def k(self):
"""
Return a range in wavenumbers, set by the minimum/maximum
allowed values, given the desired `kmin` and `kmax` and the
current values of the AP effect parameters, `alpha_perp` and `alpha_par`
"""
return np.logspace(np.log10(self.kmin), np.log10(self.kmax), self.Nk)
def k(self):
"""
Return a range in wavenumbers, set by the minimum/maximum
allowed values, given the desired `kmin` and `kmax` and the
current values of the AP effect parameters, `alpha_perp` and `alpha_par`
"""
kmin = self.kmin
if kmin < INTERP_KMIN: kmin = INTERP_KMIN
kmax = self.kmax
if kmax > INTERP_KMAX: kmax = INTERP_KMAX
return np.logspace(np.log10(kmin), np.log10(kmax), self.Nk)
def __init__(self, window, ells, kmin=1e-4, kmax=0.7, Nk=1024, Nmu=40, max_ellprime=4):
# make the grid
# NOTE: we want to use the centers of the mu bins here!
k = np.logspace(np.log10(kmin), np.log10(kmax), Nk)
mu_edges = np.linspace(0., 1., Nmu+1)
mu = 0.5 * (mu_edges[1:] + mu_edges[:-1])
grid_k, grid_mu = np.meshgrid(k, mu, indexing='ij')
weights = np.ones_like(grid_k)
grid = PkmuGrid([k,mu], grid_k, grid_mu, weights)
# init the base class
GriddedMultipoleTransfer.__init__(self, grid, ells, kmin=kmin, kmax=kmax)
# the convolver object
self.convolver = WindowConvolution(window[:,0], window[:,1:],
max_ellprime=max_ellprime,
max_ell=max(ells))
def stochasticity(self, k):
"""
The isotropic (type B) stochasticity term due to the discreteness of the
halos, i.e., Poisson noise at 1st order.
Notes
-----
* The model for the (type B) stochasticity, interpolated as a function
of sigma8(z), b1, and k using a Gaussian process
"""
_k = np.logspace(np.log10(self.k.min()), np.log10(self.k.max()), GP_NK)
params = {'sigma8_z': self.sigma8_z, 'k': _k}
if self._ib1 != self._ib1_bar:
b1_1, b1_2 = sorted([self._ib1, self._ib1_bar])
toret = self.cross_stochasticity_fits(b1_1=b1_1,
b1_2=b1_2,
**params)
else:
toret = self.auto_stochasticity_fits(b1=self._ib1, **params)
return spline(_k, toret)(k)
def __call__(self, power, k_out=None, extrap=False, mcfit_kwargs={}, **kws):
"""
Evaluate the convolved multipoles.
Parameters
----------
power : xarray.DataArray
a DataArray holding the :math:`P(k,\mu)` values on a
coordinate grid with ``k`` and ``mu`` dimensions.
k_out : array_like, optional
if provided, evaluate the convolved multipoles at these
``k`` values using a spline
**kws :
additional keywords for testing purposes
Returns
-------
Pell : xarray.DataArray
a DataArray holding the convolved :math:`P_\ell(k)` on a
coordinate grid with ``k`` and ``ell`` dimensions.
"""
from pyRSD.extern import mcfit
# get testing keywords
dry_run = kws.get('dry_run', False)
no_convolution = kws.get('no_convolution', False)
# get the unconvovled theory multipoles
Pell0 = GriddedMultipoleTransfer.__call__(self, power)
# create additional logspaced k values for zero-padding up to k=100 h/Mpc
oldk = Pell0['k'].values
dk = np.diff(np.log10(oldk))[0]
newk = 10**(np.arange(np.log10(oldk.max()) + dk, 2 + 0.5*dk, dk))
newk = np.concatenate([oldk, newk])
# now copy over with zeros
Nk = len(newk); Nell = Pell0.shape[1]
Pell = xr.DataArray(np.zeros((Nk,Nell)), coords={'k':newk, 'ell':Pell0.ell}, dims=['k', 'ell'])
Pell.loc[dict(k=Pell0['k'])] = Pell0[:]
# do the convolution
if not no_convolution:
# FFT the input power multipoles
xi = np.empty((Nk, Nell), order='F') # column-continuous
for i, ell in enumerate(self.ells):
P2xi = mcfit.P2xi(newk, l=ell, **mcfit_kwargs)
rr, xi[:,i] = P2xi(Pell.sel(ell=ell).values, extrap=extrap)
# the linear combination of multipoles
if dry_run:
xi_conv = xi.copy()
else:
xi_conv = self.convolver(self.ells, rr, xi, order='F')
# FFTLog back
Pell_conv = np.empty((Nk, Nell), order='F')
for i, ell in enumerate(self.ells):
xi2P = mcfit.xi2P(rr, l=ell, **mcfit_kwargs)
kk, Pell_conv[:,i] = xi2P(xi_conv[:,i], extrap=extrap)
else:
Pell_conv = Pell
# interpolate to k_out
coords = coords={'ell':Pell0.ell}
if k_out is not None:
shape = (len(k_out), len(self.ells))
toret = np.ones(shape) * np.nan
for i, ell in enumerate(self.ells):
idx = np.isfinite(newk)
spl = spline(newk[idx], Pell_conv[idx,i])
toret[:,i] = spl(k_out)
coords['k'] = k_out
else:
toret = Pell_conv
coords['k'] = newk
return xr.DataArray(toret, coords=coords, dims=['k', 'ell'])
class DarkMatterSpectrum(Cache, SimLoaderMixin, PTIntegralsMixin):
"""
The dark matter power spectrum in redshift space
"""
# splines and interpolation variables
k_interp = np.logspace(np.log10(INTERP_KMIN), np.log10(INTERP_KMAX), 250)
spline = tools.RSDSpline
spline_kwargs = {'bounds_error': True, 'fill_value': 0}
def __init__(self,
kmin=1e-3,
kmax=0.5,
Nk=200,
z=0.,
params=cosmology.Planck15,
include_2loop=False,
transfer_fit="CLASS",
max_mu=4,
interpolate=True,
k0_low=5e-3,
linear_power_file=None,
Pdv_model_type='jennings',
redshift_params=['f', 'sigma8_z'],
**kwargs):
"""
Parameters
----------
kmin : float, optional
The minimum wavenumber to compute the power spectrum at [units: `h/Mpc`]
kmax : float, optional
The maximum wavenumber to compute the power spectrum at [units: `h/Mpc`]
Nk : int, optional
The number of log-spaced bins to use as the underlying domain for splines
z : float, optional
The redshift to compute the power spectrum at. Default = 0.
