mirror of
https://github.com/Richard-Sti/csiborgtools_public.git
synced 2025-06-08 09:51:12 +00:00
Plots of VF (#134)
* Add VF plots * Update nb * Add CMB velocity note * rm nb * Add option to return alllikelihood * Add simulation weights * Update nb * Add bulkflow * Update nb * Add values of beta * Update imports * Update imports * Add paths to Carrick and Lilow fiels * Add Carrick and Lilow fields * Add support for more fields * Update bulkflow comp * Update nb * Update script
This commit is contained in:
Richard Stiskalek
GitHub
parent
7dad6885e8
commit
c6f49790bf
13 changed files with 1208 additions and 2680 deletions
|
|
@ -666,7 +666,8 @@ class PV_validation_model(BaseFlowValidationModel):
|
|||
self.Omega_m = Omega_m
|
||||
self.norm = - self.ndata * jnp.log(self.num_sims)
|
||||
|
||||
def __call__(self, calibration_hyperparams, distmod_hyperparams):
|
||||
def __call__(self, calibration_hyperparams, distmod_hyperparams,
|
||||
store_ll_all=False):
|
||||
"""NumPyro PV validation model."""
|
||||
Vext, sigma_v, alpha, beta = sample_calibration(**calibration_hyperparams) # noqa
|
||||
cz_err = jnp.sqrt(sigma_v**2 + self.e2_cz_obs)
|
||||
|
|
@ -698,8 +699,11 @@ class PV_validation_model(BaseFlowValidationModel):
|
|||
|
||||
ptilde *= calculate_likelihood_zobs(self.z_obs, zobs, cz_err)
|
||||
ll = jnp.log(simpson(ptilde, dx=self.dr, axis=-1)) - jnp.log(pnorm)
|
||||
ll = jnp.sum(logsumexp(ll, axis=0)) + self.norm
|
||||
|
||||
if store_ll_all:
|
||||
numpyro.deterministic("ll_all", ll)
|
||||
|
||||
ll = jnp.sum(logsumexp(ll, axis=0)) + self.norm
|
||||
numpyro.deterministic("ll_values", ll)
|
||||
numpyro.factor("ll", ll)
|
||||
|
||||
|
|
|
|||
|
|
@ -18,7 +18,8 @@ from .catalogue import (CSiBORG1Catalogue, CSiBORG2Catalogue,
|
|||
MDPL2Catalogue, fiducial_observers) # noqa
|
||||
from .snapshot import (CSiBORG1Snapshot, CSiBORG2Snapshot, QuijoteSnapshot, # noqa
|
||||
CSiBORG1Field, CSiBORG2Field, CSiBORG2XField, # noqa
|
||||
QuijoteField, BORG2Field, BORG1Field, TNG300_1Field) # noqa
|
||||
QuijoteField, BORG2Field, BORG1Field, TNG300_1Field, # noqa
|
||||
Carrick2015Field, Lilow2024Field) # noqa
|
||||
from .obs import (SDSS, MCXCClusters, PlanckClusters, TwoMPPGalaxies, # noqa
|
||||
TwoMPPGroups, ObservedCluster, match_array_to_no_masking, # noqa
|
||||
cols_to_structured) # noqa
|
||||
|
|
|
|||
|
|
@ -372,6 +372,24 @@ class Paths:
|
|||
else:
|
||||
raise ValueError(f"Unsupported CSiBORG2X field: `{kind}`.")
|
||||
|
||||
if simname == "Carrick2015":
|
||||
basedir = "/mnt/extraspace/rstiskalek/catalogs"
|
||||
if kind == "overdensity":
|
||||
return join(basedir, "twompp_density_carrick2015.npy")
|
||||
elif kind == "velocity":
|
||||
return join(basedir, "twompp_velocity_carrick2015.npy")
|
||||
else:
|
||||
raise ValueError(f"Unsupported Carrick2015 field: `{kind}`.")
|
||||
|
||||
if simname == "Lilow2024":
|
||||
basedir = "/mnt/extraspace/rstiskalek/catalogs"
|
||||
if kind == "overdensity":
|
||||
return join(basedir, "Lilow2024_density.npy")
|
||||
elif kind == "velocity":
|
||||
return join(basedir, "Lilow2024_xVelocity.npy")
|
||||
else:
|
||||
raise ValueError(f"Unsupported Lilow2024 field: `{kind}`.")
|
||||
|
||||
if MAS == "SPH" and kind in ["density", "velocity"]:
|
||||
if simname == "csiborg1":
|
||||
return join(self.csiborg1_srcdir, "field",
|
||||
|
|
|
|||
|
|
@ -20,7 +20,7 @@ observed RA-dec can be mapped into the simulation box.
