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Direct distance sampling (#155)

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* Update nb

* Update dependency

* Pass marg arg

* Add mu sampling

* Update imprts

* Move cosmography to a ceparate module

* Add mock void

* Check Vext likelihoo

* Add void mock

* Add void mocks
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Richard Stiskalek 2024-10-07 22:16:35 +02:00 committed by GitHub
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3
csiborgtools/flow/__init__.py
View file

@ -18,4 +18,5 @@ from .flow_model import (PV_LogLikelihood, PV_validation_model, dist2redshift,
Observed2CosmologicalRedshift, predict_zobs, # noqa
project_Vext, stack_pzosmo_over_realizations) # noqa
from .selection import ToyMagnitudeSelection # noqa
from .void_model import load_void_data, interpolate_void # noqa
from .void_model import (load_void_data, interpolate_void, select_void_h, # noqa
mock_void) # noqa

94
csiborgtools/flow/cosmography.py Normal file
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@ -0,0 +1,94 @@
# 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.
"""Various cosmography functions for converting between distance indicators."""
from jax import numpy as jnp
from ..params import SPEED_OF_LIGHT
H0 = 100 # km / s / Mpc
def dist2redshift(dist, Omega_m, h=1.):
"""
Convert comoving distance to cosmological redshift if the Universe is
flat and z << 1.
"""
eta = 3 * Omega_m / 2
return 1 / eta * (1 - (1 - 2 * 100 * h * dist / SPEED_OF_LIGHT * eta)**0.5)
def redshift2dist(z, Omega_m):
"""
Convert cosmological redshift to comoving distance if the Universe is
flat and z << 1.
"""
q0 = 3 * Omega_m / 2 - 1
return SPEED_OF_LIGHT * z / (2 * H0) * (2 - z * (1 + q0))
def gradient_redshift2dist(z, Omega_m):
"""
Gradient of the redshift to comoving distance conversion if the Universe is
flat and z << 1.
"""
q0 = 3 * Omega_m / 2 - 1
return SPEED_OF_LIGHT / H0 * (1 - z * (1 + q0))
def distmod2dist(mu, Om0):
"""
Convert distance modulus to distance in `Mpc / h`. The expression is valid
for a flat universe over the range of 0.00001 < z < 0.1.
"""
term1 = jnp.exp((0.443288 * mu) + (-14.286531))
term2 = (0.506973 * mu) + 12.954633
term3 = ((0.028134 * mu) ** (
((0.684713 * mu)
+ ((0.151020 * mu) + (1.235158 * Om0))) - jnp.exp(0.072229 * mu)))
term4 = (-0.045160) * mu
return (-0.000301) + (term1 * (term2 - (term3 - term4)))
def distmod2dist_gradient(mu, Om0):
"""
Calculate the derivative of comoving distance in `Mpc / h` with respect to
the distance modulus. The expression is valid for a flat universe over the
range of 0.00001 < z < 0.1.
"""
term1 = jnp.exp((0.443288 * mu) + (-14.286531))
dterm1 = 0.443288 * term1
term2 = (0.506973 * mu) + 12.954633
dterm2 = 0.506973
term3 = ((0.028134 * mu)**(((0.684713 * mu) + ((0.151020 * mu) + (1.235158 * Om0))) - jnp.exp(0.072229 * mu))) # noqa
ln_base = jnp.log(0.028134) + jnp.log(mu)
exponent = 0.835733 * mu + 1.235158 * Om0 - jnp.exp(0.072229 * mu)
exponent_derivative = 0.835733 - 0.072229 * jnp.exp(0.072229 * mu)
dterm3 = term3 * ((1 / mu) * exponent + exponent_derivative * ln_base)
term4 = (-0.045160) * mu
dterm4 = -0.045160
return (dterm1 * (term2 - (term3 - term4))
+ term1 * (dterm2 - (dterm3 - dterm4)))
def distmod2redshift(mu, Om0):
"""
Convert distance modulus to redshift, assuming `h = 1`. The expression is
valid for a flat universe over the range of 0.00001 < z < 0.1.
"""
return jnp.exp(((0.461108 * mu) - ((0.022187 * Om0) + (((0.022347 * mu)** (12.631788 - ((-6.708757) * Om0))) + 19.529852)))) # noqa