params : pyRSD.cosmology.Cosmology, str
Either a Cosmology instance or the name of a file to load
parameters from; see the 'data/params' directory for examples
include_2loop : bool, optional
If `True`, include 2-loop contributions in the model terms. Default
is `False`.
transfer_fit : str, optional
The name of the transfer function fit to use. Default is `CLASS`
and the options are {`CLASS`, `EH`, `EH_NoWiggle`, `BBKS`},
or the name of a data file holding (k, T(k))
max_mu : {0, 2, 4, 6, 8}, optional
Only compute angular terms up to mu**(``max_mu``). Default is 4.
interpolate: bool, optional
Whether to return interpolated results for underlying power moments
k0_low : float, optional (`5e-3`)
below this wavenumber, evaluate any power in "low-k mode", which
essentially just uses SPT at low-k
linear_power_file : str, optional (`None`)
string specifying the name of a file which gives the linear
power spectrum, from which the transfer function in ``cosmo``
will be initialized
Pdv_model_type : str, optional ('Jennings')
the type of model to use for the density-velocity cross-correlation
term, `Pdv`; either `Jennings` or `sims`. The Jennnings model is
from arxiv: 1207.1439
redshift_params : list of str, optional
the names of parameters to be updated when redshift changes
"""
# overload cosmo with a cosmo_filename kwargs to handle deprecated syntax
if 'cosmo_filename' in kwargs:
params = kwargs.pop('cosmo_filename')
# set and save the model version automatically
self.__version__ = __version__
# mix in the sim loader class
SimLoaderMixin.__init__(self)
# set the input parameters
self.interpolate = interpolate
self.transfer_fit = transfer_fit
self.params = params
self.max_mu = max_mu
self.include_2loop = include_2loop
self.kmin = kmin
self.kmax = kmax
self.Nk = Nk
self.k0_low = k0_low
self.linear_power_file = linear_power_file
self.Pdv_model_type = Pdv_model_type
# set these last
self.redshift_params = redshift_params
self.z = z
# initialize the cosmology parameters and set defaults
self.sigma8_z = self.cosmo.Sigma8_z(self.z)
self.f = self.cosmo.f_z(self.z)
self.alpha_par = 1.
self.alpha_perp = 1.
self.sigma_v2 = 0.
self.sigma_bv2 = 0.
self.sigma_bv4 = 0.
# set the models we want to use
# default is to use all models
for kw in self.allowable_kwargs:
if fnmatch.fnmatch(kw, 'use_*_model'):
setattr(self, kw, kwargs.pop(kw, True))
# extra keywords
if len(kwargs):
for k in kwargs:
warnings.warn("extra keyword `%s` is ignored" % k)
# mix in the PT intergrals mixin
PTIntegralsMixin.__init__(self)
def __getstate__(self):
"""
Custom pickling that removes `lru_cache` objects from
the cache, which will ensure pickling succeeds
"""
d = self.__dict__
for k in list(self._cache):
if hasattr(self._cache[k], 'cache_info'):
d['_cache'].pop(k)
return d
def initialize(self):
"""
Initialize the underlying splines, etc of the model
"""
k = 0.5 * (self.kmin + self.kmax)
return self.power(k, 0.5)
@contextlib.contextmanager
def use_cache(self):
"""
Cache repeated calls to functions defined in this class, assuming
constant `k` and `mu` input values
"""
from pyRSD.rsd.tools import cache_on, cache_off
try:
cache_on()
yield
except:
raise
finally:
cache_off()
#---------------------------------------------------------------------------
# parameters
#---------------------------------------------------------------------------
@contextlib.contextmanager
def preserve(self, **kwargs):
"""
Context manager that preserves the state of the model
upon exiting the context by first saving and then restoring it
"""
# save the current state of the model
set_params = {}
unset_params = []
for k in self._param_names:
if '__' + k in self.__dict__:
set_params[k] = getattr(self, k)
else:
unset_params.append(k)
cache = self._cache.copy()
# current model params
model_params = {}
for k in self.allowable_kwargs:
model_params[k] = getattr(self, k)
# set any kwargs passed
for k in kwargs:
if k not in self.allowable_kwargs:
raise ValueError(
"keywords to this function must be in `allowable_kwargs`")
setattr(self, k, kwargs[k])
yield
# restore model params
for k in model_params:
setattr(self, k, model_params[k])
# restore the model to previous state
for k in set_params:
setattr(self, k, set_params[k])
for k in unset_params:
if '__' + k in self.__dict__:
delattr(self, k)
for k in cache:
self._cache[k] = cache[k]
@contextlib.contextmanager
def use_spt(self):
"""
Context manager to turn off all models
"""
from collections import OrderedDict
params = OrderedDict()
for kw in self.allowable_kwargs:
