Update evaluate density scripts (#105)

* Edit docs

* Updated interpolated field paths

* Update field sampling script

* Add comments about flipping fields

* Fix little typo

* Edit docs

* Edit hard-coded values

* Fix paths issue

* Add docs

* Switch uncorrected dist to corrected

* Improve error message

* Convert numpy int to Python int

* Add flip of x and z

* Update README

* Edit README

* Fix bug in velocity field calculation

* Fix simple bug

* Add checked axes flipping

* Fix field units

* Update README
This commit is contained in:
Richard Stiskalek 2024-01-08 13:56:22 +01:00 committed by GitHub
parent f61f69dfab
commit 1a5477805a
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
6 changed files with 268 additions and 167 deletions

View file

@ -1,26 +1,41 @@
# CSiBORG Tools # CSiBORG Tools
Tools for analysing the suite of Constrained Simulations in BORG (CSiBORG) simulations. The interface is designed to work with the following suites of simulations: Tools for analysing the suite of Constrained Simulations in BORG (CSiBORG) simulations. The interface is designed to work with the following suites of simulations: *CSiBORG1* (dark matter-only RAMSES), *CSiBORG2* (dark matter-only Gadget4), *Quijote* (dark-matter only Gadget2), however with little effort it can support other simulations as well.
- CSiBORG1 dark matter-only RAMSES simulations (full support),
- CSiBORG2 dark matter-only Gadget4 simulations (planned full support), ## Ongoing projects
- Quijote dark matter-only Gadget2 simulations (partial support),
however with little effort it can support other simulations as well. ### Consistent halo reconstruction
- [ ] Make a sketch of the overlap definition and add it to the paper.
- [ ] Improve the storage system for overlaps and calculate it for all simulations.
### Enviromental dependence of galaxy properties
- [ ] Calculate the SPH density field for CSiBORG1.
- [x] Check that the velocity-field flipping of x and z coordinates is correct.
- [ ] Evaluate and share the density field for SDSS & SDSSxALFALFA for both CSiBORG2 and random fields.
- [ ] Check and verify the density field of galaxy colours (cannot do this now! Glamdring is super slow.)
#### Calculated data
##### SPH-density & velocity field:
- *CSiBORG2_main*, *CSiBORG2_random*, *CSiBORG2_varysmall*
- Evaluated for SDSS and SDSSxALFALFA in: *CSiBORG2_main*, *CSiBORG2_random*
## TODO ### Mass-assembly of massive clusters
- [x] Prune old CSiBORG1 merger tree things. - [ ] Make a list of nearby most-massive clusters.
- [x] Add visualiastion of the density field. - [ ] Write code to identify a counterpart of such clusters.
- [ ] Clear out `density` support. - [ ] Write code to make a plot of mass-assembly of all clusters within a certain mass range from the random simulations.
- [ ] Add sorting of Gadget4 initial snapshot like final snapshot. - [ ] Write code to compare mass-assembly of a specific cluster with respect to random ones.
- [ ] Add full support for CSiBORG2 suite of simulations.
- [ ] Add SPH field calculation from cosmotools.
## Adding a new simulation suite ### Effect of small-scale noise
- [ ] Study how the small-scale noise variation affects the overlap measure, halo concentration and spin.
box units ### Gravitational-wave and large-scale structure
paths - [ ] Make the velocity field data available.
readsim
halo_cat
### CSiBORG meets X-ray
- [ ] Make available one example snapshot from the simulation. Mention the issue with x- and z-coordinates.
### CSiBORG advertising
- [ ] Decide on the webpage design and what to store there.
- [ ] Write a short letter describing the simulations.