180
csiborgtools/flow/flow_model.py
View file

@ -25,10 +25,11 @@ from abc import ABC, abstractmethod
import numpy as np
from astropy import units as u
from astropy.coordinates import SkyCoord, angular_separation
from astropy.cosmology import FlatLambdaCDM, z_at_value
from interpax import interp1d
from jax import jit
from jax import numpy as jnp
from jax import vmap
from jax.scipy.special import erf, logsumexp
from numpyro import factor, plate, sample
from numpyro.distributions import MultivariateNormal, Normal, Uniform
@ -37,57 +38,19 @@ from tqdm import trange
from ..params import SPEED_OF_LIGHT
from ..utils import fprint
from .cosmography import (dist2redshift, distmod2dist, distmod2dist_gradient,
distmod2redshift, gradient_redshift2dist)
from .selection import toy_log_magnitude_selection
from .void_model import interpolate_void, load_void_data
from .void_model import (angular_distance_from_void_axis, interpolate_void,
load_void_data)
H0 = 100 # km / s / Mpc
###############################################################################
# JAX Flow model #
# Various flow utilities #
###############################################################################
def dist2redshift(dist, Omega_m, h=1.):
"""
Convert comoving distance to cosmological redshift if the Universe is
flat and z << 1.
"""
eta = 3 * Omega_m / 2
return 1 / eta * (1 - (1 - 2 * 100 * h * dist / SPEED_OF_LIGHT * eta)**0.5)
def redshift2dist(z, Omega_m):
"""
Convert cosmological redshift to comoving distance if the Universe is
flat and z << 1.
"""
q0 = 3 * Omega_m / 2 - 1
return SPEED_OF_LIGHT * z / (2 * H0) * (2 - z * (1 + q0))
def gradient_redshift2dist(z, Omega_m):
"""
Gradient of the redshift to comoving distance conversion if the Universe is
flat and z << 1.
"""
q0 = 3 * Omega_m / 2 - 1
return SPEED_OF_LIGHT / H0 * (1 - z * (1 + q0))
def distmod2dist(mu, Om0):
"""
Convert distance modulus to distance in `Mpc / h`. The expression is valid
for a flat universe over the range of 0.00001 < z < 0.1.
"""
term1 = jnp.exp((0.443288 * mu) + (-14.286531))
term2 = (0.506973 * mu) + 12.954633
term3 = ((0.028134 * mu) ** (
((0.684713 * mu)
+ ((0.151020 * mu) + (1.235158 * Om0))) - jnp.exp(0.072229 * mu)))
term4 = (-0.045160) * mu
return (-0.000301) + (term1 * (term2 - (term3 - term4)))
def project_Vext(Vext_x, Vext_y, Vext_z, RA_radians, dec_radians):
"""Project the external velocity vector onto the line of sight."""
cos_dec = jnp.cos(dec_radians)
@ -150,6 +113,37 @@ def upper_truncated_normal_logpdf(x, loc, scale, xmax):
return normal_logpdf(x, loc, scale) - jnp.log(norm)
###############################################################################
# LOS interpolation #
###############################################################################
def interpolate_los(r, los, rgrid, method="cubic"):
"""
Interpolate the LOS field at a given radial distance.
Parameters
----------
r : 1-dimensional array of shape `(n_gal, )`
Radial distances at which to interpolate the LOS field.
los : 3-dimensional array of shape `(n_sims, n_gal, n_steps)`
LOS field.
rmin, rmax : float
Minimum and maximum radial distances in the data.
order : int, optional
The order of the interpolation. Default is 1, can be 0.
Returns
-------
2-dimensional array of shape `(n_sims, n_gal)`
"""
# Vectorize over the inner loop (ngal) first, then the outer loop (nsim)
def f(rn, los_row):
return interp1d(rn, rgrid, los_row, method=method)
return vmap(vmap(f, in_axes=(0, 0)), in_axes=(None, 0))(r, los)
###############################################################################
