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Particle match & file system & phase space (#11)

Browse Source 
* Create file system

* add doc

* add n_sim n_snap directly to paths

* Move things to a single particle reader for consistency

* add docstring

* add srdcir, dumpdir and mmain_path

* make boxunits work with paths

* switch to using paths

* add tempdumpdir

* rm dependence on old functions

* rm comment

* rm unused import

* go back to all imports

* fix import bug

* rm dependence on old functions

* modernize code!

* fix typo

* fix typo

* update fits to new data structureing

* change docs

* add julia repo

* add setup

* add install commands

* ignore install files

* add array flattening

* update dependene

* add positions reader

* update manifest and projects

* add func

* update gitignore

* pos matching progress

* move file

* rm comment

* add velocities getter

* fix bug

* fix name bug

* fix path bug

* fix args func

* add redshift calculation to catalogues

* add shortcut to set n_sim and n_snap

* if cond bug

* add the cosine similarity

* add verbosit iterator

* add docs

* update README

* update README

* update README
This commit is contained in:
Richard Stiskalek 2022-11-25 10:44:08 +00:00 committed by GitHub
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commit 161c27d995
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5
.gitignore vendored
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@ -11,3 +11,8 @@ csiborgtools/fits/_filenames.py
csiborgtools/fits/analyse_voids_25.py csiborgtools/fits/analyse_voids_25.py
scripts/*.sh scripts/*.sh
scripts/*.out scripts/*.out
build/*
.eggs/*
csiborgtools.egg-info/*
scripts/playground_*
scripts/playground.ipynb

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JuliaCSiBORGTools/Manifest.toml Normal file
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@ -0,0 +1,344 @@
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12
JuliaCSiBORGTools/Project.toml Normal file
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@ -0,0 +1,12 @@
name = "JuliaCSiBORGTools"
uuid = "6ceada58-95f6-416f-bef9-d16b3bb7d5db"
authors = ["rstiskalek <richard.stiskalek@protonmail.com>"]
version = "0.1.0"
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22
JuliaCSiBORGTools/src/JuliaCSiBORGTools.jl Normal file
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@ -0,0 +1,22 @@
# 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.
module JuliaCSiBORGTools
include("./particles_match.jl")
export halo_parts
end # module JuliaCSiBORGTools

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JuliaCSiBORGTools/src/particles_match.jl Normal file
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@ -0,0 +1,29 @@
# 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.
"""
halo_parts(clumpid::Int, partids::Vector{<:Int}, clumpids::Vector{<:Int})
Return particle IDs belonging to a given clump.
# Arguments
- `clumpid::Integer`: the ID of the clump.
- `partids::Vector{<:Integer}`: vector of shape `(n_particles,)` with the particle IDs.
- `clumpids::Vector{<:Integer}`: vector of shape `(n_particles, )` with the particles' clump IDs.
"""
function halo_parts(clumpid::Integer, partids::Vector{<:Integer}, clumpids::Vector{<:Integer})
return partids[clumpids .== clumpid]
end

4
README.md
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@ -2,7 +2,7 @@
## :scroll: Short-term TODO ## :scroll: Short-term TODO
- [ ] Find the distribution of particles in the first snapshot - [ ] Find the distribution of particles in the first snapshot
- [ ] Implement Max's halo matching - [ ] Make sure I am not taking halos outside of the well-resolved region.
- [ ] Implement a custom model for matchin galaxies to halos. - [ ] Implement a custom model for matchin galaxies to halos.
@ -13,4 +13,4 @@
## :bulb: Open questions ## :bulb: Open questions
- Completeness of clusters. Optical clusters catalogues are a bit of a mess.. - What scaling of the search region? No reason for it to be a multiple of $R_{200c}$.

