def testGetAllVertexIds(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.getAllVertexIds(), [1, 2, 3, 5])
def testGetVertex(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.getVertex(1), None)
self.assertEquals(dictGraph.getVertex(2), None)
self.assertEquals(dictGraph.getVertex(3), None)
self.assertEquals(dictGraph.getVertex(5), 12)
self.assertRaises(ValueError, dictGraph.getVertex, 4)
#Directed graphs
dictGraph = DictGraph(False)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.getVertex(1), None)
self.assertEquals(dictGraph.getVertex(2), None)
self.assertEquals(dictGraph.getVertex(3), None)
self.assertEquals(dictGraph.getVertex(5), 12)
self.assertRaises(ValueError, dictGraph.getVertex, 4)
def testDensity(self):
numVertices = 10
graph = DictGraph(True)
for i in range(numVertices):
graph.setVertex(i, 0)
graph.addEdge(0, 1)
self.assertEquals(graph.density(), float(1)/45)
graph.addEdge(0, 2)
self.assertEquals(graph.density(), float(2)/45)
graph = DictGraph(False)
for i in range(numVertices):
graph.setVertex(i, 0)
graph.addEdge(0, 1)
self.assertEquals(graph.density(), float(1)/90)
graph.addEdge(0, 2)
self.assertEquals(graph.density(), float(2)/90)
#Test a graph with 1 vertex
graph = DictGraph(True)
graph.setVertex(0, 12)
self.assertEquals(graph.density(), 0)
graph.addEdge(0, 0)
self.assertEquals(graph.density(), 1)
def testGetAllEdgeIndices(self):
graph = DictGraph()
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
edgeIndices = graph.getAllEdgeIndices()
keys = graph.getAllVertexIds()
self.assertEquals(edgeIndices.shape[0], graph.getNumEdges())
for i in range(edgeIndices.shape[0]):
self.assertTrue(graph.getEdge(keys[int(edgeIndices[i, 0])], keys[edgeIndices[i, 1]]) == 1)
graph = DictGraph(False)
graph.addEdge("a", "b")
graph.addEdge("b", "a")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
edgeIndices = graph.getAllEdgeIndices()
keys = graph.getAllVertexIds()
self.assertEquals(edgeIndices.shape[0], graph.getNumEdges())
for i in range(edgeIndices.shape[0]):
self.assertTrue(graph.getEdge(keys[int(edgeIndices[i, 0])], keys[edgeIndices[i, 1]]) == 1)
def testSetItem(self):
graph = DictGraph()
graph.addEdge(1, 1, 0.1)
graph.addEdge(1, 3, 0.5)
self.assertEquals(graph[1,3], 0.5)
graph[1, 3] = 2
self.assertEquals(graph[1,3], 2)
def testGetItem(self):
graph = DictGraph()
graph.addEdge(1, 1, 0.1)
graph.addEdge(1, 3, 0.5)
graph.addEdge(2, 4, 1)
graph.addEdge(2, 3, 2)
graph.setVertex(0, "abc")
self.assertEquals(graph[1,1], 0.1)
self.assertEquals(graph[1,3], 0.5)
def testAddVertex(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.getVertex(5), 12)
dictGraph.setVertex(5, 22)
self.assertEquals(dictGraph.getVertex(5), 22)
dictGraph.addEdge(5, 11, 18)
self.assertEquals(dictGraph.getVertex(5), 22)
def testGetEdge(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
self.assertEquals(dictGraph.getEdge(1, 2), 12)
self.assertEquals(dictGraph.getEdge(2, 1), 12)
self.assertEquals(dictGraph.getEdge(2, 2), None)
self.assertRaises(ValueError, dictGraph.getEdge, 5, 8)
dictGraph = DictGraph(False)
dictGraph.addEdge(1, 2, 12)
self.assertEquals(dictGraph.getEdge(1, 2), 12)
self.assertEquals(dictGraph.getEdge(2, 1), None)
def testGetWeightMatrix(self):
graph = DictGraph()
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
W = graph.getWeightMatrix()
keys = graph.getAllVertexIds()
for i in range(len(keys)):
for j in range(len(keys)):
if W[i, j] == 1:
self.assertEquals(graph.getEdge(keys[i], keys[j]), 1)
else:
self.assertEquals(graph.getEdge(keys[i], keys[j]), None)
#Try a directed graph
graph = DictGraph(False)
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
W = graph.getWeightMatrix()
for i in range(len(keys)):
for j in range(len(keys)):
if W[i, j] == 1:
self.assertEquals(graph.getEdge(keys[i], keys[j]), 1)
else:
self.assertEquals(graph.getEdge(keys[i], keys[j]), None)
def testAdjacencyList(self):
graph = DictGraph()
graph.addEdge("a", "b", 1)
graph.addEdge("b", "c", 1)
graph.addEdge("b", "d", 1)
graph.addEdge("c", "e", 1)
graph.setVertex("f", 1)
neighbourIndices, neighbourWeights = graph.adjacencyList()
vertexIds = graph.getAllVertexIds()
for i in range(len(neighbourIndices)):
for k, j in enumerate(neighbourIndices[i]):
self.assertTrue(graph.edgeExists(vertexIds[i], vertexIds[j]))
self.assertEquals(graph[vertexIds[i], vertexIds[j]], neighbourWeights[i][k])
def testGetNumDirEdges(self):
graph = DictGraph()
graph.addEdge(0, 1, 0.1)
graph.addEdge(1, 2, 0.1)
self.assertTrue(graph.getNumDirEdges() == 4)
graph.addEdge(1, 1)
self.assertTrue(graph.getNumDirEdges() == 5)
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(1, 2)
self.assertTrue(graph.getNumDirEdges() == 2)
graph.addEdge(1, 1)
self.assertTrue(graph.getNumDirEdges() == 3)
def testBreadthFirstSearch(self):
graph = DictGraph()
graph.addEdge(0, 1)
graph.addEdge(0, 7)
graph.addEdge(7, 8)
graph.addEdge(7, 9)
graph.addEdge(1, 2)
graph.addEdge(1, 3)
graph.addEdge(2, 6)
graph.addEdge(4, 5)
self.assertEquals(graph.breadthFirstSearch(0), [0,1, 7,2,3,8,9,6])
self.assertEquals(graph.breadthFirstSearch(1), [1,0,2,3,7,6,8,9])
self.assertEquals(graph.breadthFirstSearch(6), [6, 2,1,0,3,7,8,9])
self.assertEquals(graph.breadthFirstSearch(4), [4, 5])
self.assertEquals(graph.breadthFirstSearch(5), [5, 4])
self.assertEquals(graph.breadthFirstSearch(7), [7, 0, 8, 9, 1, 2, 3, 6])
def testDepthFirstSearch(self):
graph = DictGraph()
graph.addEdge(0, 1)
graph.addEdge(1, 2)
graph.addEdge(1, 3)
graph.addEdge(2, 6)
graph.addEdge(4, 5)
self.assertEquals(graph.depthFirstSearch(0), [0,1,2,6,3])
self.assertEquals(graph.depthFirstSearch(1), [1,0,2,6,3])
self.assertEquals(graph.depthFirstSearch(6), [6,2,1,0,3])
self.assertEquals(graph.depthFirstSearch(4), [4, 5])
self.assertEquals(graph.depthFirstSearch(5), [5, 4])
def testVertexExists(self):
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
self.assertTrue(graph.vertexExists(0))
self.assertTrue(graph.vertexExists(1))
self.assertTrue(graph.vertexExists(2))
self.assertTrue(graph.vertexExists(3))
self.assertFalse(graph.vertexExists(4))
def testToSparseGraph(self):
graph = DictGraph()
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
graph.addEdge(3, 4)
graph2 = graph.toSparseGraph()
self.assertEquals(graph2[0, 1], 1)
self.assertEquals(graph2[0, 2], 1)
self.assertEquals(graph2[0, 3], 1)
self.assertEquals(graph2[2, 1], 1)
self.assertEquals(graph2[2, 3], 1)
self.assertEquals(graph2[3, 4], 1)
def testRemoveEdge(self):
dictGraph = DictGraph()
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getEdge(1, 2), 12)
self.assertEquals(dictGraph.getEdge(1, 3), 18)
self.assertEquals(dictGraph.getEdge(3, 4), 1)
dictGraph.removeEdge(1, 3)
self.assertEquals(dictGraph.getEdge(1, 3), None)
self.assertEquals(dictGraph.getEdge(1, 2), 12)
self.assertEquals(dictGraph.getEdge(3, 4), 1)
#Some tests on directed graphs
dictGraph = DictGraph(False)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(2, 1, 12)
dictGraph.removeEdge(1, 2)
self.assertEquals(dictGraph.getEdge(1, 2), None)
self.assertEquals(dictGraph.getEdge(2, 1), 12)
def testGetAllEdges(self):
dictGraph = DictGraph(True)
dictGraph.setVertex(5, 12)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
edges = dictGraph.getAllEdges()
self.assertEquals(len(edges), 2)
self.assertTrue((1,2) in edges)
self.assertTrue((1,3) in edges)
dictGraph = DictGraph(False)
dictGraph.setVertex(5, 12)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(2, 1, 12)
dictGraph.addEdge(1, 3, 18)
edges = dictGraph.getAllEdges()
self.assertEquals(len(edges), 3)
self.assertTrue((1,2) in edges)
self.assertTrue((2,1) in edges)
self.assertTrue((1,3) in edges)
class EgoSimulator:
"""
A class which simulates information diffusion processes within an Ego Network. In
this case one models information by taking as input a graph and then iterating using
a classifier for all pairs of vertices. The presence of information is stored
in the last index of the VertexList as a (0, 1) value.
