Overlapper improvements (#53)

* Store indices as f32 * Fix init sorting * Organise imports * Rename pathing * Add particle loading * Improve particle reading * Add h5py reader * edit particle path * Update particles loading * update particles loading * Fix particle dumping * Add init fitting * Fix bug due to insufficient precision * Add commnet * Add comment * Add clumps catalogue to halo cat * Add comment * Make sure PIDS never forced to float32 * fix pid reading * fix pid reading * Update matching to work with new arrays * Stop using cubical sub boxes, turn off nshift if no smoothing * Improve caching * Move function definitions * Simplify calculation * Add import * Small updates to the halo * Simplify calculation * Simplify looping calculation * fix tonew * Add initial data * Add skip condition * Add unit conversion * Add loading background in batches * Rename mmain index * Switch overlaps to h5 * Add finite lagpatch check * fix column name * Add verbosity flags * Save halo IDs instead. * Switch back to npz * Delte nbs * Reduce size of the box * Load correct bckg of halos being matched * Remove verbosity * verbosity edits * Change lower thresholds
2025-05-21 01:51:11 +00:00 · 2023-05-06 16:52:48 +01:00 · 2023-05-06 16:52:48 +01:00 · 56e39a8b1d
commit 56e39a8b1d
parent 1c9dacfde5
20 changed files with 864 additions and 3816 deletions
--- a/scripts/fit_init.py
+++ b/scripts/fit_init.py
@ -0,0 +1,104 @@
+# 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 calculate the particle centre of mass, Lagrangian patch size in the
+initial snapshot. The initial snapshot particles are read from the sorted
+files.
+"""
+from argparse import ArgumentParser
+from datetime import datetime
+
+import numpy
+from mpi4py import MPI
+
+from tqdm import tqdm
+
+try:
+    import csiborgtools
+except ModuleNotFoundError:
+    import sys
+
+    sys.path.append("../")
+    import csiborgtools
+
+
+# Get MPI things
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+nproc = comm.Get_size()
+verbose = nproc == 1
+
+# Argument parser
+parser = ArgumentParser()
+parser.add_argument("--ics", type=int, nargs="+", default=None,
+                    help="IC realisations. If `-1` processes all simulations.")
+args = parser.parse_args()
+paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
+partreader = csiborgtools.read.ParticleReader(paths)
+
+if args.ics is None or args.ics[0] == -1:
+    ics = paths.get_ics(tonew=True)
+else:
+    ics = args.ics
+
+cols_collect = [("index", numpy.int32),
+                ("x", numpy.float32),
+                ("y", numpy.float32),
+                ("z", numpy.float32),
+                ("lagpatch", numpy.float32),]
+
+
+# MPI loop over simulations
+jobs = csiborgtools.fits.split_jobs(len(ics), nproc)[rank]
+for nsim in [ics[i] for i in jobs]:
+    nsnap = max(paths.get_snapshots(nsim))
+    print(f"{datetime.now()}: rank {rank} calculating simulation `{nsim}`.",
+          flush=True)
+
+    parts = csiborgtools.read.read_h5(paths.initmatch_path(nsim, "particles"))
+    parts = parts['particles']
+    clump_map = csiborgtools.read.read_h5(paths.particles_path(nsim))
+    clump_map = clump_map["clumpmap"]
+    clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, rawdata=True,
+                                                   load_fitted=False)
+    clid2map = {clid: i for i, clid in enumerate(clump_map[:, 0])}
+    ismain = clumps_cat.ismain
+
+    out = csiborgtools.read.cols_to_structured(len(clumps_cat), cols_collect)
+    indxs = clumps_cat["index"]
+    for i, hid in enumerate(tqdm(indxs) if verbose else indxs):
+        out["index"][i] = hid
+        if not ismain[i]:
+            continue
+
+        part = csiborgtools.read.load_parent_particles(hid, parts, clump_map,
+                                                       clid2map, clumps_cat)
+        # Skip if the halo is too small.
+        if part is None or part.size < 100:
+            continue
+
+        dist, cm = csiborgtools.fits.dist_centmass(part)
+        # We enforce a maximum patchsize of 0.075 in box coordinates.
+        patchsize = min(numpy.percentile(dist, 99), 0.075)
+        out["x"][i], out["y"][i], out["z"][i] = cm
+        out["lagpatch"][i] = patchsize
+
+    out = out[ismain]
+    # Now save it
+    fout = paths.initmatch_path(nsim, "fit")
+    print(f"{datetime.now()}: dumping fits to .. `{fout}`.",
+          flush=True)
+    with open(fout, "wb") as f:
+        numpy.save(f, out)