mirror of
https://github.com/Richard-Sti/csiborgtools.git
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Remove old merger tree (#93)
* Edit docs * Delete merger tree files * Edit README * Edit docs
This commit is contained in:
Richard Stiskalek
GitHub
parent
e972f8e3f2
commit
944fea5510
@ -8,6 +8,7 @@ however with little effort it can support other simulations as well.
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## TODO
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- [x] Prune old CSiBORG1 merger tree things.
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- [ ] Add full support for CSiBORG2 suite of simulations.
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- [ ] Add SPH field calculation from cosmotools.
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@ -12,7 +12,9 @@
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""CSiBORG paths manager."""
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"""
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CSiBORG paths manager.
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"""
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from glob import glob, iglob
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from os import makedirs
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from os.path import isdir, join
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@ -312,26 +314,6 @@ class Paths:
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nsnap = str(nsnap).zfill(3)
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return join(simpath, f"snapdir_{nsnap}", f"snap_{nsnap}")
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def merger_tree_file(self, nsnap, nsim):
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"""
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Path to the CSiBORG on-the-fly generated merger tree file.
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Parameters
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----------
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nsnap : int
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Snapshot index.
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nsim : int
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IC realisation index.
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Returns
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-------
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str
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"""
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nsim = str(nsim)
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nsnap = str(nsnap).zfill(5)
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return join(self.srcdir, f"ramses_out_{nsim}",
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f"output_{nsnap}", f"mergertree_{nsnap}.dat")
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def processed_output(self, nsim, simname, halo_finder):
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"""
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Path to the files containing all particles of a CSiBORG realisation at
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@ -378,23 +360,6 @@ class Paths:
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try_create_directory(fdir)
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return join(fdir, f"phew_{str(nsim).zfill(5)}.hdf5")
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def processed_merger_tree(self, nsim):
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"""
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Path to the files containing the processed original merger tree files.
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Parameters
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----------
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nsim : int
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IC realisation index.
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Returns
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-------
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str
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"""
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fdir = join(self.postdir, "processed_output")
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try_create_directory(fdir)
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return join(fdir, f"merger_{str(nsim).zfill(5)}.hdf5")
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def halomaker_particle_membership(self, nsnap, nsim, halo_finder):
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"""
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Path to the HaloMaker particle membership file (CSiBORG only).
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@ -145,8 +145,6 @@ class CSiBORGReader(BaseReader):
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----------
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paths : py:class`csiborgtools.read.Paths`
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"""
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# _snapshot_cache = {}
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def __init__(self, paths):
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self.paths = paths
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@ -433,37 +431,6 @@ class CSiBORGReader(BaseReader):
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return parent_arr, parent_mass
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def read_merger_tree(self, nsnap, nsim):
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"""
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Read in the raw merger tree file.
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Parameters
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----------
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nsnap : int
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Snapshot index.
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nsim : int
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IC realisation index.
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Returns
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-------
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data : 2-dimensional array
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"""
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fname = self.paths.merger_tree_file(nsnap, nsim)
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# Do some checks if the file exists or is empty
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if not isfile(fname) or getsize(fname) == 0:
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raise FileExistsError(f"Merger file `{fname}` does not exist.")
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data = numpy.genfromtxt(fname)
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if data.ndim == 1:
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raise FileExistsError(f"Invalid merger file `{fname}`.")
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# Convert to Msun / h and cMpc / h but keep velocity in box units.
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data[:, 3] *= 2.6543271649678946e+19
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data[:, 5:8] *= 677.7
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return data
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###############################################################################
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# Quijote particle reader #
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@ -12,7 +12,9 @@
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""Collection of stand-off utility functions used in the scripts."""
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"""
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Collection of stand-off utility functions used in the scripts.
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"""
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import numpy
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from numba import jit
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from datetime import datetime
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@ -1,979 +0,0 @@
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# Copyright (C) 2023 Mladen Ivkovic, Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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import copy
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import os
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from os.path import exists, join
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from os import makedirs
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from sys import argv
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from datetime import datetime
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import numpy as np
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from joblib import dump, load
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from tqdm import trange
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errmsg = """
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------------------------------------
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mergertree-extract.py
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------------------------------------
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---------------
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Usage
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---------------
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This script extracts the masses of clumps and haloes written by the mergertree
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patch.
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It needs output_XXXXX/mergertree_XXXXX.txtYYYYY and
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output_XXXXX/clump_XXXXX.txtYYYYY files to work.
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You need to run it from the directory where the output_XXXXX directories are
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in.
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There are three working modes defined:
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1) do for one clump only.
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You need to provide the clump ID you want it done for.
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You can provide a starting directory, but by default the script will
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search for the directory where z = 0.
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run with `python3 mergertree-extract.py <clumpid> [--options] `
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this creates the file mergertree_XXXXX_halo-<halo-ID>.txt. Its contents are
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discussed below.
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2) do for one halo.
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You need to provide the halo ID you want it done for, and the flag
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-c or --children.
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The script will by itself find all the child clumps and walk through
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their main branches as well, and write them down.
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run with `python3 mergertree-extract.py <haloid> -c [--options]`
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or `python3 mergertree-extract.py <haloid> --children [--options]`
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this creates the hollowing files:
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- halo_hierarchy_XXXXX-<halo-ID>.txt
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contains the halo ID, how many children it has, and the children
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IDs
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- mergertree_XXXXX_halo-<halo-ID>.txt
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mergertree data for halo that you chose.
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- mergertree_XXXXX_subhalo-<child-ID>.txt
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mergertree data for subhalos of the halo you chose. One file will
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be created for each subhalo.
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The contents of the mergertree_XXXXX* files are discussed below.
