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'])):
# 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)