if fnmatch.fnmatch(kw, 'use_*_model'):
params[kw] = False
try:
# save the original state
state = {k: getattr(self, k, None) for k in params}
# update the state to low-k mode
for k, v in params.items():
if hasattr(self, k):
setattr(self, k, v)
yield
except:
pass
finally:
# restore the original state
for k, v in state.items():
if hasattr(self, k):
setattr(self, k, v)
@contextlib.contextmanager
def load_dm_sims(self, val):
"""
Context manager to load simulation data for certain dark matter terms
"""
allowed = ['teppei_lowz', 'teppei_midz', 'teppei_highz']
if val not in allowed:
raise ValueError("Allowed simulations to load are %s" % allowed)
z_tags = {
'teppei_lowz': '000',
'teppei_midz': '509',
'teppei_highz': '989'
}
z_tag = z_tags[val]
# get the data
P00_mu0_data = getattr(sim_data, 'P00_mu0_z_0_%s' % z_tag)()
P01_mu2_data = getattr(sim_data, 'P01_mu2_z_0_%s' % z_tag)()
P11_mu4_data = getattr(sim_data, 'P11_mu4_z_0_%s' % z_tag)()
Pdv_mu0_data = getattr(sim_data, 'Pdv_mu0_z_0_%s' % z_tag)()
self._load('P00_mu0', P00_mu0_data[:, 0], P00_mu0_data[:, 1])
self._load('P01_mu2', P01_mu2_data[:, 0], P01_mu2_data[:, 1])
self._load('P11_mu4', P11_mu4_data[:, 0], P11_mu4_data[:, 1])
self._load('Pdv', Pdv_mu0_data[:, 0], Pdv_mu0_data[:, 1])
yield
self._unload('P00_mu0')
self._unload('P01_mu2')
self._unload('P11_mu4')
self._unload('Pdv')
@parameter
def interpolate(self, val):
"""
Whether we want to interpolate any underlying models
"""
self._update_models('interpolate', ['hzpt'], val)
return val
@parameter
def transfer_fit(self, val):
"""
The transfer function fitting method
"""
allowed = ['CLASS', 'EH', 'EH_NoWiggle', 'BBKS']
if val not in allowed:
raise ValueError("`transfer_fit` must be one of %s" % allowed)
return val
@parameter
def cosmo_filename(self, val):
"""
The cosmology filename; this is deprecated, use attr:`params` instead
"""
self.params = val
return val
@parameter
def params(self, val, default="cosmo_filename"):
"""
The cosmology parameters by the user
"""
# check cosmology object
if val is None:
val = cosmology.Planck15
if not isinstance(
val,
(string_types, cosmology.Cosmology, dict, pygcl.Cosmology)):
raise TypeError(
("input `cosmo` keyword should be a parameter file name"
"dictionary, or a pyRSD.cosmology.Cosmology object"))
# convert from dictionary
if isinstance(val, dict):
val = cosmology.Cosmology(**val)
# name of available cosmo?
if isinstance(val, string_types) and hasattr(cosmology, val):
val = getattr(cosmology, val)
return val
@parameter
def linear_power_file(self, val):
"""
The name of the file holding the cosmological parameters
"""
return val
@parameter
def max_mu(self, val):
"""
Only compute the power terms up to and including `max_mu`. Should
be one of [0, 2, 4, 6]
"""
allowed = [0, 2, 4, 6]
if val not in allowed:
raise ValueError("`max_mu` must be one of %s" % allowed)
return val
@parameter
def include_2loop(self, val):
"""
Whether to include 2-loop terms in the power spectrum calculation
"""
return val
@parameter
def z(self, val):
"""
Redshift to evaluate power spectrum at
"""
# update the dependencies
models = ['P11_sim_model', 'Pdv_sim_model']
self._update_models('z', models, val)
# update redshift params
if len(self.redshift_params):
if 'f' in self.redshift_params:
self.f = self.cosmo.f_z(val)
if 'sigma8_z' in self.redshift_params:
self.sigma8_z = self.cosmo.Sigma8_z(val)
return val
@parameter
def k0_low(self, val):
"""
Wavenumber to transition to use only SPT for lower wavenumber
"""
if val < 5e-4:
raise ValueError("`k0_low` must be greater than 5e-4 h/Mpc")
return val
@parameter
def kmin(self, val):
"""
Minimum observed wavenumber needed for results
"""
if val < INTERP_KMIN:
raise ValueError(
"kmin = %.2e h/Mpc below PT integrals interpolation lower bound"
% val)
return val
@parameter
def kmax(self, val):
"""
Maximum observed wavenumber needed for results
"""
if val > INTERP_KMAX:
raise ValueError(
"kmax = %.2e h/Mpc above PT integrals interpolation upper bound"
% val)
return val
@parameter
def Nk(self, val):
"""
Number of log-spaced wavenumber bins to use in underlying splines
"""
return val
@parameter
def sigma8_z(self, val):
"""
The value of Sigma8(z) (mass variances within 8 Mpc/h at z) to compute
the power spectrum at, which gives the normalization of the
linear power spectrum
"""
# update the dependencies
models = ['hzpt', 'P11_sim_model', 'Pdv_sim_model']
self._update_models('sigma8_z', models, val)
return val
@parameter
def f(self, val):
"""
The growth rate, defined as the `dlnD/dlna`.
