def print_kl(out_file, true_obj):
# ''' #
res, pr, mod = bread.results_from(out_file)
# HOW CONVERGED IS THE CODE?? LET'S FIND OUT!
parnames = np.array(res['model'].theta_labels())
fig, kl_ax = plt.subplots(1, 1, figsize=(7, 7))
for i in xrange(parnames.shape[0]):
kl_ax.plot(res['kl_iteration'],
np.log10(res['kl_divergence'][:, i]),
'o',
label=parnames[i],
lw=1.5,
linestyle='-',
alpha=0.6)
kl_ax.set_ylabel('log(KL divergence)')
kl_ax.set_xlabel('iteration')
# kl_ax.set_xlim(0, nsteps*1.1)
kl_div_lim = res['run_params'].get('convergence_kl_threshold', 0.018)
kl_ax.axhline(np.log10(kl_div_lim),
linestyle='--',
color='red',
lw=2,
zorder=1)
kl_ax.legend(prop={'size': 5}, ncol=2, numpoints=1, markerscale=0.7)
plt.title(true_obj + ' kl')
plt.show()
def read_results(filename):
res, obs, mod = reader.results_from(path_res + filename)
# update data table
res['run_params']['data_table'] = path_wdir + 'data/halo7d_with_phot.fits'
mod = reader.get_model(res)
# update filters
filternames = [str(ii) for ii in obs['filters']]
obs['filters'] = load_filters(filternames, directory=filter_folder)
# load sps
sps = reader.get_sps(res)
return (res, obs, mod, sps)
def sample_posterior(outname=None, shortname=None, mass_folder=None):
# I/O
# paramfile = model_setup.import_module_from_file(param_name)
# outname = paramfile.run_params['outfile']
# sample_results, powell_results, model, eout = load_prospector_data(outname, hdf5=True, load_extra_output=True)
sample_results, powell_results, model = bread.results_from(outname)
# create useful quantities
sample_results['flatchain'] = chop_chain(sample_results['chain'],
**sample_results['run_params'])
sample_results['flatprob'] = chop_chain(sample_results['lnprobability'],
**sample_results['run_params'])
sps = model_setup.load_sps(**sample_results['run_params'])
# sps = paramfile.load_sps(**sample_results['run_params'])
# obs = paramfile.load_obs(**sample_results['run_params'])
# sample from posterior
nsamp = 3000
good = np.isfinite(sample_results['flatprob']) == True
sample_idx = np.random.choice(np.where(good)[0], nsamp)
# define outputs
mfrac = np.linspace(0, 0.95, 20)
mfrac_out = np.zeros(shape=(nsamp, mfrac.shape[0]))
for jj, idx in enumerate(sample_idx):
print(jj)
##### model call, to set parameters
thetas = copy.copy(sample_results['flatchain'][idx])
spec, mags, sm = sample_results['model'].mean_model(
thetas, sample_results['obs'], sps=sps)
##### extract sfh parameters
sfh_params = find_sfh_params(sample_results['model'],
thetas,
sample_results['obs'],
sps,
sm=sm)
for ii, m in enumerate(mfrac):
mfrac_out[jj, ii] = halfmass_assembly_time(sfh_params, c=m)
# fixing negatives
mfrac_out = np.clip(mfrac_out, 0.0, np.inf)
# write out
out = np.percentile(mfrac_out, [50, 84, 16], axis=0)
with open('out/' + mass_folder + shortname + 'mass.txt', 'w') as f:
f.write('# mass_fraction median_time err_up err_down\n')
for ii in range(out.shape[1]):
f.write("{:.2f}".format(mfrac[ii]) + ' ' +
"{:.3f}".format(out[0, ii]) + ' ' +
"{:.3f}".format(out[1, ii]) + ' ' +
"{:.3f}".format(out[2, ii]) + ' ')
f.write('\n')
def printer(out_file, percs=True, sfhtest=False, masstest=False, fast=False, five=False, quiet=False, draw1=False,
fixmet=False):
if not quiet:
print(out_file)
print(masstest)
res, pr, mod = bread.results_from(out_file)
# ''' #
# PRINT CORNERFIG CONTOURS/HISTOGRAMS FOR EACH PARAMETER
return md(res, start=-1000, thin=5, percs=percs, sfhtest=sfhtest, masstest=masstest, fast=fast, five=five,
quiet=quiet, draw1=draw1, fixmet=fixmet) # -650
def extract_posteriors():
logMs, logZs, dusts, t0s, logTaus = [], [], [], [], []
clusters = ['a370', 'a1063', 'a2744', 'm416', 'm717', 'm1149']
for cluster in clusters:
h5_files = glob.glob('{}/h5/*.h5'.format(cluster))
h5s = []
for file in h5_files:
file = file.replace(os.sep, '/') # compatibility for Windows
h5s.append(file)
for file in h5s:
result, obs, _ = reader.results_from(file, dangerous=True)
samples = sample_posterior(result['chain'],
weights=result['weights'],
nsample=len(result['chain']))
samples[:, 1] = np.log10(samples[:, 1])
samples[:, 5] = np.log10(samples[:, 5])
logMs.append(list(samples[:, 1]))
logZs.append(list(samples[:, 2]))
dusts.append(list(samples[:, 3]))
t0s.append(list(samples[:, 4]))
logTaus.append(list(samples[:, 5]))
logM = flatten_posteriors(logMs)
logZ = flatten_posteriors(logZs)
dust = flatten_posteriors(dusts)
t0 = flatten_posteriors(t0s)
logTau = flatten_posteriors(logTaus)
# np.savez('subsample_posteriors.npz', logM=logM, logZ=logZ, dust=dust,
# t0=t0, logTau=tau)
solMetal = u.def_unit(['solMetal', 'Z_sun', 'Zsun'],
prefixes=False,
format={
'latex': r'Z_{\odot}',
'unicode': 'Z\N{SUN}'
})
table = Table(
[logM / u.solMass, logZ / solMetal, dust, t0 * u.Gyr, logTau / u.Gyr],
names=('logM', 'logZ', 'dust', 't0', 'logTau'))
table.write('boneyard/subsample_posteriors.fits')
return
def get_results(cluster, ID, binNum, results_type='dynesty', version=''):
# convenience function
infile = '{}/h5/{}_ID_{}_bin_{}{}.h5'.format(cluster, cluster, ID, binNum,
version)
result, obs, _ = reader.results_from(infile, dangerous=True)
model = reader.get_model(result)
sps = reader.get_sps(result)
# t_hr = result['sampling_duration']/3600
# print('The sampling took {:.2f} hours'.format(t_hr))
return result, obs, model, sps
def post_processing(out_file, filename, **kwargs):
'''
Driver. Loads output, runs post-processing routine.
'''
sample_results, powell_results, model = read_results.results_from(out_file)
### create flatchain, run post-processing
sample_results['flatchain'] = prosp_dutils.chop_chain(sample_results['chain'], **sample_results['run_params'])
sample_results['flatprob'] = prosp_dutils.chop_chain(sample_results['lnprobability'],
**sample_results['run_params'])
extra_output = calc_extra_quantities(sample_results, **kwargs)
with open(filename, 'wb') as newfile: # 'wb' because binary format
pickle.dump(extra_output, newfile, pickle.HIGHEST_PROTOCOL)
def read_h5(filename, **kwargs):
"""
Read and return the prospector fit results saved in a given .h5 file.
Parameters
----------
filename : [string]
File name in which are saved the results to be read and returned.
Returns
-------
dict, dict, SedModel
"""
import prospect.io.read_results as reader
return reader.results_from(filename, **kwargs)
def determine_age_gradients(cluster, ID, bins, radius_array, version='') :
mwas = []
radii = []
for binNum, radius in zip(bins, radius_array) :
infile = '{}/h5/{}_ID_{}_bin_{}{}.h5'.format(
cluster, cluster, ID, binNum, version)
result, obs, _ = reader.results_from(infile, dangerous=True)
samples = sample_posterior(result['chain'], weights=result['weights'])
mwas.append(mwa_calc(samples[:, 5], samples[:, 4], power=1))
radii.append(np.full(len(samples), radius))
return np.concatenate(radii).ravel(), np.concatenate(mwas).ravel()
def post_processing(param_name, **kwargs):
'''
Driver. Loads output, runs post-processing routine.
'''
print(outname)
sample_results, powell_results, model = read_results.results_from(outname)
### create flatchain, run post-processing
sample_results['flatchain'] = prosp_dutils.chop_chain(sample_results['chain'], **sample_results['run_params'])
sample_results['flatprob'] = prosp_dutils.chop_chain(sample_results['lnprobability'],
**sample_results['run_params'])
extra_output = calc_extra_quantities(sample_results, **kwargs)
print(len(extra_output['extras']['sfh'][0]), '2000?') # YAY
'''
print('len flatchain', len(extra_output['extras']['flatchain'])) # 2000 :D
print('index 0', extra_output['extras']['flatchain'][0]) # should return set of params (half time, sfr10, etc)?
# Returns array with len 6: (half_time [units?], sfr10, sfr100, ssfr10, ssfr100, stellar_mass)?
print('thing', extra_output['extras']['flatchain']) # Returns 2000 arrays each with len(6)
'''
print(extra_output['bfit']['maxprob_params']) # [10.34, 0.33, 0.59, 0.0023, 0.03, 0.0095, 0.69, -2, -0.2, -1]
# emission_decoupled_recent: [10.32, 0.32, 0.61, 0.0246, 0.00155, 0.015, 0.7, -2, -0.2, -1]
# 10 thetas are: logmass, sfr_frac1, sfr_frac2, sfr_frac3, sfr_frac4, sfr_frac5, dust2, logzsol, gas_logz, gas_logu
# print('max', len(extra_output['bfit']['maxprob_params'])) # 10
print(extra_output['bfit']['half_time']) # -1.0216794961; emission_decoupled_recent: -1.03132084372
print(extra_output['bfit']['sfr_10']) # 66.4716596583; emission_decoupled_recent: 66.2740632613
print(extra_output['bfit']['sfr_100']) # 114.443681589; emission_decoupled_recent: 121.448368493
# plt.plot(extra_output['extras']['t_sfh'], extra_output['bfit']['sfh'])
# plt.plot(extra_output['extras']['t_sfh'], extra_output['extras']['sfh'])
plt.plot(extra_output['extras']['t_sfh'], extra_output['bfit']['sfh'])
plt.ylabel(r'M$_\odot$ yr$^{-1}$')
plt.xlabel('Gyr')
plt.show()
def post_processing(param_name, outname=None, **kwargs):
'''
Driver. Loads output, runs post-processing routine.