"""
def __init__(self, graph, egoPairClassifier, preprocessor=None):
self.graph = graph
self.egoPairClassifier = egoPairClassifier
self.preprocessor = preprocessor
self.iteration = 0
self.allTransmissionEdges = []
self.transmissionGraph = DictGraph(False)
self.numVertexFeatures = self.graph.getVertexList().getNumFeatures()
self.numPersonFeatures = self.numVertexFeatures-1
self.infoIndex = self.numVertexFeatures-1
self.edges = self.graph.getAllEdges()
def advanceGraph(self):
#First, find all the edges in the graph and create an ExampleList
blockSize = 5000
X = numpy.zeros((blockSize, self.numPersonFeatures*2))
possibleTransmissionEdges = []
possibleTransmissionEdgeIndices = []
for i in range(self.edges.shape[0]):
vertex1 = self.graph.getVertex(self.edges[i,0])
vertex2 = self.graph.getVertex(self.edges[i,1])
if vertex1[self.infoIndex] == 1 and vertex2[self.infoIndex] == 0:
X[len(possibleTransmissionEdges), :] = numpy.r_[vertex1[0:self.numPersonFeatures], vertex2[0:self.numPersonFeatures]]
possibleTransmissionEdges.append((self.edges[i,0], self.edges[i,1]))
possibleTransmissionEdgeIndices.append(i)
if vertex2[self.infoIndex] == 1 and vertex1[self.infoIndex] == 0:
X[len(possibleTransmissionEdges), :] = numpy.r_[vertex2[0:self.numPersonFeatures], vertex1[0:self.numPersonFeatures]]
possibleTransmissionEdges.append((self.edges[i,1], self.edges[i,0]))
possibleTransmissionEdgeIndices.append(i)
#Increase X if it is small
if (len(possibleTransmissionEdges) == X.shape[0]):
X = numpy.r_[X, numpy.zeros((blockSize, self.numPersonFeatures*2))]
#Now, remove from edges the ones that can possible have a transmission
self.edges = numpy.delete(self.edges, possibleTransmissionEdgeIndices, 0)
X = X[0:len(possibleTransmissionEdges), :]
name = "X"
examplesList = ExamplesList(X.shape[0])
examplesList.addDataField(name, X)
examplesList.setDefaultExamplesName(name)
if self.preprocessor != None:
X = examplesList.getDataField(examplesList.getDefaultExamplesName())
X = self.preprocessor.standardiseArray(X)
examplesList.overwriteDataField(examplesList.getDefaultExamplesName(), X)
y = self.egoPairClassifier.classify(X)
transmissionEdges = numpy.zeros((sum(y==1), 2), numpy.int)
j = 0
#Now, update the vertices to reflect transfer
for i in range(len(possibleTransmissionEdges)):
if y[i] == 1:
transmissionEdges[j, 0] = possibleTransmissionEdges[i][0]
transmissionEdges[j, 1] = possibleTransmissionEdges[i][1]
self.transmissionGraph.setVertex(int(transmissionEdges[j, 0]), self.graph.getVertex(transmissionEdges[j, 0]))
self.transmissionGraph.setVertex(int(transmissionEdges[j, 1]), self.graph.getVertex(transmissionEdges[j, 1]))
self.transmissionGraph.addEdge(int(transmissionEdges[j, 0]), int(transmissionEdges[j, 1]), 1)
j += 1
vertex = self.graph.getVertex(possibleTransmissionEdges[i][1])
vertex[self.infoIndex] = 1
self.graph.setVertex(possibleTransmissionEdges[i][1], vertex)
self.allTransmissionEdges.append(transmissionEdges)
self.iteration = self.iteration + 1
return self.graph
def fullTransGraph(self):
"""
This function will return a new graph which contains a directed edge if
a transmission will occur between two vertices.