"""
# update the dependencies
models = ['hzpt', 'Pdv_sim_model', 'P11_sim_model']
self._update_models('f', models, val)
return val
@parameter
def alpha_perp(self, val):
"""
The perpendicular Alcock-Paczynski effect scaling parameter, where
:math: `k_{perp, true} = k_{perp, true} / alpha_{perp}`
"""
return val
@parameter
def alpha_par(self, val):
"""
The parallel Alcock-Paczynski effect scaling parameter, where
:math: `k_{par, true} = k_{par, true} / alpha_{par}`
"""
return val
@parameter(default=1.0)
def alpha_drag(self, val):
"""
The ratio of the sound horizon in the fiducial cosmology
to the true cosmology
"""
return val
@parameter(default="sigma_lin")
def sigma_v(self, val):
"""
The velocity dispersion at `z`. If not provided, defaults to the
linear theory prediction (as given by `self.sigma_lin`) [units: Mpc/h]
"""
return val
@parameter
def sigma_v2(self, val):
"""
The additional, small-scale velocity dispersion, evaluated using the
halo model and weighted by the velocity squared. [units: km/s]
.. math:: (sigma_{v2})^2 = (1/\bar{rho}) * \int dM M \frac{dn}{dM} v_{\parallel}^2
"""
return val
@parameter
def sigma_bv2(self, val):
"""
The additional, small-scale velocity dispersion, evaluated using the
halo model and weighted by the bias times velocity squared. [units: km/s]
.. math:: (sigma_{bv2})^2 = (1/\bar{rho}) * \int dM M \frac{dn}{dM} b(M) v_{\parallel}^2
"""
return val
@parameter
def sigma_bv4(self, val):
"""
The additional, small-scale velocity dispersion, evaluated using the
halo model and weighted by bias times the velocity squared. [units: km/s]
.. math:: (sigma_{bv4})^4 = (1/\bar{rho}) * \int dM M \frac{dn}{dM} b(M) v_{\parallel}^4
"""
return val
#---------------------------------------------------------------------------
# cached properties
#---------------------------------------------------------------------------
@cached_property("cosmo")
def fiducial_rs_drag(self):
"""
The sound horizon at the drag redshift in the cosmology of ``cosmo``
"""
return self.cosmo.rs_drag()
@cached_property("transfer_fit")
def transfer_fit_int(self):
"""
The integer value representing the transfer function fitting method
"""
return getattr(pygcl.transfers, self.transfer_fit)
@cached_property("params", "transfer_fit", "linear_power_file")
def cosmo(self):
"""
A `pygcl.Cosmology` object holding the cosmological parameters
"""
# convert from cosmology.Cosmology to pygcl.Cosmology
if isinstance(self.params, cosmology.Cosmology):
kws = {
'transfer': self.transfer_fit_int,
'linear_power_file': self.linear_power_file
}
return self.params.to_class(**kws)
# convert string to pygcl.Cosmology
if self.linear_power_file is not None:
k, Pk = np.loadtxt(self.linear_power_file, unpack=True)
return pygcl.Cosmology.from_power(self.params, k, Pk)
else:
return pygcl.Cosmology(self.params, self.transfer_fit_int)
@cached_property("Nk", "kmin", "kmax")
def k(self):
"""
Return a range in wavenumbers, set by the minimum/maximum
allowed values, given the desired `kmin` and `kmax` and the
current values of the AP effect parameters, `alpha_perp` and `alpha_par`
"""
kmin = self.kmin
if kmin < INTERP_KMIN: kmin = INTERP_KMIN
kmax = self.kmax
if kmax > INTERP_KMAX: kmax = INTERP_KMAX
return np.logspace(np.log10(kmin), np.log10(kmax), self.Nk)
@cached_property("z", "cosmo")
def D(self):
"""
The growth function at z
"""
return self.cosmo.D_z(self.z)
@cached_property("z", "cosmo")
def conformalH(self):
"""
The conformal Hubble parameter, defined as `H(z) / (1 + z)`
"""
return self.cosmo.H_z(self.z) / (1. + self.z)
@cached_property("cosmo")
def power_lin(self):
"""
A 'pygcl.LinearPS' object holding the linear power spectrum at z = 0
"""
return pygcl.LinearPS(self.cosmo, 0.)
@cached_property("cosmo")
def power_lin_nw(self):
"""
A 'pygcl.LinearPS' object holding the linear power spectrum at z = 0,
using the Eisenstein-Hu no-wiggle transfer function
"""
cosmo = self.cosmo.clone(tf=pygcl.transfers.EH_NoWiggle)
return pygcl.LinearPS(cosmo, 0.)
@cached_property("sigma8_z", "cosmo")
def _power_norm(self):
"""
The factor needed to normalize the linear power spectrum
in `power_lin` to the desired sigma_8, as specified by `sigma8_z`,
and the desired redshift `z`
"""
return (self.sigma8_z / self.cosmo.sigma8())**2
@cached_property("_power_norm", "_sigma_lin_unnormed")
def sigma_lin(self):
"""
The dark matter velocity dispersion at z, as evaluated in
linear theory [units: Mpc/h]. Normalized to `sigma8_z`
"""
return self._power_norm**0.5 * self._sigma_lin_unnormed
@cached_property("power_lin")
def _sigma_lin_unnormed(self):
"""
The dark matter velocity dispersion at z = 0, as evaluated in
linear theory [units: Mpc/h]. This is not properly normalized
"""
return np.sqrt(self.power_lin.VelocityDispersion())
#---------------------------------------------------------------------------
# models to use
#---------------------------------------------------------------------------
@parameter
def use_P00_model(self, val):
"""
If `True`, use the `HZPT` model for P00
"""
return val
@parameter
def use_P01_model(self, val):
"""
If `True`, use the `HZPT` model for P01
"""
return val
@parameter
def use_P11_model(self, val):
"""
If `True`, use the `HZPT` model for P11
"""
return val
@parameter
def use_Pdv_model(self, val):
"""
Whether to use interpolated sim results for Pdv
"""
return val
@parameter
def use_Pvv_model(self, val):
"""
Whether to use Jennings model for Pvv or SPT
"""
return val
@parameter
def Pdv_model_type(self, val):
"""
Either `jennings` or `sims` to describe the Pdv model
"""
allowed = ['jennings', 'sims']
if val not in allowed:
raise ValueError("`Pdv_model_type` must be one of %s" %
str(allowed))
return val
@parameter
def redshift_params(self, val):
"""
A list of parameter names to be scaled with redshift
"""
if len(val) and any(par not in ['f', 'sigma8_z'] for par in val):
