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* Update verbosity messages

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2
csiborgtools/__init__.py
View file

@ -14,7 +14,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
from csiborgtools import clustering, field, match, read # noqa
from .utils import (center_of_mass, delta2ncells, number_counts,
from .utils import (center_of_mass, delta2ncells, number_counts, # noqa
periodic_distance, periodic_distance_two_points) # noqa
# Arguments to csiborgtools.read.Paths.

3
csiborgtools/match/__init__.py
View file

@ -14,4 +14,5 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
from .match import (ParticleOverlap, RealisationsMatcher, # noqa
calculate_overlap, calculate_overlap_indxs, pos2cell, # noqa
cosine_similarity, find_neighbour, get_halo_cell_limits) # noqa
cosine_similarity, find_neighbour, get_halo_cell_limits, # noqa
matching_max) # noqa

142
csiborgtools/match/match.py
View file

@ -236,8 +236,6 @@ class RealisationsMatcher(BaseMatcher):
# We begin by querying the kNN for the nearest neighbours of each halo
# in the reference simulation from the cross simulation in the initial
# snapshot.
if verbose:
print(f"{datetime.now()}: querying the KNN.", flush=True)
match_indxs = radius_neighbours(
catx.knn(in_initial=True, subtract_observer=False, periodic=True),
cat0.position(in_initial=True),
@ -261,11 +259,13 @@ class RealisationsMatcher(BaseMatcher):
return load_processed_halo(hid, particlesx, halo_mapx, hid2mapx,
nshift=0, ncells=self.box_size)
if verbose:
print(f"{datetime.now()}: calculating overlaps.", flush=True)
iterator = tqdm(
cat0["index"],
desc=f"{datetime.now()}: calculating NGP overlaps",
disable=not verbose
)
cross = [numpy.asanyarray([], dtype=numpy.float32)] * match_indxs.size
indxs = cat0["index"]
for i, k0 in enumerate(tqdm(indxs) if verbose else indxs):
for i, k0 in enumerate(iterator):
# If we have no matches continue to the next halo.
matches = match_indxs[i]
if matches.size == 0:
@ -347,12 +347,13 @@ class RealisationsMatcher(BaseMatcher):
return load_processed_halo(hid, particlesx, halo_mapx, hid2mapx,
nshift=nshift, ncells=self.box_size)
if verbose:
print(f"{datetime.now()}: calculating smoothed overlaps.",
flush=True)
iterator = tqdm(
cat0["index"],
desc=f"{datetime.now()}: calculating smoothed overlaps",
disable=not verbose
)
cross = [numpy.asanyarray([], dtype=numpy.float32)] * match_indxs.size
indxs = cat0["index"]
for i, k0 in enumerate(tqdm(indxs) if verbose else indxs):
for i, k0 in enumerate(iterator):
pos0, mass0, __, mins0, maxs0 = load_processed_halo(
k0, particles0, halo_map0, hid2map0, nshift=nshift,
ncells=self.box_size)
@ -434,7 +435,12 @@ class ParticleOverlap(BaseMatcher):
assert ((delta.shape == (ncells,) * 3)
& (delta.dtype == numpy.float32))
for hid in tqdm(halo_cat["index"]) if verbose else halo_cat["index"]:
iterator = tqdm(
halo_cat["index"],
desc=f"{datetime.now()} Calculating the background field",
disable=not verbose
)
for hid in iterator:
pos = load_halo_particles(hid, particles, halo_map, hid2map)
if pos is None:
continue
@ -993,11 +999,13 @@ def radius_neighbours(knn, X, radiusX, radiusKNN, nmult=1.0,
if radiusKNN.size != knn.n_samples_fit_:
raise ValueError("Mismatch in shape of `radiusKNN` or `knn`")
nsamples = len(X)
indxs = [None] * nsamples
patchknn_max = numpy.max(radiusKNN)
for i in trange(nsamples) if verbose else range(nsamples):
iterator = trange(len(X),
desc=f"{datetime.now()}: querying the kNN",
disable=not verbose)
indxs = [None] * len(X)
for i in iterator:
dist, indx = knn.radius_neighbors(
X[i].reshape(1, -1), radiusX[i] + patchknn_max,
sort_results=True)
@ -1082,3 +1090,107 @@ def cosine_similarity(x, y):
out /= numpy.linalg.norm(x) * numpy.linalg.norm(y, axis=1)
return out[0] if out.size == 1 else out
def matching_max(cat0, catx, mass_kind, mult, periodic, overlap=None,
match_indxs=None, verbose=True):
"""
Halo matching algorithm based on [1].
Parameters
----------
cat0 : instance of :py:class:`csiborgtools.read.BaseCatalogue`
Halo catalogue of the reference simulation.
catx : instance of :py:class:`csiborgtools.read.BaseCatalogue`
Halo catalogue of the cross simulation.
mass_kind : str
Name of the mass column.
mult : float
Multiple of R200c below which to consider a match.
periodic : bool
Whether to account for periodic boundary conditions.
overlap : array of 1-dimensional arrays, optional
Overlap of halos from `cat0` with halos from `catx`. If `overlap` or
`match_indxs` is not provided, then the overlap of the identified halos
is not calculated.
match_indxs : array of 1-dimensional arrays, optional
Indicies of halos from `catx` having a non-zero overlap with halos
from `cat0`.
verbose : bool, optional
Verbosity flag.
Returns
-------
out : structured array
Array of matches. Columns are `hid0`, `hidx`, `dist`, `success`.
References
----------
[1] Maxwell L Hutt, Harry Desmond, Julien Devriendt, Adrianne Slyz; The
effect of local Universe constraints on halo abundance and clustering;
Monthly Notices of the Royal Astronomical Society, Volume 516, Issue 3,
November 2022, Pages 3592–3601, https://doi.org/10.1093/mnras/stac2407
"""
pos0 = cat0.position(in_initial=False)
knnx = catx.knn(in_initial=False, subtract_observer=False,
periodic=periodic)
rad0 = cat0["r200c"]
mass0 = numpy.log10(cat0[mass_kind])
massx = numpy.log10(catx[mass_kind])
assert numpy.all(numpy.isfinite(mass0)) & numpy.all(numpy.isfinite(massx))
maskx = numpy.ones(len(catx), dtype=numpy.bool_)
dtypes = [("hid0", numpy.int32),
("hidx", numpy.int32),
("mass0", numpy.float32),
("massx", numpy.float32),
("dist", numpy.float32),
("success", numpy.bool_),
("match_overlap", numpy.float32),
("max_overlap", numpy.float32),
]
out = numpy.full(len(cat0), numpy.nan, dtype=dtypes)
out["success"] = False
for i in tqdm(numpy.argsort(mass0)[::-1], desc="Matching haloes",
disable=not verbose):
hid0 = cat0["index"][i]
out[i]["hid0"] = hid0
out[i]["mass0"] = 10**mass0[i]
neigh_dists, neigh_inds = knnx.radius_neighbors(pos0[i].reshape(1, -1),
mult * rad0[i])
neigh_dists, neigh_inds = neigh_dists[0], neigh_inds[0]
if neigh_dists.size == 0:
continue
# Sort the neighbours by mass difference
sort_order = numpy.argsort(numpy.abs(mass0[i] - massx[neigh_inds]))
neigh_dists = neigh_dists[sort_order]
neigh_inds = neigh_inds[sort_order]
for j, neigh_ind in enumerate(neigh_inds):
if maskx[neigh_ind]:
out[i]["hidx"] = catx["index"][neigh_ind]
out[i]["dist"] = neigh_dists[j]
out[i]["massx"] = 10**massx[neigh_ind]
out[i]["success"] = True
maskx[neigh_ind] = False
if overlap is not None and match_indxs is not None:
if neigh_ind in match_indxs[i]:
k = numpy.where(neigh_ind == match_indxs[i])[0][0]
out[i]["match_overlap"] = overlap[i][k]
if len(overlap[i]) > 0:
out[i]["max_overlap"] = numpy.max(overlap[i])
break
return out