View file

@ -249,17 +249,18 @@ class VelocityField(BaseField):
batch_vel = force_single_precision(batch_vel) batch_vel = force_single_precision(batch_vel)
batch_mass = force_single_precision(batch_mass) batch_mass = force_single_precision(batch_mass)
vel *= mass.reshape(-1, 1) batch_vel *= batch_mass.reshape(-1, 1)
for i in range(3): for i in range(3):
MASL.MA(pos, rho_vel[i], self.boxsize, self.MAS, W=vel[:, i], MASL.MA(batch_pos, rho_vel[i], self.boxsize, self.MAS,
verbose=False) W=batch_vel[:, i], verbose=False)
MASL.MA(pos, cellcounts, self.boxsize, self.MAS, W=mass, MASL.MA(batch_pos, cellcounts, self.boxsize, self.MAS,
verbose=False) W=batch_mass, verbose=False)
if end == nparts: if end == nparts:
break break
start = end start = end
for i in range(3): for i in range(3):
@ -272,7 +273,7 @@ class VelocityField(BaseField):
def radial_velocity(rho_vel, observer_velocity): def radial_velocity(rho_vel, observer_velocity):
""" """
Calculate the radial velocity field around the observer in the centre Calculate the radial velocity field around the observer in the centre
of the box. of the box, such that the observer velocity is 0.
Parameters Parameters
---------- ----------

View file

@ -367,10 +367,7 @@ class Paths:
------- -------
str str
""" """
if MAS == "SPH": if MAS == "SPH" and kind in ["density", "velocity"]:
if kind not in ["density", "velocity"]:
raise ValueError("SPH field must be either `density` or `velocity`.") # noqa
if simname == "csiborg1": if simname == "csiborg1":
raise ValueError("SPH field not available for CSiBORG1.") raise ValueError("SPH field not available for CSiBORG1.")
elif simname == "csiborg2_main": elif simname == "csiborg2_main":
@ -416,7 +413,7 @@ class Paths:
fname = f"observer_peculiar_velocity_{simname}_{MAS}_{str(nsim).zfill(5)}_{grid}.npz" # noqa fname = f"observer_peculiar_velocity_{simname}_{MAS}_{str(nsim).zfill(5)}_{grid}.npz" # noqa
return join(fdir, fname) return join(fdir, fname)
def field_interpolated(self, survey, kind, MAS, grid, nsim, in_rsp): def field_interpolated(self, survey, simname, nsim, kind, MAS, grid):
""" """
Path to the files containing the CSiBORG interpolated field for a given Path to the files containing the CSiBORG interpolated field for a given
survey. survey.
@ -425,35 +422,32 @@ class Paths:
---------- ----------
survey : str survey : str
Survey name. Survey name.
simname : str
Simulation name.
nsim : int
IC realisation index.
kind : str kind : str
Field type. Must be one of: `density`, `velocity`, `potential`, Field type.
`radvel`, `environment`.
MAS : str MAS : str
Mass-assignment scheme. Mass-assignment scheme.
grid : int grid : int
Grid size. Grid size.
nsim : int
IC realisation index.
in_rsp : bool
Whether the calculation is performed in redshift space.
Returns Returns
------- -------
str str
""" """
raise NotImplementedError("This function is not implemented yet.") if "csiborg" not in simname:
assert kind in ["density", "velocity", "potential", "radvel", raise ValueError("Interpolated field only available for CSiBORG.")
"environment"]
fdir = join(self.postdir, "environment_interpolated")
if kind not in ["density", "potential", "radvel"]:
raise ValueError("Unsupported field type.")
fdir = join(self.postdir, "field_interpolated")
try_create_directory(fdir) try_create_directory(fdir)
if in_rsp: nsim = str(nsim).zfill(5)
kind = kind + "_rsp" return join(fdir, f"{survey}_{simname}_{kind}_{MAS}_{nsim}_{grid}.npz")
fname = f"{survey}_{kind}_{MAS}_{str(nsim).zfill(5)}_grid{grid}.npz"
return join(fdir, fname)
def cross_nearest(self, simname, run, kind, nsim=None, nobs=None): def cross_nearest(self, simname, run, kind, nsim=None, nobs=None):
""" """

