mirror of
https://github.com/Richard-Sti/csiborgtools.git
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Reorganise funcs
This commit is contained in:
rstiskalek
parent
e34a791e05
commit
aa43fbf66e
2 changed files with 523 additions and 500 deletions
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@ -26,287 +26,21 @@ from abc import ABC, abstractmethod
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import numpy as np
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from astropy import units as u
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from astropy.cosmology import FlatLambdaCDM, z_at_value
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from h5py import File
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from jax import jit
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from jax import numpy as jnp
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from jax.scipy.special import logsumexp, erf
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from numpyro import factor, sample, plate
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from numpyro.distributions import Normal, Uniform, MultivariateNormal
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from jax.scipy.special import erf, logsumexp
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from numpyro import factor, plate, sample
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from numpyro.distributions import MultivariateNormal, Normal, Uniform
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from quadax import simpson
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from tqdm import trange
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from ..params import SPEED_OF_LIGHT
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from ..utils import fprint
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from .selection import toy_log_magnitude_selection
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from ..params import SPEED_OF_LIGHT, simname2Omega_m
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from ..utils import fprint, radec_to_galactic, radec_to_supergalactic
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H0 = 100 # km / s / Mpc
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###############################################################################
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# Data loader #
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###############################################################################
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class DataLoader:
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"""
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Data loader for the line of sight (LOS) interpolated fields and the
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corresponding catalogues.
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Parameters
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----------
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simname : str
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Simulation name.
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ksim : int or list of int
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Index of the simulation to read in (not the IC index).
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catalogue : str
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Name of the catalogue with LOS objects.
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catalogue_fpath : str
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Path to the LOS catalogue file.
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paths : csiborgtools.read.Paths
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Paths object.
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ksmooth : int, optional
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Smoothing index.
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store_full_velocity : bool, optional
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Whether to store the full 3D velocity field. Otherwise stores only
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the radial velocity.
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verbose : bool, optional
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Verbose flag.
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"""
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def __init__(self, simname, ksim, catalogue, catalogue_fpath, paths,
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ksmooth=None, store_full_velocity=False, verbose=True):
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fprint("reading the catalogue,", verbose)
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self._cat = self._read_catalogue(catalogue, catalogue_fpath)
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self._catname = catalogue
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fprint("reading the interpolated field.", verbose)
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self._field_rdist, self._los_density, self._los_velocity = self._read_field( # noqa
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simname, ksim, catalogue, ksmooth, paths)
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if len(self._cat) != self._los_density.shape[1]:
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raise ValueError("The number of objects in the catalogue does not "
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"match the number of objects in the field.")
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fprint("calculating the radial velocity.", verbose)
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nobject = self._los_density.shape[1]
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dtype = self._los_density.dtype
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if simname in ["Carrick2015", "Lilow2024"]:
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# Carrick+2015 and Lilow+2024 are in galactic coordinates
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d1, d2 = radec_to_galactic(self._cat["RA"], self._cat["DEC"])
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elif simname in ["CF4", "CLONES"]:
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# CF4 is in supergalactic coordinates
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d1, d2 = radec_to_supergalactic(self._cat["RA"], self._cat["DEC"])
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else:
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d1, d2 = self._cat["RA"], self._cat["DEC"]
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num_sims = len(self._los_density)
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if "IndranilVoid" in simname:
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self._los_radial_velocity = self._los_velocity
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self._los_velocity = None
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else:
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radvel = np.empty(
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(num_sims, nobject, len(self._field_rdist)), dtype)
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for k in range(num_sims):
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for i in range(nobject):
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radvel[k, i, :] = radial_velocity_los(
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self._los_velocity[k, :, i, ...], d1[i], d2[i])
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self._los_radial_velocity = radvel
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if not store_full_velocity:
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self._los_velocity = None
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self._Omega_m = simname2Omega_m(simname)
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# Normalize the CSiBORG & CLONES density by the mean matter density
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if "csiborg" in simname or simname == "CLONES":
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cosmo = FlatLambdaCDM(H0=H0, Om0=self._Omega_m)
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mean_rho_matter = cosmo.critical_density0.to("Msun/kpc^3").value
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mean_rho_matter *= self._Omega_m
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self._los_density /= mean_rho_matter
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# Since Carrick+2015 and CF4 provide `rho / <rho> - 1`
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if simname in ["Carrick2015", "CF4", "CF4gp"]:
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self._los_density += 1
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# But some CF4 delta values are < -1. Check that CF4 really reports
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# this.
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if simname in ["CF4", "CF4gp"]:
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self._los_density = np.clip(self._los_density, 1e-2, None,)
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# Lilow+2024 outside of the range data is NaN. Replace it with some
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# finite values. This is OK because the PV tracers are not so far.
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if simname == "Lilow2024":
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self._los_density[np.isnan(self._los_density)] = 1.
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self._los_radial_velocity[np.isnan(self._los_radial_velocity)] = 0.
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self._mask = np.ones(len(self._cat), dtype=bool)
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self._catname = catalogue
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@property
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def cat(self):
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"""The distance indicators catalogue (structured array)."""
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return self._cat[self._mask]
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@property
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def catname(self):
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"""Catalogue name."""
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return self._catname
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@property
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def rdist(self):
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"""Radial distances at which the field was interpolated."""
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return self._field_rdist
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@property
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def los_density(self):
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"""
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Density field along the line of sight `(n_sims, n_objects, n_steps)`
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"""
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return self._los_density[:, self._mask, ...]
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@property
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def los_velocity(self):
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"""
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Velocity field along the line of sight `(n_sims, 3, n_objects,
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n_steps)`.
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"""
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if self._los_velocity is None:
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raise ValueError("The 3D velocities were not stored.")
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return self._los_velocity[:, :, self._mask, ...]
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@property
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def los_radial_velocity(self):
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"""
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Radial velocity along the line of sight `(n_sims, n_objects, n_steps)`.
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"""
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return self._los_radial_velocity[:, self._mask, ...]
