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Overlap reader thresholds (#31)

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* Improve data

* Add comment

* Update how KNN is called

* Bring back indices

* New function output

* return catx["index"]

* Remove unnecessary arguments

* Remove useless arguments

* Rename output

* thin up catalogues

* Add thresholding

* Update README
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Richard Stiskalek 2023-03-15 20:55:50 +00:00 committed by GitHub
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9
README.md
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@ -1,21 +1,14 @@
# CSiBORG tools # CSiBORGTools
## CSiBORG Matching
### TODO
- [ ] Modify the call to tN
### Questions ### Questions
- What scaling of the search region? No reason for it to be a multiple of $R_{200c}$.
- How well can observed clusters be matched to CSiBORG? Do their masses agree? - How well can observed clusters be matched to CSiBORG? Do their masses agree?
- Is the number of clusters in CSiBORG consistent? - Is the number of clusters in CSiBORG consistent?
## CSiBORG Galaxy Environmental Dependence ## CSiBORG Galaxy Environmental Dependence
### TODO ### TODO
- [ ] Add gradient and Hessian of the overdensity field. - [ ] Add gradient and Hessian of the overdensity field.
- [x] Write a script to smoothen an overdensity field, calculate the derived fields and evaluate them at the galaxy positions.
### Questions ### Questions

25
csiborgtools/match/match.py
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@ -215,7 +215,7 @@ class RealisationsMatcher:
mapping[ind2] = ind1 mapping[ind2] = ind1
return mapping return mapping
def cross(self, nsim0, nsimx, cat0, catx, overlap=False, verbose=True): def cross(self, cat0, catx, overlap=False, verbose=True):
r""" r"""
Find all neighbours whose CM separation is less than `nmult` times the Find all neighbours whose CM separation is less than `nmult` times the
sum of their initial Lagrangian patch sizes. Enforces that the sum of their initial Lagrangian patch sizes. Enforces that the
@ -223,10 +223,9 @@ class RealisationsMatcher:
Parameters Parameters
---------- ----------
nsim0, nsimx : int
The reference and cross simulation IDs.
cat0, catx: :py:class:`csiborgtools.read.HaloCatalogue` cat0, catx: :py:class:`csiborgtools.read.HaloCatalogue`
Halo catalogues corresponding to `nsim0` and `nsimx`, respectively. Halo catalogues corresponding to the reference and cross
simulations.
overlap : bool, optional overlap : bool, optional
whether to calculate overlap between clumps in the initial whether to calculate overlap between clumps in the initial
snapshot. by default `false`. this operation is slow. snapshot. by default `false`. this operation is slow.
@ -235,22 +234,22 @@ class RealisationsMatcher:
Returns Returns
------- -------
indxs : 1-dimensional array of shape `(nhalos, )` ref_indxs : 1-dimensional array
Indices of halos in the reference catalogue. Indices of halos in the reference catalogue.
cross_indxs : 1-dimensional array
Indices of halos in the cross catalogue.
match_indxs : 1-dimensional array of arrays match_indxs : 1-dimensional array of arrays
Indices of halo counterparts in the cross catalogue. Indices of halo counterparts in the cross catalogue.
overlaps : 1-dimensional array of arrays overlaps : 1-dimensional array of arrays
Overlaps with the cross catalogue. Overlaps with the cross catalogue.
""" """
assert (nsim0 == cat0.paths.n_sim) & (nsimx == catx.paths.n_sim)
# Query the KNN # Query the KNN
if verbose: if verbose:
print("{}: querying the KNN.".format(datetime.now()), flush=True) print("{}: querying the KNN.".format(datetime.now()), flush=True)
match_indxs = radius_neighbours( match_indxs = radius_neighbours(
catx.knn0, cat0.positions0, radiusX=cat0["lagpatch"], catx.knn(select_initial=True), cat0.positions0,
radiusKNN=catx["lagpatch"], nmult=self.nmult, enforce_in32=True, radiusX=cat0["lagpatch"], radiusKNN=catx["lagpatch"],
verbose=verbose) nmult=self.nmult, enforce_in32=True, verbose=verbose)
# Remove neighbours whose mass is too large/small # Remove neighbours whose mass is too large/small
if self.dlogmass is not None: if self.dlogmass is not None:
@ -265,9 +264,9 @@ class RealisationsMatcher:
if overlap: if overlap:
if verbose: if verbose:
print("Loading the clump particles", flush=True) print("Loading the clump particles", flush=True)
with open(cat0.paths.clump0_path(nsim0), "rb") as f: with open(cat0.paths.clump0_path(cat0.n_sim), "rb") as f:
clumps0 = numpy.load(f, allow_pickle=True) clumps0 = numpy.load(f, allow_pickle=True)
with open(catx.paths.clump0_path(nsimx), 'rb') as f: with open(catx.paths.clump0_path(catx.n_sim), 'rb') as f:
clumpsx = numpy.load(f, allow_pickle=True) clumpsx = numpy.load(f, allow_pickle=True)
# Convert 3D positions to particle IDs # Convert 3D positions to particle IDs
@ -320,7 +319,7 @@ class RealisationsMatcher:
match_indxs[k] = match_indxs[k][mask] match_indxs[k] = match_indxs[k][mask]
cross[k] = cross[k][mask] cross[k] = cross[k][mask]
return cat0["index"], match_indxs, cross return cat0["index"], catx["index"], match_indxs, cross
############################################################################### ###############################################################################

