def test_model_singlepsr_noise_sw(nodmx_psrs,caplog):
# caplog.set_level(logging.CRITICAL)
m=models.model_singlepsr_noise(nodmx_psrs[1], dm_sw_deter=True,
dm_sw_gp=True)
assert hasattr(m,'get_lnlikelihood')
x0 = {pname:p.sample() for pname,p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
def test_model_singlepsr_noise_dip_cusp(nodmx_psrs, caplog):
# caplog.set_level(logging.CRITICAL)
dip_kwargs = {
'dm_expdip': True,
'dmexp_sign': 'negative',
'num_dmdips': 2,
'dm_cusp_idx': [2, 4],
'dm_expdip_tmin': [54700, 57450],
'dm_expdip_tmax': [54850, 57560],
'dmdip_seqname': ['1st_ism', '2nd_ism'],
'dm_cusp': False,
'dm_cusp_sign': 'negative',
'dm_cusp_idx': [2, 4],
'dm_cusp_sym': False,
'dm_cusp_tmin': None,
'dm_cusp_tmax': None,
'num_dm_cusps': 2,
'dm_dual_cusp': True,
'dm_dual_cusp_tmin': [54700, 57450],
'dm_dual_cusp_tmax': [54850, 57560],
}
m = models.model_singlepsr_noise(nodmx_psrs[1],
dm_sw_deter=True,
dm_sw_gp=True,
**dip_kwargs)
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
def test_model_singlepsr_noise_chrom_diag(nodmx_psrs,caplog):
# caplog.set_level(logging.CRITICAL)
m=models.model_singlepsr_noise(nodmx_psrs[1], chrom_gp=True,
chrom_gp_kernel='diag')
assert hasattr(m,'get_lnlikelihood')
x0 = {pname:p.sample() for pname,p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
def test_model_singlepsr_noise_faclike(nodmx_psrs, caplog):
# caplog.set_level(logging.CRITICAL)
# default behaviour
m=models.model_singlepsr_noise(nodmx_psrs[1],
factorized_like=True, Tspan=10*const.yr)
m.get_basis()
assert 'gw_log10_A' in m.param_names
assert 'J1713+0747_red_noise_log10_A' in m.param_names
assert m.signals["J1713+0747_gw"]._labels[''][-1] == const.fyr
# gw but no RN
m=models.model_singlepsr_noise(nodmx_psrs[1], red_var=False,
factorized_like=True, Tspan=10*const.yr)
assert hasattr(m, 'get_lnlikelihood')
assert 'gw_log10_A' in m.param_names
assert 'J1713+0747_red_noise_log10_A' not in m.param_names
def test_model_singlepsr_fact_like(nodmx_psrs, caplog):
# caplog.set_level(logging.CRITICAL)
psr = nodmx_psrs[1]
Tspan = model_utils.get_tspan([psr])
m=models.model_singlepsr_noise(psr, chrom_gp=True,
chrom_gp_kernel='diag',
factorized_like=False,
Tspan=Tspan, fact_like_gamma=13./3,
gw_components=5)
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
dm_expdip_tmin.append(57450)
dm_expdip_tmax.append(57560)
dm_expdip_idx.append(4.4)
dmdip_seqname.append('chrom_2')
dip_kwargs = {'dm_expdip':True,
'dmexp_sign': 'negative',
'num_dmdips':num_dips,
'dm_expdip_idx':dm_expdip_idx,
'dm_expdip_tmin':dm_expdip_tmin,
'dm_expdip_tmax':dm_expdip_tmax,
'dmdip_seqname':dmdip_seqname}
kwargs = copy.deepcopy(model_kwargs['5'])
kwargs.update(dip_kwargs)
ptas[ii] = model_singlepsr_noise(psr, **kwargs)
all_kwargs[ii] = kwargs
super_model = HyperModel(ptas)
sampler = super_model.setup_sampler(resume=True, outdir=args.outdir,
empirical_distr=args.emp_distr)
model_params = {}
for ky, pta in ptas.items():
model_params.update({str(ky): pta.param_names})
with open(args.outdir + '/model_params.json', 'w') as fout:
json.dump(model_params, fout, sort_keys=True,
indent=4, separators=(',', ': '))
def test_model_singlepsr_noise(nodmx_psrs, caplog):
# caplog.set_level(logging.CRITICAL)
m = models.model_singlepsr_noise(nodmx_psrs[1])
assert hasattr(m, 'get_lnlikelihood')
with open(args.model_kwargs_path, 'r') as fin:
model_kwargs = json.load(fin)
model_labels = [
['A', 'NANOGrav'],
['B', '1.13 Dip w/ Scatt GP'],
['C', 'PPTA'],