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def _read_field(self, simname, ksims, catalogue, ksmooth, paths):
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nsims = paths.get_ics(simname)
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if isinstance(ksims, int):
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ksims = [ksims]
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# For no-field read in Carrick+2015 but then zero it.
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if simname == "no_field":
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simname = "Carrick2015"
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to_wipe = simname == "no_field"
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if not all(0 <= ksim < len(nsims) for ksim in ksims):
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raise ValueError(f"Invalid simulation index: `{ksims}`")
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if "Pantheon+" in catalogue:
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fpath = paths.field_los(simname, "Pantheon+")
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elif "CF4_TFR" in catalogue:
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fpath = paths.field_los(simname, "CF4_TFR")
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else:
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fpath = paths.field_los(simname, catalogue)
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los_density = [None] * len(ksims)
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los_velocity = [None] * len(ksims)
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for n, ksim in enumerate(ksims):
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nsim = nsims[ksim]
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with File(fpath, 'r') as f:
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has_smoothed = True if f[f"density_{nsim}"].ndim > 2 else False
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if has_smoothed and (ksmooth is None or not isinstance(ksmooth, int)): # noqa
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raise ValueError("The output contains smoothed field but "
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"`ksmooth` is None. It must be provided.")
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indx = (..., ksmooth) if has_smoothed else (...)
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los_density[n] = f[f"density_{nsim}"][indx]
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los_velocity[n] = f[f"velocity_{nsim}"][indx]
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rdist = f[f"rdist_{nsim}"][...]
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los_density = np.stack(los_density)
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los_velocity = np.stack(los_velocity)
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if to_wipe:
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los_density = np.ones_like(los_density)
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los_velocity = np.zeros_like(los_velocity)
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return rdist, los_density, los_velocity
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def _read_catalogue(self, catalogue, catalogue_fpath):
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if catalogue == "A2":
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with File(catalogue_fpath, 'r') as f:
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dtype = [(key, np.float32) for key in f.keys()]
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arr = np.empty(len(f["RA"]), dtype=dtype)
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for key in f.keys():
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arr[key] = f[key][:]
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elif catalogue in ["LOSS", "Foundation", "SFI_gals", "2MTF",
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"Pantheon+", "SFI_gals_masked", "SFI_groups",
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"Pantheon+_groups", "Pantheon+_groups_zSN",
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"Pantheon+_zSN"]:
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with File(catalogue_fpath, 'r') as f:
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if "Pantheon+" in catalogue:
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grp = f["Pantheon+"]
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else:
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grp = f[catalogue]
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dtype = [(key, np.float32) for key in grp.keys()]
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arr = np.empty(len(grp["RA"]), dtype=dtype)
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for key in grp.keys():
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arr[key] = grp[key][:]
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elif "CB2_" in catalogue:
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with File(catalogue_fpath, 'r') as f:
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dtype = [(key, np.float32) for key in f.keys()]
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arr = np.empty(len(f["RA"]), dtype=dtype)
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for key in f.keys():
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arr[key] = f[key][:]
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elif "UPGLADE" in catalogue:
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with File(catalogue_fpath, 'r') as f:
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dtype = [(key, np.float32) for key in f.keys()]
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arr = np.empty(len(f["RA"]), dtype=dtype)
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for key in f.keys():
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if key == "mask":
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continue
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arr[key] = f[key][:]
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elif catalogue in ["CF4_GroupAll"] or "CF4_TFR" in catalogue:
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with File(catalogue_fpath, 'r') as f:
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dtype = [(key, np.float32) for key in f.keys()]
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dtype += [("DEC", np.float32)]
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arr = np.empty(len(f["RA"]), dtype=dtype)
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for key in f.keys():
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arr[key] = f[key][:]
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arr["DEC"] = arr["DE"]
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if "CF4_TFR" in catalogue:
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arr["RA"] *= 360 / 24
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else:
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raise ValueError(f"Unknown catalogue: `{catalogue}`.")
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return arr
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###############################################################################
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# Supplementary flow functions #
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###############################################################################
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def radial_velocity_los(los_velocity, ra, dec):
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"""
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Calculate the radial velocity along the LOS from the 3D velocity
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along the LOS `(3, n_steps)`.
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"""
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types = (float, np.float32, np.float64)
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if not isinstance(ra, types) and not isinstance(dec, types):
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raise ValueError("RA and dec must be floats.")
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if los_velocity.ndim != 2 and los_velocity.shape[0] != 3:
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raise ValueError("The shape of `los_velocity` must be (3, n_steps).")
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ra_rad, dec_rad = np.deg2rad(ra), np.deg2rad(dec)
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vx, vy, vz = los_velocity
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return (vx * np.cos(ra_rad) * np.cos(dec_rad)
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+ vy * np.sin(ra_rad) * np.cos(dec_rad)
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+ vz * np.sin(dec_rad))
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###############################################################################
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# JAX Flow model #
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###############################################################################
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@ -990,235 +724,6 @@ def PV_validation_model(models, distmod_hyperparams_per_model,
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factor("ll", ll)
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###############################################################################
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# Shortcut to create a model #
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###############################################################################
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def read_absolute_calibration(kind, data_length, calibration_fpath):
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"""
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Read the absolute calibration for the CF4 TFR sample from LEDA but
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preprocessed by me.
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Parameters
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----------
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kind : str
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Calibration kind: `Cepheids`, `TRGB`, `SBF`, ...
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data_length : int
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Number of samples in CF4 TFR (should be 9,788).
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calibration_fpath : str
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Path to the preprocessed calibration file.
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Returns
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-------
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data : 3-dimensional array of shape (data_length, max_calib, 2)
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Absolute calibration data.
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with_calibration : 1-dimensional array of shape (data_length)
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Whether the sample has a calibration.
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length_calibration : 1-dimensional array of shape (data_length)
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Number of calibration points per sample.
