def _samples(self, kappa, beta=1, return_full=False, print_progress=False):
r"""
Draws samples from the surrogate model (optionally the acquisition
function). Calls `dynesty.NestedSampler`. Runs on a single thread even
if `self.nthreads > 1`.
Parameters
----------
kappa : int
Acquisition function parameter. See class documentation for more
information.
beta : float, optional
Parallel tempering parameter :math:`L^{\beta}`, where :math:`L`
is the target function. By default 1.
return_full : bool, optional
Whether to also return the sampled log-target values and the
target evidence.
print_progress : bool, optional
Whether to print the sampler's progress bar.
Returns
-------
samples : np.ndarray
Sampled points from the surrogate model.
logtarget : np.ndarray
Optionally returned if `return_full=True`, the surrogate model
target values.
logz : int
Optionally returned if `return_full=True`, the surrogate model
evidence.
"""
sampler = NestedSampler(self.surrogate_predict,
self._prior_transform,
ndim=len(self.params),
logl_kwargs={
'kappa': kappa,
'beta': beta
},
rstate=self.generator,
**self._sampler_kwargs)
sampler.run_nested(print_progress=print_progress)
results = sampler.results
logz = results.logz[-1]
weights = numpy.exp(results.logwt - logz)
# Resample from the posterior
samples = dyfunc.resample_equal(results.samples, weights)
if return_full:
logtarget = self.surrogate_predict(samples)
# We're only interested in the contribution to the evidence the
# likelihood (our target function). The uniform prior is used only
# to provide samples, hence undo its contribution.
logprior = -numpy.log(self._prior_max - self._prior_min).sum()
logz -= logprior
return samples, logtarget, logz
return samples
def construct_analytical_functions(self):
"""Construct invertible functions based on interpolations."""
import warnings
# from dynesty import DynamicNestedSampler
from dynesty import NestedSampler
from collections import OrderedDict
import numpy as np
warnings.filterwarnings("ignore")
self._free_vars = OrderedDict(
(('r0', (0.25, 1.5)), ('mpow', (0, 5)), ('mtrunning', (-5, 5)),
('mrunning', (-5, 5)), ('tpow', (-5, 5)), ('trunning', (-5, 5)),
('tmrunning', (-5, 5)), ('zpow', (-5, 5))))
self._min_ilms, self._max_ilms = np.log10(np.min(self._ims)), np.log10(
np.max(self._ims))
self._min_ilzs, self._max_ilzs = np.min(self._ilzs), np.max(self._ilzs)
self._mlzs, self._mms, self._mts = np.meshgrid(self._ilzs,
self._ims,
self._its,
indexing='ij')
self._ndim = len(list(self._free_vars.keys()))
dsampler = NestedSampler(self.rad_log_like,
self.ptform,
self._ndim,
sample='rwalk')
# dsampler.run_nested(dlogz_init=0.01)
dsampler.run_nested(dlogz=1000)
res = dsampler.results
bbest = res['samples'][-1]
prt_ts = np.linspace(0, 1, 5)
test_masses = 10.0**np.linspace(self._min_ilms, self._max_ilms, 3)
test_lzs = np.linspace(self._min_ilzs, self._max_ilzs, 3)
for tlz in test_lzs:
for tm in test_masses:
print('Radii for logz = {} and m = {}'.format(tlz, tm))
print(self._radius_rgi([[tlz, tm, x] for x in prt_ts]))
print(self.rad_func(bbest, tlz, tm, prt_ts))
max_frac_err = np.max(
np.abs(
self.rad_func(bbest, self._mlzs, self._mms, self._mts) -
self._irs) / self._irs)
print('Maximum fractional error: {:.1%}'.format(max_frac_err))
def nestle_multi_cos():
with closing(Pool(processes=24)) as pool:
# Run nestedsampling
sampler = NestedSampler(log_likelihood_cosine, prior_transform_cos, 17,
bound='balls', nlive=1024,sample='rwalk',pool=pool,queue_size=24)
# t0 = time.time()
sampler.run_nested(dlogz=tol, print_progress=False) # don't output progress bar
# t1 = time.time()
pool.terminate
res=sampler.results
print (res.summary())
print(res.logz)
return res.logz[-1],res.logzerr[-1]
def execute(self):
from dynesty import NestedSampler, DynamicNestedSampler
ndim = self.pipeline.nvaried
sampling_method = None if self.sample == "auto" else self.sample
if self.mode == "static":
sampler = NestedSampler(log_probability_function,
prior_transform,
ndim,
nlive=self.nlive,
bound=self.bound,
sample=sampling_method,
update_interval=self.update_interval,
first_update={
'min_ncall': self.min_ncall,
'min_eff': self.min_eff
},
queue_size=self.queue_size,
pool=self.pool)
sampler.run_nested(dlogz=self.dlogz)
else:
sampler = DynamicNestedSampler(
log_probability_function,
prior_transform,
ndim,
bound=self.bound,
sample=sampling_method,
# update_interval = self.update_interval,
queue_size=self.queue_size,
pool=self.pool)
sampler.run_nested(dlogz_init=self.dlogz)
results = sampler.results
results.summary()
for sample, logwt, logl in zip(results['samples'], results['logwt'],
results['logl']):
self.output.parameters(sample, logwt, logl)
self.output.final("ncall", results['ncall'])
self.output.final("efficiency", results['eff'])
self.output.final("log_z", results['logz'])
self.output.final("log_z_err", results['logzerr'])
self.converged = True
def sampler_setup(self):
# see jupyter notebook memopy_testing_evidence_analytical (env_working)
# for background, reference and visualisations of this test
sigma = 0.001
def loglikelihood(theta):
r2 = np.sum(theta**2)
logl = - r2 / (2 * sigma**2)
return logl
def logprior_transform_2_sphere(hypercube):
# transforms a 2-dimenional vector of uniform[0, 1] random variables
# into a two-dimensional uniform vector of the 2-sphere interior
u = hypercube[0]
v = hypercube[1]
r = u**0.5 # sqrt function
theta = 2* np.pi * v
x = r*np.cos(theta)
y = r*np.sin(theta)
return np.array([x, y])
# theoretical results
# logevid_analytical = -13.122363377404328
# logl_max_analytical = 0.0
# theta means = 0.0, 0.0
nlive = 1000 # number of live points
bound = 'multi' # use MutliNest algorithm for bounds
ndims = 2 # two parameters
sample = 'unif' # unif or random walk sampling or ...
tol = 0.01 # the stopping criterion
sampler = NestedSampler(loglikelihood, logprior_transform_2_sphere, ndims,
bound=bound, sample=sample, nlive=nlive)
sampler.run_nested(dlogz=tol, print_progress=False) # don't output progress bar
return sampler
def run_inference(beta,
age,
S,
nlive=1500,
lamscale=1.0,
muscale=0.05,
gammascale=0.05,
verbose=False):
# set the std of the halfnormal priors on lam, mu, gamma
scales = np.array([lamscale, muscale, gammascale])
ndims = 7 + 2 * S + 1
# create dummy functions which takes only the params as an argument to pass
# to dynesty
prior_function = lambda flat_prior: prior_transform(flat_prior, scales)
loglikelihood_function = lambda params: loglikelihood(params, beta, S, age)
t0 = time()
print('Performing Dynesty sampling')
sampler = NestedSampler(loglikelihood_function,
prior_function,
ndims,
bound='multi',
sample='rwalk',
nlive=nlive)
sampler.run_nested(print_progress=verbose)
res = sampler.results
t1 = time()
timesampler = int(t1 - t0)
print("\nTime taken to run Dynesty is {} seconds".format(timesampler))
print(res.summary())
return res
def run(self, nlive=1000, cores=None, filename=None, **kwargs):
merge = "no"
if filename is not None and os.path.isfile(filename):
doit = input(f"There seems to be a file named {filename}. "
f"Would you like to run anyway? [y/n] ").lower()
if doit in ["no", "n"]:
with open(filename, "br") as file:
self.results = pickle.load(file)
return
if cores is None or cores > MAX_CORES:
cores = MAX_CORES
try:
with Pool(cores) as pool:
sampler = NestedSampler(
self.loglike,
self.sample,
self.N,
npdim=self.ndim,
nlive=nlive,
pool=pool,
queue_size=cores,
**kwargs,
)
sampler.run_nested()
except KeyboardInterrupt:
pass
if filename is not None and os.path.isfile(filename):
merge = input("Merge new run with previous data? [y/n] ").lower()
if merge in ["no", "n"]:
self.results = sampler.results
else:
with open(filename, "br") as file:
res = pickle.load(file)
self.results = merge_runs([sampler.results, res])
if filename is not None:
with open(filename, "bw") as file:
pickle.dump(self.results, file)
def run_multinest(self, transit_bins, transit_depths, transit_errors,
eclipse_bins, eclipse_depths, eclipse_errors,
fit_info,
include_condensation=True, rad_method="xsec",
maxiter=None, maxcall=None, nlive=100,
num_final_samples=100,
**dynesty_kwargs):
'''Runs nested sampling to retrieve atmospheric parameters.
Parameters
----------
transit_bins : array_like, shape (N,2)
Wavelength bins, where wavelength_bins[i][0] is the start
wavelength and wavelength_bins[i][1] is the end wavelength for
bin i.
transit_depths : array_like, length N
Measured transit depths for the specified wavelength bins
transit_errors : array_like, length N
Errors on the aforementioned transit depths
eclipse_bins : array_like, shape (N,2)
Wavelength bins, where wavelength_bins[i][0] is the start
wavelength and wavelength_bins[i][1] is the end wavelength for
bin i.
eclipse_depths : array_like, length N
Measured eclipse depths for the specified wavelength bins
eclipse_errors : array_like, length N
Errors on the aforementioned eclipse depths
fit_info : :class:`.FitInfo` object
Tells us what parameters to
freely vary, and in what range those parameters can vary. Also
sets default values for the fixed parameters.
include_condensation : bool, optional
When determining atmospheric abundances, whether to include
condensation.
rad_method : string, optional
"xsec" for opacity sampling, "ktables" for correlated k
nlive : int
Number of live points to use for nested sampling
**dynesty_kwargs : keyword arguments to pass to dynesty's NestedSampler
Returns
-------
result : RetrievalResult object
'''
transit_calc = None
eclipse_calc = None
if transit_bins is not None:
transit_calc = TransitDepthCalculator(
include_condensation=include_condensation, method=rad_method)
transit_calc.change_wavelength_bins(transit_bins)
self._validate_params(fit_info, transit_calc)
if eclipse_bins is not None:
eclipse_calc = EclipseDepthCalculator(
include_condensation=include_condensation, method=rad_method)
eclipse_calc.change_wavelength_bins(eclipse_bins)
def transform_prior(cube):
new_cube = np.zeros(len(cube))
for i in range(len(cube)):
new_cube[i] = fit_info._from_unit_interval(i, cube[i])
return new_cube
def multinest_ln_like(cube):
ln_like = self._ln_like(cube, transit_calc, eclipse_calc, fit_info, transit_depths, transit_errors,
eclipse_depths, eclipse_errors)
if np.random.randint(100) == 0:
print("\nEvaluated params: {}".format(self.pretty_print(fit_info)))
return ln_like
num_dim = fit_info._get_num_fit_params()
sampler = NestedSampler(multinest_ln_like, transform_prior, num_dim, bound='multi',
update_interval=float(num_dim), nlive=nlive, **dynesty_kwargs)
sampler.run_nested(maxiter=maxiter, maxcall=maxcall)
result = sampler.results
result.logp = result.logl + np.array([fit_info._ln_prior(params) for params in result.samples])
best_params_arr = result.samples[np.argmax(result.logp)]
normalized_weights = np.exp(result.logwt - np.max(result.logwt))
normalized_weights /= np.sum(normalized_weights)
result.weights = normalized_weights
equal_samples = dynesty.utils.resample_equal(result.samples, result.weights)
np.random.shuffle(equal_samples)
write_param_estimates_file(
equal_samples,
best_params_arr,
np.max(result.logp),
fit_info.fit_param_names)
best_fit_transit_depths, best_fit_transit_info, best_fit_eclipse_depths, best_fit_eclipse_info = self._ln_like(
best_params_arr, transit_calc, eclipse_calc, fit_info,
transit_depths, transit_errors,
eclipse_depths, eclipse_errors, ret_best_fit=True)
retrieval_result = RetrievalResult(
result, "dynesty",
transit_bins, transit_depths, transit_errors,
eclipse_bins, eclipse_depths, eclipse_errors,
best_fit_transit_depths, best_fit_transit_info,
best_fit_eclipse_depths, best_fit_eclipse_info,
fit_info)
retrieval_result.random_transit_depths = []
retrieval_result.random_eclipse_depths = []
for params in equal_samples[0:num_final_samples]:
_, transit_info, _, eclipse_info = self._ln_like(
params, transit_calc, eclipse_calc, fit_info,
transit_depths, transit_errors,
eclipse_depths, eclipse_errors, ret_best_fit=True)
if transit_depths is not None:
retrieval_result.random_transit_depths.append(transit_info["unbinned_depths"])
if eclipse_depths is not None:
retrieval_result.random_eclipse_depths.append(eclipse_info["unbinned_eclipse_depths"])
with open("retrieval_result.pkl", "wb") as f:
pickle.dump(retrieval_result, f)
return retrieval_result
def sample(self, quiet=False):
"""
sample using the UltraNest numerical integration method
:rtype:
:returns:
"""
if not self._is_setup:
log.info("You forgot to setup the sampler!")
return
loud = not quiet
self._update_free_parameters()
param_names = list(self._free_parameters.keys())
ndim = len(param_names)
self._kwargs["ndim"] = ndim
loglike, dynesty_prior = self._construct_unitcube_posterior(return_copy=True)
# check if we are doing to do things in parallel
if threeML_config["parallel"]["use_parallel"]:
c = ParallelClient()
view = c[:]
self._kwargs["pool"] = view
self._kwargs["queue_size"] = len(view)
sampler = NestedSampler(loglike, dynesty_prior, **self._kwargs)
self._sampler_kwargs["print_progress"] = loud
with use_astromodels_memoization(False):
log.debug("Start dynesty run")
sampler.run_nested(**self._sampler_kwargs)
log.debug("Dynesty run done")
self._sampler = sampler
results = self._sampler.results
# draw posterior samples
weights = np.exp(results["logwt"] - results["logz"][-1])
SQRTEPS = math.sqrt(float(np.finfo(np.float64).eps))
rstate = np.random
if abs(np.sum(weights) - 1.0) > SQRTEPS: # same tol as in np.random.choice.
raise ValueError("Weights do not sum to 1.")
# Make N subdivisions and choose positions with a consistent random offset.
nsamples = len(weights)
positions = (rstate.random() + np.arange(nsamples)) / nsamples
# Resample the data.
idx = np.zeros(nsamples, dtype=np.int)
cumulative_sum = np.cumsum(weights)
i, j = 0, 0
while i < nsamples:
if positions[i] < cumulative_sum[j]:
idx[i] = j
i += 1
else:
j += 1
samples_dynesty = results["samples"][idx]
self._raw_samples = samples_dynesty
# now do the same for the log likes
logl_dynesty = results["logl"][idx]
self._log_like_values = logl_dynesty
self._log_probability_values = self._log_like_values + np.array(
[self._log_prior(samples) for samples in self._raw_samples]
)
self._marginal_likelihood = self._sampler.results["logz"][-1] / np.log(10.0)
self._build_results()
# Display results
if loud:
self._results.display()
# now get the marginal likelihood
return self.samples
model_transformation = model_transformation_4
ndim = 12 + ic_cantons + 1 + 1
print("+++++++++++++++++++++++++++++")
print("+++ Nested Sampling +++")
print(" Case : ", args.case)
print(" nlive: ", args.nlive)
print(" dlogz: ", args.dlogz)
print(" cores: ", args.cores)
print("+++++++++++++++++++++++++++++")
t = -time.time()
from pathlib import Path
Path("case" + str(args.case)).mkdir(parents=True, exist_ok=True)
fname = 'case' + str(args.case) + '/samples_' + str(
args.case) + '.pickle'
pool = MyPool(args.cores)
sampler = NestedSampler(model,
model_transformation,
ndim,
nlive=args.nlive,
bound='multi',
pool=pool)
sampler.run_nested(maxiter=1e8, dlogz=args.dlogz, add_live=True)
res = sampler.results
res.summary()
with open(fname, 'wb') as f:
pickle.dump(res, f)
t += time.time()
print("Total time=", t)
def dynestyfitter(lc, model, meta, log, **kwargs):
"""Perform sampling using dynesty.