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3) do for all haloes
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The script will just walk off all haloes in the z = 0 directory. Note:
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Haloes, not clumps!
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run with `python3 mergertree-extract.py -a [--options]`
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or `python3 mergertree-extract.py --all [--options]`
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This will create the same type of files as in mode (2), just for all
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haloes.
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If only an integer is given as cmdline arg, mode (1) [one clump only] will be
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run. If no cmd line argument is given, mode (3) [--all] will be run.
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---------------
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Output
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---------------
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the mergertree_XXXXX* files have 6 columns:
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snapshot The snapshot from which this data is taken from
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redshift The redshift of that snapshot
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clump_ID The clump ID of the clump at that snapshot
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mass The mass of the clump at that snapshot, based on what's in
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the output_XXXXX/mergertree_XXXXX.txtYYYYY files, not the
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output_XXXXX/clump_XXXXX.txtYYYYY files.
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mass_from_mergers how much mass has been merged into this clump in this
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snapshot, i.e. the sum of all the clump masses that have
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been found to merge with this clump at this snapshot. This
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does not include the mass of clumps which only seem to
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merge with this clump, but re-emerge later.
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mass_from_jumpers The mass of all clumps that seem to merge with this clump,
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but re-emerge at a later time.
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----------------
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Options
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----------------
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List of all flags:
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Running modes
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-a, --all: make trees for all clumps in output where z = 0
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-c --children: make trees for a halo and all its subhaloes. You need to
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specify which halo via its halo ID.
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-h, --help: print this help and exit.
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Options:
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--start-at=INT don't start at z = 0 snapshot, but with the specified
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directory output_00INT.
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--prefix=some/path/ path where you want your output written to.
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-v, --verbose: be more verbose about what you're doing
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-----------------
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Requirements
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-----------------
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It needs output_XXXXX/mergertree_XXXXX.txtYYYYY and
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output_XXXXX/clump_XXXXX.txtYYYYY files to work, which are created using the
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mergertree patch in ramses.
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Also needs numpy.
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"""
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###############################################################################
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# Clump data #
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###############################################################################
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class ClumpData:
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"""
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Data from clump_XXXXX.txt
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Parameters
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----------
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par : params object
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"""
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def __init__(self, par):
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self.clumpids = np.zeros(1) # clump ID
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self.parent = np.zeros(1) # parent ID
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self.level = np.zeros(1) # clump level
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def read_clumpdata(self, par):
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"""Reads in the clump data for the z = 0 directory."""
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if par.verbose:
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print("Reading clump data.")
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out = p.z0
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raw_data = [None for i in range(par.ncpu)]
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dirnrstr = str(par.outputnrs[out]).zfill(5)
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dirname = 'output_' + dirnrstr
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i = 0
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for cpu in range(1):
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fname = join(par.workdir, dirname, 'clump_' + dirnrstr + '.dat')
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new_data = np.loadtxt(fname, dtype='int', skiprows=1,
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usecols=[0, 1, 2])
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if new_data.ndim == 2:
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raw_data[i] = new_data
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i += 1
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elif new_data.shape[0] == 3: # if only 1 row is present in file
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raw_data[i] = np.atleast_2d(new_data)
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i += 1
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fulldata = np.concatenate(raw_data[:i], axis=0)
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self.clumpids = fulldata[:, 0]
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self.level = fulldata[:, 1]
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self.parent = fulldata[:, 2]
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def cleanup_clumpdata(self, par, mtd):
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"""
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The particle unbinding can remove entire clumps from the catalogue.
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If the option isn't set in the namelist, the clumpfinder output will
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still be made not based on the clumpfinder. If that is the case, the
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clumpfinder catalogue will contain clumps which the mergertree data
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doesn't have, leading to problems. So remove those here.
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"""
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for i, c in enumerate(self.clumpids):
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if c not in mtd.descendants[par.z0]:
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self.clumpids[i] = 0
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self.level[i] = 0
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self.parent[i] = -1 # don't make it the same as clumpid
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def find_children(self, clumpid):
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"""Find the children for given clump ID."""
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children = []
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last_added = [clumpid]
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loopcounter = 0
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while True:
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loopcounter += 1
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this_level_parents = copy.copy(last_added)
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children += this_level_parents
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last_added = []
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for i, cid in enumerate(self.clumpids):
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if self.parent[i] in this_level_parents and cid != clumpid:
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last_added.append(cid)
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if len(last_added) == 0:
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break
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if loopcounter == 100:
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print("Finished 100 iterations, we shouldn't be this deep")
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break
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return children[1:] # don't return top level parent
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def write_children(self, par, clumpid, children):
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"""Write the children to file."""
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hfile = join(par.outdir, f"{par.halofilename}-{str(clumpid)}.txt")
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with open(hfile, 'w') as f:
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f.write("# {0:>18} {1:>18} {2:>18}\n".format("halo", "nr_of_children", "children")) # noqa
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nc = len(children)
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dumpstring = " {0:18d} {1:18d}".format(clumpid, nc)
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dumpstring = "".join([dumpstring] + [" {0:18d}".format(c) for c in children] + ['\n']) # noqa
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f.write(dumpstring)
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###############################################################################
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# Constants object #
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###############################################################################
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class Constants:
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"""
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Class holding constants.
