Speed up overlap (#27)

* Edit improt

* Simplify patch size calculation

* Add patch size percentiles

* Add various percentiles

* Remove  comment

* Update TODO

* Change to 95th percentile

* Add import

* Add KNN properties

* Add new matching initial condition

* Add import

* Remove import

* Add fast neighbours option

* Further edits to fast neighbours

* add imports

* add new overlap calculation and non-zero things

* Remove print

* Clean up code

* Fix small bug

* Remove comment

* Add run single cross match

* change values

* Edit hyperparams

* Add comment

* Add the argument parser

* Add new lagpatch calc

* New lagpatch calc

* Delete old patch definitions

* Make clump dumping once again optional

* Add lagpatch to the catalogue

* Edit print statement

* Fix small bug

* Remove init radius

* Change to lagpatch key

* Fix a small bug

* Fix little bug

scripts/run_singlematch.py

@@ -0,0 +1,66 @@
+# 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
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# 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
+from os.path import join
+try:
+    import csiborgtools
+except ModuleNotFoundError:
+    import sys
+    sys.path.append("../")
+    import csiborgtools
+import utils
+
+# Argument parser
+parser = ArgumentParser()
+parser.add_argument("--nmult", type=float)
+parser.add_argument("--overlap", type=lambda x: bool(strtobool(x)))
+parser.add_argument("--select_initial", type=lambda x: bool(strtobool(x)))
+parser.add_argument("--fast_neighbours", type=lambda x: bool(strtobool(x)))
+args = parser.parse_args()
+
+# File paths
+ic = 7468
+fperm = join(utils.dumpdir, "overlap", "cross_{}.npy")
+
+paths = csiborgtools.read.CSiBORGPaths(to_new=False)
+paths.set_info(ic, paths.get_maximum_snapshot(ic))
+
+print("{}: loading catalogues.".format(datetime.now()), flush=True)
+cat = csiborgtools.read.CombinedHaloCatalogue(paths)
+
+
+matcher = csiborgtools.match.RealisationsMatcher(cat)
+nsim0 = cat.n_sims[0]
+nsimx = cat.n_sims[1]
+
+print("{}: crossing the simulations.".format(datetime.now()), flush=True)
+
+out = matcher.cross_knn_position_single(
+    0, nmult=args.nmult, dlogmass=2., overlap=args.overlap,
+    select_initial=args.select_initial, fast_neighbours=args.fast_neighbours)
+
+# Dump the result
+fout = fperm.format(nsim0)
+print("Saving results to `{}`.".format(fout), flush=True)
+with open(fout, "wb") as f:
+    numpy.save(fout, out)
+
+print("All finished.", flush=True)