137
csiborgtools/read/overlap_summary.py
View file

@ -21,6 +21,8 @@ from os.path import isfile
import numpy
from tqdm import tqdm, trange
from ..utils import periodic_distance
###############################################################################
# Overlap of two simulations #
###############################################################################
@ -47,6 +49,7 @@ class PairOverlap:
_cat0 = None
_catx = None
_data = None
_paths = None
def __init__(self, cat0, catx, paths, min_logmass, maxdist=None):
if cat0.simname != catx.simname:
@ -55,6 +58,7 @@ class PairOverlap:
self._cat0 = cat0
self._catx = catx
self._paths = paths
self.load(cat0, catx, paths, min_logmass, maxdist)
def load(self, cat0, catx, paths, min_logmass, maxdist=None):
@ -257,6 +261,8 @@ class PairOverlap:
for i in range(len(overlap)):
if len(overlap[i]) > 0:
out[i] = numpy.sum(overlap[i])
else:
out[i] = 0
return out
def prob_nomatch(self, from_smoothed):
@ -279,9 +285,11 @@ class PairOverlap:
for i in range(len(overlap)):
if len(overlap[i]) > 0:
out[i] = numpy.product(numpy.subtract(1, overlap[i]))
else:
out[i] = 1
return out
def dist(self, in_initial, norm_kind=None):
def dist(self, in_initial, boxsize, norm_kind=None):
"""
Pair distances of matched halos between the reference and cross
simulations.
@ -290,6 +298,8 @@ class PairOverlap:
----------
in_initial : bool
Whether to calculate separation in the initial or final snapshot.
boxsize : float
The size of the simulation box.
norm_kind : str, optional
The kind of normalisation to apply to the distances.
Can be `r200c`, `ref_patch` or `sum_patch`.
@ -320,8 +330,7 @@ class PairOverlap:
# Now calculate distances
dist = [None] * len(self)
for i, ind in enumerate(self["match_indxs"]):
# n refers to the reference halo catalogue position
dist[i] = numpy.linalg.norm(pos0[i, :] - posx[ind, :], axis=1)
dist[i] = periodic_distance(posx[ind, :], pos0[i, :], boxsize)
if norm_kind is not None:
dist[i] /= norm[i]
@ -358,7 +367,7 @@ class PairOverlap:
ratio[i] = numpy.abs(ratio[i])
return numpy.array(ratio, dtype=object)
def max_overlap_key(self, key, from_smoothed):
def max_overlap_key(self, key, min_overlap, from_smoothed):
"""
Calculate the maximum overlap mass of each halo in the reference
simulation from the cross simulation.
@ -367,10 +376,10 @@ class PairOverlap:
----------
key : str
Key to the maximum overlap statistic to calculate.
min_overlap : float
Minimum pair overlap to consider.
from_smoothed : bool
Whether to use the smoothed overlap or not.
mass_kind : str, optional
The mass kind whose ratio is to be calculated.
Returns
-------
@ -384,11 +393,15 @@ class PairOverlap:
# Skip if no match
if len(match_ind) == 0:
continue
out[i] = y[match_ind][numpy.argmax(overlap[i])]
k = numpy.argmax(overlap[i])
if overlap[i][k] > min_overlap:
out[i] = y[match_ind][k]
return out
def counterpart_mass(self, from_smoothed, overlap_threshold=0.,
in_log=False, mass_kind="totpartmass"):
mass_kind="totpartmass"):
"""
Calculate the expected counterpart mass of each halo in the reference
simulation from the crossed simulation.
@ -400,9 +413,6 @@ class PairOverlap:
overlap_threshold : float, optional
Minimum overlap required for a halo to be considered a match. By
default 0.0, i.e. no threshold.
in_log : bool, optional
Whether to calculate the expectation value in log space. By default
`False`.
mass_kind : str, optional
The mass kind whose ratio is to be calculated. Must be a valid
catalogue key. By default `totpartmass`, i.e. the total particle
@ -434,15 +444,11 @@ class PairOverlap:
massx_ = massx_[mask]
overlap_ = overlap_[mask]
massx_ = numpy.log10(massx_) if in_log else massx_
massx_ = numpy.log10(massx_)
# Weighted average and *biased* standard deviation
mean_ = numpy.average(massx_, weights=overlap_)
std_ = numpy.average((massx_ - mean_)**2, weights=overlap_)**0.5
# If in log, convert back to linear
mean_ = 10**mean_ if in_log else mean_
std_ = mean_ * std_ * numpy.log(10) if in_log else std_
mean[i] = mean_
std[i] = std_
@ -544,7 +550,7 @@ def weighted_stats(x, weights, min_weight=0, verbose=False):
"""
out = numpy.full((x.size, 2), numpy.nan, dtype=numpy.float32)
for i in trange(len(x)) if verbose else range(len(x)):
for i in trange(len(x), disable=not verbose):
x_, w_ = numpy.asarray(x[i]), numpy.asarray(weights[i])
mask = w_ > min_weight
x_ = x_[mask]
@ -574,27 +580,30 @@ class NPairsOverlap:
List of cross simulation halo catalogues.
paths : py:class`csiborgtools.read.Paths`
CSiBORG paths object.
min_logmass : float
Minimum log mass of halos to consider.
verbose : bool, optional
Verbosity flag for loading the overlap objects.
"""
_pairs = None
def __init__(self, cat0, catxs, paths, verbose=True):
def __init__(self, cat0, catxs, paths, min_logmass, verbose=True):
pairs = [None] * len(catxs)
if verbose:
print("Loading individual overlap objects...", flush=True)
for i, catx in enumerate(tqdm(catxs) if verbose else catxs):
pairs[i] = PairOverlap(cat0, catx, paths)
for i, catx in enumerate(tqdm(catxs, desc="Loading overlap objects",
disable=not verbose)):
pairs[i] = PairOverlap(cat0, catx, paths, min_logmass)
self._pairs = pairs
def max_overlap(self, from_smoothed, verbose=True):
def max_overlap(self, min_overlap, from_smoothed, verbose=True):
"""
Calculate maximum overlap of each halo in the reference simulation with
the cross simulations.
Parameters
----------
min_overlap : float
Minimum pair overlap to consider.
from_smoothed : bool
Whether to use the smoothed overlap or not.
verbose : bool, optional
@ -604,21 +613,24 @@ class NPairsOverlap:
-------
max_overlap : 2-dimensional array of shape `(nhalos, ncatxs)`
"""
out = [None] * len(self)
if verbose:
print("Calculating maximum overlap...", flush=True)
def get_max(y_):
if len(y_) == 0:
return numpy.nan
return numpy.max(y_)
return 0
out = numpy.max(y_)
for i, pair in enumerate(tqdm(self.pairs) if verbose else self.pairs):
return out if out >= min_overlap else 0
iterator = tqdm(self.pairs,
desc="Calculating maximum overlap",
disable=not verbose
)
out = [None] * len(self)
for i, pair in enumerate(iterator):
out[i] = numpy.asanyarray([get_max(y_)
for y_ in pair.overlap(from_smoothed)])
return numpy.vstack(out).T
def max_overlap_key(self, key, from_smoothed, verbose=True):
def max_overlap_key(self, key, min_overlap, from_smoothed, verbose=True):
"""
Calculate maximum overlap mass of each halo in the reference
simulation with the cross simulations.
@ -627,6 +639,8 @@ class NPairsOverlap:
----------
key : str
Key to the maximum overlap statistic to calculate.
min_overlap : float
Minimum pair overlap to consider.
from_smoothed : bool
Whether to use the smoothed overlap or not.
verbose : bool, optional
@ -636,12 +650,13 @@ class NPairsOverlap:
-------
out : 2-dimensional array of shape `(nhalos, ncatxs)`
"""
iterator = tqdm(self.pairs,
desc=f"Calculating maximum overlap {key}",
disable=not verbose
)
out = [None] * len(self)
if verbose:
print(f"Calculating maximum overlap {key}...", flush=True)
for i, pair in enumerate(tqdm(self.pairs) if verbose else self.pairs):
out[i] = pair.max_overlap_key(key, from_smoothed)
for i, pair in enumerate(iterator):
out[i] = pair.max_overlap_key(key, min_overlap, from_smoothed)
return numpy.vstack(out).T
@ -661,10 +676,11 @@ class NPairsOverlap:
-------
summed_overlap : 2-dimensional array of shape `(nhalos, ncatxs)`
"""
iterator = tqdm(self.pairs,
desc="Calculating summed overlap",
disable=not verbose)
out = [None] * len(self)
if verbose:
print("Calculating summed overlap...", flush=True)
for i, pair in enumerate(tqdm(self.pairs) if verbose else self.pairs):
for i, pair in enumerate(iterator):
out[i] = pair.summed_overlap(from_smoothed)
return numpy.vstack(out).T
@ -684,16 +700,18 @@ class NPairsOverlap:
-------
prob_nomatch : 2-dimensional array of shape `(nhalos, ncatxs)`
"""
iterator = tqdm(self.pairs,
desc="Calculating probability of no match",
disable=not verbose
)
out = [None] * len(self)
if verbose:
print("Calculating probability of no match...", flush=True)
for i, pair in enumerate(tqdm(self.pairs) if verbose else self.pairs):
for i, pair in enumerate(iterator):
out[i] = pair.prob_nomatch(from_smoothed)
return numpy.vstack(out).T
def counterpart_mass(self, from_smoothed, overlap_threshold=0.,
in_log=False, mass_kind="totpartmass",
return_full=False, verbose=True):
mass_kind="totpartmass", return_full=False,
verbose=True):
"""
Calculate the expected counterpart mass of each halo in the reference
simulation from the crossed simulation.
@ -705,9 +723,6 @@ class NPairsOverlap:
overlap_threshold : float, optional
Minimum overlap required for a halo to be considered a match. By
default 0.0, i.e. no threshold.
in_log : bool, optional
Whether to calculate the expectation value in log space. By default
`False`.
mass_kind : str, optional
The mass kind whose ratio is to be calculated. Must be a valid
catalogue key. By default `totpartmass`, i.e. the total particle
@ -727,26 +742,31 @@ class NPairsOverlap:
Expected mass and standard deviation from each cross simulation.
Returned only if `return_full` is `True`.
"""
iterator = tqdm(self.pairs,
desc="Calculating counterpart masses",
disable=not verbose)
mus, stds = [None] * len(self), [None] * len(self)
if verbose:
print("Calculating counterpart masses...", flush=True)
for i, pair in enumerate(tqdm(self.pairs) if verbose else self.pairs):
for i, pair in enumerate(iterator):
mus[i], stds[i] = pair.counterpart_mass(
from_smoothed=from_smoothed,
overlap_threshold=overlap_threshold, in_log=in_log,
mass_kind=mass_kind)
overlap_threshold=overlap_threshold, mass_kind=mass_kind)
mus, stds = numpy.vstack(mus).T, numpy.vstack(stds).T
probmatch = 1 - self.prob_nomatch(from_smoothed) # Prob of > 0 matches
# Prob of > 0 matches
probmatch = 1 - self.prob_nomatch(from_smoothed)
# Normalise it for weighted sums etc.
norm_probmatch = numpy.apply_along_axis(
lambda x: x / numpy.sum(x), axis=1, arr=probmatch)
# Mean and standard deviation of weighted stacked Gaussians
mu = numpy.sum(norm_probmatch * mus, axis=1)
std = numpy.sum(norm_probmatch * (mus**2 + stds**2), axis=1) - mu**2
mu = numpy.sum((norm_probmatch * mus), axis=1)
std = numpy.sum((norm_probmatch * (mus**2 + stds**2)), axis=1) - mu**2
std **= 0.5
mask = mu <= 0
mu[mask] = numpy.nan
std[mask] = numpy.nan
if return_full:
return mu, std, mus, stds
return mu, std
@ -766,6 +786,11 @@ class NPairsOverlap:
def cat0(self):
return self.pairs[0].cat0 # All pairs have the same ref catalogue
def __getitem__(self, key):
if not isinstance(key, int):
raise TypeError("Key must be an integer.")
return self.pairs[key]
def __len__(self):
return len(self.pairs)
@ -794,7 +819,7 @@ def get_cross_sims(simname, nsim0, paths, min_logmass, smoothed):
Whether to use the smoothed overlap or not.
"""
nsimxs = []
for nsimx in paths.get_ics("csiborg"):
for nsimx in paths.get_ics(simname):
if nsimx == nsim0:
continue
f1 = paths.overlap(simname, nsim0, nsimx, min_logmass, smoothed)