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"""
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data = {}
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with File(calibration_fpath, 'r') as f:
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for key in f[kind].keys():
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x = f[kind][key][:]
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# Get rid of points without uncertainties
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x = x[~np.isnan(x[:, 1])]
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data[key] = x
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max_calib = max(len(val) for val in data.values())
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out = np.full((data_length, max_calib, 2), np.nan)
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with_calibration = np.full(data_length, False)
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length_calibration = np.full(data_length, 0)
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for i in data.keys():
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out[int(i), :len(data[i]), :] = data[i]
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with_calibration[int(i)] = True
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length_calibration[int(i)] = len(data[i])
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return out, with_calibration, length_calibration
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def get_model(loader, zcmb_min=None, zcmb_max=None, mag_selection=None,
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absolute_calibration=None, calibration_fpath=None):
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"""
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Get a model and extract the relevant data from the loader.
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Parameters
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----------
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loader : DataLoader
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DataLoader instance.
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zcmb_min : float, optional
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Minimum observed redshift in the CMB frame to include.
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zcmb_max : float, optional
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Maximum observed redshift in the CMB frame to include.
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mag_selection : dict, optional
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Magnitude selection parameters.
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add_absolute_calibration : bool, optional
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Whether to add an absolute calibration for CF4 TFRs.
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calibration_fpath : str, optional
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Returns
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-------
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model : NumPyro model
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"""
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zcmb_min = 0.0 if zcmb_min is None else zcmb_min
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zcmb_max = np.infty if zcmb_max is None else zcmb_max
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los_overdensity = loader.los_density
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los_velocity = loader.los_radial_velocity
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kind = loader._catname
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if absolute_calibration is not None and "CF4_TFR_" not in kind:
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raise ValueError("Absolute calibration supported only for the CF4 TFR sample.") # noqa
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if kind in ["LOSS", "Foundation"]:
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keys = ["RA", "DEC", "z_CMB", "mB", "x1", "c", "e_mB", "e_x1", "e_c"]
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RA, dec, zCMB, mag, x1, c, e_mag, e_x1, e_c = (
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loader.cat[k] for k in keys)
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e_zCMB = None
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mask = (zCMB < zcmb_max) & (zCMB > zcmb_min)
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calibration_params = {"mag": mag[mask], "x1": x1[mask], "c": c[mask],
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"e_mag": e_mag[mask], "e_x1": e_x1[mask],
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"e_c": e_c[mask]}
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model = PV_LogLikelihood(
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los_overdensity[:, mask], los_velocity[:, mask],
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RA[mask], dec[mask], zCMB[mask], e_zCMB, calibration_params,
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None, mag_selection, loader.rdist, loader._Omega_m, "SN",
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name=kind)
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elif "Pantheon+" in kind:
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keys = ["RA", "DEC", "zCMB", "mB", "x1", "c", "biasCor_m_b", "mBERR",
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"x1ERR", "cERR", "biasCorErr_m_b", "zCMB_SN", "zCMB_Group",
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"zCMBERR"]
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RA, dec, zCMB, mB, x1, c, bias_corr_mB, e_mB, e_x1, e_c, e_bias_corr_mB, zCMB_SN, zCMB_Group, e_zCMB = (loader.cat[k] for k in keys) # noqa
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mB -= bias_corr_mB
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e_mB = np.sqrt(e_mB**2 + e_bias_corr_mB**2)
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mask = (zCMB < zcmb_max) & (zCMB > zcmb_min)
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if kind == "Pantheon+_groups":
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mask &= np.isfinite(zCMB_Group)
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if kind == "Pantheon+_groups_zSN":
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mask &= np.isfinite(zCMB_Group)
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zCMB = zCMB_SN
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if kind == "Pantheon+_zSN":
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zCMB = zCMB_SN
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calibration_params = {"mag": mB[mask], "x1": x1[mask], "c": c[mask],
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"e_mag": e_mB[mask], "e_x1": e_x1[mask],
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"e_c": e_c[mask]}
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model = PV_LogLikelihood(
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los_overdensity[:, mask], los_velocity[:, mask],
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RA[mask], dec[mask], zCMB[mask], e_zCMB[mask], calibration_params,
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None, mag_selection, loader.rdist, loader._Omega_m, "SN",
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name=kind)
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elif kind in ["SFI_gals", "2MTF", "SFI_gals_masked"]:
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keys = ["RA", "DEC", "z_CMB", "mag", "eta", "e_mag", "e_eta"]
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RA, dec, zCMB, mag, eta, e_mag, e_eta = (loader.cat[k] for k in keys)
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mask = (zCMB < zcmb_max) & (zCMB > zcmb_min)
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calibration_params = {"mag": mag[mask], "eta": eta[mask],
|
||||
"e_mag": e_mag[mask], "e_eta": e_eta[mask]}
|
||||
model = PV_LogLikelihood(
|
||||
los_overdensity[:, mask], los_velocity[:, mask],
|
||||
RA[mask], dec[mask], zCMB[mask], None, calibration_params, None,
|
||||
mag_selection, loader.rdist, loader._Omega_m, "TFR", name=kind)
|
||||
elif "CF4_TFR_" in kind:
|
||||
# The full name can be e.g. "CF4_TFR_not2MTForSFI_i" or "CF4_TFR_i".
|
||||
band = kind.split("_")[-1]
|
||||
if band not in ['g', 'r', 'i', 'z', 'w1', 'w2']:
|
||||
raise ValueError(f"Band `{band}` not recognized.")
|
||||
|
||||
keys = ["RA", "DEC", "Vcmb", f"{band}", "lgWmxi", "elgWi",
|
||||
"not_matched_to_2MTF_or_SFI", "Qs", "Qw"]
|
||||
RA, dec, z_obs, mag, eta, e_eta, not_matched_to_2MTF_or_SFI, Qs, Qw = (
|
||||
loader.cat[k] for k in keys)
|
||||
l, b = radec_to_galactic(RA, dec)
|
||||
|
||||
not_matched_to_2MTF_or_SFI = not_matched_to_2MTF_or_SFI.astype(bool)
|
||||
# NOTE: fiducial uncertainty until we can get the actual values.
|
||||
e_mag = 0.05 * np.ones_like(mag)
|
||||
|
||||
z_obs /= SPEED_OF_LIGHT
|
||||
eta -= 2.5
|
||||
|
||||
fprint("selecting only galaxies with mag > 5 and eta > -0.3.")
