def profileSimulateGraphMatch(self):
N, matchAlpha, breakDist, purtScale = HIVModelUtils.toyABCParams()
startDate, endDate, recordStep, M, targetGraph = HIVModelUtils.toySimulationParams()
theta, stdTheta = HIVModelUtils.toyTheta()
featureInds= numpy.ones(targetGraph.vlist.getNumFeatures(), numpy.bool)
featureInds[HIVVertices.dobIndex] = False
featureInds[HIVVertices.infectionTimeIndex] = False
featureInds[HIVVertices.hiddenDegreeIndex] = False
featureInds[HIVVertices.stateIndex] = False
featureInds = numpy.arange(featureInds.shape[0])[featureInds]
#QCV is fastest and most accurate
#PATH is slowests but quite accurate
#RANK is very fast by less accurate than PATH
#U is fastest but least accurate
matcher = GraphMatch("QCV", alpha=matchAlpha, featureInds=featureInds, useWeightM=False)
matcher.lambdaM = 50
matcher.init = "rand"
graphMetrics = HIVGraphMetrics2(targetGraph, breakDist, matcher, float(endDate))
def run():
times, infectedIndices, removedIndices, graph = HIVModelUtils.simulate(theta, startDate, endDate, recordStep, M, graphMetrics)
print("Mean distance " + str(graphMetrics.meanDistance()))
ProfileUtils.profile('run()', globals(), locals())
def loadParams(ind):
if processReal:
resultsDir = PathDefaults.getOutputDir() + "viroscopy/real/theta" + str(ind) + "/"
outputDir = resultsDir + "stats/"
N, matchAlpha, breakScale, numEpsilons, epsilon, minEpsilon, matchAlg, abcMaxRuns, batchSize, pertScale = HIVModelUtils.realABCParams(True)
startDate, endDate, recordStep, M, targetGraph, numInds = HIVModelUtils.realSimulationParams(test=True, ind=ind)
realTheta, sigmaTheta, pertTheta = HIVModelUtils.estimatedRealTheta(ind)
numInds=2
prefix = "Real"
else:
resultsDir = PathDefaults.getOutputDir() + "viroscopy/toy/theta/"
outputDir = resultsDir + "stats/"
N, matchAlpha, breakScale, numEpsilons, epsilon, minEpsilon, matchAlg, abcMaxRuns, batchSize, pertScale = HIVModelUtils.toyABCParams()
startDate, endDate, recordStep, M, targetGraph = HIVModelUtils.toySimulationParams(test=True)
realTheta, sigmaTheta, pertTheta = HIVModelUtils.toyTheta()
prefix = "Toy"
numInds = 1
breakSize = (targetGraph.subgraph(targetGraph.removedIndsAt(endDate)).size - targetGraph.subgraph(targetGraph.removedIndsAt(startDate)).size) * breakScale
return N, resultsDir, outputDir, recordStep, startDate, endDate, prefix, targetGraph, breakSize, numEpsilons, M, matchAlpha, matchAlg, numInds
def testSimulate(self):
#We want to see if we can get the same simulation twice
N, matchAlpha, breakScale, numEpsilons, epsilon, minEpsilon, matchAlg, abcMaxRuns, batchSize, pertScale = HIVModelUtils.toyABCParams()
startDate, endDate, recordStep, M, targetGraph = HIVModelUtils.toySimulationParams(test=True)
breakSize = (targetGraph.subgraph(targetGraph.removedIndsAt(endDate)).size - targetGraph.subgraph(targetGraph.removedIndsAt(startDate)).size) * breakScale
theta, sigmaTheta, pertTheta = HIVModelUtils.toyTheta()
model = HIVModelUtils.createModel(theta, targetGraph, startDate, endDate, recordStep, M, matchAlpha, breakSize, matchAlg)
model.setParams(theta)
times, infectedIndices, removedIndices, graph, compTimes, graphMetrics = HIVModelUtils.simulate(model)
numEdges = graph.getNumEdges()
lastRemovedIndices = removedIndices[-1]
#Simulate again
model = HIVModelUtils.createModel(theta, targetGraph, startDate, endDate, recordStep, M, matchAlpha, breakSize, matchAlg)
model.setParams(theta)
times, infectedIndices, removedIndices, graph, compTimes, graphMetrics = HIVModelUtils.simulate(model)
numEdges2 = graph.getNumEdges()
lastRemovedIndices2 = removedIndices[-1]
self.assertEquals(numEdges, numEdges2)
self.assertEquals(lastRemovedIndices, lastRemovedIndices2)
assert False, "Must run with -O flag"
if len(sys.argv) > 1:
numProcesses = int(sys.argv[1])
else:
numProcesses = multiprocessing.cpu_count()
FORMAT = "%(levelname)s:root:%(process)d:%(message)s"
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG, format=FORMAT)
logging.debug("Number of processes: " + str(numProcesses))
numpy.set_printoptions(suppress=True, precision=4, linewidth=150)
numpy.seterr(invalid='raise')
resultsDir = PathDefaults.getOutputDir() + "viroscopy/toy/"
startDate, endDate, recordStep, M, targetGraph = HIVModelUtils.toySimulationParams()
N, matchAlpha, breakScale, numEpsilons, epsilon, minEpsilon, matchAlg, abcMaxRuns, batchSize, pertScale = HIVModelUtils.toyABCParams()
logging.debug("Total time of simulation is " + str(endDate-startDate))
logging.debug("Posterior sample size " + str(N))
epsilonArray = numpy.ones(numEpsilons)*epsilon
breakSize = (targetGraph.subgraph(targetGraph.removedIndsAt(endDate)).size - targetGraph.subgraph(targetGraph.removedIndsAt(startDate)).size) * breakScale
logging.debug("Largest acceptable graph is " + str(breakSize))
def createModel(t):
"""
The parameter t is the particle index.
"""
return HIVModelUtils.createModel(targetGraph, startDate, endDate, recordStep, M, matchAlpha, breakSize, matchAlg)
meanTheta, sigmaTheta, pertTheta = HIVModelUtils.toyTheta()