**rp)
esampler = out
edur = time.time() - tstart
if rp['verbose']:
print('done emcee in {0}s'.format(edur))
# -------------------------
# Output HDF5 (and pickles if asked for)
# -------------------------
print("Writing to {}".format(outroot))
if rp.get("output_pickles", False):
write_results.write_pickles(rp,
model,
obsdat,
esampler,
guesses,
outroot=outroot,
toptimize=0,
tsample=edur,
sampling_initial_center=initial_center)
if hfile is None:
hfile = hfilename
write_results.write_hdf5(hfile,
rp,
model,
obsdat,
esampler,
guesses,
toptimize=0,
tsample=edur,
sampling_initial_center=initial_center)
tstart = time.time()
out = fitting.run_emcee_sampler(lnprobfn, initial_center, model,
postkwargs=postkwargs, initial_prob=initial_prob,
pool=pool, hdf5=hfile, **rp)
esampler, burn_p0, burn_prob0 = out
edur = time.time() - tstart
if rp['verbose']:
print('done emcee in {0}s'.format(edur))
# -------------------------
# Output pickles (and HDF5)
# -------------------------
print("Writing to {}".format(outroot))
write_results.write_pickles(rp, model, obsdat, esampler, guesses,
outroot=outroot, toptimize=pdur, tsample=edur,
sampling_initial_center=initial_center,
post_burnin_center=burn_p0,
post_burnin_prob=burn_prob0)
if hfile is None:
hfile = hfilename
write_results.write_hdf5(hfile, rp, model, obsdat, esampler, guesses,
toptimize=pdur, tsample=edur,
sampling_initial_center=initial_center,
post_burnin_center=burn_p0,
post_burnin_prob=burn_prob0)
try:
hfile.close()
except:
pass
halt('Finished')
# -----------------------
if rp['verbose']:
print('emcee sampling...')
tstart = time.time()
out = fitting.restart_emcee_sampler(lnprobfn, initial_positions,
postkwargs=postkwargs,
pool=pool, hdf5=hfile, **rp)
esampler = out
edur = time.time() - tstart
if rp['verbose']:
print('done emcee in {0}s'.format(edur))
# -------------------------
# Output HDF5 (and pickles if asked for)
# -------------------------
print("Writing to {}".format(outroot))
if rp.get("output_pickles", False):
write_results.write_pickles(rp, model, obsdat, esampler, guesses,
outroot=outroot, toptimize=0, tsample=edur,
sampling_initial_center=initial_center)
if hfile is None:
hfile = hfilename
write_results.write_hdf5(hfile, rp, model, obsdat, esampler, guesses,
toptimize=0, tsample=edur,
sampling_initial_center=initial_center)
try:
hfile.close()
except:
pass
halt('Finished')
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--prefix',
type=str,
default='redmapper_sdssphot',
help='String to prepend to I/O files.')
parser.add_argument('--nthreads',
type=int,
default=16,
help='Number of cores to use concurrently.')
parser.add_argument('--first',
type=int,
default=0,
help='Index of first object to fit.')
parser.add_argument('--last',
type=int,
default=None,
help='Index of last object to fit.')
parser.add_argument('--seed',
type=int,
default=1,
help='Random number seed.')
parser.add_argument('--build-sample',
action='store_true',
help='Build the sample.')
parser.add_argument('--dofit', action='store_true', help='Run prospector!')
parser.add_argument(
'--refit',
action='store_true',
help='Refit even if the prospector output files exist.')
parser.add_argument('--qaplots',
action='store_true',
help='Make some neat plots.')
parser.add_argument('--verbose',
action='store_true',
help='Be loquacious.')
args = parser.parse_args()
# Specify the run parameters and initialize the SPS object.
run_params = {
'prefix': args.prefix,
'verbose': args.verbose,
'seed': args.seed,
# initial optimization choices (nmin is only for L-M optimization)
'do_levenburg': True,
'do_powell': False,
'do_nelder_mead': False,
'nmin': np.max((10, args.nthreads)),
# emcee fitting parameters monte carlo markov chain samples parameters ft. certain technique
'nwalkers': 128,
'nburn': [32, 32, 64],
'niter': 256, # 512,
'interval': 0.1, # save 10% of the chains at a time
# Nestle fitting parameters
'nestle_method': 'single',
'nestle_npoints': 200,
'nestle_maxcall': int(1e6),
# Multiprocessing
'nthreads': args.nthreads,
# SPS initialization parameters
'compute_vega_mags': False,
'vactoair_flag': False, # use wavelengths in air
'zcontinuous': 1, # interpolate in metallicity
}
rand = np.random.RandomState(args.seed)
if not args.build_sample:
t0 = time()
print('Initializing CSPSpecBasis...')