|
||||
mask = (mag > 5) & (eta > -0.3)
|
||||
fprint("selecting only galaxies with |b| > 7.5.")
|
||||
mask &= np.abs(b) > 7.5
|
||||
mask &= (z_obs < zcmb_max) & (z_obs > zcmb_min)
|
||||
|
||||
if "not2MTForSFI" in kind:
|
||||
mask &= not_matched_to_2MTF_or_SFI
|
||||
elif "2MTForSFI" in kind:
|
||||
mask &= ~not_matched_to_2MTF_or_SFI
|
||||
|
||||
fprint("employing a quality cut on the galaxies.")
|
||||
if "w" in band:
|
||||
mask &= Qw == 5
|
||||
else:
|
||||
mask &= Qs == 5
|
||||
|
||||
# Read the absolute calibration
|
||||
if absolute_calibration is not None:
|
||||
CF4_length = len(RA)
|
||||
distmod, with_calibration, length_calibration = read_absolute_calibration( # noqa
|
||||
"Cepheids", CF4_length, calibration_fpath)
|
||||
|
||||
distmod = distmod[mask]
|
||||
with_calibration = with_calibration[mask]
|
||||
length_calibration = length_calibration[mask]
|
||||
fprint(f"found {np.sum(with_calibration)} galaxies with absolute calibration.") # noqa
|
||||
|
||||
distmod = distmod[with_calibration]
|
||||
length_calibration = length_calibration[with_calibration]
|
||||
|
||||
abs_calibration_params = {
|
||||
"calibration_distmod": distmod,
|
||||
"data_with_calibration": with_calibration,
|
||||
"length_calibration": length_calibration}
|
||||
else:
|
||||
abs_calibration_params = None
|
||||
|
||||
calibration_params = {"mag": mag[mask], "eta": eta[mask],
|
||||
"e_mag": e_mag[mask], "e_eta": e_eta[mask]}
|
||||
model = PV_LogLikelihood(
|
||||
los_overdensity[:, mask], los_velocity[:, mask],
|
||||
RA[mask], dec[mask], z_obs[mask], None, calibration_params,
|
||||
abs_calibration_params, mag_selection, loader.rdist,
|
||||
loader._Omega_m, "TFR", name=kind)
|
||||
elif kind in ["CF4_GroupAll"]:
|
||||
# Note, this for some reason works terribly.
|
||||
keys = ["RA", "DE", "Vcmb", "DMzp", "eDM"]
|
||||
RA, dec, zCMB, mu, e_mu = (loader.cat[k] for k in keys)
|
||||
|
||||
zCMB /= SPEED_OF_LIGHT
|
||||
mask = (zCMB < zcmb_max) & (zCMB > zcmb_min) & np.isfinite(mu)
|
||||
|
||||
# The distance moduli in CF4 are most likely given assuming h = 0.75
|
||||
mu += 5 * np.log10(0.75)
|
||||
|
||||
calibration_params = {"mu": mu[mask], "e_mu": e_mu[mask]}
|
||||
model = PV_LogLikelihood(
|
||||
los_overdensity[:, mask], los_velocity[:, mask],
|
||||
RA[mask], dec[mask], zCMB[mask], None, calibration_params, None,
|
||||
mag_selection, loader.rdist, loader._Omega_m, "simple",
|
||||
name=kind)
|
||||
else:
|
||||
raise ValueError(f"Catalogue `{kind}` not recognized.")
|
||||
|
||||
fprint(f"selected {np.sum(mask)}/{len(mask)} galaxies in catalogue `{kind}`") # noqa
|
||||
|
||||
return model
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Predicting z_cosmo from z_obs #
|
||||
###############################################################################
|
||||
|
|
|
|||
518
csiborgtools/flow/io.py
Normal file
518
csiborgtools/flow/io.py
Normal file
|
|
@ -0,0 +1,518 @@
|
|||
# Copyright (C) 2024 Richard Stiskalek
|
||||
# This program is free software; you can redistribute it and/or modify it
|
||||
# under the terms of the GNU General Public License as published by the
|
||||
# Free Software Foundation; either version 3 of the License, or (at your
|
||||
# option) any later version.
|
||||
#
|
||||
# This program is distributed in the hope that it will be useful, but
|
||||
# WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
|
||||
# Public License for more details.
|
||||
#
|
||||
# You should have received a copy of the GNU General Public License along
|
||||
# with this program; if not, write to the Free Software Foundation, Inc.,
|
||||
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
|
||||
|
||||
import numpy as np
|
||||
from astropy.cosmology import FlatLambdaCDM
|
||||
from h5py import File
|
||||
|
||||
from ..params import SPEED_OF_LIGHT, simname2Omega_m
|
||||
from ..utils import fprint, radec_to_galactic, radec_to_supergalactic
|
||||
from .flow_model import PV_LogLikelihood
|
||||
|
||||
H0 = 100 # km / s / Mpc
|
||||
|
||||
|
||||
##############################################################################
|
||||
# Data loader #
|
||||
###############################################################################
|
||||
|
||||
|
||||
class DataLoader:
|
||||
"""
|
||||
Data loader for the line of sight (LOS) interpolated fields and the
|
||||
corresponding catalogues.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
simname : str
|
||||
Simulation name.
|
||||
ksim : int or list of int
|
||||
Index of the simulation to read in (not the IC index).
|
||||
catalogue : str
|
||||
Name of the catalogue with LOS objects.
|
||||
catalogue_fpath : str
|
||||
Path to the LOS catalogue file.
