mirror of
https://github.com/Richard-Sti/csiborgtools_public.git
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LSS projected basics (#140)
* Move files * Move files * Add galactic to RA/dec * Update sky maps * Add projected fields * Remove old import * Quick update * Add IO * Add imports * Update imports * Add basic file
This commit is contained in:
Richard Stiskalek
GitHub
parent
3b46f17ead
commit
d578c71b83
36 changed files with 365 additions and 231 deletions
128
scripts/halo_overlap/fit_init.py
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128
scripts/halo_overlap/fit_init.py
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# Copyright (C) 2022 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""
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Script to calculate the particle centre of mass and Lagrangian patch size in
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the initial snapshot. The initial snapshot particles are read from the sorted
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files.
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"""
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from argparse import ArgumentParser
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from datetime import datetime
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import csiborgtools
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import numpy
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from mpi4py import MPI
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from taskmaster import work_delegation
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from tqdm import tqdm
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from utils import get_nsims
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def _main(nsim, simname, verbose):
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"""
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Calculate and save the Lagrangian halo centre of mass and Lagrangian patch
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size in the initial snapshot.
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Parameters
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----------
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nsim : int
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IC realisation index.
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simname : str
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Simulation name.
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verbose : bool
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Verbosity flag.
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Returns
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-------
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None
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"""
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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cols = [("index", numpy.int32),
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("x", numpy.float32),
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("y", numpy.float32),
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("z", numpy.float32),
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("lagpatch_size", numpy.float32),
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("lagpatch_ncells", numpy.int32),]
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if simname == "csiborg1":
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snap = csiborgtools.read.CSiBORG1Snapshot(nsim, 1, paths,
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keep_snapshot_open=True)
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cat = csiborgtools.read.CSiBORG1Catalogue(nsim, paths, snapshot=snap)
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fout = f"/mnt/extraspace/rstiskalek/csiborg1/chain_{nsim}/initial_lagpatch.npy" # noqa
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elif "csiborg2" in simname:
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kind = simname.split("_")[-1]
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snap = csiborgtools.read.CSiBORG2Snapshot(nsim, 0, kind, paths,
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keep_snapshot_open=True)
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cat = csiborgtools.read.CSiBORG2Catalogue(nsim, 99, kind, paths,
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snapshot=snap)
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fout = f"/mnt/extraspace/rstiskalek/csiborg2_{kind}/catalogues/initial_lagpatch_{nsim}.npy" # noqa
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elif simname == "quijote":
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snap = csiborgtools.read.QuijoteSnapshot(nsim, "ICs", paths,
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keep_snapshot_open=True)
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cat = csiborgtools.read.QuijoteHaloCatalogue(nsim, paths,
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snapshot=snap)
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fout = f"/mnt/extraspace/rstiskalek/quijote/fiducial_processed/chain_{nsim}/initial_lagpatch.npy" # noqa
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else:
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raise ValueError(f"Unknown simulation name `{simname}`.")
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boxsize = csiborgtools.simname2boxsize(simname)
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# Initialise the overlapper.
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if simname == "csiborg" or "csiborg2" in simname:
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kwargs = {"box_size": 2048, "bckg_halfsize": 512}
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else:
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kwargs = {"box_size": 512, "bckg_halfsize": 256}
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overlapper = csiborgtools.match.ParticleOverlap(**kwargs)
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out = csiborgtools.read.cols_to_structured(len(cat), cols)
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for i, hid in enumerate(tqdm(cat["index"]) if verbose else cat["index"]):
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out["index"][i] = hid
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pos = snap.halo_coordinates(hid)
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mass = snap.halo_masses(hid)
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# Calculate the centre of mass and the Lagrangian patch size.
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cm = csiborgtools.center_of_mass(pos, mass, boxsize=boxsize)
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distances = csiborgtools.periodic_distance(pos, cm, boxsize=boxsize)
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out["x"][i], out["y"][i], out["z"][i] = cm
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out["lagpatch_size"][i] = numpy.percentile(distances, 99)
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pos /= boxsize # need to normalize the positions to be [0, 1).
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# Calculate the number of cells with > 0 density.
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delta = overlapper.make_delta(pos, mass, subbox=True)
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out["lagpatch_ncells"][i] = csiborgtools.delta2ncells(delta)
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# Now save it
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if verbose:
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print(f"{datetime.now()}: dumping fits to .. `{fout}`.", flush=True)
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with open(fout, "wb") as f:
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numpy.save(f, out)
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("--simname", type=str,
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choices=["csiborg1", "csiborg2_main", "csiborg2_random", "csiborg2_varysmall", "quijote"], # noqa
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help="Simulation name")
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parser.add_argument("--nsims", type=int, nargs="+", default=None,
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help="IC realisations. If `-1` processes all.")