117
csiborgtools/read/make_cat.py
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@ -31,38 +31,24 @@ class HaloCatalogue:
---------- ----------
paths : py:class:`csiborgtools.read.CSiBORGPaths` paths : py:class:`csiborgtools.read.CSiBORGPaths`
CSiBORG paths-handling object with set `n_sim` and `n_snap`. CSiBORG paths-handling object with set `n_sim` and `n_snap`.
min_m500 : float, optional min_mass : float, optional
The minimum :math:`M_{rm 500c} / M_\odot` mass. By default no The minimum :math:`M_{rm tot} / M_\odot` mass. By default no threshold.
threshold.
max_dist : float, optional max_dist : float, optional
The maximum comoving distance of a halo. By default no upper limit. The maximum comoving distance of a halo. By default no upper limit.
""" """
_box = None _box = None
_paths = None _paths = None
_data = None _data = None
_knn = None _selmask = None
_knn0 = None
_positions = None
_positions0 = None
def __init__(self, nsim, min_m500=None, max_dist=None): def __init__(self, nsim, min_mass=None, max_dist=None):
# Set up paths # Set up paths
paths = CSiBORGPaths(n_sim=nsim) paths = CSiBORGPaths(n_sim=nsim)
paths.n_snap = paths.get_maximum_snapshot() paths.n_snap = paths.get_maximum_snapshot()
self._paths = paths self._paths = paths
self._box = BoxUnits(paths) self._box = BoxUnits(paths)
min_m500 = 0 if min_m500 is None else min_m500
max_dist = numpy.infty if max_dist is None else max_dist
self._paths = paths self._paths = paths
self._set_data(min_m500, max_dist) self._set_data(min_mass, max_dist)
# Initialise the KNN at z = 0 and at z = 70
knn = NearestNeighbors()
knn.fit(self.positions)
self._knn = knn
knn0 = NearestNeighbors()
knn0.fit(self.positions0)
self._knn0 = knn0
@property @property
def data(self): def data(self):
@ -88,17 +74,6 @@ class HaloCatalogue:
""" """
return self._box return self._box
@property
def cosmo(self):
"""
The box cosmology.
Returns
-------
cosmo : `astropy` cosmology object
"""
return self.box.cosmo
@property @property
def paths(self): def paths(self):
""" """
@ -132,29 +107,23 @@ class HaloCatalogue:
""" """
return self.paths.n_sim return self.paths.n_sim
@property def knn(self, select_initial):
def knn(self):
""" """
The final snapshot k-nearest neighbour object. The final snapshot k-nearest neighbour object.
Returns Parameters
------- ----------
knn : :py:class:`sklearn.neighbors.NearestNeighbors` select_initial : bool
""" Whether to define the KNN on the initial or final snapshot.
return self._knn
@property
def knn0(self):
"""
The initial snapshot k-nearest neighbour object.
Returns Returns
------- -------
knn : :py:class:`sklearn.neighbors.NearestNeighbors` knn : :py:class:`sklearn.neighbors.NearestNeighbors`
""" """
return self._knn0 knn = NearestNeighbors()
return knn.fit(self.positions0 if select_initial else self.positions)
def _set_data(self, min_m500, max_dist): def _set_data(self, min_mass, max_dist):
""" """
Loads the data, merges with mmain, does various coordinate transforms. Loads the data, merges with mmain, does various coordinate transforms.
""" """
@ -168,7 +137,7 @@ class HaloCatalogue:
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. Do not change! Hardcoded
data = data[(data["npart"] > 100) & numpy.isfinite(data["m200"])] data = data[(data["npart"] > 100) & numpy.isfinite(data["m200"])]
# Now also load the initial positions # Now also load the initial positions
@ -177,16 +146,15 @@ class HaloCatalogue:
data = self.merge_initmatch_to_clumps(data, initcm) data = self.merge_initmatch_to_clumps(data, initcm)
flip_cols(data, "x0", "z0") flip_cols(data, "x0", "z0")
# Calculate redshift # # Calculate redshift
pos = [data["peak_{}".format(p)] - 0.5 for p in ("x", "y", "z")] # pos = [data["peak_{}".format(p)] - 0.5 for p in ("x", "y", "z")]
vel = [data["v{}".format(p)] for p in ("x", "y", "z")] # vel = [data["v{}".format(p)] for p in ("x", "y", "z")]
zpec = self.box.box2pecredshift(*vel, *pos) # zpec = self.box.box2pecredshift(*vel, *pos)
zobs = self.box.box2obsredshift(*vel, *pos) # zobs = self.box.box2obsredshift(*vel, *pos)
zcosmo = self.box.box2cosmoredshift( # zcosmo = self.box.box2cosmoredshift(
sum(pos[i]**2 for i in range(3))**0.5) # sum(pos[i]**2 for i in range(3))**0.5)