]
ptas = {}
all_kwargs = {}
kwargs = copy.deepcopy(model_kwargs['0'])
kwargs.update({'red_var': True, 'psd': 'powerlaw'})
ptas[0] = model_singlepsr_noise(psr, **kwargs)
all_kwargs[0] = kwargs
dip_kwargs = {
'dm_expdip': True,
'dmexp_sign': 'negative',
'num_dmdips': 2,
'dm_expdip_idx': [2, 1.15],
'dm_expdip_tmin': [54700, 57450],
'dm_expdip_tmax': [54850, 57560],
'dmdip_seqname': ['dm_1', 'pr_1']
}
# kwargs = copy.deepcopy(model_kwargs['0'])
kwargs.update(dip_kwargs)
ptas[1] = model_singlepsr_noise(psr, **kwargs)
'tm_marg': True
})
## Treat all other Adv Noise pulsars the same
else:
### Turn SW model off. Add in stand alone SW model and common process. Return model.
kwargs.update({
'dm_sw_deter': False,
'white_vary': False,
'extra_sigs': mean_sw,
'psr_model': True,
'chrom_df': None,
'dm_df': None,
'tm_marg': True
})
### Load the appropriate single_pulsar_model
psr_models.append(model_singlepsr_noise(new_psr,
**kwargs)) #(new_psr))
final_psrs.append(new_psr)
# Treat all other DMX pulsars in the standard way
elif not args.adv_noise_psrs_only:
s2 = s + blocks.white_noise_block(
vary=False, inc_ecorr=True, select='backend')
psr_models.append(s2) #(psr))
final_psrs.append(psr)
print(f'\r{psr.name} Complete.', end='', flush=True)
crn_models = [(m + cs)(psr) for psr, m in zip(final_psrs, psr_models)]
# gw_models = [(m + gw)(psr) for psr,m in zip(final_psrs,psr_models)]
pta_crn = signal_base.PTA(crn_models)
# pta_gw = signal_base.PTA(gw_models)
m += gp_signals.TimingModel(use_svd=False)
m += models.red_noise_block(psd=args.psd, prior=prior,
components=args.nfreqs, gamma_val=None)
m += models.common_red_noise_block(gamma_val=13/3., prior=prior,
psd=args.psd, components=args.nfreqs)
pta = signal_base.PTA(m(psr))
else:
if args.gfl:
vary_rn = False
else:
vary_rn = True
pta = models.model_singlepsr_noise(psr, red_var=vary_rn,
psd=args.psd, Tspan=args.tspan,
components=args.nfreqs,
factorized_like=args.gfl,
gw_components=args.n_gwbfreqs,
fact_like_logmin=-14.2,
fact_like_logmax=-1.2,
is_wideband=args.wideband)
emp_dist_path = args.emp_distr.replace('PSR_NAME',psr.name)
Sampler = sampler.setup_sampler(pta=pta,
outdir=Outdir,
empirical_distr = emp_dist_path,
resume=True)
if args.gfl:
freqs = bys.get_freqs(pta, signal_id='gw')
else:
freqs = bys.get_freqs(pta, signal_id='red_noise')
np.savetxt(Outdir+'achrom_freqs.txt', freqs)
# use dm_expdip for J1713+0747
use_dmdip = False
if 'J1713+0747' == psr.name:
use_dmdip = True
#################
## pta model ##
#################
red_psd = 'spectrum' if args.fs else 'powerlaw'
pta = models.model_singlepsr_noise(psr,
tm_svd=True,
white_vary=True,
red_var=True,
psd=red_psd,
components=30,
dm_var=True,
dm_type='gp',
dmgp_kernel='diag',
dm_psd='powerlaw',
dm_annual=True,
dm_expdip=use_dmdip,
upper_limit=False)
outfile = os.path.join(args.outdir, 'params.txt')
with open(outfile, 'w') as f:
for pname in pta.param_names:
f.write(pname + '\n')
###############
## sampler ##
###############
from enterprise_warp import bilby_warp
# use the tim files from wn_sp_tutorial - tim files within the -pta flag
# do not seem to work with model_singlepsr_noise
parfile = "J0030+0451_NANOGrav_12yv3.gls.par"
timfile = "J0030+0451.tim"
psr = Pulsar(parfile, timfile, drop_t2pulsar=False)
plist = ["F0", "F1"] # vary F0 and F1
pta = model_singlepsr_noise(
psr,
tmparam_list=plist,
tm_linear=False, # set to False so F0 and F1 will be varied
tm_var=True, # set to True so F0 and F1 will be varied
