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Overlapper improvements (#53)

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* Store indices as f32

* Fix init sorting

* Organise imports

* Rename pathing

* Add particle loading

* Improve particle reading

* Add h5py reader

* edit particle path

* Update particles loading

* update particles loading

* Fix particle dumping

* Add init fitting

* Fix bug due to insufficient precision

* Add commnet

* Add comment

* Add clumps catalogue to halo cat

* Add comment

* Make sure PIDS never forced to float32

* fix pid reading

* fix pid reading

* Update matching to work with new arrays

* Stop using cubical sub boxes, turn off nshift if no smoothing

* Improve caching

* Move function definitions

* Simplify calculation

* Add import

* Small updates to the halo

* Simplify calculation

* Simplify looping calculation

* fix tonew

* Add initial data

* Add skip condition

* Add unit conversion

* Add loading background in batches

* Rename mmain index

* Switch overlaps to h5

* Add finite lagpatch check

* fix column name

* Add verbosity flags

* Save halo IDs instead.

* Switch back to npz

* Delte nbs

* Reduce size of the box

* Load correct bckg of halos being matched

* Remove verbosity

* verbosity edits

* Change lower thresholds
This commit is contained in:
Richard Stiskalek 2023-05-06 16:52:48 +01:00 • committed by GitHub
parent 1c9dacfde5
commit 56e39a8b1d
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20 changed files with 864 additions and 3816 deletions
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67
scripts/match_singlematch.py
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@ -13,6 +13,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""A script to calculate overlap between two CSiBORG realisations."""
from argparse import ArgumentParser
from copy import deepcopy
from datetime import datetime
from distutils.util import strtobool
@ -26,13 +27,16 @@ except ModuleNotFoundError:
sys.path.append("../")
import csiborgtools
from csiborgtools.read import HaloCatalogue, read_h5
# 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("--sigma", type=float, default=None)
parser.add_argument("--smoothen", type=lambda x: bool(strtobool(x)),
default=None)
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
default=False)
args = parser.parse_args()
@ -43,27 +47,52 @@ matcher = csiborgtools.match.RealisationsMatcher()
# 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")
cat0 = HaloCatalogue(args.nsim0, paths, load_initial=True,
minmass=("totpartmass", 1e12), with_lagpatch=True)
catx = HaloCatalogue(args.nsimx, paths, load_initial=True,
minmass=("totpartmass", 1e12), with_lagpatch=True)
clumpmap0 = read_h5(paths.particles_path(args.nsim0))["clumpmap"]
parts0 = read_h5(paths.initmatch_path(args.nsim0, "particles"))["particles"]
clid2map0 = {clid: i for i, clid in enumerate(clumpmap0[:, 0])}
clumpmapx = read_h5(paths.particles_path(args.nsimx))["clumpmap"]
partsx = read_h5(paths.initmatch_path(args.nsimx, "particles"))["particles"]
clid2mapx = {clid: i for i, clid in enumerate(clumpmapx[:, 0])}
# We generate the background density fields. Loads halos's particles one by one
# from the archive, concatenates them and calculates the NGP density field.
if args.verbose:
print(f"{datetime.now()}: generating the background density fields.",
flush=True)
delta_bckg = overlapper.make_bckg_delta(halos0_archive, verbose=args.verbose)
delta_bckg = overlapper.make_bckg_delta(halosx_archive, delta=delta_bckg,
delta_bckg = overlapper.make_bckg_delta(parts0, clumpmap0, clid2map0, cat0,
verbose=args.verbose)
delta_bckg = overlapper.make_bckg_delta(partsx, clumpmapx, clid2mapx, catx,
delta=delta_bckg, verbose=args.verbose)
# We calculate the overlap between the NGP fields.
if args.verbose:
print(f"{datetime.now()}: crossing the simulations.", flush=True)
match_indxs, ngp_overlap = matcher.cross(cat0, catx, halos0_archive,
halosx_archive, delta_bckg)
match_indxs, ngp_overlap = matcher.cross(cat0, catx, parts0, partsx, clumpmap0,
clumpmapx, delta_bckg,
verbose=args.verbose)
# We wish 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_path(args.nsim0, args.nsimx, smoothed=False)
numpy.savez(fout, ref_hids=cat0["index"], match_hids=match_hids,
ngp_overlap=ngp_overlap)
if args.verbose:
print(f"{datetime.now()}: calculated NGP overlap, saved to {fout}.",
flush=True)
if not args.smoothen:
quit()
# We now smoothen up the background density field for the smoothed overlap
# calculation.
@ -72,16 +101,12 @@ if args.verbose:
gaussian_filter(delta_bckg, output=delta_bckg, **smooth_kwargs)
# We calculate the smoothed overlap for the pairs whose NGP overlap is > 0.
if args.verbose:
print(f"{datetime.now()}: calculating smoothed overlaps.", flush=True)
smoothed_overlap = matcher.smoothed_cross(cat0, catx, halos0_archive,
halosx_archive, delta_bckg,
smoothed_overlap = matcher.smoothed_cross(cat0, catx, parts0, partsx,
clumpmap0, clumpmapx, delta_bckg,
match_indxs, smooth_kwargs)
# We save the results at long last.
fout = paths.overlap_path(args.nsim0, args.nsimx)
fout = paths.overlap_path(args.nsim0, args.nsimx, smoothed=True)
numpy.savez(fout, smoothed_overlap=smoothed_overlap, sigma=args.sigma)
if args.verbose:
print(f"{datetime.now()}: saving results to `{fout}`.", flush=True)
numpy.savez(fout, match_indxs=match_indxs, ngp_overlap=ngp_overlap,
smoothed_overlap=smoothed_overlap, sigma=args.sigma)
print(f"{datetime.now()}: all finished.", flush=True)
print(f"{datetime.now()}: calculated smoothed overlap, saved to {fout}.",
flush=True)