def testreadSimulationHIVGraph(self):
hivReader = HIVGraphReader()
graph = hivReader.readSimulationHIVGraph()
self.assertEquals(graph.getNumVertices(), 5389)
self.assertEquals(graph.getNumEdges(), 4097)
#Check the edges of the first few vertices
nptst.assert_array_equal(graph.neighbours(0), numpy.array([50]))
nptst.assert_array_equal(graph.neighbours(1), numpy.array([1380]))
nptst.assert_array_equal(graph.neighbours(2), numpy.array([]))
nptst.assert_array_equal(graph.neighbours(3), numpy.array([]))
nptst.assert_array_equal(graph.neighbours(30), numpy.array([43, 51, 57, 151, 304, 386,913]))
#Check vertex values
v = graph.getVertex(0)
self.assertEquals(v[HIVVertices.dobIndex], 19602)
self.assertEquals(v[HIVVertices.genderIndex], HIVVertices.male)
self.assertEquals(v[HIVVertices.orientationIndex], HIVVertices.hetero)
self.assertEquals(v[HIVVertices.stateIndex], HIVVertices.removed)
self.assertEquals(v[HIVVertices.infectionTimeIndex], -1)
self.assertEquals(v[HIVVertices.detectionTimeIndex], 31563)
self.assertEquals(v[HIVVertices.detectionTypeIndex], HIVVertices.randomDetect)
self.assertEquals(v[HIVVertices.hiddenDegreeIndex], 3)
v = graph.getVertex(1)
self.assertEquals(v[HIVVertices.dobIndex], 21508)
self.assertEquals(v[HIVVertices.genderIndex], HIVVertices.male)
self.assertEquals(v[HIVVertices.orientationIndex], HIVVertices.hetero)
self.assertEquals(v[HIVVertices.stateIndex], HIVVertices.removed)
self.assertEquals(v[HIVVertices.infectionTimeIndex], -1)
self.assertEquals(v[HIVVertices.detectionTimeIndex], 31563)
self.assertEquals(v[HIVVertices.detectionTypeIndex], HIVVertices.randomDetect)
self.assertEquals(v[HIVVertices.hiddenDegreeIndex], 4)
v = graph.getVertex(6)
self.assertEquals(v[HIVVertices.dobIndex], 21676)
self.assertEquals(v[HIVVertices.genderIndex], HIVVertices.female)
self.assertEquals(v[HIVVertices.orientationIndex], HIVVertices.hetero)
self.assertEquals(v[HIVVertices.stateIndex], HIVVertices.removed)
self.assertEquals(v[HIVVertices.infectionTimeIndex], -1)
self.assertEquals(v[HIVVertices.detectionTimeIndex], 31472)
self.assertEquals(v[HIVVertices.detectionTypeIndex], HIVVertices.contactTrace)
self.assertEquals(v[HIVVertices.hiddenDegreeIndex], 1)
v = graph.getVertex(5381)
self.assertEquals(v[HIVVertices.dobIndex], 25307)
self.assertEquals(v[HIVVertices.genderIndex], HIVVertices.male)
self.assertEquals(v[HIVVertices.orientationIndex], HIVVertices.bi)
self.assertEquals(v[HIVVertices.stateIndex], HIVVertices.removed)
self.assertEquals(v[HIVVertices.infectionTimeIndex], -1)
self.assertEquals(v[HIVVertices.detectionTimeIndex], 38231)
self.assertEquals(v[HIVVertices.detectionTypeIndex], HIVVertices.randomDetect)
self.assertEquals(v[HIVVertices.hiddenDegreeIndex], 0)
def __init__(self, minGraphSize=500, monthStep=1):
startYear = 1900
daysInMonth = 30
#Start off with the HIV data
hivReader = HIVGraphReader()
graph = hivReader.readHIVGraph()
fInds = hivReader.getIndicatorFeatureIndices()
#The set of edges indexed by zeros is the contact graph
#The ones indexed by 1 is the infection graph
edgeTypeIndex1 = 0
edgeTypeIndex2 = 1
sGraphContact = graph.getSparseGraph(edgeTypeIndex1)
sGraphInfect = graph.getSparseGraph(edgeTypeIndex2)
sGraphContact = sGraphContact.union(sGraphInfect)
graph = sGraphContact
#Find max component
#Create a graph starting from the oldest point in the largest component
components = graph.findConnectedComponents()
graph = graph.subgraph(list(components[0]))
logging.debug(graph)
detectionIndex = fInds["detectDate"]
vertexArray = graph.getVertexList().getVertices()
detections = vertexArray[:, detectionIndex]
firstVertex = numpy.argmin(detections)
dayList = list(range(int(numpy.min(detections)), int(numpy.max(detections)), daysInMonth*monthStep))
dayList.append(numpy.max(detections))
subgraphIndicesList = []
#Generate subgraph indices list
for i in dayList:
logging.info("Date: " + str(DateUtils.getDateStrFromDay(i, startYear)))
subgraphIndices = numpy.nonzero(detections <= i)[0]
#Check subgraphIndices are sorted
subgraphIndices = numpy.sort(subgraphIndices)
currentSubgraph = graph.subgraph(subgraphIndices)
compIndices = currentSubgraph.depthFirstSearch(list(subgraphIndices).index(firstVertex))
subgraphIndices = subgraphIndices[compIndices]
if subgraphIndices.shape[0] >= minGraphSize:
subgraphIndicesList.append(subgraphIndices)
self.graph = graph
self.subgraphIndicesList = subgraphIndicesList
self.numGraphs = len(subgraphIndicesList)
def realSimulationParams():
hivReader = HIVGraphReader()
targetGraph = hivReader.readSimulationHIVGraph()
numRecordSteps = 10
#Note that 5% of the population is bi
M = targetGraph.size * 4
#This needs to be from 1986 to 2004
startDate = CsvConverters.dateConv("01/01/1986")
endDates = [CsvConverters.dateConv("01/01/1987"), CsvConverters.dateConv("01/01/1989"), CsvConverters.dateConv("01/01/1991"), CsvConverters.dateConv("01/01/1993"), CsvConverters.dateConv("01/01/1995"), CsvConverters.dateConv("01/01/1997")]
endDates = [float(i) for i in endDates]
return float(startDate), endDates, numRecordSteps, M, targetGraph
import numpy
from apgl.graph import *
from exp.viroscopy.HIVGraphReader import HIVGraphReader
from sandbox.util.PathDefaults import PathDefaults
from sandbox.util.DateUtils import DateUtils
from exp.clusterexp.ClusterExpHelper import ClusterExpHelper
from exp.sandbox.GraphIterators import IncreasingSubgraphListIterator, toDenseGraphListIterator
from exp.sandbox.IterativeSpectralClustering import IterativeSpectralClustering
numpy.random.seed(21)
#numpy.seterr("raise")
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
numpy.set_printoptions(suppress=True, linewidth=60)
#Start off with the HIV data
hivReader = HIVGraphReader()
graph = hivReader.readHIVGraph()
fInds = hivReader.getIndicatorFeatureIndices()
#The set of edges indexed by zeros is the contact graph
#The ones indexed by 1 is the infection graph
edgeTypeIndex1 = 0
edgeTypeIndex2 = 1
sGraphContact = graph.getSparseGraph(edgeTypeIndex1)
sGraphInfect = graph.getSparseGraph(edgeTypeIndex2)
sGraphContact = sGraphContact.union(sGraphInfect)
graph = sGraphContact
#Find max component
components = graph.findConnectedComponents()
graph = graph.subgraph(list(components[0]))
