def computeInfectConfigGraphs():
#We need the directed infection graph
hivReader = HIVGraphReader()
graph = hivReader.readHIVGraph(False)
sGraphInfect = graph.getSparseGraph(edgeTypeIndex2)
sGraph = sGraphInfect
graphFileNameBase = resultsDir + "ConfigInfectGraph"
for j in range(numGraphs):
configGraph = SparseGraph(GeneralVertexList(numVertices), False)
outDegSequence = numpy.zeros(numVertices, numpy.int)
inDegSequence = numpy.zeros(numVertices, numpy.int)
lastOutDegSequence = numpy.zeros(numVertices, numpy.int)
lastInDegSequence = numpy.zeros(numVertices, numpy.int)
generator = ConfigModelGenerator(lastOutDegSequence, lastInDegSequence)
for i in dayList:
logging.info("Date: " + str(DateUtils.getDateStrFromDay(i, startYear)))
subgraphIndices = numpy.nonzero(detections <= i)[0]
subgraphIndices = numpy.unique(subgraphIndices)
subgraph = sGraph.subgraph(subgraphIndices)
outDegSequence[subgraphIndices] = subgraph.outDegreeSequence()
inDegSequence[subgraphIndices] = subgraph.inDegreeSequence()
outDiffSequence = outDegSequence - lastOutDegSequence
inDiffSequence = inDegSequence - lastInDegSequence
generator.setInDegSequence(inDiffSequence)
generator.setOutDegSequence(outDiffSequence)
configGraph = generator.generate(configGraph, False)
lastOutDegSequence = configGraph.outDegreeSequence()
lastInDegSequence = configGraph.inDegreeSequence()
assert (outDegSequence>=lastOutDegSequence).all()
assert (inDegSequence>=lastInDegSequence).all()
configGraph.save(graphFileNameBase + str(j))
import numpy
from apgl.graph import *
from apgl.viroscopy.HIVGraphReader import HIVGraphReader
from apgl.util.PathDefaults import PathDefaults
from apgl.util.DateUtils import DateUtils
from exp.sandbox.IterativeSpectralClustering import IterativeSpectralClustering
from exp.sandbox.GraphIterators import IncreasingSubgraphListIterator
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]))
#graph = graph.subgraph(range(500))
from apgl.util.DateUtils import DateUtils from apgl.util.Latex import Latex from apgl.util.Util import Util from apgl.graph import * from apgl.viroscopy.HIVGraphReader import HIVGraphReader """ This script computes some basic statistics on the growing infection graph. """ logging.basicConfig(stream=sys.stdout, level=logging.DEBUG) numpy.set_printoptions(suppress=True, linewidth=100, precision=3) undirected = False hivReader = HIVGraphReader() graph = hivReader.readHIVGraph(undirected, indicators=False) fInds = hivReader.getNonIndicatorFeatureIndices() figureDir = PathDefaults.getOutputDir() + "viroscopy/figures/infect/" resultsDir = PathDefaults.getOutputDir() + "viroscopy/" #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) sGraph = sGraphInfect #sGraph = sGraph.subgraph(range(0, 500))
matplotlib.use('WXAgg') # do this before importing pylab
import matplotlib.pyplot as plt
"""
Let's compute some basic statistics of the infection and contact graph at the
end of the epidemic.
"""
logging.basicConfig(stream=sys.stdout, level=logging.INFO)
figureDir = PathDefaults.getOutputDir() + "viroscopy/figures/"
undirected = False
hivReader = HIVGraphReader()
graph = hivReader.readHIVGraph(undirected)
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)
numpy.set_printoptions(precision=3, suppress=True)
logging.info("Statistics over Verticies ")
logging.info("===============================")
#Other measures : infection period of tree, infection types
#PCA to find variance of data, correlation matrix, center matrix
