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)
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]))
logging.debug(graph)