# Base flow validation #
###############################################################################
@ -232,17 +226,12 @@ class BaseFlowValidationModel(ABC):
rLG_grid *= h
rLG_min, rLG_max = rLG_grid.min(), rLG_grid.max()
rgrid_min, rgrid_max = 0, 250
fprint(f"setting radial grid from {rLG_min} to {rLG_max} Mpc.")
fprint(f"setting radial grid from {rLG_min} to {rLG_max} Mpc / h.")
rgrid_max *= h
# Get angular separation (in degrees) of each object from the model
# axis.
model_axis = SkyCoord(l=117, b=4, frame='galactic', unit='deg').icrs
coords = SkyCoord(ra=RA, dec=dec, unit='deg').icrs
phi = angular_separation(coords.ra.rad, coords.dec.rad,
model_axis.ra.rad, model_axis.dec.rad)
phi = jnp.asarray(phi * 180 / np.pi, dtype=jnp.float32)
# Get angular separation of each object from the model axis.
phi = angular_distance_from_void_axis(RA, dec)
phi = jnp.asarray(phi, dtype=jnp.float32)
if kind == "density":
void_grid = jnp.log(void_grid)
@ -291,6 +280,12 @@ class BaseFlowValidationModel(ABC):
return self._los_velocity
def log_los_density_at_r(self, r):
return interpolate_los(r, self.log_los_density(), self.r_xrange, )
def los_velocity_at_r(self, r):
return interpolate_los(r, self.los_velocity(), self.r_xrange, )
@abstractmethod
def __call__(self, **kwargs):
pass
@ -514,16 +509,16 @@ class PV_LogLikelihood(BaseFlowValidationModel):
Name of the catalogue.
void_kwargs : dict, optional
Void data parameters. If `None` the data is not void data.
with_num_dist_marginalisation : bool, optional
Whether to use numerical distance marginalisation, in which case
the tracers cannot be coupled by a covariance matrix. By default
`True`.
wo_num_dist_marginalisation : bool, optional
Whether to directly sample the distance without numerical
marginalisation. in which case the tracers can be coupled by a
covariance matrix. By default `False`.
"""
def __init__(self, los_density, los_velocity, RA, dec, z_obs, e_zobs,
calibration_params, abs_calibration_params, mag_selection,
r_xrange, Omega_m, kind, name, void_kwargs=None,
with_num_dist_marginalisation=True):
wo_num_dist_marginalisation=False):
if e_zobs is not None:
e2_cz_obs = jnp.asarray((SPEED_OF_LIGHT * e_zobs)**2)
else:
@ -549,7 +544,7 @@ class PV_LogLikelihood(BaseFlowValidationModel):
values += [jnp.log(los_density), los_velocity]
# Density required only if not numerically marginalising.
if not with_num_dist_marginalisation:
if not wo_num_dist_marginalisation:
names += ["_los_density"]
values += [los_density]
@ -561,12 +556,9 @@ class PV_LogLikelihood(BaseFlowValidationModel):
self.kind = kind
self.name = name
self.Omega_m = Omega_m
self.with_num_dist_marginalisation = with_num_dist_marginalisation
self.wo_num_dist_marginalisation = wo_num_dist_marginalisation
self.norm = - self.ndata * jnp.log(self.num_sims)
# TODO: Somewhere here prepare the interpolators in case of no
# numerical marginalisation.
if mag_selection is not None:
self.mag_selection_kind = mag_selection["kind"]
@ -767,30 +759,20 @@ class PV_LogLikelihood(BaseFlowValidationModel):
else:
raise ValueError(f"Unknown kind: `{self.kind}`.")
# h = field_calibration_params["h"]
# ----------------------------------------------------------------
# 2. Log-likelihood of the true distance and observed redshifts.
# The marginalisation of the true distance can be done numerically.
# ----------------------------------------------------------------
if self.with_num_dist_marginalisation:
if not self.wo_num_dist_marginalisation:
if field_calibration_params["sample_h"]:
raise NotImplementedError("Sampling of h not implemented.")