components=1, # make smaller than default to try and speed things up
tm_marg=False,
red_var=False, # don't estimate red noise to speed things up
white_vary=True, # estimate white noise (this defaults to True anyway)
)
# run using enterprise_warp to access bilby_mcmc
priors = bilby_warp.get_bilby_prior_dict(pta)
parameters = dict.fromkeys(priors.keys())
likelihood = bilby_warp.PTABilbyLikelihood(pta, parameters)
outdir = "test/"
label = "test_bilby"
bilby.run_sampler(likelihood=likelihood,
priors=priors,
outdir=outdir,
def test_model_singlepsr_noise_chrom_nondiag(nodmx_psrs, caplog):
# caplog.set_level(logging.CRITICAL)
m=models.model_singlepsr_noise(nodmx_psrs[0], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag')
assert 'J0613-0200_chrom_gp_log10_sigma' in m.param_names
assert 'J0613-0200_chrom_gp_log10_ell' in m.param_names
assert 'J0613-0200_chrom_gp_log10_ell2' not in m.param_names
assert 'J0613-0200_chrom_gp_log10_alpha_wgt' not in m.param_names
assert 'J0613-0200_chrom_gp_log10_p' in m.param_names
assert 'J0613-0200_chrom_gp_log10_gam_p' in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[1], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag')
assert 'J1713+0747_chrom_gp_log10_sigma' in m.param_names
assert 'J1713+0747_chrom_gp_log10_ell' in m.param_names
assert 'J1713+0747_chrom_gp_log10_ell2' not in m.param_names
assert 'J1713+0747_chrom_gp_log10_alpha_wgt' not in m.param_names
assert 'J1713+0747_chrom_gp_log10_p' in m.param_names
assert 'J1713+0747_chrom_gp_log10_gam_p' in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[2], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag')
assert 'J1909-3744_chrom_gp_log10_sigma' in m.param_names
assert 'J1909-3744_chrom_gp_log10_ell' in m.param_names
assert 'J1909-3744_chrom_gp_log10_ell2' not in m.param_names
assert 'J1909-3744_chrom_gp_log10_alpha_wgt' not in m.param_names
assert 'J1909-3744_chrom_gp_log10_p' in m.param_names
assert 'J1909-3744_chrom_gp_log10_gam_p' in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[0], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag',
chrom_kernel='periodic_rfband')
assert 'J0613-0200_chrom_gp_log10_sigma' in m.param_names
assert 'J0613-0200_chrom_gp_log10_ell' in m.param_names
assert 'J0613-0200_chrom_gp_log10_ell2' in m.param_names
assert 'J0613-0200_chrom_gp_log10_alpha_wgt' in m.param_names
assert 'J0613-0200_chrom_gp_log10_p' in m.param_names
assert 'J0613-0200_chrom_gp_log10_gam_p' in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[1], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag',
chrom_kernel='periodic_rfband')
assert 'J1713+0747_chrom_gp_log10_sigma' in m.param_names
assert 'J1713+0747_chrom_gp_log10_ell' in m.param_names
assert 'J1713+0747_chrom_gp_log10_ell2' in m.param_names
assert 'J1713+0747_chrom_gp_log10_alpha_wgt' in m.param_names
assert 'J1713+0747_chrom_gp_log10_p' in m.param_names
assert 'J1713+0747_chrom_gp_log10_gam_p' in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[2], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag',
chrom_kernel='periodic_rfband')
assert 'J1909-3744_chrom_gp_log10_sigma' in m.param_names
assert 'J1909-3744_chrom_gp_log10_ell' in m.param_names
assert 'J1909-3744_chrom_gp_log10_ell2' in m.param_names
assert 'J1909-3744_chrom_gp_log10_alpha_wgt' in m.param_names
assert 'J1909-3744_chrom_gp_log10_p' in m.param_names
assert 'J1909-3744_chrom_gp_log10_gam_p' in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[0], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag',