"""
if self.iteration != 0:
raise ValueError("Must run fullTransGraph before advanceGraph")
#First, find all the edges in the graph and create an ExampleList
numEdges = self.edges.shape[0]
X = numpy.zeros((numEdges*2, self.numPersonFeatures*2))
ind = 0
for i in range(numEdges):
vertex1 = self.graph.getVertex(self.edges[i,0])
vertex2 = self.graph.getVertex(self.edges[i,1])
X[ind, :] = numpy.r_[vertex1[0:self.numPersonFeatures], vertex2[0:self.numPersonFeatures]]
X[ind+numEdges, :] = numpy.r_[vertex2[0:self.numPersonFeatures], vertex1[0:self.numPersonFeatures]]
ind = ind + 1
name = "X"
examplesList = ExamplesList(X.shape[0])
examplesList.addDataField(name, X)
examplesList.setDefaultExamplesName(name)
if self.preprocessor != None:
X = self.preprocessor.process(examplesList.getDataField(examplesList.getDefaultExamplesName()))
examplesList.overwriteDataField(examplesList.getDefaultExamplesName(), X)
y = self.egoPairClassifier.classify(examplesList.getSampledDataField(name))
fullTransmissionGraph = SparseGraph(self.graph.getVertexList(), False)
transIndices = numpy.nonzero(y==1)[0]
#Now, write out the transmission graph
for i in range(len(transIndices)):
if transIndices[i] < numEdges:
fullTransmissionGraph.addEdge(self.edges[transIndices[i],0], self.edges[transIndices[i],1])
else:
fullTransmissionGraph.addEdge(self.edges[transIndices[i]-numEdges,1], self.edges[transIndices[i]-numEdges,0])
return fullTransmissionGraph
def getGraph(self):
return self.graph
def getTransmissions(self, i=None):
if i != None:
Parameter.checkIndex(i, 0, self.iteration)
return self.allTransmissionEdges[i]
else:
return self.allTransmissionEdges
def getAlters(self, i):
Parameter.checkIndex(i, 0, self.iteration)
alters = []
for j in range(0, len(self.allTransmissionEdges[i])):
alters.append(self.allTransmissionEdges[i][j, 1])
return numpy.unique(numpy.array(alters))
def getNumIterations(self):
return self.iteration
def getTransmissionGraph(self):
return self.transmissionGraph
graph = None
egoPairClassifier = None
preprocessor = None
iteration = None
allTransmissionEdges = []
transmissionGraph = None
def testRemoveVertex(self):
graph = DictGraph()
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
graph.addEdge(3, 4)
graph.removeVertex(4)
self.assertFalse(graph.vertexExists(4))
self.assertFalse(graph.edgeExists(3, 4))
graph.removeVertex(3)
self.assertFalse(graph.vertexExists(3))
self.assertFalse(graph.edgeExists(2, 3))
self.assertFalse(graph.edgeExists(0, 3))
graph.removeVertex(2)
self.assertFalse(graph.vertexExists(2))
self.assertFalse(graph.edgeExists(1, 2))
self.assertFalse(graph.edgeExists(0, 2))
self.assertTrue(graph.getAllVertexIds() == [0, 1])
self.assertTrue(graph.getAllEdges() == [(0, 1)])
#Try directed graph
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(1, 0)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
graph.addEdge(3, 4)
graph.removeVertex(0)
self.assertFalse(graph.vertexExists(0))
self.assertFalse(graph.edgeExists(0, 1))
self.assertFalse(graph.edgeExists(0, 3))
self.assertFalse(graph.edgeExists(1, 0))
graph.removeVertex(2)
self.assertFalse(graph.vertexExists(2))
self.assertFalse(graph.edgeExists(1, 2))
self.assertFalse(graph.edgeExists(2, 3))
self.assertTrue(graph.getAllVertexIds() == [1, 3, 4])
self.assertTrue(graph.getAllEdges() == [(3, 4)])
def testInDegreeSequence(self):
graph = DictGraph(True)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
degSeq, vertices = graph.inDegreeSequence()
self.assertTrue((degSeq == numpy.array([ 3, 2, 3, 2.])).all())
self.assertTrue(vertices == [0, 1, 2, 3])
#Test results on a directed graph
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
degSeq, vertices = graph.inDegreeSequence()
self.assertTrue((degSeq == numpy.array([ 0, 1, 2, 2])).all())
class SimpleGraphWriterTest(unittest.TestCase):
def setUp(self):
#Finally, try DictGraphs
self.dctGraph1 = DictGraph(True)
self.dctGraph1.addEdge(0, 1, 1)
self.dctGraph1.addEdge(0, 2, 2)
self.dctGraph1.addEdge(2, 4, 8)
self.dctGraph1.addEdge(2, 3, 1)
self.dctGraph1.addEdge(12, 4, 1)
self.dctGraph2 = DictGraph(False)
self.dctGraph2.addEdge(0, 1, 0.5)
self.dctGraph2.addEdge(0, 2, 1)
self.dctGraph2.addEdge(2, 4, 1)
self.dctGraph2.addEdge(2, 3, 0.2)
self.dctGraph2.addEdge(12, 4, 1)
def testWriteToFile(self):
sgw = SimpleGraphWriter()
directory = PathDefaults.getOutputDir() + "test/"
#Have to check the files
fileName1 = directory + "dictTestUndirected"
sgw.writeToFile(fileName1, self.dctGraph1)
fileName2 = directory + "dictTestDirected"
sgw.writeToFile(fileName2, self.dctGraph2)
def testDijkstrasAlgorithm(self):
graph = DictGraph()
graph.addEdge(0, 1, 1)
graph.addEdge(1, 2, 1)
graph.addEdge(1, 3, 1)
graph.addEdge(2, 4, 1)
graph.setVertex(4, 1)
self.assertTrue((graph.dijkstrasAlgorithm(0) == numpy.array([0, 1, 2, 2, 3])).all())
self.assertTrue((graph.dijkstrasAlgorithm(1) == numpy.array([1, 0, 1, 1, 2])).all())
self.assertTrue((graph.dijkstrasAlgorithm(2) == numpy.array([2, 1, 0, 2, 1])).all())
self.assertTrue((graph.dijkstrasAlgorithm(3) == numpy.array([2, 1, 2, 0, 3])).all())
self.assertTrue((graph.dijkstrasAlgorithm(4) == numpy.array([3, 2, 1, 3, 0])).all())
#Test a graph which has an isolated node
graph = DictGraph()
graph.setVertex(5, 1)
graph.addEdge(0, 1, 1)
graph.addEdge(1, 2, 1)
graph.addEdge(1, 3, 1)
self.assertTrue((graph.dijkstrasAlgorithm(0) == numpy.array([0, 1, 2, 2, numpy.inf])).all())
#Test a graph in a ring
graph = DictGraph()
graph.addEdge(0, 1, 1)
graph.addEdge(1, 2, 1)
graph.addEdge(2, 3, 1)
graph.addEdge(3, 4, 1)
graph.addEdge(4, 0, 1)
self.assertTrue((graph.dijkstrasAlgorithm(0) == numpy.array([0, 1, 2, 2, 1])).all())
#Try case in which vertex ids are not numbers
graph = DictGraph()
graph.addEdge("a", "b", 1)
graph.addEdge("b", "c", 1)
graph.addEdge("b", "d", 1)
graph.addEdge("c", "e", 1)
inds = Util.argsort(graph.getAllVertexIds())
self.assertTrue((graph.dijkstrasAlgorithm("a")[inds] == numpy.array([0, 1, 2, 2, 3])).all())
self.assertTrue((graph.dijkstrasAlgorithm("b")[inds] == numpy.array([1, 0, 1, 1, 2])).all())
self.assertTrue((graph.dijkstrasAlgorithm("c")[inds] == numpy.array([2, 1, 0, 2, 1])).all())
