Aquila-Consortium/csiborgtools
0
0
Fork 0
mirror of https://github.com/Richard-Sti/csiborgtools_public.git synced 2025-05-21 01:51:11 +00:00
Code Issues Projects Releases Packages Wiki Activity Actions

Update initial matching & overlaps (#47)

Browse source 
* pep8

* fix convention

* Update script

* enforce optimisation boundaries to be finite

* Update TODO

* Remove sky matching

* FIx a small bug

* fix bug

* Remove import

* Add halo fitted quantities

* Update nbs

* update README

* Add load_initial comments

* Rename nbs

* Delete nb

* Update imports

* Rename function

* Update matcher

* Add overlap paths

* Update the matching script

* Update verbosity

* Add verbosity flags

* Simplify make_bckg_delta

* bug fix

* fix bug
This commit is contained in:
Richard Stiskalek 2023-04-21 01:35:06 +02:00 • committed by GitHub
parent 39b3498621
commit 04119a5314
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
14 changed files with 527 additions and 2836 deletions
Download patch file Download diff file Expand all files Collapse all files

106
scripts/match_singlematch.py
View file

@ -1,4 +1,3 @@
# Copyright (C) 2022 Richard Stiskalek
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
@ -15,7 +14,7 @@
"""A script to calculate overlap between two CSiBORG realisations."""
from argparse import ArgumentParser
from datetime import datetime
from os.path import join
from distutils.util import strtobool
import numpy
from scipy.ndimage import gaussian_filter
@ -24,71 +23,76 @@ try:
import csiborgtools
except ModuleNotFoundError:
import sys
sys.path.append("../")
import csiborgtools
import utils
# Argument parser
parser = ArgumentParser()
parser.add_argument("--nsim0", type=int)
parser.add_argument("--nsimx", type=int)
parser.add_argument("--nmult", type=float)
parser.add_argument("--sigma", type=float)
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)), default=False)
args = parser.parse_args()
# File paths
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
fout = join(utils.dumpdir, "overlap",
"cross_{}_{}.npz".format(args.nsim0, args.nsimx))
smooth_kwargs = {"sigma": args.sigma, "mode": "constant", "cval": 0.0}
overlapper = csiborgtools.match.ParticleOverlap()
# Load catalogues
print("{}: loading catalogues {} and {}."
.format(datetime.now(), args.nsim0, args.nsimx), flush=True)
cat0 = csiborgtools.read.ClumpsCatalogue(args.nsim0, paths)
catx = csiborgtools.read.ClumpsCatalogue(args.nsimx, paths)
print("{}: loading simulation {} and converting positions to cell numbers."
.format(datetime.now(), args.nsim0), flush=True)
with open(paths.initmatch_path(args.nsim0, "particles"), "rb") as f:
clumps0 = numpy.load(f, allow_pickle=True)
overlapper.clumps_pos2cell(clumps0)
print("{}: loading simulation {} and converting positions to cell numbers."
.format(datetime.now(), args.nsimx), flush=True)
with open(paths.initmatch_path(args.nsimx, "particles"), 'rb') as f:
clumpsx = numpy.load(f, allow_pickle=True)
overlapper.clumps_pos2cell(clumpsx)
print("{}: generating the background density fields.".format(datetime.now()),
flush=True)
delta_bckg = overlapper.make_bckg_delta(clumps0)
delta_bckg = overlapper.make_bckg_delta(clumpsx, delta=delta_bckg)
print("{}: crossing the simulations.".format(datetime.now()), flush=True)
matcher = csiborgtools.match.RealisationsMatcher()
ref_indxs, cross_indxs, match_indxs, ngp_overlap = matcher.cross(
cat0, catx, clumps0, clumpsx, delta_bckg)
# Load the raw catalogues (i.e. no selection) including the initial CM positions
# and the particle archives.
cat0 = csiborgtools.read.HaloCatalogue(
args.nsim0, paths, load_initial=True, rawdata=True
)
catx = csiborgtools.read.HaloCatalogue(
args.nsimx, paths, load_initial=True, rawdata=True
)
halos0_archive = paths.initmatch_path(args.nsim0, "particles")
halosx_archive = paths.initmatch_path(args.nsimx, "particles")
print("{}: smoothing the background field.".format(datetime.now()), flush=True)
# We generate the background density fields. Loads halos's particles one by one
# from the archive, concatenates them and calculates the NGP density field.
args.verbose and print(
"{}: generating the background density fields.".format(datetime.now()), flush=True
)
delta_bckg = overlapper.make_bckg_delta(halos0_archive, verbose=args.verbose)
delta_bckg = overlapper.make_bckg_delta(
halosx_archive, delta=delta_bckg, verbose=args.verbose
)
# We calculate the overlap between the NGP fields.
args.verbose and print(
"{}: crossing the simulations.".format(datetime.now()), flush=True
)
match_indxs, ngp_overlap = matcher.cross(
cat0, catx, halos0_archive, halosx_archive, delta_bckg
)
# We now smoothen up the background density field for the smoothed overlap calculation.
args.verbose and print(
"{}: smoothing the background field.".format(datetime.now()), flush=True
)
gaussian_filter(delta_bckg, output=delta_bckg, **smooth_kwargs)
# We calculate the smoothed overlap for the pairs whose NGP overlap is > 0.
args.verbose and print(
"{}: calculating smoothed overlaps.".format(datetime.now()), flush=True
)
smoothed_overlap = matcher.smoothed_cross(
cat0, catx, halos0_archive, halosx_archive, delta_bckg, match_indxs, smooth_kwargs
)
print("{}: calculating smoothed overlaps.".format(datetime.now()), flush=True)
smoothed_overlap = matcher.smoothed_cross(clumps0, clumpsx, delta_bckg,
ref_indxs, cross_indxs, match_indxs,
smooth_kwargs)
# Dump the result
print("Saving results to `{}`.".format(fout), flush=True)
with open(fout, "wb") as f:
numpy.savez(fout, ref_indxs=ref_indxs, cross_indxs=cross_indxs,
match_indxs=match_indxs, ngp_overlap=ngp_overlap,
smoothed_overlap=smoothed_overlap, sigma=args.sigma)
print("All finished.", flush=True)
# We save the results at long last.
fout = paths.overlap_path(args.nsim0, args.nsimx)
args.verbose and print(
"{}: saving results to `{}`.".format(datetime.now(), fout), flush=True
)
numpy.savez(
fout,
match_indxs=match_indxs,
ngp_overlap=ngp_overlap,
smoothed_overlap=smoothed_overlap,
sigma=args.sigma,
)
print("{}: all finished.".format(datetime.now()), flush=True)