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"""
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def __init__(self):
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self.Mpc = 3.086e24 # cm
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self.M_Sol = 1.98855e33 # g
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self.Gyr = (24 * 3600 * 365 * 1e9) # s
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self.G = 4.492e-15 # Mpc^3/(M_sol Gyr^2)
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self.H0 = 100 # km/s/Mpc
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self.omega_m = 0.307000011205673
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self.omega_l = 0.693000018596649
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self.omega_k = 0.0
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self.omega_b = 0.0
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###############################################################################
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# Params object #
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###############################################################################
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class Params:
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"""
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Global parameters to be stored
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"""
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def __init__(self):
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# self.workdir = f"/mnt/extraspace/hdesmond/ramses_out_{self.nsim}"
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# self.outdir = f"/mnt/extraspace/rstiskalek/CSiBORG/cleaned_mtree/ramses_out_{self.nsim}" # noqa
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# if not exists(self.outdir):
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# makedirs(self.outdir)
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self.lastdir = "" # last output_XXXXX directory
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self.lastdirnr = -1 # XXXX from lastdir
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self.ncpu = 1 # Number of CPUs used
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self.noutput = 1 # how many output_XXXXX dirs exist
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self.nout = 1 # how many outputs we're gonna deal with. (Some might not have merger tree data) # noqa
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self.outputnrs = None # numpy array of output numbers
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self.output_lowest = 0 # lowest snapshot number that we're dealing with (>= 1) # noqa
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self.z0 = 0 # index of z=0 snapshot (or whichever you want to start with) # noqa
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# NOTE: params.nout will be defined such that you can easily loop
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self.verbose = False # verbosity
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self.start_at = 0 # output dir to start with, if given
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self.output_prefix = "" # user given prefix for output files
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self.outputfilename = "" # output filename. Stores prefix/mergertree_XXXXX part of name only # noqa
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self.halofilename = "" # output filename for halo hierarchy. Stores prefix/halo_hierarchy_XXXXX part of filename only # noqa
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self.one_halo_only = False # do the tree for one clump only
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self.halo_and_children = False # do the tree for one halo, including subhaloes # noqa
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self.do_all = False # do for all clumps at z=0 output
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self.clumpid = 0 # which clump ID to work for.
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self.nsim = None
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# Dictionnary of accepted keyword command line arguments
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self.accepted_flags = {
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'-a': self.set_do_all,
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'--all': self.set_do_all,
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'-r': self.set_halo_and_children,
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'--recursive': self.set_halo_and_children,
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'-c': self.set_halo_and_children,
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'--children': self.set_halo_and_children,
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'-h': self.get_help,
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'--help': self.get_help,
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'-v': self.set_verbose,
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'--verbose': self.set_verbose,
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}
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self.accepted_flags_with_args = {
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"--nsim": self.set_nsim,
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'--start-at': self.set_startnr,
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'--prefix': self.set_prefix,
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}
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# -----------------------------
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# Setter methods
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# -----------------------------
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def set_do_all(self):
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self.do_all = True
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return
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def set_halo_and_children(self):
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self.halo_and_children = True
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return
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def get_help(self):
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print(errmsg)
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quit()
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return
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def set_verbose(self):
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self.verbose = True
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return
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def set_startnr(self, arg):
|
||||
flag, startnr = arg.split("=")
|
||||
try:
|
||||
self.start_at = int(startnr)
|
||||
except ValueError:
|
||||
print("given value for --start-at=INT isn't an integer?")
|
||||
|
||||
def set_prefix(self, arg):
|
||||
flag, prefix = arg.split("=")
|
||||
# try:
|
||||
self.output_prefix = prefix
|
||||
try:
|
||||
os.makedirs(self.output_prefix)
|
||||
except FileExistsError:
|
||||
pass
|
||||
return
|
||||
|
||||
def set_nsim(self, arg):
|
||||
flag, nsim = arg.split("=")
|
||||
try:
|
||||
self.nsim = int(nsim)
|
||||
except ValueError:
|
||||
print("given value for --nsim=INT isn't an integer?")
|
||||
|
||||
def read_cmdlineargs(self):
|
||||
"""
|
||||
Reads in the command line arguments and store them in the
|
||||
global_params object.
|
||||
"""
|
||||
nargs = len(argv)
|
||||
i = 1 # first cmdlinearg is filename of this file, so skip it
|
||||
|
||||
while i < nargs:
|
||||
arg = argv[i]
|
||||
arg = arg.strip()
|
||||
if arg in self.accepted_flags.keys():
|
||||
self.accepted_flags[arg]()
|
||||
else:
|
||||
for key in self.accepted_flags_with_args.keys():
|
||||
if arg.startswith(key):
|
||||
self.accepted_flags_with_args[key](arg)
|
||||
break
|
||||
else:
|
||||
try:
|
||||
self.clumpid = int(arg)
|
||||
except ValueError:
|
||||
print(f"I didn't recognize the argument '{arg}'. Use "
|
||||
"mergertre-extract.py -h or --help to print "
|
||||
"help message.")
|
||||
quit()
|
||||
|
||||
i += 1
|
||||
|
||||
if self.nsim is None:
|
||||
raise ValueError("nsim not set. Use --nsim=INT to set it.")
|
||||
|
||||
@property
|
||||
def workdir(self):
|
||||
return f"/mnt/extraspace/hdesmond/ramses_out_{self.nsim}"
|
||||
|
||||
@property
|
||||
def outdir(self):
|
||||
fname = f"/mnt/extraspace/rstiskalek/CSiBORG/cleaned_mtree/ramses_out_{self.nsim}" # noqa
|
||||
if not exists(fname):
|
||||
makedirs(fname)
|
||||
return fname
|
||||
|
||||
def get_output_info(self):
|
||||
"""
|
||||
Read in the output info based on the files in the current working
|
||||
directory. Reads in last directory, ncpu, noutputs. Doesn't read
|
||||
infofiles.