# Rescale the grid to account for the sampled H0. For distance
# modulus going from Mpc / h to Mpc implies larger numerical
# values, so there has to be a minus sign since h < 1.
# mu_xrange = self.mu_xrange - 5 * jnp.log(h)
# The redshift should also be boosted since now the object are
# further away?
# Actually, the redshift ought to remain the same?
else:
mu_xrange = self.mu_xrange
raise NotImplementedError(
"Sampling of 'h' is not supported if numerically "
"marginalising the true distance.")
# Calculate p(r) (Malmquist bias). Shape is (ndata, nxrange)
log_ptilde = log_ptilde_wo_bias(
mu_xrange[None, :], mu[:, None], e2_mu[:, None],
self.mu_xrange[None, :], mu[:, None], e2_mu[:, None],
self.log_r2_xrange[None, :])
if self.is_void_data:
@ -832,56 +814,52 @@ class PV_LogLikelihood(BaseFlowValidationModel):
return ll0 + jnp.sum(logsumexp(ll, axis=0)) + self.norm
else:
if field_calibration_params["sample_h"]:
raise NotImplementedError("Sampling of h not implemented.")
raise NotImplementedError(
"Sampling of distance is not implemented. Work in progress.")
raise NotImplementedError(
"Sampling of h is not yet implemented.")
e_mu = jnp.sqrt(e2_mu)
# True distance modulus, shape is `(n_data)``
with plate("plate_mu", self.ndata):
mu_true = sample("mu", Normal(mu, e_mu))
# True distance, shape is `(n_data)``
# True distance and redshift, shape is `(n_data)`.
r_true = distmod2dist(mu_true, self.Omega_m)
# TODO:
z_true = None
z_true = distmod2redshift(mu_true, self.Omega_m)
if self.is_void_data:
raise NotImplementedError(
"Void data not implemented yet for distance sampling.")
else:
# grid log(density), shape is `(n_sims, n_data, n_rad)`
log_los_density_grid = self.los_density()
# TODO: Need to add the interpolators for these
# Grid log(density), shape is `(n_sims, n_data, n_rad)`
log_los_density_grid = self.log_los_density()
# Densities and velocities at the true distances, shape is
# `(n_sims, n_data)`
log_density = None
los_velocity = None
log_density = self.log_los_density_at_r(r_true)
los_velocity = self.los_velocity_at_r(r_true)
alpha = distmod_params["alpha"]
# Check dimensions of all this
# Normalisation of p(mu), shape is `(n_sims, n_data, n_rad)`
pnorm = (
self.log_r2_xrange[None, None, :]
+ self.log_r2_xrange[None, None, :]
+ alpha * log_los_density_grid
+ normal_logpdf(
self.mu_xrange[None, :], mu[:, None], e_mu[:, None])[None, ...]) # noqa
pnorm = jnp.exp(pnorm)
# Normalization of p(mu). Shape is now (nsims, ndata)
# Now integrate over the radial steps. Shape is `(nsims, ndata)`.
# No Jacobian here because I integrate over distance, not the
# distance modulus.
pnorm = simpson(pnorm, x=self.r_xrange, axis=-1)
# TODO: There should be a Jacobian?
# Jacobian |dr / dmu|_(mu_true), shape is `(n_data)`.
jac = jnp.abs(distmod2dist_gradient(mu_true, self.Omega_m))
# Calculate unnormalized log p(mu). Shape is (nsims, ndata)
ll = (
2 * (jnp.log(r_true) - self.log_r2_xrange_mean)[None, :]
+ jnp.log(jac)[None, :]
+ (2 * jnp.log(r_true) - self.log_r2_xrange_mean)[None, :]
+ alpha * log_density
+ normal_logpdf(mu_true, mu, e_mu)[None, :])
)
# Subtract the normalization. Shape remains (nsims, ndata)
ll -= jnp.log(pnorm)
@ -933,7 +911,7 @@ def PV_validation_model(models, distmod_hyperparams_per_model,
# We sample the components of Vext with a uniform prior, which means
# there is a |Vext|^2 prior, we correct for this so that the sampling
# is effecitvely uniformly in magnitude of Vext and angles.
if "Vext" in field_calibration_params:
if "Vext" in field_calibration_params and not field_calibration_hyperparams["no_Vext"]: # noqa
ll -= jnp.log(jnp.sum(field_calibration_params["Vext"]**2))
for n in range(len(models)):

