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_hmf.py

@@ -0,0 +1,108 @@
+# 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 HMF for CSIBORG and Quijote haloes.
+"""
+from argparse import ArgumentParser
+from datetime import datetime
+from distutils.util import strtobool
+
+import numpy
+from mpi4py import MPI
+
+from taskmaster import work_delegation
+from utils import get_nsims
+
+try:
+    import csiborgtools
+except ModuleNotFoundError:
+    import sys
+
+    sys.path.append("../")
+    import csiborgtools
+
+
+def get_counts(nsim, bins, paths, parser_args):
+    """
+    Calculate and save the number of haloes in each mass bin.
+    """
+    simname = parser_args.simname
+    paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
+    bounds = {"dist": (0, parser_args.Rmax)}
+
+    if simname == "csiborg":
+        cat = csiborgtools.read.CSiBORGHaloCatalogue(
+            nsim, paths, bounds=bounds, load_fitted=False, load_initial=False)
+        logmass = numpy.log10(cat["fof_totpartmass"])
+        counts = csiborgtools.number_counts(logmass, bins)
+    elif simname == "quijote":
+        cat0 = csiborgtools.read.QuijoteHaloCatalogue(
+            nsim, paths, nsnap=4, load_fitted=False, load_initial=False)
+        nmax = int(cat0.box.boxsize // (2 * parser_args.Rmax))**3
+        counts = numpy.full((nmax, len(bins) - 1), numpy.nan,
+                            dtype=numpy.float32)
+
+        for nobs in range(nmax):
+            cat = cat0.pick_fiducial_observer(nobs, rmax=parser_args.Rmax)
+            logmass = numpy.log10(cat["group_mass"])
+            counts[nobs, :] = csiborgtools.number_counts(logmass, bins)
+    elif simname == "quijote_full":
+        cat = csiborgtools.read.QuijoteHaloCatalogue(
+            nsim, paths, nsnap=4, load_fitted=False, load_initial=False,
+            load_backup=parser_args.from_quijote_backup)
+        logmass = numpy.log10(cat["group_mass"])
+        counts = csiborgtools.number_counts(logmass, bins)
+    else:
+        raise ValueError(f"Unknown simulation name `{simname}`.")
+
+    fout = paths.halo_counts(simname, nsim, parser_args.from_quijote_backup)
+    if parser_args.verbose:
+        print(f"{datetime.now()}: saving halo counts to `{fout}`.")
+    numpy.savez(fout, counts=counts, bins=bins, rmax=parser_args.Rmax)
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser()
+    parser.add_argument("--simname", type=str,
+                        choices=["csiborg", "quijote", "quijote_full"],
+                        help="Simulation name.")
+    parser.add_argument("--nsims", type=int, nargs="+", default=None,
+                        help="Indices of simulations to cross. If `-1` all .")
+    parser.add_argument(
+        "--Rmax", type=float, default=155,
+        help="High-res region radius in Mpc / h. Ignored for `quijote_full`.")
+    parser.add_argument("--from_quijote_backup",
+                        type=lambda x: bool(strtobool(x)), default=False,
+                        help="Flag to indicate Quijote backup data.")
+    parser.add_argument("--lims", type=float, nargs="+", default=[11., 16.],
+                        help="Mass limits in Msun / h.")
+    parser.add_argument("--bw", type=float, default=0.2,
+                        help="Bin width in dex.")
+    parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
+                        default=False, help="Verbosity flag.")
+    parser_args = parser.parse_args()
+
+    paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
+    nsims = get_nsims(parser_args, paths)
+
+    if len(parser_args.lims) != 2:
+        raise ValueError("Mass limits must be a pair of floats.")
+
+    bins = numpy.arange(*parser_args.lims, parser_args.bw, dtype=numpy.float32)
+
+    def do_work(nsim):
+        get_counts(nsim, bins, paths, parser_args)
+
+    work_delegation(do_work, nsims, MPI.COMM_WORLD)