Gaussian smoothing of density fields (#33)

* 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

scripts/run_singlematch.py

@@ -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)