|
||||
"""
|
||||
# self.workdir = os.getcwd()
|
||||
filelist = os.listdir(self.workdir)
|
||||
|
||||
outputlist = []
|
||||
for filename in filelist:
|
||||
if filename.startswith('output_'):
|
||||
outputlist.append(filename)
|
||||
|
||||
if len(outputlist) < 1:
|
||||
print("I didn't find any output_XXXXX directories in current "
|
||||
"working directory. Are you in the correct workdir? "
|
||||
"Use mergertree-extract.py -h or --help to print help "
|
||||
"message.")
|
||||
quit()
|
||||
|
||||
outputlist.sort()
|
||||
|
||||
self.lastdir = outputlist[-1]
|
||||
self.lastdirnr = int(self.lastdir[-5:])
|
||||
self.noutput = len(outputlist)
|
||||
|
||||
if (self.start_at > 0):
|
||||
# check that directory exists
|
||||
startnrstr = str(self.start_at).zfill(5)
|
||||
if 'output_' + startnrstr not in outputlist:
|
||||
print("Didn't find specified starting directory "
|
||||
f"output_{startnrstr} use mergertree-extract.py -h or "
|
||||
"--help to print help message.")
|
||||
quit()
|
||||
|
||||
# read ncpu from infofile in last output directory
|
||||
infofile = join(self.workdir, self.lastdir,
|
||||
f"info_{self.lastdir[-5:]}.txt")
|
||||
with open(infofile, 'r') as f:
|
||||
ncpuline = f.readline()
|
||||
line = ncpuline.split()
|
||||
self.ncpu = int(line[-1])
|
||||
|
||||
def setup_and_checks(self, sd):
|
||||
"""
|
||||
Do checks and additional setups once you have all the cmd line args and
|
||||
output infos
|
||||
|
||||
Parameters
|
||||
----------
|
||||
sd: snapshotdata object
|
||||
"""
|
||||
# set running mode
|
||||
if not self.do_all:
|
||||
if self.clumpid <= 0:
|
||||
print("No or wrong clump id given. Setting the --all mode.")
|
||||
self.set_do_all()
|
||||
else:
|
||||
if not self.halo_and_children:
|
||||
self.one_halo_only = True
|
||||
|
||||
# generate list of outputdirnumbers
|
||||
startnr = self.lastdirnr
|
||||
self.outputnrs = np.array(range(startnr, startnr - self.noutput, -1))
|
||||
|
||||
# find starting output directory
|
||||
self.z0 = np.argmin(np.absolute(sd.redshift))
|
||||
|
||||
if self.start_at > 0:
|
||||
# replace z0 dir with starting dir
|
||||
self.z0 = self.lastdirnr - self.start_at
|
||||
|
||||
# generate output filename
|
||||
dirnrstr = str(self.outputnrs[self.z0]).zfill(5)
|
||||
fname = "mergertree_" + dirnrstr
|
||||
self.outputfilename = join(self.output_prefix, fname)
|
||||
|
||||
# generate halo output filename
|
||||
fname = "halo_hierarchy_" + dirnrstr
|
||||
self.halofilename = join(self.output_prefix, fname)
|
||||
|
||||
# rename output_prefix to something if it wasn't set
|
||||
if self.output_prefix == "":
|
||||
self.output_prefix = os.path.relpath(self.workdir)
|
||||
|
||||
# find self.nout; i.e. how many outputs we are actually going to have
|
||||
for out in range(self.noutput - 1, -1, -1):
|
||||
dirnrstr = str(self.outputnrs[out]).zfill(5)
|
||||
mtreefile = join(self.workdir,
|
||||
f"output_{dirnrstr}",
|
||||
f"mergertree_{dirnrstr}.dat")
|
||||
|
||||
if os.path.exists(mtreefile):
|
||||
print("Loading mergertree data from ", mtreefile)
|
||||
# if there is a file, this is lowest snapshot number directory
|
||||
# that we'll be dealing with, and hence will have the highest
|
||||
# index number in the arrays I'm using
|
||||
|
||||
# NOTE: params.nout will be defined such that you can easily
|
||||
# loop for out in range(p.z0, p.nout)
|
||||
self.nout = out + 1
|
||||
break
|
||||
|
||||
def print_params(self):
|
||||
"""Prints out the parameters that are set."""
|
||||
if self.do_all:
|
||||
print("Working mode: all clumps")
|
||||
else:
|
||||
if self.halo_and_children:
|
||||
print("Working mode: halo", self.clumpid, "and its children") # noqa
|
||||
else:
|
||||
print("Working mode: clump ", self.clumpid)
|
||||
|
||||
print("workdir: ", self.workdir)
|
||||
print("snapshot of tree root: ", self.outputnrs[self.z0])
|
||||
print("p.one_halo_only ", p.one_halo_only)
|
||||
print("p.do_all ", p.do_all)
|
||||
print("p.halo_and_children ", p.halo_and_children)
|
||||
print("p.one_halo_only ", p.one_halo_only)
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Merger tree data #
|
||||
###############################################################################
|
||||
|
||||
|
||||
class MTreeData:
|
||||
"""
|
||||
Merger tree data lists
|
||||
|
||||
Parameters
|
||||
----------
|
||||
par : params object
|
||||
"""
|
||||
def __init__(self, par):
|
||||
self.progenitors = [np.zeros(1) for i in range(par.noutput)] # progenitor IDs # noqa
|
||||
self.descendants = [np.zeros(1) for i in range(par.noutput)] # descendant IDs # noqa
|
||||
self.progenitor_outputnrs = [np.zeros(1) for i in range(par.noutput)] # snapshot number of progenitor # noqa
|
||||
self.mass = [np.zeros(1) for i in range(par.noutput)] # descendant mass # noqa
|
||||
self.mass_to_remove = [np.zeros(1) for i in range(par.noutput)] # descendant mass # noqa
|
||||
|
||||
def read_mergertree_data(self, par, sd):
|
||||
"""Reads in mergertree data."""
