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Gaussian smoothing of density fields (#33)

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* Simplify smoothing support and looping over nonzero

* Simplify comments

* add now()

* add cat length

* add smoothed calculation

* add smoothing

* Add sorting

* Edit what is ignored

* Move notebooks

* Add nonsymmetric smoothed overlap

* Update NB

* Add support for reading in the smoothed overlap

* Switch to the true overlap definition

* Reader of the true overlap

* rem occups

* Import moved to a class

* Move definition

* Edit submission script

* Update to account for the new definition

* backup nb

* Switch back to properly initialising arrays

* Fix addition bug

* Update NB

* Fix little bug

* Update nb
This commit is contained in:
Richard Stiskalek 2023-03-27 09:22:03 +01:00 • committed by GitHub
parent 9b524db617
commit 5dd8c668fa
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13 changed files with 10587 additions and 441 deletions
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63
scripts/run_singlematch.py
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@ -12,14 +12,12 @@
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""
Script to test running the CSiBORG realisations matcher.
"""
import numpy
from argparse import ArgumentParser
from distutils.util import strtobool
from datetime import datetime
"""A script to calculate overlap between two CSiBORG realisations."""
from os.path import join
from argparse import ArgumentParser
from datetime import datetime
import numpy
from scipy.ndimage import gaussian_filter
try:
import csiborgtools
except ModuleNotFoundError:
@ -33,26 +31,59 @@ parser = ArgumentParser()
parser.add_argument("--nsim0", type=int)
parser.add_argument("--nsimx", type=int)
parser.add_argument("--nmult", type=float)
parser.add_argument("--overlap", type=lambda x: bool(strtobool(x)))
parser.add_argument("--sigma", type=float)
args = parser.parse_args()
# File paths
fout = join(
utils.dumpdir, "overlap", "cross_{}_{}.npz".format(args.nsim0, args.nsimx))
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()
print("{}: loading catalogues.".format(datetime.now()), flush=True)
# Load catalogues
print("{}: loading catalogues {} and {}."
.format(datetime.now(), args.nsim0, args.nsimx), flush=True)
cat0 = csiborgtools.read.HaloCatalogue(args.nsim0)
catx = csiborgtools.read.HaloCatalogue(args.nsimx)
matcher = csiborgtools.match.RealisationsMatcher()
print("{}: loading simulation {} and converting positions to cell numbers."
.format(datetime.now(), args.nsim0), flush=True)
with open(cat0.paths.clump0_path(args.nsim0), "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(catx.paths.clump0_path(args.nsimx), '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)
ref_indxs, cross_indxs, match_indxs, overlap = matcher.cross(
cat0, catx, overlap=args.overlap)
matcher = csiborgtools.match.RealisationsMatcher()
ref_indxs, cross_indxs, match_indxs, ngp_overlap = matcher.cross(
cat0, catx, clumps0, clumpsx, delta_bckg)
print("{}: smoothing the background field.".format(datetime.now()), flush=True)
gaussian_filter(delta_bckg, output=delta_bckg, **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, overlap=overlap)
match_indxs=match_indxs, ngp_overlap=ngp_overlap,
smoothed_overlap=smoothed_overlap, sigma=args.sigma)
print("All finished.", flush=True)