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args = parser.parse_args()
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsims = get_nsims(args, paths)
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def main(nsim):
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_main(nsim, args.simname, MPI.COMM_WORLD.Get_size() == 1)
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work_delegation(main, nsims, MPI.COMM_WORLD)
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23
scripts/halo_overlap/fit_init.sh
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23
scripts/halo_overlap/fit_init.sh
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nthreads=6
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memory=16
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on_login=${1}
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queue="berg"
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env="/mnt/zfsusers/rstiskalek/csiborgtools/venv_csiborg/bin/python"
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file="fit_init.py"
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simname="csiborg2_varysmall"
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nsims="-1"
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pythoncm="$env $file --nsims $nsims --simname $simname"
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if [ $on_login -eq 1 ]; then
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echo $pythoncm
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$pythoncm
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else
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cm="addqueue -q $queue -n $nthreads -m $memory $pythoncm"
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echo "Submitting:"
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echo $cm
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echo
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eval $cm
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fi
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88
scripts/halo_overlap/match_overlap_all.py
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88
scripts/halo_overlap/match_overlap_all.py
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""A script to match all IC pairs of a simulation."""
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import warnings
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from argparse import ArgumentParser
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from distutils.util import strtobool
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from itertools import combinations
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from random import Random
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from mpi4py import MPI
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from taskmaster import work_delegation
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import csiborgtools
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from match_overlap_single import pair_match, pair_match_max
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def get_combs(simname):
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"""
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Get the list of all pairs of IC indices and permute them with a fixed
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seed.
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"""
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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combs = list(combinations(paths.get_ics(simname), 2))
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Random(42).shuffle(combs)
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return combs
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def main(comb, kind, simname, min_logmass, sigma, mult, verbose):
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"""
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Match a pair of simulations.
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"""
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nsim0, nsimx = comb
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if kind == "overlap":
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pair_match(nsim0, nsimx, simname, min_logmass, sigma, verbose)
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elif args.kind == "max":
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pair_match_max(nsim0, nsimx, simname, min_logmass, mult, verbose)
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else:
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raise ValueError(f"Unknown matching kind: `{kind}`.")
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("--kind", type=str, required=True,
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choices=["overlap", "max"], help="Kind of matching.")
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parser.add_argument("--simname", type=str, required=True,
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help="Simulation name.",
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choices=["csiborg1", "quijote", "csiborg2_main",
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"csiborg2_random", "csiborg2_varysmall"])
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parser.add_argument("--nsim0", type=int, default=None,
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help="Reference IC for Max's matching method.")
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parser.add_argument("--min_logmass", type=float, required=True,
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help="Minimum log halo mass.")
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parser.add_argument("--sigma", type=float, default=0,
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help="Smoothing scale in number of grid cells.")
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parser.add_argument("--mult", type=float, default=5,
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help="Search radius multiplier for Max's method.")
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parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
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default=False, help="Verbosity flag.")
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args = parser.parse_args()
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if args.kind == "overlap":
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combs = get_combs(args.simname)
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else:
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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combs = [(args.nsim0, nsimx) for nsimx in paths.get_ics(args.simname)
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if nsimx != args.nsim0]
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def _main(comb):
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with warnings.catch_warnings():
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warnings.filterwarnings("ignore",
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"invalid value encountered in cast",
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RuntimeWarning)
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main(comb, args.kind, args.simname, args.min_logmass, args.sigma,
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args.mult, args.verbose)
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work_delegation(_main, combs, MPI.COMM_WORLD)
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24
scripts/halo_overlap/match_overlap_all.sh
Executable file
24
scripts/halo_overlap/match_overlap_all.sh
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#!/bin/bash
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nthreads=41
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memory=12
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queue="berg"
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env="/mnt/zfsusers/rstiskalek/csiborgtools/venv_csiborg/bin/python"
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file="match_overlap_all.py"
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simname=${1}
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min_logmass=12.25
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sigma=1
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kind="overlap"
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mult=10 # Only for Max's method
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nsim0=0 # Only for Max's method
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verbose="false"
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pythoncm="$env $file --kind $kind --simname $simname --nsim0 $nsim0 --min_logmass $min_logmass --mult $mult --sigma $sigma --verbose $verbose"
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# $pythoncm
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cm="addqueue -q $queue -n $nthreads -m $memory $pythoncm"
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echo "Submitting:"
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echo $cm
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echo
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$cm
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218
scripts/halo_overlap/match_overlap_single.py
Normal file
218
scripts/halo_overlap/match_overlap_single.py
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@ -0,0 +1,218 @@
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""
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A script to calculate overlap between two IC realisations of the same
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simulation.