raise ValueError(
"valid parameters for redshift scaling: 'f' and 'sigma8_z'")
return val
@cached_property("cosmo")
def hzpt(self):
"""
The class holding the (possibly interpolated) HZPT models
"""
kw = {'interpolate': self.interpolate}
return InterpolatedHZPTModels(self.cosmo, self.sigma8_z, self.f, **kw)
@cached_property("power_lin")
def P11_sim_model(self):
"""
The class holding the model for the P11 dark matter term, based
on interpolating simulations
"""
return SimulationP11(self.power_lin, self.z, self.sigma8_z, self.f)
@cached_property("power_lin")
def Pdv_sim_model(self):
"""
The class holding the model for the Pdv dark matter term, based
on interpolating simulations
"""
return SimulationPdv(self.power_lin, self.z, self.sigma8_z, self.f)
def Pdv_jennings(self, k):
"""
Return the density-divergence cross spectrum using the fitting
formula from Jennings et al 2012 (arxiv: 1207.1439)
"""
a0 = -12483.8
a1 = 2.554
a2 = 1381.29
a3 = 2.540
D = self.D
s8 = self.sigma8_z / D
# z = 0 results
self.hzpt._P00.sigma8_z = s8
P00_z0 = self.hzpt.P00(k)
# redshift scaling
z_scaling = 3. / (D + D**2 + D**3)
# reset sigma8_z
self.hzpt._P00.sigma8_z = self.sigma8_z
g = (a0 * P00_z0**0.5 + a1 * P00_z0**2) / (a2 + a3 * P00_z0)
toret = (g - P00_z0) / z_scaling**2 + self.hzpt.P00(k)
return -self.f * toret
def Pvv_jennings(self, k):
"""
Return the divergence auto spectrum using the fitting
formula from Jennings et al 2012 (arxiv: 1207.1439)
"""
a0 = -12480.5
a1 = 1.824
a2 = 2165.87
a3 = 1.796
D = self.D
s8 = self.sigma8_z / D
# z = 0 results
self.hzpt._P00.sigma8_z = s8
P00_z0 = self.hzpt.P00(k)
# redshift scaling
z_scaling = 3. / (D + D**2 + D**3)
# reset sigma8_z
self.hzpt._P00.sigma8_z = self.sigma8_z
g = (a0 * P00_z0**0.5 + a1 * P00_z0**2) / (a2 + a3 * P00_z0)
toret = (g - P00_z0) / z_scaling**2 + self.hzpt.P00(k)
return self.f**2 * toret
def to_npy(self, filename):
"""
Save to a ``.npy`` file by calling :func:`numpy.save`
"""
np.save(filename, self)
@classmethod
def from_npy(cls, filename):
"""
Load a model from a ``.npy`` file
"""
from pyRSD.rsd import load_model
return load_model(filename)
#---------------------------------------------------------------------------
# utility functions
#---------------------------------------------------------------------------
def update(self, **kwargs):
"""
Update the attributes. Checks that the current value is not equal to
the new value before setting.
"""
for k, v in kwargs.items():
try:
setattr(self, k, v)
except Exception as e:
raise RuntimeError(
"failure to set parameter `%s` to value %s: %s" %
(k, str(v), str(e)))
@classmethod
def default_config(cls, **params):
"""
Return a :class:`ParameterSet` object holding the default
model configuration parameters, updated with any values passed on
as keywords
Parameters
----------
**params :
parameter values specified as key/value pairs
"""
from pyRSD.rsdfit.parameters import Parameter, ParameterSet
allowed = cls.allowable_kwargs
model = cls()
for name in allowed:
params.setdefault(name, getattr(model, name))
# make the set of parameters
toret = ParameterSet()
for name in params:
toret[name] = Parameter(name=name, value=params[name])
toret.tag = 'model'
return toret
@property
def config(self):
"""
Return a dictionary holding the model configuration
This holds the value of all attributes in the
:attr:`allowable_kwargs` list
"""
allowed = self.__class__.allowable_kwargs
return {k: getattr(self, k) for k in allowed}
def _update_models(self, name, models, val):
"""
Update the specified attribute for the models given
"""
for model in models:
if model in self._cache:
setattr(getattr(self, model), name, val)
#---------------------------------------------------------------------------
# power term attributes
#---------------------------------------------------------------------------
def normed_power_lin(self, k):
"""
The linear power evaluated at the specified `k` and at `z`,
normalized to `sigma8_z`
"""
return self._power_norm * self.power_lin(k)
def normed_power_lin_nw(self, k):
"""
The Eisenstein-Hu no-wiggle, linear power evaluated at the specified
`k` and at `self.z`, normalized to `sigma8_z`
"""
return self._power_norm * self.power_lin_nw(k)
@interpolated_function("P00", "k", interp="k")
def P_mu0(self, k):
"""
The full power spectrum term with no angular dependence. Contributions
from P00.
"""
return self.P00.mu0(k)
@interpolated_function("P01", "P11", "P02", "k", interp="k")
def P_mu2(self, k):
"""
The full power spectrum term with mu^2 angular dependence. Contributions
from P01, P11, and P02.
"""
return self.P01.mu2(k) + self.P11.mu2(k) + self.P02.mu2(k)
@interpolated_function("P11",
"P02",
"P12",
"P22",
"P03",
"P13",
"P04",
"include_2loop",
"k",
interp="k")
def P_mu4(self, k):
"""
The full power spectrum term with mu^4 angular dependence. Contributions
from P11, P02, P12, P22, P03, P13 (2-loop), and P04 (2-loop).
"""
Pk = self.P11.mu4(k) + self.P02.mu4(k) + self.P12.mu4(
k) + self.P22.mu4(k) + self.P03.mu4(k)
if self.include_2loop: Pk += self.P13.mu4(k) + self.P04.mu4(k)
return Pk
@interpolated_function("P12",
"P22",
"P13",
"P04",
"include_2loop",
"k",
interp="k")
def P_mu6(self, k):
"""
The full power spectrum term with mu^6 angular dependence. Contributions
from P12, P22, P13, and P04 (2-loop).
"""
Pk = self.P12.mu6(k) + self.P22.mu6(k) + self.P13.mu6(k)
if self.include_2loop: Pk += self.P04.mu6(k)
return Pk
@interpolated_function("z", "_power_norm", "k", interp="k")
def Pdd(self, k):
"""
The 1-loop auto-correlation of density.
"""
norm = self._power_norm
return norm * (self.power_lin(k) + norm * self._Pdd_0(k))
@interpolated_function("f",
"z",
"_power_norm",
"use_Pdv_model",
"Pdv_model_type",
"Pdv_loaded",
"k",
interp="k")
def Pdv(self, k):
"""
The 1-loop cross-correlation between dark matter density and velocity
divergence.
