraph(components[0])
        
        logging.debug("Largest component graph: " + str(self.graph))
        
        self.minGraphSize = minGraphSize
        self.maxGraphSize = maxGraphSize 
        self.dayStep = dayStep 

# 需要导入模块: from apgl.graph.DictGraph import DictGraph [as 别名]
# 或者: from apgl.graph.DictGraph.DictGraph import subgraph [as 别名]
    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())