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Absmag (#149)

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* Add spacing

* Add various cleanups of the code

* Add basic updates

* Add
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Richard Stiskalek 2024-09-21 14:51:08 +02:00 committed by GitHub
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commit 5336c0296c
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1 changed files with 75 additions and 60 deletions
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csiborgtools/flow/flow_model.py
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@ -45,13 +45,13 @@ H0 = 100 # km / s / Mpc
# JAX Flow model # # JAX Flow model #
############################################################################### ###############################################################################
def dist2redshift(dist, Omega_m): def dist2redshift(dist, Omega_m, h=1.):
""" """
Convert comoving distance to cosmological redshift if the Universe is Convert comoving distance to cosmological redshift if the Universe is
flat and z << 1. flat and z << 1.
""" """
eta = 3 * Omega_m / 2 eta = 3 * Omega_m / 2
return 1 / eta * (1 - (1 - 2 * H0 * dist / SPEED_OF_LIGHT * eta)**0.5) return 1 / eta * (1 - (1 - 2 * 100 * h * dist / SPEED_OF_LIGHT * eta)**0.5)
def redshift2dist(z, Omega_m): def redshift2dist(z, Omega_m):
@ -366,11 +366,6 @@ def sample_calibration(Vext_min, Vext_max, Vmono_min, Vmono_max, beta_min,
} }
###############################################################################
# PV calibration model #
###############################################################################
def sample_gaussian_hyperprior(param, name, xmin, xmax): def sample_gaussian_hyperprior(param, name, xmin, xmax):
"""Sample MNR Gaussian hyperprior mean and standard deviation.""" """Sample MNR Gaussian hyperprior mean and standard deviation."""
mean = sample(f"{param}_mean_{name}", Uniform(xmin, xmax)) mean = sample(f"{param}_mean_{name}", Uniform(xmin, xmax))
@ -378,9 +373,15 @@ def sample_gaussian_hyperprior(param, name, xmin, xmax):
return mean, std return mean, std
###############################################################################
# PV calibration model without absolute calibration #
###############################################################################
class PV_LogLikelihood(BaseFlowValidationModel): class PV_LogLikelihood(BaseFlowValidationModel):
""" """
Peculiar velocity validation model log-likelihood. Peculiar velocity validation model log-likelihood with numerical
integration of the true distances.
Parameters Parameters
---------- ----------
@ -408,11 +409,15 @@ class PV_LogLikelihood(BaseFlowValidationModel):
Catalogue kind, either "TFR", "SN", or "simple". Catalogue kind, either "TFR", "SN", or "simple".
name : str name : str
Name of the catalogue. Name of the catalogue.
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`.
""" """
def __init__(self, los_density, los_velocity, RA, dec, z_obs, e_zobs, def __init__(self, los_density, los_velocity, RA, dec, z_obs, e_zobs,
calibration_params, abs_calibration_params, mag_selection, calibration_params, abs_calibration_params, mag_selection,
r_xrange, Omega_m, kind, name): r_xrange, Omega_m, kind, name, with_num_dist_marginalisation):
if e_zobs is not None: if e_zobs is not None:
e2_cz_obs = jnp.asarray((SPEED_OF_LIGHT * e_zobs)**2) e2_cz_obs = jnp.asarray((SPEED_OF_LIGHT * e_zobs)**2)
else: else:
@ -433,8 +438,12 @@ class PV_LogLikelihood(BaseFlowValidationModel):
self.kind = kind self.kind = kind
self.name = name self.name = name
self.Omega_m = Omega_m self.Omega_m = Omega_m
self.with_num_dist_marginalisation = with_num_dist_marginalisation
self.norm = - self.ndata * jnp.log(self.num_sims) 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: if mag_selection is not None:
self.mag_selection_kind = mag_selection["kind"] self.mag_selection_kind = mag_selection["kind"]
@ -485,6 +494,9 @@ class PV_LogLikelihood(BaseFlowValidationModel):
Vmono = field_calibration_params["Vmono"] Vmono = field_calibration_params["Vmono"]
Vext_rad = project_Vext(Vext[0], Vext[1], Vext[2], self.RA, self.dec) Vext_rad = project_Vext(Vext[0], Vext[1], Vext[2], self.RA, self.dec)
# ------------------------------------------------------------
# 1. Sample true observables and obtain the distance estimate
# ------------------------------------------------------------
e_mu = distmod_params["e_mu"] e_mu = distmod_params["e_mu"]
if self.kind == "SN": if self.kind == "SN":
mag_cal = distmod_params["mag_cal"] mag_cal = distmod_params["mag_cal"]
@ -532,10 +544,6 @@ class PV_LogLikelihood(BaseFlowValidationModel):
mu = distmod_SN( mu = distmod_SN(
mag_true, x1_true, c_true, mag_cal, alpha_cal, beta_cal) mag_true, x1_true, c_true, mag_cal, alpha_cal, beta_cal)
if field_calibration_params["sample_h"]:
raise NotImplementedError("H0 for SN not implemented.")
elif self.kind == "TFR": elif self.kind == "TFR":
a = distmod_params["a"] a = distmod_params["a"]