'''
sample_results, powell_results, model = read_results.results_from(out_file)
### create flatchain, run post-processing
sample_results['flatchain'] = prosp_dutils.chop_chain(
sample_results['chain'], **sample_results['run_params'])
sample_results['flatprob'] = prosp_dutils.chop_chain(
sample_results['lnprobability'], **sample_results['run_params'])
extra_output = calc_extra_quantities(sample_results, **kwargs)
print('max', extra_output['bfit']['maxprob_params'])
print('half', extra_output['bfit']['half_time'])
print('sfr_10', extra_output['bfit']['sfr_10'])
print('sfr_100', extra_output['bfit']['sfr_100'])
plt.plot(extra_output['extras']['t_sfh'], extra_output['bfit']['sfh'])
plt.ylabel(r'M$_\odot$ yr$^{-1}$')
plt.xlabel('Gyr')
plt.show()
def save_mass_metallicity_images():
HFF = Table.read('output/tables/nbCGs.fits')
for cluster, ID in zip(HFF['cluster'], HFF['ID']):
# ensure the output directories for the images are available
os.makedirs('{}/logM_images'.format(cluster), exist_ok=True)
os.makedirs('{}/logZ_images'.format(cluster), exist_ok=True)
bins_image = core.open_image(cluster, ID, 'bins')
bins = np.sort(np.unique(
bins_image[~np.isnan(bins_image)])).astype(int)
mass = bins_image.copy()
metal = bins_image.copy()
if not (cluster == 'm717') & (ID == 3692): # fitting issue for bin_4
for binNum in bins: # loop over all the bins
result, obs, _ = reader.results_from(
'{}/h5/{}_ID_{}_bin_{}.h5'.format(cluster, cluster, ID,
binNum),
dangerous=True)
samples = sample_posterior(result['chain'],
weights=result['weights'])
mass[mass == binNum] = np.percentile(samples[:, 1], 50)
metal[metal == binNum] = np.percentile(samples[:, 2], 50)
hdu = fits.PrimaryHDU(mass)
hdu.writeto('{}/logM_images/{}_ID_{}_logM.fits'.format(
cluster, cluster, ID))
hdu = fits.PrimaryHDU(metal)
hdu.writeto('{}/logZ_images/{}_ID_{}_logZ.fits'.format(
cluster, cluster, ID))
return
from prospect.io import write_results
from prospect.io import read_results as pr
from prospect import fitting
from prospect.likelihood import lnlike_spec, lnlike_phot, write_log, chi_spec, chi_phot
# --------------
# Read command line arguments
# --------------
sargv = sys.argv
argdict = {'restart_from': '', 'niter': 1024}
clargs = model_setup.parse_args(sargv, argdict=argdict)
# ----------
# Result object and Globals
# ----------
result, global_obs, global_model = pr.results_from(clargs["restart_from"])
is_emcee = (len(result["chain"].shape) == 3) & (result["chain"].shape[0] > 1)
assert is_emcee, "Result file does not have a chain of the proper shape."
# SPS Model instance (with libraries check)
sps = pr.get_sps(result)
run_params = result["run_params"]
run_params.update(clargs)
# Noise model (this should be doable via read_results)
from prospect.models.model_setup import import_module_from_string
param_file = (result['run_params'].get('param_file',
''), result.get("paramfile_text", ''))
path, filename = os.path.split(param_file[0])
modname = filename.replace('.py', '')
user_module = import_module_from_string(param_file[1], modname)
def main(field, galaxy_seq):
#vers = (np.__version__, scipy.__version__, h5py.__version__, fsps.__version__, prospect.__version__)
#print("Numpy: {}\nScipy: {}\nH5PY: {}\nFSPS: {}\nProspect: {}".format(*vers))
# -------------- Decide field and filters
# Read in catalog from Lou
if 'North' in field:
df = pandas.read_pickle(adap_dir + 'GOODS_North_SNeIa_host_phot.pkl')
all_filters = [
'LBC_U_FLUX', 'ACS_F435W_FLUX', 'ACS_F606W_FLUX', 'ACS_F775W_FLUX',
'ACS_F814W_FLUX', 'ACS_F850LP_FLUX', 'WFC3_F105W_FLUX',
'WFC3_F125W_FLUX', 'WFC3_F140W_FLUX', 'WFC3_F160W_FLUX',
'MOIRCS_K_FLUX', 'CFHT_Ks_FLUX', 'IRAC_CH1_SCANDELS_FLUX',
'IRAC_CH2_SCANDELS_FLUX', 'IRAC_CH3_FLUX', 'IRAC_CH4_FLUX'
]
#all_filters = ['LBC_U_FLUX', 'ACS_F435W_FLUX', 'ACS_F606W_FLUX',
#'ACS_F775W_FLUX', 'ACS_F850LP_FLUX']
seq = np.array(df['ID'])
i = int(np.where(seq == galaxy_seq)[0])
elif 'South' in field:
df = pandas.read_pickle(adap_dir + 'GOODS_South_SNeIa_host_phot.pkl')
all_filters = [
'CTIO_U_FLUX', 'ACS_F435W_FLUX', 'ACS_F606W_FLUX',
'ACS_F775W_FLUX', 'ACS_F814W_FLUX', 'ACS_F850LP_FLUX',
'WFC3_F098M_FLUX', 'WFC3_F105W_FLUX', 'WFC3_F125W_FLUX',
'WFC3_F160W_FLUX', 'HAWKI_KS_FLUX', 'IRAC_CH1_FLUX',
'IRAC_CH2_FLUX', 'IRAC_CH3_FLUX', 'IRAC_CH4_FLUX'
]
#all_filters = ['CTIO_U_FLUX', 'ACS_F435W_FLUX', 'ACS_F606W_FLUX',
#'ACS_F775W_FLUX', 'ACS_F850LP_FLUX']
seq = np.array(df['Seq'])
i = int(np.where(seq == galaxy_seq)[0])
#print('Read in pickle with the following columns:')
#print(df.columns)
#print('Rows in DataFrame:', len(df)
print("Match index:", i, "for Seq:", galaxy_seq)
# -------------- Preliminary stuff
# Set up for emcee
nwalkers = 1000
niter = 500
ndim = 12
# Other set up
obj_ra = df['RA'][i]
obj_dec = df['DEC'][i]
obj_z = df['zbest'][i]
print("Object redshift:", obj_z)
age_at_z = astropy_cosmo.age(obj_z).value
print("Age of Universe at object redshift [Gyr]:", age_at_z)
# ------------- Get obs data
fluxes = []
fluxes_unc = []
useable_filters = []
for ft in range(len(all_filters)):
filter_name = all_filters[ft]
flux = df[filter_name][i]
fluxerr = df[filter_name + 'ERR'][i]
if np.isnan(flux):
continue
if flux <= 0.0:
continue
if (fluxerr < 0) or np.isnan(fluxerr):
fluxerr = 0.1 * flux
fluxes.append(flux)
fluxes_unc.append(fluxerr)
useable_filters.append(filter_name)
#print("\n")
#print(df.loc[i])
#print(fluxes, len(fluxes))
#print(useable_filters, len(useable_filters))
fluxes = np.array(fluxes)
fluxes_unc = np.array(fluxes_unc)
# Now build the prospector observation
obs = build_obs(fluxes, fluxes_unc, useable_filters)
# Set params for run
run_params = {}
run_params["object_redshift"] = obj_z
run_params["fixed_metallicity"] = None
run_params["add_duste"] = True
#run_params["dust_type"] = 4
run_params["zcontinuous"] = 1
# Generate the model SED at the initial value of theta
#theta = model.theta.copy()
#initial_spec, initial_phot, initial_mfrac = model.sed(theta, obs=obs, sps=sps)
verbose = True
run_params["verbose"] = verbose
model = build_model(**run_params)
print("\nInitial free parameter vector theta:\n {}\n".format(model.theta))
#print("Initial parameter dictionary:\n{}".format(model.params))
print("\n----------------------- Model details: -----------------------")
print(model)
print(
"----------------------- End model details. -----------------------\n")
# Here we will run all our building functions
obs = build_obs(fluxes, fluxes_unc, useable_filters)
sps = build_sps(**run_params)
#plot_data(obs)
#sys.exit(0)
# --- start fitting ----
# Set this to False if you don't want to do another optimization
# before emcee sampling (but note that the "optimization" entry
# in the output dictionary will be (None, 0.) in this case)
# If set to true then another round of optmization will be performed
# before sampling begins and the "optmization" entry of the output
# will be populated.
"""
run_params["optimize"] = False
run_params["min_method"] = 'lm'
# We'll start minimization from "nmin" separate places,
# the first based on the current values of each parameter and the
# rest drawn from the prior. Starting from these extra draws
# can guard against local minima, or problems caused by
# starting at the edge of a prior (e.g. dust2=0.0)
run_params["nmin"] = 5
run_params["emcee"] = True
run_params["dynesty"] = False
# Number of emcee walkers
run_params["nwalkers"] = nwalkers
# Number of iterations of the MCMC sampling
run_params["niter"] = niter
# Number of iterations in each round of burn-in
# After each round, the walkers are reinitialized based on the
# locations of the highest probablity half of the walkers.
run_params["nburn"] = [8, 16, 32, 64]
run_params["progress"] = True
hfile = adap_dir + "emcee_" + field + "_" + str(galaxy_seq) + ".h5"
if not os.path.isfile(hfile):
print("Now running with Emcee.")
output = fit_model(obs, model, sps, lnprobfn=lnprobfn, **run_params)
print('done emcee in {0}s'.format(output["sampling"][1]))
writer.write_hdf5(hfile, run_params, model, obs,
output["sampling"][0], output["optimization"][0],
tsample=output["sampling"][1],
toptimize=output["optimization"][1])
print('Finished with Seq: ' + str(galaxy_seq))
"""
hfile = adap_dir + "dynesty_" + field + "_" + str(galaxy_seq) + ".h5"
if not os.path.isfile(hfile):
print("Now running with Dynesty.")