View file

@ -516,10 +516,12 @@ class BaseField(ABC):
Base class for reading fields such as density or velocity fields. Base class for reading fields such as density or velocity fields.
""" """
def __init__(self, nsim, paths): def __init__(self, nsim, paths):
if isinstance(nsim, numpy.integer):
nsim = int(nsim)
if not isinstance(nsim, int): if not isinstance(nsim, int):
raise TypeError("`nsim` must be an integer") raise TypeError(f"`nsim` must be an integer. Received `{type(nsim)}`.") # noqa
self._nsim = nsim
self._nsim = nsim
self._paths = paths self._paths = paths
@property @property
@ -542,6 +544,8 @@ class BaseField(ABC):
------- -------
Paths Paths
""" """
if self._paths is None:
self._paths = Paths(**paths_glamdring)
return self._paths return self._paths
@abstractmethod @abstractmethod
@ -594,11 +598,12 @@ class CSiBORG1Field(BaseField):
---------- ----------
nsim : int nsim : int
Simulation index. Simulation index.
paths : Paths paths : Paths, optional
Paths object. Paths object. By default, the paths are set to the `glamdring` paths.
""" """
def __init__(self, nsim, paths): def __init__(self, nsim, paths=None):
super().__init__(nsim, paths) super().__init__(nsim, paths)
self._simname = "csiborg1"
def density_field(self, MAS, grid): def density_field(self, MAS, grid):
fpath = self.paths.field("density", MAS, grid, self.nsim, "csiborg1") fpath = self.paths.field("density", MAS, grid, self.nsim, "csiborg1")
@ -606,9 +611,14 @@ class CSiBORG1Field(BaseField):
if MAS == "SPH": if MAS == "SPH":
with File(fpath, "r") as f: with File(fpath, "r") as f:
field = f["density"][:] field = f["density"][:]
field /= (677.7 * 1e3 / grid)**3 # Convert to h^2 Msun / kpc^3
else: else:
field = numpy.load(fpath) field = numpy.load(fpath)
# Flip x- and z-axes
if self._simname == "csiborg1":
field = field.T
return field return field
def velocity_field(self, MAS, grid): def velocity_field(self, MAS, grid):
@ -624,6 +634,13 @@ class CSiBORG1Field(BaseField):
else: else:
field = numpy.load(fpath) field = numpy.load(fpath)
# Flip x- and z-axes
if self._simname == "csiborg1":
field[0, ...] = field[0, ...].T
field[1, ...] = field[1, ...].T
field[2, ...] = field[2, ...].T
field[[0, 2], ...] = field[[2, 0], ...]
return field return field
@ -640,13 +657,13 @@ class CSiBORG2Field(BaseField):
---------- ----------
nsim : int nsim : int
Simulation index. Simulation index.
paths : Paths
Paths object.
kind : str kind : str
CSiBORG2 run kind. One of `main`, `random`, or `varysmall`. CSiBORG2 run kind. One of `main`, `random`, or `varysmall`.
paths : Paths, optional
Paths object. By default, the paths are set to the `glamdring` paths.
""" """
def __init__(self, nsim, paths, kind): def __init__(self, nsim, kind, paths=None):
super().__init__(nsim, paths) super().__init__(nsim, paths)
self.kind = kind self.kind = kind
@ -675,11 +692,11 @@ class CSiBORG2Field(BaseField):
with File(fpath, "r") as f: with File(fpath, "r") as f:
field = f["density"][:] field = f["density"][:]
field *= 1e10 # Convert to Msun / h field *= 1e10 # Convert to Msun / h
field /= (676.6 * 1e3 / 1024)**3 # Convert to h^2 Msun / kpc^3 field /= (676.6 * 1e3 / grid)**3 # Convert to h^2 Msun / kpc^3
field = field.T # Flip x- and z-axes
else: else:
field = numpy.load(fpath) field = numpy.load(fpath)
field = field.T # Flip x- and z-axes
return field return field
def velocity_field(self, MAS, grid): def velocity_field(self, MAS, grid):
@ -688,7 +705,6 @@ class CSiBORG2Field(BaseField):
if MAS == "SPH": if MAS == "SPH":
with File(fpath, "r") as f: with File(fpath, "r") as f:
# TODO: the x and z still have to be flipped.
density = f["density"][:] density = f["density"][:]
v0 = f["p0"][:] / density v0 = f["p0"][:] / density
v1 = f["p1"][:] / density v1 = f["p1"][:] / density
@ -697,6 +713,12 @@ class CSiBORG2Field(BaseField):
else: else:
field = numpy.load(fpath) field = numpy.load(fpath)
# Flip x- and z-axes
field[0, ...] = field[0, ...].T
field[1, ...] = field[1, ...].T
field[2, ...] = field[2, ...].T
field[[0, 2], ...] = field[[2, 0], ...]
return field return field
@ -718,6 +740,7 @@ class QuijoteField(CSiBORG1Field):
""" """
def __init__(self, nsim, paths): def __init__(self, nsim, paths):
super().__init__(nsim, paths) super().__init__(nsim, paths)
self._simname = "quijote"
############################################################################### ###############################################################################