|
||||
paths : csiborgtools.read.Paths
|
||||
Paths object.
|
||||
ksmooth : int, optional
|
||||
Smoothing index.
|
||||
store_full_velocity : bool, optional
|
||||
Whether to store the full 3D velocity field. Otherwise stores only
|
||||
the radial velocity.
|
||||
verbose : bool, optional
|
||||
Verbose flag.
|
||||
"""
|
||||
def __init__(self, simname, ksim, catalogue, catalogue_fpath, paths,
|
||||
ksmooth=None, store_full_velocity=False, verbose=True):
|
||||
fprint("reading the catalogue,", verbose)
|
||||
self._cat = self._read_catalogue(catalogue, catalogue_fpath)
|
||||
self._catname = catalogue
|
||||
|
||||
fprint("reading the interpolated field.", verbose)
|
||||
self._field_rdist, self._los_density, self._los_velocity = self._read_field( # noqa
|
||||
simname, ksim, catalogue, ksmooth, paths)
|
||||
|
||||
if len(self._cat) != self._los_density.shape[1]:
|
||||
raise ValueError("The number of objects in the catalogue does not "
|
||||
"match the number of objects in the field.")
|
||||
|
||||
fprint("calculating the radial velocity.", verbose)
|
||||
nobject = self._los_density.shape[1]
|
||||
dtype = self._los_density.dtype
|
||||
|
||||
if simname in ["Carrick2015", "Lilow2024"]:
|
||||
# Carrick+2015 and Lilow+2024 are in galactic coordinates
|
||||
d1, d2 = radec_to_galactic(self._cat["RA"], self._cat["DEC"])
|
||||
elif simname in ["CF4", "CLONES"]:
|
||||
# CF4 is in supergalactic coordinates
|
||||
d1, d2 = radec_to_supergalactic(self._cat["RA"], self._cat["DEC"])
|
||||
else:
|
||||
d1, d2 = self._cat["RA"], self._cat["DEC"]
|
||||
|
||||
num_sims = len(self._los_density)
|
||||
if "IndranilVoid" in simname:
|
||||
self._los_radial_velocity = self._los_velocity
|
||||
self._los_velocity = None
|
||||
else:
|
||||
radvel = np.empty(
|
||||
(num_sims, nobject, len(self._field_rdist)), dtype)
|
||||
for k in range(num_sims):
|
||||
for i in range(nobject):
|
||||
radvel[k, i, :] = radial_velocity_los(
|
||||
self._los_velocity[k, :, i, ...], d1[i], d2[i])
|
||||
self._los_radial_velocity = radvel
|
||||
|
||||
if not store_full_velocity:
|
||||
self._los_velocity = None
|
||||
|
||||
self._Omega_m = simname2Omega_m(simname)
|
||||
|
||||
# Normalize the CSiBORG & CLONES density by the mean matter density
|
||||
if "csiborg" in simname or simname == "CLONES":
|
||||
cosmo = FlatLambdaCDM(H0=H0, Om0=self._Omega_m)
|
||||
mean_rho_matter = cosmo.critical_density0.to("Msun/kpc^3").value
|
||||
mean_rho_matter *= self._Omega_m
|
||||
self._los_density /= mean_rho_matter
|
||||
|
||||
# Since Carrick+2015 and CF4 provide `rho / <rho> - 1`
|
||||
if simname in ["Carrick2015", "CF4", "CF4gp"]:
|
||||
self._los_density += 1
|
||||
|
||||
# But some CF4 delta values are < -1. Check that CF4 really reports
|
||||
# this.
|
||||
if simname in ["CF4", "CF4gp"]:
|
||||
self._los_density = np.clip(self._los_density, 1e-2, None,)
|
||||
|
||||
# Lilow+2024 outside of the range data is NaN. Replace it with some
|
||||
# finite values. This is OK because the PV tracers are not so far.
|
||||
if simname == "Lilow2024":
|
||||
self._los_density[np.isnan(self._los_density)] = 1.
|
||||
self._los_radial_velocity[np.isnan(self._los_radial_velocity)] = 0.
|
||||
|
||||
self._mask = np.ones(len(self._cat), dtype=bool)
|
||||
self._catname = catalogue
|
||||
|
||||
@property
|
||||
def cat(self):
|
||||
"""The distance indicators catalogue (structured array)."""
|
||||
return self._cat[self._mask]
|
||||
|
||||
@property
|
||||
def catname(self):
|
||||
"""Catalogue name."""
|
||||
return self._catname
|
||||
|
||||
@property
|
||||
def rdist(self):
|
||||
"""Radial distances at which the field was interpolated."""
|
||||
return self._field_rdist
|
||||
|
||||
@property
|
||||
def los_density(self):
|
||||
"""
|
||||
Density field along the line of sight `(n_sims, n_objects, n_steps)`
|
||||
"""
|
||||
return self._los_density[:, self._mask, ...]
|
||||
|
||||
@property
|
||||
def los_velocity(self):
|
||||
"""
|
||||
Velocity field along the line of sight `(n_sims, 3, n_objects,
|
||||
n_steps)`.
|
||||
"""
|
||||
if self._los_velocity is None:
|
||||
raise ValueError("The 3D velocities were not stored.")
|
||||
|
||||
return self._los_velocity[:, :, self._mask, ...]
|
||||
|
||||
@property
|
||||
def los_radial_velocity(self):
|
||||
"""
|
||||
Radial velocity along the line of sight `(n_sims, n_objects, n_steps)`.
|
||||
"""
|
||||
return self._los_radial_velocity[:, self._mask, ...]
