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
2025-05-14 06:31:11 +00:00 · 2023-12-07 14:23:32 +00:00 · 2023-12-07 14:23:32 +00:00 · e972f8e3f2
commit e972f8e3f2
parent 5500fbd2b9
53 changed files with 4627 additions and 1774 deletions
--- a/old/cluster_knn_cross.py
+++ b/old/cluster_knn_cross.py
@ -0,0 +1,144 @@
+# 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 KNN-CDF for a set of CSiBORG halo catalogues.
+
+TODO:
+    - [ ] Add support for new catalogue readers. Currently will not work.
+    - [ ] Update catalogue readers.
+    - [ ] Update paths.
+    - [ ] Update to cross-correlate different mass populations from different
+    simulations.
+"""
+raise NotImplementedError("This script is currently not working.")
+from argparse import ArgumentParser
+from datetime import datetime
+from itertools import combinations
+from warnings import warn
+
+import joblib
+import numpy
+import yaml
+from mpi4py import MPI
+from sklearn.neighbors import NearestNeighbors
+from taskmaster import master_process, worker_process
+
+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("--simname", type=str, choices=["csiborg", "quijote"])
+args = parser.parse_args()
+with open("../scripts/knn_cross.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(**csiborgtools.paths_glamdring)
+ics = paths.get_ics("csiborg")
+knncdf = csiborgtools.clustering.kNN_1DCDF()
+
+###############################################################################
+#                               Analysis                                      #
+###############################################################################
+
+
+def read_single(selection, cat):
+    mmask = numpy.ones(len(cat), dtype=bool)
+    pos = cat.positions(False)
+    # Primary selection
+    psel = selection["primary"]
+    pmin, pmax = psel.get("min", None), psel.get("max", None)
+    if pmin is not None:
+        mmask &= cat[psel["name"]] >= pmin
+    if pmax is not None:
+        mmask &= cat[psel["name"]] < pmax
+    return pos[mmask, ...]
+
+
+def do_cross(run, ics):
+    _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)
+    knn1, knn2 = NearestNeighbors(), NearestNeighbors()
+
+    cat1 = csiborgtools.read.ClumpsCatalogue(ics[0], paths, max_dist=Rmax)
+    pos1 = read_single(_config, cat1)
+    knn1.fit(pos1)
+
+    cat2 = csiborgtools.read.ClumpsCatalogue(ics[1], paths, max_dist=Rmax)
+    pos2 = read_single(_config, cat2)
+    knn2.fit(pos2)
+
+    rs, cdf0, cdf1, joint_cdf = knncdf.joint(
+        knn1,
+        knn2,
+        rvs_gen=rvs_gen,
+        nneighbours=int(config["nneighbours"]),
+        rmin=config["rmin"],
+        rmax=config["rmax"],
+        nsamples=int(config["nsamples"]),
+        neval=int(config["neval"]),
+        batch_size=int(config["batch_size"]),
+        random_state=config["seed"],
+    )
+
+    corr = knncdf.joint_to_corr(cdf0, cdf1, joint_cdf)
+    fout = paths.knncross(args.simname, run, ics)
+    joblib.dump({"rs": rs, "corr": corr}, fout)
+
+
+def do_runs(nsims):
+    for run in args.runs:
+        do_cross(run, nsims)
+
+
+###############################################################################
+#                         Crosscorrelation calculation                        #
+###############################################################################
+
+
+if nproc > 1:
+    if rank == 0:
+        tasks = list(combinations(ics, 2))
+        master_process(tasks, comm, verbose=True)
+    else:
+        worker_process(do_runs, comm, verbose=False)
+else:
+    tasks = list(combinations(ics, 2))
+    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