46
csiborgtools/flow/io.py
View file

@ -20,6 +20,7 @@ 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
from .void_model import load_void_data, mock_void, select_void_h
H0 = 100 # km / s / Mpc
@ -242,6 +243,25 @@ class DataLoader:
arr = np.empty(len(f["RA"]), dtype=dtype)
for key in f.keys():
arr[key] = f[key][:]
elif "IndranilVoidTFRMock" in catalogue:
# The name can be e.g. "IndranilVoidTFRMock_exp_34_0", where the
# first and second number are the LG observer index and random
# seed.
profile, rLG_index, seed = catalogue.split("_")[1:]
rLG_index = int(rLG_index)
seed = int(seed)
rLG, vrad_data = load_void_data(profile, "vrad")
h = select_void_h(profile)
print(f"Mock observed galaxies for LG observer with index "
f"{rLG_index} at {rLG[rLG_index] * h} Mpc / h and "
f"seed {seed}.")
mock_data = mock_void(vrad_data, rLG_index, profile, seed=seed)[0]
# Convert the dictionary to a structured array
dtype = [(key, np.float32) for key in mock_data.keys()]
arr = np.empty(len(mock_data["RA"]), dtype=dtype)
for key in mock_data.keys():
arr[key] = mock_data[key]
elif "UPGLADE" in catalogue:
with File(catalogue_fpath, 'r') as f:
dtype = [(key, np.float32) for key in f.keys()]
@ -354,8 +374,8 @@ def mask_fields(density, velocity, mask, return_none):
def get_model(loader, zcmb_min=None, zcmb_max=None, mag_selection=None,
absolute_calibration=None, calibration_fpath=None,
void_kwargs=None):
wo_num_dist_marginalisation=False, absolute_calibration=None,
calibration_fpath=None, void_kwargs=None):
"""
Get a model and extract the relevant data from the loader.
@ -369,9 +389,14 @@ def get_model(loader, zcmb_min=None, zcmb_max=None, mag_selection=None,
Maximum observed redshift in the CMB frame to include.
mag_selection : dict, optional
Magnitude selection parameters.
wo_num_dist_marginalisation : bool, optional
Whether to directly sample the distance without numerical
marginalisation. in which case the tracers can be coupled by a
covariance matrix. By default `False`.
add_absolute_calibration : bool, optional
Whether to add an absolute calibration for CF4 TFRs.
calibration_fpath : str, optional
Path to the file containing the absolute calibration of CF4 TFR.
Returns
-------
@ -418,7 +443,8 @@ def get_model(loader, zcmb_min=None, zcmb_max=None, mag_selection=None,
los_overdensity, los_velocity,
RA[mask], dec[mask], zCMB[mask], e_zCMB, calibration_params,
None, mag_selection, loader.rdist, loader._Omega_m, "SN",
name=kind, void_kwargs=void_kwargs)
name=kind, void_kwargs=void_kwargs,
wo_num_dist_marginalisation=wo_num_dist_marginalisation)
elif "Pantheon+" in kind:
keys = ["RA", "DEC", "zCMB", "mB", "x1", "c", "biasCor_m_b", "mBERR",
"x1ERR", "cERR", "biasCorErr_m_b", "zCMB_SN", "zCMB_Group",
@ -451,8 +477,9 @@ def get_model(loader, zcmb_min=None, zcmb_max=None, mag_selection=None,
los_overdensity, los_velocity,
RA[mask], dec[mask], zCMB[mask], e_zCMB[mask], calibration_params,
None, mag_selection, loader.rdist, loader._Omega_m, "SN",
name=kind, void_kwargs=void_kwargs)
elif kind in ["SFI_gals", "2MTF", "SFI_gals_masked"]:
name=kind, void_kwargs=void_kwargs,
wo_num_dist_marginalisation=wo_num_dist_marginalisation)
elif kind in ["SFI_gals", "2MTF", "SFI_gals_masked"] or "IndranilVoidTFRMock" in kind: # noqa
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)
@ -467,7 +494,8 @@ def get_model(loader, zcmb_min=None, zcmb_max=None, mag_selection=None,
los_overdensity, los_velocity,
RA[mask], dec[mask], zCMB[mask], None, calibration_params, None,
mag_selection, loader.rdist, loader._Omega_m, "TFR", name=kind,
void_kwargs=void_kwargs)
void_kwargs=void_kwargs,
wo_num_dist_marginalisation=wo_num_dist_marginalisation)
elif "CF4_TFR_" in kind:
# The full name can be e.g. "CF4_TFR_not2MTForSFI_i" or "CF4_TFR_i".
band = kind.split("_")[-1]
@ -535,7 +563,8 @@ def get_model(loader, zcmb_min=None, zcmb_max=None, mag_selection=None,
los_overdensity, los_velocity,
RA[mask], dec[mask], z_obs[mask], None, calibration_params,
abs_calibration_params, mag_selection, loader.rdist,
loader._Omega_m, "TFR", name=kind, void_kwargs=void_kwargs)
loader._Omega_m, "TFR", name=kind, void_kwargs=void_kwargs,
wo_num_dist_marginalisation=wo_num_dist_marginalisation)
elif kind in ["CF4_GroupAll"]:
# Note, this for some reason works terribly.
keys = ["RA", "DE", "Vcmb", "DMzp", "eDM"]
@ -556,7 +585,8 @@ def get_model(loader, zcmb_min=None, zcmb_max=None, mag_selection=None,
los_overdensity, los_velocity,
RA[mask], dec[mask], zCMB[mask], None, calibration_params, None,
mag_selection, loader.rdist, loader._Omega_m, "simple",
name=kind, void_kwargs=void_kwargs)
name=kind, void_kwargs=void_kwargs,
wo_num_dist_marginalisation=wo_num_dist_marginalisation)
else:
raise ValueError(f"Catalogue `{kind}` not recognized.")

