def get_overall_best_fit(self, pars, **specargs):
"""Returns the overall best-fit, the chi-square and the N.d.o.f."""
if type(pars) == str: pars = [pars]
for s, v in enumerate(self.p.get("data_vectors")):
d = DataManager(self.p, v, self.cosmo, all_data=False)
self.d = d
lik = Likelihood(self.p.get('params'),
d.data_vector,
d.covar,
self._th,
template=d.templates)
sam = Sampler(lik.lnprob, lik.p0, lik.p_free_names,
self.p.get_sampler_prefix(v['name']),
self.p.get('mcmc'))
sam.get_chain()
sam.update_p0(sam.chain[np.argmax(sam.probs)])
kwargs = lik.build_kwargs(sam.p0)
w = kwargs["width"]
zz, NN = self._get_dndz(d.tracers[0][0].dndz, w)
zmean = np.average(zz, weights=NN)
kwargs["z"] = zmean
kwargs["chi2"] = lik.chi2(sam.p0)
all_pars = self.p.p.get("params")
dof = np.sum(
[param["vary"] for param in all_pars if "vary" in param])
kwargs["dof"] = len(lik.dv) - dof
kwargs["PTE"] = 1 - chi2.cdf(kwargs["chi2"], kwargs["dof"])
if s == 0:
keys = ["z", "chi2", "dof", "PTE"] + pars
OV_BF = {k: kwargs[k] for k in keys}
else:
for k in keys:
OV_BF[k] = np.vstack((OV_BF[k], kwargs[k]))
return OV_BF
if vv['name']==sample:
v=vv
dat = DataManager(p, v, cosmo, all_data=False)
gat = DataManager(p, v, cosmo, all_data=True)
def th(pars,d):
if not cosmo_vary:
cosmo_fid = cosmo
hmc_fid = hmc
else:
cosmo_fid = COSMO_ARGS(kwargs)
hmc_fid = get_hmcalc(cosmo_fid, **kwargs)
return get_theory(p, d, cosmo_fid, hmc_fid,
hm_correction=hm_correction,
selection=None,**pars)
likd = Likelihood(p.get('params'), dat.data_vector, dat.covar, th,
template=dat.templates)
likg = Likelihood(p.get('params'), gat.data_vector, gat.covar, th,
template=gat.templates)
sam = Sampler(likd.lnprob, likd.p0, likd.p_free_names,
p.get_sampler_prefix(v['name']), p.get('mcmc'))
sam.get_chain()
sam.update_p0(sam.chain[np.argmax(sam.probs)])
params = likd.build_kwargs(sam.p0)
clth=th(params,gat)[:len(ls)]
l=np.geomspace(ls[0],ls[-1],1024)
clthp=np.exp(interp1d(np.log(ls),np.log(clth),kind='quadratic')(np.log(l)))
# grey boundaries
z, nz = np.loadtxt(dat.tracers[0][0].dndz, unpack=True)
zmean = np.average(z, weights=nz)
def get_chains(self, pars, **specargs):
"""Returns a dictionary containing the chains of `pars`. """
def bias_one(p0, num):
"""Calculates the halo model bias for a set of parameters."""
bb = hm_bias(self.cosmo, 1 / (1 + zarr), d.tracers[num][1].profile,
**lik.build_kwargs(p0))
return bb
def bias_avg(num, skip):
"""Calculates the halo model bias of a profile, from a chain."""
#from pathos.multiprocessing import ProcessingPool as Pool
#with Pool() as pool:
# bb = pool.map(lambda p0: bias_one(p0, num),
# sam.chain[::skip])
bb = list(map(lambda p0: bias_one(p0, num), sam.chain[::skip]))
bb = np.mean(np.array(bb), axis=1)
return bb
# path to chain
fname = lambda s: self.p.get("global")["output_dir"] + "/sampler_" + \
self.p.get("mcmc")["run_name"] + "_" + s + "_chain"
if type(pars) == str: pars = [pars]
import os
print(os.getcwd())
preCHAINS = {}
fid_pars = pars.copy()
for par in pars:
try:
print(fname(par))
preCHAINS[par] = np.load(fname(par) + ".npy")
fid_pars.remove(par)
print("Found saved chains for %s." % par)
except FileNotFoundError:
continue
if "bg" or "by" in fid_pars:
# skip every (for computationally expensive hm_bias)
b_skip = specargs.get("reduce_by_factor")
if b_skip is None:
print("'reduce_by_factor' not given. Defaulting to 100.")