Parameters
----------
lc: eureka.S5_lightcurve_fitting.lightcurve.LightCurve
The lightcurve data object
model: eureka.S5_lightcurve_fitting.models.CompositeModel
The composite model to fit
meta: MetaClass
The metadata object
log: logedit.Logedit
The open log in which notes from this step can be added.
**kwargs:
Arbitrary keyword arguments.
Returns
-------
best_model: eureka.S5_lightcurve_fitting.models.CompositeModel
The composite model after fitting
Notes
-----
History:
- December 29, 2021 Taylor Bell
Updated documentation. Reduced repeated code.
- January 7-22, 2022 Megan Mansfield
Adding ability to do a single shared fit across all channels
- February 23-25, 2022 Megan Mansfield
Added log-uniform and Gaussian priors.
- February 28-March 1, 2022 Caroline Piaulet
Adding scatter_ppm parameter.
"""
# Group the different variable types
freenames, freepars, prior1, prior2, priortype, indep_vars = group_variables(
model)
if hasattr(meta, 'old_fitparams') and meta.old_fitparams is not None:
freepars = load_old_fitparams(meta, log, lc.channel, freenames)
# DYNESTY
nlive = meta.run_nlive # number of live points
bound = meta.run_bound # use MutliNest algorithm for bounds
ndims = len(freepars) # two parameters
sample = meta.run_sample # uniform sampling
tol = meta.run_tol # the stopping criterion
start_lnprob = lnprob(freepars, lc, model, prior1, prior2, priortype,
freenames)
log.writelog(f'Starting lnprob: {start_lnprob}', mute=(not meta.verbose))
# START DYNESTY
l_args = [lc, model, freenames]
log.writelog('Running dynesty...')
min_nlive = int(np.ceil(ndims * (ndims + 1) // 2))
if nlive < min_nlive:
log.writelog(
f'**** WARNING: You should set run_nlive to at least {min_nlive} ****'
)
if hasattr(meta, 'ncpu') and meta.ncpu > 1:
pool = Pool(meta.ncpu)
queue_size = meta.ncpu
else:
meta.ncpu = 1
pool = None
queue_size = None
sampler = NestedSampler(ln_like,
ptform,
ndims,
pool=pool,
queue_size=queue_size,
bound=bound,
sample=sample,
nlive=nlive,
logl_args=l_args,
ptform_args=[prior1, prior2, priortype])
sampler.run_nested(dlogz=tol, print_progress=True) # output progress bar
res = sampler.results # get results dictionary from sampler
if meta.ncpu > 1:
pool.close()
pool.join()
logZdynesty = res.logz[-1] # value of logZ
logZerrdynesty = res.logzerr[
-1] # estimate of the statistcal uncertainty on logZ
log.writelog('', mute=(not meta.verbose))
# Need to temporarily redirect output since res.summar() prints rather than returns a string
old_stdout = sys.stdout
sys.stdout = mystdout = StringIO()
res.summary()
sys.stdout = old_stdout
log.writelog(mystdout.getvalue(), mute=(not meta.verbose))
# get function that resamples from the nested samples to give sampler with equal weight
# draw posterior samples
weights = np.exp(res['logwt'] - res['logz'][-1])
samples = resample_equal(res.samples, weights)
log.writelog('Number of posterior samples is {}'.format(len(samples)),
mute=(not meta.verbose))
# Compute the medians and uncertainties
fit_params = []
upper_errs = []
lower_errs = []
for i in range(ndims):
q = np.percentile(samples[:, i], [16, 50, 84])
lower_errs.append(q[0])
fit_params.append(q[1])
upper_errs.append(q[2])
fit_params = np.array(fit_params)
upper_errs = np.array(upper_errs) - fit_params
lower_errs = fit_params - np.array(lower_errs)
model.update(fit_params, freenames)
if "scatter_ppm" in freenames:
ind = [
i for i in np.arange(len(freenames))
if freenames[i][0:11] == "scatter_ppm"
]
for chan in range(len(ind)):
lc.unc_fit[chan * lc.time.size:(chan + 1) *
lc.time.size] = fit_params[ind[chan]] * 1e-6
elif "scatter_mult" in freenames:
ind = [
i for i in np.arange(len(freenames))
if freenames[i][0:12] == "scatter_mult"
]
for chan in range(len(ind)):
lc.unc_fit[chan * lc.time.size:(chan + 1) *
lc.time.size] = fit_params[
ind[chan]] * lc.unc[chan * lc.time.size:(chan + 1) *
lc.time.size]
else:
lc.unc_fit = lc.unc
# Save the fit ASAP so plotting errors don't make you lose everything
save_fit(meta,
lc,
model,
'dynesty',
fit_params,
freenames,
samples,
upper_errs=upper_errs,
lower_errs=lower_errs)
end_lnprob = lnprob(fit_params, lc, model, prior1, prior2, priortype,
freenames)
log.writelog(f'Ending lnprob: {end_lnprob}', mute=(not meta.verbose))
# plot using corner.py
if meta.isplots_S5 >= 5:
plots.plot_corner(samples, lc, meta, freenames, fitter='dynesty')
# Make a new model instance
best_model = copy.copy(model)
best_model.components[0].update(fit_params, freenames)
#Plot GP fit + components
if model.GP:
plots.plot_GP_components(lc, model, meta, fitter='dynesty')
# Plot fit
if meta.isplots_S5 >= 1:
plots.plot_fit(lc, model, meta, fitter='dynesty')
# Compute reduced chi-squared
chi2red = computeRedChiSq(lc, log, model, meta, freenames)
log.writelog('\nDYNESTY RESULTS:')
for i in range(ndims):
if 'scatter_mult' in freenames[i]:
chan = freenames[i].split('_')[-1]
if chan.isnumeric():
chan = int(chan)
else:
chan = 0
scatter_ppm = fit_params[i] * np.ma.median(
lc.unc[chan * lc.time.size:(chan + 1) * lc.time.size]) * 1e6
scatter_ppm_upper = upper_errs[i] * np.ma.median(
lc.unc[chan * lc.time.size:(chan + 1) * lc.time.size]) * 1e6
scatter_ppm_lower = lower_errs[i] * np.ma.median(
lc.unc[chan * lc.time.size:(chan + 1) * lc.time.size]) * 1e6
log.writelog('{0}: {1} (+{2}, -{3}); {4} (+{5}, -{6}) ppm'.format(
freenames[i], fit_params[i], upper_errs[i], lower_errs[i],
scatter_ppm, scatter_ppm_upper, scatter_ppm_lower))
else:
log.writelog('{0}: {1} (+{2}, -{3})'.format(
freenames[i], fit_params[i], upper_errs[i], lower_errs[i]))
log.writelog('')
# Plot Allan plot
if meta.isplots_S5 >= 3:
plots.plot_rms(lc, model, meta, fitter='dynesty')
# Plot residuals distribution
if meta.isplots_S5 >= 3:
plots.plot_res_distr(lc, model, meta, fitter='dynesty')
best_model.__setattr__('chi2red', chi2red)
best_model.__setattr__('fit_params', fit_params)
return best_model
def MCMC_diagnostic(path, ndim, p, loglike, ptform, galname, nlive, **pdict):
pdict = pdict['pdict']
start = time.time()
pdict['start'] = start
if ndim == 10:
nparams = '_10P'
sampler = NestedSampler(loglike,
ptform,
ndim=ndim,
nlive=nlive,
sample='unif',
bound='multi',
logl_kwargs=pdict,
update_interval=.8,
dlogz=0.5,
first_update={
'min_ncall': nlive,
'min_eff': 50.