70
csiborgtools/fits/halo.py
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@ -22,7 +22,7 @@ from os import remove
from warnings import warn from warnings import warn
from os.path import join from os.path import join
from tqdm import trange from tqdm import trange
from ..read import nparts_to_start_ind from ..read import ParticleReader
def clump_with_particles(particle_clumps, clumps): def clump_with_particles(particle_clumps, clumps):
@ -44,14 +44,14 @@ def clump_with_particles(particle_clumps, clumps):
return numpy.isin(clumps["index"], particle_clumps) return numpy.isin(clumps["index"], particle_clumps)
def distribute_halos(Nsplits, clumps): def distribute_halos(n_splits, clumps):
""" """
Evenly distribute clump indices to smaller splits. Clumps should only be Evenly distribute clump indices to smaller splits. Clumps should only be
clumps that contain particles. clumps that contain particles.
Parameters Parameters
---------- ----------
Nsplits : int n_splits : int
Number of splits. Number of splits.
clumps : structured array clumps : structured array
The clumps array. The clumps array.
@ -59,22 +59,23 @@ def distribute_halos(Nsplits, clumps):
Returns Returns
------- -------
splits : 2-dimensional array splits : 2-dimensional array
Array of starting and ending indices of each CPU of shape `(Njobs, 2)`. Array of starting and ending indices of each CPU of shape
`(njobs, 2)`.
""" """
# Make sure these are unique IDs # Make sure these are unique IDs
indxs = clumps["index"] indxs = clumps["index"]
if indxs.size > numpy.unique((indxs)).size: if indxs.size > numpy.unique((indxs)).size:
raise ValueError("`clump_indxs` constains duplicate indices.") raise ValueError("`clump_indxs` constains duplicate indices.")
Ntotal = indxs.size Ntotal = indxs.size
Njobs_per_cpu = numpy.ones(Nsplits, dtype=int) * Ntotal // Nsplits njobs_per_cpu = numpy.ones(n_splits, dtype=int) * Ntotal // n_splits
# Split the remainder Ntotal % Njobs among the CPU # Split the remainder Ntotal % njobs among the CPU
Njobs_per_cpu[:Ntotal % Nsplits] += 1 njobs_per_cpu[:Ntotal % n_splits] += 1
start = nparts_to_start_ind(Njobs_per_cpu) start = ParticleReader.nparts_to_start_ind(njobs_per_cpu)
return numpy.vstack([start, start + Njobs_per_cpu]).T return numpy.vstack([start, start + njobs_per_cpu]).T
def dump_split_particles(particles, particle_clumps, clumps, Nsplits, def dump_split_particles(particles, particle_clumps, clumps, n_splits,
dumpfolder, Nsim, Nsnap, verbose=True): paths, verbose=True):
""" """
Save the data needed for each split so that a process does not have to load Save the data needed for each split so that a process does not have to load
everything. everything.
@ -87,14 +88,10 @@ def dump_split_particles(particles, particle_clumps, clumps, Nsplits,
Array of particles' clump IDs. Array of particles' clump IDs.
clumps : structured array clumps : structured array
The clumps array. The clumps array.
Nsplits : int n_splits : int
Number of times to split the clumps. Number of times to split the clumps.
dumpfolder : str paths : py:class`csiborgtools.read.CSiBORGPaths`
Path to the folder where to dump the splits. CSiBORG paths-handling object with set `n_sim` and `n_snap`.
Nsim : int
CSiBORG simulation index.
Nsnap : int
Snapshot index.
verbose : bool, optional verbose : bool, optional
Verbosity flag. By default `True`. Verbosity flag. By default `True`.
@ -112,10 +109,10 @@ def dump_split_particles(particles, particle_clumps, clumps, Nsplits,
.format(with_particles.sum() / with_particles.size * 100)) .format(with_particles.sum() / with_particles.size * 100))
# The starting clump index of each split # The starting clump index of each split
splits = distribute_halos(Nsplits, clumps) splits = distribute_halos(n_splits, clumps)
fname = join(dumpfolder, "out_{}_snap_{}_{}.npz") fname = join(paths.temp_dumpdir, "out_{}_snap_{}_{}.npz")
iters = trange(Nsplits) if verbose else range(Nsplits) iters = trange(n_splits) if verbose else range(n_splits)
tot = 0 tot = 0
for n in iters: for n in iters:
# Lower and upper array index of the clumps array # Lower and upper array index of the clumps array
@ -133,7 +130,7 @@ def dump_split_particles(particles, particle_clumps, clumps, Nsplits,
"with no particles.".format(n, indxs.size, npart_unique)) "with no particles.".format(n, indxs.size, npart_unique))
# Dump it! # Dump it!
tot += mask.sum() tot += mask.sum()
fout = fname.format(Nsim, Nsnap, n) fout = fname.format(paths.n_sim, paths.n_snap, n)
numpy.savez(fout, particles[mask], particle_clumps[mask], clumps[i:j]) numpy.savez(fout, particles[mask], particle_clumps[mask], clumps[i:j])
# There are particles whose clump ID is > 1 and have no counterpart in the # There are particles whose clump ID is > 1 and have no counterpart in the
@ -144,15 +141,15 @@ def dump_split_particles(particles, particle_clumps, clumps, Nsplits,
"size `{}`.".format(tot, particle_clumps.size)) "size `{}`.".format(tot, particle_clumps.size))
def split_jobs(Njobs, Ncpu): def split_jobs(njobs, ncpu):
""" """
Split `Njobs` amongst `Ncpu`. Split `njobs` amongst `ncpu`.
Parameters Parameters
---------- ----------
Njobs : int njobs : int
Number of jobs. Number of jobs.
Ncpu : int ncpu : int
Number of CPUs. Number of CPUs.
Returns Returns
@ -160,29 +157,25 @@ def split_jobs(Njobs, Ncpu):
jobs : list of lists of integers jobs : list of lists of integers
Outer list of each CPU and inner lists for CPU's jobs. Outer list of each CPU and inner lists for CPU's jobs.
""" """
njobs_per_cpu, njobs_remainder = divmod(Njobs, Ncpu) njobs_per_cpu, njobs_remainder = divmod(njobs, ncpu)
jobs = numpy.arange(njobs_per_cpu * Ncpu).reshape((njobs_per_cpu, Ncpu)).T jobs = numpy.arange(njobs_per_cpu * ncpu).reshape((njobs_per_cpu, ncpu)).T
jobs = jobs.tolist() jobs = jobs.tolist()
for i in range(njobs_remainder): for i in range(njobs_remainder):
jobs[i].append(njobs_per_cpu * Ncpu + i) jobs[i].append(njobs_per_cpu * ncpu + i)
return jobs return jobs
def load_split_particles(Nsplit, dumpfolder, Nsim, Nsnap, remove_split=False): def load_split_particles(n_split, paths, remove_split=False):
""" """
Load particles of a split saved by `dump_split_particles`. Load particles of a split saved by `dump_split_particles`.
Parameters Parameters
-------- --------
Nsplit : int n_split : int
Split index. Split index.
dumpfolder : str paths : py:class`csiborgtools.read.CSiBORGPaths`
Path to the folder where the splits were dumped. CSiBORG paths-handling object with set `n_sim` and `n_snap`.
Nsim : int
CSiBORG simulation index.
Nsnap : int
Snapshot index.
remove_split : bool, optional remove_split : bool, optional
Whether to remove the split file. By default `False`. Whether to remove the split file. By default `False`.
@ -196,7 +189,8 @@ def load_split_particles(Nsplit, dumpfolder, Nsim, Nsnap, remove_split=False):
Clumps belonging to this split. Clumps belonging to this split.
""" """
fname = join( fname = join(
dumpfolder, "out_{}_snap_{}_{}.npz".format(Nsim, Nsnap, Nsplit)) paths.temp_dumpdir, "out_{}_snap_{}_{}.npz".format(
paths.n_sim, paths.n_snap, n_split))
file = numpy.load(fname) file = numpy.load(fname)
particles, clump_indxs, clumps = (file[f] for f in file.files) particles, clump_indxs, clumps = (file[f] for f in file.files)
if remove_split: if remove_split:

40
csiborgtools/match/match.py
View File

@ -122,7 +122,38 @@ class RealisationsMatcher:
""" """
return [i for i in range(self.cats.N) if i != n_sim] return [i for i in range(self.cats.N) if i != n_sim]
def cross_knn_position_single(self, n_sim, nmult=5, dlogmass=2): def cosine_similarity(self, x, y):
r"""
Calculate the cosine similarity between two Cartesian vectors. Defined
as :math:`\Sum_{i} x_i y_{i} / (|x| |y|)`.
Parameters
----------
x : 1-dimensional array
The first vector.
y : 1- or 2-dimensional array
The second vector. Can be 2-dimensional of shape `(n_samples, 3)`,
in which case the calculation is broadcasted.
Returns
-------
out : float or 1-dimensional array
The cosine similarity. If y is 1-dimensinal returns only a float.
"""
# Quick check of dimensions
if x.ndim != 1:
raise ValueError("`x` must be a 1-dimensional array.")
y = y.reshape(-1, 3) if y.ndim == 1 else y
out = numpy.sum(x * y, axis=1)
out /= numpy.linalg.norm(x) * numpy.linalg.norm(y, axis=1)
if out.size == 1:
return out[0]
return out
def cross_knn_position_single(self, n_sim, nmult=5, dlogmass=2,
verbose=True):
r""" r"""
Find all neighbours within :math:`n_{\rm mult} R_{200c}` of halos in Find all neighbours within :math:`n_{\rm mult} R_{200c}` of halos in
the `nsim`th simulation. Also enforces that the neighbours' the `nsim`th simulation. Also enforces that the neighbours'
@ -153,8 +184,13 @@ class RealisationsMatcher:
pos = self.cats[n_sim].positions pos = self.cats[n_sim].positions
matches = [None] * (self.cats.N - 1) matches = [None] * (self.cats.N - 1)
# Verbose iterator
if verbose:
iters = enumerate(tqdm(self.search_sim_indices(n_sim)))
else:
iters = enumerate(self.search_sim_indices(n_sim))
# Search for neighbours in the other simulations # Search for neighbours in the other simulations
for count, i in enumerate(self.search_sim_indices(n_sim)): for count, i in iters:
dist, indxs = self.cats[i].radius_neigbours(pos, r200 * nmult) dist, indxs = self.cats[i].radius_neigbours(pos, r200 * nmult)
# Get rid of neighbors whose mass is too off # Get rid of neighbors whose mass is too off
for j, indx in enumerate(indxs): for j, indx in enumerate(indxs):

6
csiborgtools/read/__init__.py
View File

@ -13,11 +13,7 @@
# with this program; if not, write to the Free Software Foundation, Inc., # with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
from .readsim import (get_csiborg_ids, get_sim_path, get_snapshots, # noqa from .readsim import (CSiBORGPaths, ParticleReader, read_mmain, get_positions) # noqa
get_snapshot_path, get_maximum_snapshot, read_info, nparts_to_start_ind, # noqa
open_particle, open_unbinding, read_particle, # noqa
drop_zero_indx, # noqa
read_clumpid, read_clumps, read_mmain) # noqa
from .make_cat import (HaloCatalogue, CombinedHaloCatalogue) # noqa from .make_cat import (HaloCatalogue, CombinedHaloCatalogue) # noqa
from .readobs import (PlanckClusters, MCXCClusters, TwoMPPGalaxies, TwoMPPGroups) # noqa from .readobs import (PlanckClusters, MCXCClusters, TwoMPPGalaxies, TwoMPPGroups) # noqa
from .outsim import (dump_split, combine_splits) # noqa from .outsim import (dump_split, combine_splits) # noqa