run_params["emcee"] = False
run_params["dynesty"] = True
run_params["nested_method"] = "rwalk"
run_params["nlive_init"] = 400
run_params["nlive_batch"] = 200
run_params["nested_dlogz_init"] = 0.05
run_params["nested_posterior_thresh"] = 0.05
run_params["nested_maxcall"] = int(1e6)
#from multiprocessing import Pool
#with Pool(6) as pool:
# run_params["pool"] = pool
output = fit_model(obs, model, sps, lnprobfn=lnprobfn, **run_params)
print('done dynesty in {0}s'.format(output["sampling"][1]))
writer.write_hdf5(hfile,
run_params,
model,
obs,
output["sampling"][0],
output["optimization"][0],
tsample=output["sampling"][1],
toptimize=output["optimization"][1])
print('Finished with Seq: ' + str(galaxy_seq))
# -------------------------
# Visualizing results
results_type = "dynesty" # "emcee" | "dynesty"
# grab results (dictionary), the obs dictionary, and our corresponding models
# When using parameter files set `dangerous=True`
#result, obs, _ = reader.results_from("{}_" + str(galaxy_seq) + \
# ".h5".format(results_type), dangerous=False)
result, obs, _ = reader.results_from(adap_dir + results_type + "_" + \
field + "_" + str(galaxy_seq) + ".h5", dangerous=False)
#The following commented lines reconstruct the model and sps object,
# if a parameter file continaing the `build_*` methods was saved along with the results
#model = reader.get_model(result)
#sps = reader.get_sps(result)
# let's look at what's stored in the `result` dictionary
print(result.keys())
parnames = np.array(result['theta_labels'])
print('Parameters in this model:', parnames)
"""
if results_type == "emcee":
chosen = np.random.choice(result["run_params"]["nwalkers"], size=150, replace=False)
tracefig = reader.traceplot(result, figsize=(10,6), chains=chosen)
tracefig.savefig(adap_dir + 'trace_' + field + '_' + str(galaxy_seq) + '.pdf',
dpi=200, bbox_inches='tight')
else:
tracefig = reader.traceplot(result, figsize=(10,6))
tracefig.savefig(adap_dir + 'trace_' + field + '_' + str(galaxy_seq) + '.pdf',
dpi=200, bbox_inches='tight')
"""
# Get chain for corner plot
if results_type == 'emcee':
trace = result['chain']
thin = 5
trace = trace[:, ::thin, :]
samples = trace.reshape(trace.shape[0] * trace.shape[1],
trace.shape[2])
else:
samples = result['chain']
# Plot SFH
#print(model) # to copy paste agebins from print out
nagebins = 6
agebins = np.array([[0., 8.], [8., 8.47712125], [8.47712125, 9.],
[9., 9.47712125], [9.47712125, 9.77815125],
[9.77815125, 10.13353891]])
# Get the zfractions from corner quantiles
zf1 = corner.quantile(samples[:, 2], q=[0.16, 0.5, 0.84])
zf2 = corner.quantile(samples[:, 3], q=[0.16, 0.5, 0.84])
zf3 = corner.quantile(samples[:, 4], q=[0.16, 0.5, 0.84])
zf4 = corner.quantile(samples[:, 5], q=[0.16, 0.5, 0.84])
zf5 = corner.quantile(samples[:, 6], q=[0.16, 0.5, 0.84])
zf_arr = np.array([zf1[1], zf2[1], zf3[1], zf4[1], zf5[1]])
zf_arr_l = np.array([zf1[0], zf2[0], zf3[0], zf4[0], zf5[0]])
zf_arr_u = np.array([zf1[2], zf2[2], zf3[2], zf4[2], zf5[2]])
cq_mass = corner.quantile(samples[:, 7], q=[0.16, 0.5, 0.84])
print("Total mass:", "{:.3e}".format(cq_mass[1]), "+",
"{:.3e}".format(cq_mass[2] - cq_mass[1]), "-",
"{:.3e}".format(cq_mass[1] - cq_mass[0]))
# -----------
new_agebins = pt.zred_to_agebins(zred=obj_z, agebins=agebins)
print("New agebins:", new_agebins)
# -----------------------
# now convert to sfh and its errors
sfr = pt.zfrac_to_sfr(total_mass=cq_mass[1],
z_fraction=zf_arr,
agebins=new_agebins)
sfr_l = pt.zfrac_to_sfr(total_mass=cq_mass[1],
z_fraction=zf_arr_l,
agebins=new_agebins)
sfr_u = pt.zfrac_to_sfr(total_mass=cq_mass[1],
z_fraction=zf_arr_u,
agebins=new_agebins)
print("----------")
print("z fractions: ", zf_arr)
print("Lower z fractions:", zf_arr_l)
print("Upper z fractions:", zf_arr_u)
print("----------")
print("Inferred SFR: ", sfr)
print("Lower sfr vals:", sfr_l)
print("Upper sfr vals:", sfr_u)
#############
x_agebins = 10**new_agebins / 1e9
fig = plt.figure(figsize=(8, 4))
ax = fig.add_subplot(111)
ax.set_xlabel(r'$\mathrm{Time\, [Gyr];\, since\ galaxy\ formation}$',
fontsize=20)
ax.set_ylabel(r'$\mathrm{SFR\, [M_\odot/yr]}$', fontsize=20)
for a in range(len(agebins)):
ax.plot(x_agebins[a],
np.ones(len(x_agebins[a])) * sfr[a],
color='mediumblue',
lw=3.0)
# put in some poisson errors
sfr_err = np.ones(len(x_agebins[a])) * np.sqrt(sfr[a])
sfr_plt = np.ones(len(x_agebins[a])) * sfr[a]
sfr_low_fill = sfr_plt - sfr_err
sfr_up_fill = sfr_plt + sfr_err
ax.fill_between(x_agebins[a],
sfr_low_fill,
sfr_up_fill,
color='gray',
alpha=0.6)
#ax.set_ylim(np.min(sfr_low_fill) * 0.3, np.max(sfr_up_fill) * 1.1)
fig.savefig(adap_dir + 'sfh_' + field + '_' + str(galaxy_seq) + '.pdf',
dpi=200,
bbox_inches='tight')
sys.exit(0)
# Keep code block for future use if needed
"""
# combination of linear and log axis from
# https://stackoverflow.com/questions/21746491/combining-a-log-and-linear-scale-in-matplotlib
# linear part i.e., first age bin
ax.plot(x_agebins[0], np.ones(len(x_agebins[0])) * sfr[0], color='mediumblue', lw=3.5)
#ax.fill_between(x_agebins[0], np.ones(len(x_agebins[0])) * sfr_l[0],
# np.ones(len(x_agebins[0])) * sfr_u[0], color='gray', alpha=0.5)
ax.set_xlim(0.0, 8.0)
ax.spines['right'].set_visible(False)
ax.yaxis.set_ticks_position('left')
ax.xaxis.set_label_coords(x=1.2,y=-0.06)
# now log axis
divider = make_axes_locatable(ax)
axlog = divider.append_axes("right", size=3.0, pad=0, sharey=ax)
axlog.set_xscale('log')
for a in range(1, nagebins):
axlog.plot(x_agebins[a], np.ones(len(x_agebins[a])) * sfr[a], color='mediumblue', lw=3.5)
#axlog.fill_between(x_agebins[a], np.ones(len(x_agebins[a])) * sfr_l[a],
# np.ones(len(x_agebins[a])) * sfr_u[a], color='gray', alpha=0.5)
axlog.set_xlim(8.0, x_agebins[-1, -1] + 0.1)
axlog.spines['left'].set_visible(False)
axlog.yaxis.set_ticks_position('right')
axlog.tick_params(labelright=False)
axlog.xaxis.set_ticks(ticks=[8.0, 9.0])
axlog.xaxis.set_ticks(ticks=[8.2, 8.4, 8.6, 8.8, 9.2, 9.4, 9.6], minor=True)
axlog.set_xticklabels(['8', '9'])
axlog.set_xticklabels(labels=[], minor=True)
fig.savefig(adap_dir + 'sfh_' + field + '_' + str(galaxy_seq) + '.pdf',
dpi=200, bbox_inches='tight')
"""
# ---------- corner plot
# set up corner ranges and labels
math_parnames = [
r'$\mathrm{log(Z_\odot)}$', r'$\mathrm{dust2}$', r'$zf_1$', r'$zf_2$',
r'$zf_3$', r'$zf_4$', r'$zf_5$', r'$\mathrm{M_s}$',
r'$\mathrm{f_{agn}}$', r'$\mathrm{agn_\tau}$',
r'$\mathrm{dust_{ratio}}$', r'$\mathrm{dust_{index}}$'
]
#math_parnames = [r'$\mathrm{M_s}$', r'$\mathrm{log(Z_\odot)}$',
#r'$\mathrm{dust2}$', r'$\mathrm{t_{age}}$', r'$\mathrm{log(\tau)}$']
# Fix labels for corner plot and
# Figure out ranges for corner plot
corner_range = []
for d in range(ndim):
# Get corner estimate and errors
cq = corner.quantile(x=samples[:, d], q=[0.16, 0.5, 0.84])
low_err = cq[1] - cq[0]
up_err = cq[2] - cq[1]
# Decide the padding for the plot range
# depending on how large the error is relative
# to the central estimate.
if low_err * 2.5 >= cq[1]:
sigma_padding_low = 1.2
else:
sigma_padding_low = 3.0
if up_err * 2.5 >= cq[1]:
sigma_padding_up = 1.2
else:
sigma_padding_up = 3.0
low_lim = cq[1] - sigma_padding_low * low_err
up_lim = cq[1] + sigma_padding_up * up_err
corner_range.append((low_lim, up_lim))
# Print estimate to screen
if 'mass' in parnames[d]:
pn = '{:.3e}'.format(cq[1])
pnu = '{:.3e}'.format(up_err)
pnl = '{:.3e}'.format(low_err)
else:
pn = '{:.3f}'.format(cq[1])
pnu = '{:.3f}'.format(up_err)
pnl = '{:.3f}'.format(low_err)
print(parnames[d], ": ", pn, "+", pnu, "-", pnl)
# Corner plot
cornerfig = corner.corner(samples,
quantiles=[0.16, 0.5, 0.84],
labels=math_parnames,
label_kwargs={"fontsize": 14},
range=corner_range,
smooth=0.5,
smooth1d=0.5)