|
|||
from abc import ABC, abstractmethod
|
||||
from os.path import join
|
||||
|
||||
import numpy
|
||||
import numpy as np
|
||||
from h5py import File
|
||||
|
||||
from ..params import paths_glamdring, simname2boxsize, simname2Omega_m
|
||||
|
|
@ -40,11 +40,11 @@ class BaseSnapshot(ABC):
|
|||
flip_xz=False):
|
||||
self._keep_snapshot_open = None
|
||||
|
||||
if not isinstance(nsim, (int, numpy.integer)):
|
||||
if not isinstance(nsim, (int, np.integer)):
|
||||
raise TypeError("`nsim` must be an integer")
|
||||
self._nsim = int(nsim)
|
||||
|
||||
if not isinstance(nsnap, (int, numpy.integer)):
|
||||
if not isinstance(nsnap, (int, np.integer)):
|
||||
raise TypeError("`nsnap` must be an integer")
|
||||
self._nsnap = int(nsnap)
|
||||
|
||||
|
|
@ -409,16 +409,16 @@ class CSiBORG2Snapshot(BaseSnapshot):
|
|||
with File(self._snapshot_path, "r") as f:
|
||||
if kind == "Masses":
|
||||
npart = f["Header"].attrs["NumPart_Total"][1]
|
||||
x = numpy.ones(npart, dtype=numpy.float32)
|
||||
x = np.ones(npart, dtype=np.float32)
|
||||
x *= f["Header"].attrs["MassTable"][1]
|
||||
else:
|
||||
x = f[f"PartType1/{kind}"][...]
|
||||
|
||||
if not high_resolution_only:
|
||||
if x.ndim == 1:
|
||||
x = numpy.hstack([x, f[f"PartType5/{kind}"][...]])
|
||||
x = np.hstack([x, f[f"PartType5/{kind}"][...]])
|
||||
else:
|
||||
x = numpy.vstack([x, f[f"PartType5/{kind}"][...]])
|
||||
x = np.vstack([x, f[f"PartType5/{kind}"][...]])
|
||||
|
||||
if self.flip_xz and kind in ["Coordinates", "Velocities"]:
|
||||
x[:, [0, 2]] = x[:, [2, 0]]
|
||||
|
|
@ -453,7 +453,7 @@ class CSiBORG2Snapshot(BaseSnapshot):
|
|||
|
||||
if i1 is not None and j1 - i1 > 0:
|
||||
if kind == "Masses":
|
||||
x1 = numpy.ones(j1 - i1, dtype=numpy.float32)
|
||||
x1 = np.ones(j1 - i1, dtype=np.float32)
|
||||
x1 *= f["Header"].attrs["MassTable"][1]
|
||||
else:
|
||||
x1 = f[f"PartType1/{kind}"][i1:j1]
|
||||
|
|
@ -481,9 +481,9 @@ class CSiBORG2Snapshot(BaseSnapshot):
|
|||
return x5
|
||||
|
||||
if x1.ndim > 1:
|
||||
x1 = numpy.vstack([x1, x5])
|
||||
x1 = np.vstack([x1, x5])
|
||||
else:
|
||||
x1 = numpy.hstack([x1, x5])
|
||||
x1 = np.hstack([x1, x5])
|
||||
|
||||
return x1
|
||||
|
||||
|
|
@ -565,7 +565,7 @@ class BaseField(ABC):
|
|||
Base class for reading fields such as density or velocity fields.
|
||||
"""
|
||||
def __init__(self, nsim, paths, flip_xz=False):
|
||||
if isinstance(nsim, numpy.integer):
|
||||
if isinstance(nsim, np.integer):
|
||||
nsim = int(nsim)
|
||||
if not isinstance(nsim, int):
|
||||
raise TypeError(f"`nsim` must be an integer. Received `{type(nsim)}`.") # noqa
|
||||
|
|
@ -644,7 +644,7 @@ class CSiBORG1Field(BaseField):
|
|||
field = f["density"][:]
|
||||
field /= (677.7 * 1e3 / grid)**3 # Convert to h^2 Msun / kpc^3
|
||||
else:
|
||||
field = numpy.load(fpath)
|
||||
field = np.load(fpath)
|
||||
|
||||
if self.flip_xz:
|
||||
field = field.T
|
||||
|
|
@ -660,9 +660,9 @@ class CSiBORG1Field(BaseField):
|
|||
v0 = f["p0"][:] / density
|
||||
v1 = f["p1"][:] / density
|
||||
v2 = f["p2"][:] / density
|
||||
field = numpy.array([v0, v1, v2])
|
||||
field = np.array([v0, v1, v2])
|
||||
else:
|
||||
field = numpy.load(fpath)
|
||||
field = np.load(fpath)
|
||||
|
||||
if self.flip_xz:
|
||||
field[0, ...] = field[0, ...].T
|
||||
|
|
@ -678,7 +678,7 @@ class CSiBORG1Field(BaseField):
|
|||
"for the flipped x- and z-axes.")