View file

@ -30,7 +30,21 @@ from utils import get_nsims
def density_field(nsim, parser_args): def density_field(nsim, parser_args):
"""Calculate the density field.""" """
Calculate and save the density field from the particle positions and
masses.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Command line arguments.
Returns
-------
density_field : 3-dimensional array
"""
if parser_args.MAS == "SPH": if parser_args.MAS == "SPH":
raise NotImplementedError("SPH is not implemented here. Use cosmotool") raise NotImplementedError("SPH is not implemented here. Use cosmotool")
@ -70,7 +84,21 @@ def density_field(nsim, parser_args):
def velocity_field(nsim, parser_args): def velocity_field(nsim, parser_args):
"""Calculate the velocity field.""" """
Calculate and save the velocity field from the particle positions,
velocities and masses.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Command line arguments.
Returns
-------
velocity_field : 4-dimensional array
"""
if parser_args.MAS == "SPH": if parser_args.MAS == "SPH":
raise NotImplementedError("SPH is not implemented here. Use cosmotool") raise NotImplementedError("SPH is not implemented here. Use cosmotool")
@ -81,7 +109,7 @@ def velocity_field(nsim, parser_args):
snapshot = csiborgtools.read.CSIBORG1Snapshot(nsim, nsnap, paths) snapshot = csiborgtools.read.CSIBORG1Snapshot(nsim, nsnap, paths)
elif "csiborg2" in parser_args.simname: elif "csiborg2" in parser_args.simname:
kind = parser_args.simname.split("_")[-1] kind = parser_args.simname.split("_")[-1]
snapshot = csiborgtools.read.CSIBORG2Snapshot(nsim, nsnap, paths, kind) snapshot = csiborgtools.read.CSIBORG2Snapshot(nsim, nsnap, kind, paths)
elif parser_args.simname == "quijote": elif parser_args.simname == "quijote":
snapshot = csiborgtools.read.QuijoteSnapshot(nsim, nsnap, paths) snapshot = csiborgtools.read.QuijoteSnapshot(nsim, nsnap, paths)
else: else:
@ -108,14 +136,27 @@ def velocity_field(nsim, parser_args):
def radvel_field(nsim, parser_args): def radvel_field(nsim, parser_args):
"""Calculate the radial velocity field.""" """
Calculate and save the radial velocity field.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Command line arguments.
Returns
-------
radvel_field : 3-dimensional array
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring) paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
if parser_args.simname == "csiborg1": if parser_args.simname == "csiborg1":
field = csiborgtools.read.CSiBORG1Field(nsim, paths) field = csiborgtools.read.CSiBORG1Field(nsim, paths)
elif "csiborg2" in parser_args.simname: elif "csiborg2" in parser_args.simname:
kind = parser_args.simname.split("_")[-1] kind = parser_args.simname.split("_")[-1]
field = csiborgtools.read.CSiBORG2Field(nsim, paths, kind) field = csiborgtools.read.CSiBORG2Field(nsim, kind, paths)
elif parser_args.simname == "quijote": elif parser_args.simname == "quijote":
field = csiborgtools.read.QuijoteField(nsim, paths) field = csiborgtools.read.QuijoteField(nsim, paths)
else: else:
@ -136,11 +177,22 @@ def radvel_field(nsim, parser_args):
def observer_peculiar_velocity(nsim, parser_args): def observer_peculiar_velocity(nsim, parser_args):
""" """
Calculate the peculiar velocity of an observer in the centre of the box Calculate the peculiar velocity of an observer in the centre of the box
for several smoothing scales. for several hard-coded smoothing scales.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Command line arguments.
Returns
-------
observer_vp : 4-dimensional array
""" """
boxsize = csiborgtools.simname2boxsize(parser_args.simname) boxsize = csiborgtools.simname2boxsize(parser_args.simname)
# NOTE thevse values are hard-coded. # NOTE these values are hard-coded.
smooth_scales = numpy.array([0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0]) smooth_scales = numpy.array([0., 2.0, 4.0, 8.0, 16.])
smooth_scales /= boxsize smooth_scales /= boxsize
if parser_args.simname == "csiborg1": if parser_args.simname == "csiborg1":

