Add pynbody and other support (#92)

* Simplify box units

* Move old scripts

* Add printing

* Update readers

* Disable boundscheck

* Add new ordering

* Clean up imports

* Enforce dtype and add mass to quijote

* Simplify print statements

* Fix little typos

* Fix key bug

* Bug fixing

* Delete boring comments

* Improve ultimate clumps for PHEW

* Delete boring comments

* Add basic reading

* Remove 0th index HID

* Add flipping of X and Z

* Updates to halo catalogues

* Add ordered caching

* Fix flipping

* Add new flags

* Fix PHEW empty clumps

* Stop over-wrriting

* Little improvements to angular neighbours

* Add catalogue masking

* Change if-else statements

* Cache only filtered data

* Add PHEW cats

* Add comments

* Sort imports

* Get Quijote workign

* Docs

* Add HMF calculation

* Move to old

* Fix angular

* Add great circle distance

* Update imports

* Update impotrts

* Update docs

* Remove unused import

* Fix a quick bug

* Update compatibility

* Rename files

* Renaming

* Improve compatiblity

* Rename snapsht

* Fix snapshot bug

* Update interface

* Finish updating interface

* Update all paths

* Add old scripts

* Add basic halo

* Update imports

* Improve snapshot processing

* Update ordering

* Fix how CM positions accessed

* Add merger paths

* Add imports

* Add merger reading

* Add making a merger tree

* Add a basic merger tree reader

* Add imports

* Add main branch walking + comments + debuggin

* Get tree running

* Add working merger tree walking along main branch

* Add units conversion for merger data

* Add hid_to_array_index

* Update merger tree

* Add mergertree mass to PHEWcat

* Edit comments

* Add this to track changes...

* Fix a little bug

* Add mergertree mass

* Add cache clearing

* Improve summing substructure code

* Littbe bug

* Little updates to the merger tree reader

* Update .giignore

* Add box selection

* Add optional deletingf of a group

* add to keep track of changes

* Update changes

* Remove

* Add manual tracker

* Fix bug

* Add m200c_to_r200c

* Add manual halo tracking

* Remove skipped snapshots

* update cosmo params to match csiborg

* remove old comments

* Add SDSSxALFALFA

* Fix bugs

* Rename

* Edit paths

* Updates

* Add comments

* Add comment

* Add hour conversion

* Add imports

* Add new observation class

* Add selection

* Add imports

* Fix small bug

* Add field copying for safety

* Add matching to survey without masking

* Add P(k) calculation

* Add nb

* Edit comment

* Move files

* Remove merger import

* Edit setup.yp

* Fix typo

* Edit import warnigns

* update nb

* Update README

* Update README

* Update README

* Add skeleton

* Add skeleton

old/fit_profiles.py

@@ -0,0 +1,109 @@
+# Copyright (C) 2023 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 the particle's separation from the CM and save it.
+Currently MPI is not supported.
+"""
+from argparse import ArgumentParser
+from datetime import datetime
+from gc import collect
+
+import numpy
+from mpi4py import MPI
+from tqdm import trange
+
+try:
+    import csiborgtools
+except ModuleNotFoundError:
+    import sys
+
+    sys.path.append("../")
+    import csiborgtools
+
+parser = ArgumentParser()
+parser.add_argument("--ics", type=int, nargs="+", default=None,
+                    help="IC realisatiosn. If `-1` processes all simulations.")
+args = parser.parse_args()
+
+# Get MPI things
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+nproc = comm.Get_size()
+
+if nproc > 1:
+    raise NotImplementedError("MPI is not implemented implemented yet.")
+
+paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
+cols_collect = [("r", numpy.float32), ("M", numpy.float32)]
+if args.ics is None or args.ics == -1:
+    nsims = paths.get_ics("csiborg")
+else:
+    nsims = args.ics
+
+
+# We loop over simulations. Here later optionally add MPI.
+for i, nsim in enumerate(nsims):
+    if rank == 0:
+        now = datetime.now()
+        print(f"{now}: calculating {i}th simulation `{nsim}`.", flush=True)
+    nsnap = max(paths.get_snapshots(nsim, "csiborg"))
+    box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
+
+    f = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
+    particles = f["particles"]
+    clump_map = f["clumpmap"]
+    clid2map = {clid: i for i, clid in enumerate(clump_map[:, 0])}
+    clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, rawdata=True,
+                                                   load_fitted=False)
+    ismain = clumps_cat.ismain
+    ntasks = len(clumps_cat)
+
+    # We loop over halos and add ther particle positions to this dictionary,
+    # which we will later save as an archive.
+    out = {}
+    for j in trange(ntasks) if nproc == 1 else range(ntasks):
+        # If we are fitting halos and this clump is not a main, then continue.
+        if not ismain[j]:
+            continue
+
+        clumpid = clumps_cat["index"][j]
+        parts = csiborgtools.read.load_parent_particles(
+            clumpid, particles, clump_map, clid2map, clumps_cat)
+        # If we have no particles, then do not save anything.
+        if parts is None:
+            continue
+        obj = csiborgtools.fits.Clump(parts, clumps_cat[j], box)
+        r200m, m200m = obj.spherical_overdensity_mass(200, npart_min=10,
+                                                      kind="matter")
+        r = obj.r()
+        mask = r <= r200m
+
+        _out = csiborgtools.read.cols_to_structured(numpy.sum(mask),
+                                                    cols_collect)
+
+        _out["r"] = r[mask]
+        _out["M"] = obj["M"][mask]
+        out[str(clumpid)] = _out
+
+    # Finished, so we save everything.
+    fout = paths.radpos_path(nsnap, nsim)
+    now = datetime.now()
+    print(f"{now}: saving radial profiles for simulation {nsim} to `{fout}`",
+          flush=True)
+    numpy.savez(fout, **out)
+
+    # Clean up the memory just to be sure.
+    del out
+    collect()