# loop over all axes *again* and set title
# because it won't let me set the
# format for soem titles separately
# Looping has to be done twice because corner
# plotting has to be done to get the figure.
corner_axes = np.array(cornerfig.axes).reshape((ndim, ndim))
for d in range(ndim):
# Get corner estimate and errors
cq = corner.quantile(x=samples[:, d], q=[0.16, 0.5, 0.84])
low_err = cq[1] - cq[0]
up_err = cq[2] - cq[1]
ax_c = corner_axes[d, d]
if 'mass' in parnames[d]:
ax_c.set_title(math_parnames[d] + r"$ \, =\,$" + csn(cq[1], sigfigs=3) + \
r"$\substack{+$" + csn(up_err, sigfigs=3) + r"$\\ -$" + \
csn(low_err, sigfigs=3) + r"$}$", fontsize=11, pad=15)
else:
ax_c.set_title(math_parnames[d] + r"$ \, =\,$" + r"${:.3f}$".format(cq[1]) + \
r"$\substack{+$" + r"${:.3f}$".format(up_err) + r"$\\ -$" + \
r"${:.3f}$".format(low_err) + r"$}$", fontsize=11, pad=10)
cornerfig.savefig(adap_dir + 'corner_' + field + '_' + \
str(galaxy_seq) + '.pdf', dpi=200, bbox_inches='tight')
sys.exit(0)
# maximum a posteriori (of the locations visited by the MCMC sampler)
pmax = np.argmax(result['lnprobability'])
if results_type == "emcee":
p, q = np.unravel_index(pmax, result['lnprobability'].shape)
theta_max = result['chain'][p, q, :].copy()
else:
theta_max = result["chain"][pmax, :]
#print('Optimization value: {}'.format(theta_best))
#print('MAP value: {}'.format(theta_max))
# make SED plot for MAP model and some random model
# randomly chosen parameters from chain
randint = np.random.randint
if results_type == "emcee":
theta = result['chain'][randint(nwalkers), randint(niter)]
else:
theta = result["chain"][randint(len(result["chain"]))]
# generate models
a = 1.0 + model.params.get('zred', 0.0) # cosmological redshifting
# photometric effective wavelengths
wphot = obs["phot_wave"]
# spectroscopic wavelengths
if obs["wavelength"] is None:
# *restframe* spectral wavelengths, since obs["wavelength"] is None
wspec = sps.wavelengths
wspec *= a #redshift them
else:
wspec = obs["wavelength"]
# sps = reader.get_sps(result) # this works if using parameter files
mspec, mphot, mextra = model.mean_model(theta, obs, sps=sps)
mspec_map, mphot_map, _ = model.mean_model(theta_max, obs, sps=sps)
# establish bounds
xmin, xmax = np.min(wphot) * 0.8, np.max(wphot) / 0.8
ymin, ymax = obs["maggies"].min() * 0.8, obs["maggies"].max() / 0.4
# Make plot of data and model
fig3 = plt.figure(figsize=(9, 4))
ax3 = fig3.add_subplot(111)
ax3.set_xlabel(r'$\mathrm{\lambda\ [\AA]}$', fontsize=15)
#ax3.set_ylabel(r'$\mathrm{f_\lambda\ [erg\, s^{-1}\, cm^{-2}\, \AA^{-1}]}$', fontsize=15)
ax3.set_ylabel(r'$\mathrm{Flux\ Density\ [maggies]}$', fontsize=15)
ax3.loglog(wspec,
mspec,
label='Model spectrum (random draw)',
lw=0.7,
color='navy',
alpha=0.7)
ax3.loglog(wspec,
mspec_map,
label='Model spectrum (MAP)',
lw=0.7,
color='green',
alpha=0.7)
ax3.errorbar(wphot,
mphot,
label='Model photometry (random draw)',
marker='s',
markersize=10,
alpha=0.8,
ls='',
lw=3,
markerfacecolor='none',
markeredgecolor='blue',
markeredgewidth=3)
ax3.errorbar(wphot,
mphot_map,
label='Model photometry (MAP)',
marker='s',
markersize=10,
alpha=0.8,
ls='',
lw=3,
markerfacecolor='none',
markeredgecolor='green',
markeredgewidth=3)
ax3.errorbar(wphot,
obs['maggies'],
yerr=obs['maggies_unc'],
label='Observed photometry',
ecolor='red',
marker='o',
markersize=10,
ls='',
lw=3,
alpha=0.8,
markerfacecolor='none',
markeredgecolor='red',
markeredgewidth=3)
# plot transmission curves
for f in obs['filters']:
w, t = f.wavelength.copy(), f.transmission.copy()
t = t / t.max()
t = 10**(0.2 * (np.log10(ymax / ymin))) * t * ymin
ax3.loglog(w, t, lw=3, color='gray', alpha=0.7)
ax3.set_xlim([xmin, xmax])
ax3.set_ylim([ymin, ymax])
ax3.legend(loc='best', fontsize=11)
fig3.savefig(adap_dir + 'sedplot_' + field + '_' + str(galaxy_seq) +
'.pdf',
dpi=200,
bbox_inches='tight')
plt.clf()
plt.cla()
plt.close()
return None
def post_processing(param_name, outname=None, **kwargs):
'''
Driver. Loads output, runs post-processing routine.
'''
''' # MACHETE
from brown_io import load_prospector_data, create_prosp_filename
'''
# I/O
if outname is None:
parmfile = model_setup.import_module_from_file(param_name)
outname = parmfile.run_params['outfile']
model_filename = outname[:-6] + 'odel' # ADDED
sample_results, powell_results, model = read_results.results_from(
outname, model_file=model_filename, inmod=None) # ADDED
cornerfig = read_results.subtriangle(sample_results,
start=400,
thin=5,
show_titles=True) # ADDED
plt.show(
) # ADDED to give idea what sfh should look like based on sfr_fraction
''' # MACHETE
outfolder = os.getenv('APPS') + '/threedhst_bsfh/plots/' + outname.split('/')[-2] + '/'
# check for output folder, create if necessary
if not os.path.isdir(outfolder):
os.makedirs(outfolder)
try:
sample_results, powell_results, model, _ = load_prospector_data(outname, hdf5=True, load_extra_output=False)
except AttributeError:
print
'Failed to load chain for ' + sample_results['run_params']['objname'] + '. Returning.'
return
'''
print
'Performing post-processing on ' + sample_results['run_params']['objname']
### create flatchain, run post-processing
sample_results['flatchain'] = prosp_dutils.chop_chain(
sample_results['chain'], **sample_results['run_params'])
sample_results['flatprob'] = prosp_dutils.chop_chain(
sample_results['lnprobability'], **sample_results['run_params'])
extra_output = calc_extra_quantities(sample_results, **kwargs)
''' # MACHETE
### create post-processing name, dump info
mcmc_filename, model_filename, extra_filename = create_prosp_filename(outname)
hickle.dump(extra_output, open(extra_filename, "w"))
### MAKE PLOTS HERE
try:
prosp_diagnostic_plots.make_all_plots(sample_results=sample_results, extra_output=extra_output,
filebase=outname, outfolder=outfolder, param_name=param_name + '.py')
except NameError:
print
"Unable to make plots for " + sample_results['run_params']['objname'] + " due to import error. Passing."
pass
'''
### ADDED to quickly print out SFH
plt.plot(extra_output['extras']['t_sfh'], extra_output['bfit']['sfh'])
plt.ylabel(r'M$_\odot$ yr$^{-1}$')
plt.xlabel('Gyr')
plt.show()
def post_processing(out_file, param_file, out_incl=False, full_h5file=False): # , **kwargs):
"""
Driver. Loads output, runs post-processing routine.
"""
obj = ''
field = ''
base = ''
count = 0
slash = 0
for i in out_file:
if i == '/':
slash += 1
elif i == '_':
count += 1
elif out_incl:
if slash == 1 and count == 1:
obj += i
elif count == 2:
field += i
elif count == 3:
base += i
elif count == 4:
break
elif full_h5file:
if slash == 13 and count == 1: # slash=12
obj += i
elif count == 2:
field += i
elif count == 3:
base += i
elif count == 4:
break
elif count == 0:
obj += i
elif count == 1:
field += i
elif count == 2:
base += i
elif count == 3 and not outy:
break
print(field)
git = '/home/jonathan/.conda/envs/snowflakes/lib/python2.7/site-packages/prospector/git/'
full_base = 'pkl_tfn/' + obj + '_' + field + '_' + base # 'pkl_efastnoem/' # 'pkl_efico/'
pkl = 'out.pkl'
res, pr, mod = bread.results_from(out_file)
print('bread')
# create flatchain, run post-processing
res['flatchain'] = prosp_dutils.chop_chain(res['chain'], **res['run_params'])
res['flatprob'] = prosp_dutils.chop_chain(res['lnprobability'], **res['run_params'])
'''
extra_output = calc_extra_quantities(res) # , **kwargs)
print('extra calculated')
extra = full_base + '_extra_' + pkl
with open(extra, 'wb') as newfile: # 'wb' because binary format
pickle.dump(extra_output, newfile, pickle.HIGHEST_PROTOCOL)
print('extra pickled')
'''
prob = res['lnprobability'][:, 0:]
# PRINT TRACE SHOWING HOW ITERATIONS CONVERGE FOR EACH PARAMETER
# tracefig, prob = bread.param_evol(res) # print tracefig, store probability
# plt.title(full_base) # BUCKET just added
# plt.savefig('img/' + full_base + '_tracefig.png', bbox_inches='tight')
# plt.show()
# FIND WALKER, ITERATION THAT GIVE MAX PROBABILITY
print('max', prob.max())
row = prob.argmax() / len(prob[0])
col = prob.argmax() - row * len(prob[0])
walker, iteration = row, col
print(walker, iteration)
# PRINT CORNERFIG CONTOURS/HISTOGRAMS FOR EACH PARAMETER
'''
bread.subtriangle(res, start=0, thin=5, show_titles=True)
plt.title(full_base) # BUCKET just added
plt.savefig('img/' + full_base + '_cornerfig.png', bbox_inches='tight')
# plt.show()
'''
# For FAST: truths=[mass, age, tau, dust2] (for 1824: [9.78, 0.25, -1., 0.00])
# We need the correct sps object to generate models
sargv = sys.argv
argdict = {'param_file': param_file}
clargs = model_setup.parse_args(sargv, argdict=argdict)
run_params = model_setup.get_run_params(argv=sargv, **clargs)
sps = model_setup.load_sps(**run_params)
print('sps')