|
||||
|
||||
if par.verbose:
|
||||
print("Reading in mergertree data")
|
||||
|
||||
# Preparation
|
||||
|
||||
# define new datatype for mergertree output
|
||||
mtree = np.dtype([('clump', 'i4'),
|
||||
('prog', 'i4'),
|
||||
('prog_outnr', 'i4'),
|
||||
('mass', 'f8'),
|
||||
('npart', 'f8'),
|
||||
('x', 'f8'),
|
||||
('y', 'f8'),
|
||||
('z', 'f8'),
|
||||
('vx', 'f8'),
|
||||
('vy', 'f8'),
|
||||
('vz', 'f8')
|
||||
])
|
||||
|
||||
# ---------------------------
|
||||
# Loop over directories
|
||||
# ---------------------------
|
||||
|
||||
startnr = par.lastdirnr
|
||||
# READ THE ONES BEFORE z0 TOO!
|
||||
for output in trange(par.nout, desc="Reading merger"):
|
||||
dirnr = str(startnr - output).zfill(5)
|
||||
srcdir = 'output_' + dirnr
|
||||
|
||||
fnames = [srcdir + '/' + "mergertree_" + dirnr + '.dat']
|
||||
fnames[0] = join(par.workdir, fnames[0])
|
||||
|
||||
datalist = [np.zeros((1, 3)) for i in range(par.ncpu)]
|
||||
i = 0
|
||||
nofile = 0
|
||||
for f in fnames:
|
||||
if os.path.exists(f):
|
||||
datalist[i] = np.atleast_1d(np.genfromtxt(f, dtype=mtree,
|
||||
skip_header=1))
|
||||
i += 1
|
||||
else:
|
||||
nofile += 1
|
||||
|
||||
if nofile == p.ncpu:
|
||||
print("Didn't find any mergertree data in", srcdir)
|
||||
|
||||
# ---------------------------------
|
||||
# Sort out data
|
||||
# ---------------------------------
|
||||
if i > 0:
|
||||
fulldata = np.concatenate(datalist[:i], axis=0)
|
||||
|
||||
self.descendants[output] = fulldata[:]['clump']
|
||||
self.progenitors[output] = fulldata[:]['prog']
|
||||
self.progenitor_outputnrs[output] = fulldata[:]['prog_outnr']
|
||||
self.mass[output] = fulldata[:]['mass']
|
||||
# self.npart[output] = fulldata[:]['npart']
|
||||
# self.x[output] = fulldata[:]['x']
|
||||
# self.y[output] = fulldata[:]['y']
|
||||
# self.z[output] = fulldata[:]['z']
|
||||
# self.vx[output] = fulldata[:]['vx']
|
||||
# self.vy[output] = fulldata[:]['vy']
|
||||
# self.vz[output] = fulldata[:]['vz']
|
||||
|
||||
# --------------------------------------
|
||||
# Transform units to physical units
|
||||
# --------------------------------------
|
||||
|
||||
# transform units to physical units
|
||||
for i in range(len(self.descendants)):
|
||||
self.mass[i] *= sd.unit_m[i]
|
||||
# self.x[i] *= sd.unit_l[i] # only transform later when needed; Need to check for periodicity first! # noqa
|
||||
# self.y[i] *= sd.unit_l[i]
|
||||
# self.z[i] *= sd.unit_l[i]
|
||||
# self.vx[i] *= sd.unit_l[i]/sd.unit_t[i]
|
||||
# self.vy[i] *= sd.unit_l[i]/sd.unit_t[i]
|
||||
# self.vz[i] *= sd.unit_l[i]/sd.unit_t[i]
|
||||
|
||||
def clean_up_jumpers(self, par):
|
||||
"""
|
||||
Remove jumpers from the merger list. Take note of how much mass should
|
||||
be removed from the descendant because the jumper is to be removed.
|
||||
"""
|
||||
# First initialize mass_to_remove arrays
|
||||
self.mass_to_remove = [np.zeros(self.descendants[out].shape)
|
||||
for out in range(par.noutput)]
|
||||
nreplaced = 0
|
||||
for out in trange(par.nout + par.z0 - 1, desc="Cleaning jumpers"):
|
||||
for i, pr in enumerate(self.progenitors[out]):
|
||||
if pr < 0:
|
||||
# Subtract 1 here from snapind:
|
||||
# progenitor_outputnrs gives the snapshot number where the
|
||||
# jumper was a descendant for the last time
|
||||
# so you need to overwrite the merging one snapshot later,
|
||||
# where the clump is the progenitor
|
||||
snapind = get_snap_ind(p, self.progenitor_outputnrs[out][i]) - 1 # noqa
|
||||
|
||||
# NOTE bottleneck
|
||||
jumpind = self.progenitors[snapind] == -pr
|
||||
|
||||
# NOTE bottleneck
|
||||
# find index of descendant into which this clump will
|
||||
# appearingly merge into
|
||||
mergerind = self.descendants[snapind] == - self.descendants[snapind][jumpind] # noqa
|
||||
# overwrite merging event so it won't count
|
||||
self.descendants[snapind][jumpind] = 0
|
||||
|
||||
# find mass of jumper in previous snapshot
|
||||
jumpmassind = self.descendants[snapind + 1] == -pr
|
||||
# note how much mass might need to be removed for whatever
|
||||
# you need it
|
||||
self.mass_to_remove[snapind][mergerind] += self.mass[snapind + 1][jumpmassind] # noqa
|
||||
|
||||
nreplaced += 1
|
||||
|
||||
print("Cleaned out", nreplaced, "jumpers")
|
||||
|
||||
def get_tree(self, par, tree, sd, clumpid):
|
||||
"""Follow the main branch down."""