# data = add_columns(data, [zpec, zobs, zcosmo],
data = add_columns(data, [zpec, zobs, zcosmo], # ["zpec", "zobs", "zcosmo"])
["zpec", "zobs", "zcosmo"])
# Unit conversion # Unit conversion
convert_cols = ["m200", "m500", "totpartmass", "mass_mmain", convert_cols = ["m200", "m500", "totpartmass", "mass_mmain",
@ -194,29 +162,15 @@ class HaloCatalogue:
"peak_x", "peak_y", "peak_z"] "peak_x", "peak_y", "peak_z"]
data = self.box.convert_from_boxunits(data, convert_cols) data = self.box.convert_from_boxunits(data, convert_cols)
# Cut on mass. Note that this is in Msun
data = data[data["m500"] > min_m500]
# Now calculate spherical coordinates # Now calculate spherical coordinates
d, ra, dec = cartesian_to_radec( d, ra, dec = cartesian_to_radec(
data["peak_x"], data["peak_y"], data["peak_z"]) data["peak_x"], data["peak_y"], data["peak_z"])
data = add_columns(data, [d, ra, dec], ["dist", "ra", "dec"]) data = add_columns(data, [d, ra, dec], ["dist", "ra", "dec"])
# Cut on separation
data = data[data["dist"] < max_dist]
# Pre-allocate the positions arrays
self._positions = numpy.vstack(
[data["peak_{}".format(p)] for p in ("x", "y", "z")]).T
self._positions = self._positions.astype(numpy.float32)
# And do the unit transform # And do the unit transform
if initcm is not None: if initcm is not None:
data = self.box.convert_from_boxunits( data = self.box.convert_from_boxunits(
data, ["x0", "y0", "z0", "lagpatch"]) data, ["x0", "y0", "z0", "lagpatch"])
self._positions0 = numpy.vstack(
[data["{}0".format(p)] for p in ("x", "y", "z")]).T
self._positions0 = self._positions0.astype(numpy.float32)
# Convert all that is not an integer to float32 # Convert all that is not an integer to float32
names = list(data.dtype.names) names = list(data.dtype.names)
@ -227,9 +181,13 @@ class HaloCatalogue:
else: else:
formats.append(numpy.float32) formats.append(numpy.float32)
dtype = numpy.dtype({"names": names, "formats": formats}) dtype = numpy.dtype({"names": names, "formats": formats})
data = data.astype(dtype)
self._data = data # Apply cuts on distance and min500 if any
data = data[data["dist"] < max_dist] if max_dist is not None else data
data = (data[data["totpartmass"] > min_mass]
if min_mass is not None else data)
self._data = data.astype(dtype)
def merge_mmain_to_clumps(self, clumps, mmain): def merge_mmain_to_clumps(self, clumps, mmain):
""" """
@ -288,8 +246,8 @@ class HaloCatalogue:
@property @property
def positions(self): def positions(self):
""" r"""
3D positions of halos in comoving units of Mpc. 3D positions of halos in :math:`\mathrm{cMpc}`.
Returns Returns
------- -------
@ -297,12 +255,13 @@ class HaloCatalogue:
Array of shape `(n_halos, 3)`, where the latter axis represents Array of shape `(n_halos, 3)`, where the latter axis represents
`x`, `y` and `z`. `x`, `y` and `z`.
""" """
return self._positions return numpy.vstack(
[self._data["peak_{}".format(p)] for p in ("x", "y", "z")]).T
@property @property
def positions0(self): def positions0(self):
r""" r"""
3D positions of halos in the initial snapshot in comoving units of Mpc. 3D positions of halos in the initial snapshot in :math:`\mathrm{cMpc}`.
Returns Returns
------- -------
@ -310,9 +269,11 @@ class HaloCatalogue:
Array of shape `(n_halos, 3)`, where the latter axis represents Array of shape `(n_halos, 3)`, where the latter axis represents
`x`, `y` and `z`. `x`, `y` and `z`.
""" """
if self._positions0 is None: try:
return numpy.vstack(
[self._data["{}".format(p)] for p in ("x0", "y0", "z0")]).T
except KeyError:
raise RuntimeError("Initial positions are not set!") raise RuntimeError("Initial positions are not set!")
return self._positions0
@property @property
def velocities(self): def velocities(self):
@ -365,7 +326,7 @@ class HaloCatalogue:
""" """
if not (X.ndim == 2 and X.shape[1] == 3): if not (X.ndim == 2 and X.shape[1] == 3):
raise TypeError("`X` must be an array of shape `(n_samples, 3)`.") raise TypeError("`X` must be an array of shape `(n_samples, 3)`.")
knn = self.knn0 if select_initial else self.knn # Pick the right KNN knn = self.knn(select_initial)
return knn.radius_neighbors(X, radius, sort_results=True) return knn.radius_neighbors(X, radius, sort_results=True)
@property @property