103
csiborgtools/read/make_cat.py
View File

@ -19,9 +19,9 @@ Functions to read in the particle and clump files.
import numpy import numpy
from os.path import join from os.path import join
from tqdm import trange from tqdm import trange
from copy import deepcopy
from sklearn.neighbors import NearestNeighbors from sklearn.neighbors import NearestNeighbors
from .readsim import (get_sim_path, read_mmain, get_csiborg_ids, from .readsim import read_mmain
get_maximum_snapshot)
from ..utils import (flip_cols, add_columns) from ..utils import (flip_cols, add_columns)
from ..units import (BoxUnits, cartesian_to_radec) from ..units import (BoxUnits, cartesian_to_radec)
@ -32,35 +32,23 @@ class HaloCatalogue:
Parameters Parameters
---------- ----------
n_sim: int paths : py:class:`csiborgtools.read.CSiBORGPaths`
Initial condition index. CSiBORG paths-handling object with set `n_sim` and `n_snap`.
n_snap: int
Snapshot index.
minimum_m500 : float, optional minimum_m500 : float, optional
The minimum :math:`M_{rm 500c} / M_\odot` mass. By default no The minimum :math:`M_{rm 500c} / M_\odot` mass. By default no
threshold. threshold.
dumpdir : str, optional
Path to where files from `run_fit_halos` are stored. By default
`/mnt/extraspace/rstiskalek/csiborg/`.
mmain_path : str, optional
Path to where mmain files are stored. By default
`/mnt/zfsusers/hdesmond/Mmain`.
""" """
_box = None _box = None
_n_sim = None _paths = None
_n_snap = None
_data = None _data = None
_knn = None _knn = None
_positions = None _positions = None
def __init__(self, n_sim, n_snap, minimum_m500=None, def __init__(self, paths, minimum_m500=None):
dumpdir="/mnt/extraspace/rstiskalek/csiborg/", self._box = BoxUnits(paths)
mmain_path="/mnt/zfsusers/hdesmond/Mmain"):
self._box = BoxUnits(n_snap, get_sim_path(n_sim))
minimum_m500 = 0 if minimum_m500 is None else minimum_m500 minimum_m500 = 0 if minimum_m500 is None else minimum_m500
self._set_data(n_sim, n_snap, dumpdir, mmain_path, minimum_m500) self._paths = paths
self._nsim = n_sim self._set_data(minimum_m500)
self._nsnap = n_snap
# Initialise the KNN # Initialise the KNN
knn = NearestNeighbors() knn = NearestNeighbors()
knn.fit(self.positions) knn.fit(self.positions)
@ -74,7 +62,6 @@ class HaloCatalogue:
Returns Returns
------- -------
cat : structured array cat : structured array
Catalogue.
""" """
if self._data is None: if self._data is None:
raise ValueError("`data` is not set!") raise ValueError("`data` is not set!")
@ -88,7 +75,6 @@ class HaloCatalogue:
Returns Returns
------- -------
box : :py:class:`csiborgtools.units.BoxUnits` box : :py:class:`csiborgtools.units.BoxUnits`
The box object.
""" """
return self._box return self._box
@ -100,10 +86,20 @@ class HaloCatalogue:
Returns Returns
------- -------
cosmo : `astropy` cosmology object cosmo : `astropy` cosmology object
Box cosmology.
""" """
return self.box.cosmo return self.box.cosmo
@property
def paths(self):
"""
The paths-handling object.
Returns
-------
paths : :py:class:`csiborgtools.read.CSiBORGPaths`
"""
return self._paths
@property @property
def n_snap(self): def n_snap(self):
""" """
@ -112,9 +108,8 @@ class HaloCatalogue:
Returns Returns
------- -------
n_snap : int n_snap : int
Snapshot ID.
""" """
return self._n_snap return self.paths.n_snap
@property @property
def n_sim(self): def n_sim(self):
@ -124,27 +119,37 @@ class HaloCatalogue:
Returns Returns
------- -------
n_sim : int n_sim : int
The IC ID.
""" """
return self._n_sim return self.paths.n_sim
def _set_data(self, n_sim, n_snap, dumpdir, mmain_path, minimum_m500): def _set_data(self, minimum_m500):
""" """
Loads the data, merges with mmain, does various coordinate transforms. Loads the data, merges with mmain, does various coordinate transforms.
""" """
# Load the processed data # Load the processed data
fname = "ramses_out_{}_{}.npy".format( fname = "ramses_out_{}_{}.npy".format(
str(n_sim).zfill(5), str(n_snap).zfill(5)) str(self.n_sim).zfill(5), str(self.n_snap).zfill(5))
data = numpy.load(join(dumpdir, fname)) data = numpy.load(join(self.paths.dumpdir, fname))
# Load the mmain file and add it to the data # Load the mmain file and add it to the data
mmain = read_mmain(n_sim, mmain_path) mmain = read_mmain(self.n_sim, self.paths.mmain_path)
data = self.merge_mmain_to_clumps(data, mmain) data = self.merge_mmain_to_clumps(data, mmain)
flip_cols(data, "peak_x", "peak_z") flip_cols(data, "peak_x", "peak_z")
# Cut on number of particles and finite m200 # Cut on number of particles and finite m200
data = data[(data["npart"] > 100) & numpy.isfinite(data["m200"])] data = data[(data["npart"] > 100) & numpy.isfinite(data["m200"])]
# Calculate redshift
pos = [data["peak_{}".format(p)] - 0.5 for p in ("x", "y", "z")]
vel = [data["v{}".format(p)] for p in ("x", "y", "z")]
zpec = self.box.box2pecredshift(*vel, *pos)
zobs = self.box.box2obsredshift(*vel, *pos)
zcosmo = self.box.box2cosmoredshift(
sum(pos[i]**2 for i in range(3))**0.5)
data = add_columns(data, [zpec, zobs, zcosmo],
["zpec", "zobs", "zcosmo"])
# Unit conversion # Unit conversion
convert_cols = ["m200", "m500", "totpartmass", "mass_mmain", convert_cols = ["m200", "m500", "totpartmass", "mass_mmain",
"r200", "r500", "Rs", "rho0", "r200", "r500", "Rs", "rho0",
@ -203,6 +208,18 @@ class HaloCatalogue:
""" """
return self._positions return self._positions
@property
def velocities(self):
"""
Cartesian velocities of halos.
Returns
-------
vel : 2-dimensional array
Array of shape `(n_halos, 3)`.
"""
return numpy.vstack([self["v{}".format(p)] for p in ("x", "y", "z")]).T
def radius_neigbours(self, X, radius): def radius_neigbours(self, X, radius):
""" """
Return sorted nearest neigbours within `radius` or `X`. Return sorted nearest neigbours within `radius` or `X`.
@ -245,15 +262,12 @@ class CombinedHaloCatalogue:
Parameters Parameters
---------- ----------
paths : py:class`csiborgtools.read.CSiBORGPaths`
CSiBORG paths-handling object. Doest not have to have set set `n_sim`
and `n_snap`.
minimum_m500 : float, optional minimum_m500 : float, optional
The minimum :math:`M_{rm 500c} / M_\odot` mass. By default no The minimum :math:`M_{rm 500c} / M_\odot` mass. By default no
threshold. threshold.
dumpdir : str, optional
Path to where files from `run_fit_halos` are stored. By default
`/mnt/extraspace/rstiskalek/csiborg/`.
mmain_path : str, optional
Path to where mmain files are stored. By default
`/mnt/zfsusers/hdesmond/Mmain`.
verbose : bool, optional verbose : bool, optional
Verbosity flag for reading the catalogues. Verbosity flag for reading the catalogues.
""" """
@ -261,19 +275,18 @@ class CombinedHaloCatalogue:
_n_snaps = None _n_snaps = None
_cats = None _cats = None
def __init__(self, minimum_m500=None, def __init__(self, paths, minimum_m500=None, verbose=True):
dumpdir="/mnt/extraspace/rstiskalek/csiborg/",
mmain_path="/mnt/zfsusers/hdesmond/Mmain", verbose=True):
# Read simulations and their maximum snapshots # Read simulations and their maximum snapshots
# NOTE remove this later and take all cats # NOTE remove this later and take all cats
self._n_sims = get_csiborg_ids("/mnt/extraspace/hdesmond")[:10] self._n_sims = paths.ic_ids[:10]
n_snaps = [get_maximum_snapshot(get_sim_path(i)) for i in self._n_sims] n_snaps = [paths.get_maximum_snapshot(i) for i in self._n_sims]
self._n_snaps = numpy.asanyarray(n_snaps) self._n_snaps = numpy.asanyarray(n_snaps)
cats = [None] * self.N cats = [None] * self.N
for i in trange(self.N) if verbose else range(self.N): for i in trange(self.N) if verbose else range(self.N):
cats[i] = HaloCatalogue(self._n_sims[i], self._n_snaps[i], paths = deepcopy(paths)
minimum_m500, dumpdir, mmain_path) paths.set_info(self.n_sims[i], self.n_snaps[i])
cats[i] = HaloCatalogue(paths, minimum_m500)
self._cats = cats self._cats = cats
@property @property