self.assertTrue((graph.dijkstrasAlgorithm("d")[inds] == numpy.array([2, 1, 2, 0, 3])).all())
self.assertTrue((graph.dijkstrasAlgorithm("e")[inds] == numpy.array([3, 2, 1, 3, 0])).all())
"""
Name: Generate Graph:
Author: Jia_qiu Wang(王佳秋)
Data: December, 2016
function:
"""
from apgl.graph.DictGraph import DictGraph
from apgl.graph.SparseGraph import SparseGraph
from apgl.graph.GeneralVertexList import GeneralVertexList
graph = DictGraph()
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
edgeIndices = graph.getAllEdgeIndices()
graph2 = SparseGraph(GeneralVertexList(graph.getNumVertices()))
graph2.addEdges(edgeIndices)
# -*- coding: utf-8 -*-
from apgl.graph.DictGraph import DictGraph
from apgl.graph.SparseGraph import SparseGraph
from apgl.graph.GeneralVertexList import GeneralVertexList
graph = DictGraph()
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
edgeIndices = graph.getAllEdgeIndices()
graph2 = SparseGraph(GeneralVertexList(graph.getNumVertices()))
graph2.addEdges(edgeIndices)
class DictGraphTest(unittest.TestCase):
def setUp(self):
self.graph = DictGraph()
self.graph.addEdge(0, 1, 1)
self.graph.addEdge(1, 3, 1)
self.graph.addEdge(0, 2, 2)
self.graph.addEdge(2, 3, 5)
self.graph.addEdge(0, 4, 1)
self.graph.addEdge(3, 4, 1)
self.graph.setVertex(5, None)
self.graph2 = DictGraph(False)
self.graph2.addEdge(0, 1, 1)
self.graph2.addEdge(1, 3, 1)
self.graph2.addEdge(0, 2, 2)
self.graph2.addEdge(2, 3, 5)
self.graph2.addEdge(0, 4, 1)
self.graph2.addEdge(3, 4, 1)
self.graph2.setVertex(5, 1)
def testInit(self):
dictGraph = DictGraph()
def testAddEdge(self):
dictGraph = DictGraph()
dictGraph.addEdge("A", "B", [1,2,3])
dictGraph.addEdge("A", "C", "HelloThere")
dictGraph.addEdge(12, 8, [1,2,3, 12])
self.assertEquals(dictGraph.getEdge("A", "B"), [1,2,3])
self.assertEquals(dictGraph.getEdge("B", "A"), [1,2,3])
self.assertEquals(dictGraph.getEdge("A", "C"), "HelloThere")
self.assertEquals(dictGraph.getEdge("C", "A"), "HelloThere")
self.assertEquals(dictGraph.getEdge(12, 8), [1,2,3, 12])
self.assertEquals(dictGraph.getEdge(8, 12), [1,2,3, 12])
dictGraph.addEdge(2, 8)
dictGraph = DictGraph(False)
dictGraph.addEdge("A", "B", [1,2,3])
dictGraph.addEdge("A", "C", "HelloThere")
dictGraph.addEdge(12, 8, [1,2,3, 12])
self.assertEquals(dictGraph.getEdge("A", "B"), [1,2,3])
self.assertEquals(dictGraph.getEdge("B", "A"), None)
self.assertEquals(dictGraph.getEdge("A", "C"), "HelloThere")
self.assertEquals(dictGraph.getEdge("C", "A"), None)
self.assertEquals(dictGraph.getEdge(12, 8), [1,2,3, 12])
self.assertEquals(dictGraph.getEdge(8, 12), None)
dictGraph.addEdge(2, 8)
#Test directed graphs
def testRemoveEdge(self):
dictGraph = DictGraph()
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getEdge(1, 2), 12)
self.assertEquals(dictGraph.getEdge(1, 3), 18)
self.assertEquals(dictGraph.getEdge(3, 4), 1)
dictGraph.removeEdge(1, 3)
self.assertEquals(dictGraph.getEdge(1, 3), None)
self.assertEquals(dictGraph.getEdge(1, 2), 12)
self.assertEquals(dictGraph.getEdge(3, 4), 1)
#Some tests on directed graphs
dictGraph = DictGraph(False)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(2, 1, 12)
dictGraph.removeEdge(1, 2)
self.assertEquals(dictGraph.getEdge(1, 2), None)
self.assertEquals(dictGraph.getEdge(2, 1), 12)
def testIsUndirected(self):
dictGraph = DictGraph(True)
self.assertEquals(dictGraph.isUndirected(), True)
dictGraph = DictGraph(False)
self.assertEquals(dictGraph.isUndirected(), False)
def testGetNumEdges(self):
dictGraph = DictGraph(True)
self.assertEquals(dictGraph.getNumEdges(), 0)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getNumEdges(), 3)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getNumEdges(), 3)
dictGraph.addEdge(3, 5, 1)
self.assertEquals(dictGraph.getNumEdges(), 4)
dictGraph.addEdge(3, 3, 1)
self.assertEquals(dictGraph.getNumEdges(), 5)
#Identical tests with directed graphs
dictGraph = DictGraph(False)
self.assertEquals(dictGraph.getNumEdges(), 0)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getNumEdges(), 3)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getNumEdges(), 3)
dictGraph.addEdge(3, 5, 1)
self.assertEquals(dictGraph.getNumEdges(), 4)
dictGraph.addEdge(3, 3, 1)
self.assertEquals(dictGraph.getNumEdges(), 5)
def testGetEdge(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
self.assertEquals(dictGraph.getEdge(1, 2), 12)
self.assertEquals(dictGraph.getEdge(2, 1), 12)
self.assertEquals(dictGraph.getEdge(2, 2), None)
self.assertRaises(ValueError, dictGraph.getEdge, 5, 8)
dictGraph = DictGraph(False)
dictGraph.addEdge(1, 2, 12)
self.assertEquals(dictGraph.getEdge(1, 2), 12)
self.assertEquals(dictGraph.getEdge(2, 1), None)
def testGetNeighbours(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(1, 4, 1)
dictGraph.addEdge(3, 4, 1)
dictGraph.addEdge(2, 2, 1)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.neighbours(1), [2, 3, 4])
self.assertEquals(dictGraph.neighbours(3), [1, 4])
self.assertEquals(dictGraph.neighbours(2), [1, 2])
self.assertEquals(dictGraph.neighbours(5), [])
#Directed graphs
dictGraph = DictGraph(False)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(1, 4, 1)
dictGraph.addEdge(3, 4, 1)
dictGraph.addEdge(2, 2, 1)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.neighbours(1), [2,3,4])
self.assertEquals(dictGraph.neighbours(3), [4])
self.assertEquals(dictGraph.neighbours(2), [2])
self.assertEquals(dictGraph.neighbours(5), [])
def testGetVertex(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.getVertex(1), None)
self.assertEquals(dictGraph.getVertex(2), None)
self.assertEquals(dictGraph.getVertex(3), None)
self.assertEquals(dictGraph.getVertex(5), 12)
self.assertRaises(ValueError, dictGraph.getVertex, 4)
#Directed graphs
dictGraph = DictGraph(False)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.getVertex(1), None)
self.assertEquals(dictGraph.getVertex(2), None)
self.assertEquals(dictGraph.getVertex(3), None)
self.assertEquals(dictGraph.getVertex(5), 12)
self.assertRaises(ValueError, dictGraph.getVertex, 4)
def testAddVertex(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.getVertex(5), 12)
dictGraph.setVertex(5, 22)
self.assertEquals(dictGraph.getVertex(5), 22)
dictGraph.addEdge(5, 11, 18)