View file

@ -13,12 +13,13 @@
# with this program; if not, write to the Free Software Foundation, Inc., # with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
""" """
Sample a CSiBORG field at galaxy positions and save the result to disk. Script to sample a CSiBORG field at galaxy positions and save the result.
Supports additional smoothing of the field as well.
""" """
from argparse import ArgumentParser from argparse import ArgumentParser
from distutils.util import strtobool
from os.path import join from os.path import join
import csiborgtools
import numpy import numpy
from astropy.cosmology import FlatLambdaCDM from astropy.cosmology import FlatLambdaCDM
from h5py import File from h5py import File
@ -26,54 +27,42 @@ from mpi4py import MPI
from taskmaster import work_delegation from taskmaster import work_delegation
from tqdm import tqdm from tqdm import tqdm
import csiborgtools
from utils import get_nsims from utils import get_nsims
# TODO get rid of this.
# MPC2BOX = 1 / 677.7
SIM2BOXSIZE = {"csiborg1": 677.7,
"csiborg2_main": None,
"csiborg2_random": None,
"csiborg2_varysmall": None,
}
def steps(cls, survey_name):
"""Make a list of selection criteria to apply to a survey."""
if survey_name == "SDSS":
return [
# (lambda x: cls[x], ("IN_DR7_LSS",)),
# (lambda x: cls[x] < 17.6, ("ELPETRO_APPMAG_r", )),
(lambda x: cls[x] < 155.5, ("DIST", ))
]
else:
raise NotImplementedError(f"Survey `{survey_name}` not implemented.")
def open_galaxy_positions(survey_name, comm): def open_galaxy_positions(survey_name, comm):
""" """
Load the survey galaxy positions and indices, broadcasting them to all Load the survey's galaxy positions , broadcasting them to all ranks.
ranks.
Parameters
----------
survey_name : str
Name of the survey.
comm : mpi4py.MPI.Comm
MPI communicator.
Returns
-------
pos : 2-dimensional array
Galaxy positions in the form of (distance, RA, DEC).
""" """
rank, size = comm.Get_rank(), comm.Get_size() rank, size = comm.Get_rank(), comm.Get_size()
if rank == 0: if rank == 0:
if survey_name == "SDSS": if survey_name == "SDSS":
survey = csiborgtools.SDSS()() survey = csiborgtools.SDSS()()
pos = numpy.vstack([survey["DIST_UNCORRECTED"], pos = numpy.vstack([survey["DIST"],
survey["RA"], survey["RA"],
survey["DEC"]], survey["DEC"]],
).T ).T
pos = pos.astype(numpy.float32) pos = pos.astype(numpy.float32)
indxs = survey["INDEX"] elif survey_name == "SDSSxALFALFA":
if survey_name == "SDSSxALFALFA":
survey = csiborgtools.SDSSxALFALFA()() survey = csiborgtools.SDSSxALFALFA()()
pos = numpy.vstack([survey["DIST_UNCORRECTED"], pos = numpy.vstack([survey["DIST"],
survey["RA_1"], survey["RA_1"],
survey["DEC_1"]], survey["DEC_1"]],
).T ).T
pos = pos.astype(numpy.float32) pos = pos.astype(numpy.float32)
indxs = survey["INDEX"]
elif survey_name == "GW170817": elif survey_name == "GW170817":
samples = File("/mnt/extraspace/rstiskalek/GWLSS/H1L1V1-EXTRACT_POSTERIOR_GW170817-1187008600-400.hdf", 'r')["samples"] # noqa samples = File("/mnt/extraspace/rstiskalek/GWLSS/H1L1V1-EXTRACT_POSTERIOR_GW170817-1187008600-400.hdf", 'r')["samples"] # noqa