},
pool=p)
sampler.run_nested(maxiter=15000, maxcall=50000)
res1 = sampler.results
# Save nested data
# obtain KL divergence
klds = []
for i in range(500):
kld = dyfunc.kld_error(res1, error='simulate')
klds.append(kld[-1])
print(np.mean(klds))
res1['KLval'] = np.mean(klds)
with open(path + '/result_nested_P' + '{}'.format(nlive) + '.json',
'w') as ff:
ff.write(json.dumps(res1, cls=NumpyEncoder))
lnz_truth = 10 * -np.log(2 * 30.)
fig, axes = dyplot.runplot(res1, lnz_truth=lnz_truth)
plt.savefig(path + '/runplot_' + galname + nparams + '.png')
plt.close()
fig, axes = dyplot.traceplot(
res1,
truths=np.array([
pdict['vrot'][0], pdict['vrot'][1], pdict['vrot'][2],
pdict['vrot'][3], pdict['vdisp'][0], pdict['vdisp'][1],
pdict['vdisp'][2], pdict['vdisp'][3], pdict['inc'],
pdict['phi']
]),
truth_color='black',
show_titles=True,
trace_cmap='viridis',
connect=True,
smooth=0.02,
connect_highlight=range(8),
labels=[
r'$v_{rot,225}$', r'$v_{rot,450}$', r'$v_{rot,675}$',
r'$v_{rot,900}$', r'$\sigma_{225}$', r'$\sigma_{450}$',
r'$\sigma_{675}$', r'$\sigma_{900}$', r'$i$', r'$\phi$'
])
plt.savefig(path + '/traceplot_' + galname + nparams + '.png')
plt.close()
# initialize figure
fig, axes = plt.subplots(2, 3, figsize=(15, 10))
# plot 6 snapshots over the course of the run
for i, a in enumerate(axes.flatten()):
it = int((i + 1) * res1.niter / 8.)
# overplot the result onto each subplot
temp = dyplot.boundplot(res1,
dims=(0, 1),
it=it,
prior_transform=ptform,
max_n_ticks=3,
show_live=True,
span=[(70, 150), (70, 150)],
fig=(fig, a))
a.set_title('Iteration {0}'.format(it), fontsize=26)
fig.tight_layout()
plt.savefig(path + '/boundplot_' + galname + nparams + '.png')
plt.close()
fg, ax = dyplot.cornerplot(
res1,
color='blue',
truths=np.array([
pdict['vrot'][0], pdict['vrot'][1], pdict['vrot'][2],
pdict['vrot'][3], pdict['vdisp'][0], pdict['vdisp'][1],
pdict['vdisp'][2], pdict['vdisp'][3], pdict['inc'],
pdict['phi']
]), # 91.8,98.3,8.88,6.5,60,60
truth_color='black',
show_titles=True,
smooth=0.02,
max_n_ticks=5,
quantiles=None,
labels=[
r'$v_{rot,225}$', r'$v_{rot,450}$', r'$v_{rot,675}$',
r'$v_{rot,900}$', r'$\sigma_{225}$', r'$\sigma_{450}$',
r'$\sigma_{675}$', r'$\sigma_{900}$', r'$i$', r'$\phi$'
])
plt.savefig(path + '/cornerplot_' + galname + nparams + '.png')
plt.close()
with open(path + '/' + galname + '.txt', 'w+') as f:
f.write('Running took: {} hours'.format(
(time.time() - start) / 3600))
# Save the model data
samples, weights = res1.samples, np.exp(res1.logwt - res1.logz[-1])
mean, cov = dyfunc.mean_and_cov(samples, weights)
MaP = res1['samples'][res1['logl'].tolist().index(
max(res1['logl'].tolist()))]
quantiles = [
dyfunc.quantile(samps, [0.025, 0.5, 0.975], weights=weights)
for samps in samples.T
]
print(quantiles)
# vrotsigma
sigmavrot1_l = [i for i in samples[:, 0] if (i - MaP[0]) < 0]
sigmavrot1_r = [i for i in samples[:, 0] if (i - MaP[0]) > 0]
sigmavrot2_l = [i for i in samples[:, 1] if (i - MaP[1]) < 0]
sigmavrot2_r = [i for i in samples[:, 1] if (i - MaP[1]) > 0]
sigmavrot3_l = [i for i in samples[:, 2] if (i - MaP[2]) < 0]
sigmavrot3_r = [i for i in samples[:, 2] if (i - MaP[2]) > 0]
sigmavrot4_l = [i for i in samples[:, 3] if (i - MaP[3]) < 0]
sigmavrot4_r = [i for i in samples[:, 3] if (i - MaP[3]) > 0]
if len(sigmavrot1_l) == 0: sigmavrot1_l.append(0)
if len(sigmavrot1_r) == 0: sigmavrot1_r.append(0)
if len(sigmavrot2_l) == 0: sigmavrot2_l.append(0)
if len(sigmavrot2_r) == 0: sigmavrot2_r.append(0)
if len(sigmavrot3_l) == 0: sigmavrot3_l.append(0)
if len(sigmavrot3_r) == 0: sigmavrot3_r.append(0)
if len(sigmavrot4_l) == 0: sigmavrot4_l.append(0)
if len(sigmavrot4_r) == 0: sigmavrot4_r.append(0)
# vdispsigma
sigmavdisp1_l = [i for i in samples[:, 4] if (i - MaP[4]) < 0]
sigmavdisp1_r = [i for i in samples[:, 4] if (i - MaP[4]) > 0]
sigmavdisp2_l = [i for i in samples[:, 5] if (i - MaP[5]) < 0]
sigmavdisp2_r = [i for i in samples[:, 5] if (i - MaP[5]) > 0]
sigmavdisp3_l = [i for i in samples[:, 6] if (i - MaP[6]) < 0]
sigmavdisp3_r = [i for i in samples[:, 6] if (i - MaP[6]) > 0]
sigmavdisp4_l = [i for i in samples[:, 7] if (i - MaP[7]) < 0]
sigmavdisp4_r = [i for i in samples[:, 7] if (i - MaP[7]) > 0]
if len(sigmavdisp1_l) == 0: sigmavdisp1_l.append(0)
if len(sigmavdisp1_r) == 0: sigmavdisp1_r.append(0)
if len(sigmavdisp2_l) == 0: sigmavdisp2_l.append(0)
if len(sigmavdisp2_r) == 0: sigmavdisp2_r.append(0)
if len(sigmavdisp3_l) == 0: sigmavdisp3_l.append(0)
if len(sigmavdisp3_r) == 0: sigmavdisp3_r.append(0)
if len(sigmavdisp4_l) == 0: sigmavdisp4_l.append(0)
if len(sigmavdisp4_r) == 0: sigmavdisp4_r.append(0)
pdict['sigmavrot'] = [(np.std(sigmavrot1_l), np.std(sigmavrot1_r)),
(np.std(sigmavrot2_l), np.std(sigmavrot2_r)),
(np.std(sigmavrot3_l), np.std(sigmavrot3_r)),
(np.std(sigmavrot4_l), np.std(sigmavrot4_r))]
pdict['sigmavdisp'] = [(np.std(sigmavdisp1_l), np.std(sigmavdisp1_r)),
(np.std(sigmavdisp2_l), np.std(sigmavdisp2_r)),
(np.std(sigmavdisp3_l), np.std(sigmavdisp3_r)),
(np.std(sigmavdisp4_l), np.std(sigmavdisp4_r))]
if len(MaP) == 8:
pdict['vrot'] = MaP[0:4]
pdict['vdisp'] = MaP[4:8]
if len(MaP) == 9:
pdict['vrot'] = MaP[0:4]
pdict['vdisp'] = MaP[4:8]
pdict['inc'] = MaP[8]
# inc
sigmainc_l = [i for i in samples[:, 8] if (i - MaP[8]) < 0]
sigmainc_r = [i for i in samples[:, 8] if (i - MaP[8]) > 0]
if len(sigmainc_l) == 0: sigmainc_l.append(0)
if len(sigmainc_r) == 0: sigmainc_r.append(0)
pdict['sigmainc'] = [(np.std(sigmainc_l), np.std(sigmainc_r))]
if len(MaP) == 10:
pdict['vrot'] = MaP[0:4]
pdict['vdisp'] = MaP[4:8]
pdict['inc'] = MaP[8]
pdict['phi'] = MaP[9]
# inc
sigmainc_l = [i for i in samples[:, 8] if (i - MaP[8]) < 0]
sigmainc_r = [i for i in samples[:, 8] if (i - MaP[8]) > 0]
if len(sigmainc_l) == 0: sigmainc_l.append(0)
if len(sigmainc_r) == 0: sigmainc_r.append(0)
pdict['sigmainc'] = [(np.std(sigmainc_l), np.std(sigmainc_r))]
# phi
sigmaphi_l = [i for i in samples[:, 9] if (i - MaP[9]) < 0]
sigmaphi_r = [i for i in samples[:, 9] if (i - MaP[9]) > 0]
if len(sigmaphi_l) == 0: sigmaphi_l.append(0)
if len(sigmaphi_r) == 0: sigmaphi_r.append(0)
pdict['sigmaphi'] = [(np.std(sigmaphi_l), np.std(sigmaphi_r))]
# We don't need data entry
pdict['Data'] = None
with open(path + '/params_model.json', 'w') as f:
f.write(json.dumps(pdict, cls=NumpyEncoder))
def runMCMC(path, ndim, p, loglike, ptform, galname, **pdict):
pdict = pdict['pdict']
start = time.time()
pdict['start'] = start
if ndim == 8:
nparams = '_8P'
sampler = NestedSampler(loglike,
ptform,
ndim=ndim,
nlive=250,
sample='unif',
bound='multi',
logl_kwargs=pdict,
update_interval=0.8,
dlogz=0.5,
first_update={
'min_ncall': 300,
'min_eff': 50.