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"""
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from argparse import ArgumentParser
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from copy import deepcopy
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from datetime import datetime
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from distutils.util import strtobool
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import numpy
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from scipy.ndimage import gaussian_filter
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import csiborgtools
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def pair_match_max(nsim0, nsimx, simname, min_logmass, mult, verbose):
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"""
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Match a pair of simulations using the Max method.
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Parameters
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----------
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nsim0, nsimx : int
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The reference and cross simulation IC index.
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simname : str
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Simulation name.
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min_logmass : float
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Minimum log halo mass.
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mult : float
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Multiplicative factor for search radius.
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verbose : bool
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Verbosity flag.
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"""
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if simname == "csiborg1":
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maxdist = 155
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periodic = False
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bounds = {"dist": (0, maxdist), "totmass": (10**min_logmass, None)}
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cat0 = csiborgtools.read.CSiBORG1Catalogue(nsim0, bounds=bounds)
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catx = csiborgtools.read.CSiBORG1Catalogue(nsimx, bounds=bounds)
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elif "csiborg2" in simname:
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raise RuntimeError("CSiBORG2 currently not implemented..")
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elif simname == "quijote":
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maxdist = None
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periodic = True
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bounds = {"totmass": (10**min_logmass, None)}
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cat0 = csiborgtools.read.QuijoteCatalogue(nsim0, bounds=bounds)
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catx = csiborgtools.read.QuijoteHaloCatalogue(nsimx, bounds=bounds)
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else:
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raise ValueError(f"Unknown simulation `{simname}`.")
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reader = csiborgtools.summary.PairOverlap(cat0, catx, min_logmass, maxdist)
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out = csiborgtools.match.matching_max(
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cat0, catx, "totmass", mult=mult, periodic=periodic,
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overlap=reader.overlap(from_smoothed=True),
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match_indxs=reader["match_indxs"], verbose=verbose)
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fout = cat0.paths.match_max(simname, nsim0, nsimx, min_logmass, mult)
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if verbose:
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print(f"{datetime.now()}: saving to ... `{fout}`.", flush=True)
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numpy.savez(fout, **{p: out[p] for p in out.dtype.names})
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def pair_match(nsim0, nsimx, simname, min_logmass, sigma, verbose):
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"""
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Calculate overlaps between two simulations.
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Parameters
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----------
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nsim0 : int
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The reference simulation IC index.
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nsimx : int
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The cross simulation IC index.
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simname : str
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Simulation name.
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min_logmass : float
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Minimum log halo mass.
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sigma : float
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Smoothing scale in number of grid cells.
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verbose : bool
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Verbosity flag.
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Returns
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-------
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None
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"""
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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smooth_kwargs = {"sigma": sigma, "mode": "constant", "cval": 0}
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bounds = {"lagpatch_radius": (0, None)}
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if simname == "csiborg1":
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overlapper_kwargs = {"box_size": 2048, "bckg_halfsize": 512}
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bounds |= {"dist": (0, 135), "totmass": (10**min_logmass, None)}
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# Reference simulation.
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snap0 = csiborgtools.read.CSiBORG1Snapshot(
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nsim0, 1, keep_snapshot_open=True)
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cat0 = csiborgtools.read.CSiBORG1Catalogue(
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nsim0, snapshot=snap0, bounds=bounds)
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# Cross simulation.
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snapx = csiborgtools.read.CSiBORG1Snapshot(
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nsimx, 1, keep_snapshot_open=True)
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catx = csiborgtools.read.CSiBORG1Catalogue(
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nsimx, snapshot=snapx, bounds=bounds)
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elif "csiborg2" in simname:
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kind = simname.split("_")[-1]
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overlapper_kwargs = {"box_size": 2048, "bckg_halfsize": 512}
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bounds |= {"dist": (0, 135), "totmass": (10**min_logmass, None)}
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# Reference simulation.
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snap0 = csiborgtools.read.CSiBORG2Snapshot(
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nsim0, 99, kind, keep_snapshot_open=True)
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cat0 = csiborgtools.read.CSiBORG2Catalogue(
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nsim0, 99, kind, snapshot=snap0, bounds=bounds)
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# Cross simulation.
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snapx = csiborgtools.read.CSiBORG2Snapshot(
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nsimx, 99, kind, keep_snapshot_open=True)
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catx = csiborgtools.read.CSiBORG2Catalogue(
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nsimx, 99, kind, snapshot=snapx, bounds=bounds)
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elif simname == "quijote":
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overlapper_kwargs = {"box_size": 512, "bckg_halfsize": 256}
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bounds |= {"totmass": (10**min_logmass, None)}
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# Reference simulation.
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snap0 = csiborgtools.read.QuijoteSnapshot(
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nsim0, "ICs", keep_snapshot_open=True)
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cat0 = csiborgtools.read.QuijoteCatalogue(
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nsim0, snapshot=snap0, bounds=bounds)
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# Cross simulation.