142
csiborgtools/flow/void_model.py
View file

@ -19,11 +19,44 @@ from os.path import join
from re import search
import numpy as np
from astropy.coordinates import SkyCoord, angular_separation
from jax import numpy as jnp
from jax import vmap
from jax.scipy.ndimage import map_coordinates
from scipy.interpolate import RegularGridInterpolator
from tqdm import tqdm
from ..utils import galactic_to_radec
from ..params import SPEED_OF_LIGHT
from .cosmography import distmod2dist, distmod2redshift
###############################################################################
# Basic void computations #
###############################################################################
def angular_distance_from_void_axis(RA, dec):
"""
Calculate the angular distance of a galaxy from the void axis, all in
degrees.
"""
# Calculate the separation angle between the galaxy and the model axis.
model_axis = SkyCoord(l=117, b=4, frame='galactic', unit='deg').icrs
coords = SkyCoord(ra=RA, dec=dec, unit='deg').icrs
return angular_separation(
coords.ra.rad, coords.dec.rad,
model_axis.ra.rad, model_axis.dec.rad) * 180 / np.pi
def select_void_h(kind):
"""Select 'little h' for void profile `kind`."""
hs = {"mb": 0.7615, "gauss": 0.7724, "exp": 0.7725}
try:
return hs[kind]
except KeyError:
raise ValueError(f"Unknown void kind: `{kind}`.")
###############################################################################
# I/O of the void data #
###############################################################################
@ -97,9 +130,9 @@ def interpolate_void(rLG, r, phi, data, rgrid_min, rgrid_max, rLG_min, rLG_max,
----------
rLG : float
The observer's distance from the center of the void.
r : 1-dimensional array
r : 1-dimensional array of shape `(nsteps,)
The radial distances at which to interpolate the velocities.
phi : 1-dimensional array
phi : 1-dimensional array of shape `(ngal,)`
The angles at which to interpolate the velocities, in degrees,
defining the galaxy position.
data : 3-dimensional array of shape (nLG, nrad, nphi)
@ -114,7 +147,7 @@ def interpolate_void(rLG, r, phi, data, rgrid_min, rgrid_max, rLG_min, rLG_max,
Returns
-------
vel : 2-dimensional array of shape (len(phi), len(r))
vel : 2-dimensional array of shape `(ngal, nsteps)`
"""
nLG, nrad, nphi = data.shape
@ -139,3 +172,106 @@ def interpolate_void(rLG, r, phi, data, rgrid_min, rgrid_max, rLG_min, rLG_max,
return map_coordinates(data, X, order=order, mode='nearest')
return vmap(interpolate_single_phi)(phi)
###############################################################################
# Mock void data #
###############################################################################
def mock_void(vrad_data, rLG_index, profile,
a_TF=-22.8, b_TF=-7.2, sigma_TF=0.1, sigma_v=100.,
mean_eta=0.069, std_eta=0.078, mean_e_eta=0.012,
mean_mag=10.31, std_mag=0.83, mean_e_mag=0.044,