},
pool=p)
sampler.run_nested(maxiter=15000, maxcall=50000)
res1 = sampler.results
with open(path + '/result_nested_P' + '{}'.format(ndim) + '.json',
'w') as ff:
ff.write(json.dumps(res1, cls=NumpyEncoder))
lnz_truth = 10 * -np.log(2 * 30.)
fig, axes = dyplot.runplot(res1, lnz_truth=lnz_truth)
plt.savefig(path + '/runplot_' + galname + nparams + '.png')
plt.close()
fig, axes = dyplot.traceplot(res1,
truths=np.array([
pdict['vrot'][0], pdict['vrot'][1],
pdict['vrot'][2], pdict['vrot'][3],
pdict['vdisp'][0], pdict['vdisp'][1],
pdict['vdisp'][2], pdict['vdisp'][3]
]),
truth_color='black',
show_titles=True,
trace_cmap='viridis',
connect=True,
smooth=0.02,
connect_highlight=range(8),
labels=[
r'$v_{rot,225}$', r'$v_{rot,450}$',
r'$v_{rot,675}$', r'$v_{rot,900}$',
r'$\sigma_{225}$', r'$\sigma_{450}$',
r'$\sigma_{675}$', r'$\sigma_{900}$'
])
plt.savefig(path + '/traceplot_' + galname + nparams + '.png')
plt.close()
# plot 6 snapshots over the course of the run
for i, a in enumerate(axes.flatten()):
it = int((i + 1) * res1.niter / 8.)
# overplot the result onto each subplot
temp = dyplot.boundplot(res1,
dims=(0, 1),
it=it,
prior_transform=ptform,
max_n_ticks=5,
show_live=True,
span=[(70, 150), (70, 150)],
fig=(fig, a))
a.set_title('Iteration {0}'.format(it), fontsize=26)
fig.tight_layout()
plt.savefig(path + '/boundplot_' + galname + nparams + '.png')
plt.close()
matplotlib.rcParams.update({'font.size': 16})
fig, axes = dyplot.cornerplot(
res1,
color='blue',
truths=np.array([
pdict['vrot'][0], pdict['vrot'][1], pdict['vrot'][2],
pdict['vrot'][3], pdict['vdisp'][0], pdict['vdisp'][1],
pdict['vdisp'][2], pdict['vdisp'][3], pdict['inc'],
pdict['phi']
]),
truth_color='black',
show_titles=True,
smooth=0.02,
max_n_ticks=5,
quantiles=[0.16, 0.5, 0.84],
labels=[
r'$V_{225}[km/s]$', r'$V_{450}[km/s]$', r'$V_{675}[km/s]$',
r'$V_{900}[km/s]$', r'$\sigma_{gas,225}[km/s]$',
r'$\sigma_{gas,450}[km/s]$', r'$\sigma_{gas,675}[km/s]$',
r'$\sigma_{gas,900}[km/s]$', r'$i[deg]$', r'$\phi[deg]$'
])
# Save the model data
samples, weights = res1.samples, np.exp(res1.logwt - res1.logz[-1])
mean, cov = dyfunc.mean_and_cov(samples, weights)
MaP = res1['samples'][res1['logl'].tolist().index(
max(res1['logl'].tolist()))]
quantiles = [
dyfunc.quantile(samps, [0.16, 0.5, 0.84], weights=weights)
for samps in samples.T
]
labels = [
r'$V_{225}$', r'$V_{450}$', r'$V_{675}$', r'$V_{900}$',
r'$\sigma_{gas,225}$', r'$\sigma_{gas,450}$',
r'$\sigma_{gas,675}$', r'$\sigma_{gas,900}$', r'$i$', r'$\phi$'
]
units = [
' [km/s]', ' [km/s]', ' [km/s]', ' [km/s]', ' [km/s]', ' [km/s]',
' [km/s]', ' [km/s]', ' [deg]', ' [deg]'
]
for i in range(ndim):
ax = axes[i, i]
q5 = np.round(quantiles[i][1], 2)
q14 = np.round(quantiles[i][0], 2)
q84 = np.round(quantiles[i][2], 2)
ax.set_title(r"$%.2f_{%.2f}^{+%.2f}$" %
(q5, -1 * abs(q5 - q14), abs(q5 - q84)) + units[i])
# Loop over the histograms
for yi in range(ndim):
axes[yi, 0].set_ylabel(labels[yi] + units[yi],
labelpad=30,
fontsize=20)
axes[-1, yi].set_xlabel(labels[yi] + units[yi],
labelpad=30,
fontsize=20)
axes[yi, 0].tick_params(axis='y', which='major', labelsize=14)
axes[-1, yi].tick_params(axis='x', which='major', labelsize=14)
fig.tight_layout()
plt.savefig(path + '/cornerplot_' + galname + nparams + '.pdf')
plt.close()
with open(path + '/' + galname + '.txt', 'w+') as f:
f.write('Running took: {} hours'.format(
(time.time() - start) / 3600))
elif ndim == 9:
nparams = '_9P'
sampler = NestedSampler(loglike,
ptform,
ndim=ndim,
nlive=250,
sample='unif',
bound='multi',
logl_kwargs=pdict,
update_interval=0.8,
dlogz=0.5,
first_update={
'min_ncall': 300,
'min_eff': 50.
},
pool=p)
sampler.run_nested(maxiter=15000, maxcall=50000)
res1 = sampler.results
with open(path + '/result_nested_P' + '{}'.format(ndim) + '.json',
'w') as ff:
ff.write(json.dumps(res1, cls=NumpyEncoder))
lnz_truth = 10 * -np.log(2 * 30.)
fig, axes = dyplot.runplot(res1, lnz_truth=lnz_truth)
plt.savefig(path + '/runplot_' + galname + nparams + '.png')
plt.close()
fig, axes = dyplot.traceplot(
res1,
truths=np.array([
pdict['vrot'][0], pdict['vrot'][1], pdict['vrot'][2],
pdict['vrot'][3], pdict['vdisp'][0], pdict['vdisp'][1],
pdict['vdisp'][2], pdict['vdisp'][3], pdict['inc']
]),
truth_color='black',
show_titles=True,
trace_cmap='viridis',
connect=True,
smooth=0.02,
connect_highlight=range(8),
labels=[
r'$v_{rot,225}$', r'$v_{rot,450}$', r'$v_{rot,675}$',
r'$v_{rot,900}$', r'$\sigma_{225}$', r'$\sigma_{450}$',
r'$\sigma_{675}$', r'$\sigma_{900}$', r'$i$'
])
plt.savefig(path + '/traceplot_' + galname + nparams + '.png')
plt.close()
# initialize figure
fig, axes = plt.subplots(2, 3, figsize=(15, 10))
# plot 6 snapshots over the course of the run
for i, a in enumerate(axes.flatten()):
it = int((i + 1) * res1.niter / 8.)
