Quijote kNN adding (#62)

* Fix small bug

* Add fiducial observers

* Rename 1D knn

* Add new bounds system

* rm whitespace

* Add boudns

* Add simname to paths

* Add fiducial obserevrs

* apply bounds only if not none

* Add TODO

* add simnames

* update script

* Fix distance bug

* update yaml

* Update file reading

* Update gitignore

* Add plots

* add check if empty list

* add func to obtaining cross

* Update nb

* Remove blank lines

* update ignroes

* loop over a few ics

* update gitignore

* add comments

scripts/cluster_tpcf_auto.py

@@ -0,0 +1,121 @@
+# 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.
+"""
+A script to calculate the auto-2PCF of CSiBORG catalogues.
+"""
+from argparse import ArgumentParser
+from copy import deepcopy
+from datetime import datetime
+from warnings import warn
+
+import joblib
+import numpy
+import yaml
+from mpi4py import MPI
+
+from taskmaster import master_process, worker_process
+
+from .cluster_knn_auto import read_single
+
+try:
+    import csiborgtools
+except ModuleNotFoundError:
+    import sys
+
+    sys.path.append("../")
+    import csiborgtools
+
+
+###############################################################################
+#                            MPI and arguments                                #
+###############################################################################
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+nproc = comm.Get_size()
+
+parser = ArgumentParser()
+parser.add_argument("--runs", type=str, nargs="+")
+parser.add_argument("--ics", type=int, nargs="+", default=None,
+                    help="IC realisations. If `-1` processes all simulations.")
+parser.add_argument("--simname", type=str, choices=["csiborg", "quijote"])
+args = parser.parse_args()
+with open("../scripts/tpcf_auto.yml", "r") as file:
+    config = yaml.safe_load(file)
+
+Rmax = 155 / 0.705  # Mpc (h = 0.705) high resolution region radius
+paths = csiborgtools.read.Paths()
+tpcf = csiborgtools.clustering.Mock2PCF()
+
+if args.ics is None or args.ics[0] == -1:
+    if args.simname == "csiborg":
+        ics = paths.get_ics()
+    else:
+        ics = paths.get_quijote_ics()
+else:
+    ics = args.ics
+
+###############################################################################
+#                                 Analysis                                    #
+###############################################################################
+
+
+def do_auto(run, nsim):
+    _config = config.get(run, None)
+    if _config is None:
+        warn("No configuration for run {}.".format(run), stacklevel=1)
+        return
+
+    rvs_gen = csiborgtools.clustering.RVSinsphere(Rmax)
+    bins = numpy.logspace(
+        numpy.log10(config["rpmin"]),
+        numpy.log10(config["rpmax"]),
+        config["nrpbins"] + 1,
+    )
+    cat = read_single(nsim, _config)
+    pos = cat.position(in_initial=False, cartesian=True)
+    nrandom = int(config["randmult"] * pos.shape[0])
+    rp, wp = tpcf(pos, rvs_gen, nrandom, bins)
+
+    fout = paths.tpcfauto_path(args.simname, run, nsim)
+    joblib.dump({"rp": rp, "wp": wp}, fout)
+
+
+def do_runs(nsim):
+    for run in args.runs:
+        do_auto(run, nsim)
+
+
+###############################################################################
+#                             MPI task delegation                             #
+###############################################################################
+
+
+if nproc > 1:
+    if rank == 0:
+        tasks = deepcopy(ics)
+        master_process(tasks, comm, verbose=True)
+    else:
+        worker_process(do_runs, comm, verbose=False)
+else:
+    tasks = deepcopy(ics)
+    for task in tasks:
+        print("{}: completing task `{}`.".format(datetime.now(), task))
+        do_runs(task)
+comm.Barrier()
+
+
+if rank == 0:
+    print("{}: all finished.".format(datetime.now()))
+quit()  # Force quit the script