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Add Quijote (#61)

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* Rename paths object

* Remove redshift calculation

* Explicit keywrod arg

* Rename box units

* Basic renaming

* Little docs

* Rename paths

* add imports

* Sort imports

* Add Quijote cat

* Split boxes

* add Quijote path

* Add origin argument

* Update nbs
This commit is contained in:
Richard Stiskalek 2023-05-13 17:37:34 +01:00 • committed by GitHub
parent b3fd14b81f
commit 1d847cbd06
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34 changed files with 1401 additions and 292 deletions
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3
csiborgtools/__init__.py
View file

@ -14,7 +14,8 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
from csiborgtools import clustering, field, fits, match, read # noqa
# Arguments to csiborgtools.read.CSiBORGPaths.
# Arguments to csiborgtools.read.Paths.
paths_glamdring = {"srcdir": "/mnt/extraspace/hdesmond/",
"postdir": "/mnt/extraspace/rstiskalek/CSiBORG/",
"quijote_dir": "/mnt/extraspace/rstiskalek/Quijote",
}

10
csiborgtools/field/density.py
View file

@ -52,7 +52,7 @@ class BaseField(ABC):
Returns
-------
box : :py:class:`csiborgtools.units.BoxUnits`
box : :py:class:`csiborgtools.units.CSiBORGBox`
"""
return self._box
@ -94,7 +94,7 @@ class DensityField(BaseField):
Parameters
----------
box : :py:class:`csiborgtools.read.BoxUnits`
box : :py:class:`csiborgtools.read.CSiBORGBox`
The simulation box information and transformations.
MAS : str
Mass assignment scheme. Options are Options are: 'NGP' (nearest grid
@ -204,7 +204,7 @@ class VelocityField(BaseField):
Parameters
----------
box : :py:class:`csiborgtools.read.BoxUnits`
box : :py:class:`csiborgtools.read.CSiBORGBox`
The simulation box information and transformations.
MAS : str
Mass assignment scheme. Options are Options are: 'NGP' (nearest grid
@ -295,7 +295,7 @@ class PotentialField(BaseField):
Parameters
----------
box : :py:class:`csiborgtools.read.BoxUnits`
box : :py:class:`csiborgtools.read.CSiBORGBox`
The simulation box information and transformations.
MAS : str
Mass assignment scheme. Options are Options are: 'NGP' (nearest grid
@ -334,7 +334,7 @@ class TidalTensorField(BaseField):
Parameters
----------
box : :py:class:`csiborgtools.read.BoxUnits`
box : :py:class:`csiborgtools.read.CSiBORGBox`
The simulation box information and transformations.
MAS : str
Mass assignment scheme. Options are Options are: 'NGP' (nearest grid

2
csiborgtools/field/interp.py
View file

@ -67,7 +67,7 @@ def evaluate_sky(*fields, pos, box, isdeg=True):
pos : 2-dimensional array of shape `(n_samples, 3)`
Spherical coordinates to evaluate the field. Columns are distance,
right ascension, declination, respectively.
box : :py:class:`csiborgtools.read.BoxUnits`
box : :py:class:`csiborgtools.read.CSiBORGBox`
The simulation box information and transformations.
isdeg : bool, optional
Whether `ra` and `dec` are in degres. By default `True`.

6
csiborgtools/fits/halo.py
View file

@ -67,7 +67,7 @@ class BaseStructure(ABC):
Returns
-------
box : :py:class:`csiborgtools.units.BoxUnits`
box : :py:class:`csiborgtools.units.CSiBORGBox`
"""
return self._box
@ -280,7 +280,7 @@ class Clump(BaseStructure):
Particle array. Must contain `['x', 'y', 'z', 'vx', 'vy', 'vz', 'M']`.
info : structured array
Array containing information from the clump finder.
box : :py:class:`csiborgtools.read.BoxUnits`
box : :py:class:`csiborgtools.read.CSiBORGBox`
Box units object.
"""
@ -301,7 +301,7 @@ class Halo(BaseStructure):
Particle array. Must contain `['x', 'y', 'z', 'vx', 'vy', 'vz', 'M']`.
info : structured array
Array containing information from the clump finder.
box : :py:class:`csiborgtools.read.BoxUnits`
box : :py:class:`csiborgtools.read.CSiBORGBox`
Box units object.
"""