# overplot the result onto each subplot
temp = dyplot.boundplot(res1,
dims=(0, 1),
it=it,
prior_transform=ptform,
max_n_ticks=3,
show_live=True,
span=[(70, 150), (70, 150)],
fig=(fig, a))
a.set_title('Iteration {0}'.format(it), fontsize=26)
fig.tight_layout()
plt.savefig(path + '/boundplot_' + galname + nparams + '.png')
plt.close()
matplotlib.rcParams.update({'font.size': 16})
fig, axes = dyplot.cornerplot(
res1,
color='blue',
truths=np.array([
pdict['vrot'][0], pdict['vrot'][1], pdict['vrot'][2],
pdict['vrot'][3], pdict['vdisp'][0], pdict['vdisp'][1],
pdict['vdisp'][2], pdict['vdisp'][3], pdict['inc']
]),
truth_color='black',
show_titles=True,
smooth=0.02,
max_n_ticks=5,
quantiles=[0.16, 0.5, 0.84],
labels=[
r'$V_{225}[km/s]$', r'$V_{450}[km/s]$', r'$V_{675}[km/s]$',
r'$V_{900}[km/s]$', r'$\sigma_{gas,225}[km/s]$',
r'$\sigma_{gas,450}[km/s]$', r'$\sigma_{gas,675}[km/s]$',
r'$\sigma_{gas,900}[km/s]$', r'$i[deg]$'
])
# Save the model data
samples, weights = res1.samples, np.exp(res1.logwt - res1.logz[-1])
mean, cov = dyfunc.mean_and_cov(samples, weights)
MaP = res1['samples'][res1['logl'].tolist().index(
max(res1['logl'].tolist()))]
quantiles = [
dyfunc.quantile(samps, [0.16, 0.5, 0.84], weights=weights)
for samps in samples.T
]
labels = [
r'$V_{225}$', r'$V_{450}$', r'$V_{675}$', r'$V_{900}$',
r'$\sigma_{gas,225}$', r'$\sigma_{gas,450}$',
r'$\sigma_{gas,675}$', r'$\sigma_{gas,900}$', r'$i$', r'$\phi$'
]
units = [
' [km/s]', ' [km/s]', ' [km/s]', ' [km/s]', ' [km/s]', ' [km/s]',
' [km/s]', ' [km/s]', ' [deg]', ' [deg]'
]
for i in range(ndim):
ax = axes[i, i]
q5 = np.round(quantiles[i][1], 2)
q14 = np.round(quantiles[i][0], 2)
q84 = np.round(quantiles[i][2], 2)
ax.set_title(r"$%.2f_{%.2f}^{+%.2f}$" %
(q5, -1 * abs(q5 - q14), abs(q5 - q84)) + units[i])
# Loop over the histograms
for yi in range(ndim):
axes[yi, 0].set_ylabel(labels[yi] + units[yi],
labelpad=30,
fontsize=20)
axes[-1, yi].set_xlabel(labels[yi] + units[yi],
labelpad=30,
fontsize=20)
axes[yi, 0].tick_params(axis='y', which='major', labelsize=14)
axes[-1, yi].tick_params(axis='x', which='major', labelsize=14)
fig.tight_layout()
plt.savefig(path + '/cornerplot_' + galname + nparams + '.pdf')
plt.close()
with open(path + '/' + galname + '.txt', 'w+') as f:
f.write('Running took: {} hours'.format(
(time.time() - start) / 3600))
elif ndim == 10:
nparams = '_10P'
sampler = NestedSampler(loglike,
ptform,
ndim=ndim,
nlive=250,
sample='unif',
bound='multi',
logl_kwargs=pdict,
update_interval=.8,
dlogz=0.5,
first_update={
'min_ncall': 300,
'min_eff': 50.
},
pool=p)
sampler.run_nested(maxiter=15000, maxcall=50000)
res1 = sampler.results
with open(path + '/result_nested_P' + '{}'.format(ndim) + '.json',
'w') as ff:
ff.write(json.dumps(res1, cls=NumpyEncoder))
lnz_truth = 10 * -np.log(2 * 30.)
fig, axes = dyplot.runplot(res1, lnz_truth=lnz_truth)
plt.savefig(path + '/runplot_' + galname + nparams + '.png')
plt.close()
fig, axes = dyplot.traceplot(
res1,
truths=np.array([
pdict['vrot'][0], pdict['vrot'][1], pdict['vrot'][2],
pdict['vrot'][3], pdict['vdisp'][0], pdict['vdisp'][1],
pdict['vdisp'][2], pdict['vdisp'][3], pdict['inc'],
pdict['phi']
]),
truth_color='black',
show_titles=True,
trace_cmap='viridis',
connect=True,
smooth=0.02,
connect_highlight=range(8),
labels=[
r'$v_{rot,225}$', r'$v_{rot,450}$', r'$v_{rot,675}$',
r'$v_{rot,900}$', r'$\sigma_{225}$', r'$\sigma_{450}$',
r'$\sigma_{675}$', r'$\sigma_{900}$', r'$i$', r'$\phi$'
])
plt.savefig(path + '/traceplot_' + galname + nparams + '.png')
plt.close()
# initialize figure
fig, axes = plt.subplots(2, 3, figsize=(15, 10))
# plot 6 snapshots over the course of the run
for i, a in enumerate(axes.flatten()):
it = int((i + 1) * res1.niter / 8.)
# overplot the result onto each subplot
temp = dyplot.boundplot(res1,
dims=(0, 1),
it=it,
prior_transform=ptform,
max_n_ticks=3,
show_live=True,
span=[(70, 150), (70, 150)],
fig=(fig, a))
a.set_title('Iteration {0}'.format(it), fontsize=26)
fig.tight_layout()
plt.savefig(path + '/boundplot_' + galname + nparams + '.png')
plt.close()
matplotlib.rcParams.update({'font.size': 16})
fig, axes = dyplot.cornerplot(
res1,
color='blue',
truths=np.array([
pdict['vrot'][0], pdict['vrot'][1], pdict['vrot'][2],
pdict['vrot'][3], pdict['vdisp'][0], pdict['vdisp'][1],
pdict['vdisp'][2], pdict['vdisp'][3], pdict['inc'],
pdict['phi']
]),
truth_color='black',
show_titles=True,
smooth=0.02,
max_n_ticks=5,
quantiles=[0.16, 0.5, 0.84],
labels=[
r'$V_{225}[km/s]$', r'$V_{450}[km/s]$', r'$V_{675}[km/s]$',
r'$V_{900}[km/s]$', r'$\sigma_{gas,225}[km/s]$',
r'$\sigma_{gas,450}[km/s]$', r'$\sigma_{gas,675}[km/s]$',
r'$\sigma_{gas,900}[km/s]$', r'$i[deg]$', r'$\phi[deg]$'
])
# Save the model data
samples, weights = res1.samples, np.exp(res1.logwt - res1.logz[-1])
mean, cov = dyfunc.mean_and_cov(samples, weights)
MaP = res1['samples'][res1['logl'].tolist().index(
max(res1['logl'].tolist()))]
quantiles = [
dyfunc.quantile(samps, [0.16, 0.5, 0.84], weights=weights)
for samps in samples.T
]
labels = [
r'$V_{225}$', r'$V_{450}$', r'$V_{675}$', r'$V_{900}$',
r'$\sigma_{gas,225}$', r'$\sigma_{gas,450}$',
r'$\sigma_{gas,675}$', r'$\sigma_{gas,900}$', r'$i$', r'$\phi$'
]
units = [
' [km/s]', ' [km/s]', ' [km/s]', ' [km/s]', ' [km/s]', ' [km/s]',
' [km/s]', ' [km/s]', ' [deg]', ' [deg]'
]
for i in range(ndim):
ax = axes[i, i]
q5 = np.round(quantiles[i][1], 2)
q14 = np.round(quantiles[i][0], 2)
q84 = np.round(quantiles[i][2], 2)
ax.set_title(r"$%.2f_{%.2f}^{+%.2f}$" %
(q5, -1 * abs(q5 - q14), abs(q5 - q84)) + units[i])
# Loop over the histograms
for yi in range(ndim):
axes[yi, 0].set_ylabel(labels[yi] + units[yi],
labelpad=30,
fontsize=20)
axes[-1, yi].set_xlabel(labels[yi] + units[yi],
labelpad=30,
fontsize=20)
axes[yi, 0].tick_params(axis='y', which='major', labelsize=14)
axes[-1, yi].tick_params(axis='x', which='major', labelsize=14)
fig.tight_layout()
plt.savefig(path + '/cornerplot_' + galname + nparams + '.pdf')
plt.close()
with open(path + '/' + galname + '.txt', 'w+') as f:
f.write('Running took: {} hours'.format(
(time.time() - start) / 3600))
# Save the model data
samples, weights = res1.samples, np.exp(res1.logwt - res1.logz[-1])
mean, cov = dyfunc.mean_and_cov(samples, weights)
MaP = res1['samples'][res1['logl'].tolist().index(
max(res1['logl'].tolist()))]
quantiles = [
dyfunc.quantile(samps, [0.16, 0.5, 0.84], weights=weights)
for samps in samples.T
]
pdict['sigmavrot'] = [(quantiles[0][0], quantiles[0][2]),
(quantiles[1][0], quantiles[1][2]),
(quantiles[2][0], quantiles[2][2]),
(quantiles[3][0], quantiles[3][2])]
pdict['sigmavdisp'] = [(quantiles[4][0], quantiles[4][2]),
(quantiles[5][0], quantiles[5][2]),
