Example #1
0
                        action='store_true',
                        help='restart an old run')
    parser.add_argument('--init',
                        metavar='FILE',
                        help='file storing initial point')
    parser.add_argument('--delta',
                        metavar='DPARAM',
                        type=float,
                        default=1e-3,
                        help='fractional width about initial point')

    args = parser.parse_args()

    ts, rvs = load_data(args.rvs)

    pmin, pmax = cl.prior_bounds_from_data(args.nplanets, ts, rvs)

    ndim = 5 * args.nplanets + 4 * len(ts)

    # If re-starting a run, burnin = nthin, so that output continues
    # to be evenly-spaced
    if args.restart:
        args.nburnin = args.nthin - 1

    if args.restart:
        pts = []
        logls = []
        lnprobs = []

        for i in range(args.ntemps):
            data = np.loadtxt('%s.%02d.txt.gz' % (args.prefix, i))
Example #2
0
    parser.add_argument('--nburnin', metavar='N', type=int, default=100, help='number of initial ensembles to discard as burnin')

    parser.add_argument('--ntemps', metavar='N', type=int, default=20, help='number of temperatures')
    parser.add_argument('--nwalkers', metavar='N', type=int, default=100, help='number of walkers')

    parser.add_argument('--rvs', metavar='FILE', required=True, default=[], action='append', help='file of times and RV\'s')

    parser.add_argument('--restart', action='store_true', help='restart an old run')
    parser.add_argument('--init', metavar='FILE', help='file storing initial point')
    parser.add_argument('--delta', metavar='DPARAM', type=float, default=1e-3, help='fractional width about initial point')

    args=parser.parse_args()

    ts, rvs=load_data(args.rvs)

    pmin,pmax=cl.prior_bounds_from_data(args.nplanets, ts, rvs)
    
    ndim = 5*args.nplanets + 4*len(ts)

    # If re-starting a run, burnin = nthin, so that output continues
    # to be evenly-spaced
    if args.restart:
        args.nburnin = args.nthin - 1

    if args.restart:
        pts=[]
        logls=[]
        lnprobs=[]

        for i in range(args.ntemps):
            data=np.loadtxt('%s.%02d.txt.gz'%(args.prefix, i))
Example #3
0
    parser.add_argument('--ntemps', metavar='N', default=20, type=int, help='number of temperatures')

    args=parser.parse_args()

    ts=[]
    rvs=[]
    for f in args.rvs:
        data=np.loadtxt(f)
        ts.append(data[:,0])
        rvs.append(data[:,1])

    nobs = len(ts)
    npl = args.npl
    newnpl = npl + 1

    pmin,pmax = cl.prior_bounds_from_data(newnpl, ts, rvs)

    chain = pr.Parameters(arr=np.loadtxt(args.input)[-args.nwalkers:, 2:], npl=npl, nobs=nobs)
    newchain = pr.Parameters(arr=np.zeros((args.nwalkers, chain.shape[1]+5)), npl=newnpl, nobs=nobs)

    newchain[:, :-5] = chain
    
    newks = newchain.K
    newks[:, -1] = draw_logarithmic(pmin.K[0], pmax.K[0], size=args.nwalkers)
    newchain.K = newks

    newes = newchain.e
    newes[:,-1] = nr.uniform(low=0.0, high=1.0, size=args.nwalkers)
    newchain.e = newes

    newchis = newchain.chi
Example #4
0
                        help='number of temperatures')

    args = parser.parse_args()

    ts = []
    rvs = []
    for f in args.rvs:
        data = np.loadtxt(f)
        ts.append(data[:, 0])
        rvs.append(data[:, 1])

    nobs = len(ts)
    npl = args.npl
    newnpl = npl + 1

    pmin, pmax = cl.prior_bounds_from_data(newnpl, ts, rvs)

    chain = pr.Parameters(arr=np.loadtxt(args.input)[-args.nwalkers:, 2:],
                          npl=npl,
                          nobs=nobs)
    newchain = pr.Parameters(arr=np.zeros((args.nwalkers, chain.shape[1] + 5)),
                             npl=newnpl,
                             nobs=nobs)

    newchain[:, :-5] = chain

    newks = newchain.K
    newks[:, -1] = draw_logarithmic(pmin.K[0], pmax.K[0], size=args.nwalkers)
    newchain.K = newks

    newes = newchain.e