6
csiborgtools/read/__init__.py
View file

@ -12,14 +12,14 @@
# 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.
from .box_units import BoxUnits # noqa
from .halo_cat import ClumpsCatalogue, HaloCatalogue # noqa
from .box_units import CSiBORGBox, QuijoteBox # noqa
from .halo_cat import ClumpsCatalogue, HaloCatalogue, QuijoteHaloCatalogue # noqa
from .knn_summary import kNNCDFReader # noqa
from .obs import (SDSS, MCXCClusters, PlanckClusters, TwoMPPGalaxies, # noqa
TwoMPPGroups)
from .overlap_summary import (NPairsOverlap, PairOverlap, # noqa
binned_resample_mean)
from .paths import CSiBORGPaths # noqa
from .paths import Paths # noqa
from .pk_summary import PKReader # noqa
from .readsim import (MmainReader, ParticleReader, halfwidth_mask, # noqa
load_clump_particles, load_parent_particles, read_initcm)

221
csiborgtools/read/box_units.py
View file

@ -15,14 +15,15 @@
"""
Simulation box unit transformations.
"""
from abc import ABC
import numpy
from astropy import constants, units
from astropy.cosmology import LambdaCDM
from scipy.interpolate import interp1d
from .readsim import ParticleReader
# Map of unit conversions
# Map of CSiBORG unit conversions
CONV_NAME = {
"length": ["x", "y", "z", "peak_x", "peak_y", "peak_z", "Rs", "rmin",
"rmax", "r200c", "r500c", "r200m", "x0", "y0", "z0",
@ -33,53 +34,18 @@ CONV_NAME = {
"density": ["rho0"]}
class BoxUnits:
r"""
Box units class for converting between box and physical units.
###############################################################################
# Base box #
###############################################################################
Paramaters
----------
nsnap : int
Snapshot index.
nsim : int
IC realisation index.
paths : py:class`csiborgtools.read.CSiBORGPaths`
CSiBORG paths object.
class BaseBox(ABC):
"""
Base class for box units.
"""
_name = "box_units"
_cosmo = None
def __init__(self, nsnap, nsim, paths):
"""
Read in the snapshot info file and set the units from it.
"""
partreader = ParticleReader(paths)
info = partreader.read_info(nsnap, nsim)
pars = [
"boxlen",
"time",
"aexp",
"H0",
"omega_m",
"omega_l",
"omega_k",
"omega_b",
"unit_l",
"unit_d",
"unit_t",
]
for par in pars:
setattr(self, "_" + par, float(info[par]))
self._cosmo = LambdaCDM(
H0=self._H0,
Om0=self._omega_m,
Ode0=self._omega_l,
Tcmb0=2.725 * units.K,
Ob0=self._omega_b,
)
self._Msuncgs = constants.M_sun.cgs.value # Solar mass in grams
@property
def cosmo(self):
"""
@ -89,6 +55,8 @@ class BoxUnits:
-------
cosmo : `astropy.cosmology.LambdaCDM`
"""
if self._cosmo is None:
raise ValueError("Cosmology not set.")
return self._cosmo
@property
@ -101,7 +69,7 @@ class BoxUnits:
-------
H0 : float
"""
return self._H0
return self.cosmo.H0.value
@property
def h(self):
@ -112,7 +80,54 @@ class BoxUnits:
-------
h : float
"""
return self._H0 / 100
return self.H0 / 100
@property
def Om0(self):
r"""
The matter density parameter.
Returns
-------
Om0 : float
"""
return self.cosmo.Om0
###############################################################################
# CSiBORG box #
###############################################################################
class CSiBORGBox(BaseBox):
r"""
CSiBORG box units class for converting between box and physical units.
Paramaters
----------
nsnap : int
Snapshot index.
nsim : int
IC realisation index.
paths : py:class`csiborgtools.read.Paths`
CSiBORG paths object.
"""
def __init__(self, nsnap, nsim, paths):
"""
Read in the snapshot info file and set the units from it.
"""
partreader = ParticleReader(paths)
info = partreader.read_info(nsnap, nsim)
pars = ["boxlen", "time", "aexp", "H0", "omega_m", "omega_l",
"omega_k", "omega_b", "unit_l", "unit_d", "unit_t"]
for par in pars:
setattr(self, "_" + par, float(info[par]))
self._cosmo = LambdaCDM(H0=self._H0, Om0=self._omega_m,
Ode0=self._omega_l, Tcmb0=2.725 * units.K,
Ob0=self._omega_b)
self._Msuncgs = constants.M_sun.cgs.value # Solar mass in grams
@property
def box_G(self):
@ -157,7 +172,6 @@ class BoxUnits:
-------
rhoc : float
"""
return 3 * self.box_H0**2 / (8 * numpy.pi * self.box_G)