cosmo = FlatLambdaCDM(H0=100, Om0=0.3175) cosmo = FlatLambdaCDM(H0=100, Om0=0.3175)
@ -82,121 +71,155 @@ def open_galaxy_positions(survey_name, comm):
samples["ra"][:] * 180 / numpy.pi, samples["ra"][:] * 180 / numpy.pi,
samples["dec"][:] * 180 / numpy.pi], samples["dec"][:] * 180 / numpy.pi],
).T ).T
indxs = numpy.arange(pos.shape[0])
else: else:
raise NotImplementedError(f"Survey `{survey_name}` not " raise NotImplementedError(f"Survey `{survey_name}` not "
"implemented.") "implemented.")
else: else:
pos = None pos = None
indxs = None
comm.Barrier() comm.Barrier()
if size > 1: if size > 1:
pos = comm.bcast(pos, root=0) pos = comm.bcast(pos, root=0)
indxs = comm.bcast(indxs, root=0)
return pos, indxs return pos
def evaluate_field(field, pos, nrand, smooth_scales=None, seed=42, def evaluate_field(field, pos, boxsize, smooth_scales, verbose=True):
verbose=True):
""" """
Evaluate the field at the given sky positions. Additionally, evaluate the Evaluate the field at the given galaxy positions.
field at `nrand` random positions.
Parameters
----------
field : 3-dimensional array
Cartesian field to be evaluated.
pos : 2-dimensional array
Galaxy positions in the form of (distance, RA, DEC).
boxsize : float
Box size in `Mpc / h`.
smooth_scales : list
List of smoothing scales in `Mpc / h`.
verbose : bool
Verbosity flag.
Returns
-------
val : 2-dimensional array
Evaluated field.
""" """
if smooth_scales is None: mpc2box = 1. / boxsize
smooth_scales = [0.] val = numpy.full((pos.shape[0], len(smooth_scales)), numpy.nan,
dtype=field.dtype)
nsample = pos.shape[0]
nsmooth = len(smooth_scales)
val = numpy.full((nsample, nsmooth), numpy.nan, dtype=field.dtype)
if nrand > 0:
rand_val = numpy.full((nsample, nsmooth, nrand), numpy.nan,
dtype=field.dtype)
else:
rand_val = None
for i, scale in enumerate(tqdm(smooth_scales, desc="Smoothing", for i, scale in enumerate(tqdm(smooth_scales, desc="Smoothing",
disable=not verbose)): disable=not verbose)):
if scale > 0: if scale > 0:
field_smoothed = csiborgtools.field.smoothen_field( field_smoothed = csiborgtools.field.smoothen_field(
field, scale * MPC2BOX, boxsize=1, make_copy=True) field, scale * mpc2box, boxsize=1, make_copy=True)
else: else:
field_smoothed = numpy.copy(field) field_smoothed = numpy.copy(field)
val[:, i] = csiborgtools.field.evaluate_sky( val[:, i] = csiborgtools.field.evaluate_sky(
field_smoothed, pos=pos, mpc2box=MPC2BOX) field_smoothed, pos=pos, mpc2box=mpc2box)
if nrand == 0: return val
continue
for j in range(nrand):
gen = numpy.random.default_rng(seed + j)
pos_rand = numpy.vstack([
gen.permutation(pos[:, 0]),
gen.uniform(0, 360, nsample),
90 - numpy.rad2deg(numpy.arccos(gen.uniform(-1, 1, nsample))),
]).T
rand_val[:, i, j] = csiborgtools.field.evaluate_sky(
field_smoothed, pos=pos_rand, mpc2box=MPC2BOX)
return val, rand_val, smooth_scales
def match_to_no_selection(val, rand_val, parser_args): def match_to_no_selection(val, parser_args):
if parser_args.survey == "SDSSxALFALFA": """