|
||||
|
||||
def _read_field(self, simname, ksims, catalogue, ksmooth, paths):
|
||||
nsims = paths.get_ics(simname)
|
||||
if isinstance(ksims, int):
|
||||
ksims = [ksims]
|
||||
|
||||
# For no-field read in Carrick+2015 but then zero it.
|
||||
if simname == "no_field":
|
||||
simname = "Carrick2015"
|
||||
to_wipe = simname == "no_field"
|
||||
|
||||
if not all(0 <= ksim < len(nsims) for ksim in ksims):
|
||||
raise ValueError(f"Invalid simulation index: `{ksims}`")
|
||||
|
||||
if "Pantheon+" in catalogue:
|
||||
fpath = paths.field_los(simname, "Pantheon+")
|
||||
elif "CF4_TFR" in catalogue:
|
||||
fpath = paths.field_los(simname, "CF4_TFR")
|
||||
else:
|
||||
fpath = paths.field_los(simname, catalogue)
|
||||
|
||||
los_density = [None] * len(ksims)
|
||||
los_velocity = [None] * len(ksims)
|
||||
|
||||
for n, ksim in enumerate(ksims):
|
||||
nsim = nsims[ksim]
|
||||
|
||||
with File(fpath, 'r') as f:
|
||||
has_smoothed = True if f[f"density_{nsim}"].ndim > 2 else False
|
||||
if has_smoothed and (ksmooth is None or not isinstance(ksmooth, int)): # noqa
|
||||
raise ValueError("The output contains smoothed field but "
|
||||
"`ksmooth` is None. It must be provided.")
|
||||
|
||||
indx = (..., ksmooth) if has_smoothed else (...)
|
||||
los_density[n] = f[f"density_{nsim}"][indx]
|
||||
los_velocity[n] = f[f"velocity_{nsim}"][indx]
|
||||
rdist = f[f"rdist_{nsim}"][...]
|
||||
|
||||
los_density = np.stack(los_density)
|
||||
los_velocity = np.stack(los_velocity)
|
||||
|
||||
if to_wipe:
|
||||
los_density = np.ones_like(los_density)
|
||||
los_velocity = np.zeros_like(los_velocity)
|
||||
|
||||
return rdist, los_density, los_velocity
|
||||
|
||||
def _read_catalogue(self, catalogue, catalogue_fpath):
|
||||
if catalogue == "A2":
|
||||
with File(catalogue_fpath, 'r') as f:
|
||||
dtype = [(key, np.float32) for key in f.keys()]
|
||||
arr = np.empty(len(f["RA"]), dtype=dtype)
|
||||
for key in f.keys():
|
||||
arr[key] = f[key][:]
|
||||
elif catalogue in ["LOSS", "Foundation", "SFI_gals", "2MTF",
|
||||
"Pantheon+", "SFI_gals_masked", "SFI_groups",
|
||||
"Pantheon+_groups", "Pantheon+_groups_zSN",
|
||||
"Pantheon+_zSN"]:
|
||||
with File(catalogue_fpath, 'r') as f:
|
||||
if "Pantheon+" in catalogue:
|
||||
grp = f["Pantheon+"]
|
||||
else:
|
||||
grp = f[catalogue]
|
||||
|
||||
dtype = [(key, np.float32) for key in grp.keys()]
|
||||
arr = np.empty(len(grp["RA"]), dtype=dtype)
|
||||
for key in grp.keys():
|
||||
arr[key] = grp[key][:]
|
||||
elif "CB2_" in catalogue:
|
||||
with File(catalogue_fpath, 'r') as f:
|
||||
dtype = [(key, np.float32) for key in f.keys()]
|
||||
arr = np.empty(len(f["RA"]), dtype=dtype)
|
||||
for key in f.keys():
|
||||
arr[key] = f[key][:]
|
||||
elif "UPGLADE" in catalogue:
|
||||
with File(catalogue_fpath, 'r') as f:
|
||||
dtype = [(key, np.float32) for key in f.keys()]
|
||||
arr = np.empty(len(f["RA"]), dtype=dtype)
|
||||
for key in f.keys():
|
||||
if key == "mask":
|
||||
continue
|
||||
|
||||
arr[key] = f[key][:]
|
||||
elif catalogue in ["CF4_GroupAll"] or "CF4_TFR" in catalogue:
|
||||
with File(catalogue_fpath, 'r') as f:
|
||||
dtype = [(key, np.float32) for key in f.keys()]
|
||||
dtype += [("DEC", np.float32)]
|
||||
arr = np.empty(len(f["RA"]), dtype=dtype)
|
||||
|
||||
for key in f.keys():
|
||||
arr[key] = f[key][:]
|
||||
arr["DEC"] = arr["DE"]
|
||||
|
||||
if "CF4_TFR" in catalogue:
|
||||
arr["RA"] *= 360 / 24
|
||||
else:
|
||||
raise ValueError(f"Unknown catalogue: `{catalogue}`.")
|
||||
|
||||
return arr
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Supplementary flow functions #
|
||||
###############################################################################
|
||||
|
||||
|
||||
def radial_velocity_los(los_velocity, ra, dec):
|
||||
"""
|
||||
Calculate the radial velocity along the LOS from the 3D velocity
|
||||
along the LOS `(3, n_steps)`.
|
||||
"""
|
||||
types = (float, np.float32, np.float64)
|
||||
if not isinstance(ra, types) and not isinstance(dec, types):
|
||||
raise ValueError("RA and dec must be floats.")
|
||||
|
||||
if los_velocity.ndim != 2 and los_velocity.shape[0] != 3:
|
||||
raise ValueError("The shape of `los_velocity` must be (3, n_steps).")
|
||||
|
||||
ra_rad, dec_rad = np.deg2rad(ra), np.deg2rad(dec)
|
||||
|
||||
vx, vy, vz = los_velocity
|
||||
return (vx * np.cos(ra_rad) * np.cos(dec_rad)
|
||||
+ vy * np.sin(ra_rad) * np.cos(dec_rad)
|
||||
+ vz * np.sin(dec_rad))
|
||||
|
||||
|
||||
##############################################################################
|
||||
# Shortcut to create a model #
|
||||
###############################################################################
|
||||
|
||||
|
||||
def read_absolute_calibration(kind, data_length, calibration_fpath):
|
||||
"""
|
||||
Read the absolute calibration for the CF4 TFR sample from LEDA but
|
||||
preprocessed by me.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
kind : str
|
||||
Calibration kind: `Cepheids`, `TRGB`, `SBF`, ...