def box2kpc(self, length):
@ -244,83 +258,6 @@ class BoxUnits:
"""
return vel * (1e-2 * self._unit_l / self._unit_t / self._aexp) * 1e-3
def box2cosmoredshift(self, dist):
r"""
Convert the box comoving distance to cosmological redshift.
NOTE: this likely is already the observed redshift.
Parameters
----------
dist : float
Distance in box units.
Returns
-------
cosmo_redshift : foat
Cosmological redshift.
"""
x = numpy.linspace(0.0, 1.0, 5001)
y = self.cosmo.comoving_distance(x)
return interp1d(y, x)(self.box2mpc(dist))
def box2pecredshift(self, vx, vy, vz, px, py, pz, p0x=0, p0y=0, p0z=0):
"""
Convert the box phase-space information to a peculiar redshift.
NOTE: there is some confusion about this.
Parameters
----------
vx, vy, vz : 1-dimensional arrays
Cartesian velocity components.
px, py, pz : 1-dimensional arrays
Cartesian position vectors components.
p0x, p0y, p0z : floats
Centre of the box coordinates. By default 0, in which it is assumed
that the coordinates are already centred.
Returns
-------
pec_redshift : 1-dimensional array
Peculiar redshift.
"""
# Peculiar velocity along the radial distance
r = numpy.vstack([px - p0x, py - p0y, pz - p0z]).T
norm = numpy.sum(r**2, axis=1) ** 0.5
v = numpy.vstack([vx, vy, vz]).T
vpec = numpy.sum(r * v, axis=1) / norm
# Ratio between the peculiar velocity and speed of light
x = self.box2vel(vpec) / constants.c.value
# Doppler shift
return numpy.sqrt((1 + x) / (1 - x)) - 1
def box2obsredshift(self, vx, vy, vz, px, py, pz, p0x=0, p0y=0, p0z=0):
"""
Convert the box phase-space information to an 'observed' redshift.
NOTE: there is some confusion about this.
Parameters
----------
vx, vy, vz : 1-dimensional arrays
Cartesian velocity components.
px, py, pz : 1-dimensional arrays
Cartesian position vectors components.
p0x, p0y, p0z : floats
Centre of the box coordinates. By default 0, in which it is assumed
that the coordinates are already centred.
Returns
-------
obs_redshift : 1-dimensional array
Observed redshift.
"""
r = numpy.vstack([px - p0x, py - p0y, pz - p0z]).T
zcosmo = self.box2cosmoredshift(numpy.sum(r**2, axis=1) ** 0.5)
zpec = self.box2pecredshift(vx, vy, vz, px, py, pz, p0x, p0y, p0z)
return (1 + zpec) * (1 + zcosmo) - 1
def solarmass2box(self, mass):
r"""
Convert mass from :math:`M_\odot` (with :math:`h=0.705`) to box units.
@ -391,7 +328,7 @@ class BoxUnits:
return (density / self._unit_d * self._Msuncgs
/ (units.Mpc.to(units.cm)) ** 3)
def convert_from_boxunits(self, data, names):
def convert_from_box(self, data, names):
r"""
Convert columns named `names` in array `data` from box units to
physical units, such that
@ -421,13 +358,12 @@ class BoxUnits:
transforms = {"length": self.box2mpc,
"mass": self.box2solarmass,
"velocity": self.box2vel,
"density": self.box2dens,
}
"density": self.box2dens}
for name in names:
# Check that the name is even in the array
if name not in data.dtype.names:
raise ValueError("Name `{}` not in `data` array.".format(name))
raise ValueError(f"Name `{name}` not in `data` array.")
# Convert
found = False
@ -439,11 +375,36 @@ class BoxUnits:
# If nothing found
if not found:
raise NotImplementedError(
"Conversion of `{}` is not defined.".format(name)
)
f"Conversion of `{name}` is not defined.")
# Center at the observer
if name in ["peak_x", "peak_y", "peak_z", "x0", "y0", "z0"]:
data[name] -= transforms["length"](0.5)
return data
###############################################################################
# Quijote fiducial cosmology box #
###############################################################################
class QuijoteBox(BaseBox):
"""
Quijote fiducial cosmology box.
Parameters
----------
nsnap : int
Snapshot number.
**kwargs : dict
Empty keyword arguments. For backwards compatibility.
"""
def __init__(self, nsnap, **kwargs):
zdict = {4: 0.0, 3: 0.5, 2: 1.0, 1: 2.0, 0: 3.0}
assert nsnap in zdict.keys(), f"`nsnap` must be in {zdict.keys()}."
self._aexp = 1 / (1 + zdict[nsnap])
self._cosmo = LambdaCDM(H0=67.11, Om0=0.3175, Ode0=0.6825,
Tcmb0=2.725 * units.K, Ob0=0.049)