b_skip = 100
for s, v in enumerate(self.p.get("data_vectors")):
d = DataManager(self.p, v, self.cosmo, all_data=False)
self.d = d
lik = Likelihood(self.p.get('params'),
d.data_vector,
d.covar,
self._th,
template=d.templates)
sam = Sampler(lik.lnprob, lik.p0, lik.p_free_names,
self.p.get_sampler_prefix(v['name']),
self.p.get('mcmc'))
sam.get_chain()
chains = lik.build_kwargs(sam.chain.T)
sam.update_p0(sam.chain[np.argmax(sam.probs)])
kwargs = lik.build_kwargs(sam.p0)
w = kwargs["width"]
zz, NN = self._get_dndz(d.tracers[0][0].dndz, w)
zmean = np.average(zz, weights=NN)
chains["z"] = zmean
if "probs" in pars:
chains["probs"] = sam.probs
if ("by" or "bg") in fid_pars:
sigz = np.sqrt(np.sum(NN * (zz - zmean)**2) / np.sum(NN))
zarr = np.linspace(zmean - sigz, zmean + sigz, 10)
if "bg" in pars:
chains["bg"] = bias_avg(num=0, skip=b_skip)
if "by" in pars:
chains["by"] = bias_avg(num=1, skip=b_skip)
# Construct tomographic dictionary
if s == 0:
keys = ["z"] + fid_pars
CHAINS = {k: chains[k] for k in keys}
else:
for k in keys:
CHAINS[k] = np.vstack((CHAINS[k], chains[k]))
# save bias chains to save time if not already saved
if "bg" in fid_pars: np.save(fname("bg"), CHAINS["bg"])
if "by" in fid_pars: np.save(fname("by"), CHAINS["by"])
return {**preCHAINS, **CHAINS}
# Theory predictor wrapper
def th(kwargs):
"""Theory for free cosmology."""
cosmo_use = p.get_cosmo(pars=kwargs) # optimized internally
return get_theory(p,
d,
cosmo_use,
hmc,
hm_correction=hm_correction,
**kwargs)
# Set up likelihood
lik = Likelihood(p.get('params'),
d.data_vector,
d.covar,
th,
template=d.templates,
debug=p.get('mcmc')['debug'])
# Set up sampler
p0 = p.get_map_p0(lik.p_free_names) # p0 for particular map
sam = Sampler(lik.lnprob, p0, lik.p_free_names,
p.get_sampler_prefix(v['name']), p.get('mcmc'))
# print(dict(zip(lik.p_free_names, p0)))
# print("chisq:", lik.chi2(p0))
# exit(1)
# Compute best fit and covariance
if not sam.read_properties():
print(" Computing best-fit and covariance")
sam.get_best_fit(update_p0=True)
if not cosmo_vary:
pars_fid = pars
cosmo_fid = cosmo
hmc_fid = hmc
else:
pars_fid = {**p.get_cosmo_pars(), **pars}
cosmo_fid = COSMO_ARGS(pars_fid)
hmc_fid = get_hmcalc(cosmo_fid, **pars_fid)
return get_theory(p, d, cosmo_fid, hmc_fid,
return_separated=False,
hm_correction=None,
include_1h=False, include_2h=True,
**pars_fid)
# Set up likelihood
lik = Likelihood(p.get('params'), d.data_vector, d.covar, th,
debug=p.get('mcmc')['debug'])
# Set up sampler
sam = Sampler(lik.lnprob, lik.p0, lik.p_free_names,
p.get_sampler_prefix(v['name']), p.get('mcmc'))
# Read chains and best-fit
sam.get_chain()
