Python DictGraph.getVertices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 getVertices [as 别名]
    def testSetVertices(self):
        graph = DictGraph()

        vertexIndices = [1, 2, 3]
        vertices = ["a", "b", "c"]

        graph.setVertices(vertexIndices, vertices)

        vertexIndices2 = graph.getAllVertexIds()
        vertices2 = graph.getVertices(vertexIndices2)

        self.assertEquals(vertexIndices, vertexIndices2)
        self.assertEquals(vertices, vertices2)

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