250
csiborgtools/read/halo_cat.py
View file

@ -12,24 +12,29 @@
# 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.
"""CSiBORG halo and clumps catalogues."""
from abc import ABC
"""
Simulation catalogues:
- CSiBORG: halo and clump catalogue.
- Quijote: halo catalogue.
"""
from abc import ABC, abstractproperty
from os.path import join
import numpy
from readfof import FoF_catalog
from sklearn.neighbors import NearestNeighbors
from .box_units import BoxUnits
from .paths import CSiBORGPaths
from .box_units import CSiBORGBox, QuijoteBox
from .paths import Paths
from .readsim import ParticleReader
from .utils import (add_columns, cartesian_to_radec, flip_cols,
radec_to_cartesian, real2redshift)
from .utils import (add_columns, cartesian_to_radec, cols_to_structured,
flip_cols, radec_to_cartesian, real2redshift)
class BaseCatalogue(ABC):
"""
Base (sub)halo catalogue.
"""
_data = None
_paths = None
_nsim = None
@ -51,14 +56,25 @@ class BaseCatalogue(ABC):
def nsim(self, nsim):
self._nsim = nsim
@property
def paths(self):
@abstractproperty
def nsnap(self):
"""
CSiBORG paths manager.
Catalogue's snapshot index.
Returns
-------
paths : :py:class:`csiborgtools.read.CSiBORGPaths`
nsnap : int
"""
pass
@property
def paths(self):
"""
Paths manager.
Returns
-------
paths : :py:class:`csiborgtools.read.Paths`
"""
if self._paths is None:
raise RuntimeError("`paths` is not set!")
@ -66,7 +82,7 @@ class BaseCatalogue(ABC):
@paths.setter
def paths(self, paths):
assert isinstance(paths, CSiBORGPaths)
assert isinstance(paths, Paths)
self._paths = paths
@property
@ -82,36 +98,16 @@ class BaseCatalogue(ABC):
raise RuntimeError("Catalogue data not loaded!")
return self._data
@property
def nsnap(self):
"""
Catalogue's snapshot index corresponding to the maximum simulation
snapshot index.
Returns
-------
nsnap : int
"""
return max(self.paths.get_snapshots(self.nsim))
@property
@abstractproperty
def box(self):
"""
CSiBORG box object handling unit conversion.
Box object.
Returns
-------
box : :py:class:`csiborgtools.units.BoxUnits`
box : instance of :py:class:`csiborgtools.units.BoxUnits`
"""
return BoxUnits(self.nsnap, self.nsim, self.paths)
@box.setter
def box(self, box):
try:
assert box._name == "box_units"
self._box = box
except AttributeError as err:
raise TypeError from err
pass
def position(self, in_initial=False, cartesian=True):
r"""
@ -143,8 +139,8 @@ class BaseCatalogue(ABC):
return pos
def velocity(self):
"""
Cartesian velocity components in box units.
r"""
Cartesian velocity components in :math:`\mathrm{km} / \mathrm{s}`.
Returns
-------
@ -204,7 +200,7 @@ class BaseCatalogue(ABC):
knn : :py:class:`sklearn.neighbors.NearestNeighbors`
"""
knn = NearestNeighbors()
return knn.fit(self.position(in_initial))
return knn.fit(self.position(in_initial=in_initial))
def radius_neigbours(self, X, radius, in_initial):
r"""
@ -299,20 +295,56 @@ class BaseCatalogue(ABC):
@property
def keys(self):
"""Catalogue keys."""
"""
Catalogue keys.
Returns
-------
keys : list of strings
"""
return self.data.dtype.names