227
csiborgtools/read/summaries.py
View File

@ -17,9 +17,8 @@ Tools for summarising various results.
""" """
import numpy import numpy
import joblib import joblib
from os.path import isfile from os.path import (join, isfile)
from tqdm import tqdm from tqdm import tqdm
from .make_cat import HaloCatalogue
class PKReader: class PKReader:
@ -171,73 +170,64 @@ class PKReader:
class OverlapReader: class OverlapReader:
""" r"""
A shortcut object for reading in the results of matching two simulations. A shortcut object for reading in the results of matching two simulations.
Parameters Parameters
---------- ----------
nsim0 : int cat0, catx: :py:class:`csiborgtools.read.HaloCatalogue`
The reference simulation ID. Halo catalogues corresponding to the reference and cross
nsimx : int simulations.
The cross simulation ID.
fskel : str, optional fskel : str, optional
Path to the overlap. By default `None`, i.e. Path to the overlap. By default `None`, i.e.
`/mnt/extraspace/rstiskalek/csiborg/overlap/cross_{}_{}.npz`. `/mnt/extraspace/rstiskalek/csiborg/overlap/cross_{}_{}.npz`.
min_mass : float, optional
The minimum :math:`M_{\rm tot} / M_\odot` mass. By default no
threshold.
max_dist : float, optional
The maximum comoving distance of a halo. By default no upper limit.
""" """
def __init__(self, nsim0, nsimx, fskel=None): _cat0 = None
if fskel is None: _catx = None
fskel = "/mnt/extraspace/rstiskalek/csiborg/overlap/" _refmask = None
fskel += "cross_{}_{}.npz"
fpath = fskel.format(nsim0, nsimx) def __init__(self, cat0, catx, fskel=None, min_mass=None, max_dist=None):
fpath_inv = fskel.format(nsimx, nsim0) self._cat0 = cat0
is_inverted = False self._catx = catx
if fskel is None:
fskel = join("/mnt/extraspace/rstiskalek/csiborg/overlap",
"cross_{}_{}.npz")
fpath = fskel.format(cat0.n_sim, catx.n_sim)
fpath_inv = fskel.format(catx.n_sim, cat0.n_sim)
if isfile(fpath): if isfile(fpath):
pass is_inverted = False
elif isfile(fpath_inv): elif isfile(fpath_inv):
fpath = fpath_inv fpath = fpath_inv
is_inverted = True is_inverted = True
nsim0, nsimx = nsimx, nsim0
else: else:
raise FileNotFoundError( raise FileNotFoundError(
"No overlap file found for combination `{}` and `{}`." "No overlap file found for combination `{}` and `{}`."
.format(nsim0, nsimx)) .format(cat0.n_sim, catx.n_sim))
# We can set catalogues already now even if inverted # We can set catalogues already now even if inverted
self._set_cats(nsim0, nsimx)
print(is_inverted)
data = numpy.load(fpath, allow_pickle=True) data = numpy.load(fpath, allow_pickle=True)
if is_inverted: if is_inverted:
inv_match_indxs, inv_overlap = self._invert_match( inv_match_indxs, inv_overlap = self._invert_match(
data["match_indxs"], data["cross"], self.cat0["index"].size,) data["match_indxs"], data["overlap"],
# Overwrite the original file and store as a dictionary data["cross_indxs"].size,)
data = {"indxs": self.cat0["index"], self._data = {
"match_indxs": inv_match_indxs, "index": data["cross_indxs"],
"cross": inv_overlap, "match_indxs": inv_match_indxs,
} "overlap": inv_overlap}
self._data = data else:
self._data = {
"index": data["ref_indxs"],
"match_indxs": data["match_indxs"],
"overlap": data["overlap"]}
