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Dump radial profile information (#48)

Browse source 
* add radial position path

* pep8

* Add basic fit profile dumping

* pep8

* pep8

* pep8

* pep8

* pep8

* pep8

* Update TODO

* Fix parts is None bug

* Update nb
This commit is contained in:
Richard Stiskalek 2023-04-27 01:18:30 +02:00 committed by GitHub
parent 1a115f481d
commit f48eb6dcb0
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29 changed files with 512 additions and 395 deletions
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2
.gitignore vendored
View file

@ -1,4 +1,4 @@
venv_galomatch/
venv_csiborg/
share/
bin/
.bashrc

7
csiborgtools/__init__.py
View file

@ -15,7 +15,6 @@
from csiborgtools import clustering, field, fits, match, read # noqa
# Arguments to csiborgtools.read.CSiBORGPaths.
paths_glamdring = {
"srcdir": "/mnt/extraspace/hdesmond/",
"postdir": "/mnt/extraspace/rstiskalek/csiborg/"
}
paths_glamdring = {"srcdir": "/mnt/extraspace/hdesmond/",
"postdir": "/mnt/extraspace/rstiskalek/csiborg/",
}

2
csiborgtools/clustering/__init__.py
View file

@ -28,4 +28,4 @@ try:
from .tpcf import Mock2PCF # noqa
except ImportError:
warn("`Corrfunc` not installed. 2PCF modules will not be available (`Mock2PCF`).") # noqa
warn("`Corrfunc` not installed. 2PCF modules will not be available .") # noqa

2
csiborgtools/clustering/utils.py
View file

@ -66,7 +66,7 @@ class RVSinsphere(BaseRVS):
def __call__(self, nsamples, random_state=42, dtype=numpy.float32):
gen = numpy.random.default_rng(random_state)
# Spherical
r = gen.random(nsamples, dtype=dtype)**(1/3) * self.R
r = gen.random(nsamples, dtype=dtype)**(1 / 3) * self.R
theta = 2 * numpy.arcsin(gen.random(nsamples, dtype=dtype))
phi = 2 * numpy.pi * gen.random(nsamples, dtype=dtype)
# Cartesian

2
csiborgtools/field/density.py
View file

@ -105,7 +105,7 @@ class DensityField:
@box.setter
def box(self, box):
try:
assert box._name == "box_units"
assert box._name == "box_units"
self._box = box
except AttributeError as err:
raise TypeError from err

11
csiborgtools/fits/halo.py
View file

@ -40,7 +40,7 @@ class BaseStructure(ABC):
@particles.setter
def particles(self, particles):
pars = ["x", "y", "z", "vx", "vy", "vz", "M"]
pars = ["x", "y", "z", "M"]
assert all(p in particles.dtype.names for p in pars)
self._particles = particles
@ -204,11 +204,12 @@ class BaseStructure(ABC):
return numpy.nan
mass = self.enclosed_mass(radius)
V = numpy.sqrt(self.box.box_G * mass / radius)
return numpy.linalg.norm(self.angular_momentum(radius)) / (
numpy.sqrt(2) * mass * V * radius
)
out = numpy.linalg.norm(self.angular_momentum(radius))
out /= numpy.sqrt(2) * mass * V * radius
return out
def spherical_overdensity_mass(self, delta_mult, npart_min=10, kind="crit"):
def spherical_overdensity_mass(self, delta_mult, npart_min=10,
kind="crit"):
r"""
Calculate spherical overdensity mass and radius. The mass is defined as
the enclosed mass within an outermost radius where the mean enclosed

4
csiborgtools/fits/haloprofile.py
View file

@ -364,9 +364,7 @@ class NFWPosterior(NFWProfile):
if not (numpy.all(numpy.isfinite(bounds)) and bounds[0] < bounds[1]):
return numpy.nan, numpy.nan
res = minimize_scalar(
loss, bounds=(numpy.log10(rmin), numpy.log10(rmax)), method="bounded"
)
res = minimize_scalar(loss, bounds=bounds, method="bounded")
# Check whether the fit converged to radius sufficienly far from `rmax`
# and that its a success. Otherwise return NaNs.
if numpy.log10(rmax) - res.x < eps:

210
csiborgtools/match/match.py
View file

@ -105,13 +105,13 @@ class RealisationsMatcher:
"""
return self._overlapper
def cross(
self, cat0, catx, halos0_archive, halosx_archive, delta_bckg, verbose=True
):
def cross(self, cat0, catx, halos0_archive, halosx_archive, delta_bckg,
verbose=True):
r"""
Find all neighbours whose CM separation is less than `nmult` times the
sum of their initial Lagrangian patch sizes and calculate their overlap.
Enforces that the neighbours' are similar in mass up to `dlogmass` dex.
sum of their initial Lagrangian patch sizes and calculate their
overlap. Enforces that the neighbours' are similar in mass up to
`dlogmass` dex.
Parameters
----------
@ -121,12 +121,12 @@ class RealisationsMatcher:
Halo catalogue of the cross simulation.
halos0_archive : `NpzFile` object
Archive of halos' particles of the reference simulation, keys must
include `x`, `y`, `z` and `M`. The positions must already be converted
to cell numbers.
include `x`, `y`, `z` and `M`. The positions must already be
converted to cell numbers.
halosx_archive : `NpzFile` object
Archive of halos' particles of the cross simulation, keys must
include `x`, `y`, `z` and `M`. The positions must already be converted
to cell numbers.
include `x`, `y`, `z` and `M`. The positions must already be
converted to cell numbers.
delta_bckg : 3-dimensional array
Summed background density field of the reference and cross
simulations calculated with particles assigned to halos at the
@ -138,25 +138,23 @@ class RealisationsMatcher:
Returns
-------
match_indxs : 1-dimensional array of arrays
The outer array corresponds to halos in the reference catalogue, the
inner array corresponds to the array positions of matches in the cross
catalogue.
The outer array corresponds to halos in the reference catalogue,
the inner array corresponds to the array positions of matches in
the cross catalogue.
overlaps : 1-dimensional array of arrays
Overlaps with the cross catalogue. Follows similar pattern as `match_indxs`.
Overlaps with the cross catalogue. Follows similar pattern as
`match_indxs`.
"""
# We begin by querying the kNN for the nearest neighbours of each halo
# in the reference simulation from the cross simulation in the initial
# snapshot.
verbose and print("{}: querying the KNN.".format(datetime.now()), flush=True)
if verbose:
now = datetime.now()
print(f"{now}: querying the KNN.", flush=True)
match_indxs = radius_neighbours(
catx.knn(select_initial=True),
cat0.positions(in_initial=True),
radiusX=cat0["lagpatch"],
radiusKNN=catx["lagpatch"],
nmult=self.nmult,
enforce_int32=True,
verbose=verbose,
)
catx.knn(select_initial=True), cat0.positions(in_initial=True),
radiusX=cat0["lagpatch"], radiusKNN=catx["lagpatch"],
nmult=self.nmult, enforce_int32=True, verbose=verbose)
# We next remove neighbours whose mass is too large/small.
if self.dlogmass is not None:
for i, indx in enumerate(match_indxs):
@ -165,34 +163,35 @@ class RealisationsMatcher:
aratio = numpy.abs(numpy.log10(catx[p][indx] / cat0[p][i]))
match_indxs[i] = match_indxs[i][aratio < self.dlogmass]
# We will make a dictionary to keep in memory the halos' particles from the
# cross simulations so that they are not loaded in several times and we only
# convert their positions to cells once. Possibly make an option to not do
# this to lower memory requirements?
# We will make a dictionary to keep in memory the halos' particles from
# the cross simulations so that they are not loaded in several times
# and we only convert their positions to cells once. Possibly make an
# option to not do this to lower memory requirements?
cross_halos = {}
cross_lims = {}
cross = [numpy.asanyarray([], dtype=numpy.float32)] * match_indxs.size
for i, k0 in enumerate(tqdm(cat0["index"]) if verbose else cat0["index"]):
indxs = cat0["index"]
for i, k0 in enumerate(tqdm(indxs) if verbose else indxs):
# If we have no matches continue to the next halo.
matches = match_indxs[i]
if matches.size == 0:
continue
# Next, we find this halo's particles, total mass and minimum/maximum cells
# and convert positions to cells.
# Next, we find this halo's particles, total mass, minimum and
# maximum cells and convert positions to cells.
halo0 = halos0_archive[str(k0)]
mass0 = numpy.sum(halo0["M"])
mins0, maxs0 = get_halolims(
halo0, ncells=self.overlapper.inv_clength, nshift=self.overlapper.nshift
)
mins0, maxs0 = get_halolims(halo0,
ncells=self.overlapper.inv_clength,
nshift=self.overlapper.nshift)
for p in ("x", "y", "z"):
halo0[p] = self.overlapper.pos2cell(halo0[p])
# We now loop over matches of this halo and calculate their overlap,
# storing them in `_cross`.
# We now loop over matches of this halo and calculate their
# overlap, storing them in `_cross`.
_cross = numpy.full(matches.size, numpy.nan, dtype=numpy.float32)
for j, kf in enumerate(catx["index"][matches]):
# Attempt to load this cross halo from memory, if it fails get it from
# from the halo archive (and similarly for the limits) and convert the
# particle positions to cells.
# Attempt to load this cross halo from memory, if it fails get
# it from from the halo archive (and similarly for the limits)
# and convert the particle positions to cells.
try:
halox = cross_halos[kf]
minsx, maxsx = cross_lims[kf]
@ -208,17 +207,9 @@ class RealisationsMatcher:
cross_halos[kf] = halox
cross_lims[kf] = (minsx, maxsx)
massx = numpy.sum(halox["M"])
_cross[j] = self.overlapper(
halo0,
halox,
delta_bckg,
mins0,
maxs0,
minsx,
maxsx,
mass1=mass0,
mass2=massx,
)
_cross[j] = self.overlapper(halo0, halox, delta_bckg, mins0,
maxs0, minsx, maxsx, mass1=mass0,
mass2=massx)
cross[i] = _cross
# We remove all matches that have zero overlap to save space.
@ -233,17 +224,8 @@ class RealisationsMatcher:
cross = numpy.asanyarray(cross, dtype=object)
return match_indxs, cross
def smoothed_cross(
self,
cat0,
catx,
halos0_archive,
halosx_archive,
delta_bckg,
match_indxs,
smooth_kwargs,
verbose=True,
):
def smoothed_cross(self, cat0, catx, halos0_archive, halosx_archive,
delta_bckg, match_indxs, smooth_kwargs, verbose=True):
r"""
Calculate the smoothed overlaps for pair previously identified via
`self.cross(...)` to have a non-zero overlap.
@ -256,12 +238,12 @@ class RealisationsMatcher:
Halo catalogue of the cross simulation.
halos0_archive : `NpzFile` object
Archive of halos' particles of the reference simulation, keys must
include `x`, `y`, `z` and `M`. The positions must already be converted
to cell numbers.
include `x`, `y`, `z` and `M`. The positions must already be
converted to cell numbers.
halosx_archive : `NpzFile` object
Archive of halos' particles of the cross simulation, keys must
include `x`, `y`, `z` and `M`. The positions must already be converted
to cell numbers.
include `x`, `y`, `z` and `M`. The positions must already be
converted to cell numbers.
delta_bckg : 3-dimensional array
Smoothed summed background density field of the reference and cross
simulations calculated with particles assigned to halos at the
@ -287,40 +269,32 @@ class RealisationsMatcher:
cross_lims = {}
cross = [numpy.asanyarray([], dtype=numpy.float32)] * match_indxs.size
for i, k0 in enumerate(tqdm(cat0["index"]) if verbose else cat0["index"]):
indxs = cat0["index"]
for i, k0 in enumerate(tqdm(indxs) if verbose else indxs):
halo0 = halos0_archive[str(k0)]
mins0, maxs0 = get_halolims(
halo0, ncells=self.overlapper.inv_clength, nshift=self.overlapper.nshift
)
mins0, maxs0 = get_halolims(halo0,
ncells=self.overlapper.inv_clength,
nshift=self.overlapper.nshift)
# Now loop over the matches and calculate the smoothed overlap.
_cross = numpy.full(match_indxs[i].size, numpy.nan, numpy.float32)
for j, kf in enumerate(catx["index"][match_indxs[i]]):
# Attempt to load this cross halo from memory, if it fails get it from
# from the halo archive (and similarly for the limits).
# Attempt to load this cross halo from memory, if it fails get
# it from from the halo archive (and similarly for the limits).
try:
halox = cross_halos[kf]
minsx, maxsx = cross_lims[kf]
except KeyError:
halox = halosx_archive[str(kf)]
minsx, maxsx = get_halolims(
halox,
ncells=self.overlapper.inv_clength,
nshift=self.overlapper.nshift,
)
halox, ncells=self.overlapper.inv_clength,
nshift=self.overlapper.nshift)
cross_halos[kf] = halox
cross_lims[kf] = (minsx, maxsx)
_cross[j] = self.overlapper(
halo0,
halox,
delta_bckg,
mins0,
maxs0,
minsx,
maxsx,
smooth_kwargs=smooth_kwargs,
)
_cross[j] = self.overlapper(halo0, halox, delta_bckg, mins0,
maxs0, minsx, maxsx,
smooth_kwargs=smooth_kwargs)
cross[i] = _cross
return numpy.asanyarray(cross, dtype=object)
@ -398,9 +372,9 @@ class ParticleOverlap:
def make_bckg_delta(self, halo_archive, delta=None, verbose=False):
"""
Calculate a NGP density field of particles belonging to halos within the
central :math:`1/2^3` high-resolution region of the simulation. Smoothing
must be applied separately.
Calculate a NGP density field of particles belonging to halos within
the central :math:`1/2^3` high-resolution region of the simulation.
Smoothing must be applied separately.
Parameters
----------
@ -417,16 +391,16 @@ class ParticleOverlap:
-------
delta : 3-dimensional array
"""
# We obtain the minimum/maximum cell IDs and number of cells along each dim.
# We obtain the minimum/maximum cell IDs and number of cells
cellmin = self.inv_clength // 4 # The minimum cell ID
cellmax = 3 * self.inv_clength // 4 # The maximum cell ID
ncells = cellmax - cellmin
# We then pre-allocate the density field or check it is of the right shape
# if already given.
# We then pre-allocate the density field/check it is of the right shape
if delta is None:
delta = numpy.zeros((ncells,) * 3, dtype=numpy.float32)
else:
assert (delta.shape == (ncells,) * 3) & (delta.dtype == numpy.float32)
assert ((delta.shape == (ncells,) * 3)
& (delta.dtype == numpy.float32))
# We now loop one-by-one over the halos fill the density field.
files = halo_archive.files
@ -436,21 +410,20 @@ class ParticleOverlap:
mass = parts["M"]
# We mask out particles outside the cubical high-resolution region
mask = (
(cellmin <= cells[0])
& (cells[0] < cellmax)
& (cellmin <= cells[1])
& (cells[1] < cellmax)
& (cellmin <= cells[2])
& (cells[2] < cellmax)
)
mask = ((cellmin <= cells[0])
& (cells[0] < cellmax)
& (cellmin <= cells[1])
& (cells[1] < cellmax)
& (cellmin <= cells[2])
& (cells[2] < cellmax))
cells = [c[mask] for c in cells]
mass = mass[mask]
fill_delta(delta, *cells, *(cellmin,) * 3, mass)
return delta
def make_delta(self, clump, mins=None, maxs=None, subbox=False, smooth_kwargs=None):
def make_delta(self, clump, mins=None, maxs=None, subbox=False,
smooth_kwargs=None):
"""
Calculate a NGP density field of a halo on a cubic grid. Optionally can
be smoothed with a Gaussian kernel.
@ -505,16 +478,8 @@ class ParticleOverlap:
gaussian_filter(delta, output=delta, **smooth_kwargs)
return delta
def make_deltas(
self,
clump1,
clump2,
mins1=None,
maxs1=None,
mins2=None,
maxs2=None,
smooth_kwargs=None,
):
def make_deltas(self, clump1, clump2, mins1=None, maxs1=None, mins2=None,
maxs2=None, smooth_kwargs=None):
"""
Calculate a NGP density fields of two halos on a grid that encloses
them both. Optionally can be smoothed with a Gaussian kernel.
@ -596,19 +561,9 @@ class ParticleOverlap:
gaussian_filter(delta2, output=delta2, **smooth_kwargs)
return delta1, delta2, cellmins, nonzero
def __call__(
self,
clump1,
clump2,
delta_bckg,
mins1=None,
maxs1=None,
mins2=None,
maxs2=None,
mass1=None,
mass2=None,
smooth_kwargs=None,
):
def __call__(self, clump1, clump2, delta_bckg, mins1=None, maxs1=None,
mins2=None, maxs2=None, mass1=None, mass2=None,
smooth_kwargs=None):
"""
Calculate overlap between `clump1` and `clump2`. See
`calculate_overlap(...)` for further information. Be careful so that
@ -647,8 +602,8 @@ class ParticleOverlap:
overlap : float
"""
delta1, delta2, cellmins, nonzero = self.make_deltas(
clump1, clump2, mins1, maxs1, mins2, maxs2, smooth_kwargs=smooth_kwargs
)
clump1, clump2, mins1, maxs1, mins2, maxs2,
smooth_kwargs=smooth_kwargs)
if smooth_kwargs is not None:
return calculate_overlap(delta1, delta2, cellmins, delta_bckg)
@ -656,8 +611,7 @@ class ParticleOverlap:
mass1 = numpy.sum(clump1["M"]) if mass1 is None else mass1
mass2 = numpy.sum(clump2["M"]) if mass2 is None else mass2
return calculate_overlap_indxs(
delta1, delta2, cellmins, delta_bckg, nonzero, mass1, mass2
)
delta1, delta2, cellmins, delta_bckg, nonzero, mass1, mass2)
###############################################################################
@ -963,8 +917,8 @@ def radius_neighbours(
for i in trange(nsamples) if verbose else range(nsamples):
dist, indx = knn.radius_neighbors(
X[i, :].reshape(-1, 3), radiusX[i] + patchknn_max, sort_results=True
)
X[i, :].reshape(-1, 3), radiusX[i] + patchknn_max,
sort_results=True)
# Note that `dist` and `indx` are wrapped in 1-element arrays
# so we take the first item where appropriate
mask = (dist[0] / (radiusX[i] + radiusKNN[indx[0]])) < nmult

6
csiborgtools/match/utils.py
View file

@ -41,9 +41,9 @@ def concatenate_parts(list_parts, include_velocities=False):
else:
posdtype = numpy.float32
# We pre-allocate an empty array. By default, we include just particle positions,
# which may be specified by cell IDs if integers, and masses. Additionally also
# outputs velocities.
# We pre-allocate an empty array. By default, we include just particle
# positions, which may be specified by cell IDs if integers, and masses.
# Additionally also outputs velocities.
if include_velocities:
dtype = {
"names": ["x", "y", "z", "vx", "vy", "vz", "M"],

44
csiborgtools/read/box_units.py
View file

@ -24,27 +24,12 @@ from .readsim import ParticleReader
# Map of unit conversions
CONV_NAME = {
"length": [
"x",
"y",
"z",
"peak_x",
"peak_y",
"peak_z",
"Rs",
"rmin",
"rmax",
"r200c",
"r500c",
"r200m",
"x0",
"y0",
"z0",
"lagpatch",
],
"mass": ["mass_cl", "totpartmass", "m200c", "m500c", "mass_mmain", "M", "m200m"],
"density": ["rho0"],
}
"length": ["x", "y", "z", "peak_x", "peak_y", "peak_z", "Rs", "rmin",
"rmax", "r200c", "r500c", "r200m", "x0", "y0", "z0",
"lagpatch"],
"mass": ["mass_cl", "totpartmass", "m200c", "m500c", "mass_mmain", "M",
"m200m"],
"density": ["rho0"]}
class BoxUnits:
@ -367,7 +352,8 @@ class BoxUnits:
density : float
Density in :math:`M_\odot / \mathrm{pc}^3`.
"""
return density * self._unit_d / self._Msuncgs * (units.Mpc.to(units.cm)) ** 3
return (density * self._unit_d
/ self._Msuncgs * (units.Mpc.to(units.cm)) ** 3)
def dens2box(self, density):
r"""
@ -384,7 +370,8 @@ class BoxUnits:
density : float
Density in box units.
"""
return density / self._unit_d * self._Msuncgs / (units.Mpc.to(units.cm)) ** 3
return (density / self._unit_d * self._Msuncgs
/ (units.Mpc.to(units.cm)) ** 3)
def convert_from_boxunits(self, data, names):
r"""
@ -412,13 +399,10 @@ class BoxUnits:
Input array with converted columns.
"""
names = [names] if isinstance(names, str) else names
# Shortcut for the transform functions
transforms = {
"length": self.box2mpc,
"mass": self.box2solarmass,
"density": self.box2dens,
}
transforms = {"length": self.box2mpc,
"mass": self.box2solarmass,
"density": self.box2dens,
}
for name in names:
# Check that the name is even in the array

79
csiborgtools/read/halo_cat.py
View file

@ -21,7 +21,8 @@ from sklearn.neighbors import NearestNeighbors
from .box_units import BoxUnits
from .paths import CSiBORGPaths
from .readsim import ParticleReader
from .utils import add_columns, cartesian_to_radec, flip_cols, radec_to_cartesian
from .utils import (add_columns, cartesian_to_radec, flip_cols,
radec_to_cartesian)
class BaseCatalogue(ABC):
@ -249,7 +250,8 @@ class BaseCatalogue(ABC):
knn.fit(pos)
# Convert angular radius to cosine difference.
metric_maxdist = 1 - numpy.cos(numpy.deg2rad(ang_radius))
dist, ind = knn.radius_neighbors(X, radius=metric_maxdist, sort_results=True)
dist, ind = knn.radius_neighbors(X, radius=metric_maxdist,
sort_results=True)
# And the cosine difference to angular distance.
for i in range(X.shape[0]):
dist[i] = numpy.rad2deg(numpy.arccos(1 - dist[i]))
@ -302,15 +304,8 @@ class ClumpsCatalogue(BaseCatalogue):
transformations.
"""
def __init__(
self,
nsim,
paths,
maxdist=155.5 / 0.705,
minmass=("mass_cl", 1e12),
load_fitted=True,
rawdata=False,
):
def __init__(self, nsim, paths, maxdist=155.5 / 0.705,
minmass=("mass_cl", 1e12), load_fitted=True, rawdata=False):
self.nsim = nsim
self.paths = paths
# Read in the clumps from the final snapshot
@ -333,27 +328,12 @@ class ClumpsCatalogue(BaseCatalogue):
flip_cols(self._data, "x", "z")
for p in ("x", "y", "z"):
self._data[p] -= 0.5
self._data = self.box.convert_from_boxunits(
self._data,
[
"x",
"y",
"z",
"mass_cl",
"totpartmass",
"rho0",
"r200c",
"r500c",
"m200c",
"m500c",
"r200m",
"m200m",
],
)
names = ["x", "y", "z", "mass_cl", "totpartmass", "rho0", "r200c",
"r500c", "m200c", "m500c", "r200m", "m200m"]
self._data = self.box.convert_from_boxunits(self._data, names)
if maxdist is not None:
dist = numpy.sqrt(
self._data["x"] ** 2 + self._data["y"] ** 2 + self._data["z"] ** 2
)
dist = numpy.sqrt(self._data["x"]**2 + self._data["y"]**2
+ self._data["z"]**2)
self._data = self._data[dist < maxdist]
if minmass is not None:
self._data = self._data[self._data[minmass[0]] > minmass[1]]
@ -397,16 +377,8 @@ class HaloCatalogue(BaseCatalogue):
transformations.
"""
def __init__(
self,
nsim,
paths,
maxdist=155.5 / 0.705,
minmass=("M", 1e12),
load_fitted=True,
load_initial=False,
rawdata=False,
):
def __init__(self, nsim, paths, maxdist=155.5 / 0.705, minmass=("M", 1e12),
load_fitted=True, load_initial=False, rawdata=False):
self.nsim = nsim
self.paths = paths
# Read in the mmain catalogue of summed substructure
@ -426,28 +398,13 @@ class HaloCatalogue(BaseCatalogue):
flip_cols(self._data, "x", "z")
for p in ("x", "y", "z"):
self._data[p] -= 0.5
self._data = self.box.convert_from_boxunits(
self._data,
[
"x",
"y",
"z",
"M",
"totpartmass",
"rho0",
"r200c",
"r500c",
"m200c",
"m500c",
"r200m",
"m200m",
],
)
names = ["x", "y", "z", "M", "totpartmass", "rho0", "r200c",
"r500c", "m200c", "m500c", "r200m", "m200m"]
self._data = self.box.convert_from_boxunits(self._data, names)
if maxdist is not None:
dist = numpy.sqrt(
self._data["x"] ** 2 + self._data["y"] ** 2 + self._data["z"] ** 2
)
dist = numpy.sqrt(self._data["x"]**2 + self._data["y"]**2
+ self._data["z"]**2)
self._data = self._data[dist < maxdist]
if minmass is not None:
self._data = self._data[self._data[minmass[0]] > minmass[1]]

2
csiborgtools/read/obs.py
View file

@ -163,7 +163,7 @@ class TwoMPPGroups(TextSurvey):
# Convert galactic coordinates to RA, dec
glon = data[:, 1]
glat = data[:, 2]
coords = SkyCoord(l=glon*units.degree, b=glat*units.degree,
coords = SkyCoord(l=glon * units.degree, b=glat * units.degree,
frame='galactic')
coords = coords.transform_to("icrs")
data["RA"] = coords.ra

2
csiborgtools/read/overlap_summary.py
View file

@ -82,7 +82,7 @@ class PairOverlap:
"match_indxs": match_indxs,
"ngp_overlap": ngp_overlap,
"smoothed_overlap": smoothed_overlap,
}
}
self._make_refmask(min_mass, max_dist)

64
csiborgtools/read/paths.py
View file

@ -97,7 +97,7 @@ class CSiBORGPaths:
fpath = join(self.postdir, "temp")
if not isdir(fpath):
mkdir(fpath)
warn("Created directory `{}`.".format(fpath), UserWarning, stacklevel=1)
warn(f"Created directory `{fpath}`.", UserWarning, stacklevel=1)
return fpath
def mmain_path(self, nsnap, nsim):
@ -118,10 +118,9 @@ class CSiBORGPaths:
fdir = join(self.postdir, "mmain")
if not isdir(fdir):
mkdir(fdir)
warn("Created directory `{}`.".format(fdir), UserWarning, stacklevel=1)
return join(
fdir, "mmain_{}_{}.npz".format(str(nsim).zfill(5), str(nsnap).zfill(5))
)
warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
return join(fdir,
f"mmain_{str(nsim).zfill(5)}_{str(nsnap).zfill(5)}.npz")
def initmatch_path(self, nsim, kind):
"""
@ -143,8 +142,8 @@ class CSiBORGPaths:
fdir = join(self.postdir, "initmatch")
if not isdir(fdir):
mkdir(fdir)
warn("Created directory `{}`.".format(fdir), UserWarning, stacklevel=1)
return join(fdir, "{}_{}.npy".format(kind, str(nsim).zfill(5)))
warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
return join(fdir, f"{kind}_{str(nsim).zfill(5)}.npy")
def split_path(self, nsnap, nsim):
"""
@ -164,10 +163,9 @@ class CSiBORGPaths:
fdir = join(self.postdir, "split")
if not isdir(fdir):
mkdir(fdir)
warn("Created directory `{}`.".format(fdir), UserWarning, stacklevel=1)
warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
return join(
fdir, "clumps_{}_{}.npz".format(str(nsim).zfill(5), str(nsnap).zfill(5))
)
fdir, f"clumps_{str(nsim).zfill(5)}_{str(nsnap).zfill(5)}.npz")
def get_ics(self, tonew):
"""
@ -256,7 +254,7 @@ class CSiBORGPaths:
"""
tonew = nsnap == 1
simpath = self.ic_path(nsim, tonew=tonew)
return join(simpath, "output_{}".format(str(nsnap).zfill(5)))
return join(simpath, f"output_{str(nsnap).zfill(5)}")
def structfit_path(self, nsnap, nsim, kind):
"""
@ -279,9 +277,8 @@ class CSiBORGPaths:
fdir = join(self.postdir, "structfit")
if not isdir(fdir):
mkdir(fdir)
warn("Created directory `{}`.".format(fdir), UserWarning, stacklevel=1)
fname = "{}_out_{}_{}.npy".format(kind, str(nsim).zfill(5), str(nsnap).zfill(5))
warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
fname = f"{kind}_out_{str(nsim).zfill(5)}_{str(nsnap).zfill(5)}.npy"
return join(fdir, fname)
def overlap_path(self, nsim0, nsimx):
@ -302,8 +299,31 @@ class CSiBORGPaths:
fdir = join(self.postdir, "overlap")
if not isdir(fdir):
mkdir(fdir)
warn("Created directory `{}`.".format(fdir), UserWarning, stacklevel=1)
fname = "ovelrap_{}_{}.npz".format(str(nsim0).zfill(5), str(nsimx).zfill(5))
warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
fname = f"overlap_{str(nsim0).zfill(5)}_{str(nsimx).zfill(5)}.npz"
return join(fdir, fname)
def radpos_path(self, nsnap, nsim):
"""
Path to the files containing radial positions of halo particles (with
summed substructure).
Parameters
----------
nsnap : int
Snapshot index.
nsim : int
IC realisation index.
Returns
-------
path : str
"""
fdir = join(self.postdir, "radpos")
if not isdir(fdir):
mkdir(fdir)
warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
fname = f"radpos_{str(nsim).zfill(5)}_{str(nsnap).zfill(5)}.npz"
return join(fdir, fname)
def knnauto_path(self, run, nsim=None):
@ -325,9 +345,9 @@ class CSiBORGPaths:
fdir = join(self.postdir, "knn", "auto")
if not isdir(fdir):
makedirs(fdir)
warn("Created directory `{}`.".format(fdir), UserWarning, stacklevel=1)
warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
if nsim is not None:
return join(fdir, "knncdf_{}_{}.p".format(str(nsim).zfill(5), run))
return join(fdir, f"knncdf_{str(nsim).zfill(5)}_{run}.p")
files = glob(join(fdir, "knncdf*"))
run = "__" + run
@ -352,12 +372,12 @@ class CSiBORGPaths:
fdir = join(self.postdir, "knn", "cross")
if not isdir(fdir):
makedirs(fdir)
warn("Created directory `{}`.".format(fdir), UserWarning, stacklevel=1)
warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
if nsims is not None:
assert isinstance(nsims, (list, tuple)) and len(nsims) == 2
nsim0 = str(nsims[0]).zfill(5)
nsimx = str(nsims[1]).zfill(5)
return join(fdir, "knncdf_{}_{}__{}.p".format(nsim0, nsimx, run))
return join(fdir, f"knncdf_{nsim0}_{nsimx}__{run}.p")
files = glob(join(fdir, "knncdf*"))
run = "__" + run
@ -382,9 +402,9 @@ class CSiBORGPaths:
fdir = join(self.postdir, "tpcf", "auto")
if not isdir(fdir):
makedirs(fdir)
warn("Created directory `{}`.".format(fdir), UserWarning, stacklevel=1)
warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
if nsim is not None:
return join(fdir, "tpcf{}_{}.p".format(str(nsim).zfill(5), run))
return join(fdir, f"tpcf{str(nsim).zfill(5)}_{run}.p")
files = glob(join(fdir, "tpcf*"))
run = "__" + run

2
csiborgtools/read/readsim.py
View file

@ -345,7 +345,7 @@ class ParticleReader:
.format(fname))
data = numpy.genfromtxt(fname)
# How the data is stored in the clump file.
clump_cols = {"index": (0, numpy.int32),
clump_cols = {"index": (0, numpy.int32),
"level": (1, numpy.int32),
"parent": (2, numpy.int32),
"ncell": (3, numpy.float32),

7
csiborgtools/read/utils.py
View file

@ -101,7 +101,8 @@ def cols_to_structured(N, cols):
if not isinstance(cols, list) and all(isinstance(c, tuple) for c in cols):
raise TypeError("`cols` must be a list of tuples.")
dtype = {"names": [col[0] for col in cols], "formats": [col[1] for col in cols]}
dtype = {"names": [col[0] for col in cols],
"formats": [col[1] for col in cols]}
return numpy.full(N, numpy.nan, dtype=dtype)
@ -236,9 +237,7 @@ def array_to_structured(arr, cols):
"""
cols = [cols] if isinstance(cols, str) else cols
if arr.ndim != 2 and arr.shape[1] != len(cols):
raise TypeError(
"`arr` must be a 2-dimensional array of " "shape `(n_samples, n_cols)`."
)
raise TypeError("`arr` must be a 2D array `(n_samples, n_cols)`.")
dtype = {"names": cols, "formats": [arr.dtype] * len(cols)}
out = numpy.full(arr.shape[0], numpy.nan, dtype=dtype)

93
notebooks/fits.ipynb Normal file
View file

@ -0,0 +1,93 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "5a38ed25",
"metadata": {
"ExecuteTime": {
"end_time": "2023-04-12T14:25:46.519408Z",
"start_time": "2023-04-12T14:25:03.003304Z"
},
"scrolled": true
},
"outputs": [],
"source": [
"import sys\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
"\n",
"sys.path.append(\"../\")\n",
"import csiborgtools\n",
"\n",
"%matplotlib widget \n",
"%load_ext autoreload\n",
"%autoreload 2"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "312c96c9",
"metadata": {},
"outputs": [],
"source": [
"paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)\n",
"nsim0 = 7444\n",
"nsimx = 7444 + 24\n",
"nsnap0 = max(paths.get_snapshots(nsim0))\n",
"nsnapx = max(paths.get_snapshots(nsimx))\n",
"overlapper = csiborgtools.match.ParticleOverlap()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "b097637b",
"metadata": {},
"outputs": [],
"source": [
"halo0_archive = np.load(paths.split_path(nsnap0, nsim0))\n",
"halox_archive = np.load(paths.split_path(nsnapx, nsimx))"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "c3cf4c91",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 204873/204873 [16:48<00:00, 203.15it/s]\n",
"100%|██████████| 204960/204960 [16:42<00:00, 204.55it/s]\n"
]
}
],
"source": [
"# delta_bckg = overlapper.make_bckg_delta(halo0_archive, verbose=True)\n",
"# delta_bckg = overlapper.make_bckg_delta(halox_archive, delta=delta_bckg, verbose=True)\n",
"# np.save(\"./bckg_{}_{}.npy\".format(nsim0, nsimx), delta_bckg)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f2986dd2",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "venv_galomatch",
"language": "python",
"name": "venv_galomatch"
}
},
"nbformat": 4,
"nbformat_minor": 5
}

4
scripts/cluster_crosspk.py
View file

@ -63,7 +63,7 @@ fout = join(dumpdir, "crosspk",
jobs = csiborgtools.utils.split_jobs(nsims, nproc)[rank]
for n in jobs:
print("Rank {}@{}: saving {}th delta.".format(rank, datetime.now(), n))
print(f"Rank {rank} at {datetime.now()}: saving {n}th delta.", flush=True)
nsim = ics[n]
particles = reader.read_particle(max(paths.get_snapshots(nsim)), nsim,
["x", "y", "z", "M"], verbose=False)
@ -155,4 +155,4 @@ if rank == 0:
remove(ftemp.format(ic, "delta") + ".npy")
remove(ftemp.format(ic, "lengths") + ".p")
print("All finished!")
print("All finished!")

34
scripts/cluster_knn_auto.py
View file

@ -23,7 +23,7 @@ import numpy
import yaml
from mpi4py import MPI
from sklearn.neighbors import NearestNeighbors
from TaskmasterMPI import master_process, worker_process
from taskmaster import master_process, worker_process
try:
import csiborgtools
@ -98,7 +98,7 @@ def do_auto(run, cat, ic):
"""Calculate the kNN-CDF single catalgoue autocorrelation."""
_config = config.get(run, None)
if _config is None:
warn("No configuration for run {}.".format(run), UserWarning, stacklevel=1)
warn(f"No configuration for run {run}.", UserWarning, stacklevel=1)
return
rvs_gen = csiborgtools.clustering.RVSinsphere(Rmax)
@ -106,16 +106,10 @@ def do_auto(run, cat, ic):
knn = NearestNeighbors()
knn.fit(pos)
rs, cdf = knncdf(
knn,
rvs_gen=rvs_gen,
nneighbours=config["nneighbours"],
rmin=config["rmin"],
rmax=config["rmax"],
nsamples=int(config["nsamples"]),
neval=int(config["neval"]),
batch_size=int(config["batch_size"]),
random_state=config["seed"],
)
knn, rvs_gen=rvs_gen, nneighbours=config["nneighbours"],
rmin=config["rmin"], rmax=config["rmax"],
nsamples=int(config["nsamples"]), neval=int(config["neval"]),
batch_size=int(config["batch_size"]), random_state=config["seed"])
joblib.dump(
{"rs": rs, "cdf": cdf, "ndensity": pos.shape[0] / totvol},
@ -127,7 +121,7 @@ def do_cross_rand(run, cat, ic):
"""Calculate the kNN-CDF cross catalogue random correlation."""
_config = config.get(run, None)
if _config is None:
warn("No configuration for run {}.".format(run), UserWarning, stacklevel=1)
warn(f"No configuration for run {run}.", UserWarning, stacklevel=1)
return
rvs_gen = csiborgtools.clustering.RVSinsphere(Rmax)
@ -140,16 +134,10 @@ def do_cross_rand(run, cat, ic):
knn2.fit(pos2)
rs, cdf0, cdf1, joint_cdf = knncdf.joint(
knn1,
knn2,
rvs_gen=rvs_gen,
nneighbours=int(config["nneighbours"]),
rmin=config["rmin"],
rmax=config["rmax"],
nsamples=int(config["nsamples"]),
neval=int(config["neval"]),
batch_size=int(config["batch_size"]),
random_state=config["seed"],
knn1, knn2, rvs_gen=rvs_gen, nneighbours=int(config["nneighbours"]),
rmin=config["rmin"], rmax=config["rmax"],
nsamples=int(config["nsamples"]), neval=int(config["neval"]),
batch_size=int(config["batch_size"]), random_state=config["seed"],
)
corr = knncdf.joint_to_corr(cdf0, cdf1, joint_cdf)
joblib.dump({"rs": rs, "corr": corr}, paths.knnauto_path(run, ic))

2
scripts/cluster_knn_cross.py
View file

@ -23,7 +23,7 @@ import numpy
import yaml
from mpi4py import MPI
from sklearn.neighbors import NearestNeighbors
from TaskmasterMPI import master_process, worker_process
from taskmaster import master_process, worker_process
try:
import csiborgtools

2
scripts/cluster_tcpf_auto.py
View file

@ -22,7 +22,7 @@ import joblib
import numpy
import yaml
from mpi4py import MPI
from TaskmasterMPI import master_process, worker_process
from taskmaster import master_process, worker_process
try:
import csiborgtools

2
scripts/field_prop.py
View file

@ -124,4 +124,4 @@ if rank == 0:
print("Saving results to `{}`.".format(fperm), flush=True)
with open(fperm, "wb") as f:
numpy.save(f, out)
numpy.save(f, out)

46
scripts/fit_halos.py
View file

@ -77,9 +77,12 @@ def fit_clump(particles, clump_info, box):
for i, v in enumerate(["vx", "vy", "vz"]):
out[v] = numpy.average(obj.vel[:, i], weights=obj["M"])
# Overdensity masses
out["r200c"], out["m200c"] = obj.spherical_overdensity_mass(200, kind="crit")
out["r500c"], out["m500c"] = obj.spherical_overdensity_mass(500, kind="crit")
out["r200m"], out["m200m"] = obj.spherical_overdensity_mass(200, kind="matter")
out["r200c"], out["m200c"] = obj.spherical_overdensity_mass(200,
kind="crit")
out["r500c"], out["m500c"] = obj.spherical_overdensity_mass(500,
kind="crit")
out["r200m"], out["m200m"] = obj.spherical_overdensity_mass(200,
kind="matter")
# NFW fit
if out["npart"] > 10 and numpy.isfinite(out["r200c"]):
Rs, rho0 = nfwpost.fit(obj)
@ -108,8 +111,8 @@ def load_parent_particles(clumpid, particle_archive, clumps_cat):
Load a parent halo's particles.
"""
indxs = clumps_cat["index"][clumps_cat["parent"] == clumpid]
# We first load the particles of each clump belonging to this parent and then
# concatenate them for further analysis.
# We first load the particles of each clump belonging to this parent
# and then concatenate them for further analysis.
clumps = []
for ind in indxs:
parts = load_clump_particles(ind, particle_archive)
@ -118,24 +121,23 @@ def load_parent_particles(clumpid, particle_archive, clumps_cat):
if len(clumps) == 0:
return None
return csiborgtools.match.concatenate_parts(clumps, include_velocities=True)
return csiborgtools.match.concatenate_parts(clumps,
include_velocities=True)
# We now start looping over all simulations
for i, nsim in enumerate(paths.get_ics(tonew=False)):
if rank == 0:
print(
"{}: calculating {}th simulation `{}`.".format(datetime.now(), i, nsim),
flush=True,
)
print(f"{datetime.now()}: calculating {i}th simulation `{nsim}`.",
flush=True)
nsnap = max(paths.get_snapshots(nsim))
box = csiborgtools.read.BoxUnits(nsnap, nsim, paths)
# Archive of clumps, keywords are their clump IDs
particle_archive = numpy.load(paths.split_path(nsnap, nsim))
clumps_cat = csiborgtools.read.ClumpsCatalogue(
nsim, paths, maxdist=None, minmass=None, rawdata=True, load_fitted=False
)
clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, maxdist=None,
minmass=None, rawdata=True,
load_fitted=False)
# We check whether we fit halos or clumps, will be indexing over different
# iterators.
if args.kind == "halos":
@ -171,25 +173,23 @@ for i, nsim in enumerate(paths.get_ics(tonew=False)):
fout = ftemp.format(str(nsim).zfill(5), str(nsnap).zfill(5), rank)
if nproc == 0:
print(
"{}: rank {} saving to `{}`.".format(datetime.now(), rank, fout), flush=True
)
print(f"{datetime.now()}: rank {rank} saving to `{fout}`.", flush=True)
numpy.save(fout, out)
# We saved this CPU's results in a temporary file. Wait now for the other
# CPUs and then collect results from the 0th rank and save them.
comm.Barrier()
if rank == 0:
print(
"{}: collecting results for simulation `{}`.".format(datetime.now(), nsim),
flush=True,
)
print(f"{datetime.now()}: collecting results for simulation `{nsim}`.",
flush=True)
# We write to the output array. Load data from each CPU and append to
# the output array.
out = csiborgtools.read.cols_to_structured(ntasks, cols_collect)
clumpid2outpos = {indx: i for i, indx in enumerate(clumps_cat["index"])}
clumpid2outpos = {indx: i
for i, indx in enumerate(clumps_cat["index"])}
for i in range(nproc):
inp = numpy.load(ftemp.format(str(nsim).zfill(5), str(nsnap).zfill(5), i))
inp = numpy.load(ftemp.format(str(nsim).zfill(5),
str(nsnap).zfill(5), i))
for j, clumpid in enumerate(inp["index"]):
k = clumpid2outpos[clumpid]
for key in inp.dtype.names:
@ -201,7 +201,7 @@ for i, nsim in enumerate(paths.get_ics(tonew=False)):
out = out[ismain]
fout = paths.structfit_path(nsnap, nsim, args.kind)
print("Saving to `{}`.".format(fout), flush=True)
print(f"Saving to `{fout}`.", flush=True)
numpy.save(fout, out)
# We now wait before moving on to another simulation.

140
scripts/fit_profiles.py Normal file
View file

@ -0,0 +1,140 @@
# Copyright (C) 2023 Richard Stiskalek
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""
A script to calculate the particle's separation from the CM and save it.
Currently MPI is not supported.
"""
from argparse import ArgumentParser
from datetime import datetime
from gc import collect
import numpy
from mpi4py import MPI
from tqdm import trange
try:
import csiborgtools
except ModuleNotFoundError:
import sys
sys.path.append("../")
import csiborgtools
parser = ArgumentParser()
parser.add_argument("--ics", type=int, nargs="+", default=None,
help="IC realisatiosn. If `-1` processes all simulations.")
args = parser.parse_args()
# Get MPI things
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nproc = comm.Get_size()
if nproc > 1:
raise NotImplementedError("MPI is not implemented implemented yet.")
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
partreader = csiborgtools.read.ParticleReader(paths)
cols_collect = [("r", numpy.float32), ("M", numpy.float32)]
if args.ics is None or args.ics == -1:
nsims = paths.get_ics(tonew=False)
else:
nsims = args.ics
def load_clump_particles(clumpid, particle_archive):
"""
Load a clump's particles from the particle archive. If it is not there, i.e
clump has no associated particles, return `None`.
"""
try:
part = particle_archive[str(clumpid)]
except KeyError:
part = None
return part
def load_parent_particles(clumpid, particle_archive, clumps_cat):
"""
Load a parent halo's particles.
"""
indxs = clumps_cat["index"][clumps_cat["parent"] == clumpid]
# We first load the particles of each clump belonging to this
# parent and then concatenate them for further analysis.
clumps = []
for ind in indxs:
parts = load_clump_particles(ind, particle_archive)
if parts is not None:
clumps.append(parts)
if len(clumps) == 0:
return None
return csiborgtools.match.concatenate_parts(clumps)
# We loop over simulations. Here later optionlaly add MPI.
for i, nsim in enumerate(nsims):
if rank == 0:
now = datetime.now()
print(f"{now}: calculating {i}th simulation `{nsim}`.", flush=True)
nsnap = max(paths.get_snapshots(nsim))
box = csiborgtools.read.BoxUnits(nsnap, nsim, paths)
# Archive of clumps, keywords are their clump IDs
particle_archive = numpy.load(paths.split_path(nsnap, nsim))
clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, maxdist=None,
minmass=None, rawdata=True,
load_fitted=False)
ismain = clumps_cat.ismain
ntasks = len(clumps_cat)
# We loop over halos and add ther particle positions to this dictionary,
# which we will later save as an archive.
out = {}
for j in trange(ntasks) if nproc == 1 else range(ntasks):
# If we are fitting halos and this clump is not a main, then continue.
if not ismain[j]:
continue
clumpid = clumps_cat["index"][j]
parts = load_parent_particles(clumpid, particle_archive, clumps_cat)
# If we have no particles, then do not save anything.
if parts is None:
continue
obj = csiborgtools.fits.Clump(parts, clumps_cat[j], box)
r200m, m200m = obj.spherical_overdensity_mass(200, npart_min=10,
kind="matter")
r = obj.r()
mask = r <= r200m
_out = csiborgtools.read.cols_to_structured(numpy.sum(mask),
cols_collect)
_out["r"] = r[mask]
_out["M"] = obj["M"][mask]
out[str(clumps_cat["index"][i])] = _out
# Finished, so we save everything.
fout = paths.radpos_path(nsnap, nsim)
now = datetime.now()
print(f"{now}: saving radial profiles for simulation {nsim} to `{fout}`",
flush=True)
numpy.savez(fout, **out)
# Clean up the memory just to be sure.
del out
collect()

73
scripts/match_singlematch.py
View file

@ -33,66 +33,55 @@ parser.add_argument("--nsim0", type=int)
parser.add_argument("--nsimx", type=int)
parser.add_argument("--nmult", type=float)
parser.add_argument("--sigma", type=float)
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)), default=False)
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
default=False)
args = parser.parse_args()
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
smooth_kwargs = {"sigma": args.sigma, "mode": "constant", "cval": 0.0}
overlapper = csiborgtools.match.ParticleOverlap()
matcher = csiborgtools.match.RealisationsMatcher()
# Load the raw catalogues (i.e. no selection) including the initial CM positions
# and the particle archives.
cat0 = csiborgtools.read.HaloCatalogue(
args.nsim0, paths, load_initial=True, rawdata=True
)
catx = csiborgtools.read.HaloCatalogue(
args.nsimx, paths, load_initial=True, rawdata=True
)
# Load the raw catalogues (i.e. no selection) including the initial CM
# positions and the particle archives.
cat0 = csiborgtools.read.HaloCatalogue(args.nsim0, paths, load_initial=True,
rawdata=True)
catx = csiborgtools.read.HaloCatalogue(args.nsimx, paths, load_initial=True,
rawdata=True)
halos0_archive = paths.initmatch_path(args.nsim0, "particles")
halosx_archive = paths.initmatch_path(args.nsimx, "particles")
# We generate the background density fields. Loads halos's particles one by one
# from the archive, concatenates them and calculates the NGP density field.
args.verbose and print(
"{}: generating the background density fields.".format(datetime.now()), flush=True
)
if args.verbose:
print(f"{datetime.now()}: generating the background density fields.",
flush=True)
delta_bckg = overlapper.make_bckg_delta(halos0_archive, verbose=args.verbose)
delta_bckg = overlapper.make_bckg_delta(
halosx_archive, delta=delta_bckg, verbose=args.verbose
)
delta_bckg = overlapper.make_bckg_delta(halosx_archive, delta=delta_bckg,
verbose=args.verbose)
# We calculate the overlap between the NGP fields.
args.verbose and print(
"{}: crossing the simulations.".format(datetime.now()), flush=True
)
match_indxs, ngp_overlap = matcher.cross(
cat0, catx, halos0_archive, halosx_archive, delta_bckg
)
if args.verbose:
print(f"{datetime.now()}: crossing the simulations.", flush=True)
match_indxs, ngp_overlap = matcher.cross(cat0, catx, halos0_archive,
halosx_archive, delta_bckg)
# We now smoothen up the background density field for the smoothed overlap calculation.
args.verbose and print(
"{}: smoothing the background field.".format(datetime.now()), flush=True
)
# We now smoothen up the background density field for the smoothed overlap
# calculation.
if args.verbose:
print(f"{datetime.now()}: smoothing the background field.", flush=True)
gaussian_filter(delta_bckg, output=delta_bckg, **smooth_kwargs)
# We calculate the smoothed overlap for the pairs whose NGP overlap is > 0.
args.verbose and print(
"{}: calculating smoothed overlaps.".format(datetime.now()), flush=True
)
smoothed_overlap = matcher.smoothed_cross(
cat0, catx, halos0_archive, halosx_archive, delta_bckg, match_indxs, smooth_kwargs
)
if args.verbose:
print(f"{datetime.now()}: calculating smoothed overlaps.", flush=True)
smoothed_overlap = matcher.smoothed_cross(cat0, catx, halos0_archive,
halosx_archive, delta_bckg,
match_indxs, smooth_kwargs)
# We save the results at long last.
fout = paths.overlap_path(args.nsim0, args.nsimx)
args.verbose and print(
"{}: saving results to `{}`.".format(datetime.now(), fout), flush=True
)
numpy.savez(
fout,
match_indxs=match_indxs,
ngp_overlap=ngp_overlap,
smoothed_overlap=smoothed_overlap,
sigma=args.sigma,
)
print("{}: all finished.".format(datetime.now()), flush=True)
if args.verbose:
print(f"{datetime.now()}: saving results to `{fout}`.", flush=True)
numpy.savez(fout, match_indxs=match_indxs, ngp_overlap=ngp_overlap,
smoothed_overlap=smoothed_overlap, sigma=args.sigma)
print(f"{datetime.now()}: all finished.", flush=True)

53
scripts/pre_initmatch.py
View file

@ -13,8 +13,9 @@
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""
Script to calculate the particle centre of mass and Lagrangian patch size in the initial
snapshot. Optinally dumps the particle files, however this requires a lot of memory.
Script to calculate the particle centre of mass and Lagrangian patch size in
the initial snapshot. Optinally dumps the particle files, however this requires
a lot of memory.
"""
from argparse import ArgumentParser
from datetime import datetime
@ -54,15 +55,14 @@ ftemp = join(paths.temp_dumpdir, "initmatch_{}_{}_{}.npy")
# initial snapshot and dumping them.
for i, nsim in enumerate(paths.get_ics(tonew=True)):
if rank == 0:
print("{}: reading simulation {}.".format(datetime.now(), nsim), flush=True)
print(f"{datetime.now()}: reading simulation {nsim}.", flush=True)
nsnap = max(paths.get_snapshots(nsim))
# We first load particles in the initial and final snapshots and sort them
# by their particle IDs so that we can match them by array position.
# `clump_ids` are the clump IDs of particles.
part0 = partreader.read_particle(
1, nsim, ["x", "y", "z", "M", "ID"], verbose=verbose
)
part0 = partreader.read_particle(1, nsim, ["x", "y", "z", "M", "ID"],
verbose=verbose)
part0 = part0[numpy.argsort(part0["ID"])]
pid = partreader.read_particle(nsnap, nsim, ["ID"], verbose=verbose)["ID"]
@ -85,17 +85,14 @@ for i, nsim in enumerate(paths.get_ics(tonew=True)):
# size and optionally the initial snapshot particles belonging to this
# parent halo. Dumping the particles will take majority of time.
if rank == 0:
print(
"{}: calculating {}th simulation {}.".format(datetime.now(), i, nsim),
flush=True,
)
print(f"{datetime.now()}: calculating {i}th simulation {nsim}.",
flush=True)
# We load up the clump catalogue which contains information about the
# ultimate parent halos of each clump. We will loop only over the clump
# IDs of ultimate parent halos and add their substructure particles and at
# the end save these.
cat = csiborgtools.read.ClumpsCatalogue(
nsim, paths, load_fitted=False, rawdata=True
)
cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, load_fitted=False,
rawdata=True)
parent_ids = cat["index"][cat.ismain][:500]
jobs = csiborgtools.fits.split_jobs(parent_ids.size, nproc)[rank]
for i in tqdm(jobs) if verbose else jobs:
@ -106,7 +103,8 @@ for i, nsim in enumerate(paths.get_ics(tonew=True)):
mmain_particles = part0[mmain_mask]
raddist, cmpos = csiborgtools.match.dist_centmass(mmain_particles)
patchsize = csiborgtools.match.dist_percentile(raddist, [99], distmax=0.075)
patchsize = csiborgtools.match.dist_percentile(raddist, [99],
distmax=0.075)
with open(ftemp.format(nsim, clid, "fit"), "wb") as f:
numpy.savez(f, cmpos=cmpos, patchsize=patchsize)
@ -118,15 +116,13 @@ for i, nsim in enumerate(paths.get_ics(tonew=True)):
del part0, clump_ids
collect()
# We now wait for all processes and then use the 0th process to collect the results.
# We first collect just the Lagrangian patch size information.
# We now wait for all processes and then use the 0th process to collect
# the results. We first collect just the Lagrangian patch size information.
comm.Barrier()
if rank == 0:
print("{}: collecting fits...".format(datetime.now()), flush=True)
dtype = {
"names": ["index", "x", "y", "z", "lagpatch"],
"formats": [numpy.int32] + [numpy.float32] * 4,
}
print(f"{datetime.now()}: collecting fits...", flush=True)
dtype = {"names": ["index", "x", "y", "z", "lagpatch"],
"formats": [numpy.int32] + [numpy.float32] * 4}
out = numpy.full(parent_ids.size, numpy.nan, dtype=dtype)
for i, clid in enumerate(parent_ids):
fpath = ftemp.format(nsim, clid, "fit")
@ -140,14 +136,15 @@ for i, nsim in enumerate(paths.get_ics(tonew=True)):
remove(fpath)
fout = paths.initmatch_path(nsim, "fit")
print("{}: dumping fits to .. `{}`.".format(datetime.now(), fout), flush=True)
print(f"{datetime.now()}: dumping fits to .. `{fout}`.", flush=True)
with open(fout, "wb") as f:
numpy.save(f, out)
# We now optionally collect the individual clumps and store them in an archive,
# which has the benefit of being a single file that can be easily read in.
# We now optionally collect the individual clumps and store them in an
# archive, which has the benefit of being a single file that can be
# easily read in.
if args.dump:
print("{}: collecting particles...".format(datetime.now()), flush=True)
print(f"{datetime.now()}: collecting particles...", flush=True)
out = {}
for clid in parent_ids:
fpath = ftemp.format(nsim, clid, "particles")
@ -155,10 +152,8 @@ for i, nsim in enumerate(paths.get_ics(tonew=True)):
out.update({str(clid): numpy.load(f)})
fout = paths.initmatch_path(nsim, "particles")
print(
"{}: dumping particles to .. `{}`.".format(datetime.now(), fout),
flush=True,
)
print(f"{datetime.now()}: dumping particles to .. `{fout}`.",
flush=True)
with open(fout, "wb") as f:
numpy.savez(f, **out)

6
scripts/pre_mmain.py
View file

@ -19,7 +19,7 @@ from datetime import datetime
import numpy
from mpi4py import MPI
from TaskmasterMPI import master_process, worker_process
from taskmaster import master_process, worker_process
try:
import csiborgtools
@ -58,7 +58,7 @@ if nproc > 1:
else:
tasks = paths.get_ics(tonew=False)
for task in tasks:
print("{}: completing task `{}`.".format(datetime.now(), task))
print(f"{datetime.now()}: completing task `{task}`.", flush=True)
do_mmain(task)
comm.Barrier()
comm.Barrier()

2
scripts/pre_splithalos.py
View file

@ -24,7 +24,7 @@ from os.path import join
import numpy
from mpi4py import MPI
from TaskmasterMPI import master_process, worker_process
from taskmaster import master_process, worker_process
from tqdm import tqdm
try:

4
scripts/utils.py
View file

@ -30,12 +30,12 @@ dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
# Some chosen clusters
_coma = {"RA": (12 + 59/60 + 48.7 / 60**2) * 15,
_coma = {"RA": (12 + 59 / 60 + 48.7 / 60**2) * 15,
"DEC": 27 + 58 / 60 + 50 / 60**2,
"COMDIST": 102.975}
_virgo = {"RA": (12 + 27 / 60) * 15,
"DEC": 12 + 43/60,
"DEC": 12 + 43 / 60,
"COMDIST": 16.5}
specific_clusters = {"Coma": _coma, "Virgo": _virgo}