def __getitem__(self, key):
initpars = ["x0", "y0", "z0"]
if key in initpars and key not in self.keys:
raise RuntimeError("Initial positions are not set!")
if key not in self.keys:
raise KeyError(f"Key '{key}' not in catalogue.")
return self.data[key]
def __len__(self):
return self.data.size
class ClumpsCatalogue(BaseCatalogue):
###############################################################################
# CSiBORG base catalogue #
###############################################################################
class BaseCSiBORG(BaseCatalogue):
"""
Base CSiBORG catalogue class.
"""
@property
def nsnap(self):
return max(self.paths.get_snapshots(self.nsim))
@property
def box(self):
"""
CSiBORG box object handling unit conversion.
Returns
-------
box : instance of :py:class:`csiborgtools.units.BaseBox`
"""
return CSiBORGBox(self.nsnap, self.nsim, self.paths)
###############################################################################
# CSiBORG clumps catalogue #
###############################################################################
class ClumpsCatalogue(BaseCSiBORG):
r"""
Clumps catalogue, defined in the final snapshot.
@ -320,8 +352,8 @@ class ClumpsCatalogue(BaseCatalogue):
----------
sim : int
IC realisation index.
paths : py:class`csiborgtools.read.CSiBORGPaths`
CSiBORG paths object.
paths : py:class`csiborgtools.read.Paths`
Paths object.
maxdist : float, optional
The maximum comoving distance of a halo. By default
:math:`155.5 / 0.705 ~ \mathrm{Mpc}` with assumed :math:`h = 0.705`,
@ -363,7 +395,7 @@ class ClumpsCatalogue(BaseCatalogue):
names = ["x", "y", "z", "mass_cl", "totpartmass", "rho0", "r200c",
"r500c", "m200c", "m500c", "r200m", "m200m",
"vx", "vy", "vz"]
self._data = self.box.convert_from_boxunits(self._data, names)
self._data = self.box.convert_from_box(self._data, names)
if maxdist is not None:
dist = numpy.sqrt(self._data["x"]**2 + self._data["y"]**2
+ self._data["z"]**2)
@ -383,7 +415,12 @@ class ClumpsCatalogue(BaseCatalogue):
return self["index"] == self["parent"]
class HaloCatalogue(BaseCatalogue):
###############################################################################
# CSiBORG halo catalogue #
###############################################################################
class HaloCatalogue(BaseCSiBORG):
r"""
Halo catalogue, i.e. parent halos with summed substructure, defined in the
final snapshot.
@ -392,8 +429,8 @@ class HaloCatalogue(BaseCatalogue):
----------
nsim : int
IC realisation index.
paths : py:class`csiborgtools.read.CSiBORGPaths`
CSiBORG paths object.
paths : py:class`csiborgtools.read.Paths`
Paths object.
maxdist : float, optional
The maximum comoving distance of a halo. By default
:math:`155.5 / 0.705 ~ \mathrm{Mpc}` with assumed :math:`h = 0.705`,
@ -455,11 +492,11 @@ class HaloCatalogue(BaseCatalogue):
names = ["x", "y", "z", "M", "totpartmass", "rho0", "r200c",
"r500c", "m200c", "m500c", "r200m", "m200m",
"vx", "vy", "vz"]
self._data = self.box.convert_from_boxunits(self._data, names)
