def build_model_data(self, ctx):
"""Compute all data defined by this core and add it to the context."""
# Update parameters
logger.debug(f"Updating parameters: {ctx.getParams()}")
astro_params, cosmo_params = self._update_params(ctx.getParams())
logger.debug(f"AstroParams: {astro_params}")
logger.debug(f"CosmoParams: {cosmo_params}")
# Call C-code
coeval = p21.run_coeval(
redshift=self.redshift,
astro_params=astro_params,
cosmo_params=cosmo_params,
flag_options=self.flag_options,
user_params=self.user_params,
regenerate=False,
random_seed=self.initial_conditions_seed,
write=self.io_options["cache_mcmc"],
direc=self.io_options["cache_dir"],
**self.global_params,
)
logger.debug(f"Adding {self.ctx_variables} to context data")
for key in self.ctx_variables:
try:
ctx.add(key, [getattr(c, key) for c in coeval])
except AttributeError:
raise ValueError(
f"ctx_variable {key} not an attribute of Coeval")
def produce_coeval_power_spectra(redshift, **kwargs):
options = get_all_options(redshift, **kwargs)
coeval = run_coeval(**options)
p, k = get_power(
coeval.brightness_temp,
boxlength=coeval.user_params.BOX_LEN,
)
return k, p, coeval
def produce_coeval_power_spectra(redshift, **kwargs):
options = get_all_options(redshift, **kwargs)
coeval = run_coeval(write=write_ics_only_hook, **options)
p = {}
for field in COEVAL_FIELDS:
if hasattr(coeval, field):
p[field], k = get_power(getattr(coeval, field),
boxlength=coeval.user_params.BOX_LEN)
return k, p, coeval
def setup(self):
"""
Perform setup of the core.
Notes
-----
This method is called automatically by its parent
:class:`~LikelihoodComputationChain`, and should not be invoked directly.
"""
super().setup()
# If the chain has different parameter truths, we want to use those for our defaults.
self.astro_params, self.cosmo_params = self._update_params(
self.chain.createChainContext().getParams())
# Here we save to disk the full default realization.
# The init and perturb boxes here can usually be re-used, and the box serves
# as a nice thing to compare to after MCMC.
# If modifying cosmo, we don't want to do this, because we'll create them
# on the fly on every iteration.
if (all(p not in self.cosmo_params.self.keys()
for p in self.parameter_names)
and not self.change_seed_every_iter):
logger.info("Initializing default boxes for the entire chain.")
coeval = p21.run_coeval(
redshift=self.redshift,
user_params=self.user_params,
cosmo_params=self.cosmo_params,
astro_params=self.astro_params,
flag_options=self.flag_options,
write=True,
regenerate=self.regenerate,
direc=self.io_options["cache_dir"],
random_seed=self.initial_conditions_seed,
**self.global_params,
)
# update the seed
self.initial_conditions_seed = coeval[0].random_seed
logger.info("Initialization done.")
# late, middle and early stage of reionization
bins = np.array([[0.18, 0.22], [0.48, 0.52], [0.78, 0.82]])
compare_tobs_mean = np.zeros((bins.shape[0], tobs.size))
compare_tobs_std = np.zeros((bins.shape[0], tobs.size))
ic = p21c.initial_conditions(user_params=params,
cosmo_params=c_params,
random_seed=2021)
compare_tobs = np.zeros((redshift.size, tobs.size))
for i in tqdm(range(len(redshift))):
z = redshift[i]
cube = p21c.run_coeval(redshift=z,
init_box=ic,
astro_params=a_params,
zprime_step_factor=1.05)
dT = cube.brightness_temp
xH = cube.xH_box
uv = uvs['%.3f' % z]
Nant = uvs['Nant']
print('z = %.3f x_n = %.3f zeta = %.3f R_mfp = %.3f T_vir = %.3f' %
(z, np.mean(cube.xH_box), zeta, Rmfp, Tvir))
for j, t in enumerate(tobs):
noise_cube = t2c.noise_cube_coeval(params['HII_DIM'],
z,
depth_mhz=None,
def coeval(ic):
return run_coeval(
redshift=25.0, init_box=ic, write=True, flag_options={"USE_TS_FLUCT": True}
)
def coeval(ic):
return run_coeval(redshift=10.0, init_box=ic)
snapshot = snapshot2
NITER = 50
init = initial_conditions(user_params={
"HII_DIM": 50,
"BOX_LEN": 125.0
},
regenerate=True)
perturb = (
perturb_field(redshift=7, init_boxes=init),
perturb_field(redshift=8, init_boxes=init),
perturb_field(redshift=9, init_boxes=init),
)
astro_params = {"HII_EFF_FACTOR": np.random.normal(30, 0.1)}
for i in range(NITER):
trace_print()
coeval = run_coeval(
redshift=[7, 8, 9],
astro_params=astro_params,
init_box=init,
perturb=perturb,
regenerate=True,
random_seed=init.random_seed,
write=False,
)