43
csiborgtools/read/outsim.py
View File

@ -21,13 +21,12 @@ import numpy
from os.path import join from os.path import join
from os import remove from os import remove
from tqdm import trange from tqdm import trange
from .readsim import (get_sim_path, read_clumps)
I64 = numpy.int64 I64 = numpy.int64
F64 = numpy.float64 F64 = numpy.float64
def dump_split(arr, Nsplit, Nsim, Nsnap, outdir): def dump_split(arr, n_split, paths):
""" """
Dump an array from a split. Dump an array from a split.
@ -35,11 +34,13 @@ def dump_split(arr, Nsplit, Nsim, Nsnap, outdir):
---------- ----------
arr : n-dimensional or structured array arr : n-dimensional or structured array
Array to be saved. Array to be saved.
Nsplit : int n_split: int
The split index. The split index.
Nsim : int paths : py:class`csiborgtools.read.CSiBORGPaths`
CSiBORG paths-handling object with set `n_sim` and `n_snap`.
n_sim : int
The CSiBORG realisation index. The CSiBORG realisation index.
Nsnap : int n_snap : int
The index of a redshift snapshot. The index of a redshift snapshot.
outdir : string outdir : string
Directory where to save the temporary files. Directory where to save the temporary files.
@ -48,13 +49,14 @@ def dump_split(arr, Nsplit, Nsim, Nsnap, outdir):
------- -------
None None
""" """
Nsim = str(Nsim).zfill(5) n_sim = str(paths.n_sim).zfill(5)
Nsnap = str(Nsnap).zfill(5) n_snap = str(paths.n_snap).zfill(5)
fname = join(outdir, "ramses_out_{}_{}_{}.npy".format(Nsim, Nsnap, Nsplit)) fname = join(paths.temp_dumpdir, "ramses_out_{}_{}_{}.npy"
.format(n_sim, n_snap, n_split))
numpy.save(fname, arr) numpy.save(fname, arr)
def combine_splits(Nsplits, Nsim, Nsnap, outdir, cols_add, remove_splits=False, def combine_splits(n_splits, part_reader, cols_add, remove_splits=False,
verbose=True): verbose=True):
""" """
Combine results of many splits saved from `dump_split`. Identifies to which Combine results of many splits saved from `dump_split`. Identifies to which
@ -64,14 +66,10 @@ def combine_splits(Nsplits, Nsim, Nsnap, outdir, cols_add, remove_splits=False,
Paramaters Paramaters
---------- ----------
Nsplits : int n_splits : int
The total number of clump splits. The total number of clump splits.
Nsim : int part_reader : py:class`csiborgtools.read.ParticleReadear`
The CSiBORG realisation index. CSiBORG particle reader.
Nsnap : int
The index of a redshift snapshot.
outdir : str
Directory where to save the new array.
cols_add : list of `(str, dtype)` cols_add : list of `(str, dtype)`
Colums to add. Must be formatted as, for example, Colums to add. Must be formatted as, for example,
`[("npart", numpy.float64), ("totpartmass", numpy.float64)]`. `[("npart", numpy.float64), ("totpartmass", numpy.float64)]`.
@ -86,8 +84,10 @@ def combine_splits(Nsplits, Nsim, Nsnap, outdir, cols_add, remove_splits=False,
Clump array with appended results from the splits. Clump array with appended results from the splits.
""" """
# Load clumps to see how many there are and will add to this array # Load clumps to see how many there are and will add to this array
simpath = get_sim_path(Nsim) n_sim = part_reader.paths.n_sim
clumps = read_clumps(Nsnap, simpath, cols=None) n_snap = part_reader.paths.n_snap
clumps = part_reader.read_clumps(cols=None)
# Get the old + new dtypes and create an empty array # Get the old + new dtypes and create an empty array
descr = clumps.dtype.descr + cols_add descr = clumps.dtype.descr + cols_add
out = numpy.full(clumps.size, numpy.nan, dtype=descr) out = numpy.full(clumps.size, numpy.nan, dtype=descr)
@ -96,12 +96,13 @@ def combine_splits(Nsplits, Nsim, Nsnap, outdir, cols_add, remove_splits=False,
out[par] = clumps[par] out[par] = clumps[par]
# Filename of splits data # Filename of splits data
froot = "ramses_out_{}_{}".format(str(Nsim).zfill(5), str(Nsnap).zfill(5)) froot = "ramses_out_{}_{}".format(
fname = join(outdir, froot + "_{}.npy") str(n_sim).zfill(5), str(n_snap).zfill(5))
fname = join(part_reader.paths.temp_dumpdir, froot + "_{}.npy")
# Iterate over splits and add to the output array # Iterate over splits and add to the output array
cols_add_names = [col[0] for col in cols_add] cols_add_names = [col[0] for col in cols_add]
iters = trange(Nsplits) if verbose else range(Nsplits) iters = trange(n_splits) if verbose else range(n_splits)
for n in iters: for n in iters:
fnamesplit = fname.format(n) fnamesplit = fname.format(n)
arr = numpy.load(fnamesplit) arr = numpy.load(fnamesplit)