Match the shape of the evaluated field to the shape of the survey without
any masking. Missing values are filled with `numpy.nan`.
Parameters
----------
val : n-dimensional array
Evaluated field.
parser_args : argparse.Namespace
Command line arguments.
Returns
-------
n-dimensional array
"""
if parser_args.survey == "SDSS":
survey = csiborgtools.SDSS()()
elif parser_args.survey == "SDSSxALFALFA":
survey = csiborgtools.SDSSxALFALFA()() survey = csiborgtools.SDSSxALFALFA()()
else: else:
raise NotImplementedError( raise NotImplementedError(
f"Survey `{parser_args.survey}` not implemented for matching to no selection.") # noqa f"Survey `{parser_args.survey}` not implemented for matching to no selection.") # noqa
if val is not None: return csiborgtools.read.match_array_to_no_masking(val, survey)
val = csiborgtools.read.match_array_to_no_masking(val, survey)
if rand_val is not None:
rand_val = csiborgtools.read.match_array_to_no_masking(rand_val,
survey)
return val, rand_val
def main(nsim, parser_args, pos, indxs, paths, verbose): def main(nsim, parser_args, pos, verbose):
"""Load the field, interpolate it and save it to disk.""" """
fpath_field = paths.field(parser_args.kind, parser_args.MAS, Main function to load the field, interpolate (and smooth it) it and save
parser_args.grid, nsim, parser_args.in_rsp) the results to the disk.
field = numpy.load(fpath_field)
val, rand_val, smooth_scales = evaluate_field( Parameters
field, pos, nrand=parser_args.nrand, ----------
smooth_scales=parser_args.smooth_scales, verbose=verbose) nsim : int
IC realisation.
parser_args : argparse.Namespace
Command line arguments.
pos : numpy.ndarray
Galaxy coordinates in the form of (distance, RA, DEC) where to evaluate
the field.
verbose : bool
Verbosity flag.
Returns
-------
None
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
boxsize = csiborgtools.simname2boxsize(parser_args.simname)
# Get the appropriate field loader
if parser_args.simname == "csiborg1":
freader = csiborgtools.read.CSiBORG1Field(nsim)
elif "csiborg2" in parser_args.simname:
kind = parser_args.simname.split("_")[-1]
freader = csiborgtools.read.CSiBORG2Field(nsim, kind)
else:
raise NotImplementedError(f"Simulation `{parser_args.simname}` is not supported.") # noqa
# Get the appropriate field
if parser_args.kind == "density":
field = freader.density_field(parser_args.MAS, parser_args.grid)
else:
raise NotImplementedError(f"Field `{parser_args.kind}` is not supported.") # noqa
val = evaluate_field(field, pos, boxsize, parser_args.smooth_scales,
verbose=verbose)
if parser_args.survey == "GW170817": if parser_args.survey == "GW170817":
kind = parser_args.kind
kind = kind + "_rsp" if parser_args.in_rsp else kind
fout = join( fout = join(
"/mnt/extraspace/rstiskalek/GWLSS/", "/mnt/extraspace/rstiskalek/GWLSS/",
f"{kind}_{parser_args.MAS}_{parser_args.grid}_{nsim}_H1L1V1-EXTRACT_POSTERIOR_GW170817-1187008600-400.npz") # noqa f"{parser_args.kind}_{parser_args.MAS}_{parser_args.grid}_{nsim}_H1L1V1-EXTRACT_POSTERIOR_GW170817-1187008600-400.npz") # noqa