sps = CSPSpecBasis(zcontinuous=run_params['zcontinuous'],
compute_vega_mags=run_params['compute_vega_mags'],
vactoair_flag=run_params['vactoair_flag'])
print('...took {:.1f} seconds.'.format(time() - t0))
if args.build_sample:
# READ OUR SHIT INSTEAD.
# Read the parent redmapper catalog, choose a subset of objects and
# write out.
cat = read_redmapper()
# Choose objects with masses from iSEDfit, Kravtsov, and pymorph, but
# for now just pick three random galaxies.
#these = np.arange(2) # [300, 301, 302]
these = np.arange(100) # [300, 301, 302]
print('Selecting {} galaxies.'.format(len(these)))
out = cat[these]
#out = cat[:200]
outfile = os.path.join(datadir(),
'{}_sample.fits'.format(run_params['prefix']))
print('Writing {}'.format(outfile))
fitsio.write(outfile, out, clobber=True)
if args.dofit:
import h5py
import emcee
from prospect import fitting
from prospect.io import write_results
# MAKE THIS SHIT WORK WITH OUR SHIT TOO ft getobs
# Read the parent sample and loop on each object.
cat = read_parent(
prefix=run_params['prefix']) #, first=args.first, last=args.last)
for ii, obj in enumerate(cat):
objprefix = '{0:05}'.format(obj['ISEDFIT_ID'])
print('Working on object {}/{} with prefix {}.'.format(
ii + 1, len(cat), objprefix))
# Check for the HDF5 output file / fitting results --
outroot = os.path.join(
datadir(), '{}_{}'.format(run_params['prefix'], objprefix))
hfilename = os.path.join(
datadir(), '{}_{}_mcmc.h5'.format(run_params['prefix'],
objprefix))
if os.path.isfile(hfilename):
if args.refit:
os.remove(hfilename)
else:
print('Prospector fitting results {} exist; skipping.'.
format(hfilename))
continue
# Grab the photometry for this object and then initialize the priors
# and the SED model.
obs = getobs(obj)
model = load_model(zred=obs['zred'], seed=args.seed)
# Get close to the right answer doing a simple minimization.
if run_params['verbose']:
print('Free parameters: {}'.format(model.free_params))
print('Initial parameter values: {}'.format(
model.initial_theta))
initial_theta = model.rectify_theta(
model.initial_theta) # make zeros tiny numbers
if bool(run_params.get('do_powell', True)):
tstart = time()
# optimization options
powell_opt = {
'ftol': run_params.get('ftol', 0.5e-5),
'xtol': 1e-6,
'maxfev': run_params.get('maxfev', 5000)
}
chi2args = (model, obs, sps, run_params['verbose']
) # extra arguments for chisqfn
guesses, pinit = fitting.pminimize(
chisqfn,
initial_theta,
args=chi2args,
model=model,
method='powell',
opts=powell_opt,
pool=pool,
nthreads=run_params['nthreads'])
best = np.argmin([p.fun for p in guesses])
# Hack to recenter values outside the parameter bounds!
initial_center = fitting.reinitialize(
guesses[best].x,
model,
edge_trunc=run_params.get('edge_trunc', 0.1))
initial_prob = -1 * guesses[best]['fun']
pdur = time() - tstart
if run_params['verbose']:
print('Powell initialization took {:.1f} seconds.'.format(
pdur))
print('Best Powell guesses: {}'.format(initial_center))
print('Initial probability: {}'.format(initial_prob))
elif bool(run_params.get('do_nelder_mead', True)):
from scipy.optimize import minimize
tstart = time()
chi2args = (model, obs, sps, run_params['verbose']
) # extra arguments for chisqfn
guesses = minimize(chisqfn,
initial_theta,
args=chi2args,
method='nelder-mead')
pdur = time() - tstart
# Hack to recenter values outside the parameter bounds!
initial_center = fitting.reinitialize(
guesses.x,
model,
edge_trunc=run_params.get('edge_trunc', 0.1))
initial_prob = -1 * guesses['fun']
if run_params['verbose']:
print('Nelder-Mead initialization took {:.1f} seconds.'.
format(pdur))
print('Best guesses: {}'.format(initial_center))
print('Initial probability: {}'.format(initial_prob))
elif bool(run_params.get('do_levenburg', True)):
tstart = time()
nmin = run_params['nmin']
chi2args = (model, obs, sps)
pinitial = fitting.minimizer_ball(initial_theta,
nmin,
model,
seed=run_params['seed'])
lsargs = list()
for pinit in pinitial:
lsargs.append((chivecfn, pinit, chi2args))
if run_params['nthreads'] > 1:
p = multiprocessing.Pool(run_params['nthreads'])
guesses = p.map(_doleast_squares, lsargs)
p.close()
else:
guesses = list()
for lsargs1 in lsargs:
guesses.append(_doleast_squares(lsargs1))
chisq = [np.sum(r.fun**2) for r in guesses]
best = np.argmin(chisq)
initial_prob = -np.log(chisq[best] / 2)
#initial_center = guesses[best].x
initial_center = fitting.reinitialize(
guesses[best].x,
model,
edge_trunc=run_params.get('edge_trunc', 0.1))
pdur = time() - tstart
if run_params['verbose']:
print(
'Levenburg-Marquardt initialization took {:.1f} seconds.'
