Overlap calculation (#19)

* Rm comment

* Add new fixed particle overlap

* Fix overlap calculation

* Update docs

* Add new overlapper support in matcher

* add filter optin

* Add the real space filter.

* Change filtering to real space only

* Update TODO

* add high-resolution switch

* add cross script

* Remove comment

* Add smoothing option

scripts/run_crossmatch.py

@@ -0,0 +1,78 @@
+# 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.
+"""
+MPI script to run the CSiBORG realisations matcher.
+"""
+import numpy
+from datetime import datetime
+from mpi4py import MPI
+from os.path import join
+from os import remove
+try:
+    import csiborgtools
+except ModuleNotFoundError:
+    import sys
+    sys.path.append("../")
+    import csiborgtools
+import utils
+
+# Get MPI things
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+nproc = comm.Get_size()
+
+# File paths
+ftemp = join(utils.dumpdir, "temp_match", "match_{}.npy")
+fperm = join(utils.dumpdir, "match", "cross_matches.npy")
+
+# Set up the catalogue
+paths = csiborgtools.read.CSiBORGPaths(to_new=False)
+print("{}: started reading in the combined catalogue.".format(datetime.now()),
+      flush=True)
+cat = csiborgtools.read.CombinedHaloCatalogue(
+    paths, min_m500=None, max_dist=None, verbose=False)
+print("{}: finished reading in the combined catalogue with `{}`."
+      .format(datetime.now(), cat.n_sims), flush=True)
+matcher = csiborgtools.match.RealisationsMatcher(cat)
+
+
+for i in csiborgtools.fits.split_jobs(len(cat.n_sims), nproc)[rank]:
+    n = cat.n_sims[i]
+    print("{}: rank {} working on simulation `{}`."
+          .format(datetime.now(), rank, n), flush=True)
+    out = matcher.cross_knn_position_single(
+        i, nmult=15, dlogmass=2, init_dist=True, overlap=True, verbose=False,
+        overlapper_kwargs={"smooth_scale": 0.5})
+
+    # Dump the result
+    with open(ftemp.format(n), "wb") as f:
+        numpy.save(f, out)
+
+
+comm.Barrier()
+if rank == 0:
+    print("Collecting files...", flush=True)
+
+    dtype = {"names": ["match", "nsim"], "formats": [object, numpy.int32]}
+    matches = numpy.full(len(cat.n_sims), numpy.nan, dtype=dtype)
+    for i, n in enumerate(cat.n_sims):
+        with open(ftemp.format(n), "rb") as f:
+            matches["match"][i] = numpy.load(f, allow_pickle=True)
+        matches["nsim"][i] = n
+        remove(ftemp.format(n))
+
+    print("Saving results to `{}`.".format(fperm))
+    with open(fperm, "wb") as f:
+        numpy.save(f, matches)