@property self._make_refmask(min_mass, max_dist)
def nsim0(self):
"""
The reference simulation ID.
Returns
-------
nsim0 : int
"""
return self._nsim0
@property
def nsimx(self):
"""
The cross simulation ID.
Returns
-------
nsimx : int
"""
return self._nsimx
@property @property
def cat0(self): def cat0(self):
@ -261,24 +251,6 @@ class OverlapReader:
""" """
return self._catx return self._catx
def _set_cats(self, nsim0, nsimx):
"""
Set the simulation IDs and catalogues.
Parameters
----------
nsim0, nsimx : int
The reference and cross simulation IDs.
Returns
-------
None
"""
self._nsim0 = nsim0
self._nsimx = nsimx
self._cat0 = HaloCatalogue(nsim0)
self._catx = HaloCatalogue(nsimx)
@staticmethod @staticmethod
def _invert_match(match_indxs, overlap, cross_size): def _invert_match(match_indxs, overlap, cross_size):
""" """
@ -304,8 +276,8 @@ class OverlapReader:
The corresponding overlaps to `inv_match_indxs`. The corresponding overlaps to `inv_match_indxs`.
""" """
# 1. Invert the match. Each reference halo has a list of counterparts # 1. Invert the match. Each reference halo has a list of counterparts
# so loop over those to each counterpart assign a reference halo. # so loop over those to each counterpart assign a reference halo
# Add the same time also add the overlaps # and at the same time also add the overlaps
inv_match_indxs = [[] for __ in range(cross_size)] inv_match_indxs = [[] for __ in range(cross_size)]
inv_overlap = [[] for __ in range(cross_size)] inv_overlap = [[] for __ in range(cross_size)]
for ref_id in range(match_indxs.size): for ref_id in range(match_indxs.size):
@ -330,6 +302,35 @@ class OverlapReader:
return inv_match_indxs, inv_overlap return inv_match_indxs, inv_overlap
def _make_refmask(self, min_mass, max_dist):
r"""
Create a mask for the reference catalogue that accounts for the mass
and distance cuts. Note that *no* masking is applied to the cross
catalogue.
Parameters
----------
min_mass : float, optional
The minimum :math:`M_{rm tot} / M_\odot` mass.
max_dist : float, optional
The maximum comoving distance of a halo.
Returns
-------
None
"""
# Enforce a cut on the reference catalogue
min_mass = 0 if min_mass is None else min_mass
max_dist = numpy.infty if max_dist is None else max_dist
m = ((self.cat0["totpartmass"] > min_mass)
& (self.cat0["dist"] < max_dist))
# Now remove indices that are below this cut
self._data["index"] = self._data["index"][m]
self._data["match_indxs"] = self._data["match_indxs"][m]
self._data["overlap"] = self._data["overlap"][m]
self._refmask = m
@property @property
def indxs(self): def indxs(self):
""" """
@ -339,7 +340,7 @@ class OverlapReader:
------- -------
indxs : 1-dimensional array indxs : 1-dimensional array
""" """
return self._data["indxs"] return self._data["index"]
@property @property
def match_indxs(self): def match_indxs(self):
@ -361,47 +362,73 @@ class OverlapReader:
------- -------
overlap : array of 1-dimensional arrays of shape `(nhalos, )` overlap : array of 1-dimensional arrays of shape `(nhalos, )`
""" """
return self._data["cross"] return self._data["overlap"]
def dist(self, in_initial, norm=None): @property
def refmask(self):
""" """
Final snapshot pair distances. Mask of the reference catalogue to match the calculated overlaps.
Returns
-------
refmask : 1-dimensional boolean array
"""
return self._refmask
def dist(self, in_initial, norm_kind=None):
"""
Pair distances of matched halos between the reference and cross
simulations.
Parameters Parameters
---------- ----------
in_initial : bool in_initial : bool
Whether to calculate separation in the initial or final snapshot. Whether to calculate separation in the initial or final snapshot.
norm_kind : str, optional
The kind of normalisation to apply to the distances. Can be `r200`,
`ref_patch` or `sum_patch`.
Returns Returns
------- -------
dist : array of 1-dimensional arrays of shape `(nhalos, )` dist : array of 1-dimensional arrays of shape `(nhalos, )`
""" """
assert norm is None or norm in ("r200", "ref_patch", "sum_patch") assert (norm_kind is None
# Positions either in the initial or final snapshot or norm_kind in ("r200", "ref_patch", "sum_patch"))
# Get positions either in the initial or final snapshot
if in_initial: if in_initial:
pos0 = self.cat0.positions0 pos0, posx = self.cat0.positions0, self.catx.positions0
posx = self.catx.positions0
else: else:
pos0 = self.cat0.positions pos0, posx = self.cat0.positions, self.catx.positions
posx = self.catx.positions pos0 = pos0[self.refmask, :] # Apply the reference catalogue mask
# Get the normalisation array if applicable
if norm_kind == "r200":
norm = self.cat0["r200"][self.refmask]
if norm_kind == "ref_patch":
norm = self.cat0["lagpatch"][self.refmask]
if norm_kind == "sum_patch":
patch0 = self.cat0["lagpatch"][self.refmask]
patchx = self.catx["lagpatch"]
norm = [None] * self.indxs.size
for i, ind in enumerate(self.match_indxs):
norm[i] = patch0[i] + patchx[ind]
norm = numpy.array(norm, dtype=object)
# Now calculate distances
dist = [None] * self.indxs.size dist = [None] * self.indxs.size
for n, ind in enumerate(self.match_indxs): for i, ind in enumerate(self.match_indxs):
dist[n] = numpy.linalg.norm(pos0[n, :] - posx[ind, :], axis=1) # n refers to the reference halo catalogue position
dist[i] = numpy.linalg.norm(pos0[i, :] - posx[ind, :], axis=1)
if norm_kind is not None:
dist[i] /= norm[i]
# Normalisation
if norm == "r200":
dist[n] /= self.cat0["r200"][n]
if norm == "ref_patch":
dist[n] /= self.cat0["lagpatch"][n]
if norm == "sum_patch":
dist[n] /= (self.cat0["lagpatch"][n]
+ self.catx["lagpatch"][ind])
return numpy.array(dist, dtype=object) return numpy.array(dist, dtype=object)
def mass_ratio(self, mass_kind="totpartmass", in_log=True, in_abs=True): def mass_ratio(self, mass_kind="totpartmass", in_log=True, in_abs=True):
""" """
Pair mass ratio. Pair mass ratio of matched halos between the reference and cross
simulations.
Parameters Parameters
---------- ----------
@ -418,16 +445,16 @@ class OverlapReader:
------- -------
ratio : array of 1-dimensional arrays of shape `(nhalos, )` ratio : array of 1-dimensional arrays of shape `(nhalos, )`
""" """
mass0 = self.cat0[mass_kind] mass0 = self.cat0[mass_kind][self.refmask]
massx = self.catx[mass_kind] massx = self.catx[mass_kind]
ratio = [None] * self.indxs.size ratio = [None] * self.indxs.size
