Exemplo n.º 1
0
logging.basicConfig(filename=rdir + 'log.log', level=logging.INFO)
log_message('Beginning Chronostar run', symbol='_', surround=True)

log_message('Setting up', symbol='.', surround=True)

assert os.access(rdir, os.W_OK)

# ------------------------------------------------------------
# -----  SETTING UP ALL DATA PREP  ---------------------------
# ------------------------------------------------------------

# Set up some filename constants (INPUT files) FOR COMPARISON and expectmax
final_comps_file_with_rv = '../data/no_rv_paper/beta_pic_sphere_component.npy'
final_memb_probs_file_with_rv = '../data/no_rv_paper/beta_memb_probs.npy'

bp_comp_with_rv = SphereComponent.load_components(final_comps_file_with_rv)
bp_probs_with_rv = np.load(final_memb_probs_file_with_rv)
print(bp_probs_with_rv)

# Set up some filename constants (OUTPUT files)
final_comps_file = 'final_comps.npy'
final_med_and_spans_file = 'final_med_and_spans.npy'
final_memb_probs_file = 'final_membership.npy'

# TODO: data_loadfile: mask out rows with nans

# First see if a data savefile path has been provided, and if
# so, then just assume this script has already been performed
# and the data prep has already been done
if (config.config['data_savefile'] != ''
        and os.path.isfile(config.config['data_savefile'])):
# Fit the first component
log_message(msg='FITTING {} COMPONENT'.format(ncomps),
            symbol='*', surround=True)
run_dir = rdir + '{}/'.format(ncomps)

# Initialise all stars in dataset to be full members of first component
init_memb_probs = np.zeros((len(data_dict['means']),2))
init_memb_probs[:,0] = 1.

# Try and recover any results from previous run
try:
    prev_med_and_spans = np.load(run_dir + 'final/'
                            + final_med_and_spans_file)
    prev_memb_probs = np.load(run_dir + 'final/' + final_memb_probs_file)
    try:
        prev_comps = Component.load_components(
                str(run_dir+'final/'+final_comps_file))
    # Final comps are there, they just can't be read by current module
    # so quickly fit them based on fixed prev membership probabilities
    except AttributeError:
        logging.info('Component class has been modified, reconstructing '
                     'from chain')
        prev_comps = ncomps * [None]
        for i in range(ncomps):
            final_cdir = run_dir + 'final/comp{}/'.format(i)
            chain = np.load(final_cdir + 'final_chain.npy')
            lnprob = np.load(final_cdir + 'final_lnprob.npy')
            npars = len(Component.PARAMETER_FORMAT)
            best_ix = np.argmax(lnprob)
            best_pars = chain.reshape(-1,npars)[best_ix]
            prev_comps[i] = Component(emcee_pars=best_pars)
        np.save(str(run_dir+'final/'+final_comps_file), prev_comps)
log_message('Beginning Chronostar run',
            symbol='_', surround=True)

log_message('Setting up', symbol='.', surround=True)

assert os.access(rdir, os.W_OK)

# ------------------------------------------------------------
# -----  SETTING UP ALL DATA PREP  ---------------------------
# ------------------------------------------------------------

# Set up some filename constants (INPUT files) FOR COMPARISON and expectmax
final_comps_file_with_rv = '../data/no_rv_paper/beta_pic_sphere_component.npy'
final_memb_probs_file_with_rv = '../data/no_rv_paper/beta_memb_probs.npy'

bp_comp_with_rv = SphereComponent.load_components(final_comps_file_with_rv)
bp_probs_with_rv = np.load(final_memb_probs_file_with_rv)
print(bp_probs_with_rv)

# Set up some filename constants (OUTPUT files)
final_comps_file = 'final_comps.npy'
final_med_and_spans_file = 'final_med_and_spans.npy'
final_memb_probs_file = 'final_membership.npy'

# TODO: data_loadfile: mask out rows with nans

# First see if a data savefile path has been provided, and if
# so, then just assume this script has already been performed
# and the data prep has already been done
if (config.config['data_savefile'] != '' and
        os.path.isfile(config.config['data_savefile'])):
Exemplo n.º 4
0
# Fit the first component
log_message(msg='FITTING {} COMPONENT'.format(ncomps),
            symbol='*',
            surround=True)
run_dir = rdir + '{}/'.format(ncomps)

# Initialise all stars in dataset to be full members of first component
init_memb_probs = np.zeros((len(data_dict['means']), 2))
init_memb_probs[:, 0] = 1.

# Try and recover any results from previous run
try:
    prev_med_and_spans = np.load(run_dir + 'final/' + final_med_and_spans_file)
    prev_memb_probs = np.load(run_dir + 'final/' + final_memb_probs_file)
    try:
        prev_comps = Component.load_components(
            str(run_dir + 'final/' + final_comps_file))
    # Final comps are there, they just can't be read by current module
    # so quickly fit them based on fixed prev membership probabilities
    except AttributeError:
        logging.info('Component class has been modified, reconstructing '
                     'from chain')
        prev_comps = ncomps * [None]
        for i in range(ncomps):
            final_cdir = run_dir + 'final/comp{}/'.format(i)
            chain = np.load(final_cdir + 'final_chain.npy')
            lnprob = np.load(final_cdir + 'final_lnprob.npy')
            npars = len(Component.PARAMETER_FORMAT)
            best_ix = np.argmax(lnprob)
            best_pars = chain.reshape(-1, npars)[best_ix]
            prev_comps[i] = Component(emcee_pars=best_pars)
        np.save(str(run_dir + 'final/' + final_comps_file), prev_comps)