|
||||
if par.verbose:
|
||||
print("Computing tree for clump", clumpid)
|
||||
|
||||
dind = self.descendants[par.z0] == clumpid
|
||||
desc_snap_ind = p.z0
|
||||
desc = self.descendants[p.z0][dind]
|
||||
prog = self.progenitors[p.z0][dind]
|
||||
|
||||
def get_prog_indices(prog, desc_snap_ind):
|
||||
"""
|
||||
Compute snapshot index at which given progenitor has been a
|
||||
descendant and its index in the array
|
||||
|
||||
prog: progenitor ID
|
||||
desc_snap_ind: snapshot index of descendant of given prog
|
||||
|
||||
returns:
|
||||
p_snap_ind: snapshot index of the progenitor
|
||||
pind: progenitor index (np.array mask) of progenitor in
|
||||
array where it is descendant
|
||||
"""
|
||||
if prog > 0: # if progenitor isn't jumper
|
||||
# find progenitor's index in previous snapshot
|
||||
p_snap_ind = desc_snap_ind + 1
|
||||
pind = self.descendants[p_snap_ind] == prog
|
||||
|
||||
elif prog < 0:
|
||||
p_snap_ind = get_snap_ind(
|
||||
par, self.progenitor_outputnrs[desc_snap_ind][dind])
|
||||
pind = self.descendants[p_snap_ind] == -prog
|
||||
|
||||
return p_snap_ind, pind
|
||||
|
||||
while True:
|
||||
# first calculate merger mass
|
||||
mergers = self.descendants[desc_snap_ind] == -desc
|
||||
mergermass = 0.0
|
||||
if mergers.any():
|
||||
for m in self.progenitors[desc_snap_ind][mergers]:
|
||||
# find mass of merger. That's been written down at the
|
||||
# place where merger was descendant.
|
||||
m_snap_ind, mergerind = get_prog_indices(m, desc_snap_ind)
|
||||
mergermass += self.mass[m_snap_ind][mergerind]
|
||||
|
||||
# add the descendant to the tree
|
||||
tree.add_snap(par.outputnrs[desc_snap_ind],
|
||||
sd.redshift[desc_snap_ind], desc,
|
||||
self.mass[desc_snap_ind][dind], mergermass,
|
||||
self.mass_to_remove[desc_snap_ind][dind])
|
||||
|
||||
# now descend down the main branch
|
||||
if prog != 0:
|
||||
p_snap_ind, pind = get_prog_indices(prog, desc_snap_ind)
|
||||
else:
|
||||
# stop at progenitor = 0
|
||||
break
|
||||
|
||||
# prepare for next round
|
||||
desc_snap_ind = p_snap_ind
|
||||
dind = pind
|
||||
desc = abs(prog)
|
||||
prog = self.progenitors[p_snap_ind][pind]
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Snapshot data #
|
||||
###############################################################################
|
||||
|
||||
|
||||
class SnapshotData():
|
||||
"""Snapshot specific data"""
|
||||
def __init__(self, par):
|
||||
# read in
|
||||
self.aexp = np.zeros(par.noutput)
|
||||
self.unit_l = np.zeros(par.noutput)
|
||||
self.unit_m = np.zeros(par.noutput)
|
||||
self.unit_t = np.zeros(par.noutput)
|
||||
self.unit_dens = np.zeros(par.noutput)
|
||||
# to be computed
|
||||
self.redshift = np.zeros(par.noutput) # z
|
||||
|
||||
def read_infofiles(self, par, const):
|
||||
"""Read the info_XXXXX.txt files."""
|
||||
if par.verbose:
|
||||
print("Reading info files.")
|
||||
|
||||
startnr = par.lastdirnr
|
||||
|
||||
for output in range(p.noutput):
|
||||
# Start with last directory (e.g. output_00060),
|
||||
# work your way to first directory (e.g. output_00001)
|
||||
# p.z0 isn't decided yet, so just read in everything here.
|
||||
dirnr = str(startnr - output).zfill(5)
|
||||
srcdir = 'output_' + dirnr
|
||||
|
||||
try:
|
||||
# ------------------------------------------------------
|
||||
# get time, redshift, and units even for output_00001
|
||||
# ------------------------------------------------------
|
||||
fileloc = srcdir + '/info_' + dirnr + '.txt'
|
||||
fileloc = join(par.workdir, fileloc)
|
||||
infofile = open(fileloc)
|
||||
for i in range(9):
|
||||
infofile.readline() # skip first 9 lines
|
||||
|
||||
# get expansion factor
|
||||
aline = infofile.readline()
|
||||
astring, equal, aval = aline.partition("=")
|
||||
afloat = float(aval)
|
||||
sd.aexp[output] = afloat
|
||||
|
||||
for i in range(5):
|
||||
infofile.readline() # skip 5 lines
|
||||
|
||||
# get unit_l
|
||||
unitline = infofile.readline()
|
||||
unitstring, equal, unitval = unitline.partition("=")
|
||||
unitfloat = float(unitval)
|
||||
sd.unit_l[output] = unitfloat
|
||||
|
||||
# get unit_dens
|
||||
unitline = infofile.readline()
|
||||
unitstring, equal, unitval = unitline.partition("=")
|
||||
unitfloat = float(unitval)
|
||||
sd.unit_dens[output] = unitfloat
|
||||
|
||||
# get unit_t
|
||||
unitline = infofile.readline()
|
||||
unitstring, equal, unitval = unitline.partition("=")
|
||||
unitfloat = float(unitval)
|
||||
sd.unit_t[output] = unitfloat
|
||||
|
||||
infofile.close()
|
||||
|
||||
except IOError: # If file doesn't exist
|
||||
print("Didn't find any info data in ", srcdir)
|
||||
break
|
||||
|
||||
self.unit_m = self.unit_dens * self.unit_l ** 3 / const.M_Sol
|
||||
self.unit_l /= const.Mpc
|
||||
self.unit_t /= const.Gyr
|
||||
|
||||
self.redshift = 1. / self.aexp - 1
|
||||
|
||||
###############################################################################
|
||||
# Tree object #
|
||||
###############################################################################
|
||||
|
||||
|
||||
class Tree:
|
||||
"""
|
||||
Holds tree result data. It's not really a tree, it's just the values along
|
||||
the main branch, but let's call it a tree anyway. Sue me.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
nelements : int
|
||||
Estimate for how many snapshots you need to allocate space for.