1080
csiborgtools/read/readsim.py
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File diff suppressed because it is too large Load Diff

51
csiborgtools/units/box_units.py
View File

@ -20,7 +20,7 @@ import numpy
from scipy.interpolate import interp1d from scipy.interpolate import interp1d
from astropy.cosmology import LambdaCDM from astropy.cosmology import LambdaCDM
from astropy import (constants, units) from astropy import (constants, units)
from ..read import read_info from ..read import ParticleReader
# Map of unit conversions # Map of unit conversions
@ -38,18 +38,17 @@ class BoxUnits:
Paramaters Paramaters
---------- ----------
Nsnap : int paths : py:class`csiborgtools.read.CSiBORGPaths`
Snapshot index. CSiBORG paths-handling object with set `n_sim` and `n_snap`.
simpath : str
Path to the simulation where its snapshot index folders are stored.
""" """
_cosmo = None _cosmo = None
def __init__(self, Nsnap, simpath): def __init__(self, paths):
""" """
Read in the snapshot info file and set the units from it. Read in the snapshot info file and set the units from it.
""" """
info = read_info(Nsnap, simpath) partreader = ParticleReader(paths)
info = partreader.read_info()
pars = ["boxlen", "time", "aexp", "H0", pars = ["boxlen", "time", "aexp", "H0",
"omega_m", "omega_l", "omega_k", "omega_b", "omega_m", "omega_l", "omega_k", "omega_b",
"unit_l", "unit_d", "unit_t"] "unit_l", "unit_d", "unit_t"]
@ -220,6 +219,8 @@ class BoxUnits:
r""" r"""
Convert the box comoving distance to cosmological redshift. Convert the box comoving distance to cosmological redshift.
NOTE: this likely is already the observed redshift.
Parameters Parameters
---------- ----------
dist : float dist : float
@ -236,8 +237,24 @@ class BoxUnits:
def box2pecredshift(self, vx, vy, vz, px, py, pz, p0x=0, p0y=0, p0z=0): def box2pecredshift(self, vx, vy, vz, px, py, pz, p0x=0, p0y=0, p0z=0):
""" """
TODO: docs Convert the box phase-space information to a peculiar redshift.
NOTE: there is some confusion about this.
Parameters
----------
vx, vy, vz : 1-dimensional arrays
The Cartesian velocity components.
px, py, pz : 1-dimensional arrays
The Cartesian position vectors components.
p0x, p0y, p0z : floats
The centre of the box. By default 0, in which it is assumed that
the coordinates are already centred.
Returns
-------
pec_redshift : 1-dimensional array
The peculiar redshift.
""" """
# Peculiar velocity along the radial distance # Peculiar velocity along the radial distance
r = numpy.vstack([px - p0x, py - p0y, pz - p0z]).T r = numpy.vstack([px - p0x, py - p0y, pz - p0z]).T
@ -251,8 +268,24 @@ class BoxUnits:
def box2obsredshift(self, vx, vy, vz, px, py, pz, p0x=0, p0y=0, p0z=0): def box2obsredshift(self, vx, vy, vz, px, py, pz, p0x=0, p0y=0, p0z=0):
""" """
TODO: docs Convert the box phase-space information to an 'observed' redshift.
NOTE: there is some confusion about this.
Parameters
----------
vx, vy, vz : 1-dimensional arrays
The Cartesian velocity components.
px, py, pz : 1-dimensional arrays
The Cartesian position vectors components.
p0x, p0y, p0z : floats
The centre of the box. By default 0, in which it is assumed that
the coordinates are already centred.
Returns
-------
obs_redshift : 1-dimensional array
The observed redshift.
""" """
r = numpy.vstack([px - p0x, py - p0y, pz - p0z]).T r = numpy.vstack([px - p0x, py - p0y, pz - p0z]).T
zcosmo = self.box2cosmoredshift(numpy.sum(r**2, axis=1)**0.5) zcosmo = self.box2cosmoredshift(numpy.sum(r**2, axis=1)**0.5)

2
csiborgtools/utils/__init__.py
View File

@ -15,4 +15,4 @@
from .recarray_manip import (cols_to_structured, add_columns, rm_columns, # noqa from .recarray_manip import (cols_to_structured, add_columns, rm_columns, # noqa
list_to_ndarray, array_to_structured, # noqa list_to_ndarray, array_to_structured, # noqa
flip_cols) # noqa flip_cols, extract_from_structured) # noqa