sam.update_p0(sam.chain[np.argmax(sam.probs)])
# Compute galaxy bias
# zarr = np.linspace(zmean - sigz, zmean + sigz, 10)
# bgchain = np.array([hm_bias(cosmo, 1./(1 + zarr), d.tracers[0][0],
# **(lik.build_kwargs(p0))) for p0 in sam.chain[::100]])
# bychain = np.array([hm_bias(cosmo, 1./(1 + zarr), d.tracers[1][1],
# **(lik.build_kwargs(p0))) for p0 in sam.chain[::100]])
for s, v in enumerate(p.get("data_vectors")):
# Construct data vector and covariance
d = DataManager(p, v, cosmo, all_data=False)
g = DataManager(p, v, cosmo, all_data=True)
thd = thr(d)
thg = thr(g)
z, nz = np.loadtxt(d.tracers[0][0].dndz, unpack=True)
zmean = np.average(z, weights=nz)
# Set up likelihood
likd = Likelihood(p.get('params'),
d.data_vector,
d.covar,
thd.th,
template=d.templates)
likg = Likelihood(p.get('params'),
g.data_vector,
g.covar,
thg.th,
template=g.templates)
# Set up sampler
sam = Sampler(likd.lnprob, likd.p0, likd.p_free_names,
p.get_sampler_prefix(v['name']), p.get('mcmc'))
# Read chains and best-fit
sam.get_chain()
sam.update_p0(sam.chain[np.argmax(sam.probs)])
def get_chains(self, pars=None, **specargs):
"""Returns a dictionary containing the chains of `pars`. """
# if `pars` is not set, collect chains for all free parameters
if pars is None:
pars = [
par["name"] for par in self.p.get("params") if par.get("vary")
]
def bias_one(p0, num):
"""Calculates the halo model bias for a set of parameters."""
if self.cosmo_vary:
cosmo = COSMO_ARGS(pars)
hmc = get_hmcalc(
cosmo, **{
"mass_function": self.p.get_massfunc(),
"halo_bias": self.p.get_halobias()
})
else:
cosmo = self.cosmo
hmc = self.hmc
bb = hm_bias(cosmo, hmc, 1 / (1 + zarr), d.tracers[num][1],
**lik.build_kwargs(p0))
return bb
def bias_avg(num, skip):
"""Calculates the halo model bias of a profile, from a chain."""
from pathos.multiprocessing import ProcessingPool as Pool
with Pool() as pool:
bb = pool.map(lambda p0: bias_one(p0, num), sam.chain[::skip])
# bb = list(map(lambda p0: bias_one(p0, num), sam.chain[::skip]))
bb = np.mean(np.array(bb), axis=1)
return bb
# path to chain
fname = lambda s: self.p.get("global")["output_dir"] + "/sampler_" + \
self.p.get("mcmc")["run_name"] + "_" + s + "_chain"
if type(pars) == str: pars = [pars]
preCHAINS = {}
fid_pars = pars.copy()
for par in pars:
try:
preCHAINS[par] = np.load(fname(par) + ".npy")
fid_pars.remove(par)
print("Found saved chains for %s." % par)
except FileNotFoundError:
continue
if ("bg" in fid_pars) or ("by" in fid_pars) or ("bk" in fid_pars):
# thin sample (for computationally expensive hm_bias)
b_skip = specargs.get("thin")
if b_skip is None:
print("Chain 'thin' factor not given. Defaulting to 100.")