"""
# check for any user-loaded values
if self.Pdv_loaded:
return self._get_loaded_data('Pdv', k)
else:
if self.use_Pdv_model:
if self.Pdv_model_type == 'jennings':
return self.Pdv_jennings(k)
elif self.Pdv_model_type == 'sims':
return self.Pdv_sim_model(k)
else:
norm = self._power_norm
return (-self.f) * norm * (self.power_lin(k) +
norm * self._Pdv_0(k))
@interpolated_function("f",
"z",
"_power_norm",
"use_Pvv_model",
"k",
interp="k")
def Pvv(self, k):
"""
The 1-loop auto-correlation of velocity divergence.
"""
if self.use_Pvv_model:
return self.Pvv_jennings(k)
else:
norm = self._power_norm
return self.f**2 * norm * (self.power_lin(k) +
norm * self._Pvv_0(k))
@cached_property("z", "sigma8_z", "use_P00_model", "power_lin",
"P00_mu0_loaded")
def P00(self):
"""
The isotropic, zero-order term in the power expansion, corresponding
to the density field auto-correlation. No angular dependence.
"""
from .P00 import P00PowerTerm
return P00PowerTerm(self)
@cached_property("f", "z", "sigma8_z", "use_P01_model", "power_lin",
"max_mu", "P01_mu2_loaded")
def P01(self):
"""
The correlation of density and momentum density, which contributes
mu^2 terms to the power expansion.
"""
from .P01 import P01PowerTerm
return P01PowerTerm(self)
@cached_property("f", "z", "sigma8_z", "use_P11_model", "power_lin",
"max_mu", "include_2loop", "P11_mu2_loaded",
"P11_mu4_loaded")
def P11(self):
"""
The auto-correlation of momentum density, which has a scalar portion
which contributes mu^4 terms and a vector term which contributes
mu^2*(1-mu^2) terms to the power expansion. This is the last term to
contain a linear contribution.
"""
from .P11 import P11PowerTerm
return P11PowerTerm(self)
@cached_property("f", "z", "sigma8_z", "power_lin", "max_mu",
"include_2loop", "sigma_v", "sigma_bv2", "P00")
def P02(self):
"""
The correlation of density and energy density, which contributes
mu^2 and mu^4 terms to the power expansion. There are no
linear contributions here.
"""
from .P02 import P02PowerTerm
return P02PowerTerm(self)
@cached_property("f", "z", "sigma8_z", "power_lin", "max_mu",
"include_2loop", "sigma_v", "sigma_bv2", "P01")
def P12(self):
"""
The correlation of momentum density and energy density, which contributes
mu^4 and mu^6 terms to the power expansion. There are no linear
contributions here. Two-loop contribution uses the mu^2 contribution
from the P01 term.
"""
from .P12 import P12PowerTerm
return P12PowerTerm(self)
@cached_property("f", "z", "sigma8_z", "power_lin", "max_mu",
"include_2loop", "sigma_v", "sigma_bv2", "P00", "P02")
def P22(self):
"""
The autocorelation of energy density, which contributes
mu^4, mu^6, mu^8 terms to the power expansion. There are no linear
contributions here.
"""
from .P22 import P22PowerTerm
return P22PowerTerm(self)
@cached_property("f", "z", "sigma8_z", "power_lin", "max_mu",
"include_2loop", "sigma_v", "sigma_v2", "P01")
def P03(self):
"""
The cross-corelation of density with the rank three tensor field
((1+delta)v)^3, which contributes mu^4 terms.
"""
from .P03 import P03PowerTerm
return P03PowerTerm(self)
@cached_property("f", "z", "sigma8_z", "power_lin", "max_mu",
"include_2loop", "sigma_v", "sigma_bv2", "sigma_v2",
"P11")
def P13(self):
"""
The cross-correlation of momentum density with the rank three tensor field
((1+delta)v)^3, which contributes mu^6 terms at 1-loop order and
mu^4 terms at 2-loop order.
"""
from .P13 import P13PowerTerm
return P13PowerTerm(self)
@cached_property("f", "z", "sigma8_z", "power_lin", "max_mu",
"include_2loop", "sigma_v", "sigma_bv4", "P02", "P00")
def P04(self):
"""
The cross-correlation of density with the rank four tensor field
((1+delta)v)^4, which contributes mu^4 and mu^6 terms, at 2-loop order.
"""
from .P04 import P04PowerTerm
return P04PowerTerm(self)
#---------------------------------------------------------------------------
# main user callables
#---------------------------------------------------------------------------
@tools.broadcast_kmu
def power(self, k, mu, flatten=False):
"""
The redshift space power spectrum as a function of ``k`` and ``mu``
This includes terms up to ``mu**self.max_mu``.
Parameters
----------
k : float or array_like
The wavenumbers in `h/Mpc` to evaluate the model at
mu : float, array_like
The mu values to evaluate the power at.
Returns
-------
pkmu : float, array_like
The power model P(k, mu). If `mu` is a scalar, return dimensions
are `(len(self.k), )`. If `mu` has dimensions (N, ), the return
dimensions are `(len(k), N)`, i.e., each column corresponds is the
model evaluated at different `mu` values. If `flatten = True`, then
the returned array is raveled, with dimensions of `(N*len(self.k), )`
"""
# the return array
pkmu = self._power(k, mu)
if flatten:
pkmu = np.ravel(pkmu, order='F')
return pkmu
def poles(self, k, ells, Nmu=40):
"""
The multipole moments of the redshift-space power spectrum
Parameters
----------
k : float, array_like
The wavenumbers to evaluate the power spectrum at, in `h/Mpc`
ells : int, array_like
The `ell` values of the multipole moments
Nmu : int, optional
the number of ``mu`` bins to use when performing the multipole
integration
Returns
-------
poles : array_like
returns tuples of arrays for each ell value in ``poles``
"""
from pyRSD.rsd.transfers import MultipoleTransfer
# the transfer
t = MultipoleTransfer(k, ells, Nmu=Nmu)
# evaluate the model on the grid
P = self.power(t.flatk, t.flatmu)
# return the transferred power
return t(P)
def apply_transfer(self, transfer):
"""
Return the power spectrum with the specified transfer functions
applied, e.g., grid binning, multipole integration, etc.
