Python HIVGraph.getVertex方法代码示例

# 需要导入模块: from exp.viroscopy.model.HIVGraph import HIVGraph [as 别名]
# 或者: from exp.viroscopy.model.HIVGraph.HIVGraph import getVertex [as 别名]
    def testContactRates(self):
        undirected = True 
        numVertices = 10
        graph = HIVGraph(numVertices, undirected)

        t = 0.2

        contactList = range(numVertices)

        hiddenDegSeq = self.gen.rvs(size=graph.getNumVertices())
        rates = HIVRates(graph, hiddenDegSeq)
        contactRateInds, contactRates = rates.contactRates([0, 5, 7], contactList, t)
        self.assertEquals(contactRates.shape[0], 3)

        #Now we have that 0 had contact with another
        rates.contactEvent(0, 3, 0.2)
        rates.contactEvent(1, 9, 0.1)
        
        infectedInds = numpy.arange(numVertices)
        contactRateInds, contactRates = rates.contactRates(infectedInds, contactList, t)

        #Note that in some cases an infected has no contacted as the persons do not match 
        for i in range(infectedInds.shape[0]): 
            if contactRateInds[i] != -1: 
                if graph.getVertex(infectedInds[i])[HIVVertices.genderIndex]==graph.getVertex(contactRateInds[i])[HIVVertices.genderIndex]:
                    self.assertEquals(contactRates[i], rates.heteroContactRate)
                elif graph.getVertex(infectedInds[i])[HIVVertices.genderIndex]!=graph.getVertex(contactRateInds[1])[HIVVertices.genderIndex] and graph.getVertex(infectedInds[i])[HIVVertices.orientationIndex]==HIVVertices.bi and graph.getVertex(contactRateInds[i])[HIVVertices.orientationIndex]==HIVVertices.bi:
                    self.assertEquals(contactRates[i],rates.biContactRate)

# 需要导入模块: from exp.viroscopy.model.HIVGraph import HIVGraph [as 别名]
# 或者: from exp.viroscopy.model.HIVGraph.HIVGraph import getVertex [as 别名]
    def testInfectionProbability(self):
        undirected = True
        numVertices = 10
        graph = HIVGraph(numVertices, undirected)
        hiddenDegSeq = self.gen.rvs(size=graph.getNumVertices())
        rates = HIVRates(graph, hiddenDegSeq)
        t = 0.1

        graph.getVertex(0)[HIVVertices.stateIndex] = HIVVertices.infected
        graph.getVertex(1)[HIVVertices.stateIndex] = HIVVertices.removed
        graph.getVertex(2)[HIVVertices.stateIndex] = HIVVertices.infected

        for vertexInd1 in range(numVertices):
            for vertexInd2 in range(numVertices): 
                vertex1 = graph.getVertex(vertexInd1)
                vertex2 = graph.getVertex(vertexInd2)

                if vertex1[HIVVertices.stateIndex]!=HIVVertices.infected or vertex2[HIVVertices.stateIndex]!=HIVVertices.susceptible:
                    self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), 0.0)
                elif vertex1[HIVVertices.genderIndex] == HIVVertices.female and vertex2[HIVVertices.genderIndex] == HIVVertices.male:
                    self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), rates.infectProb) 
                elif vertex1[HIVVertices.genderIndex] == HIVVertices.male and vertex2[HIVVertices.genderIndex] == HIVVertices.female:
                    self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), rates.infectProb)
                elif vertex1[HIVVertices.genderIndex] == HIVVertices.male and vertex2[HIVVertices.orientationIndex]==HIVVertices.bi:
                    self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), rates.infectProb)
                else:
                    self.assertEquals(rates.infectionProbability(vertexInd1, vertexInd2, t), 0.0)

# 需要导入模块: from exp.viroscopy.model.HIVGraph import HIVGraph [as 别名]
# 或者: from exp.viroscopy.model.HIVGraph.HIVGraph import getVertex [as 别名]
 def testPickle(self): 
     numVertices = 10
     graph = HIVGraph(numVertices)  
     graph[0, 0] = 1
     graph[3, 5] = 0.1
     
     output = pickle.dumps(graph)
     newGraph = pickle.loads(output)
     
     graph[2, 2] = 1
     
     self.assertEquals(newGraph[0, 0], 1)
     self.assertEquals(newGraph[3, 5], 0.1)
     self.assertEquals(newGraph[2, 2], 0.0)
     self.assertEquals(newGraph.getNumEdges(), 2)
     self.assertEquals(newGraph.getNumVertices(), numVertices)
     self.assertEquals(newGraph.isUndirected(), True)
     