32
csiborgtools/utils/recarray_manip.py
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@ -209,3 +209,35 @@ def flip_cols(arr, col1, col2):
dum = numpy.copy(arr[col1]) dum = numpy.copy(arr[col1])
arr[col1] = arr[col2] arr[col1] = arr[col2]
arr[col2] = dum arr[col2] = dum
def extract_from_structured(arr, cols):
"""
Extract columns `cols` from a structured array. The array dtype is set
to be that of the first column in `cols`.
Parameters
----------
arr : structured array
Array from which to extract columns.
cols : list of str or str
Column to extract.
Returns
-------
out : 2- or 1-dimensional array
Array with shape `(n_particles, len(cols))`. If `len(cols)` is 1
flattens the array.
"""
cols = [cols] if isinstance(cols, str) else cols
for col in cols:
if col not in arr.dtype.names:
raise ValueError("Invalid column `{}`!".format(col))
# Preallocate an array and populate it
out = numpy.zeros((arr.size, len(cols)), dtype=arr[cols[0]].dtype)
for i, col in enumerate(cols):
out[:, i] = arr[col]
# Optionally flatten
if len(cols) == 1:
return out.reshape(-1,)
return out

2
pymake.sh Normal file
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@ -0,0 +1,2 @@
cmd="/mnt/zfsusers/rstiskalek/csiborgtools/venv_galomatch/bin/python -m pip install ."
$cmd

2
pyremove.sh Normal file
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@ -0,0 +1,2 @@
cmd="/mnt/zfsusers/rstiskalek/csiborgtools/venv_galomatch/bin/python -m pip uninstall csiborgtools"
$cmd

3633
scripts/playground.ipynb
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File diff suppressed because one or more lines are too long

49
scripts/run_find_initpos.jl Normal file
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@ -0,0 +1,49 @@
# 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.
using Pkg: activate, build
activate("../JuliaCSiBORGTools/")
using JuliaCSiBORGTools
using NPZ: npzread
using PyCall: pyimport
csiborgtools = pyimport("csiborgtools")
verbose = true
paths = csiborgtools.read.CSiBORGPaths()
nsims = paths.ic_ids[:1]
for nsim in nsims
nsnap_min = convert(Int64, paths.get_minimum_snapshot(nsim))
nsnap_max = convert(Int64, paths.get_maximum_snapshot(nsim))
# Get the maximum snapshot properties
verbose ? println("Loading snapshot $nsnap_max from simulation $nsim") : nothing
pids, ppos, pmass, clumpids = csiborgtools.read.get_positions(nsim, nsnap_max, get_clumpid=true, verbose=false)
println("Sizes are: ")
println(size(pids))
println(size(ppos))
println(size(pmass))
# # Get the minimum snapshot properties
# verbose ? println("Loading snapshot $nsnap_min from simulation $nsim") : nothing
# pids, ppos, pmass = csiborgtools.read.get_positions(nsim, nsnap_max, get_clumpid=false, verbose=false)
JuliaCSiBORGTools.halo_parts(0, partids, clumpids)
end

33
scripts/run_fit_halos.py
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@ -46,20 +46,21 @@ cols_collect = [("npart", I64), ("totpartmass", F64), ("Rs", F64),
("rho0", F64), ("conc", F64), ("rmin", F64), ("rho0", F64), ("conc", F64), ("rmin", F64),
("rmax", F64), ("r200", F64), ("r500", F64), ("rmax", F64), ("r200", F64), ("r500", F64),
("m200", F64), ("m500", F64)] ("m200", F64), ("m500", F64)]
paths = csiborgtools.read.CSiBORGPaths()
Nsims = csiborgtools.read.get_csiborg_ids("/mnt/extraspace/hdesmond") for i, n_sim in enumerate(paths.ic_ids):
for i, Nsim in enumerate(Nsims):
if rank == 0: if rank == 0:
print("{}: calculating {}th simulation.".format(datetime.now(), i)) print("{}: calculating {}th simulation.".format(datetime.now(), i))
# Correctly set the paths!
n_snap = paths.get_maximum_snapshot(n_sim)
paths.set_info(n_sim, n_snap)
simpath = csiborgtools.read.get_sim_path(Nsim) box = csiborgtools.units.BoxUnits(paths)
Nsnap = csiborgtools.read.get_maximum_snapshot(simpath)
box = csiborgtools.units.BoxUnits(Nsnap, simpath)
jobs = csiborgtools.fits.split_jobs(utils.Nsplits, nproc)[rank] jobs = csiborgtools.fits.split_jobs(utils.Nsplits, nproc)[rank]
for Nsplit in jobs: for n_split in jobs:
parts, part_clumps, clumps = csiborgtools.fits.load_split_particles( parts, part_clumps, clumps = csiborgtools.fits.load_split_particles(
Nsplit, loaddir, Nsim, Nsnap, remove_split=False) n_split, paths, remove_split=False)
N = clumps.size N = clumps.size
cols = [("index", I64), ("npart", I64), ("totpartmass", F64), cols = [("index", I64), ("npart", I64), ("totpartmass", F64),
@ -79,9 +80,9 @@ for i, Nsim in enumerate(Nsims):
out["rmin"][n] = clump.rmin out["rmin"][n] = clump.rmin
out["rmax"][n] = clump.rmax out["rmax"][n] = clump.rmax
out["totpartmass"][n] = clump.total_particle_mass out["totpartmass"][n] = clump.total_particle_mass
out["vx"] = numpy.average(clump.vel[:, 0], weights=clump.m) out["vx"][n] = numpy.average(clump.vel[:, 0], weights=clump.m)
out["vy"] = numpy.average(clump.vel[:, 1], weights=clump.m) out["vy"][n] = numpy.average(clump.vel[:, 1], weights=clump.m)
out["vz"] = numpy.average(clump.vel[:, 2], weights=clump.m) out["vz"][n] = numpy.average(clump.vel[:, 2], weights=clump.m)
# Spherical overdensity radii and masses # Spherical overdensity radii and masses
rs, ms = clump.spherical_overdensity_mass([200, 500]) rs, ms = clump.spherical_overdensity_mass([200, 500])
@ -100,7 +101,7 @@ for i, Nsim in enumerate(Nsims):
out["rho0"][n] = nfwpost.rho0_from_Rs(Rs) out["rho0"][n] = nfwpost.rho0_from_Rs(Rs)
out["conc"][n] = out["r200"][n] / Rs out["conc"][n] = out["r200"][n] / Rs
csiborgtools.read.dump_split(out, Nsplit, Nsim, Nsnap, dumpdir) csiborgtools.read.dump_split(out, n_split, paths)
# Wait until all jobs finished before moving to another simulation # Wait until all jobs finished before moving to another simulation
comm.Barrier() comm.Barrier()
@ -108,11 +109,13 @@ for i, Nsim in enumerate(Nsims):
# Use the rank 0 to combine outputs for this CSiBORG realisation # Use the rank 0 to combine outputs for this CSiBORG realisation
if rank == 0: if rank == 0:
print("Collecting results!") print("Collecting results!")
partreader = csiborgtools.read.ParticleReader(paths)
out_collected = csiborgtools.read.combine_splits( out_collected = csiborgtools.read.combine_splits(
utils.Nsplits, Nsim, Nsnap, utils.dumpdir, cols_collect, utils.Nsplits, partreader, cols_collect, remove_splits=True,
remove_splits=True, verbose=False) verbose=False)
fname = join(utils.dumpdir, "ramses_out_{}_{}.npy" fname = join(paths.dumpdir, "ramses_out_{}_{}.npy"
.format(str(Nsim).zfill(5), str(Nsnap).zfill(5))) .format(str(paths.n_sim).zfill(5),
str(paths.n_snap).zfill(5)))
print("Saving results to `{}`.".format(fname)) print("Saving results to `{}`.".format(fname))
numpy.save(fname, out_collected) numpy.save(fname, out_collected)