b_skip = 100
for s, v in enumerate(self.p.get("data_vectors")):
print(v["name"])
d = DataManager(self.p, v, all_data=False)
self.d = d
lik = Likelihood(self.p.get('params'),
d.data_vector,
d.covar,
self._th,
template=d.templates)
sam = Sampler(lik.lnprob, lik.p0, lik.p_free_names,
self.p.get_sampler_prefix(v['name']),
self.p.get('mcmc'))
sam.get_chain()
chains = lik.build_kwargs(sam.chain.T)
sam.update_p0(sam.chain[np.argmax(sam.probs)])
# print(sam.p0)
kwargs = lik.build_kwargs(sam.p0)
w = kwargs["width"]
zz, NN = self._get_dndz(d.tracers[0][0].dndz, w)
zmean = np.average(zz, weights=NN)
chains["z"] = zmean
if "probs" in pars:
chains["probs"] = sam.probs
if ("bg" in fid_pars) or ("by" in fid_pars) or ("bk" in fid_pars):
sigz = np.sqrt(np.sum(NN * (zz - zmean)**2) / np.sum(NN))
zarr = np.linspace(zmean - sigz, zmean + sigz, 10)
if "bg" in pars:
chains["bg"] = bias_avg(num=0, skip=b_skip)
if "by" in pars:
chains["by"] = bias_avg(num=1, skip=b_skip)
if "bk" in pars:
chains["bk"] = bias_avg(num=2, skip=b_skip)
# Construct tomographic dictionary
if s == 0:
keys = ["z"] + fid_pars
CHAINS = {k: [chains[k]] for k in keys}
else:
for k in keys:
CHAINS[k].append(chains[k])
# save bias chains to save time if not already saved
if "bg" in fid_pars: np.save(fname("bg"), CHAINS["bg"])
if "by" in fid_pars: np.save(fname("by"), CHAINS["by"])
if "bk" in fid_pars: np.save(fname("bk"), CHAINS["bk"])
return {**preCHAINS, **CHAINS}
# Construct data vector and covariance
d = DataManager(p, v, cosmo, jk_region=jk_region)
# Theory predictor wrapper
def th(pars):
return get_theory(p,
d,
cosmo,
hm_correction=hm_correction,
selection=sel,
**pars)
# Set up likelihood
lik = Likelihood(p.get('params'),
d.data_vector,
d.covar,
th,
template=d.templates,
debug=p.get('mcmc')['debug'])
# Set up sampler
sam = Sampler(lik.lnprob, lik.p0, lik.p_free_names,
p.get_sampler_prefix(v['name']) + "jk%d" % jk_region,
p.get('mcmc'))
# Compute best fit and covariance around it
if not sam.read_properties():
print(" Computing best-fit and covariance")
sam.get_best_fit(update_p0=True)
cov0 = sam.get_covariance(update_cov=True)
sam.save_properties()
def th2h(pars):
return get_theory(p,
d,
cosmo,
return_separated=False,
hm_correction=hm_correction,
selection=sel,
include_2h=True,
include_1h=False,
**pars)
# Set up likelihood
lik = Likelihood(p.get('params'),
d.data_vector,
d.covar,
th,
debug=p.get('mcmc')['debug'])
# Set up sampler
sam = Sampler(lik.lnprob, lik.p0, lik.p_free_names,
p.get_sampler_prefix(v['name']), p.get('mcmc'))
# Read chains and best-fit
sam.get_chain()
sam.update_p0(sam.chain[np.argmax(sam.probs)])
# Compute galaxy bias
zarr = np.linspace(zmean - sigz, zmean + sigz, 10)
bgchain = np.array([
hm_bias(cosmo, 1. / (1 + zarr), d.tracers[0][0].profile,
hm_correction = None
for v in p.get('data_vectors'):
if v['name'] == bin_name:
d = DataManager(p, v, cosmo)
z, nz = np.loadtxt(d.tracers[0][0].dndz, unpack=True)
zmean = np.average(z, weights=nz)
sigz = np.sqrt(np.sum(nz * (z - zmean)**2) / np.sum(nz))
# Theory predictor wrapper
def th(pars):
return get_theory(p,
d,
cosmo,
return_separated=False,
hm_correction=hm_correction,
selection=sel,
**pars)
lik = Likelihood(p.get('params'),
d.data_vector,
d.covar,
th,
debug=p.get('mcmc')['debug'])
sam = Sampler(lik.lnprob, lik.p0, lik.p_free_names,
p.get_sampler_prefix(v['name']), p.get('mcmc'))
sam.get_chain()
figs_ch = lik.plot_chain(sam.chain,
save_figure=True,
prefix='notes/paper/')
plt.show()