for n, ind in enumerate(self.match_indxs): for i, ind in enumerate(self.match_indxs):
ratio[n] = mass0[n] / massx[ind] ratio[i] = mass0[i] / massx[ind]
if in_log: if in_log:
ratio[n] = numpy.log10(ratio[n]) ratio[i] = numpy.log10(ratio[i])
if in_abs: if in_abs:
ratio[n] = numpy.abs(ratio[n]) ratio[i] = numpy.abs(ratio[i])
return numpy.array(ratio, dtype=object) return numpy.array(ratio, dtype=object)
def summed_overlap(self): def summed_overlap(self):
@ -456,9 +483,10 @@ class OverlapReader:
------- -------
out : 1-dimensional array of shape `(nhalos, )` out : 1-dimensional array of shape `(nhalos, )`
""" """
vals = self.cat0[par][self.refmask]
out = [None] * self.indxs.size out = [None] * self.indxs.size
for n, ind in enumerate(self.match_indxs): for i, ind in enumerate(self.match_indxs):
out[n] = numpy.ones(ind.size) * self.cat0[par][n] out[i] = numpy.ones(ind.size) * vals[i]
return numpy.array(out, dtype=object) return numpy.array(out, dtype=object)
def prob_nomatch(self): def prob_nomatch(self):
@ -504,14 +532,13 @@ class OverlapReader:
massx = self.catx[mass_kind] # Create references to the arrays here massx = self.catx[mass_kind] # Create references to the arrays here
overlap = self.overlap # to speed up the loop below. overlap = self.overlap # to speed up the loop below.
# Is the iterator verbose? for i, match_ind in enumerate(self.match_indxs):
for n, match_ind in enumerate((self.match_indxs)):
# Skip if no match # Skip if no match
if match_ind.size == 0: if match_ind.size == 0:
continue continue
massx_ = massx[match_ind] # Again just create references massx_ = massx[match_ind] # Again just create references
overlap_ = overlap[n] # to the appropriate elements overlap_ = overlap[i] # to the appropriate elements
# Optionally apply overlap threshold # Optionally apply overlap threshold
if overlap_threshold > 0.: if overlap_threshold > 0.:
@ -530,8 +557,8 @@ class OverlapReader:
mean_ = 10**mean_ if in_log else mean_ mean_ = 10**mean_ if in_log else mean_
std_ = mean_ * std_ * numpy.log(10) if in_log else std_ std_ = mean_ * std_ * numpy.log(10) if in_log else std_
mean[n] = mean_ mean[i] = mean_
std[n] = std_ std[i] = std_
return mean, std return mean, std

7
scripts/run_singlematch.py
View File

@ -46,12 +46,13 @@ catx = csiborgtools.read.HaloCatalogue(args.nsimx)
matcher = csiborgtools.match.RealisationsMatcher() matcher = csiborgtools.match.RealisationsMatcher()
print("{}: crossing the simulations.".format(datetime.now()), flush=True) print("{}: crossing the simulations.".format(datetime.now()), flush=True)
indxs, match_indxs, cross = matcher.cross( ref_indxs, cross_indxs, match_indxs, overlap = matcher.cross(
args.nsim0, args.nsimx, cat0, catx, overlap=args.overlap) cat0, catx, overlap=args.overlap)
# Dump the result # Dump the result
print("Saving results to `{}`.".format(fout), flush=True) print("Saving results to `{}`.".format(fout), flush=True)
with open(fout, "wb") as f: with open(fout, "wb") as f:
numpy.savez(fout, indxs=indxs, match_indxs=match_indxs, cross=cross) numpy.savez(fout, ref_indxs=ref_indxs, cross_indxs=cross_indxs,
match_indxs=match_indxs, overlap=overlap)
print("All finished.", flush=True) print("All finished.", flush=True)