     self.assertEquals(graph[0, 0], 1)
     self.assertEquals(graph[3, 5], 0.1)
     self.assertEquals(graph[2, 2], 1)
     self.assertEquals(graph.getNumEdges(), 3)
     self.assertEquals(graph.getNumVertices(), numVertices)
     self.assertEquals(graph.isUndirected(), True)        
     
     for i in range(numVertices): 
         nptst.assert_array_equal(graph.getVertex(i), newGraph.getVertex(i))

# 需要导入模块: from exp.viroscopy.model.HIVGraph import HIVGraph [as 别名]
# 或者: from exp.viroscopy.model.HIVGraph.HIVGraph import getVertex [as 别名]
class HIVGraphMetricsProfile():
    def __init__(self):
        #Total number of people in population
        self.M = 1000
        numInitialInfected = 5

        #The graph is one in which edges represent a contact
        undirected = True
        self.graph = HIVGraph(self.M, undirected)

        for i in range(self.M):
            vertex = self.graph.getVertex(i)

            #Set the infection time of a number of individuals to 0
            if i < numInitialInfected:
                vertex[HIVVertices.stateIndex] = HIVVertices.infected
            

        p = 0.01
        generator = ErdosRenyiGenerator(p)
        self.graph = generator.generate(self.graph)
        
        perm1 = numpy.random.permutation(self.M)
        perm2 = numpy.random.permutation(self.M)        
        
        sizes = [200, 300, 500, 1000]
        self.summary1 = [] 
        self.summary2 = [] 

        for size in sizes: 
            self.summary1.append(self.graph.subgraph(perm1[0:size]))
            self.summary2.append(self.graph.subgraph(perm2[0:int(size/10)]))
        
        print(self.graph)

    def profileDistance(self): 
        times = numpy.arange(len(self.summary1))
        #metrics = HIVGraphMetrics2(times, GraphMatch("RANK"))
        metrics = HIVGraphMetrics2(times, GraphMatch("U"))
        
        #Can try RANK and Umeyama algorithm - Umeyama is faster      
        self.summary2 = self.summary2[0:2]
        
        ProfileUtils.profile('metrics.distance(self.summary1, self.summary2)', globals(), locals())

# 需要导入模块: from exp.viroscopy.model.HIVGraph import HIVGraph [as 别名]
# 或者: from exp.viroscopy.model.HIVGraph.HIVGraph import getVertex [as 别名]
    def testContactRates2(self):
        undirected = True
        numVertices = 10
        graph = HIVGraph(numVertices, undirected)

        maleVertex = graph.getVertex(0)
        maleVertex[HIVVertices.genderIndex] = HIVVertices.male
        femaleVertex = maleVertex.copy()
        femaleVertex[HIVVertices.genderIndex] = HIVVertices.female

        for i in range(5): 
            graph.setVertex(i, maleVertex)
            graph.setVertex(i+5, femaleVertex)

        V = graph.getVertexList().getVertices()

        contactList = range(numVertices)

        #Test that the parameters alpha and C do the right thing
        hiddenDegSeq = self.gen.rvs(size=graph.getNumVertices())
        rates = HIVRates(graph, hiddenDegSeq)
        t = 0.2
        logging.debug("Rates with no existing contacts")
        contactRateInds, contactRates = rates.contactRates(range(numVertices), contactList, t)

        #When there are no contacts the choice is easy and some random new contacts
        #are chosen.
        #Now test differences in choice between existing and new contact.
        t = 0.3
        for i in range(5):
            rates.contactEvent(i, i+5, t)

        rates.alpha = 1.0
        logging.debug("Rates with default alpha=" + str(rates.alpha))
        contactRateInds, contactRates = rates.contactRates(range(numVertices), contactList, 0.4)


        for i in range(5):
            self.assertTrue(contactRates[i] == rates.contactRate)
            self.assertTrue(contactRateInds[i] == i+5)

        #Now try changing alpha
        logging.debug("Rates with alpha=0.5")
        rates.setAlpha(0.5)
        contactRateInds, contactRates = rates.contactRates(range(numVertices), contactList, 0.4)
        #Observed probabilities change as expected


        #Now increase time and observe probabilities
        logging.debug("Rates with t=20")
        contactRateInds, contactRates = rates.contactRates(range(numVertices), contactList, 20)