bmin=None, add_malmquist=False, nsamples=2000, seed=42,
Om0=0.3175, verbose=False, **kwargs):
"""Mock 2MTF-like TFR data with void velocities."""
truths = {"a": a_TF, "b": b_TF, "e_mu": sigma_TF, "sigma_v": sigma_v,
"mean_eta": mean_eta, "std_eta": std_eta,
"mean_mag": mean_mag, "std_mag": std_mag,
}
gen = np.random.default_rng(seed)
# Sample the sky-distribution, either full-sky or mask out the Galactic
# plane.
l = gen.uniform(0, 360, size=nsamples) # noqa
if bmin is None:
b = np.arcsin(gen.uniform(-1, 1, size=nsamples))
else:
b = np.arcsin(gen.uniform(np.sin(np.deg2rad(bmin)), 1,
size=nsamples))
b[gen.rand(nsamples) < 0.5] *= -1
b = np.rad2deg(b)
RA, DEC = galactic_to_radec(l, b)
# Calculate the angular separation from the void axis, in degrees.
phi = angular_distance_from_void_axis(RA, DEC)
# Sample the linewidth of each galaxy from a Gaussian distribution to mimic
# the MNR procedure.
eta_true = gen.normal(mean_eta, std_eta, nsamples)
eta_obs = gen.normal(eta_true, mean_e_eta)
# Subtract the mean of the observed linewidths, so that they are
# centered around zero. For consistency subtract from both observed
# and true values.
eta_mean_sampled = np.mean(eta_obs)
eta_true -= eta_mean_sampled
eta_obs -= eta_mean_sampled
# Sample the magnitude from some Gaussian distribution to replicate MNR.
mag_true = gen.normal(mean_mag, std_mag, nsamples)
mag_obs = gen.normal(mag_true, mean_e_mag)
# Calculate the 'true' distance modulus and redshift from the TFR distance.
mu_TFR = mag_true - (a_TF + b_TF * eta_true)
if add_malmquist:
raise NotImplementedError("Malmquist bias not implemented yet.")
else:
mu_true = gen.normal(mu_TFR, sigma_TF)
# Convert the true distance modulus to true distance and cosmological
# redshift.
r = distmod2dist(mu_true, Om0)
zcosmo = distmod2redshift(mu_true, Om0)
# Little h of this void profile
h = select_void_h(profile)
# Extract the velocities for the galaxies from the grid for this LG
# index.
vrad_data_rLG = vrad_data[rLG_index]
r_grid = np.arange(0, 251) * h
phi_grid = np.arange(0, 181)
Vr = RegularGridInterpolator((r_grid, phi_grid), vrad_data_rLG,
fill_value=np.nan, bounds_error=False,
method="cubic")(np.vstack([r, phi]).T)
# The true redshift of the source.
zCMB_true = (1 + zcosmo) * (1 + Vr / SPEED_OF_LIGHT) - 1
zCMB_obs = gen.normal(zCMB_true, sigma_v / SPEED_OF_LIGHT)
sample = {"RA": RA,
"DEC": DEC,
"z_CMB": zCMB_obs,
"eta": eta_obs,
"mag": mag_obs,
"e_eta": np.ones(nsamples) * mean_e_eta,
"e_mag": np.ones(nsamples) * mean_e_mag,
"r": r,
"distmod_true": mu_true,
"distmod_TFR": mu_TFR}
# Apply a true distance cut to the mocks.
mask = r < np.max(r_grid)
for key in sample:
sample[key] = sample[key][mask]
if verbose and np.any(~mask):
print(f"Removed {(~mask).sum()} out of {mask.size} samples "
"due to the true distance cutoff.")
return sample, truths

