if len(sys.argv) > 2:
i = int(sys.argv[2])
else:
i = 0
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))
logging.debug("Epidemic period index " + str(i))
numpy.set_printoptions(suppress=True, precision=4, linewidth=150)
numpy.seterr(invalid='raise')
resultsDir = PathDefaults.getOutputDir() + "viroscopy/real/"
startDate, endDate, recordStep, M, targetGraph, numInds = HIVModelUtils.realSimulationParams(ind=i)
N, matchAlpha, breakScale, numEpsilons, epsilon, minEpsilon, matchAlg, abcMaxRuns, batchSize, pertScale = HIVModelUtils.realABCParams(i)
logging.debug("Posterior sample size " + str(N))
logging.debug("Matching algorithm " + str(matchAlg))
logging.debug("="*10 + "Starting new simulation batch with index " + str(i) + "="*10)
logging.debug("Total time of simulation is " + str(endDate-startDate))
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)
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
