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)
def saveStats(args):
i, theta = args
resultsFileName = outputDir + "SimStats" + str(i) + ".pkl"
lock = FileLock(resultsFileName)
if not lock.fileExists() and not lock.isLocked():
lock.lock()
model = HIVModelUtils.createModel(targetGraph, startDate, endDate, recordStep, M, matchAlpha, breakSize, matchAlg, theta=thetaArray[i])
times, infectedIndices, removedIndices, graph, compTimes, graphMetrics = HIVModelUtils.simulate(model)
times = numpy.arange(startDate, endDate+1, recordStep)
vertexArray, infectedIndices, removedIndices, contactGraphStats, removedGraphStats, finalRemovedDegrees = HIVModelUtils.generateStatistics(graph, times)
stats = times, vertexArray, infectedIndices, removedGraphStats, finalRemovedDegrees, graphMetrics.objectives, compTimes
Util.savePickle(stats, resultsFileName)
lock.unlock()
else:
logging.debug("Results already computed: " + str(resultsFileName))
def createModel(t):
"""
The parameter t is the particle index.
"""
return HIVModelUtils.createModel(targetGraph, startDate, endDate, recordStep, M, matchAlpha, breakSize, matchAlg)