b = distmod_params["b"] b = distmod_params["b"]
@ -605,11 +613,6 @@ class PV_LogLikelihood(BaseFlowValidationModel):
e2_mu = jnp.ones_like(mag_true) * e_mu**2 e2_mu = jnp.ones_like(mag_true) * e_mu**2
mu = distmod_TFR(mag_true, eta_true, a, b, c) mu = distmod_TFR(mag_true, eta_true, a, b, c)
if field_calibration_params["sample_h"]:
raise NotImplementedError("H0 for TFR not implemented.")
# mu -= 5 * jnp.log10(field_calibration_params["h"])
elif self.kind == "simple": elif self.kind == "simple":
dmu = distmod_params["dmu"] dmu = distmod_params["dmu"]
@ -628,61 +631,73 @@ class PV_LogLikelihood(BaseFlowValidationModel):
e2_mu = jnp.ones_like(mag_true) * e_mu**2 e2_mu = jnp.ones_like(mag_true) * e_mu**2
mu = mu_true + dmu mu = mu_true + dmu
if field_calibration_params["sample_h"]:
raise NotImplementedError("H0 for simple not implemented.")
else: else:
raise ValueError(f"Unknown kind: `{self.kind}`.") raise ValueError(f"Unknown kind: `{self.kind}`.")
# Calculate p(r) (Malmquist bias). Shape is (ndata, nxrange) # h = field_calibration_params["h"]
log_ptilde = log_ptilde_wo_bias( # ----------------------------------------------------------------
self.mu_xrange[None, :], mu[:, None], e2_mu[:, None], # 2. Log-likelihood of the true distance and observed redshifts.
self.log_r2_xrange[None, :]) # The marginalisation of the true distance can be done numerically.
# ----------------------------------------------------------------
if self.with_num_dist_marginalisation:
# Inhomogeneous Malmquist bias. Shape is (n_sims, ndata, nxrange) if field_calibration_params["sample_h"]:
alpha = distmod_params["alpha"] raise NotImplementedError("Sampling of h not implemented.")
log_ptilde = log_ptilde[None, ...] + alpha * self.log_los_density # 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)
ptilde = jnp.exp(log_ptilde) # The redshift should also be boosted since now the object are
# further away?
# Normalization of p(r). Shape is (n_sims, ndata) # Actually, the redshift ought to remain the same?
pnorm = simpson(ptilde, x=self.r_xrange, axis=-1) else:
mu_xrange = self.mu_xrange
# Calculate z_obs at each distance. Shape is (n_sims, ndata, nxrange) # Calculate p(r) (Malmquist bias). Shape is (ndata, nxrange)
vrad = field_calibration_params["beta"] * self.los_velocity log_ptilde = log_ptilde_wo_bias(
vrad += (Vext_rad[None, :, None] + Vmono) mu_xrange[None, :], mu[:, None], e2_mu[:, None],
zobs = (1 + self.z_xrange[None, None, :]) * (1 + vrad / SPEED_OF_LIGHT) self.log_r2_xrange[None, :])
zobs -= 1.
# Shape remains (n_sims, ndata, nxrange) # Inhomogeneous Malmquist bias. Shape: (nsims, ndata, nxrange)
ptilde *= likelihood_zobs( alpha = distmod_params["alpha"]
self.z_obs[None, :, None], zobs, e2_cz[None, :, None]) log_ptilde = log_ptilde[None, ...] + alpha * self.log_los_density
if self.with_absolute_calibration: ptilde = jnp.exp(log_ptilde)
raise NotImplementedError("Absolute calibration not implemented.")
# Absolute calibration likelihood, the shape is now
# (ndata_with_calibration, ncalib, nxrange)
# ll_calibration = normal_logpdf(
# self.mu_xrange[None, None, :],
# self.calibration_distmod[..., None],
# self.calibration_edistmod[..., None])
# # Average the likelihood over the calibration points. The shape # Normalization of p(r). Shape: (nsims, ndata)
# is pnorm = simpson(ptilde, x=self.r_xrange, axis=-1)
# # now (ndata, nxrange)
# ll_calibration = logsumexp(
# jnp.nan_to_num(ll_calibration, nan=-jnp.inf), axis=1)
# # This is the normalisation because we want the *average*.
# ll_calibration -= self.log_length_calibration[:, None]
# ptilde = ptilde.at[:, self.data_with_calibration, :]. # Calculate z_obs at each distance. Shape: (nsims, ndata, nxrange)
# multiply(jnp.exp(ll_calibration)) vrad = field_calibration_params["beta"] * self.los_velocity
vrad += (Vext_rad[None, :, None] + Vmono)
zobs = 1 + self.z_xrange[None, None, :]
zobs *= 1 + vrad / SPEED_OF_LIGHT
zobs -= 1.
# Integrate over the radial distance. Shape is (n_sims, ndata) # Shape remains (nsims, ndata, nxrange)
ll = jnp.log(simpson(ptilde, x=self.r_xrange, axis=-1)) ptilde *= likelihood_zobs(
ll -= jnp.log(pnorm) self.z_obs[None, :, None], zobs, e2_cz[None, :, None])
return ll0 + jnp.sum(logsumexp(ll, axis=0)) + self.norm if self.with_absolute_calibration:
raise NotImplementedError(
"Absolute calibration not implemented for this model. "
"Use `PV_LogLikelihood_NoDistMarg` instead.")
# Integrate over the radial distance. Shape: (nsims, ndata)
ll = jnp.log(simpson(ptilde, x=self.r_xrange, axis=-1))
ll -= jnp.log(pnorm)
return ll0 + jnp.sum(logsumexp(ll, axis=0)) + self.norm
else:
raise NotImplementedError(
"No distance marginalisation not implemented yet.")
###############################################################################
# Combining several catalogues #
###############################################################################
def PV_validation_model(models, distmod_hyperparams_per_model, def PV_validation_model(models, distmod_hyperparams_per_model,