self.assertEquals(dictGraph.getVertex(5), 22)
def testGetAllVertexIds(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.getAllVertexIds(), [1, 2, 3, 5])
def testGetAllEdges(self):
dictGraph = DictGraph(True)
dictGraph.setVertex(5, 12)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
edges = dictGraph.getAllEdges()
self.assertEquals(len(edges), 2)
self.assertTrue((1,2) in edges)
self.assertTrue((1,3) in edges)
dictGraph = DictGraph(False)
dictGraph.setVertex(5, 12)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(2, 1, 12)
dictGraph.addEdge(1, 3, 18)
edges = dictGraph.getAllEdges()
self.assertEquals(len(edges), 3)
self.assertTrue((1,2) in edges)
self.assertTrue((2,1) in edges)
self.assertTrue((1,3) in edges)
def testDensity(self):
numVertices = 10
graph = DictGraph(True)
for i in range(numVertices):
graph.setVertex(i, 0)
graph.addEdge(0, 1)
self.assertEquals(graph.density(), float(1)/45)
graph.addEdge(0, 2)
self.assertEquals(graph.density(), float(2)/45)
graph = DictGraph(False)
for i in range(numVertices):
graph.setVertex(i, 0)
graph.addEdge(0, 1)
self.assertEquals(graph.density(), float(1)/90)
graph.addEdge(0, 2)
self.assertEquals(graph.density(), float(2)/90)
#Test a graph with 1 vertex
graph = DictGraph(True)
graph.setVertex(0, 12)
self.assertEquals(graph.density(), 0)
graph.addEdge(0, 0)
self.assertEquals(graph.density(), 1)
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)
def testGetWeightMatrix(self):
graph = DictGraph()
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
W = graph.getWeightMatrix()
keys = graph.getAllVertexIds()
for i in range(len(keys)):
for j in range(len(keys)):
if W[i, j] == 1:
self.assertEquals(graph.getEdge(keys[i], keys[j]), 1)
else:
self.assertEquals(graph.getEdge(keys[i], keys[j]), None)
#Try a directed graph
graph = DictGraph(False)
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
W = graph.getWeightMatrix()
for i in range(len(keys)):
for j in range(len(keys)):
if W[i, j] == 1:
self.assertEquals(graph.getEdge(keys[i], keys[j]), 1)
else:
self.assertEquals(graph.getEdge(keys[i], keys[j]), None)
def testGetSparseWeightMatrix(self):
graph = DictGraph()
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d", "blah")
graph.addEdge("d", "e", -1.1)
graph.addEdge("c", "b", 2)
W = graph.getSparseWeightMatrix()
keys = graph.getAllVertexIds()
for i in range(len(keys)):
for j in range(len(keys)):
if graph.edgeExists(keys[i], keys[j]) and not isinstance(graph.getEdge(keys[i], keys[j]), numbers.Number):
self.assertEquals(1, W[i, j])
elif W[i, j] != 0:
self.assertEquals(graph.getEdge(keys[i], keys[j]), W[i, j])
else:
self.assertEquals(graph.getEdge(keys[i], keys[j]), None)
#Try a directed graph
graph = DictGraph(False)
graph.addEdge("a", "b")
graph.addEdge("a", "c", "test")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
graph.addEdge("c", "a", 0.1)
W = graph.getSparseWeightMatrix()
for i in range(len(keys)):
for j in range(len(keys)):
if graph.edgeExists(keys[i], keys[j]) and not isinstance(graph.getEdge(keys[i], keys[j]), numbers.Number):
self.assertEquals(1, W[i, j])
elif W[i, j] != 0:
self.assertEquals(graph.getEdge(keys[i], keys[j]), W[i, j])
else:
self.assertEquals(graph.getEdge(keys[i], keys[j]), None)
def testGetAllEdgeIndices(self):
graph = DictGraph()
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
edgeIndices = graph.getAllEdgeIndices()
keys = graph.getAllVertexIds()
self.assertEquals(edgeIndices.shape[0], graph.getNumEdges())
for i in range(edgeIndices.shape[0]):
self.assertTrue(graph.getEdge(keys[int(edgeIndices[i, 0])], keys[edgeIndices[i, 1]]) == 1)
graph = DictGraph(False)
graph.addEdge("a", "b")
graph.addEdge("b", "a")
graph.addEdge("a", "c")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
edgeIndices = graph.getAllEdgeIndices()
keys = graph.getAllVertexIds()
self.assertEquals(edgeIndices.shape[0], graph.getNumEdges())
for i in range(edgeIndices.shape[0]):
self.assertTrue(graph.getEdge(keys[int(edgeIndices[i, 0])], keys[edgeIndices[i, 1]]) == 1)
def testGetItem(self):
graph = DictGraph()
graph.addEdge(1, 1, 0.1)
graph.addEdge(1, 3, 0.5)
graph.addEdge(2, 4, 1)
graph.addEdge(2, 3, 2)
graph.setVertex(0, "abc")
self.assertEquals(graph[1,1], 0.1)
self.assertEquals(graph[1,3], 0.5)
def testSetItem(self):
graph = DictGraph()
graph.addEdge(1, 1, 0.1)
graph.addEdge(1, 3, 0.5)
self.assertEquals(graph[1,3], 0.5)
graph[1, 3] = 2
self.assertEquals(graph[1,3], 2)
def testAddEdges(self):
graph = DictGraph()
edgeList = [(1, 2), (2, 1), (5, 2), (8, 8)]
graph.addEdges(edgeList)
self.assertEquals(graph.getNumEdges(), 3)
self.assertEquals(graph.getEdge(1, 2), 1)
self.assertEquals(graph.getEdge(5, 2), 1)
self.assertEquals(graph.getEdge(2, 1), 1)
self.assertEquals(graph.getEdge(8, 8), 1)
edgeValues = [1, 2, 3, 4]
graph.addEdges(edgeList, edgeValues)
self.assertEquals(graph.getEdge(1, 2), 2)
self.assertEquals(graph.getEdge(5, 2), 3)
self.assertEquals(graph.getEdge(2, 1), 2)
self.assertEquals(graph.getEdge(8, 8), 4)
#Now test directed graphs
graph = DictGraph(False)
graph.addEdges(edgeList)
self.assertEquals(graph.getNumEdges(), 4)
self.assertEquals(graph.getEdge(1, 2), 1)
self.assertEquals(graph.getEdge(5, 2), 1)
self.assertEquals(graph.getEdge(2, 1), 1)
self.assertEquals(graph.getEdge(8, 8), 1)
edgeValues = [1, 2, 3, 4]
graph.addEdges(edgeList, edgeValues)
self.assertEquals(graph.getEdge(1, 2), 1)
self.assertEquals(graph.getEdge(5, 2), 3)
self.assertEquals(graph.getEdge(2, 1), 2)
self.assertEquals(graph.getEdge(8, 8), 4)
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)
def testNeighbourOf(self):
graph = DictGraph(True)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
for i in range(4):
self.assertEquals(graph.neighbours(i), graph.neighbourOf(i))
#Now test directed graph
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
self.assertEquals(graph.neighbourOf(0), [])
self.assertEquals(graph.neighbourOf(1), [0])
self.assertEquals(graph.neighbourOf(2), [0,1])
self.assertEquals(graph.neighbourOf(3), [0, 2])
def testOutDegreeSequence(self):
graph = DictGraph(True)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
degSeq, vertices = graph.outDegreeSequence()
self.assertTrue((degSeq == numpy.array([ 3, 2, 3, 2.])).all())