else: else:
fout = paths.field_interpolated(parser_args.survey, parser_args.kind, fout = paths.field_interpolated(
parser_args.MAS, parser_args.grid, parser_args.survey, parser_args.simname, nsim, parser_args.kind,
nsim, parser_args.in_rsp) parser_args.MAS, parser_args.grid)
# The survey above had some cuts, however for compatibility we want # The survey above had some cuts, however for compatibility we want
# the same shape as the `uncut` survey # the same shape as the `uncut` survey
val, rand_val = match_to_no_selection(val, rand_val, parser_args) val = match_to_no_selection(val, parser_args)
if verbose: if verbose:
print(f"Saving to ... `{fout}`.") print(f"Saving to ... `{fout}`.")
numpy.savez(fout, val=val, rand_val=rand_val, indxs=indxs,
smooth_scales=smooth_scales) numpy.savez(fout, val=val, smooth_scales=parser_args.smooth_scales)
if __name__ == "__main__": if __name__ == "__main__":
parser = ArgumentParser() parser = ArgumentParser()
parser.add_argument("--nsims", type=int, nargs="+", default=None, parser.add_argument("--nsims", type=int, nargs="+", default=None,
help="IC realisations. If `-1` processes all.") help="IC realisations. If `-1` processes all.")
parser.add_argument("--simname", type=str, default="csiborg1",
choices=["csiborg1", "csiborg2_main", "csiborg2_random", "csiborg2_varysmall"], # noqa
help="Simulation name")
parser.add_argument("--survey", type=str, required=True, parser.add_argument("--survey", type=str, required=True,
choices=["SDSS", "SDSSxALFALFA", "GW170817"], choices=["SDSS", "SDSSxALFALFA", "GW170817"],
help="Galaxy survey") help="Galaxy survey")
@ -207,24 +230,17 @@ if __name__ == "__main__":
"potential"], "potential"],
help="What field to interpolate.") help="What field to interpolate.")
parser.add_argument("--MAS", type=str, parser.add_argument("--MAS", type=str,
choices=["NGP", "CIC", "TSC", "PCS"], choices=["NGP", "CIC", "TSC", "PCS", "SPH"],
help="Mass assignment scheme.") help="Mass assignment scheme.")
parser.add_argument("--grid", type=int, help="Grid resolution.") parser.add_argument("--grid", type=int, help="Grid resolution.")
parser.add_argument("--in_rsp", type=lambda x: bool(strtobool(x)),
help="Field in RSP?")
parser.add_argument("--nrand", type=int, required=True,
help="Number of rand. positions to evaluate the field")
parser.add_argument("--simname", type=str, default="csiborg1",
choices=["csiborg1"], help="Simulation name")
args = parser.parse_args() args = parser.parse_args()
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring) paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsims = get_nsims(args, paths) nsims = get_nsims(args, paths)
pos, indxs = open_galaxy_positions(args.survey, MPI.COMM_WORLD) pos = open_galaxy_positions(args.survey, MPI.COMM_WORLD)
def _main(nsim): def _main(nsim):
main(nsim, args, pos, indxs, paths, main(nsim, args, pos, verbose=MPI.COMM_WORLD.Get_size() == 1)
verbose=MPI.COMM_WORLD.Get_size() == 1)
work_delegation(_main, nsims, MPI.COMM_WORLD) work_delegation(_main, nsims, MPI.COMM_WORLD)