Parameters
----------
transfer : subclass of :class:`pyRSD.rsd.transfers.TransferBase`
the transfer class
"""
# check some bounds for window convolution
from pyRSD.rsd.transfers import WindowFunctionTransfer
if isinstance(transfer, WindowFunctionTransfer):
kmin = transfer.kmin
kmax = transfer.kmax
if (kmin < self.kmin):
warnings.warn(
"min k of window transfer (%s) is less than model's kmin (%.2e)"
% (kmin, self.kmin))
if (kmax > self.kmax):
warnings.warn(
"max k of window transfer (%s) is greater than model's kmax (%.2e)"
% (kmax, self.kmax))
# check bad values
if self.kmin > 5e-3:
warnings.warn(
"doing window convolution with dangerous model kmin (%.2e)"
% self.kmin)
if self.kmax < 0.5:
warnings.warn(
"doing window convolution with dangerous model kmax (%.2e)"
% self.kmax)
# evaluate the model on the grid
P = self.power(transfer.flatk, transfer.flatmu)
# return power with transfer applied
return transfer(P)
@tools.alcock_paczynski
def _P_mu0(self, k, mu):
"""
Return the AP-distorted P[mu^0]
"""
return self.P_mu0(k)
@tools.alcock_paczynski
def _P_mu2(self, k, mu):
"""
Return the AP-distorted mu^2 P[mu^2]
"""
return mu**2 * self.P_mu2(k)
@tools.alcock_paczynski
def _P_mu4(self, k, mu):
"""
Return the AP-distorted mu^4 P[mu^4]
"""
return mu**4 * self.P_mu4(k)
@tools.alcock_paczynski
def _P_mu6(self, k, mu):
"""
Return the AP-distorted mu^6 P[mu^6]
"""
return mu**6 * self.P_mu6(k)
@tools.broadcast_kmu
@tools.alcock_paczynski
def derivative_k(self, k, mu):
"""
Return the derivative of :func:`power` with
respect to `k`
"""
toret = 0
funcs = [self.P_mu0, self.P_mu2, self.P_mu4, self.P_mu6]
i = 0
while i <= (self.max_mu // 2):
toret += mu**(2 * i) * funcs[i](k, derivative=True)
i += 1
return toret
@tools.broadcast_kmu
@tools.alcock_paczynski
def derivative_mu(self, k, mu):
"""
Return the derivative of :func:`power` with
respect to `mu`
"""
toret = 0
funcs = [self.P_mu0, self.P_mu2, self.P_mu4, self.P_mu6]
i = 0
while i <= (self.max_mu // 2):
# derivative of mu^(2i)
if i != 0: toret += (2. * i) * mu**(2 * i - 1) * funcs[i](k)
i += 1
return toret
def _power(self, k, mu):
"""
Return the power as sum of mu powers
"""
if self.max_mu > 6:
raise NotImplementedError(
"cannot compute power spectrum including terms with order higher than mu^6"
)
toret = 0
funcs = [self._P_mu0, self._P_mu2, self._P_mu4, self._P_mu6]
i = 0
while i <= (self.max_mu // 2):
toret += funcs[i](k, mu)
i += 1
return np.nan_to_num(toret)
@tools.monopole
def monopole(self, k, mu, **kwargs):
"""
The monopole moment of the power spectrum. Include mu terms up to
mu**max_mu.
"""
return self.power(k, mu, **kwargs)
@tools.quadrupole
def quadrupole(self, k, mu, **kwargs):
"""
The quadrupole moment of the power spectrum. Include mu terms up to
mu**max_mu.
"""
return self.power(k, mu, **kwargs)
@tools.hexadecapole
def hexadecapole(self, k, mu, **kwargs):
"""
The hexadecapole moment of the power spectrum. Include mu terms up to
mu**max_mu.
"""
return self.power(k, mu, **kwargs)
@tools.tetrahexadecapole
def tetrahexadecapole(self, k, mu, **kwargs):
"""
The tetrahexadecapole (ell=6) moment of the power spectrum
"""
return self.power(k, mu, **kwargs)
class QuasarSpectrum(HaloSpectrum):
"""
The quasar redshift space power spectrum, a subclass of
:class:`~pyRSD.rsd.HaloSpectrum` for biased redshift space power spectra
"""
k_interp = np.logspace(np.log10(1e-8), np.log10(100.0), 500)
def __init__(self, fog_model='gaussian', **kwargs):
"""
Initialize the QuasarSpectrum
Parameters
----------
fog_model : str, optional
the string specifying the FOG model to use; one of
['modified_lorentzian', 'lorentzian', 'gaussian'].
