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 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 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