(quantiles[6][0], quantiles[6][2]),
(quantiles[7][0], quantiles[7][2])]
pdict['vrot'] = [
quantiles[0][1], quantiles[1][1], quantiles[2][1], quantiles[3][1]
]
pdict['vdisp'] = [
quantiles[4][1], quantiles[5][1], quantiles[6][1], quantiles[7][1]
]
if len(quantiles) == 9:
pdict['inc'] = quantiles[8][1]
pdict['sigmainc'] = [(quantiles[8][0], quantiles[8][2])]
if len(quantiles) == 10:
pdict['inc'] = quantiles[8][1]
pdict['sigmainc'] = [(quantiles[8][0], quantiles[8][2])]
pdict['phi'] = quantiles[9][1]
pdict['sigmaphi'] = [(quantiles[9][0], quantiles[9][2])]
# We don't need data entry, waste of space
pdict['Data'] = None
with open(path + '/params_model.json', 'w') as f:
f.write(json.dumps(pdict, cls=NumpyEncoder))
dlogZdynesty = dres.logz[-1] # value of logZ
dlogZerrdynesty = dres.logzerr[-1] # estimate of the statistcal uncertainty on logZ
# output marginal likelihood
print('Marginalised evidence (using dynamic sampler) is {} ± {}'.format(dlogZdynesty, dlogZerrdynesty))
# get the posterior samples
dweights = np.exp(dres['logwt'] - dres['logz'][-1])
dpostsamples = resample_equal(dres.samples, dweights)
print('Number of posterior samples (using dynamic sampler) is {}'.format(dpostsamples.shape[0]))
# Now run with the static sampler
sampler = NestedSampler(loglikelihood_dynesty, prior_transform, ndims,
bound=bound, sample=sample, nlive=nlive)
sampler.run_nested(dlogz=0.1)
res = sampler.results
logZdynesty = res.logz[-1] # value of logZ
logZerrdynesty = res.logzerr[-1] # estimate of the statistcal uncertainty on logZ
# output marginal likelihood
print('Marginalised evidence (using static sampler) is {} ± {}'.format(logZdynesty, logZerrdynesty))
# get the posterior samples
weights = np.exp(res['logwt'] - res['logz'][-1])
postsamples = resample_equal(res.samples, weights)
print('Number of posterior samples (using static sampler) is {}'.format(postsamples.shape[0]))
# get the posterior samples
dweights = np.exp(dres['logwt'] - dres['logz'][-1])
dpostsamples = resample_equal(dres.samples, dweights)
print('Number of posterior samples (using dynamic sampler) is {}'.format(
dpostsamples.shape[0]))
# Now run with the static sampler
sampler = NestedSampler(loglikelihood_dynesty,
prior_transform,
ndims,
bound=bound,
sample=sample,
nlive=nlive)
sampler.run_nested(dlogz=0.1)
res = sampler.results
logZdynesty = res.logz[-1] # value of logZ
logZerrdynesty = res.logzerr[
-1] # estimate of the statistcal uncertainty on logZ
# output marginal likelihood
print('Marginalised evidence (using static sampler) is {} ± {}'.format(
logZdynesty, logZerrdynesty))
# get the posterior samples
weights = np.exp(res['logwt'] - res['logz'][-1])
postsamples = resample_equal(res.samples, weights)
obs_times, obs_wavs, obs_excess, obs_excess_error = get_obs_data(
config["spectrum"], config["error"], config["min_wav"], config["max_wav"])
def multinest_ln_like(cube):
return get_ln_like(cube, config, obs_times, obs_wavs, obs_excess,
obs_excess_error)
sampler = NestedSampler(multinest_ln_like,
transform_prior,
3,
bound='multi',
nlive=100)
sampler.run_nested()
result = sampler.results
normalized_weights = np.exp(result.logwt - np.max(result.logwt))
normalized_weights /= np.sum(normalized_weights)
result.weights = normalized_weights
with open("dynesty_result.pkl", "wb") as f:
pickle.dump(result, f)
best_params = result.samples[np.argmax(result.logl)]
get_ln_like(best_params,
config,
obs_times,
obs_wavs,
obs_excess,
obs_excess_error,
plot=True)
def rebuild_current_distribution(
fields: np.ndarray,
ics: np.ndarray,
jj_size: float,
current_pattern: List[Union[Literal["f"], str]],
sweep_invariants: List[Union[Literal["offset"], Literal["field_to_k"]]] = [
"offset",
"field_to_k",
],
precision: float = 100,
n_points: int = 2 ** 10 + 1,
) -> dict:
"""Rebuild a current distribution from a Fraunhofer pattern.
This assumes a uniform field focusing since allowing a non uniform focusing
would lead to a much larger space to explore.
Parameters
----------
fields : np.ndarray
Out of plane field for which the critical current was measured.
ics : np.ndarray
Critical current of the junction.
jj_size : float
Size of the junction.
current_pattern : List[Union[Literal["f"], str]]
Describe in how many pieces to use to represent the junction. If the
input arrays are more than 1D, "f" means that value is the same across
all outer dimension, "v" means that the slice takes different value
for all outer dimension (ie. one value per sweep).
sweep_invariants : Tuple[Union[Literal["offset", "field_to_k"]]]
Indicate what quantities are invariants across sweep for more the 1D
inputs.
precision : float, optional
pass
n_points : int, optional
Returns
-------
dict
"""
# Get the offset and estimated amplitude used in the prior
# We do not use the estimated current and phase distribution to give the
# more space to the algorithm.
offsets, first_node_locs, _, _, _ = guess_current_distribution(
field, fraunhofer, site_number, jj_size
)
# Gives a Fraunhofer pattern at the first node for v[1] = 1
field_to_ks = 2 * np.pi / jj_size / np.abs(first_node_locs - offsets)
# Determine the dimensionality of the problem based on the invariants and
# the shape of the inputs.
if len(sweep_invariants) > 2:
raise ValueError("There are at most 2 invariants.")
if any(k for k in sweep_invariants if k not in ("offset", "field_to_k")):
raise ValueError(
f"Invalid invariant specified {sweep_invariants}, "
"valid values are 'offset', 'field_to_k'."
)
shape = fields.shape[:-1]
shape_product = prod(shape) if shape else 0
if shape_product == 0 and any(p.startswith("v") for p in current_pattern):
raise ValueError(
"Found variable current in the distribution but the measurements are 1D."
)
dim = len(sweep_invariants) + current_pattern.count("f")
dim += shape_product * (current_pattern.count("v") + 2 - len(sweep_invariants))
# Pre-compute slices to access elements in the prior and log-like
offset_access = slice(
0, 1 if "offset" in sweep_invariants else (shape_product or 1)
)
field_to_k_access = slice(
offset_access.stop,
offset_access.stop + 1
if "field_to_k" in sweep_invariants
else (shape_product or 1),
)
stop = field_to_k_access.stop
current_density_accesses = []
for p in current_pattern:
if p == "f":
current_density_accesses.append(slice(stop, stop + 1))
stop += 1
elif p == "v":
current_density_accesses.append(slice(stop, stop + (shape_product or 1)))
stop += current_density_accesses[-1].stop
else:
raise ValueError(
f"Valid values in current_pattern are 'f' and 'v', found '{p}'"
)
def prior(u):
"""Map the sampled in 0-1 to the relevant values range.
For all values we consider the values in the prior to be the log of the
values we are looking for.