# GET MODELED SPECTRA AND PHOTOMETRY
# These have the same shape as the obs['spectrum'] and obs['maggies'] arrays.
spec, phot, mfrac = mod.mean_model(res['chain'][walker, iteration, :], obs=res['obs'], sps=sps)
print('spec')
# PLOT SPECTRUM
wave = [f.wave_effective for f in res['obs']['filters']]
wave = np.asarray(wave)
# CHANGING OBSERVED TO REST FRAME WAVELENGTH
if field == 'cdfs':
datname = '/home/jonathan/cdfs/cdfs.v1.6.11.cat'
zname = '/home/jonathan/cdfs/cdfs.v1.6.9.awk.zout'
elif field == 'cosmos':
datname = '/home/jonathan/cosmos/cosmos.v1.3.8.cat' # main catalog
zname = '/home/jonathan/cosmos/cosmos.v1.3.6.awk.zout' # redshift catalog
elif field == 'uds':
datname = '/home/jonathan/uds/uds.v1.5.10.cat'
zname = '/home/jonathan/uds/uds.v1.5.8.awk.zout'
with open(datname, 'r') as f:
hdr = f.readline().split()
dtype = np.dtype([(hdr[1], 'S20')] + [(n, np.float) for n in hdr[2:]])
dat = np.loadtxt(datname, comments='#', delimiter=' ', dtype=dtype)
with open(zname, 'r') as fz:
hdr_z = fz.readline().split()
dtype_z = np.dtype([(hdr_z[1], 'S20')] + [(n, np.float) for n in hdr_z[2:]])
zout = np.loadtxt(zname, comments='#', delimiter=' ', dtype=dtype_z)
idx = dat['id'] == obj # array filled: False when dat['id'] != obj, True when dat['id'] == obj
print(obj)
zred = zout['z_spec'][idx][0] # z = z_spec
if zred == -99:
zred = zout['z_peak'][idx][0] # if z_spec does not exist, z = z_phot
print('redshift', zred)
wave_rest = [] # REST FRAME WAVELENGTH
for j in range(len(wave)):
wave_rest.append(wave[j] / (1 + zred)) # 1 + z = l_obs / l_emit --> l_emit = l_obs / (1 + z)
wave_rest = np.asarray(wave_rest)
# OUTPUT SED results to files
write_res = full_base + '_res_' + pkl # results
with open(write_res, 'wb') as newfile: # 'wb' because binary format
pickle.dump(res, newfile, pickle.HIGHEST_PROTOCOL) # res includes res['obs']['maggies'] and ...['maggies_unc']
write_sed = full_base + '_sed_' + pkl # model sed
with open(write_sed, 'wb') as newfile: # 'wb' because binary format
pickle.dump(phot, newfile, pickle.HIGHEST_PROTOCOL)
write_restwave = full_base + '_restwave_' + pkl # rest frame wavelengths
with open(write_restwave, 'wb') as newfile: # 'wb' because binary format
pickle.dump(wave_rest, newfile, pickle.HIGHEST_PROTOCOL)
write_spec = full_base + '_spec_' + pkl # spectrum
with open(write_spec, 'wb') as newfile: # 'wb' because binary format
pickle.dump(spec, newfile, pickle.HIGHEST_PROTOCOL)
write_sps = full_base + '_spswave_' + pkl # wavelengths that go with spectrum
with open(write_sps, 'wb') as newfile: # 'wb' because binary format
try:
wlengths = sps.wavelengths
except AttributeError:
wlengths = sps.csp.wavelengths
pickle.dump(wlengths, newfile, pickle.HIGHEST_PROTOCOL)
# pickle.dump(sps.wavelengths, newfile, pickle.HIGHEST_PROTOCOL)
# OUTPUT CHI_SQ results to files
chi_sq = ((res['obs']['maggies'] - phot) / res['obs']['maggies_unc']) ** 2
write_chisq = full_base + '_chisq_' + pkl
with open(write_chisq, 'wb') as newfile: # 'wb' because binary format
pickle.dump(chi_sq, newfile, pickle.HIGHEST_PROTOCOL)
write_justchi = full_base + '_justchi_' + pkl
with open(write_justchi, 'wb') as newfile:
pickle.dump((res['obs']['maggies'] - phot) / res['obs']['maggies_unc'], newfile, pickle.HIGHEST_PROTOCOL)
# PLOT CHISQ
'''
plt.plot(wave_rest, chi_sq, 'o', color='b')
plt.title(str(obj) + r' $\chi^2$')
plt.xlabel('Rest frame wavelength [angstroms]')
plt.ylabel(r'$\chi^2$')
plt.savefig('img/' + full_base + '_chisq.png', bbox_inches='tight')
# plt.show()
'''
# HOW CONVERGED IS THE CODE?? LET'S FIND OUT!
'''
parnames = np.array(res['model'].theta_labels())
fig, kl_ax = plt.subplots(1, 1, figsize=(7, 7))
for l in xrange(parnames.shape[0]):
kl_ax.plot(res['kl_iteration'], np.log10(res['kl_divergence'][:, l]), 'o', label=parnames[l], lw=1.5,
linestyle='-', alpha=0.6)
'''
write_klit = full_base + '_klit_' + pkl
with open(write_klit, 'wb') as newfile:
pickle.dump(res['kl_iteration'], newfile, pickle.HIGHEST_PROTOCOL)
write_kldvg = full_base + '_kldvg_' + pkl
with open(write_kldvg, 'wb') as newfile:
pickle.dump(res['kl_divergence'], newfile, pickle.HIGHEST_PROTOCOL)
'''
sys.path.append(prosp_dir)
from run_prosp import build_model, build_sps
sfr_50 = []
sfr_16 = []
sfr_84 = []
print('now reading files')
galaxy_num = "{:03d}".format(galaxy)
infile = prosp_dir + '/galaxy' + str(galaxy) + '.h5'
globfiles = glob.glob(infile)
try:
for prosp_output in glob.glob(infile):
print(prosp_output)
res, obs, _ = pread.results_from(prosp_output)
pdfile = pd_dir + '/grid_physical_properties.305_galaxy' + str(
galaxy_num) + '.npz'
pd_data = np.load(pdfile)
int_mass = np.sum(pd_data['grid_star_mass'])
except:
print('file not found')
print('sps and model')
sps = build_sps()
mod = build_model()
thetas = mod.theta_labels()
#print(mod)
thetas_50 = []
thetas_16 = []
thetas_84 = []
post_burnin_center=burn_p0,
post_burnin_prob=burn_prob0)
if hfile is None:
hfile = hfilename
write_results.write_hdf5(hfile, run_params, model, obs, esampler,
guesses,
toptimize=pdur, tsample=edur,
sampling_initial_center=initial_center,
post_burnin_center=burn_p0,
post_burnin_prob=burn_prob0)
#print('Finished')
# grab results, powell results, and our corresponding models
res, pr, mod = results_from("{}_mcmc.h5".format(outroot))
'''
if os.path.isfile("{}_mcmc.h5".format(outroot)):
print('the files are IN the computer!')
res, pr, mod = results_from("{}_mcmc.h5".format(outroot))
else:
tstart = time.time() # time it
out = fitting.run_emcee_sampler(lnprobfn, initial_center, model, postkwargs=postkwargs, initial_prob=initial_prob, pool=None, hdf5=hfile, **run_params)
esampler, burn_p0, burn_prob0 = out
edur = time.time() - tstart
#sys.stdout = fout
#print('done emcee in {0}s'.format(edur))
dirich_timelist = np.unique(np.array([ 1.38000000e+01, 1.37000000e+01, 1.37000000e+01, 1.34688689e+01,
1.34688689e+01, 1.32487758e+01, 1.32487758e+01, 1.28823933e+01,
1.28823933e+01, 1.22724872e+01, 1.22724872e+01, 1.12571945e+01,
1.12571945e+01, 9.56706658e+00, 9.56706658e+00, 6.75356055e+00,
6.75356055e+00, 2.07, 0.]))
#sfr50 = output_file['data'][()]['SFR_50']
#print(sfr50)
#massfrac = output_file['data'][()]['Massfrac']
#mass50 = output_file['data'][()]['Mass_50']
true_mstar = output_file['data'][()]['True Mass'] / 1.989e33
print('loading prosp results')
res, _, _ = pread.results_from(prosp_dir+'/galaxy'+str(galaxy)+'.h5')
thetas = mod.theta_labels()
print(thetas)
imax = np.argmax(res['lnprobability'])
theta_max = res["chain"][imax, :]
smass_idx = [i for i, s in enumerate(thetas) if 'massmet_1' in s][0]
smass = theta_max[smass_idx]
duste_gamma_idx = [i for i, s in enumerate(thetas) if 'duste_gamma' in s][0]
gamma = theta_max[duste_gamma_idx]#[item[duste_gamma_idx] for item in res['chain']]
duste_umin_idx = [i for i, s in enumerate(thetas) if 'duste_umin' in s][0]
umin = theta_max[duste_umin_idx]#[item[duste_umin_idx] for item in res['chain']]
#duste_qpah_idx = [i for i, s in enumerate(thetas) if 'duste_qpah' in s][0]
#pah = theta_max[duste_qpah_idx]#[item[duste_qpah_idx] for item in res['chain']]
dust2_idx = [i for i, s in enumerate(thetas) if 'dust2' in s][0]
d2 = theta_max[dust2_idx]#[item[dust2_idx] for item in res['chain']]
def post_processing(out_file, param_file, full_h5file=True, out_incl=False, **kwargs):
"""
Driver. Loads output, runs post-processing routine.