chrom_kernel='sq_exp')
assert 'J0613-0200_chrom_gp_log10_sigma' in m.param_names
assert 'J0613-0200_chrom_gp_log10_ell' in m.param_names
assert 'J0613-0200_chrom_gp_log10_p' not in m.param_names
assert 'J0613-0200_chrom_gp_log10_gam_p' not in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[1], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag',
chrom_kernel='sq_exp')
assert 'J1713+0747_chrom_gp_log10_sigma' in m.param_names
assert 'J1713+0747_chrom_gp_log10_ell' in m.param_names
assert 'J1713+0747_chrom_gp_log10_p' not in m.param_names
assert 'J1713+0747_chrom_gp_log10_gam_p' not in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[2], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag',
chrom_kernel='sq_exp')
assert 'J1909-3744_chrom_gp_log10_sigma' in m.param_names
assert 'J1909-3744_chrom_gp_log10_ell' in m.param_names
assert 'J1909-3744_chrom_gp_log10_p' not in m.param_names
assert 'J1909-3744_chrom_gp_log10_gam_p' not in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[0], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag',
chrom_kernel='sq_exp_rfband')
assert 'J0613-0200_chrom_gp_log10_sigma' in m.param_names
assert 'J0613-0200_chrom_gp_log10_ell' in m.param_names
assert 'J0613-0200_chrom_gp_log10_ell2' in m.param_names
assert 'J0613-0200_chrom_gp_log10_alpha_wgt' in m.param_names
assert 'J0613-0200_chrom_gp_log10_p' not in m.param_names
assert 'J0613-0200_chrom_gp_log10_gam_p' not in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[1], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag',
chrom_kernel='sq_exp_rfband')
assert 'J1713+0747_chrom_gp_log10_sigma' in m.param_names
assert 'J1713+0747_chrom_gp_log10_ell' in m.param_names
assert 'J1713+0747_chrom_gp_log10_ell2' in m.param_names
assert 'J1713+0747_chrom_gp_log10_alpha_wgt' in m.param_names
assert 'J1713+0747_chrom_gp_log10_p' not in m.param_names
assert 'J1713+0747_chrom_gp_log10_gam_p' not in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
m=models.model_singlepsr_noise(nodmx_psrs[2], dm_var=True,
dm_type=None, chrom_gp=True,
chrom_gp_kernel='nondiag',
chrom_kernel='sq_exp_rfband')
assert 'J1909-3744_chrom_gp_log10_sigma' in m.param_names
assert 'J1909-3744_chrom_gp_log10_ell' in m.param_names
assert 'J1909-3744_chrom_gp_log10_ell2' in m.param_names
assert 'J1909-3744_chrom_gp_log10_alpha_wgt' in m.param_names
assert 'J1909-3744_chrom_gp_log10_p' not in m.param_names
assert 'J1909-3744_chrom_gp_log10_gam_p' not in m.param_names
assert hasattr(m, 'get_lnlikelihood')
x0 = {pname: p.sample() for pname, p in zip(m.param_names, m.params)}
m.get_lnlikelihood(x0)
# Add to exponential dips for J1713+0747
if args.psr == 'J1713+0747':
dip_kwargs = {
'dm_expdip': True,
'dmexp_sign': 'negative',
'num_dmdips': 2,
'dm_expdip_tmin': [54700, 57450],
'dm_expdip_tmax': [54850, 57560],
'dmdip_seqname': 'ism'
}
for dict in model_kwargs.values():
dict.update(dip_kwargs)
ptas = {}
for ky, kwargs in model_kwargs.items():
ptas[int(ky)] = model_singlepsr_noise(psr, **kwargs)
model_labels = [['A', 'powerlaw', 'None', True],
['B', 'powerlaw', 'None', False],
['C', 'powerlaw', 'sq_exp', True],
['D', 'powerlaw', 'sq_exp', False],
['E', 'powerlaw', 'periodic', True],
['F', 'powerlaw', 'periodic', False]]
super_model = HyperModel(ptas)
sampler = super_model.setup_sampler(resume=True,
outdir=args.outdir,
empirical_distr=args.emp_distr)
model_params = {}