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snapx = csiborgtools.read.QuijoteSnapshot(
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nsimx, "ICs", keep_snapshot_open=True)
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catx = csiborgtools.read.QuijoteCatalogue(
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nsimx, snapshot=snapx, bounds=bounds)
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else:
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raise ValueError(f"Unknown simulation name: `{simname}`.")
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overlapper = csiborgtools.match.ParticleOverlap(**overlapper_kwargs)
|
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delta_bckg = overlapper.make_bckg_delta(cat0, verbose=verbose)
|
||||
delta_bckg = overlapper.make_bckg_delta(catx, delta=delta_bckg,
|
||||
verbose=verbose)
|
||||
|
||||
matcher = csiborgtools.match.RealisationsMatcher(**overlapper_kwargs)
|
||||
match_indxs, ngp_overlap = matcher.cross(cat0, catx, delta_bckg,
|
||||
verbose=verbose)
|
||||
|
||||
# We want to store the halo IDs of the matches, not their array positions
|
||||
# in the catalogues.
|
||||
match_hids = deepcopy(match_indxs)
|
||||
for i, matches in enumerate(match_indxs):
|
||||
for j, match in enumerate(matches):
|
||||
match_hids[i][j] = catx["index"][match]
|
||||
|
||||
fout = paths.overlap(simname, nsim0, nsimx, min_logmass, smoothed=False)
|
||||
if verbose:
|
||||
print(f"{datetime.now()}: saving to ... `{fout}`.", flush=True)
|
||||
numpy.savez(fout, ref_hids=cat0["index"], match_hids=match_hids,
|
||||
ngp_overlap=ngp_overlap)
|
||||
|
||||
if not sigma > 0:
|
||||
return
|
||||
|
||||
if verbose:
|
||||
print(f"{datetime.now()}: smoothing the background field.", flush=True)
|
||||
gaussian_filter(delta_bckg, output=delta_bckg, **smooth_kwargs)
|
||||
|
||||
# We calculate the smoothed overlap for the pairs whose NGP overlap is > 0.
|
||||
smoothed_overlap = matcher.smoothed_cross(cat0, catx, delta_bckg,
|
||||
match_indxs, smooth_kwargs,
|
||||
verbose=verbose)
|
||||
|
||||
fout = paths.overlap(simname, nsim0, nsimx, min_logmass, smoothed=True)
|
||||
if verbose:
|
||||
print(f"{datetime.now()}: saving to ... `{fout}`.", flush=True)
|
||||
numpy.savez(fout, smoothed_overlap=smoothed_overlap, sigma=sigma)
|
||||
|
||||
|
||||
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,
|
||||
help="Cross simulation IC index.")
|
||||
parser.add_argument("--simname", type=str, required=True,
|
||||
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}`.")
|
||||
50
scripts/halo_overlap/match_overlap_single.sh
Executable file
50
scripts/halo_overlap/match_overlap_single.sh
Executable file
|
|
@ -0,0 +1,50 @@
|
|||
#!/bin/bash
|
||||
nthreads=1
|
||||
memory=7
|
||||
queue="berg"
|
||||
env="/mnt/zfsusers/rstiskalek/csiborgtools/venv_csiborg/bin/python"
|
||||
verbose="true"
|
||||
file="match_overlap_single.py"
|
||||
|
||||
simname="csiborg2_main"
|
||||
kind="overlap"
|
||||
min_logmass=12
|
||||
mult=5 # Only for Max's method
|
||||
sigma=1
|
||||
|
||||
# sims=(7444 7468)
|
||||
sims=(16417 16517)
|
||||
# sims=(0 1)
|
||||
# sims=(7468 7588)
|
||||
nsims=${#sims[@]}
|
||||
|
||||
for i in $(seq 0 $((nsims-1)))
|
||||
do
|
||||
for j in $(seq 0 $((nsims-1)))
|
||||
do
|
||||
if [ $i -eq $j ]
|
||||
then
|
||||
continue
|
||||
elif [ $i -gt $j ]
|
||||
then
|
||||
continue
|
||||
else
|
||||
:
|
||||
fi
|
||||
|
||||
nsim0=${sims[$i]}
|
||||
nsimx=${sims[$j]}
|
||||
|
||||
pythoncm="$env $file --kind $kind --nsim0 $nsim0 --nsimx $nsimx --simname $simname --min_logmass $min_logmass --sigma $sigma --mult $mult --verbose $verbose"
|
||||
|
||||
$pythoncm
|
||||
|
||||
# cm="addqueue -q $queue -n 1x1 -m $memory $pythoncm"
|
||||
# echo "Submitting:"
|
||||
# echo $cm
|
||||
# echo
|
||||
# $cm
|
||||
# sleep 0.05
|
||||
|
||||
done
|
||||
done
|
||||
Loading…
Add table
Add a link
Reference in a new issue