self._data = self.box.convert_from_box(self._data, names)
if load_initial:
names = ["x0", "y0", "z0", "lagpatch"]
self._data = self.box.convert_from_boxunits(self._data, names)
self._data = self.box.convert_from_box(self._data, names)
if maxdist is not None:
dist = numpy.sqrt(self._data["x"]**2 + self._data["y"]**2
@ -480,3 +517,112 @@ class HaloCatalogue(BaseCatalogue):
if self._clumps_cat is None:
raise ValueError("`clumps_cat` is not loaded.")
return self._clumps_cat
###############################################################################
# Quijote halo catalogue #
###############################################################################
class QuijoteHaloCatalogue(BaseCatalogue):
"""
Quijote halo catalogue.
Parameters
----------
nsim : int
IC realisation index.
paths : py:class`csiborgtools.read.Paths`
Paths object.
nsnap : int
Snapshot index.
origin : len-3 tuple, optional
Where to place the origin of the box. By default the centre of the box.
In units of :math:`cMpc`.
maxdist : float, optional
The maximum comoving distance of a halo in the new reference frame, in
units of :math:`cMpc`.
minmass : len-2 tuple
Minimum mass. The first element is the catalogue key and the second is
the value.
rawdata : bool, optional
Whether to return the raw data. In this case applies no cuts and
transformations.
**kwargs : dict
Keyword arguments for backward compatibility.
"""
_nsnap = None
def __init__(self, nsim, paths, nsnap,
origin=[500 / 0.6711, 500 / 0.6711, 500 / 0.6711],
maxdist=None, minmass=("group_mass", 1e12), rawdata=False,
**kwargs):
self.paths = paths
self.nsnap = nsnap
fpath = join(self.paths.quijote_dir, "halos", str(nsim))
fof = FoF_catalog(fpath, self.nsnap, long_ids=False, swap=False,
SFR=False, read_IDs=False)
cols = [("x", numpy.float32), ("y", numpy.float32),
("z", numpy.float32), ("vx", numpy.float32),
("vy", numpy.float32), ("vz", numpy.float32),
("group_mass", numpy.float32), ("npart", numpy.int32)]
data = cols_to_structured(fof.GroupLen.size, cols)
pos = fof.GroupPos / 1e3 / self.box.h
for i in range(3):
pos -= origin[i]
vel = fof.GroupVel * (1 + self.redshift)
for i, p in enumerate(["x", "y", "z"]):
data[p] = pos[:, i]
data["v" + p] = vel[:, i]
data["group_mass"] = fof.GroupMass * 1e10 / self.box.h
data["npart"] = fof.GroupLen
if not rawdata:
if maxdist is not None:
pos = numpy.vstack([data["x"], data["y"], data["z"]]).T
data = data[numpy.linalg.norm(pos, axis=1) < maxdist]
if minmass is not None:
data = data[data[minmass[0]] > minmass[1]]
self._data = data
@property
def nsnap(self):
"""
Snapshot number.
Returns
-------
nsnap : int
"""
return self._nsnap
@nsnap.setter
def nsnap(self, nsnap):
assert nsnap in [0, 1, 2, 3, 4]
self._nsnap = nsnap
@property
def redshift(self):
"""
Redshift of the snapshot.
Returns
-------
redshift : float
"""
z_dict = {4: 0.0, 3: 0.5, 2: 1.0, 1: 2.0, 0: 3.0}
return z_dict[self.nsnap]
@property
def box(self):
"""
Quijote box object.
Returns
-------
box : instance of :py:class:`csiborgtools.units.BaseBox`
"""
return QuijoteBox(self.nsnap)