|
||||
|
||||
fpath = self.paths.field("radvel", MAS, grid, self.nsim, "csiborg1")
|
||||
return numpy.load(fpath)
|
||||
return np.load(fpath)
|
||||
|
||||
|
||||
###############################################################################
|
||||
|
|
@ -727,7 +727,7 @@ class CSiBORG2Field(BaseField):
|
|||
field *= 1e10 # Convert to Msun / h
|
||||
field /= (676.6 * 1e3 / grid)**3 # Convert to h^2 Msun / kpc^3
|
||||
else:
|
||||
field = numpy.load(fpath)
|
||||
field = np.load(fpath)
|
||||
|
||||
if self.flip_xz:
|
||||
field = field.T
|
||||
|
|
@ -744,9 +744,9 @@ class CSiBORG2Field(BaseField):
|
|||
v0 = f["p0"][:] / density
|
||||
v1 = f["p1"][:] / density
|
||||
v2 = f["p2"][:] / density
|
||||
field = numpy.array([v0, v1, v2])
|
||||
field = np.array([v0, v1, v2])
|
||||
else:
|
||||
field = numpy.load(fpath)
|
||||
field = np.load(fpath)
|
||||
|
||||
if self.flip_xz:
|
||||
field[0, ...] = field[0, ...].T
|
||||
|
|
@ -763,7 +763,7 @@ class CSiBORG2Field(BaseField):
|
|||
|
||||
fpath = self.paths.field("radvel", MAS, grid, self.nsim,
|
||||
f"csiborg2_{self.kind}")
|
||||
return numpy.load(fpath)
|
||||
return np.load(fpath)
|
||||
|
||||
|
||||
class CSiBORG2XField(BaseField):
|
||||
|
|
@ -784,7 +784,7 @@ class CSiBORG2XField(BaseField):
|
|||
fpath = self.paths.field(
|
||||
"overdensity", None, None, self.nsim, "csiborg2X")
|
||||
with File(fpath, "r") as f:
|
||||
field = f["delta_cic"][...].astype(numpy.float32)
|
||||
field = f["delta_cic"][...].astype(np.float32)
|
||||
|
||||
return field
|
||||
|
||||
|
|
@ -803,7 +803,7 @@ class CSiBORG2XField(BaseField):
|
|||
v0 = f["v_0"][...]
|
||||
v1 = f["v_1"][...]
|
||||
v2 = f["v_2"][...]
|
||||
field = numpy.array([v0, v1, v2])
|
||||
field = np.array([v0, v1, v2])
|
||||
|
||||
return field
|
||||
|
||||
|
|
@ -833,7 +833,7 @@ class BORG1Field(BaseField):
|
|||
def overdensity_field(self):
|
||||
fpath = self.paths.field(None, None, None, self.nsim, "borg1")
|
||||
with File(fpath, "r") as f:
|
||||
field = f["scalars/BORG_final_density"][:].astype(numpy.float32)
|
||||
field = f["scalars/BORG_final_density"][:].astype(np.float32)
|
||||
|
||||
return field
|
||||
|
||||
|
|
@ -874,7 +874,7 @@ class BORG2Field(BaseField):
|
|||
def overdensity_field(self):
|
||||
fpath = self.paths.field(None, None, None, self.nsim, "borg2")
|
||||
with File(fpath, "r") as f:
|
||||
field = f["scalars/BORG_final_density"][:].astype(numpy.float32)
|
||||
field = f["scalars/BORG_final_density"][:].astype(np.float32)
|
||||
|
||||
return field
|
||||
|
||||
|
|
@ -894,7 +894,7 @@ class BORG2Field(BaseField):
|
|||
|
||||
|
||||
###############################################################################
|
||||
# TNG300-1 field #
|
||||
# Additional fields #
|
||||
###############################################################################
|
||||
|
||||
class TNG300_1Field(BaseField):
|
||||
|
|
@ -922,7 +922,7 @@ class TNG300_1Field(BaseField):
|
|||
def density_field(self, MAS, grid):
|
||||
fpath = join(self.paths.tng300_1(), "postprocessing", "density_field",
|
||||
f"rho_dm_099_{grid}_{MAS}.npy")
|
||||
return numpy.load(fpath)
|
||||
return np.load(fpath)
|
||||
|
||||
def velocity_field(self, MAS, grid):
|
||||
raise RuntimeError("The velocity field is not available.")