44
csiborgtools/read/paths.py
View file

@ -501,6 +501,50 @@ class Paths:
fname = fname.replace("overlap", "overlap_smoothed")
return join(fdir, fname)
def match_max(self, simname, nsim0, nsimx, min_logmass, mult):
"""
Path to the files containing matching based on [1].
Parameters
----------
simname : str
Simulation name.
nsim0 : int
IC realisation index of the first simulation.
nsimx : int
IC realisation index of the second simulation.
min_logmass : float
Minimum log mass of halos to consider.
mult : float
Multiplicative search radius factor.
Returns
-------
path : str
References
----------
[1] Maxwell L Hutt, Harry Desmond, Julien Devriendt, Adrianne Slyz; The
effect of local Universe constraints on halo abundance and clustering;
Monthly Notices of the Royal Astronomical Society, Volume 516, Issue 3,
November 2022, Pages 3592–3601, https://doi.org/10.1093/mnras/stac2407
"""
if simname == "csiborg":
fdir = join(self.postdir, "match_max")
elif simname == "quijote":
fdir = join(self.quijote_dir, "match_max")
else:
ValueError(f"Unknown simulation name `{simname}`.")
try_create_directory(fdir)
nsim0 = str(nsim0).zfill(5)
nsimx = str(nsimx).zfill(5)
min_logmass = float('%.4g' % min_logmass)
fname = f"match_max_{nsim0}_{nsimx}_{min_logmass}_{str(mult)}.npz"
return join(fdir, fname)
def field(self, kind, MAS, grid, nsim, in_rsp, smooth_scale=None):
r"""
Path to the files containing the calculated density fields in CSiBORG.

47
scripts/match_all.py
View file

@ -12,6 +12,7 @@
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""A script to match all IC pairs of a simulation."""
import warnings
from argparse import ArgumentParser
from distutils.util import strtobool
from itertools import combinations
@ -20,15 +21,8 @@ from random import Random
from mpi4py import MPI
from taskmaster import work_delegation
from match_singlematch import pair_match
try:
import csiborgtools
except ModuleNotFoundError:
import sys
sys.path.append("../")
import csiborgtools
import csiborgtools
from match_singlematch import pair_match, pair_match_max
def get_combs(simname):
@ -53,7 +47,7 @@ def get_combs(simname):
return combs
def main(comb, simname, min_logmass, sigma, verbose):
def main(comb, kind, simname, min_logmass, sigma, mult, verbose):
"""
Match a pair of simulations.
@ -61,12 +55,16 @@ def main(comb, simname, min_logmass, sigma, verbose):
----------
comb : tuple
Pair of simulation IC indices.
kind : str
Kind of matching.
simname : str
Simulation name.
min_logmass : float
Minimum log halo mass.
sigma : float
Smoothing scale in number of grid cells.
mult : float
Multiplicative factor for search radius.
verbose : bool
Verbosity flag.
@ -75,25 +73,46 @@ def main(comb, simname, min_logmass, sigma, verbose):
None
"""
nsim0, nsimx = comb
if kind == "overlap":
pair_match(nsim0, nsimx, simname, min_logmass, sigma, verbose)
elif args.kind == "max":
pair_match_max(nsim0, nsimx, simname, min_logmass, mult, verbose)
else:
raise ValueError(f"Unknown matching kind: `{kind}`.")
if __name__ == "__main__":
parser = ArgumentParser()
parser.add_argument("--kind", type=str, required=True,
choices=["overlap", "max"], help="Kind of matching.")
parser.add_argument("--simname", type=str, required=True,
help="Simulation name.", choices=["csiborg", "quijote"])
help="Simulation name.",
choices=["csiborg", "quijote"])
parser.add_argument("--nsim0", type=int, default=None,
help="Reference IC for Max's matching method.")
parser.add_argument("--min_logmass", type=float, required=True,
help="Minimum log halo mass.")
parser.add_argument("--sigma", type=float, default=0,
help="Smoothing scale in number of grid cells.")
parser.add_argument("--mult", type=float, default=5,
help="Search radius multiplier for Max's method.")
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
default=False, help="Verbosity flag.")
args = parser.parse_args()
combs = get_combs()
if args.kind == "overlap":
combs = get_combs(args.simname)
else:
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
combs = [(args.nsim0, nsimx) for nsimx in paths.get_ics(args.simname)
if nsimx != args.nsim0]
def _main(comb):
main(comb, args.simname, args.min_logmass, args.sigma, args.verbose)
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
"invalid value encountered in cast",
RuntimeWarning)
main(comb, args.kind, args.simname, args.min_logmass, args.sigma,
args.mult, args.verbose)
work_delegation(_main, combs, MPI.COMM_WORLD)

94
scripts/match_singlematch.py
View file

@ -23,13 +23,75 @@ from distutils.util import strtobool
import numpy
from scipy.ndimage import gaussian_filter
try:
import csiborgtools
except ModuleNotFoundError:
import sys
import csiborgtools
sys.path.append("../")
import csiborgtools
def pair_match_max(nsim0, nsimx, simname, min_logmass, mult, verbose):
"""
Match a pair of simulations using the method of [1].
Parameters
----------
nsim0 : int
The reference simulation IC index.
nsimx : int
The cross simulation IC index.
simname : str
Simulation name.
min_logmass : float
Minimum log halo mass.
mult : float
Multiplicative factor for search radius.
verbose : bool
Verbosity flag.
Returns
-------
None
References
----------
[1] Maxwell L Hutt, Harry Desmond, Julien Devriendt, Adrianne Slyz; The
effect of local Universe constraints on halo abundance and clustering;
Monthly Notices of the Royal Astronomical Society, Volume 516, Issue 3,
November 2022, Pages 3592–3601, https://doi.org/10.1093/mnras/stac2407
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
if simname == "csiborg":
mass_kind = "fof_totpartmass"
maxdist = 155
periodic = False
bounds = {"dist": (0, maxdist), mass_kind: (10**min_logmass, None)}
cat0 = csiborgtools.read.CSiBORGHaloCatalogue(
nsim0, paths, bounds=bounds, load_fitted=True, load_initial=False)
catx = csiborgtools.read.CSiBORGHaloCatalogue(
nsimx, paths, bounds=bounds, load_fitted=True, load_initial=False)
elif simname == "quijote":
mass_kind = "group_mass"
maxdist = None
periodic = True
bounds = {mass_kind: (10**min_logmass, None)}
cat0 = csiborgtools.read.QuijoteHaloCatalogue(
nsim0, paths, 4, bounds=bounds, load_fitted=True,
load_initial=False)
catx = csiborgtools.read.QuijoteHaloCatalogue(
nsimx, paths, 4, bounds=bounds, load_fitted=True,
load_initial=False)
else:
raise ValueError(f"Unknown simulation `{simname}`.")
reader = csiborgtools.read.PairOverlap(cat0, catx, paths, min_logmass,
maxdist=maxdist)
out = csiborgtools.match.matching_max(
cat0, catx, mass_kind, mult=mult, periodic=periodic,
overlap=reader.overlap(from_smoothed=True),
match_indxs=reader["match_indxs"], verbose=verbose)
fout = paths.match_max(simname, nsim0, nsimx, min_logmass, mult)
if verbose:
print(f"{datetime.now()}: saving to ... `{fout}`.", flush=True)
numpy.savez(fout, **{p: out[p] for p in out.dtype.names})
def pair_match(nsim0, nsimx, simname, min_logmass, sigma, verbose):
@ -95,27 +157,17 @@ def pair_match(nsim0, nsimx, simname, min_logmass, sigma, verbose):
paths.initmatch(nsimx, simname, "particles"))["particles"]
hid2mapx = {hid: i for i, hid in enumerate(halomapx[:, 0])}
if verbose:
print(f"{datetime.now()}: calculating the background density fields.",
flush=True)
overlapper = csiborgtools.match.ParticleOverlap(**overlapper_kwargs)
delta_bckg = overlapper.make_bckg_delta(parts0, halomap0, hid2map0, cat0,
verbose=verbose)
delta_bckg = overlapper.make_bckg_delta(partsx, halomapx, hid2mapx, catx,
delta=delta_bckg, verbose=verbose)
if verbose:
print()
if verbose:
print(f"{datetime.now()}: NGP crossing the simulations.", flush=True)
matcher = csiborgtools.match.RealisationsMatcher(
mass_kind=mass_kind, **overlapper_kwargs)
match_indxs, ngp_overlap = matcher.cross(cat0, catx, parts0, partsx,
halomap0, halomapx, delta_bckg,
verbose=verbose)
if verbose:
print()
# We want to store the halo IDs of the matches, not their array positions
# in the catalogues.
@ -151,6 +203,8 @@ def pair_match(nsim0, nsimx, simname, min_logmass, sigma, verbose):
if __name__ == "__main__":
parser = ArgumentParser()
parser.add_argument("--kind", type=str, required=True,
choices=["overlap", "max"], help="Kind of matching.")
parser.add_argument("--nsim0", type=int, required=True,
help="Reference simulation IC index.")
parser.add_argument("--nsimx", type=int, required=True,
@ -159,11 +213,19 @@ if __name__ == "__main__":
help="Simulation name.")
parser.add_argument("--min_logmass", type=float, required=True,
help="Minimum log halo mass.")
parser.add_argument("--mult", type=float, default=5,
help="Search radius multiplier for Max's method.")
parser.add_argument("--sigma", type=float, default=0,
help="Smoothing scale in number of grid cells.")
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
default=False, help="Verbosity flag.")
args = parser.parse_args()
if args.kind == "overlap":
pair_match(args.nsim0, args.nsimx, args.simname, args.min_logmass,
args.sigma, args.verbose)
elif args.kind == "max":
pair_match_max(args.nsim0, args.nsimx, args.simname, args.min_logmass,
args.mult, args.verbose)
else:
raise ValueError(f"Unknown matching kind: `{args.kind}`.")

677
scripts_plots/plot_1nn.py
View file

@ -14,17 +14,15 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
from argparse import ArgumentParser
from gc import collect
from os.path import join
import matplotlib as mpl
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
import numpy
import scienceplots # noqa
from cache_to_disk import cache_to_disk, delete_disk_caches_for_function
from scipy.stats import kendalltau
from tqdm import trange, tqdm
from tqdm import tqdm
import plt_utils
@ -36,11 +34,7 @@ except ModuleNotFoundError:
import csiborgtools
###############################################################################
# IC overlap plotting #
###############################################################################
def open_cat(nsim: int, simname: str):
def open_cat(nsim, simname):
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
if simname == "csiborg":
@ -57,647 +51,16 @@ def open_cat(nsim: int, simname: str):
return cat
def open_cats(nsims, simname):
catxs = [None] * len(nsims)
for i, nsim in enumerate(tqdm(nsims, desc="Opening catalogues")):
catxs[i] = open_cat(nsim, simname)
@cache_to_disk(7)
def get_overlap(simname, nsim0):
"""
Calculate the summed overlap and probability of no match for a single
reference simulation.
Parameters
----------
simname : str
Simulation name.
nsim0 : int
Simulation index.
Returns
-------
mass : 1-dimensional array
Mass of halos in the reference simulation.
hindxs : 1-dimensional array
Halo indices in the reference simulation.
max_overlap : 2-dimensional array
Maximum overlap for each halo in the reference simulation.
summed_overlap : 2-dimensional array
Summed overlap for each halo in the reference simulation.
prob_nomatch : 2-dimensional array
Probability of no match for each halo in the reference simulation.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsimxs = csiborgtools.read.get_cross_sims(simname, nsim0, paths,
smoothed=True)
cat0 = open_cat(nsim0)
catxs = []
print("Opening catalogues...", flush=True)
for nsimx in tqdm(nsimxs):
catxs.append(open_cat(nsimx))
reader = csiborgtools.read.NPairsOverlap(cat0, catxs, paths)
mass = reader.cat0("totpartmass")
hindxs = reader.cat0("index")
summed_overlap = reader.summed_overlap(True)
max_overlap = reader.max_overlap(True)
prob_nomatch = reader.prob_nomatch(True)
return mass, hindxs, max_overlap, summed_overlap, prob_nomatch
@cache_to_disk(7)
def get_max_key(simname, nsim0, key):
"""
Get the value of a maximum overlap halo's property.
Parameters
----------
simname : str
Simulation name.
nsim0 : int
Reference simulation index.
key : str
Property to get.
Returns
-------
mass0 : 1-dimensional array
Mass of the reference haloes.
key_val : 1-dimensional array
Value of the property of the reference haloes.
max_overlap : 2-dimensional array
Maximum overlap of the reference haloes.
stat : 2-dimensional array
Value of the property of the maximum overlap halo.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsimxs = csiborgtools.read.get_cross_sims(simname, nsim0, paths,
smoothed=True)
nsimxs = nsimxs
cat0 = open_cat(nsim0)
catxs = []
print("Opening catalogues...", flush=True)
for nsimx in tqdm(nsimxs):
catxs.append(open_cat(nsimx))
reader = csiborgtools.read.NPairsOverlap(cat0, catxs, paths)
mass0 = reader.cat0("totpartmass")
key_val = reader.cat0(key)
max_overlap = reader.max_overlap(True)
stat = reader.max_overlap_key(key, True)
return mass0, key_val, max_overlap, stat
def plot_mass_vs_pairoverlap(nsim0, nsimx):
"""
Plot the pair overlap of a reference simulation with a single cross
simulation as a function of the reference halo mass.
Parameters
----------
nsim0 : int
Reference simulation index.
nsimx : int
Cross simulation index.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
cat0 = open_cat(nsim0)
catx = open_cat(nsimx)
reader = csiborgtools.read.PairOverlap(cat0, catx, paths)
x = reader.copy_per_match("totpartmass")
y = reader.overlap(True)
x = numpy.log10(numpy.concatenate(x))
y = numpy.concatenate(y)
with plt.style.context(plt_utils.mplstyle):
plt.figure()
plt.hexbin(x, y, mincnt=1, bins="log",
gridsize=50)
plt.colorbar(label="Counts in bins")
plt.xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
plt.ylabel("Pair overlap")
plt.ylim(0., 1.)
plt.tight_layout()
for ext in ["png"]:
fout = join(plt_utils.fout, f"mass_vs_pair_overlap{nsim0}.{ext}")
print(f"Saving to `{fout}`.")
plt.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
def plot_mass_vs_maxpairoverlap(nsim0, nsimx):
"""
Plot the maximum pair overlap of a reference simulation haloes with a
single cross simulation.
Parameters
----------
nsim0 : int
Reference simulation index.
nsimx : int
Cross simulation index.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
cat0 = open_cat(nsim0)
catx = open_cat(nsimx)
reader = csiborgtools.read.PairOverlap(cat0, catx, paths)
x = numpy.log10(cat0["totpartmass"])
y = reader.overlap(True)
def get_max(y_):
if len(y_) == 0:
return numpy.nan
return numpy.max(y_)
y = numpy.array([get_max(y_) for y_ in y])
with plt.style.context(plt_utils.mplstyle):
plt.figure()
plt.hexbin(x, y, mincnt=1, bins="log",
gridsize=50)
plt.colorbar(label="Counts in bins")
plt.xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
plt.ylabel("Maximum pair overlap")
plt.ylim(0., 1.)
plt.tight_layout()
for ext in ["png"]:
fout = join(plt_utils.fout, f"mass_vs_maxpairoverlap{nsim0}.{ext}")
print(f"Saving to `{fout}`.")
plt.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
def plot_mass_vsmedmaxoverlap(nsim0):
"""
Plot the mean maximum overlap of a reference simulation haloes with all the
cross simulations.
Parameters
----------
nsim0 : int
Reference simulation index.
"""
x, __, max_overlap, __, __ = get_overlap("csiborg", nsim0)
for i in trange(max_overlap.shape[0]):
if numpy.sum(numpy.isnan(max_overlap[i, :])) > 0:
max_overlap[i, :] = numpy.nan
x = numpy.log10(x)
with plt.style.context(plt_utils.mplstyle):
fig, axs = plt.subplots(ncols=3, figsize=(3.5 * 2, 2.625))
im1 = axs[0].hexbin(x, numpy.nanmean(max_overlap, axis=1), gridsize=30,
mincnt=1, bins="log")
im2 = axs[1].hexbin(x, numpy.nanstd(max_overlap, axis=1), gridsize=30,
mincnt=1, bins="log")
im3 = axs[2].hexbin(numpy.nanmean(max_overlap, axis=1),
numpy.nanstd(max_overlap, axis=1), gridsize=30,
C=x, reduce_C_function=numpy.nanmean)
axs[0].set_xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
axs[0].set_ylabel(r"Mean max. pair overlap")
axs[1].set_xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
axs[1].set_ylabel(r"Uncertainty of max. pair overlap")
axs[2].set_xlabel(r"Mean max. pair overlap")
axs[2].set_ylabel(r"Uncertainty of max. pair overlap")
label = ["Bin counts", "Bin counts", r"$\log M_{\rm tot} / M_\odot$"]
ims = [im1, im2, im3]
for i in range(3):
axins = inset_axes(axs[i], width="100%", height="5%",
loc='upper center', borderpad=-0.75)
fig.colorbar(ims[i], cax=axins, orientation="horizontal",
label=label[i])
axins.xaxis.tick_top()
axins.xaxis.set_tick_params(labeltop=True)
axins.xaxis.set_label_position("top")
fig.tight_layout()
for ext in ["png"]:
fout = join(plt_utils.fout, f"maxpairoverlap_{nsim0}.{ext}")
print(f"Saving to `{fout}`.")
fig.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
def plot_summed_overlap_vs_mass(nsim0):
"""
Plot the summed overlap of probability of no matching for a single
reference simulations as a function of the reference halo mass, along with
their comparison.
Parameters
----------
nsim0 : int
Simulation index.
Returns
-------
None
"""
x, __, __, summed_overlap, prob_nomatch = get_overlap("csiborg", nsim0)
del __
collect()
for i in trange(summed_overlap.shape[0]):
if numpy.sum(numpy.isnan(summed_overlap[i, :])) > 0:
summed_overlap[i, :] = numpy.nan
x = numpy.log10(x)
mean_overlap = numpy.nanmean(summed_overlap, axis=1)
std_overlap = numpy.nanstd(summed_overlap, axis=1)
mean_prob_nomatch = numpy.nanmean(prob_nomatch, axis=1)
mask = mean_overlap > 0
x = x[mask]
mean_overlap = mean_overlap[mask]
std_overlap = std_overlap[mask]
mean_prob_nomatch = mean_prob_nomatch[mask]
with plt.style.context(plt_utils.mplstyle):
fig, axs = plt.subplots(ncols=3, figsize=(3.5 * 2, 2.625))
im1 = axs[0].hexbin(x, mean_overlap, mincnt=1, bins="log",
gridsize=30)
im2 = axs[1].hexbin(x, std_overlap, mincnt=1, bins="log",
gridsize=30)
im3 = axs[2].scatter(1 - mean_overlap, mean_prob_nomatch, c=x, s=2,
rasterized=True)
t = numpy.linspace(0.3, 1, 100)
axs[2].plot(t, t, color="red", linestyle="--")
axs[0].set_ylim(0.)
axs[1].set_ylim(0.)
axs[0].set_xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
axs[0].set_ylabel("Mean summed overlap")
axs[1].set_xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
axs[1].set_ylabel("Uncertainty of summed overlap")
axs[2].set_xlabel(r"$1 - $ mean summed overlap")
axs[2].set_ylabel("Mean prob. of no match")
label = ["Bin counts", "Bin counts",
r"$\log M_{\rm tot} ~ [M_\odot / h]$"]
ims = [im1, im2, im3]
for i in range(3):
axins = inset_axes(axs[i], width="100%", height="5%",
loc='upper center', borderpad=-0.75)
fig.colorbar(ims[i], cax=axins, orientation="horizontal",
label=label[i])
axins.xaxis.tick_top()
axins.xaxis.set_tick_params(labeltop=True)
axins.xaxis.set_label_position("top")
fig.tight_layout()
for ext in ["png"]:
fout = join(plt_utils.fout, f"overlap_stat_{nsim0}.{ext}")
print(f"Saving to `{fout}`.")
fig.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
def plot_mass_vs_separation(nsim0, nsimx, plot_std=False, min_overlap=0.0):
"""
Plot the mass of a reference halo against the weighted separation of
its counterparts.
Parameters
----------
nsim0 : int
Reference simulation index.
nsimx : int
Cross simulation index.
plot_std : bool, optional
Whether to plot thestd instead of mean.
min_overlap : float, optional
Minimum overlap to consider.
Returns
-------
None
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
cat0 = open_cat(nsim0)
catx = open_cat(nsimx)
reader = csiborgtools.read.PairOverlap(cat0, catx, paths,
maxdist=155)
mass = numpy.log10(reader.cat0("totpartmass"))
dist = reader.dist(in_initial=False, norm_kind="r200c")
overlap = reader.overlap(True)
dist = csiborgtools.read.weighted_stats(dist, overlap,
min_weight=min_overlap)
mask = numpy.isfinite(dist[:, 0])
mass = mass[mask]
dist = dist[mask, :]
dist = numpy.log10(dist)
if not plot_std:
p = numpy.polyfit(mass, dist[:, 0], 1)
else:
p = numpy.polyfit(mass, dist[:, 1], 1)
xrange = numpy.linspace(numpy.min(mass), numpy.max(mass), 1000)
txt = r"$m = {}$, $c = {}$".format(*plt_utils.latex_float(*p, n=3))
with plt.style.context(plt_utils.mplstyle):
fig, ax = plt.subplots()
ax.set_title(txt, fontsize="small")
if not plot_std:
cx = ax.hexbin(mass, dist[:, 0], mincnt=1, bins="log", gridsize=50)
ax.set_ylabel(r"$\log \langle \Delta R / R_{\rm 200c}\rangle$")
else:
cx = ax.hexbin(mass, dist[:, 1], mincnt=1, bins="log", gridsize=50)
ax.set_ylabel(
r"$\delta \log \langle \Delta R / R_{\rm 200c}\rangle$")
ax.plot(xrange, numpy.polyval(p, xrange), color="red",
linestyle="--")
fig.colorbar(cx, label="Bin counts")
ax.set_xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
ax.set_ylabel(r"$\log \langle \Delta R / R_{\rm 200c}\rangle$")
fig.tight_layout()
for ext in ["png"]:
fout = join(plt_utils.fout,
f"mass_vs_sep_{nsim0}_{nsimx}_{min_overlap}.{ext}")
if plot_std:
fout = fout.replace(f".{ext}", f"_std.{ext}")
print(f"Saving to `{fout}`.")
fig.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
def plot_maxoverlap_mass(nsim0):
"""
Plot the mass of the reference haloes against the mass of the maximum
overlap haloes.
Parameters
----------
nsim0 : int
Reference simulation index.
"""
mass0, __, __, stat = get_max_key("csiborg", nsim0, "totpartmass")
mu = numpy.mean(stat, axis=1)
std = numpy.std(numpy.log10(stat), axis=1)
mu = numpy.log10(mu)
mass0 = numpy.log10(mass0)
with plt.style.context(plt_utils.mplstyle):
fig, axs = plt.subplots(ncols=2, figsize=(3.5 * 1.75, 2.625))
im0 = axs[0].hexbin(mass0, mu, mincnt=1, bins="log", gridsize=50)
im1 = axs[1].hexbin(mass0, std, mincnt=1, bins="log", gridsize=50)
m = numpy.isfinite(mass0) & numpy.isfinite(mu)
print("True to expectation corr: ", kendalltau(mass0[m], mu[m]))
t = numpy.linspace(*numpy.percentile(mass0, [0, 100]), 1000)
axs[0].plot(t, t, color="red", linestyle="--")
axs[0].plot(t, t + 0.2, color="red", linestyle="--", alpha=0.5)
axs[0].plot(t, t - 0.2, color="red", linestyle="--", alpha=0.5)
axs[0].set_xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
axs[1].set_xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
axs[0].set_ylabel(
r"Max. overlap mean of $\log M_{\rm tot} ~ [M_\odot / h]$")
axs[1].set_ylabel(
r"Max. overlap std. of $\log M_{\rm tot} ~ [M_\odot / h]$")
ims = [im0, im1]
for i in range(2):
axins = inset_axes(axs[i], width="100%", height="5%",
loc='upper center', borderpad=-0.75)
fig.colorbar(ims[i], cax=axins, orientation="horizontal",
label="Bin counts")
axins.xaxis.tick_top()
axins.xaxis.set_tick_params(labeltop=True)
axins.xaxis.set_label_position("top")
fig.tight_layout()
for ext in ["png"]:
fout = join(plt_utils.fout,
f"max_totpartmass_{nsim0}.{ext}")
print(f"Saving to `{fout}`.")
fig.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
def plot_maxoverlapstat(nsim0, key):
"""
Plot the mass of the reference haloes against the value of the maximum
overlap statistic.
Parameters
----------
nsim0 : int
Reference simulation index.
key : str
Property to get.
"""
assert key != "totpartmass"
mass0, key_val, __, stat = get_max_key("csiborg", nsim0, key)
xlabels = {"lambda200c": r"\log \lambda_{\rm 200c}"}
key_label = xlabels.get(key, key)
mass0 = numpy.log10(mass0)
key_val = numpy.log10(key_val)
mu = numpy.mean(stat, axis=1)
std = numpy.std(numpy.log10(stat), axis=1)
mu = numpy.log10(mu)
with plt.style.context(plt_utils.mplstyle):
fig, axs = plt.subplots(ncols=3, figsize=(3.5 * 2, 2.625))
im0 = axs[0].hexbin(mass0, mu, mincnt=1, bins="log", gridsize=30)
im1 = axs[1].hexbin(mass0, std, mincnt=1, bins="log", gridsize=30)
im2 = axs[2].hexbin(key_val, mu, mincnt=1, bins="log", gridsize=30)
m = numpy.isfinite(key_val) & numpy.isfinite(mu)
print("True to expectation corr: ", kendalltau(key_val[m], mu[m]))
axs[0].set_xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
axs[0].set_ylabel(r"Max. overlap mean of ${}$".format(key_label))
axs[1].set_xlabel(r"$\log M_{\rm tot} ~ [M_\odot / h]$")
axs[1].set_ylabel(r"Max. overlap std. of ${}$".format(key_label))
axs[2].set_xlabel(r"${}$".format(key_label))
axs[2].set_ylabel(r"Max. overlap mean of ${}$".format(key_label))
ims = [im0, im1, im2]
for i in range(3):
axins = inset_axes(axs[i], width="100%", height="5%",
loc='upper center', borderpad=-0.75)
fig.colorbar(ims[i], cax=axins, orientation="horizontal",
label="Bin counts")
axins.xaxis.tick_top()
axins.xaxis.set_tick_params(labeltop=True)
axins.xaxis.set_label_position("top")
fig.tight_layout()
for ext in ["png"]:
fout = join(plt_utils.fout,
f"max_{key}_{nsim0}.{ext}")
print(f"Saving to `{fout}`.")
fig.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
@cache_to_disk(7)
def get_expected_mass(simname, nsim0, min_overlap):
"""
Get the expected mass of a reference halo given its overlap with halos
from other simulations.
Parameters
----------
simname : str
Simulation name.
nsim0 : int
Reference simulation index.
min_overlap : float
Minimum overlap to consider between a pair of haloes.
Returns
-------
mass : 1-dimensional array
Mass of the reference haloes.
mu : 1-dimensional array
Expected mass of the matched haloes.
std : 1-dimensional array
Standard deviation of the expected mass of the matched haloes.
prob_nomatch : 2-dimensional array
Probability of not matching the reference halo.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsimxs = csiborgtools.read.get_cross_sims(simname, nsim0, paths,
smoothed=True)
nsimxs = nsimxs
cat0 = open_cat(nsim0)
catxs = []
print("Opening catalogues...", flush=True)
for nsimx in tqdm(nsimxs):
catxs.append(open_cat(nsimx))
reader = csiborgtools.read.NPairsOverlap(cat0, catxs, paths)
mass = reader.cat0("totpartmass")
mu, std = reader.counterpart_mass(True, overlap_threshold=min_overlap,
in_log=False, return_full=False)
prob_nomatch = reader.prob_nomatch(True)
return mass, mu, std, prob_nomatch
def plot_mass_vs_expected_mass(nsim0, min_overlap=0, max_prob_nomatch=1):
"""
Plot the mass of a reference halo against the expected mass of its
counterparts.
Parameters
----------
nsim0 : int
Reference simulation index.
min_overlap : float, optional
Minimum overlap between a pair of haloes to consider.
max_prob_nomatch : float, optional
Maximum probability of no match to consider.
"""
mass, mu, std, prob_nomatch = get_expected_mass("csiborg", nsim0,
min_overlap)
std = std / mu / numpy.log(10)
mass = numpy.log10(mass)
mu = numpy.log10(mu)
prob_nomatch = numpy.nanmedian(prob_nomatch, axis=1)
mask = numpy.isfinite(mass) & numpy.isfinite(mu)
mask &= (prob_nomatch < max_prob_nomatch)
with plt.style.context(plt_utils.mplstyle):
fig, axs = plt.subplots(ncols=3, figsize=(3.5 * 2, 2.625))
im0 = axs[0].hexbin(mass[mask], mu[mask], mincnt=1, bins="log",
gridsize=50,)
im1 = axs[1].hexbin(mass[mask], std[mask], mincnt=1, bins="log",
gridsize=50)
im2 = axs[2].hexbin(1 - prob_nomatch[mask], mass[mask] - mu[mask],
gridsize=50, C=mass[mask],
reduce_C_function=numpy.nanmedian)
axs[2].axhline(0, color="red", linestyle="--", alpha=0.5)
axs[0].set_xlabel(r"True $\log M_{\rm tot} ~ [M_\odot / h]$")
axs[0].set_ylabel(r"Expected $\log M_{\rm tot} ~ [M_\odot / h]$")
axs[1].set_xlabel(r"True $\log M_{\rm tot} ~ [M_\odot / h]$")
axs[1].set_ylabel(r"Std. of $\sigma_{\log M_{\rm tot}}$")
axs[2].set_xlabel(r"1 - median prob. of no match")
axs[2].set_ylabel(r"$\log M_{\rm tot} - \log M_{\rm tot, exp}$")
t = numpy.linspace(*numpy.percentile(mass[mask], [0, 100]), 1000)
axs[0].plot(t, t, color="red", linestyle="--")
axs[0].plot(t, t + 0.2, color="red", linestyle="--", alpha=0.5)
axs[0].plot(t, t - 0.2, color="red", linestyle="--", alpha=0.5)
ims = [im0, im1, im2]
labels = ["Bin counts", "Bin counts",
r"$\log M_{\rm tot} ~ [M_\odot / h]$"]
for i in range(3):
axins = inset_axes(axs[i], width="100%", height="5%",
loc='upper center', borderpad=-0.75)
fig.colorbar(ims[i], cax=axins, orientation="horizontal",
label=labels[i])
axins.xaxis.tick_top()
axins.xaxis.set_tick_params(labeltop=True)
axins.xaxis.set_label_position("top")
fig.tight_layout()
for ext in ["png"]:
fout = join(plt_utils.fout,
f"mass_vs_expmass_{nsim0}_{max_prob_nomatch}.{ext}")
print(f"Saving to `{fout}`.")
fig.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
###############################################################################
# Nearest neighbour plotting #
###############################################################################
return catxs
def read_dist(simname, run, kind, kwargs):
"""
Read PDF/CDF of a nearest neighbour distribution.
Parameters
----------
simname : str
Simulation name. Must be either `csiborg` or `quijote`.
run : str
Run name.
kind : str
Kind of distribution. Must be either `pdf` or `cdf`.
kwargs : dict
Nearest neighbour reader keyword arguments.
Returns
-------
dist : 2-dimensional array
Distribution of distances in radial and neighbour bins.
"""
paths = csiborgtools.read.Paths(**kwargs["paths_kind"])
reader = csiborgtools.read.NearestNeighbourReader(**kwargs, paths=paths)
@ -707,26 +70,6 @@ def read_dist(simname, run, kind, kwargs):
def pull_cdf(x, fid_cdf, test_cdf):
"""
Pull a CDF so that it matches the fiducial CDF at 0.5. Rescales the x-axis,
while keeping the corresponding CDF values fixed.
Parameters
----------
x : 1-dimensional array
The x-axis of the CDF.
fid_cdf : 1-dimensional array
The fiducial CDF.
test_cdf : 1-dimensional array
The test CDF to be pulled.
Returns
-------
xnew : 1-dimensional array
The new x-axis of the test CDF.
test_cdf : 1-dimensional array
The new test CDF.
"""
xnew = x * numpy.interp(0.5, fid_cdf, x) / numpy.interp(0.5, test_cdf, x)
return xnew, test_cdf
@ -1360,7 +703,7 @@ def plot_kl_vs_overlap(runs, nsim, kwargs, runs_to_mass, plot_std=True,
for run in runs:
nn_data = nn_reader.read_single("csiborg", run, nsim, nobs=None)
nn_hindxs = nn_data["ref_hindxs"]
mass, overlap_hindxs, __, summed_overlap, prob_nomatch = get_overlap("csiborg", nsim) # noqa
mass, overlap_hindxs, __, summed_overlap, prob_nomatch = get_overlap_summary("csiborg", nsim) # noqa
# We need to match the hindxs between the two.
hind2overlap_array = {hind: i for i, hind in enumerate(overlap_hindxs)}
@ -1457,8 +800,8 @@ if __name__ == "__main__":
"mass009": (14.0, 14.4), # There is no upper limit.
}
# cached_funcs = ["get_overlap", "read_dist", "make_kl", "make_ks"]
cached_funcs = ["get_max_key"]
# cached_funcs = ["get_overlap_summary", "read_dist", "make_kl", "make_ks"]
cached_funcs = ["get_property_maxoverlap"]
if args.clean:
for func in cached_funcs:
print(f"Cleaning cache for function {func}.")

2130
scripts_plots/plot_match.py
View file

File diff suppressed because it is too large Load diff

101
scripts_plots/plt_utils.py
View file

@ -15,6 +15,7 @@
import numpy
from scipy.stats import binned_statistic
from scipy.special import erf
dpi = 600
fout = "../plots/"
@ -56,38 +57,74 @@ def latex_float(*floats, n=2):
return latex_floats
def binned_trend(x, y, weights, bins):
"""
Calculate the weighted mean and standard deviation of `y` in bins of `x`.
def nan_weighted_average(arr, weights=None, axis=None):
if weights is None:
weights = numpy.ones_like(arr)
Parameters
----------
x : 1-dimensional array
The x-coordinates of the data points.
y : 1-dimensional array
The y-coordinates of the data points.
weights : 1-dimensional array
The weights of the data points.
bins : 1-dimensional array
The bin edges.
valid_entries = ~numpy.isnan(arr)
Returns
-------
stat_x : 1-dimensional array
The x-coordinates of the binned data points.
stat_mu : 1-dimensional array
The weighted mean of `y` in bins of `x`.
stat_std : 1-dimensional array
The weighted standard deviation of `y` in bins of `x`.
"""
stat_mu, __, __ = binned_statistic(x, y * weights, bins=bins,
statistic="sum")
stat_std, __, __ = binned_statistic(x, y * weights, bins=bins,
statistic=numpy.var)
stat_w, __, __ = binned_statistic(x, weights, bins=bins, statistic="sum")
# Set NaN entries in arr to 0 for computation
arr = numpy.where(valid_entries, arr, 0)
stat_x = (bins[1:] + bins[:-1]) / 2
stat_mu /= stat_w
stat_std /= stat_w
stat_std = numpy.sqrt(stat_std)
return stat_x, stat_mu, stat_std
# Set weights of NaN entries to 0
weights = numpy.where(valid_entries, weights, 0)
# Compute the weighted sum and the sum of weights along the axis
weighted_sum = numpy.sum(arr * weights, axis=axis)
sum_weights = numpy.sum(weights, axis=axis)
return weighted_sum / sum_weights
def nan_weighted_std(arr, weights=None, axis=None, ddof=0):
if weights is None:
weights = numpy.ones_like(arr)
valid_entries = ~numpy.isnan(arr)
# Set NaN entries in arr to 0 for computation
arr = numpy.where(valid_entries, arr, 0)
# Set weights of NaN entries to 0
weights = numpy.where(valid_entries, weights, 0)
# Calculate weighted mean
weighted_mean = numpy.sum(
arr * weights, axis=axis) / numpy.sum(weights, axis=axis)
# Calculate the weighted variance
variance = numpy.sum(
weights * (arr - numpy.expand_dims(weighted_mean, axis))**2, axis=axis)
variance /= numpy.sum(weights, axis=axis) - ddof
return numpy.sqrt(variance)
def compute_error_bars(x, y, xbins, sigma):
bin_indices = numpy.digitize(x, xbins)
y_medians = numpy.array([numpy.median(y[bin_indices == i])
for i in range(1, len(xbins))])
lower_pct = 100 * 0.5 * (1 - erf(sigma / numpy.sqrt(2)))
upper_pct = 100 - lower_pct
y_lower = numpy.full(len(y_medians), numpy.nan)
y_upper = numpy.full(len(y_medians), numpy.nan)
for i in range(len(y_medians)):
if numpy.sum(bin_indices == i + 1) == 0:
continue
y_lower[i] = numpy.percentile(y[bin_indices == i + 1], lower_pct)
y_upper[i] = numpy.percentile(y[bin_indices == i + 1], upper_pct)
yerr = (y_medians - numpy.array(y_lower), numpy.array(y_upper) - y_medians)
return y_medians, yerr
def normalize_hexbin(hb):
hexagon_counts = hb.get_array()
normalized_counts = hexagon_counts / hexagon_counts.sum()
hb.set_array(normalized_counts)
hb.set_clim(normalized_counts.min(), normalized_counts.max())