"""
# Dense, complex, terrible bookkeeping on my part here based on my naming system for prospector output files
obj = ''
field = ''
base = ''
count = 0
slash = 0
for i in kwargs['outname']:
if i == '/':
slash += 1
elif i == '_':
count += 1
elif out_incl:
if slash == 2 and count == 1:
obj += i
elif count == 2:
field += i
elif count == 3:
base += i
elif count == 4:
break
elif full_h5file:
if slash == 13 and count == 1:
obj += i
elif count == 2:
field += i
elif count == 3:
base += i
elif count == 4:
break
elif count == 0:
obj += i
elif count == 1:
field += i
elif count == 2:
base += i
elif count == 3 and not outy:
break
print(obj, field)
full_base = obj + '_' + field + '_' + base
img_base = 'img/' + full_base # /home/jonathan/img' +
print(full_base, img_base)
pkl = 'out.pkl'
res, pr, mod = bread.results_from(out_file)
print('bread')
# create flatchain, run post-processing!
res['flatchain'] = prosp_dutils.chop_chain(res['chain'], **res['run_params'])
res['flatprob'] = prosp_dutils.chop_chain(res['lnprobability'], **res['run_params'])
extra_output = calc_extra_quantities(res, **kwargs)
print('extra calculated')
print(base)
# choose correct folder where .h5 file is stored based on param file name
if base == 'corr':
folder = 'pkl_ecorr/' # 'pkl_ncorr/'
elif base == 'fico':
folder = 'pkl_efico/' # 'pkl_nfico/'
elif base == 'masstest':
folder = 'pkl_masstest/'
elif base == 'tt':
folder = 'pkl_tt/'
else:
folder = 'pkl_simsfh/'
'''
if base == 'thirty':
folder = 'etpkls/'
elif base == 'nth':
folder = 'ntpkls/'
elif base == 'fixedmet':
folder = 'pkls/'
elif base == 'otherbins':
folder = 'opkls/'
elif base == 'noelg':
folder = 'nmpkls/'
elif base == 'nother':
folder = 'nopkls/'
elif base == 'vary':
folder = 'ecorr_pkl/'
# folder = 'evar_pkl/'
elif base == 'noneb' or 'evarnoneb':
folder = 'nonebpkls/'
elif base == 'efifty2':
folder = 'efifty2_pkls/'
elif base == 'evar2':
folder = 'evar2_pkls/'
elif base == 'masstest':
folder = 'pkl_masstest'
'''
# folder = 'evar2_pkls/' # 'efifty2_pkls/'
# pkl extra output!
extra = folder + full_base + '_extra_' + pkl # full_base + '_extra_' + pkl
print(extra)
with open(extra, 'wb') as newfile: # 'wb' because binary format
pickle.dump(extra_output, newfile, pickle.HIGHEST_PROTOCOL)
print('extra pickled')
# PRINT TRACE SHOWING HOW ITERATIONS PROGRESS FOR EACH PARAMETER
# I edited param_evol to also store lnprob, but this is a silly and long-obsolete way of doing this
tracefig = bread.param_evol(res) # prints tracefig
plt.title(full_base) # BUCKET just added
# plt.savefig(img_base + '_tracefig.png', bbox_inches='tight')
# plt.show()
# FIND WALKER, ITERATION THAT GIVE MAX PROBABILITY
# a result of the silly, long-obsolete way I'm grabbing lnprob above
prob = res['lnprobability'][..., 0:]
print('max', prob.max())
row = prob.argmax() / len(prob[0])
col = prob.argmax() - row * len(prob[0])
walker, iteration = row, col
print(walker, iteration)
# PRINT CORNERFIG CONTOURS/HISTOGRAMS FOR EACH PARAMETER
bread.subtriangle(res, start=-1000, thin=5, show_titles=True)
plt.title(full_base) # BUCKET just added
# plt.savefig(img_base + '_cornerfig.png', bbox_inches='tight')
# plt.show()
# For FAST: truths=[mass, age, tau, dust2] (for 1824: [9.78, 0.25, -1., 0.00])
# We need the correct sps object to generate models
sargv = sys.argv
argdict = {'param_file': param_file}
clargs = model_setup.parse_args(sargv, argdict=argdict)
run_params = model_setup.get_run_params(argv=sargv, **clargs)
sps = model_setup.load_sps(**run_params)
print('sps')
# GET MODELED SPECTRA AND PHOTOMETRY
# These have the same shape as the obs['spectrum'] and obs['maggies'] arrays.
spec, phot, mfrac = mod.mean_model(res['chain'][walker, iteration, :], obs=res['obs'], sps=sps)
print('spec')
# PLOT SPECTRUM
wave = [f.wave_effective for f in res['obs']['filters']]
wave = np.asarray(wave)
# CHANGING OBSERVED TO REST FRAME WAVELENGTH
# grabbing data from catalogs
if field == 'cdfs':
datname = '/home/jonathan/cdfs/cdfs.v1.6.11.cat'
zname = '/home/jonathan/cdfs/cdfs.v1.6.9.awk.zout'
elif field == 'cosmos':
datname = '/home/jonathan/cosmos/cosmos.v1.3.8.cat' # main catalog
zname = '/home/jonathan/cosmos/cosmos.v1.3.6.awk.zout' # redshift catalog
elif field == 'uds':
datname = '/home/jonathan/uds/uds.v1.5.10.cat'
zname = '/home/jonathan/uds/uds.v1.5.8.awk.zout'
elif field == 'sim': # hacking for now
datname = '/home/jonathan/cosmos/cosmos.v1.3.8.cat' # main catalog
zname = '/home/jonathan/cosmos/cosmos.v1.3.6.awk.zout' # redshift catalog
# photometry catalog
with open(datname, 'r') as f:
hdr = f.readline().split()
dtype = np.dtype([(hdr[1], 'S20')] + [(n, np.float) for n in hdr[2:]])
dat = np.loadtxt(datname, comments='#', delimiter=' ', dtype=dtype)
# redshift catalog
with open(zname, 'r') as fz:
hdr_z = fz.readline().split()
dtype_z = np.dtype([(hdr_z[1], 'S20')] + [(n, np.float) for n in hdr_z[2:]])
zout = np.loadtxt(zname, comments='#', delimiter=' ', dtype=dtype_z)
# if z_spec exists, use it; else use best-fit z_phot
idx = dat['id'] == obj # array filled with: False for all dat['id'] != obj, True for dat['id'] == obj
zred = zout['z_spec'][idx][0]
if zred == -99:
zred = zout['z_peak'][idx][0]
print('redshift', zred)
# convert stored wavelengths to rest frame wavelengths
wave_rest = []
for j in range(len(wave)):
wave_rest.append(wave[j]/(1 + zred)) # 1 + z = l_obs / l_emit --> l_emit = l_obs / (1 + z)
wave_rest = np.asarray(wave_rest)
# OUTPUT SED results to pkls
full_base = folder + full_base
write_res = full_base + '_res_' + pkl # results
with open(write_res, 'wb') as newfile: # 'wb' because binary format
pickle.dump(res, newfile, pickle.HIGHEST_PROTOCOL) # res includes res['obs']['maggies'], ['maggies_unc'], etc.
write_sed = full_base + '_sed_' + pkl # model sed
with open(write_sed, 'wb') as newfile: # 'wb' because binary format
pickle.dump(phot, newfile, pickle.HIGHEST_PROTOCOL)
write_restwave = full_base + '_restwave_' + pkl # rest frame wavelengths
with open(write_restwave, 'wb') as newfile: # 'wb' because binary format
pickle.dump(wave_rest, newfile, pickle.HIGHEST_PROTOCOL)
write_spec = full_base + '_spec_' + pkl # spectrum
with open(write_spec, 'wb') as newfile: # 'wb' because binary format
pickle.dump(spec, newfile, pickle.HIGHEST_PROTOCOL)
write_sps = full_base + '_spswave_' + pkl # wavelengths that go with spectrum
with open(write_sps, 'wb') as newfile: # 'wb' because binary format
pickle.dump(sps.wavelengths, newfile, pickle.HIGHEST_PROTOCOL)
# OUTPUT chi_sq results to pkls
chi_sq = ((res['obs']['maggies'] - phot) / res['obs']['maggies_unc']) ** 2
write_chisq = full_base + '_chisq_' + pkl
with open(write_chisq, 'wb') as newfile: # 'wb' because binary format
pickle.dump(chi_sq, newfile, pickle.HIGHEST_PROTOCOL)
write_justchi = full_base + '_justchi_' + pkl
with open(write_justchi, 'wb') as newfile:
pickle.dump((res['obs']['maggies'] - phot) / res['obs']['maggies_unc'], newfile, pickle.HIGHEST_PROTOCOL)
# PLOT chi_sq
plt.plot(wave_rest, chi_sq, 'o', color='b')
plt.title(str(obj) + r' $\chi^2$')
plt.xlabel('Rest frame wavelength [angstroms]')
plt.ylabel(r'$\chi^2$')
# plt.savefig(img_base + '_chisq.png', bbox_inches='tight')
# plt.show()
# HOW CONVERGED IS THE CODE?? LET'S FIND OUT! --> kl test
parnames = np.array(res['model'].theta_labels())
fig, kl_ax = plt.subplots(1, 1, figsize=(7, 7))
for l in xrange(parnames.shape[0]):
kl_ax.plot(res['kl_iteration'], np.log10(res['kl_divergence'][:, l]), 'o', label=parnames[l], lw=1.5,
linestyle='-', alpha=0.6)
# OUTPUT kl test to pkls
write_klit = full_base + '_klit_' + pkl
with open(write_klit, 'wb') as newfile:
pickle.dump(res['kl_iteration'], newfile, pickle.HIGHEST_PROTOCOL)
write_kldvg = full_base + '_kldvg_' + pkl
with open(write_kldvg, 'wb') as newfile:
pickle.dump(res['kl_divergence'], newfile, pickle.HIGHEST_PROTOCOL)
kl_ax.set_ylabel('log(KL divergence)')
kl_ax.set_xlabel('iteration')
# kl_ax.set_xlim(0, nsteps*1.1)
kl_div_lim = res['run_params'].get('convergence_kl_threshold', 0.018)
kl_ax.axhline(np.log10(kl_div_lim), linestyle='--', color='red', lw=2, zorder=1)
kl_ax.legend(prop={'size': 5}, ncol=2, numpoints=1, markerscale=0.7)
plt.title(str(obj) + ' kl')
def main():
"""
Main wrapper script.