"""
v = np.empty_like(u)
v[offset_access] = 4 * u[offset_access] - 2
v[field_to_k_access] = 4 * u[field_to_k_access] - 2
stop += step
# For all the amplitude we map the value between 0 and -X since the
# amplitude of a single segment cannot be larger than the total current
# X is determined based on the number of segments
ampl = -np.log10(len(current_pattern))
for sl in current_density_accesses:
v[sl] = u[sl] * ampl
return v
def loglike(v):
"""Compute the distance to the data"""
# We turn invariant input into their variant form (from 1 occurence in v
# to n repetition in w) to ease a systematic writing of the loglike.
stop = step = shape_product or 1
w = np.empty((2 + len(current_pattern)) * (shape_product or 1))
stop = step = shape_product or 1
w[0:stop] = w_offset = v[offset_access]
w[stop : stop + step] = w_f2k = v[field_to_k_access]
stop += step
for sl in current_density_accesses:
w[stop : stop + step] = v[sl]
# Pack the current distribution so that each line corresponds to different
# conditions
c_density = w[stop + step :].reshape((len(current_pattern), -1)).T
err = np.empty_like(ics)
it = np.nditer((offsets, first_node_locs, field_to_ks), ["multi_index"])
for i, (off, fnloc, f2k) in enumerate(it):
# Compute the offset
f_off = off + np.sign(w_off[i]) * 10 ** -abs(w_off[i]) * fnloc
# Compute the Fraunhofer pattern
f = produce_fraunhofer_fast(
(fields[it.multi_index] - f_off[i]),
f2k * 10 ** w_f2k[i],
jj_size,
c_density[i],
2 ** 10 + 1,
)
# Compute and store the error
err[it.multi_index] = np.sum(
(100 * (ics[it.multi_index] - f) / amplitude) ** 2
)
return -np.ravel(err)
# XXX do that nasty part later
sampler = NestedSampler(loglike, prior, dim)
sampler.run_nested(dlogz=precision)
res = sampler.results
weights = np.exp(res.logwt - res.logz[-1])
mu, cov = utils.mean_and_cov(res["samples"], weights)
res["fraunhofer_params"] = {
"offset": offset + np.sign(mu[0]) * 10 ** -abs(mu[0]) * first_node_loc,
"field_to_k": 2 * np.pi / jj_size / abs(first_node_loc - offset) * 10 ** mu[1],
"amplitude": amplitude * 10 ** mu[2],
"current_distribution": np.array(
[1 - np.sum(mu[3 : 3 + site_number - 1])]
+ list(mu[3 : 3 + site_number - 1])
),
"phase_distribution": np.array(
[0] + list(mu[3 + site_number - 1 : 3 + 2 * site_number - 2])
),
}
return res
def main(path2config):
# load the yaml parameters
config = yaml.load(open(path2config))
sim_params = config['sim_params']
HOD_params = config['HOD_params']
clustering_params = config['clustering_params']
data_params = config['data_params']
dynesty_config_params = config['dynesty_config_params']
fit_params = config['dynesty_fit_params']
# create a new abacushod object and load the subsamples
newBall = AbacusHOD(sim_params, HOD_params, clustering_params)
# read data parameters
newData = wp_Data(data_params, HOD_params)
# parameters to fit
nparams = len(fit_params.keys())
param_mapping = {}
param_tracer = {}
params = np.zeros((nparams, 2))
for key in fit_params.keys():
mapping_idx = fit_params[key][0]
tracer_type = fit_params[key][-1]
param_mapping[key] = mapping_idx
param_tracer[key] = tracer_type
params[mapping_idx, :] = fit_params[key][1:-1]
# Make path to output
if not os.path.isdir(
os.path.expanduser(dynesty_config_params['path2output'])):
try:
os.makedirs(
os.path.expanduser(dynesty_config_params['path2output']))
except:
pass
# dynesty parameters
nlive = dynesty_config_params['nlive']
maxcall = dynesty_config_params['maxcall']
method = dynesty_config_params['method']
bound = dynesty_config_params['bound']
# where to record
prefix_chain = os.path.join(
os.path.expanduser(dynesty_config_params['path2output']),
dynesty_config_params['chainsPrefix'])
# initiate sampler
found_file = os.path.isfile(prefix_chain + '.dill')
if (not found_file) or (not dynesty_config_params['rerun']):
# initialize our nested sampler
sampler = NestedSampler(
lnprob,
prior_transform,
nparams,
logl_args=[param_mapping, param_tracer, newData, newBall],
ptform_args=[params[:, 0], params[:, 1]],
nlive=nlive,
sample=method,
rstate=np.random.RandomState(dynesty_config_params['rseed']))
# first_update = {'min_eff': 20})
else:
# load sampler to continue the run
with open(prefix_chain + '.dill', "rb") as f:
sampler = dill.load(f)
sampler.rstate = np.load(prefix_chain + '_results.npz')['rstate']
print("run sampler")
sampler.run_nested(maxcall=maxcall)
# save sampler itself
with open(prefix_chain + '.dill', "wb") as f:
dill.dump(sampler, f)
res1 = sampler.results
np.savez(prefix_chain + '_results.npz',
res=res1,
rstate=np.random.get_state())
def run_multinest(self,
transit_bins,
transit_depths,
transit_errors,
eclipse_bins,
eclipse_depths,
eclipse_errors,
fit_info,
include_condensation=True,
plot_best=False,
maxiter=None,
maxcall=None,
nlive=100,
**dynesty_kwargs):
'''Runs nested sampling to retrieve atmospheric parameters.
Parameters
----------
transit_bins : array_like, shape (N,2)
Wavelength bins, where wavelength_bins[i][0] is the start
wavelength and wavelength_bins[i][1] is the end wavelength for
bin i.
transit_depths : array_like, length N
Measured transit depths for the specified wavelength bins
transit_errors : array_like, length N
Errors on the aforementioned transit depths
eclipse_bins : array_like, shape (N,2)
Wavelength bins, where wavelength_bins[i][0] is the start
wavelength and wavelength_bins[i][1] is the end wavelength for
bin i.
eclipse_depths : array_like, length N
Measured eclipse depths for the specified wavelength bins
eclipse_errors : array_like, length N
Errors on the aforementioned eclipse depths
fit_info : :class:`.FitInfo` object
Tells us what parameters to
freely vary, and in what range those parameters can vary. Also
sets default values for the fixed parameters.
include_condensation : bool, optional
When determining atmospheric abundances, whether to include
condensation.
plot_best : bool, optional
If True, plots the best fit model with the data
nlive : int
Number of live points to use for nested sampling
**dynesty_kwargs : keyword arguments to pass to dynesty's NestedSampler
Returns
-------
result : Result object
This returns dynesty's NestedSampler 'results' field, slightly
modified. The object is
dictionary-like and has many useful items. For example,
result.samples (or alternatively, result["samples"]) are the
parameter values of each sample, result.logwt contains the
log(weights), result.weights contains the normalized weights
(this is added by PLATON),
result.logl contains the ln likelihoods, and result.logp
contains the ln posteriors (this is added by PLATON). result.logz
is the natural logarithm of the evidence.
'''
transit_calc = TransitDepthCalculator(
include_condensation=include_condensation)
transit_calc.change_wavelength_bins(transit_bins)
eclipse_calc = EclipseDepthCalculator()
eclipse_calc.change_wavelength_bins(eclipse_bins)
self._validate_params(fit_info, transit_calc)
def transform_prior(cube):
new_cube = np.zeros(len(cube))
for i in range(len(cube)):
new_cube[i] = fit_info._from_unit_interval(i, cube[i])
return new_cube
def multinest_ln_like(cube):
ln_like = self._ln_like(cube, transit_calc, eclipse_calc, fit_info,
transit_depths, transit_errors,
eclipse_depths, eclipse_errors)
if np.random.randint(100) == 0:
print("\nEvaluated params: {}".format(
self.pretty_print(fit_info)))
return ln_like
num_dim = fit_info._get_num_fit_params()
sampler = NestedSampler(multinest_ln_like,
transform_prior,
num_dim,
bound='multi',
sample='rwalk',
update_interval=float(num_dim),
nlive=nlive,
**dynesty_kwargs)
sampler.run_nested(maxiter=maxiter, maxcall=maxcall)
result = sampler.results
result.logp = result.logl + np.array(
[fit_info._ln_prior(params) for params in result.samples])
best_params_arr = result.samples[np.argmax(result.logp)]
normalized_weights = np.exp(result.logwt) / np.sum(np.exp(
result.logwt))
result.weights = normalized_weights
write_param_estimates_file(
dynesty.utils.resample_equal(result.samples, normalized_weights),
best_params_arr, np.max(result.logp), fit_info.fit_param_names)
if plot_best:
self._ln_prob(best_params_arr,
transit_calc,
eclipse_calc,
fit_info,
transit_depths,
transit_errors,
eclipse_depths,
eclipse_errors,
plot=True)
plt.figure(3)
dyplot.runplot(result)
plt.savefig("dyplot_runplot.png")
plt.figure(4)
dyplot.traceplot(result)
plt.savefig("dyplot_traceplot.png")
return result