5
csiborgtools/read/knn_summary.py
View file

@ -24,7 +24,7 @@ class kNNCDFReader:
Parameters
----------
paths : py:class`csiborgtools.read.CSiBORGPaths`
paths : py:class`csiborgtools.read.Paths`
"""
_paths = None
@ -38,13 +38,12 @@ class kNNCDFReader:
Parameters
----------
paths : py:class`csiborgtools.read.CSiBORGPaths`
paths : py:class`csiborgtools.read.Paths`
"""
return self._paths
@paths.setter
def paths(self, paths):
# assert isinstance(paths, CSiBORGPaths) # REMOVE
self._paths = paths
def read(self, run, kind, rmin=None, rmax=None, to_clip=True):

10
csiborgtools/read/overlap_summary.py
View file

@ -36,7 +36,7 @@ class PairOverlap:
Halo catalogue corresponding to the reference simulation.
catx : :py:class:`csiborgtools.read.HaloCatalogue`
Halo catalogue corresponding to the cross simulation.
paths : py:class`csiborgtools.read.CSiBORGPaths`
paths : py:class`csiborgtools.read.Paths`
CSiBORG paths object.
"""
_cat0 = None
@ -59,7 +59,7 @@ class PairOverlap:
Halo catalogue corresponding to the reference simulation.
catx : :py:class:`csiborgtools.read.HaloCatalogue`
Halo catalogue corresponding to the cross simulation.
paths : py:class`csiborgtools.read.CSiBORGPaths`
paths : py:class`csiborgtools.read.Paths`
CSiBORG paths object.
Returns
@ -268,8 +268,8 @@ class PairOverlap:
assert (norm_kind is None
or norm_kind in ("r200c", "ref_patch", "sum_patch"))
# Get positions either in the initial or final snapshot
pos0 = self.cat0().position(in_initial)
posx = self.catx().position(in_initial)
pos0 = self.cat0().position(in_initial=in_initial)
posx = self.catx().position(in_initial=in_initial)
# Get the normalisation array if applicable
if norm_kind == "r200c":
@ -474,7 +474,7 @@ class NPairsOverlap:
Single reference simulation halo catalogue.
catxs : list of :py:class:`csiborgtools.read.HaloCatalogue`
List of cross simulation halo catalogues.
paths : py:class`csiborgtools.read.CSiBORGPaths`
paths : py:class`csiborgtools.read.Paths`
CSiBORG paths object.
verbose : bool, optional
Verbosity flag for loading the overlap objects.