"""
parser = argparse.ArgumentParser()
parser.add_argument('--priors',
default='delayed-tau',
type=str,
choices=['delayed-tau', 'bursty'],
help='Choose the model priors.')
parser.add_argument('--prefix',
default='ngc5322',
type=str,
help='Output file prefix.')
parser.add_argument('--seed',
default=1,
type=int,
help='Seed for random number generation.')
parser.add_argument('--nproc',
default=1,
type=int,
help='Number of cores to use.')
parser.add_argument('--sedfit',
action='store_true',
help='Do the SED fit.')
parser.add_argument('--qaplots',
action='store_true',
help='Make pretty plots.')
parser.add_argument('--verbose', action='store_true', help='Be verbose.')
args = parser.parse_args()
ngc5322dir = os.path.join(os.getenv('LSLGA_DIR'), 'science', 'proposals',
'nasa-adap-2019')
hfile = os.path.join(ngc5322dir, '{}-{}.h5'.format(args.prefix,
args.priors))
if args.sedfit:
import prospect.io
import prospect.fitting
# Initialize the SPS library (takes a bit), the photometry, the "run
# parameters" dictionary, and the model priors.
sps = load_sps(verbose=args.verbose)
obs, rp = load_obs(seed=args.seed,
nproc=args.nproc,
verbose=args.verbose,
sps=sps)
model = load_model(obs, args.priors, verbose=args.verbose)
#with multiprocessing.Pool(args.nproc) as P:
P = None
output = prospect.fitting.fit_model(
obs,
model,
sps,
noise=(None, None),
#optimize=True, dynesty=False, emcee=False,
optimize=False,
dynesty=True,
emcee=False,
#nested_posterior_thresh=0.05,
pool=P,
**rp)
if os.path.isfile(hfile):
os.remove(hfile)
print('Writing {}'.format(hfile))
prospect.io.write_results.write_hdf5(
hfile,
rp,
model,
obs,
output['sampling'][0],
output['optimization'][0],
tsample=output['sampling'][1],
toptimize=output['optimization'][1])
if args.qaplots:
from prospect.io import read_results as reader
print('Reading {}...'.format(hfile), end='')
t0 = time.time()
result, obs, _ = reader.results_from(hfile, dangerous=False)
print('...took {:.2f} sec'.format(time.time() - t0))
sps = load_sps(verbose=args.verbose)
model = load_model(obs, args.priors, verbose=args.verbose)
##################################################
# P(M, SFR)
print('Hack!')
png = os.path.join(ngc5322dir,
'{}-{}-pofm.png'.format(args.prefix, args.priors))
chain = result['chain']
lnprobability = result['lnprobability']
# infer the SFR
sfr = np.zeros_like(lnprobability)
for ii in np.arange(len(lnprobability)):
_, _, _ = model.mean_model(chain[ii, :], obs=obs, sps=sps)
sfr[ii] = sps.ssp.sfr * model.params['mass']
pdb.set_trace()
#ax.set_xlabel(r'$\log_{10}({\rm Stellar\ Mass})\ (\mathcal{M}_{\odot})$')
#ax.set_ylabel(r'Marginalized Posterior Probability')
fig, ax = plt.subplots(figsize=(8, 6))
ax.hist(chain[:, 4],
bins=50,
histtype='step',
linewidth=2,
edgecolor='k',
fill=True)
ax.set_xlim(11, 11.8)
ax.set_yticklabels([])
ax.set_xlabel(r'$\log_{10}(\mathcal{M}/\mathcal{M}_{\odot})$')
ax.set_ylabel(r'$P(\mathcal{M})$')
ax.xaxis.set_major_locator(MultipleLocator(0.2))
#for item in ([ax.title, ax.xaxis.label, ax.yaxis.label] +
# ax.get_xticklabels() + ax.get_yticklabels()):
# item.set_fontsize(22)
print('Writing {}'.format(png))
plt.subplots_adjust(left=0.1, right=0.95, bottom=0.18, top=0.95)
fig.savefig(png)
pdb.set_trace()
##################################################
# SED.
png = os.path.join(ngc5322dir,
'{}-{}-sed.png'.format(args.prefix, args.priors))
bestfit_sed(obs,
chain=result['chain'],
lnprobability=result['lnprobability'],
sps=sps,
model=model,
seed=1,
nrand=100,
png=png)
pdb.set_trace()
# Corner plot.
png = os.path.join(ngc5322dir,
'{}-{}-corner.png'.format(args.prefix, args.priors))
subtriangle(result,
showpars=['logmass', 'sfr', 'tau', 'dust2', 'dust_ratio'],
logify=['tau'],
png=png)
pdb.set_trace()
#reader.subcorner(result, start=0, thin=1, fig=plt.subplots(5,5,figsize=(27,27))[0])
pdb.set_trace()
def run_prospector(tde_name, path, z, withmpi, n_cores, gal_ebv, show_figs=True, init_theta=None, n_walkers=None,
n_inter=None, n_burn=None, read_only=False):
os.chdir(os.path.join(path, tde_name, 'host'))
if init_theta is None:
init_theta = [1e10, -1.0, 6, 0.5]
if n_walkers is None:
n_walkers = 100
if n_inter is None:
n_inter = 1000
if n_burn is None:
n_burn = [500]
obs, sps, model, run_params = configure(tde_name, path, z, init_theta, n_walkers, n_inter, n_burn, gal_ebv)
if not withmpi:
n_cores = 1
if not read_only:
print("Initial guess: {}".format(model.initial_theta))
print('Sampling the the SPS grid..')
if withmpi & ('logzsol' in model.free_params):
dummy_obs = dict(filters=None, wavelength=None)
logzsol_prior = model.config_dict["logzsol"]['prior']
lo, hi = logzsol_prior.range
logzsol_grid = np.around(np.arange(lo, hi, step=0.1), decimals=2)
sps.update(**model.params) # make sure we are caching the correct IMF / SFH / etc
for logzsol in logzsol_grid:
model.params["logzsol"] = np.array([logzsol])
_ = model.predict(model.theta, obs=dummy_obs, sps=sps)
print('Done')
from functools import partial
lnprobfn_fixed = partial(lnprobfn, sps=sps)
print('Starting posterior emcee sampling..')
if withmpi:
from multiprocessing import Pool
from multiprocessing import cpu_count
with Pool(int(n_cores)) as pool:
nprocs = n_cores
output = fit_model(obs, model, sps, pool=pool, queue_size=nprocs, lnprobfn=lnprobfn_fixed,
**run_params)
else:
output = fit_model(obs, model, sps, lnprobfn=lnprobfn_fixed, **run_params)
# output = fit_model(obs, model, sps, lnprobfn=lnprobfn, **run_params)
print('done emcee in {0}s'.format(output["sampling"][1]))
if os.path.exists("prospector_result.h5"):
os.system('rm prospector_result.h5')
hfile = "prospector_result.h5"
writer.write_hdf5(hfile, run_params, model, obs,
output["sampling"][0], output["optimization"][0],
tsample=output["sampling"][1],
toptimize=output["optimization"][1])
print('Finished')
# Loading results file
result, _, _ = reader.results_from("prospector_result.h5", dangerous=False)
# Finding the Maximum A Posteriori (MAP) model
imax = np.argmax(result['lnprobability'])
i, j = np.unravel_index(imax, result['lnprobability'].shape)
theta_max = result['chain'][i, j, :].copy()
# saving results
save_results(result, model, obs, sps, theta_max, tde_name, path, n_walkers, n_inter, n_burn, n_cores)
print('MAP value: {}'.format(theta_max))
fit_plot = plot_resulting_fit(tde_name, path)
try:
os.mkdir(os.path.join(path, tde_name, 'plots'))
except:
pass
fit_plot.savefig(os.path.join(path, tde_name, 'plots', tde_name + '_host_fit.png'), bbox_inches='tight', dpi=300)
if show_figs:
plt.show()
corner_fig = corner_plot(result)
corner_fig.savefig(os.path.join(path, tde_name, 'plots', tde_name + '_cornerplot.png'), bbox_inches='tight',
dpi=300)
if show_figs:
plt.show()
os.chdir(path)
estTaus[i, k] = float(
lines[j].split('tau: ')[1]) * 1e9 # convert from Gyr to yr
textFile.close()
# Calculate Prospector attenuation curves
# Take bestfit parameters from dust fit, use only
# non-dust related parameters with nodust model
# to give dust-free spectrum
if attBool:
nodust_path = '/scratch/ntf229/RT_fit/projects/' + galaxies[
i] + '/maxLevel13/wavelengths601/numPhotons1e9/niter4096/inc0/nodust/' + phot[
k] + '/walkers512/Prospector_files/fit.h5'
dust_path = '/scratch/ntf229/RT_fit/projects/' + galaxies[
i] + '/maxLevel13/wavelengths601/numPhotons1e9/niter4096/inc0/dust/dustFraction0.2/maxTemp8000/' + phot[
k] + '/walkers512/Prospector_files/fit.h5'
nodust_res, nodust_obs, nodust_model = reader.results_from(
nodust_path)
nodust_sps = reader.get_sps(nodust_res)
dust_res, dust_obs, dust_model = reader.results_from(dust_path)
dust_sps = reader.get_sps(dust_res)
# generate fake obs to get full resolution spectra
nodust_fake_obs = nodust_obs.copy()
nodust_fake_obs['spectrum'] = None
nodust_fake_obs['wavelength'] = None
nodust_theta_max = [
estMasses[i, k], estLogzsol[i, k], estAges[i, k], estTaus[i, k]
] # non-dust related bestfit parameters from dust fit
nodust_full_spec = nodust_model.predict(nodust_theta_max,
obs=nodust_fake_obs,
sps=nodust_sps)[0]
from prospect.io import read_results as pr
from prospect import fitting
from prospect.likelihood import lnlike_spec, lnlike_phot, write_log, chi_spec, chi_phot
# --------------
# Read command line arguments
# --------------
sargv = sys.argv
argdict = {'restart_from': '', 'niter': 1024}
clargs = model_setup.parse_args(sargv, argdict=argdict)
# ----------
# Result object and Globals
# ----------
result, global_obs, global_model = pr.results_from(clargs["restart_from"])
is_emcee = (len(result["chain"].shape) == 3) & (result["chain"].shape[0] > 1)
assert is_emcee, "Result file does not have a chain of the proper shape."