|
||||
data_length : int
|
||||
Number of samples in CF4 TFR (should be 9,788).
|
||||
calibration_fpath : str
|
||||
Path to the preprocessed calibration file.
|
||||
|
||||
Returns
|
||||
-------
|
||||
data : 3-dimensional array of shape (data_length, max_calib, 2)
|
||||
Absolute calibration data.
|
||||
with_calibration : 1-dimensional array of shape (data_length)
|
||||
Whether the sample has a calibration.
|
||||
length_calibration : 1-dimensional array of shape (data_length)
|
||||
Number of calibration points per sample.
|
||||
"""
|
||||
data = {}
|
||||
with File(calibration_fpath, 'r') as f:
|
||||
for key in f[kind].keys():
|
||||
x = f[kind][key][:]
|
||||
|
||||
# Get rid of points without uncertainties
|
||||
x = x[~np.isnan(x[:, 1])]
|
||||
|
||||
data[key] = x
|
||||
|
||||
max_calib = max(len(val) for val in data.values())
|
||||
|
||||
out = np.full((data_length, max_calib, 2), np.nan)
|
||||
with_calibration = np.full(data_length, False)
|
||||
length_calibration = np.full(data_length, 0)
|
||||
for i in data.keys():
|
||||
out[int(i), :len(data[i]), :] = data[i]
|
||||
with_calibration[int(i)] = True
|
||||
length_calibration[int(i)] = len(data[i])
|
||||
|
||||
return out, with_calibration, length_calibration
|
||||
|
||||
|
||||
def get_model(loader, zcmb_min=None, zcmb_max=None, mag_selection=None,
|
||||
absolute_calibration=None, calibration_fpath=None):
|
||||
"""
|
||||
Get a model and extract the relevant data from the loader.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
loader : DataLoader
|
||||
DataLoader instance.
|
||||
zcmb_min : float, optional
|
||||
Minimum observed redshift in the CMB frame to include.
|
||||
zcmb_max : float, optional
|
||||
Maximum observed redshift in the CMB frame to include.
|
||||
mag_selection : dict, optional
|
||||
Magnitude selection parameters.
|
||||
add_absolute_calibration : bool, optional
|
||||
Whether to add an absolute calibration for CF4 TFRs.
|
||||
calibration_fpath : str, optional
|
||||
|
||||
Returns
|
||||
-------
|
||||
model : NumPyro model
|
||||
"""
|
||||
zcmb_min = 0.0 if zcmb_min is None else zcmb_min
|
||||
zcmb_max = np.infty if zcmb_max is None else zcmb_max
|
||||
|
||||
los_overdensity = loader.los_density
|
||||
los_velocity = loader.los_radial_velocity
|
||||
kind = loader._catname
|
||||
|
||||
if absolute_calibration is not None and "CF4_TFR_" not in kind:
|
||||
raise ValueError("Absolute calibration supported only for the CF4 TFR sample.") # noqa
|
||||
|
||||
if kind in ["LOSS", "Foundation"]:
|
||||
keys = ["RA", "DEC", "z_CMB", "mB", "x1", "c", "e_mB", "e_x1", "e_c"]
|
||||
RA, dec, zCMB, mag, x1, c, e_mag, e_x1, e_c = (
|
||||
loader.cat[k] for k in keys)
|
||||
e_zCMB = None
|
||||
|
||||
mask = (zCMB < zcmb_max) & (zCMB > zcmb_min)
|
||||
calibration_params = {"mag": mag[mask], "x1": x1[mask], "c": c[mask],
|
||||
"e_mag": e_mag[mask], "e_x1": e_x1[mask],
|
||||
"e_c": e_c[mask]}
|
||||
|
||||
model = PV_LogLikelihood(
|
||||
los_overdensity[:, mask], los_velocity[:, mask],
|
||||
RA[mask], dec[mask], zCMB[mask], e_zCMB, calibration_params,
|
||||
None, mag_selection, loader.rdist, loader._Omega_m, "SN",
|
||||
name=kind)
|
||||
elif "Pantheon+" in kind:
|
||||
keys = ["RA", "DEC", "zCMB", "mB", "x1", "c", "biasCor_m_b", "mBERR",
|
||||
"x1ERR", "cERR", "biasCorErr_m_b", "zCMB_SN", "zCMB_Group",
|
||||
"zCMBERR"]
|
||||
|
||||
RA, dec, zCMB, mB, x1, c, bias_corr_mB, e_mB, e_x1, e_c, e_bias_corr_mB, zCMB_SN, zCMB_Group, e_zCMB = (loader.cat[k] for k in keys) # noqa
|
||||
mB -= bias_corr_mB
|
||||
e_mB = np.sqrt(e_mB**2 + e_bias_corr_mB**2)
|
||||
|
||||
mask = (zCMB < zcmb_max) & (zCMB > zcmb_min)
|
||||
|
||||
if kind == "Pantheon+_groups":
|
||||
mask &= np.isfinite(zCMB_Group)
|
||||
|
||||
if kind == "Pantheon+_groups_zSN":
|
||||
mask &= np.isfinite(zCMB_Group)
|
||||
zCMB = zCMB_SN
|
||||
|
||||
if kind == "Pantheon+_zSN":
|
||||
zCMB = zCMB_SN
|
||||
|
||||
calibration_params = {"mag": mB[mask], "x1": x1[mask], "c": c[mask],
|
||||
"e_mag": e_mB[mask], "e_x1": e_x1[mask],
|
||||
"e_c": e_c[mask]}
|
||||
model = PV_LogLikelihood(
|
||||
los_overdensity[:, mask], los_velocity[:, mask],
|
||||
RA[mask], dec[mask], zCMB[mask], e_zCMB[mask], calibration_params,
|
||||
None, mag_selection, loader.rdist, loader._Omega_m, "SN",
|
||||
name=kind)
|
||||
elif kind in ["SFI_gals", "2MTF", "SFI_gals_masked"]:
|
||||
keys = ["RA", "DEC", "z_CMB", "mag", "eta", "e_mag", "e_eta"]
|
||||
RA, dec, zCMB, mag, eta, e_mag, e_eta = (loader.cat[k] for k in keys)
|
||||
|
||||
mask = (zCMB < zcmb_max) & (zCMB > zcmb_min)
|
||||
calibration_params = {"mag": mag[mask], "eta": eta[mask],
|
||||
"e_mag": e_mag[mask], "e_eta": e_eta[mask]}
|
||||
model = PV_LogLikelihood(
|
||||
los_overdensity[:, mask], los_velocity[:, mask],
|
||||
RA[mask], dec[mask], zCMB[mask], None, calibration_params, None,
|
||||
mag_selection, loader.rdist, loader._Omega_m, "TFR", name=kind)
|
||||
elif "CF4_TFR_" in kind:
|
||||
# The full name can be e.g. "CF4_TFR_not2MTForSFI_i" or "CF4_TFR_i".
|
||||
band = kind.split("_")[-1]
|
||||
if band not in ['g', 'r', 'i', 'z', 'w1', 'w2']:
|
||||
raise ValueError(f"Band `{band}` not recognized.")
|
||||
|
||||
keys = ["RA", "DEC", "Vcmb", f"{band}", "lgWmxi", "elgWi",
|
||||
"not_matched_to_2MTF_or_SFI", "Qs", "Qw"]
|
||||
RA, dec, z_obs, mag, eta, e_eta, not_matched_to_2MTF_or_SFI, Qs, Qw = (
|
||||
loader.cat[k] for k in keys)
|
||||
l, b = radec_to_galactic(RA, dec)
|
||||
|
||||
not_matched_to_2MTF_or_SFI = not_matched_to_2MTF_or_SFI.astype(bool)
|
||||
# NOTE: fiducial uncertainty until we can get the actual values.
|
||||
e_mag = 0.05 * np.ones_like(mag)
|
||||
|
||||
z_obs /= SPEED_OF_LIGHT
|
||||
eta -= 2.5
|
||||
|
||||
fprint("selecting only galaxies with mag > 5 and eta > -0.3.")
|
||||
mask = (mag > 5) & (eta > -0.3)
|
||||
fprint("selecting only galaxies with |b| > 7.5.")
|
||||
mask &= np.abs(b) > 7.5
|
||||
mask &= (z_obs < zcmb_max) & (z_obs > zcmb_min)
|
||||
|
||||
if "not2MTForSFI" in kind:
|
||||
mask &= not_matched_to_2MTF_or_SFI
|
||||
elif "2MTForSFI" in kind:
|
||||
mask &= ~not_matched_to_2MTF_or_SFI
|
||||
|
||||
fprint("employing a quality cut on the galaxies.")
|
||||
if "w" in band:
|
||||
mask &= Qw == 5
|
||||
else:
|
||||
mask &= Qs == 5
|
||||
|
||||
# Read the absolute calibration
|
||||
if absolute_calibration is not None:
|
||||
CF4_length = len(RA)
|
||||
distmod, with_calibration, length_calibration = read_absolute_calibration( # noqa
|
||||
"Cepheids", CF4_length, calibration_fpath)
|
||||
|
||||
distmod = distmod[mask]
|
||||
with_calibration = with_calibration[mask]
|
||||
length_calibration = length_calibration[mask]
|
||||
fprint(f"found {np.sum(with_calibration)} galaxies with absolute calibration.") # noqa
|
||||
|
||||
distmod = distmod[with_calibration]
|
||||
length_calibration = length_calibration[with_calibration]
|
||||
|
||||
abs_calibration_params = {
|
||||
"calibration_distmod": distmod,
|
||||
"data_with_calibration": with_calibration,
|
||||
"length_calibration": length_calibration}
|
||||
else:
|
||||
abs_calibration_params = None
|
||||
|
||||
calibration_params = {"mag": mag[mask], "eta": eta[mask],
|
||||
"e_mag": e_mag[mask], "e_eta": e_eta[mask]}
|
||||
model = PV_LogLikelihood(
|
||||
los_overdensity[:, mask], los_velocity[:, mask],
|
||||
RA[mask], dec[mask], z_obs[mask], None, calibration_params,
|
||||
abs_calibration_params, mag_selection, loader.rdist,
|
||||
loader._Omega_m, "TFR", name=kind)
|
||||
elif kind in ["CF4_GroupAll"]:
|
||||
# Note, this for some reason works terribly.
|
||||
keys = ["RA", "DE", "Vcmb", "DMzp", "eDM"]
|
||||
RA, dec, zCMB, mu, e_mu = (loader.cat[k] for k in keys)
|
||||
|
||||
zCMB /= SPEED_OF_LIGHT
|
||||
mask = (zCMB < zcmb_max) & (zCMB > zcmb_min) & np.isfinite(mu)
|
||||
|
||||
# The distance moduli in CF4 are most likely given assuming h = 0.75
|
||||
mu += 5 * np.log10(0.75)
|
||||
|
||||
calibration_params = {"mu": mu[mask], "e_mu": e_mu[mask]}
|
||||
model = PV_LogLikelihood(
|
||||
los_overdensity[:, mask], los_velocity[:, mask],
|
||||
RA[mask], dec[mask], zCMB[mask], None, calibration_params, None,
|
||||
mag_selection, loader.rdist, loader._Omega_m, "simple",
|
||||
name=kind)
|
||||
else:
|
||||
raise ValueError(f"Catalogue `{kind}` not recognized.")
|
||||
|
||||
fprint(f"selected {np.sum(mask)}/{len(mask)} galaxies in catalogue `{kind}`") # noqa
|
||||
|
||||
return model
|
||||
Loading…
Add table
Reference in a new issue