self.assertTrue(vertices == [0, 1, 2, 3])
#Test results on a directed graph
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
degSeq, vertices = graph.outDegreeSequence()
self.assertTrue((degSeq == numpy.array([ 3, 1, 1, 0])).all())
def testInDegreeSequence(self):
graph = DictGraph(True)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
degSeq, vertices = graph.inDegreeSequence()
self.assertTrue((degSeq == numpy.array([ 3, 2, 3, 2.])).all())
self.assertTrue(vertices == [0, 1, 2, 3])
#Test results on a directed graph
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
degSeq, vertices = graph.inDegreeSequence()
self.assertTrue((degSeq == numpy.array([ 0, 1, 2, 2])).all())
def testVertexExists(self):
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
self.assertTrue(graph.vertexExists(0))
self.assertTrue(graph.vertexExists(1))
self.assertTrue(graph.vertexExists(2))
self.assertTrue(graph.vertexExists(3))
self.assertFalse(graph.vertexExists(4))
def testRemoveVertex(self):
graph = DictGraph()
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
graph.addEdge(3, 4)
graph.removeVertex(4)
self.assertFalse(graph.vertexExists(4))
self.assertFalse(graph.edgeExists(3, 4))
graph.removeVertex(3)
self.assertFalse(graph.vertexExists(3))
self.assertFalse(graph.edgeExists(2, 3))
self.assertFalse(graph.edgeExists(0, 3))
graph.removeVertex(2)
self.assertFalse(graph.vertexExists(2))
self.assertFalse(graph.edgeExists(1, 2))
self.assertFalse(graph.edgeExists(0, 2))
self.assertTrue(graph.getAllVertexIds() == [0, 1])
self.assertTrue(graph.getAllEdges() == [(0, 1)])
#Try directed graph
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(1, 0)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
graph.addEdge(3, 4)
graph.removeVertex(0)
self.assertFalse(graph.vertexExists(0))
self.assertFalse(graph.edgeExists(0, 1))
self.assertFalse(graph.edgeExists(0, 3))
self.assertFalse(graph.edgeExists(1, 0))
graph.removeVertex(2)
self.assertFalse(graph.vertexExists(2))
self.assertFalse(graph.edgeExists(1, 2))
self.assertFalse(graph.edgeExists(2, 3))
self.assertTrue(graph.getAllVertexIds() == [1, 3, 4])
self.assertTrue(graph.getAllEdges() == [(3, 4)])
def testToSparseGraph(self):
graph = DictGraph()
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
graph.addEdge(3, 4)
graph2 = graph.toSparseGraph()
self.assertEquals(graph2[0, 1], 1)
self.assertEquals(graph2[0, 2], 1)
self.assertEquals(graph2[0, 3], 1)
self.assertEquals(graph2[2, 1], 1)
self.assertEquals(graph2[2, 3], 1)
self.assertEquals(graph2[3, 4], 1)
def testDepthFirstSearch(self):
graph = DictGraph()
graph.addEdge(0, 1)
graph.addEdge(1, 2)
graph.addEdge(1, 3)
graph.addEdge(2, 6)
graph.addEdge(4, 5)
self.assertEquals(graph.depthFirstSearch(0), [0,1,2,6,3])
self.assertEquals(graph.depthFirstSearch(1), [1,0,2,6,3])
self.assertEquals(graph.depthFirstSearch(6), [6,2,1,0,3])
self.assertEquals(graph.depthFirstSearch(4), [4, 5])
self.assertEquals(graph.depthFirstSearch(5), [5, 4])
def testBreadthFirstSearch(self):
graph = DictGraph()
graph.addEdge(0, 1)
graph.addEdge(0, 7)
graph.addEdge(7, 8)
graph.addEdge(7, 9)
graph.addEdge(1, 2)
graph.addEdge(1, 3)
graph.addEdge(2, 6)
graph.addEdge(4, 5)
self.assertEquals(graph.breadthFirstSearch(0), [0,1, 7,2,3,8,9,6])
self.assertEquals(graph.breadthFirstSearch(1), [1,0,2,3,7,6,8,9])
self.assertEquals(graph.breadthFirstSearch(6), [6, 2,1,0,3,7,8,9])
self.assertEquals(graph.breadthFirstSearch(4), [4, 5])
self.assertEquals(graph.breadthFirstSearch(5), [5, 4])
self.assertEquals(graph.breadthFirstSearch(7), [7, 0, 8, 9, 1, 2, 3, 6])
def testDegreeSequence(self):
graph = DictGraph()
graph.setVertex("a", 10)
graph["b", "c"] = 1
graph["b", "d"] = 1
graph["d", "e"] = 1
graph["e", "e"] = 1
degreeDict = {}
degreeDict2 = {"a": 0, "b": 2, "c": 1, "d": 2, "e": 3}
for i, id in enumerate(graph.getAllVertexIds()):
degreeDict[id] = graph.degreeSequence()[i]
self.assertEquals(degreeDict, degreeDict2)
def testGetNumDirEdges(self):
graph = DictGraph()
graph.addEdge(0, 1, 0.1)
graph.addEdge(1, 2, 0.1)
self.assertTrue(graph.getNumDirEdges() == 4)
graph.addEdge(1, 1)
self.assertTrue(graph.getNumDirEdges() == 5)
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(1, 2)
self.assertTrue(graph.getNumDirEdges() == 2)
graph.addEdge(1, 1)
self.assertTrue(graph.getNumDirEdges() == 3)
def testDijkstrasAlgorithm(self):
graph = DictGraph()
graph.addEdge(0, 1, 1)
graph.addEdge(1, 2, 1)
graph.addEdge(1, 3, 1)
graph.addEdge(2, 4, 1)
graph.setVertex(4, 1)
self.assertTrue((graph.dijkstrasAlgorithm(0) == numpy.array([0, 1, 2, 2, 3])).all())
self.assertTrue((graph.dijkstrasAlgorithm(1) == numpy.array([1, 0, 1, 1, 2])).all())
self.assertTrue((graph.dijkstrasAlgorithm(2) == numpy.array([2, 1, 0, 2, 1])).all())
self.assertTrue((graph.dijkstrasAlgorithm(3) == numpy.array([2, 1, 2, 0, 3])).all())
self.assertTrue((graph.dijkstrasAlgorithm(4) == numpy.array([3, 2, 1, 3, 0])).all())
#Test a graph which has an isolated node
graph = DictGraph()
graph.setVertex(5, 1)
graph.addEdge(0, 1, 1)
graph.addEdge(1, 2, 1)
graph.addEdge(1, 3, 1)
self.assertTrue((graph.dijkstrasAlgorithm(0) == numpy.array([0, 1, 2, 2, numpy.inf])).all())
#Test a graph in a ring
graph = DictGraph()
graph.addEdge(0, 1, 1)
graph.addEdge(1, 2, 1)
graph.addEdge(2, 3, 1)
graph.addEdge(3, 4, 1)
graph.addEdge(4, 0, 1)
self.assertTrue((graph.dijkstrasAlgorithm(0) == numpy.array([0, 1, 2, 2, 1])).all())
#Try case in which vertex ids are not numbers
graph = DictGraph()
graph.addEdge("a", "b", 1)
graph.addEdge("b", "c", 1)
graph.addEdge("b", "d", 1)
graph.addEdge("c", "e", 1)
inds = Util.argsort(graph.getAllVertexIds())
self.assertTrue((graph.dijkstrasAlgorithm("a")[inds] == numpy.array([0, 1, 2, 2, 3])).all())
self.assertTrue((graph.dijkstrasAlgorithm("b")[inds] == numpy.array([1, 0, 1, 1, 2])).all())
self.assertTrue((graph.dijkstrasAlgorithm("c")[inds] == numpy.array([2, 1, 0, 2, 1])).all())
self.assertTrue((graph.dijkstrasAlgorithm("d")[inds] == numpy.array([2, 1, 2, 0, 3])).all())
self.assertTrue((graph.dijkstrasAlgorithm("e")[inds] == numpy.array([3, 2, 1, 3, 0])).all())
def testAdjacencyList(self):
graph = DictGraph()
graph.addEdge("a", "b", 1)