        #Test we don't pick from removed
        graph.getVertexList().setInfected(0, t)
        graph.getVertexList().setInfected(4, t)
        graph.getVertexList().setInfected(7, t)
        graph.getVertexList().setInfected(8, t)
        #graph.getVertexList().setDetected(4, t, HIVVertices.randomDetect)
        #graph.getVertexList().setDetected(7, t, HIVVertices.randomDetect)
        rates.removeEvent(4, HIVVertices.randomDetect, t)
        rates.removeEvent(7, HIVVertices.randomDetect, t)

        infectedSet = graph.getInfectedSet()
        susceptibleSet = graph.getSusceptibleSet()
        removedSet = graph.getRemovedSet()
        contactSet = infectedSet.union(susceptibleSet)

        infectedList = list(infectedSet)
        removedList = list(removedSet)
        contactList = list(contactSet)

        contactRateInds, contactRates = rates.contactRates(infectedList, contactList, 20)
        
        #Contacts cannot be in removed set 
        self.assertTrue(numpy.intersect1d(contactRateInds, numpy.array(removedList)).shape[0]==0)        

# 需要导入模块: from exp.viroscopy.model.HIVGraph import HIVGraph [as 别名]
# 或者: from exp.viroscopy.model.HIVGraph.HIVGraph import getVertex [as 别名]
    def testContactTracingRate(self):
        undirected = True
        numVertices = 10
        graph = HIVGraph(numVertices, undirected)

        hiddenDegSeq = self.gen.rvs(size=graph.getNumVertices())
        rates = HIVRates(graph, hiddenDegSeq)
        t = 0.1
        graph.getVertexList().setInfected(0, t)
        rates.contactEvent(0, 3, 0.2)
        rates.contactEvent(0, 9, 0.1)

        t = 0.3
        graph.getVertexList().setInfected(3, t)
        graph.getVertexList().setInfected(9, t)

        t = 0.4
        rates.removeEvent(0, HIVVertices.randomDetect, t)

        removedSet = graph.getRemovedSet()
        infectedList = [3, 9]
        ctRates = rates.contactTracingRates(infectedList, removedSet, t)
        self.assertTrue((ctRates==numpy.array([0.0, 0.0])).all())

        ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)
        self.assertTrue((ctRates == numpy.array([rates.ctRatePerPerson, rates.ctRatePerPerson])).all())

        #Test contact tracing is within correct time period
        ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctEndTime-0.01)
        self.assertTrue((ctRates == numpy.array([rates.ctRatePerPerson, rates.ctRatePerPerson])).all())

        ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctEndTime+1)
        self.assertTrue((ctRates == numpy.array([0, 0])).all())

        rates.contactEvent(3, 5, t)
        graph.getVertexList().setInfected(5, t)
        rates.removeEvent(5, HIVVertices.randomDetect, t)
        removedSet = graph.getRemovedSet()
        ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)

        self.assertTrue((ctRates == numpy.array([rates.ctRatePerPerson, rates.ctRatePerPerson])).all())
        
        rates.contactEvent(3, 6, t)
        graph.getVertexList().setInfected(6, t)
        infectedList = [3, 6, 9]
        removedSet = graph.getRemovedSet()
 
        ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)
        self.assertTrue((ctRates == numpy.array([rates.ctRatePerPerson, 0, rates.ctRatePerPerson])).all())

        #Now make removedSet bigger than infectedList
        graph.getVertexList().setInfected(4, t)
        graph.getVertexList().setInfected(7, t)
        graph.getVertexList().setInfected(8, t)
        graph.getVertexList().setDetected(4, t, HIVVertices.randomDetect)
        graph.getVertexList().setDetected(7, t, HIVVertices.randomDetect)
        graph.getVertexList().setDetected(8, t, HIVVertices.randomDetect)

        #Note: InfectedList is out of order 
        infectedList = list(graph.getInfectedSet())
        sortInds = numpy.argsort(numpy.array(infectedList))
        removedSet = graph.getRemovedSet()

        ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)
        ctRates2 = numpy.array([rates.ctRatePerPerson, 0, rates.ctRatePerPerson])
        self.assertTrue((ctRates[sortInds] == ctRates2).all())

