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More ABSMAG (#152)

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* Add draft of code

* Update defaults

* Update nb

* Update nb

* Update script

* Update script

* Update script

* Indicate that not implemented
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Richard Stiskalek 2024-09-25 15:30:06 +02:00 committed by GitHub
parent c881f8eb39
commit f7d16a9cd0
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6 changed files with 155 additions and 271 deletions
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116
csiborgtools/flow/flow_model.py
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@ -74,6 +74,20 @@ def gradient_redshift2dist(z, Omega_m):
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)
@ -113,6 +127,15 @@ def likelihood_zobs(zobs, zobs_pred, e2_cz):
return jnp.exp(-0.5 * dcz**2 / e2_cz) / jnp.sqrt(2 * np.pi * e2_cz)
def log_likelihood_zobs(zobs, zobs_pred, e2_cz):
"""
Calculate the log-likelihood of the observed redshift given the predicted
redshift. Multiplies the redshifts by the speed of light.
"""
dcz = SPEED_OF_LIGHT * (zobs - zobs_pred)
return -0.5 * dcz**2 / e2_cz - 0.5 * jnp.log(2 * np.pi * e2_cz)
def normal_logpdf(x, loc, scale):
"""Log of the normal probability density function."""
return (-0.5 * ((x - loc) / scale)**2
@ -180,9 +203,12 @@ class BaseFlowValidationModel(ABC):
r_xrange = jnp.asarray(r_xrange)
r2_xrange = r_xrange**2
r2_xrange /= r2_xrange.mean()
r2_xrange_mean = r2_xrange.mean()
r2_xrange /= r2_xrange_mean
self.r_xrange = r_xrange
self.log_r2_xrange = jnp.log(r2_xrange)
self.log_r2_xrange_mean = jnp.log(r2_xrange_mean)
# Require `zmin` < 0 because the first radial step is likely at 0.
z_xrange = z_at_value(
@ -235,6 +261,13 @@ class BaseFlowValidationModel(ABC):
return len(self.log_los_density())
def los_density(self, **kwargs):
if self.is_void_data:
# Currently we have no densities for the void.
return jnp.ones((1, self.ndata, len(self.r_xrange)))
return self._los_density
def log_los_density(self, **kwargs):
if self.is_void_data:
# Currently we have no densities for the void.
@ -499,11 +532,16 @@ class PV_LogLikelihood(BaseFlowValidationModel):
names = ["RA", "dec", "z_obs", "e2_cz_obs"]
values = [RA, dec, z_obs, e2_cz_obs]
# If ever start running out of memory, may be better not to store
# both the density and log_density
if not self.is_void_data:
names += ["_log_los_density", "_los_velocity"]
values += [jnp.log(los_density), los_velocity]
# Set the void data
# Density required only if not numerically marginalising.
if not with_num_dist_marginalisation:
names += ["_los_density"]
values += [los_density]
self._setattr_as_jax(names, values)
self._set_calibration_params(calibration_params)
@ -699,13 +737,12 @@ class PV_LogLikelihood(BaseFlowValidationModel):
if inference_method == "bayes":
raise NotImplementedError("Bayes for simple not implemented.")
else:
mu_true = self.mu
if inference_method == "mike":
e2_mu = e_mu**2 + self.e2_mu
else:
e2_mu = jnp.ones_like(mag_true) * e_mu**2
mu = mu_true + dmu
mu = self.mu + dmu
else:
raise ValueError(f"Unknown kind: `{self.kind}`.")
@ -773,8 +810,77 @@ 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(
"No distance marginalisation not implemented yet.")
"Sampling of distance is not implemented. Work in progress.")
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)``
r_true = distmod2dist(mu_true, self.Omega_m)
# TODO:
z_true = None
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
# Densities and velocities at the true distances, shape is
# `(n_sims, n_data)`
log_density = None
los_velocity = None
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, :]
+ 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)
pnorm = simpson(pnorm, x=self.r_xrange, axis=-1)
# TODO: There should be a Jacobian?
# Calculate unnormalized log p(mu). Shape is (nsims, ndata)
ll = (
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)
# Calculate z_obs at the true distance. Shape: (nsims, ndata)
vrad = field_calibration_params["beta"] * los_velocity
vrad += (Vext_rad[None, :] + Vmono)
zobs = 1 + z_true[None, :]
zobs *= 1 + vrad / SPEED_OF_LIGHT
zobs -= 1.
ll += log_likelihood_zobs(
self.z_obs[None, :], zobs, e2_cz[None, :])
if self.with_absolute_calibration:
raise NotImplementedError(
"Absolute calibration not implemented for this model. "
"Use `PV_LogLikelihood_NoDistMarg` instead.")
return ll0 + jnp.sum(logsumexp(ll, axis=0)) + self.norm
###############################################################################

257
notebooks/flow/reconstruction_comparison.ipynb
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45
notebooks/overlap/lagrangian_patch_example.ipynb
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3
scripts/field_prop/field_los.sh
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@ -18,7 +18,8 @@ then
fi
for simname in "csiborg1" "csiborg2_main" "csiborg2X" "Lilow2024" "Carrick2015" "CF4" "manticore_2MPP_N128_DES_V1"; do
# for simname in "csiborg1" "csiborg2_main" "csiborg2X" "Lilow2024" "Carrick2015" "CF4" "manticore_2MPP_N128_DES_V1"; do
for simname in "CLONES"; do
for catalogue in "LOSS" "Foundation" "2MTF" "SFI_gals" "CF4_TFR"; do
pythoncm="$env $file --catalogue $catalogue --nsims $nsims --simname $simname --MAS $MAS --grid $grid"
if [ $on_login -eq 1 ]; then

2
scripts/flow/flow_validation.py
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@ -305,7 +305,7 @@ if __name__ == "__main__":
zcmb_max = 0.05
nchains_harmonic = 10
num_epochs = 50
inference_method = "bayes"
inference_method = "mike"
mag_selection = None
sample_alpha = False if "IndranilVoid_" in ARGS.simname or ARGS.simname == "no_field" else True # noqa
sample_beta = None

3
scripts/flow/flow_validation.sh
View file

@ -39,7 +39,8 @@ fi
# for simname in "IndranilVoid_exp" "IndranilVoid_gauss" "IndranilVoid_mb"; do
for simname in "Carrick2015" "Lilow2024" "csiborg2_main" "csiborg2X" "manticore_2MPP_N128_DES_V1" "CF4" "CLONES"; do
# for simname in "Carrick2015" "Lilow2024" "csiborg2_main" "csiborg2X" "manticore_2MPP_N128_DES_V1" "CF4" "CLONES"; do
for simname in "Carrick2015"; do
# for simname in "no_field"; do
for catalogue in "LOSS" "Foundation" "2MTF" "SFI_gals" "CF4_TFR_i" "CF4_TFR_w1"; do
# for catalogue in "2MTF"; do