|
||||
|
|
@ -930,10 +930,6 @@ class TNG300_1Field(BaseField):
|
|||
def radial_velocity_field(self, MAS, grid):
|
||||
raise RuntimeError("The radial velocity field is not available.")
|
||||
|
||||
###############################################################################
|
||||
# Quijote field class #
|
||||
###############################################################################
|
||||
|
||||
|
||||
class QuijoteField(CSiBORG1Field):
|
||||
"""
|
||||
|
|
@ -951,6 +947,90 @@ class QuijoteField(CSiBORG1Field):
|
|||
self._simname = "quijote"
|
||||
|
||||
|
||||
class Carrick2015Field(BaseField):
|
||||
"""
|
||||
Carrick+2015 `z = 0` field class. The field is in galactic coordinates.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
paths : Paths, optional
|
||||
Paths object. By default, the paths are set to the `glamdring` paths.
|
||||
"""
|
||||
def __init__(self, paths=None):
|
||||
super().__init__(0, paths, False)
|
||||
|
||||
def overdensity_field(self, **kwargs):
|
||||
fpath = self.paths.field(
|
||||
"overdensity", None, None, self.nsim, "Carrick2015")
|
||||
return np.load(fpath)
|
||||
|
||||
def density_field(self, **kwargs):
|
||||
field = self.overdensity_field()
|
||||
omega0 = simname2Omega_m("Carrick2015")
|
||||
rho_mean = omega0 * 277.53662724583074 # Msun / kpc^3
|
||||
field += 1
|
||||
field *= rho_mean
|
||||
return field
|
||||
|
||||
def velocity_field(self, **kwargs):
|
||||
fpath = self.paths.field(
|
||||
"velocity", None, None, self.nsim, "Carrick2015")
|
||||
field = np.load(fpath)
|
||||
# Because the Carrick+2015 data is in the following form:
|
||||
# "The velocities are predicted peculiar velocities in the CMB
|
||||
# frame in Galactic Cartesian coordinates, generated from the
|
||||
# \(\delta_g^*\) field with \(\beta^* = 0.43\) and an external
|
||||
# dipole \(V_\mathrm{ext} = [89,-131,17]\) (Carrick et al Table 3)
|
||||
# has already been added.""
|
||||
field[0] -= 89
|
||||
field[1] -= -131
|
||||
field[2] -= 17
|
||||
field /= 0.43
|
||||
return field
|
||||
|
||||
def radial_velocity_field(self, **kwargs):
|
||||
raise RuntimeError("The radial velocity field is not available.")
|
||||
|
||||
|
||||
class Lilow2024Field(BaseField):
|
||||
"""
|
||||
Lilow+2024 `z = 0` field class. The field is in galactic coordinates.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
paths : Paths, optional
|
||||
Paths object. By default, the paths are set to the `glamdring` paths.
|
||||
"""
|
||||
def __init__(self, paths=None):
|
||||
super().__init__(0, paths, False)
|
||||
|
||||
def overdensity_field(self, **kwargs):
|
||||
fpath = self.paths.field(
|
||||
"overdensity", None, None, self.nsim, "Lilow2024")
|
||||
return np.load(fpath) - 1
|
||||
|
||||
def density_field(self, **kwargs):
|
||||
field = self.overdensity_field()
|
||||
omega0 = simname2Omega_m("Lilow2024")
|
||||
rho_mean = omega0 * 277.53662724583074 # Msun / kpc^3
|
||||
field += 1
|
||||
field *= rho_mean
|
||||
return field
|
||||
|
||||
def velocity_field(self, **kwargs):
|
||||
fpath = self.paths.field(
|
||||
"velocity", None, None, self.nsim, "Lilow2024")
|
||||
|
||||
vx = np.load(fpath)
|
||||
vy = np.load(fpath.replace("xVelocity", "yVelocity"))
|
||||
vz = np.load(fpath.replace("xVelocity", "zVelocity"))
|
||||
|
||||
return np.stack([vx, vy, vz])
|
||||
|
||||
def radial_velocity_field(self, **kwargs):
|
||||
raise RuntimeError("The radial velocity field is not available.")
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Supplementary functions #
|
||||
###############################################################################
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue