def do_it_all(outdir):
with bz2.BZ2File('../../Kepler/chain.npy.bz2', 'r') as inp:
chain = np.load(inp)
tchain = ac.emcee_thinned_chain(chain)
candidates = dp.load_candidate_properties('../../Kepler/candidates.dat.bz2')
systems = dp.load_system_properties('../../Kepler/systems.dat.bz2')
logpost = pos.Posterior(candidates, systems)
eas = eta_earths(logpost, tchain)
setup()
paper_plots(logpost, tchain, eas, outdir)
parser.add_argument('--candidates', required=True, help='candidate file')
parser.add_argument('--systems', required=True, help='system file')
parser.add_argument('--outdir', default='.', help='output directory')
parser.add_argument('--threads', type=int, default=15, help='number of threads')
parser.add_argument('--walkers', type=int, default=100, help='number of walkers')
parser.add_argument('--nstep', type=int, default=100, help='steps between saves')
parser.add_argument('--nthin', type=int, default=10, help='steps between stored samples')
parser.add_argument('--fburnin', type=float, default=0.1, help='fraction of samples to discard as burnin')
args = parser.parse_args()
candidates = dp.load_candidate_properties(args.candidates)
systems = dp.load_system_properties(args.systems)
logpost = posterior.Posterior(candidates, systems)
sampler = emcee.EnsembleSampler(args.walkers, logpost.nparams,
logpost, threads=args.threads)
with bz2.BZ2File(op.join(args.outdir, 'chain.npy.bz2'), 'r') as inp:
chain = np.load(inp)
with bz2.BZ2File(op.join(args.outdir, 'lnprob.npy.bz2'), 'r') as inp:
lnprob = np.load(inp)
sampler._chain = chain
sampler._lnprob = lnprob