746
notebooks/flow/reconstruction_comparison.ipynb
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File diff suppressed because one or more lines are too long

28
scripts/flow/flow_validation.py
View file

@ -88,7 +88,7 @@ def print_variables(names, variables):
def get_models(ksim, get_model_kwargs, mag_selection, void_kwargs,
verbose=True):
wo_num_dist_marginalisation, verbose=True):
"""Load the data and create the NumPyro models."""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
folder = "/mnt/extraspace/rstiskalek/catalogs/"
@ -120,6 +120,8 @@ def get_models(ksim, get_model_kwargs, mag_selection, void_kwargs,
fpath = join(folder, "PV/CF4/CF4_TF-distances.hdf5")
elif cat in ["CF4_GroupAll"]:
fpath = join(folder, "PV/CF4/CF4_GroupAll.hdf5")
elif "IndranilVoidTFRMock" in cat:
fpath = None
else:
raise ValueError(f"Unsupported catalogue: `{ARGS.catalogue}`.")
@ -128,20 +130,13 @@ def get_models(ksim, get_model_kwargs, mag_selection, void_kwargs,
ksmooth=ARGS.ksmooth)
models[i] = csiborgtools.flow.get_model(
loader, mag_selection=mag_selection[i], void_kwargs=void_kwargs,
wo_num_dist_marginalisation=wo_num_dist_marginalisation,
**get_model_kwargs)
fprint(f"num. radial steps is {len(loader.rdist)}")
return models
def select_void_h(kind):
hs = {"mb": 0.7615, "gauss": 0.7724, "exp": 0.7725}
try:
return hs[kind]
except KeyError:
raise ValueError(f"Unknown void kind: `{kind}`.")
def get_harmonic_evidence(samples, log_posterior, nchains_harmonic, epoch_num):
"""Compute evidence using the `harmonic` package."""
data, names = csiborgtools.dict_samples_to_array(samples)
@ -243,7 +238,7 @@ def get_distmod_hyperparams(catalogue, sample_alpha, sample_mag_dipole):
"alpha_min": alpha_min, "alpha_max": alpha_max,
"sample_alpha": sample_alpha
}
elif catalogue in ["SFI_gals", "2MTF"] or "CF4_TFR" in catalogue:
elif catalogue in ["SFI_gals", "2MTF"] or "CF4_TFR" in catalogue or "IndranilVoidTFRMock" in catalogue: # noqa
return {"e_mu_min": 0.001, "e_mu_max": 1.0,
"a_mean": -21., "a_std": 5.0,
"b_mean": -5.95, "b_std": 4.0,
@ -299,7 +294,7 @@ if __name__ == "__main__":
###########################################################################
# `None` means default behaviour
nsteps = 10_000
nsteps = 2_000
nburn = 2_000
zcmb_min = None
zcmb_max = 0.05
@ -313,8 +308,9 @@ if __name__ == "__main__":
sample_Vmag_vax = False
sample_Vmono = False
sample_mag_dipole = False
wo_num_dist_marginalisation = False
absolute_calibration = None
calculate_harmonic = False if inference_method == "bayes" else True
calculate_harmonic = (False if inference_method == "bayes" else True) and (not wo_num_dist_marginalisation) # noqa
sample_h = True if absolute_calibration is not None else False
fname_kwargs = {"inference_method": inference_method,
@ -341,6 +337,7 @@ if __name__ == "__main__":
"num_epochs": num_epochs,
"inference_method": inference_method,
"sample_mag_dipole": sample_mag_dipole,
"wo_dist_marg": wo_num_dist_marginalisation,
"absolute_calibration": absolute_calibration,
"sample_h": sample_h,
}
@ -358,7 +355,7 @@ if __name__ == "__main__":
"`IndranilVoid` does not have multiple realisations.")
profile = ARGS.simname.split("_")[-1]
h = select_void_h(profile)
h = csiborgtools.flow.select_void_h(profile)
rdist = np.arange(0, 165, 0.5)
void_kwargs = {"profile": profile, "h": h, "order": 1, "rdist": rdist}
else:
@ -377,7 +374,7 @@ if __name__ == "__main__":
calibration_hyperparams = {"Vext_min": -3000, "Vext_max": 3000,
"Vmono_min": -1000, "Vmono_max": 1000,
"beta_min": -10.0, "beta_max": 10.0,
"sigma_v_min": 1.0, "sigma_v_max": 5000 if "IndranilVoid_" in ARGS.simname else 750., # noqa
"sigma_v_min": 1.0, "sigma_v_max": 1000 if "IndranilVoid_" in ARGS.simname else 750., # noqa
"h_min": 0.01, "h_max": 5.0,
"no_Vext": False if no_Vext is None else no_Vext, # noqa
"sample_Vmag_vax": sample_Vmag_vax,
@ -420,7 +417,8 @@ if __name__ == "__main__":
print(f"{'Current simulation:':<20} {i + 1} ({ksim}) out of {len(ksim_iterator)}.") # noqa
fname_kwargs["nsim"] = ksim
models = get_models(ksim, get_model_kwargs, mag_selection, void_kwargs)
models = get_models(ksim, get_model_kwargs, mag_selection, void_kwargs,
wo_num_dist_marginalisation)
model_kwargs = {
"models": models,
"field_calibration_hyperparams": calibration_hyperparams,

1
setup.py
View file

@ -11,6 +11,7 @@ INSTALL_REQ += [
"mpi4py",
"numba",
"numpyro",
"interpax"
"quadax",
"scikit-learn",
"tqdm",