|
||||
"""
|
||||
def __init__(self, nelements):
|
||||
self.n = 0 # number of elements in tree # noqa
|
||||
self.snapshotnr = -np.ones(nelements, dtype=int) # snapshot number of array values # noqa
|
||||
self.redshift = -np.ones(nelements, dtype=float) # redshift at that snapshot # noqa
|
||||
self.clumpids = -np.ones(nelements, dtype=int) # clump id of halo in that snapshot # noqa
|
||||
self.mass = np.zeros(nelements, dtype=float) # mass at that snapshot # noqa
|
||||
self.mergermass = np.zeros(nelements, dtype=float) # sum of mass of swallowed up clumps # noqa
|
||||
self.mass_to_remove = np.zeros(nelements, dtype=float) # sum of mass of swallowed up clumps # noqa
|
||||
|
||||
def add_snap(self, nr, z, ID, m, mm, mdel):
|
||||
"""Add new result."""
|
||||
n = self.n
|
||||
self.snapshotnr[n] = nr
|
||||
self.redshift[n] = z
|
||||
self.clumpids[n] = ID
|
||||
self.mass[n] = m
|
||||
self.mergermass[n] = mm
|
||||
self.mass_to_remove[n] = mdel
|
||||
self.n += 1
|
||||
|
||||
def write_tree(self, par, case='halo'):
|
||||
"""Write the results to file."""
|
||||
resfile = join(
|
||||
par.outdir,
|
||||
f"{par.outputfilename}_{case}-{str(self.clumpids[0])}.txt")
|
||||
|
||||
with open(resfile, 'w') as f:
|
||||
f.write('# {0:>12} {1:>12} {2:>16} {3:>18} {4:>18} {5:>18}\n'.format( # noqa
|
||||
"snapshot", "redshift", "clump_ID", "mass[M_sol]",
|
||||
"mass_from_mergers", "mass_from_jumpers"))
|
||||
|
||||
for i in range(self.n):
|
||||
f.write(' {0:12d} {1:12.4f} {2:16d} {3:18.6e} {4:18.6e} {5:18.6e}\n'.format( # noqa
|
||||
self.snapshotnr[i], self.redshift[i], self.clumpids[i],
|
||||
self.mass[i], self.mergermass[i], self.mass_to_remove[i]))
|
||||
|
||||
return
|
||||
|
||||
|
||||
def get_snap_ind(p, snap):
|
||||
"""
|
||||
Computes the snapshot index in mtreedata/halodata/snapshotdata arrays for a
|
||||
given snapshot number snap
|
||||
"""
|
||||
return (p.noutput - snap).item()
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
|
||||
p = Params()
|
||||
c = Constants()
|
||||
|
||||
# Read cmdlineargs, available output, get global parameters
|
||||
p.read_cmdlineargs()
|
||||
p.get_output_info()
|
||||
|
||||
sd = SnapshotData(p)
|
||||
sd.read_infofiles(p, c)
|
||||
|
||||
# finish setup
|
||||
p.setup_and_checks(sd)
|
||||
p.print_params()
|
||||
|
||||
# now read in mergertree data
|
||||
fname = join(p.outdir, "mtreedata.p")
|
||||
if exists(fname):
|
||||
print(f"{datetime.now()}: loading mergertree data from `{fname}`.",
|
||||
flush=True)
|
||||
mtd = load(fname)
|
||||
print(f"{datetime.now()}: finished loading mergertree data from `{fname}`.", # noqa
|
||||
flush=True)
|
||||
else:
|
||||
print("Generating mergertree data.", flush=True)
|
||||
mtd = MTreeData(p)
|
||||
mtd.read_mergertree_data(p, sd)
|
||||
# clean up jumpers
|
||||
mtd.clean_up_jumpers(p)
|
||||
|
||||
print("Saving mergertree data.", flush=True)
|
||||
dump(mtd, fname)
|
||||
|
||||
# read in clump data if required
|
||||
if p.do_all or p.halo_and_children:
|
||||
cd = ClumpData(p)
|
||||
cd.read_clumpdata(p)
|
||||
|
||||
# clean up halo catalogue
|
||||
cd.cleanup_clumpdata(p, mtd)
|
||||
|
||||
# find children, and write them down
|
||||
if p.verbose:
|
||||
print("Searching for child clumps.")