28
scripts/run_split_halos.py
View File

@ -18,7 +18,6 @@ membership for faster manipulation. Currently does this for the maximum
snapshot of each simulation. Running this will require a lot of memory. snapshot of each simulation. Running this will require a lot of memory.
""" """
from os.path import join
from mpi4py import MPI from mpi4py import MPI
from datetime import datetime from datetime import datetime
try: try:
@ -34,29 +33,28 @@ comm = MPI.COMM_WORLD
rank = comm.Get_rank() rank = comm.Get_rank()
nproc = comm.Get_size() nproc = comm.Get_size()
Nsims = csiborgtools.read.get_csiborg_ids("/mnt/extraspace/hdesmond") paths = csiborgtools.read.CSiBORGPaths()
n_sims = paths.ic_ids[:1]
partcols = ["x", "y", "z", "vx", "vy", "vz", "M", "level"] partcols = ["x", "y", "z", "vx", "vy", "vz", "M", "level"]
dumpdir = join(utils.dumpdir, "temp")
jobs = csiborgtools.fits.split_jobs(len(Nsims), nproc)[rank] jobs = csiborgtools.fits.split_jobs(len(n_sims), nproc)[rank]
for icount, sim_index in enumerate(jobs): for icount, sim_index in enumerate(jobs):
print("{}: rank {} working {} / {} jobs.".format(datetime.now(), rank, print("{}: rank {} working {} / {} jobs.".format(datetime.now(), rank,
icount + 1, len(jobs))) icount + 1, len(jobs)))
Nsim = Nsims[sim_index] n_sim = n_sims[sim_index]
simpath = csiborgtools.read.get_sim_path(Nsim) n_snap = paths.get_maximum_snapshot(n_sim)
Nsnap = csiborgtools.read.get_maximum_snapshot(simpath) # Set paths and inifitalise a particle reader
paths.set_info(n_sim, n_snap)
partreader = csiborgtools.read.ParticleReader(paths)
# Load the clumps, particles' clump IDs and particles. # Load the clumps, particles' clump IDs and particles.
clumps = csiborgtools.read.read_clumps(Nsnap, simpath) clumps = partreader.read_clumps()
particle_clumps = csiborgtools.read.read_clumpid(Nsnap, simpath, particle_clumps = partreader.read_clumpid(verbose=False)
verbose=False) particles = partreader.read_particle(partcols, verbose=False)
particles = csiborgtools.read.read_particle(partcols, Nsnap, simpath,
verbose=False)
# Drop all particles whose clump index is 0 (not assigned to any halo) # Drop all particles whose clump index is 0 (not assigned to any halo)
particle_clumps, particles = csiborgtools.read.drop_zero_indx( particle_clumps, particles = partreader.drop_zero_indx(
particle_clumps, particles) particle_clumps, particles)
# Dump it! # Dump it!
csiborgtools.fits.dump_split_particles(particles, particle_clumps, clumps, csiborgtools.fits.dump_split_particles(particles, particle_clumps, clumps,
utils.Nsplits, dumpdir, Nsim, Nsnap, utils.Nsplits, paths, verbose=False)
verbose=False)
print("All finished!") print("All finished!")

31
setup.py Normal file
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@ -0,0 +1,31 @@
from setuptools import find_packages, setup
BUILD_REQ = ["numpy>=1.17.3", "scipy<1.9.0"]
INSTALL_REQ = BUILD_REQ
INSTALL_REQ += ["scikit-learn>=1.1.0",
"jax[cpu]>=0.3.23",
"tqdm>=4.64.1",
"astropy>=5.1",
],
setup(
name="csiborgtools",
version="0.1",
description="CSiBORG analysis tools",
url="https://github.com/Richard-Sti/csiborgtools",
author="Richard Stiskalek",
author_email="richard.stiskalek@protonmail.com",
license="GPL-3.0",
packages=find_packages(),
python_requires=">=3.8",
build_requires=BUILD_REQ,
setup_requires=BUILD_REQ,
install_requires=INSTALL_REQ,
classifiers=[
"Development Status :: 1 - Planning",
"Intended Audience :: Science/Research",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9"]
)