Default is 'gaussian'
"""
# the base class
super(QuasarSpectrum, self).__init__(**kwargs)
# set the defaults
self.fog_model = fog_model
self.sigma_fog = 4.0
self.include_2loop = False
self.N = 0
# fnl parameters
self.f_nl = 0
self.p = 1.6 # good for quasars
@cached_property("Nk", "kmin", "kmax")
def k(self):
"""
Return a range in wavenumbers, set by the minimum/maximum
allowed values, given the desired `kmin` and `kmax` and the
current values of the AP effect parameters, `alpha_perp` and `alpha_par`
"""
return np.logspace(np.log10(self.kmin), np.log10(self.kmax), self.Nk)
@parameter
def kmin(self, val):
"""
Minimum observed wavenumber needed for results
"""
return val
@parameter
def kmax(self, val):
"""
Maximum observed wavenumber needed for results
"""
return val
def default_params(self):
"""
Return a QuasarPowerParameters instance holding the default
model parameters configuration
The model associated with the parameter is ``self``
"""
from pyRSD.rsdfit.theory import QuasarPowerParameters
return QuasarPowerParameters.from_defaults(model=self)
@parameter
def p(self, val):
"""
The bias type for PNG; either 1.6 or 1 usually
"""
return val
@parameter
def fog_model(self, val):
"""
Function to return the FOG suppression factor, which reads in a
single variable `x = k \mu \sigma`
"""
allowable = ['modified_lorentzian', 'lorentzian', 'gaussian']
if val not in allowable:
raise ValueError("`fog_model` must be one of %s" % allowable)
return val
@parameter
def sigma_fog(self, val):
"""
The FOG velocity dispersion in Mpc/h
"""
return val
@parameter
def p(self, val):
"""
The value encoding the type of tracer; must be between 1 and 1.6,
with p=1 suitable for LRGs and p=1.6 suitable for quasars
The scale-dependent bias is proportional to: ``b1 - p``
"""
if not 1 <= val <= 1.6:
raise ValueError(
"f_nl ``p`` value should be between 1 and 1.6 (inclusive)")
return val
@parameter
def f_nl(self, val):
"""
The amplitude of the local-type non-Gaussianity
"""
return val
@parameter
def N(self, val):
"""
Constant offset to model, set to 0 by default
"""
return val
@cached_property("fog_model")
def FOG(self):
"""
Return the FOG function
"""
return FOGKernel.factory(self.fog_model)
#---------------------------------------------------------------------------
# primordial non-Gaussianity functions
#---------------------------------------------------------------------------
@cached_property()
def delta_crit(self):
"""
The usual critical overdensity value for collapse from Press-Schechter
"""
return 1.686
@interpolated_function("k", "cosmo", "D")
def alpha_png(self, k):
"""
The primordial non-Gaussianity alpha value
see e.g., equation 2 of Mueller et al 2017
"""
# transfer function, normalized to unity
Tk = (self.normed_power_lin(k)/k**self.cosmo.n_s())**0.5
Tk /= Tk.max()
# normalization
c = pygcl.Constants.c_light / pygcl.Constants.km # in km/s
H0 = 100 # in units of h km/s/Mpc
# normalizes growth function to unity in matter-dominated epoch
g_ratio = growth_function(self.cosmo, 0.)
g_ratio /= (1+100.) * growth_function(self.cosmo, 100.)
return 2*k**2 * Tk * self.D / (3*self.cosmo.Omega0_m()) * (c/H0)**2 * g_ratio
@interpolated_function("k", "b1", "f_nl", "p")
def delta_bias(self, k):
"""
The scale-dependent bias introduced by primordial non-Gaussianity
"""
if self.f_nl == 0:
return k*0.
return 2*(self.b1-self.p)*self.f_nl*self.delta_crit/self.alpha_png(k)
@interpolated_function("k", "b1", "delta_bias")
def btot(self, k):
"""
The total bias, accounting for scale-dependent bias introduced by
primordial non-Gaussianity
"""
return self.b1 + self.delta_bias(k)
#---------------------------------------------------------------------------
# power as a function of mu
#---------------------------------------------------------------------------
@interpolated_function("k", "sigma8_z", "_power_norm", "btot")
def P_mu0(self, k):
"""
The isotropic part of the Kaiser formula
"""
return self.btot(k)**2 * self.normed_power_lin(k)
@interpolated_function("k", "sigma8_z", "f", "_power_norm", "btot")
def P_mu2(self, k):
"""
The mu^2 term of the Kaiser formula
"""
return 2*self.f*self.btot(k) * self.normed_power_lin(k)
@interpolated_function("k", "sigma8_z", "f", "_power_norm")
def P_mu4(self, k):
"""
The mu^4 term of the Kaiser formula
"""
return self.f**2 * self.normed_power_lin(k)
@interpolated_function(interp="k")
def P_mu6(self, k):
"""
The mu^6 term is zero in the Kaiser formula
"""
return k*0.
@tools.broadcast_kmu
@tools.alcock_paczynski
def power(self, k, mu, flatten=False):
"""
Return the redshift space power spectrum at the specified value of mu,
including terms up to ``mu**self.max_mu``.
Parameters
----------
k : float or array_like
The wavenumbers in `h/Mpc` to evaluate the model at
mu : float, array_like
The mu values to evaluate the power at.
Returns
-------
pkmu : float, array_like
The power model P(k, mu). If `mu` is a scalar, return dimensions
are `(len(self.k), )`. If `mu` has dimensions (N, ), the return
dimensions are `(len(k), N)`, i.e., each column corresponds is the
model evaluated at different `mu` values. If `flatten = True`, then
the returned array is raveled, with dimensions of `(N*len(self.k), )`
"""
# the linear kaiser P(k,mu)
pkmu = super(QuasarSpectrum, self).power(k, mu)
# add FOG damping
G = self.FOG(k, mu, self.sigma_fog)
pkmu *= G**2
# add shot noise offset
pkmu += self.N
if flatten:
pkmu = np.ravel(pkmu, order='F')
return pkmu
@tools.broadcast_kmu
@tools.alcock_paczynski
def derivative_k(self, k, mu):
"""
The derivative with respect to `k_AP`
"""
G = self.FOG(k, mu, self.sigma_fog)
Gprime = self.FOG.derivative_k(k, mu, self.sigma_fog)
deriv = super(QuasarSpectrum, self).derivative_k(k, mu)
power = super(QuasarSpectrum, self).power(k, mu)
return G**2 * deriv + 2 * G*Gprime * power
@tools.broadcast_kmu
@tools.alcock_paczynski
def derivative_mu(self, k, mu):
"""
The derivative with respect to `mu_AP`
"""
G = self.FOG(k, mu, self.sigma_fog)
Gprime = self.FOG.derivative_mu(k, mu, self.sigma_fog)
deriv = super(QuasarSpectrum, self).derivative_mu(k, mu)
power = super(QuasarSpectrum, self).power(k, mu)
return G**2 * deriv + 2 * G*Gprime * power
def get_gradient(self, pars):
"""
Return a :class:`PkmuGradient` object which can compute
the gradient of :func:`GalaxySpectrum.power` for a set of
desired parameters
Parameters
----------
pars : ParameterSet
"""
from pyRSD.rsd.power.qso.derivatives import PqsoDerivative
from pyRSD.rsd.power.gradient import PkmuGradient
registry = PqsoDerivative.registry()
return PkmuGradient(self, registry, pars)