|
||||
|
||||
if p.halo_and_children:
|
||||
children = cd.find_children(p.clumpid)
|
||||
cd.write_children(p, p.clumpid, children)
|
||||
|
||||
if p.do_all:
|
||||
is_halo = cd.clumpids == cd.parent
|
||||
childlist = [None for c in cd.clumpids[is_halo]]
|
||||
for i, halo in enumerate(cd.clumpids[is_halo]):
|
||||
children = cd.find_children(halo)
|
||||
cd.write_children(p, halo, children)
|
||||
childlist[i] = children
|
||||
|
||||
# finally, get the bloody tree
|
||||
|
||||
if p.one_halo_only:
|
||||
newtree = Tree(p.nout)
|
||||
mtd.get_tree(p, newtree, sd, p.clumpid)
|
||||
newtree.write_tree(p, 'halo')
|
||||
|
||||
if p.halo_and_children:
|
||||
newtree = Tree(p.nout)
|
||||
mtd.get_tree(p, newtree, sd, p.clumpid)
|
||||
newtree.write_tree(p, 'halo')
|
||||
|
||||
for c in children:
|
||||
newtree = Tree(p.nout)
|
||||
mtd.get_tree(p, newtree, sd, c)
|
||||
newtree.write_tree(p, 'subhalo')
|
||||
|
||||
if p.do_all:
|
||||
for i, halo in enumerate(cd.clumpids[is_halo]):
|
||||
newtree = Tree(p.nout)
|
||||
mtd.get_tree(p, newtree, sd, halo)
|
||||
newtree.write_tree(p, 'halo')
|
||||
|
||||
for c in childlist[i]:
|
||||
newtree = Tree(p.nout)
|
||||
mtd.get_tree(p, newtree, sd, c)
|
||||
newtree.write_tree(p, 'subhalo')
|
||||
|
||||
print('Finished.')
|
||||
@ -337,78 +337,6 @@ def make_phew_halo_catalogue(nsim, verbose):
|
||||
f.close()
|
||||
|
||||
|
||||
def make_merger_tree_file(nsim, verbose):
|
||||
"""
|
||||
Process the `.dat` merger tree files and dump them into a HDF5 file.
|
||||
"""
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
reader = csiborgtools.read.CSiBORGReader(paths)
|
||||
snaps = paths.get_snapshots(nsim, "csiborg")
|
||||
|
||||
fname = paths.processed_merger_tree(nsim)
|
||||
with h5py.File(fname, "w") as f:
|
||||
f.close()
|
||||
|
||||
for nsnap in tqdm(snaps, desc="Loading merger files",
|
||||
disable=not verbose):
|
||||
try:
|
||||
data = reader.read_merger_tree(nsnap, nsim)
|
||||
except FileExistsError:
|
||||
continue
|
||||
|
||||
with h5py.File(fname, "r+") as f:
|
||||
grp = f.create_group(str(nsnap))
|
||||
|
||||
grp.create_dataset("clump",
|
||||
data=data[:, 0].astype(numpy.int32))
|
||||
grp.create_dataset("progenitor",
|
||||
data=data[:, 1].astype(numpy.int32))
|
||||
grp.create_dataset("progenitor_outputnr",
|
||||
data=data[:, 2].astype(numpy.int32))
|
||||
grp.create_dataset("desc_mass",
|
||||
data=data[:, 3].astype(numpy.float32))
|
||||
grp.create_dataset("desc_npart",
|
||||
data=data[:, 4].astype(numpy.int32))
|
||||
grp.create_dataset("desc_pos",
|
||||
data=data[:, 5:8].astype(numpy.float32))
|
||||
grp.create_dataset("desc_vel",
|
||||
data=data[:, 8:11].astype(numpy.float32))
|
||||
f.close()
|
||||
|
||||
|
||||
def append_merger_tree_mass_to_phew_catalogue(nsim, verbose):
|
||||
"""
|
||||
Append mass of haloes from mergertree files to the PHEW catalogue. The
|
||||
difference between this and the PHEW value is that the latter is written
|
||||
before unbinding is performed.
|
||||
|
||||
Note that currently only does this for the highest snapshot.
|
||||
"""
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
snapshots = paths.get_snapshots(nsim, "csiborg")
|
||||
merger_reader = csiborgtools.read.MergerReader(nsim, paths)
|
||||
|
||||
for nsnap in tqdm(snapshots, disable=not verbose, desc="Snapshot"):
|
||||
# TODO do this for all later
|
||||
if nsnap < 930:
|
||||
continue
|
||||
try:
|
||||
phewcat = csiborgtools.read.CSiBORGPHEWCatalogue(nsnap, nsim,
|
||||
paths)
|
||||
except ValueError:
|
||||
phewcat.close()
|
||||
continue
|
||||
|
||||
mergertree_mass = merger_reader.match_mass_to_phewcat(phewcat)
|
||||
phewcat.close()
|
||||
|
||||
fname = paths.processed_phew(nsim)
|
||||
with h5py.File(fname, "r+") as f:
|
||||
grp = f[str(nsnap)]
|
||||
grp.create_dataset("mergertree_mass_new", data=mergertree_mass)
|
||||
f.close()
|
||||
|
||||
|
||||
def main(nsim, args):
|
||||
if args.make_final:
|
||||
process_snapshot(nsim, args.simname, args.halofinder, True)
|
||||
@ -420,12 +348,6 @@ def main(nsim, args):
|
||||
if args.make_phew:
|
||||
make_phew_halo_catalogue(nsim, True)
|
||||
|
||||
if args.make_merger:
|
||||
make_merger_tree_file(nsim, True)
|
||||
|
||||
if args.append_merger_mass:
|
||||
append_merger_tree_mass_to_phew_catalogue(nsim, True)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
parser = ArgumentParser()
|
||||
@ -441,11 +363,6 @@ if __name__ == "__main__":
|
||||
help="Process the initial snapshot.")
|
||||
parser.add_argument("--make_phew", action="store_true", default=False,
|
||||
help="Process the PHEW halo catalogue.")
|
||||
parser.add_argument("--make_merger", action="store_true", default=False,
|
||||
help="Process the merger tree files.")
|
||||
parser.add_argument("--append_merger_mass", action="store_true",
|
||||
default=False,
|
||||
help="Append the merger tree mass to the PHEW cat.")
|
||||
|
||||
args = parser.parse_args()
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user