45
csiborgtools/read/paths.py
View file

@ -21,29 +21,32 @@ from warnings import warn
import numpy
class CSiBORGPaths:
class Paths:
"""
Paths manager for CSiBORG IC realisations.
Paths manager for CSiBORG and Quijote simulations.
Parameters
----------
srcdir : str
Path to the folder where the RAMSES outputs are stored.
postdir: str
Path to the folder where post-processed files are stored.
Parameters
----------
srcdir : str, optional
Path to the folder where the RAMSES outputs are stored.
postdir: str, optional
Path to the folder where post-processed files are stored.
quiote_dir : str, optional
Path to the folder where Quijote simulations are stored.
"""
_srcdir = None
_postdir = None
_quijote_dir = None
def __init__(self, srcdir=None, postdir=None):
def __init__(self, srcdir=None, postdir=None, quijote_dir=None):
self.srcdir = srcdir
self.postdir = postdir
self.quijote_dir = quijote_dir
@staticmethod
def _check_directory(path):
if not isdir(path):
raise IOError("Invalid directory `{}`!".format(path))
raise IOError(f"Invalid directory `{path}`!")
@property
def srcdir(self):
@ -65,6 +68,26 @@ class CSiBORGPaths:
self._check_directory(path)
self._srcdir = path
@property
def quijote_dir(self):
"""
Path to the folder where Quijote simulations are stored.
Returns
-------
path : str
"""
if self._quijote_dir is None:
raise ValueError("`quijote_dir` is not set!")
return self._quijote_dir
@quijote_dir.setter
def quijote_dir(self, path):
if path is None:
return
self._check_directory(path)
self._quijote_dir = path
@property
def postdir(self):
"""

14
csiborgtools/read/readsim.py
View file

@ -22,7 +22,7 @@ import numpy
from scipy.io import FortranFile
from tqdm import tqdm, trange
from .paths import CSiBORGPaths
from .paths import Paths
from .utils import cols_to_structured
###############################################################################
@ -36,7 +36,7 @@ class ParticleReader:
Parameters
----------
paths : py:class`csiborgtools.read.CSiBORGPaths`
paths : py:class`csiborgtools.read.Paths`
"""
_paths = None
@ -50,13 +50,13 @@ class ParticleReader:
Parameters
----------
paths : py:class`csiborgtools.read.CSiBORGPaths`
paths : py:class`csiborgtools.read.Paths`
"""
return self._paths
@paths.setter
def paths(self, paths):
assert isinstance(paths, CSiBORGPaths)
assert isinstance(paths, Paths)
self._paths = paths
def read_info(self, nsnap, nsim):
@ -396,17 +396,17 @@ class ParticleReader:
class MmainReader:
"""
Object to generate the summed substructure catalogue.
Object to generate the summed substructure CSiBORG PHEW catalogue.
Parameters
----------
paths : :py:class:`csiborgtools.read.CSiBORGPaths`
paths : :py:class:`csiborgtools.read.Paths`
Paths objects.
"""
_paths = None
def __init__(self, paths):
assert isinstance(paths, CSiBORGPaths)
assert isinstance(paths, Paths)
self._paths = paths
@property

8
csiborgtools/read/tpcf_summary.py
View file

@ -16,7 +16,7 @@
import joblib
import numpy
from .paths import CSiBORGPaths
from .paths import Paths
class TPCFReader:
@ -25,7 +25,7 @@ class TPCFReader:
Parameters
----------
paths : py:class`csiborgtools.read.CSiBORGPaths`
paths : py:class`csiborgtools.read.Paths`
"""
_paths = None
@ -39,13 +39,13 @@ class TPCFReader:
Parameters
----------
paths : py:class`csiborgtools.read.CSiBORGPaths`
paths : py:class`csiborgtools.read.Paths`
"""
return self._paths
@paths.setter
def paths(self, paths):
assert isinstance(paths, CSiBORGPaths)
assert isinstance(paths, Paths)
self._paths = paths
def read(self, run):

2
csiborgtools/read/utils.py
View file

@ -93,7 +93,7 @@ def real2redshift(pos, vel, origin, box, in_box_units, periodic_wrap=True,
Cartesian velocity components.
origin : 1-dimensional array `(3,)`
Origin of the coordinate system in the `pos` reference frame.
box : py:class:`csiborg.read.BoxUnits`
box : py:class:`csiborg.read.CSiBORGBox`
Box units.
in_box_units: bool
Whether `pos` and `vel` are in box units. If not, position is assumed