# SPS Model instance (with libraries check)
sps = pr.get_sps(result)
run_params = result["run_params"]
run_params.update(clargs)
# Noise model (this should be doable via read_results)
from prospect.models.model_setup import import_module_from_string
param_file = (result['run_params'].get('param_file', ''),
result.get("paramfile_text", ''))
path, filename = os.path.split(param_file[0])
modname = filename.replace('.py', '')
user_module = import_module_from_string(param_file[1], modname)
from scipy import stats
from scipy.interpolate import griddata
from scipy.stats import kde
import argparse
import os
#currentPath = os.path.dirname(__file__)
parser = argparse.ArgumentParser()
parser.add_argument("--filename")
parser.add_argument("--path")
args = parser.parse_args()
filePath = '{0}/Prospector_files/{1}'.format(args.path, args.filename)
res, obs, model = reader.results_from(filePath)
best = res["bestfit"]
# Maximum posterior probability sample
imax = np.argmax(res['lnprobability'])
csz = res["chain"].shape
#print('prob shape', res['lnprobability'].shape)
i, j = np.unravel_index(imax, res['lnprobability'].shape)
theta_max = res['chain'][i, j, :].copy()
flatchain = res["chain"].reshape(csz[0] * csz[1], csz[2])
flatprob = res['lnprobability'].reshape(csz[0] * csz[1])
# flatchain[:,0] is all mass parameters
import corner
import prospect.models.transforms as pt
import prospect.io.read_results as reader
home = os.getenv('HOME')
adap_dir = home + '/Documents/adap2021/'
field = 'North'
galaxy_seq = 27438
obj_z = 1.557
galaxy_age = 10**4.06
results_type = "dynesty"
result, obs, _ = reader.results_from(adap_dir + results_type + "_" + \
field + "_" + str(galaxy_seq) + ".h5", dangerous=False)
# ----------- non param
nagebins = 6
agebins = np.array([[ 0. , 8. ],
[ 8. , 8.47712125],
[ 8.47712125, 9. ],
[ 9. , 9.47712125],
[ 9.47712125, 9.77815125],
[ 9.77815125, 10.13353891]])
samples = result['chain']
# Get the zfractions from corner quantiles
zf1 = corner.quantile(samples[:, 2], q=[0.16, 0.5, 0.84])
zf2 = corner.quantile(samples[:, 3], q=[0.16, 0.5, 0.84])
import numpy as np
from glob import glob
import tqdm
import sys
from corner import quantile
prosp_dir = '/ufrc/narayanan/s.lower/simSEDs/simbam25n512_newfof/prod_runs/dirichlet/old/'
sys.path.append(prosp_dir)
from run_prosp import build_model, build_sps
sps = build_sps()
mod = build_model()
files_ = glob(prosp_dir + '/galaxy*.h5')
mass_sigma = []
mass_chains = []
for galaxy in tqdm.tqdm(files_):
res, obs, _ = pread.results_from(galaxy)
thetas = mod.theta_labels()
mass = [item[thetas.index('massmet_1')] for item in res['chain']]
mass_chains.append(mass)
mass_std = np.std(mass)
mass_sigma.append(mass_std)
np.savez(prosp_dir + 'mass_posterior_widths.npz',
sigma=mass_sigma,
posterior=mass_chains)
clargs = {'param_file': paramfile}
run_params = model_setup.get_run_params(argv=paramfile, **clargs)
print(run_params)
obs = model_setup.load_obs(**run_params)
sps = model_setup.load_sps(**run_params)
model = model_setup.load_model(**run_params)
wspec = sps.csp.wavelengths # *restframe* spectral wavelengths
a = 1.0 + model.params.get('zred', 0.6) # cosmological redshifting
wphot = np.array([f.wave_effective for f in obs['filters']])
# In [21]
# grab results, powell results, and our corresponding models
#res, pr, mod = results_from("{}_mcmc.h5".format(outroot))
res, pr, mod = results_from("demo_galphot_1508433060_mcmc.h5")
# In [22]
# To see how our MCMC samples look, we can examine a few traces
choice = np.random.choice
tracefig = pread.param_evol(res,
figsize=(20, 10),
chains=choice(128, size=10, replace=False))
# In [23]
# Show samples in a triangle or corner plot
#theta_truth = np.array([pr[i]
# for i in ['mass','logzsol','tau','tage','dust2']])
theta_truth = pr[0]['x']
theta_truth[0] = np.log10(theta_truth[0])
#cornerfig = pread.subtriangle(res, start=0, thin=5, truths=theta_truth, showpars='mass')#, fig=plt.subplots(5,5,figsize=(27,27))[0])
def ems(param_file, out_file, objname='21442', field='cdfs', enames=None):
res, pr, model = bread.results_from(out_file)
# get lnprob, based on bread.param_evol()
chain = res['chain'][..., 0:, :]
lnprob = res['lnprobability'][..., 0:]
# deal with single chain (i.e. nested sampling) results
if len(chain.shape) == 2:
lnprob = lnprob[None, ...]
# tracefig, prob = bread.param_evol(res) # store probability
# plt.show()
print('max', lnprob.max())
row = lnprob.argmax() / len(lnprob[0])
col = lnprob.argmax() - row * len(lnprob[0])
walker, iteration = row, col
print(walker, iteration)
# Get emission lines!
# We need the correct sps object to generate models
sargv = sys.argv
argdict = {'param_file': param_file}
clargs = model_setup.parse_args(sargv, argdict=argdict)
run_params = model_setup.get_run_params(argv=sargv, **clargs)
sps = model_setup.load_sps(**run_params)
print('sps')
# spec, mags, sm = model.mean_model(res['chain'][walker, iteration, :], obs=res['obs'], sps=sps) # spec [maggies/Hz]
print('mean model')
w = sps.wavelengths
### save redshift, lumdist
z = model.params.get('zred', np.array(0.0))
lumdist = model.params.get('lumdist', np.array(0.0))
nebinspec = model.params.get('nebemlineinspec', True)
model.params['zred'] = np.array(0.0)
if lumdist:
model.params['lumdist'] = np.array(1e-5)
if nebinspec == False:
model.params['nebemlineinspec'] = True
### if we want restframe optical photometry, generate fake obs file
### else generate NO obs file (don't do extra filter convolutions if not necessary)
obs = {'filters': [], 'wavelength': None}
### calculate SED. comes out as maggies per Hz, @ 10pc
spec, mags, sm = model.mean_model(res['chain'][walker, iteration, :],
obs=obs,
sps=sps) # maggies/Hz at 10pc
w = sps.wavelengths
### reset model
model.params['zred'] = z
if lumdist:
model.params['lumdist'] = lumdist
if nebinspec == False:
model.params['nebemlineinspec'] = False
spec *= dfactor_10pc / constants.L_sun.cgs.value * to_ergs # spec * cm^2 * (s/erg) * erg/maggies = s*cm^2 / Hz
# note erg = [g cm^2 / s^2]
# according to measure_restframe_properties(), above line converts to Lsun / Hz
to_flam = 3e18 / w**2 # for f_nu in erg s^-1 Hz^-1 cm^-2: to_flam [(Ang / s^-1) * (1 / Ang^2)]
spec_flam = spec * to_flam # erg cm^-2 s^-1 ang^-1
smooth_spec = smooth_spectrum(w, spec_flam, 250.0, minlam=3e3, maxlam=7e3)
### load fsps emission line list
loc = os.getenv('SPS_HOME') + '/data/emlines_info.dat'
dat = np.loadtxt(loc,
delimiter=',',
dtype={
'names': ('lam', 'name'),
'formats': ('f16', 'S40')
})
print('env')
print(type(enames))
### define emission lines
# legacy code compatible
if type(enames) == bool:
lines = np.array(
['Hdelta', 'Hbeta', '[OIII]1', '[OIII]2', 'Halpha', '[NII]'])
fsps_name = np.array([
'H delta 4102', 'H beta 4861', '[OIII]4960', '[OIII]5007',
'H alpha 6563', '[NII]6585'
])
else:
lines = enames
fsps_name = enames
print(lines, enames) # None, None
# lines = np.array(['Hdelta', 'Hbeta', '[OIII]1', '[OIII]2', 'Halpha', '[NII]'])
# fsps_name = np.array(['H delta 4102', 'H beta 4861', '[OIII]4960', '[OIII]5007', 'H alpha 6563', '[NII]6585'])
lines = np.array([
'[OII]1', '[OII]2', 'Hdelta', 'Hbeta', '[OIII]1', '[OIII]2', 'Halpha',
'[NII]'
])
fsps_name = np.array([
'[OII]3726', '[OII]3729', 'H delta 4102', 'H beta 4861', '[OIII]4960',
'[OIII]5007', 'H alpha 6563', '[NII]6585'
])
##### measure emission line flux + EQW
out = {}
# print(1, sps.emline_wavelengths) # big long array, 900 to 6*1e6
for jj in xrange(len(lines)):
# if we don't do nebular emission, zero this out
if not hasattr(sps, 'get_nebline_luminosity'):
print('hi')
out[lines[jj]] = {'flux': 0.0, 'eqw': 0.0}
continue
### calculate luminosity (in Lsun)
idx = fsps_name[jj] == dat['name']
# L_so = 3.84*10**33 erg/s
print(sps.params['mass'].sum())
eflux = float(sps.get_nebline_luminosity[idx] *
sps.params['mass'].sum()) # L_sun
elam = float(sps.emline_wavelengths[idx]) # Angstroms!
print(sps.get_nebline_luminosity[idx])
print(eflux, 'e luminosity') # typically 10**40 to 10**42
print(elam, 'elam') # Angstroms
# simple continuum estimation
tidx = np.abs(
sps.wavelengths - elam
) < 100 # True for sps.wavelengths within 100 Angstroms of elam wavelengths
eqw = eflux / np.median(
smooth_spec[tidx]
) # (erg/s) / (erg cm^-2 s^-1 Ang^-1) = Ang * cm**2
eflux *= 3.84 * 10**33 # erg/s (Lum, not flux)
out[lines[jj]] = {'flux': eflux, 'eqw': eqw}
return out, fsps_name
str(galaxy))
table = Table.read(photometry)
vorbins = table['vorbin']
logmasses = []
for vorbin in vorbins :
if table['use'][vorbin] :
h5_file = '{}{}/{}_ID_{}_BIN_{}_dynesty.h5'.format(inDir,
str(galaxy),
cluster,
str(galaxy),
str(vorbin))
result, obs, model = reader.results_from(h5_file, dangerous=False)
imax = np.argmax(result['lnprobability'])
logmass = result['chain'][imax, :][2]
logmasses.append(logmass)
else :
logmasses.append(np.nan)
table['logmass'] = np.array(logmasses)
final = '{}{}_ID_{}_results.fits'.format(outDir, cluster, str(galaxy))
table.write(final)
'''
import glob
h5_files = '{}{}/{}_ID_{}_BIN_*_dynesty.h5'.format(inDir, str(galaxy),
import numpy as np
import matplotlib.pyplot as plt
import prospect.io.read_results as reader
results_type = 'dynesty' # 'emcee' or 'dynesty'
verbose = True
plots = True
# get the results and observation dictionaries
result, obs, _ = reader.results_from('demo_params_{}.h5'.format(results_type),
dangerous=True)
# also get the sps and model objects. This works if using a parameter file with
# `build_*` methods
sps = reader.get_sps(result)
model = reader.get_model(result)
# print the contents of the `results` dictionary
if verbose:
print(result.keys())
# STEP 1: invetigate the parameter traces
if plots:
if results_type == 'emcee':
chosen = np.random.choice(result['run_params']['nwalkers'],
size=10,
replace=False)
tracefig = reader.traceplot(result, figsize=(16, 9), chains=chosen)
else:
tracefig = reader.traceplot(result, figsize=(16, 9))