Add mmain and other major updates (#44)

* Move paths to a separate file * Add mmain reader * Add a verbosity flag * Fix imports * Fix bug * Rename files * Return ultimate parents * Add script to generate mmain * Remove mmain path * edit path * Add mmain path * Change function name * Rename function * Turn off verbose * Fix list requirement * Edit init match paths * Fix init pathing * Edit paths docs * Edit dumpdir name * Rename path * Fix split paths * Remove unused import * Add comment * Update readme * remove read mmain * Rename haloatalogue * Fix minor bugs * Update nbs * Add create directory option * Move split jobs * Move spliot jobs * Remove splitting * Add import * Edit script * Deeper split folder * Fix paths bug * Rename catalogue * Rename Catalogue * Add new clumpread * Edit paths * add knn paths * Update commenting * Update imports * Add more conversions * Update temp file * Add a note * Add catalogue * Cooment * Update TODO * Update script * add nb * Update * pep8 * edit paths & pep8 * Fix knn auto paths * add paths docs * Add auto and cross knn paths * Add new paths * Simplify tpcf reading * pep8 patch * update readme * Update progress * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * Pep 8 and restructure * add lambda spin * add clump and halo * add checks * Edit halo profile fit * Update gitignore * backup script
2025-05-21 01:51:11 +00:00 · 2023-04-18 11:02:36 +02:00 · 2023-04-18 11:02:36 +02:00 · fdb0df8d4c
commit fdb0df8d4c
parent e0d3854277
50 changed files with 2152 additions and 1844 deletions
--- a/scripts/match_singlematch.py
+++ b/scripts/match_singlematch.py
@ -0,0 +1,94 @@
+# 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.
+"""A script to calculate overlap between two CSiBORG realisations."""
+from argparse import ArgumentParser
+from datetime import datetime
+from os.path import join
+
+import numpy
+from scipy.ndimage import gaussian_filter
+
+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)
+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)
+
+
+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, ngp_overlap=ngp_overlap,
+                smoothed_overlap=smoothed_overlap, sigma=args.sigma)
+print("All finished.", flush=True)