refactor emcee scripts

1 files changed, 0 insertions, 145 deletions

diff --git a/plot_llh/sample.py b/plot_llh/sample.py
deleted file mode 100644
index 4309627..0000000
--- a/plot_llh/sample.py
+++ /dev/null
@@ -1,145 +0,0 @@
-#! /usr/bin/env python
-"""
-Sample points for a specific scenario
-"""
-
-from __future__ import absolute_import, division
-
-import sys
-sys.path.extend(['.', '../'])
-
-import argparse
-from functools import partial
-
-import numpy as np
-from scipy.stats import multivariate_normal
-
-from utils import fr as fr_utils
-from utils import llh as llh_utils
-from utils import mcmc as mcmc_utils
-from utils import misc as misc_utils
-from utils.param import Param, ParamSet, get_paramsets
-from utils.enums import MixingScenario, MCMCSeedType
-
-
-def triangle_llh(theta, args):
-    """-Log likelihood function for a given theta."""
-    fr = fr_utils.angles_to_fr(theta)
-    fr_bf = args.measured_ratio
-    cov_fr = np.identity(3) * args.sigma_ratio
-    return np.log(multivariate_normal.pdf(fr, mean=fr_bf, cov=cov_fr))
-
-
-def ln_prior(theta):
-    """Priors on theta."""
-    sphi4, c2psi = theta
-    # Flavour ratio bounds
-    if 0. <= sphi4 <= 1.0 and -1.0 <= c2psi <= 1.0:
-        pass
-    else: return -np.inf
-    return 0.
-
-
-def ln_prob(theta, args):
-    """Prob function for mcmc."""
-    lp = ln_prior(theta)
-    if not np.isfinite(lp):
-        return -np.inf
-    return lp + triangle_llh(theta, args)
-
-
-def process_args(args):
-    """Process the input args."""
-    if args.fix_mixing is MixingScenario.NONE:
-        raise AssertionError('Must set a mixing scenario using --fix-mixing')
-    if not args.fix_source_ratio:
-        raise AssertionError('Must set source ratio using --fix-source-ratio')
-
-    args.source_ratio = fr_utils.normalise_fr(args.source_ratio)
-    if args.fix_mixing is MixingScenario.T12:
-        s12_2, c13_4, s23_2, dcp = 0.5, 1.0, 0.0, 0.
-    elif args.fix_mixing is MixingScenario.T13:
-        s12_2, c13_4, s23_2, dcp = 0.0, 0.25, 0.0, 0.
-    elif args.fix_mixing is MixingScenario.T23:
-        s12_2, c13_4, s23_2, dcp = 0.0, 1.0, 0.5, 0.
-
-    mm = np.array(
-        fr_utils.angles_to_u((s12_2, c13_4, s23_2, dcp)), dtype=np.complex256
-    )
-    args.measured_ratio = fr_utils.u_to_fr(args.source_ratio, mm)
-
-    if not args.fix_scale:
-        args.scale, args.scale_region = fr_utils.estimate_scale(args)
-
-
-def parse_args(args=None):
-    """Parse command line arguments"""
-    parser = argparse.ArgumentParser(
-        description="BSM flavour ratio analysis",
-        formatter_class=misc_utils.SortingHelpFormatter,
-    )
-    parser.add_argument(
-        '--seed', type=misc_utils.seed_parse, default='25',
-        help='Set the random seed value'
-    )
-    parser.add_argument(
-        '--threads', type=misc_utils.thread_type, default='1',
-        help='Set the number of threads to use (int or "max")'
-    )
-    parser.add_argument(
-        '--outfile', type=str, default='./untitled',
-        help='Path to output chains'
-    )
-    parser.add_argument(
-        '--plot-statistic', type=misc_utils.parse_bool, default='False',
-        help='Plot MultiNest evidence or LLH value'
-    )
-    fr_utils.fr_argparse(parser)
-    llh_utils.likelihood_argparse(parser)
-    mcmc_utils.mcmc_argparse(parser)
-    if args is None: return parser.parse_args()
-    else: return parser.parse_args(args.split())
-
-
-def main():
-    args = parse_args()
-    process_args(args)
-    misc_utils.print_args(args)
-
-    if args.seed is not None:
-        np.random.seed(args.seed)
-
-    paramset = ParamSet([
-        Param(name='sphi4', value=0.5, ranges=[0.0,  1.0], std=0.2),
-        Param(name='c2psi', value=0.0, ranges=[-1.0, 1.0], std=0.2)
-    ])
-
-    outfile = misc_utils.gen_outfile_name(args)
-    print '== {0:<25} = {1}'.format('outfile', outfile)
-
-    if args.run_mcmc:
-        ndim = len(paramset)
-        print paramset
-
-        if args.mcmc_seed_type == MCMCSeedType.UNIFORM:
-            p0 = mcmc_utils.flat_seed(paramset, nwalkers=args.nwalkers)
-
-        samples = mcmc_utils.mcmc(
-            p0       = p0,
-            ln_prob  = partial(ln_prob, args=args),
-            ndim     = ndim,
-            nwalkers = args.nwalkers,
-            burnin   = args.burnin,
-            nsteps   = args.nsteps,
-            threads  = args.threads
-        )
-        fr_chains = np.array(map(fr_utils.angles_to_fr, samples), dtype=float)
-        mcmc_utils.save_chains(fr_chains, outfile)
-    print "DONE!"
-
-
-main.__doc__ = __doc__
-
-
-if __name__ == '__main__':
-    main()