        #Test the case where InfectedList is out of order and removedSet is small
        graph.getVertexList().setInfected(4, t)
        graph.getVertex(7)[HIVVertices.stateIndex] = HIVVertices.susceptible
        graph.getVertex(8)[HIVVertices.stateIndex] = HIVVertices.susceptible

        infectedList = list(graph.getInfectedSet())
        sortInds = numpy.argsort(numpy.array(infectedList))
        removedSet = graph.getRemovedSet()

        ctRates = rates.contactTracingRates(infectedList, removedSet, t+rates.ctStartTime)
        ctRates2 = numpy.array([rates.ctRatePerPerson, 0, 0, rates.ctRatePerPerson])
        self.assertTrue((ctRates[sortInds] == ctRates2).all())

# 需要导入模块: from exp.viroscopy.model.HIVGraph import HIVGraph [as 别名]
# 或者: from exp.viroscopy.model.HIVGraph.HIVGraph import getVertex [as 别名]
class HIVRatesProfile():
    def __init__(self):
        #Total number of people in population
        self.M = 10000
        numInitialInfected = 5

        #The graph is one in which edges represent a contact
        undirected = True
        self.graph = HIVGraph(self.M, undirected)

        for i in range(self.M):
            vertex = self.graph.getVertex(i)

            #Set the infection time of a number of individuals to 0
            if i < numInitialInfected:
                vertex[HIVVertices.stateIndex] = HIVVertices.infected

        outputDirectory = PathDefaults.getOutputDir()
        directory = outputDirectory + "test/"
        self.profileFileName = directory + "profile.cprof"


    def profileContactRate(self):
        susceptibleList = list(range(1, self.graph.getNumVertices()))
        t = 10

        s = 3
        gen = scipy.stats.zipf(s)
        hiddenDegSeq = gen.rvs(size=self.graph.getNumVertices())
        rates = HIVRates(self.graph, hiddenDegSeq)

        numContactEvents = 5000
        for i in range(numContactEvents):
            vertexInd1 = numpy.random.randint(0, self.graph.getNumVertices())
            vertexInd2 = numpy.random.randint(0, self.graph.getNumVertices())
            rates.contactEvent(vertexInd1, vertexInd2, 5)

        print((self.graph.getNumEdges()))

        infectedList = range(0, 100)
        contactList = range(100, self.M)
        t = 10

        def runContactRates():
            for i in range(100):
                rates.contactRates(infectedList, contactList, t)

        ProfileUtils.profile('runContactRates()', globals(), locals())


    def profileInfectionProbability(self):
        s = 3
        gen = scipy.stats.zipf(s)
        hiddenDegSeq = gen.rvs(size=self.graph.getNumVertices())
        rates = HIVRates(self.graph, hiddenDegSeq)
        t = 5

        #Getting vertices and checking parameters takes the most time 
        def runInfectionProbs():
            for i in range(10000):
                vertexInd1 = numpy.random.randint(0, self.graph.getNumVertices())
                vertexInd2 = numpy.random.randint(0, self.graph.getNumVertices())
                rates.infectionProbability(vertexInd1, vertexInd2, t)

        ProfileUtils.profile('runInfectionProbs()', globals(), locals())

    def profileContactTracingRate(self):
        s = 3
        gen = scipy.stats.zipf(s)
        hiddenDegSeq = gen.rvs(size=self.graph.getNumVertices())
        rates = HIVRates(self.graph, hiddenDegSeq)

        #Create a network of sexual contacts 
        numContactEvents = 10000
        for i in range(numContactEvents):
            vertexInd1 = numpy.random.randint(0, self.graph.getNumVertices())
            vertexInd2 = numpy.random.randint(0, self.graph.getNumVertices())
            rates.contactEvent(vertexInd1, vertexInd2, 5)

        print((self.graph))
        print((self.graph.degreeDistribution()))

        #Choose some individuals as being infected and then detected 
        p = 0.3
        q = 0.4
        for i in range(self.graph.getNumVertices()):
            if numpy.random.rand() < p and not self.graph.getVertex(i)[HIVVertices.stateIndex] == HIVVertices.infected:
                self.graph.getVertexList().setInfected(i, 5.0)

                if numpy.random.rand() < q:
                    self.graph.getVertexList().setDetected(i, 6.0, HIVVertices.randomDetect)

        infectedSet = self.graph.getInfectedSet()
        print((len(infectedSet)))
        print((len(self.graph.getRemovedSet())))

        removedSet = self.graph.getRemovedSet()

        t = 200
        def runContactTracingRate():
#.........这里部分代码省略.........