.format(pdur))
print('Best guesses: {}'.format(initial_center))
print('Initial probability: {}'.format(initial_prob))
from prospector_plot_utilities import bestfit_sed
fig = bestfit_sed(obs,
theta=initial_center,
sps=sps,
model=model)
fig.savefig('test.png')
else:
if run_params['verbose']:
print('Skipping initial minimization.')
guesses = None
pdur = 0.0
initial_center = initial_theta.copy()
initial_prob = None
# Write some basic info to the HDF5 file--
hfile = h5py.File(hfilename, 'a')
write_results.write_h5_header(hfile, run_params, model)
write_results.write_obs_to_h5(hfile, obs)
if run_params['verbose']:
print('Started emcee sampling on {}'.format(asctime()))
tstart = time()
out = fitting.run_emcee_sampler(lnprobfn,
initial_center,
model,
verbose=run_params['verbose'],
nthreads=run_params['nthreads'],
nwalkers=run_params['nwalkers'],
nburn=run_params['nburn'],
niter=run_params['niter'],
prob0=initial_prob,
hdf5=hfile,
postargs=(model, obs, sps),
pool=pool)
esampler, burn_p0, burn_prob0 = out
del out
edur = time() - tstart
if run_params['verbose']:
print('Finished emcee sampling in {:.2f} minutes.'.format(
edur / 60.0))
# Update the HDF5 file with the results.
write_results.write_pickles(run_params,
model,
obs,
esampler,
guesses,
outroot=outroot,
toptimize=pdur,
tsample=edur,
sampling_initial_center=initial_center,
post_burnin_center=burn_p0,
post_burnin_prob=burn_prob0)
write_results.write_hdf5(hfilename,
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)
hfile.close()
if args.qaplots:
import h5py
from prospect.io import read_results
from prospector_plot_utilities import param_evol, subtriangle, bestfit_sed
# Read the parent sample and loop on each object.
cat = read_parent(
prefix=run_params['prefix']) #, first=args.first, last=args.last)
for obj in cat:
objprefix = '{0:05}'.format(obj['ISEDFIT_ID'])
# Grab the emcee / prospector outputs.
h5file = os.path.join(
datadir(), '{}_{}_mcmc.h5'.format(run_params['prefix'],
objprefix))
if not os.path.isfile(h5file):
print('HDF5 file {} not found; skipping.'.format(h5file))
continue
print('Reading {}'.format(h5file))
results, guesses, model = read_results.results_from(h5file)
nwalkers, niter, nparams = results['chain'][:, :, :].shape
# --------------------------------------------------
# Figure: Generate the best-fitting SED.
qafile = os.path.join(
datadir(), '{}_{}_sed.png'.format(args.prefix, objprefix))
print('Writing {}'.format(qafile))
fig = bestfit_sed(results['obs'],
chain=results['chain'],
lnprobability=results['lnprobability'],
sps=sps,
model=model,
seed=results['run_params']['seed'])
fig.savefig(qafile)
# --------------------------------------------------
# Figure: Visualize a random sampling of the MCMC chains.
qafile = os.path.join(
datadir(), '{}_{}_chains.png'.format(args.prefix, objprefix))
print('Writing {}'.format(qafile))
thesechains = rand.choice(nwalkers,
size=int(0.3 * nwalkers),
replace=False)
fig = param_evol(results, chains=thesechains)
fig.savefig(qafile)
# --------------------------------------------------
# Figure: Generate a corner/triangle plot of the free parameters.
qafile = os.path.join(
datadir(), '{}_{}_corner.png'.format(args.prefix, objprefix))
print('Writing {}'.format(qafile))
fig = subtriangle(results, thin=2)
fig.savefig(qafile)
# -------
# Sample
# -------
if rp['verbose']:
print('emcee sampling...')
tstart = time.time()
out = fitting.run_emcee_sampler(lnprobfn, initial_center, model,
postkwargs=postkwargs, initial_prob=initial_prob,
pool=pool, hdf5=hfile, **rp)
esampler, burn_p0, burn_prob0 = out
edur = time.time() - tstart
if rp['verbose']:
print('done emcee in {0}s'.format(edur))
# -------------------------
# Output pickles (and HDF5)
# -------------------------
write_results.write_pickles(rp, model, obsdat, esampler, powell_guesses,
outroot=outroot, toptimize=pdur, tsample=edur,
sampling_initial_center=initial_center,
post_burnin_center=burn_p0,
post_burnin_prob=burn_prob0)
if hfile is None:
hfile = hfilename
write_results.write_hdf5(hfile, rp, model, obsdat, esampler, powell_guesses,
toptimize=pdur, tsample=edur,
sampling_initial_center=initial_center,
post_burnin_center=burn_p0,
post_burnin_prob=burn_prob0)
halt('Finished')