graph.addEdge("b", "c", 1)
graph.addEdge("b", "d", 1)
graph.addEdge("c", "e", 1)
graph.setVertex("f", 1)
neighbourIndices, neighbourWeights = graph.adjacencyList()
vertexIds = graph.getAllVertexIds()
for i in range(len(neighbourIndices)):
for k, j in enumerate(neighbourIndices[i]):
self.assertTrue(graph.edgeExists(vertexIds[i], vertexIds[j]))
self.assertEquals(graph[vertexIds[i], vertexIds[j]], neighbourWeights[i][k])
def testFindAllDistances(self):
P = self.graph.findAllDistances()
P2 = numpy.zeros((self.graph.size, self.graph.size))
P2[0, :] = numpy.array([0, 1, 2, 2, 1, numpy.inf])
P2[1, :] = numpy.array([1, 0, 3, 1, 2, numpy.inf])
P2[2, :] = numpy.array([2, 3, 0, 4, 3, numpy.inf])
P2[3, :] = numpy.array([2, 1, 4, 0, 1, numpy.inf])
P2[4, :] = numpy.array([1, 2, 3, 1, 0, numpy.inf])
P2[5, :] = numpy.array([numpy.inf, numpy.inf, numpy.inf, numpy.inf, numpy.inf, 0])
self.assertTrue((P == P2).all())
#Now test the directed graph
P = self.graph2.findAllDistances()
P2 = numpy.zeros((self.graph.size, self.graph.size))
P2[0, :] = numpy.array([0, 1, 2, 2, 1, numpy.inf])
P2[1, :] = numpy.array([numpy.inf, 0, numpy.inf, 1, 2, numpy.inf])
P2[2, :] = numpy.array([numpy.inf, numpy.inf, 0, 5, 6, numpy.inf])
P2[3, :] = numpy.array([numpy.inf, numpy.inf, numpy.inf, 0, 1, numpy.inf])
P2[4, :] = numpy.array([numpy.inf, numpy.inf, numpy.inf, numpy.inf, 0, numpy.inf])
P2[5, :] = numpy.array([numpy.inf, numpy.inf, numpy.inf, numpy.inf, numpy.inf, 0])
self.assertTrue((P == P2).all())
def testToIGraph(self):
try:
import igraph
except ImportError as error:
logging.debug(error)
return
graph = DictGraph()
graph["a", "b"] = 1
graph["b", "c"] = 2
ig = graph.toIGraph()
self.assertEquals(len(ig.vs), 3)
self.assertEquals(ig[0, 2], 1)
self.assertEquals(ig[1, 2], 1)
def testAddEdge(self):
dictGraph = DictGraph()
dictGraph.addEdge("A", "B", [1,2,3])
dictGraph.addEdge("A", "C", "HelloThere")
dictGraph.addEdge(12, 8, [1,2,3, 12])
self.assertEquals(dictGraph.getEdge("A", "B"), [1,2,3])
self.assertEquals(dictGraph.getEdge("B", "A"), [1,2,3])
self.assertEquals(dictGraph.getEdge("A", "C"), "HelloThere")
self.assertEquals(dictGraph.getEdge("C", "A"), "HelloThere")
self.assertEquals(dictGraph.getEdge(12, 8), [1,2,3, 12])
self.assertEquals(dictGraph.getEdge(8, 12), [1,2,3, 12])
dictGraph.addEdge(2, 8)
dictGraph = DictGraph(False)
dictGraph.addEdge("A", "B", [1,2,3])
dictGraph.addEdge("A", "C", "HelloThere")
dictGraph.addEdge(12, 8, [1,2,3, 12])
self.assertEquals(dictGraph.getEdge("A", "B"), [1,2,3])
self.assertEquals(dictGraph.getEdge("B", "A"), None)
self.assertEquals(dictGraph.getEdge("A", "C"), "HelloThere")
self.assertEquals(dictGraph.getEdge("C", "A"), None)
self.assertEquals(dictGraph.getEdge(12, 8), [1,2,3, 12])
self.assertEquals(dictGraph.getEdge(8, 12), None)
dictGraph.addEdge(2, 8)
class DatedPurchasesGraphListIterator(object):
def __init__(self, purchasesByWeek, nb_purchases_per_it=None):
"""
The background graph is a bi-partite graph of purchases. Purchases are
grouped by date (week by week), and we consider the graph of purchases
between first week and $i$-th week.
The returned graph considers only users and counts the number of common
purchases between two users.
Purchases are given in a list of [user, prod, week, year] with increasing
date.
nb_purchases_per_it is the maximum number of purchases to put in each
week (if there is more, randomly split the week). None corresponds to
no-limit case.
"""
# args
self.group_by_iterator = DatedPurchasesGroupByIterator(
purchasesByWeek, nb_purchases_per_it)
# init variables
self.dictUser = MyDictionary()
self.dictProd = MyDictionary()
for user, prod, week, year in purchasesByWeek:
self.dictUser.index(user)
self.dictProd.index(prod)
self.backgroundGraph = DictGraph(False) # directed
self.W = scipy.sparse.csr_matrix(
(len(self.dictUser), len(self.dictUser)), dtype='int16')
self.usefullEdges = numpy.array([])
def __iter__(self):
return self
def __next__(self):
# next group of purchases (StopIteration is raised here)
purchases_sublist = next(self.group_by_iterator)
#logging.debug(" nb purchases: " + str(len(purchases_sublist)))
# to check that the group really induces new edges
W_has_changed = False
# update graphs adding current-week purchases
for user, prod, week, year in purchases_sublist:
# update only if this purchase is seen for the first time
try:
newEdge = not self.backgroundGraph.getEdge(prod, user)
except ValueError:
newEdge = True
if newEdge:
self.backgroundGraph.addEdge(prod, user)
newCommonPurchases = self.backgroundGraph.neighbours(prod)
# print prod, newCommonPurchases
for neighbour in filter(lambda neighbour: neighbour != user,
newCommonPurchases):
W_has_changed = True
self.W[neighbour, user] += 1
self.W[user, neighbour] += 1
# the returned graph will be restricted to usefull edges
currentUsefullEdges = numpy.array(self.W.sum(1)).ravel().nonzero()[0]
newUsefullEdges = numpy.setdiff1d(currentUsefullEdges,
self.usefullEdges)
self.usefullEdges = numpy.r_[self.usefullEdges, newUsefullEdges]
if W_has_changed:
return self.W[self.usefullEdges, :][:, self.usefullEdges]
else:
return next(self)
next = __next__
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)
def testNeighbourOf(self):
graph = DictGraph(True)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
for i in range(4):
self.assertEquals(graph.neighbours(i), graph.neighbourOf(i))
#Now test directed graph
graph = DictGraph(False)
graph.addEdge(0, 1)
graph.addEdge(0, 2)
graph.addEdge(0, 3)
graph.addEdge(1, 2)
graph.addEdge(2, 3)
self.assertEquals(graph.neighbourOf(0), [])
self.assertEquals(graph.neighbourOf(1), [0])
self.assertEquals(graph.neighbourOf(2), [0,1])
self.assertEquals(graph.neighbourOf(3), [0, 2])
def testGetSparseWeightMatrix(self):
graph = DictGraph()
graph.addEdge("a", "b")
graph.addEdge("a", "c")
graph.addEdge("a", "d", "blah")
graph.addEdge("d", "e", -1.1)
graph.addEdge("c", "b", 2)
W = graph.getSparseWeightMatrix()
keys = graph.getAllVertexIds()
for i in range(len(keys)):
for j in range(len(keys)):
if graph.edgeExists(keys[i], keys[j]) and not isinstance(graph.getEdge(keys[i], keys[j]), numbers.Number):
self.assertEquals(1, W[i, j])
elif W[i, j] != 0:
self.assertEquals(graph.getEdge(keys[i], keys[j]), W[i, j])
else:
self.assertEquals(graph.getEdge(keys[i], keys[j]), None)
#Try a directed graph
graph = DictGraph(False)
graph.addEdge("a", "b")
graph.addEdge("a", "c", "test")
graph.addEdge("a", "d")
graph.addEdge("d", "e")
graph.addEdge("c", "a", 0.1)
W = graph.getSparseWeightMatrix()
for i in range(len(keys)):
for j in range(len(keys)):
if graph.edgeExists(keys[i], keys[j]) and not isinstance(graph.getEdge(keys[i], keys[j]), numbers.Number):
self.assertEquals(1, W[i, j])
elif W[i, j] != 0:
self.assertEquals(graph.getEdge(keys[i], keys[j]), W[i, j])
else:
self.assertEquals(graph.getEdge(keys[i], keys[j]), None)
def testGetNeighbours(self):
dictGraph = DictGraph(True)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(1, 4, 1)
dictGraph.addEdge(3, 4, 1)
dictGraph.addEdge(2, 2, 1)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.neighbours(1), [2, 3, 4])
self.assertEquals(dictGraph.neighbours(3), [1, 4])
self.assertEquals(dictGraph.neighbours(2), [1, 2])
self.assertEquals(dictGraph.neighbours(5), [])
#Directed graphs
dictGraph = DictGraph(False)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(1, 4, 1)
dictGraph.addEdge(3, 4, 1)
dictGraph.addEdge(2, 2, 1)
dictGraph.setVertex(5, 12)
self.assertEquals(dictGraph.neighbours(1), [2,3,4])
self.assertEquals(dictGraph.neighbours(3), [4])
self.assertEquals(dictGraph.neighbours(2), [2])
self.assertEquals(dictGraph.neighbours(5), [])
def testGetNumEdges(self):
dictGraph = DictGraph(True)
self.assertEquals(dictGraph.getNumEdges(), 0)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getNumEdges(), 3)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getNumEdges(), 3)
dictGraph.addEdge(3, 5, 1)
self.assertEquals(dictGraph.getNumEdges(), 4)
dictGraph.addEdge(3, 3, 1)
self.assertEquals(dictGraph.getNumEdges(), 5)
#Identical tests with directed graphs
dictGraph = DictGraph(False)
self.assertEquals(dictGraph.getNumEdges(), 0)
dictGraph.addEdge(1, 2, 12)
dictGraph.addEdge(1, 3, 18)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getNumEdges(), 3)
dictGraph.addEdge(3, 4, 1)
self.assertEquals(dictGraph.getNumEdges(), 3)
dictGraph.addEdge(3, 5, 1)
self.assertEquals(dictGraph.getNumEdges(), 4)
dictGraph.addEdge(3, 3, 1)
self.assertEquals(dictGraph.getNumEdges(), 5)
class PajekWriterTest(unittest.TestCase):
def setUp(self):
#Let's set up a very simple graph
numVertices = 5
numFeatures = 1
edges = []
vList = VertexList(numVertices, numFeatures)
#An undirected dense graph
self.dGraph1 = DenseGraph(vList, True)
self.dGraph1.addEdge(0, 1, 1)
self.dGraph1.addEdge(0, 2, 1)
self.dGraph1.addEdge(2, 4, 1)
self.dGraph1.addEdge(2, 3, 1)
self.dGraph1.addEdge(3, 4, 1)
#A directed sparse graph
self.dGraph2 = DenseGraph(vList, False)
self.dGraph2.addEdge(0, 1, 1)
self.dGraph2.addEdge(0, 2, 1)
self.dGraph2.addEdge(2, 4, 1)
self.dGraph2.addEdge(2, 3, 1)
self.dGraph2.addEdge(3, 4, 1)
#Now try sparse graphs
vList = VertexList(numVertices, numFeatures)
self.sGraph1 = SparseGraph(vList, True)
self.sGraph1.addEdge(0, 1, 1)
self.sGraph1.addEdge(0, 2, 1)
self.sGraph1.addEdge(2, 4, 1)
self.sGraph1.addEdge(2, 3, 1)
self.sGraph1.addEdge(3, 4, 1)
self.sGraph2 = SparseGraph(vList, False)
self.sGraph2.addEdge(0, 1, 1)
self.sGraph2.addEdge(0, 2, 1)
self.sGraph2.addEdge(2, 4, 1)
self.sGraph2.addEdge(2, 3, 1)
self.sGraph2.addEdge(3, 4, 1)
#Finally, try DictGraphs
self.dctGraph1 = DictGraph(True)
self.dctGraph1.addEdge(0, 1, 1)
self.dctGraph1.addEdge(0, 2, 2)
self.dctGraph1.addEdge(2, 4, 8)
self.dctGraph1.addEdge(2, 3, 1)
self.dctGraph1.addEdge(12, 4, 1)
self.dctGraph2 = DictGraph(False)
self.dctGraph2.addEdge(0, 1, 1)
self.dctGraph2.addEdge(0, 2, 1)
self.dctGraph2.addEdge(2, 4, 1)
self.dctGraph2.addEdge(2, 3, 1)
self.dctGraph2.addEdge(12, 4, 1)
def tearDown(self):
pass
def testInit(self):
pass
def testWriteToFile(self):
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
#Have to check the files
fileName1 = directory + "denseTestUndirected"
pw.writeToFile(fileName1, self.dGraph1)
fileName2 = directory + "denseTestDirected"
pw.writeToFile(fileName2, self.dGraph2)
fileName3 = directory + "sparseTestUndirected"
pw.writeToFile(fileName3, self.sGraph1)
fileName4 = directory + "sparseTestDirected"
pw.writeToFile(fileName4, self.sGraph2)
fileName5 = directory + "dictTestUndirected"
pw.writeToFile(fileName5, self.dctGraph1)
fileName6 = directory + "dictTestDirected"
pw.writeToFile(fileName6, self.dctGraph2)
def testWriteToFile2(self):
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
def setVertexColour(vertexIndex, graph):
colours = ["grey05", "grey10", "grey15", "grey20", "grey25"]
return colours[vertexIndex]
def setVertexSize(vertexIndex, graph):
return vertexIndex
def setEdgeColour(vertexIndex1, vertexIndex2, graph):
colours = ["grey05", "grey10", "grey15", "grey20", "grey25"]
return colours[vertexIndex1]
def setEdgeSize(vertexIndex1, vertexIndex2, graph):
return vertexIndex1+vertexIndex2
pw.setVertexColourFunction(setVertexColour)
fileName1 = directory + "vertexColourTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setVertexColourFunction(None)
pw.setVertexSizeFunction(setVertexSize)
fileName1 = directory + "vertexSizeTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setVertexSizeFunction(None)
pw.setEdgeColourFunction(setEdgeColour)
fileName1 = directory + "edgeColourTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setEdgeColourFunction(None)
pw.setEdgeSizeFunction(setEdgeSize)
fileName1 = directory + "edgeSizeTest"
pw.writeToFile(fileName1, self.dGraph1)
pw.setEdgeColourFunction(None)
def testWriteToFile3(self):
"""
We will test out writing out some random graphs to Pajek
"""
numVertices = 20
numFeatures = 0
vList = VertexList(numVertices, numFeatures)
graph = SparseGraph(vList)
p = 0.1
generator = ErdosRenyiGenerator(p)
graph = generator.generate(graph)
pw = PajekWriter()
directory = PathDefaults.getOutputDir() + "test/"
pw.writeToFile(directory + "erdosRenyi20", graph)
#Now write a small world graph
p = 0.2
k = 3
graph.removeAllEdges()
generator = SmallWorldGenerator(p, k)
graph = generator.generate(graph)
pw.writeToFile(directory + "smallWorld20", graph)
