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Velocity observer (#86)

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* Continue if r200c not defined

* Remove smooth scale

* Remove smooth scale

* Edit Max Matching plot

* Add peculiar velocity

* Add Vobs calculation

* Edit docs

* Add Vobs plot

* Improve plotting

* Edit naming convention

* Make a note

* Add new cat options

* Update density field RSP calculation

* Update field 2 rsp

* Move functions and shorten documentation

* Improve transforms and comments

* Update docs

* Update imports

* Edit calculation

* Add docs

* Remove imports

* Add Quijote flags

* Edit documentation

* Shorten documentation

* Edit func calls

* Shorten

* Docs edits

* Edit docs

* Shorten docs

* Short docs edits

* Simplify docs a little bit

* Save plotting

* Update env
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Richard Stiskalek 2023-08-30 23:27:20 +01:00 committed by GitHub
parent 8e3127f4d9
commit ae92fd9b72
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18 changed files with 761 additions and 788 deletions
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65
csiborgtools/field/density.py
View File

@ -22,7 +22,6 @@ import numpy
from numba import jit
from tqdm import trange
from ..read.utils import real2redshift
from .interp import divide_nonzero
from .utils import force_single_precision
@ -32,18 +31,6 @@ class BaseField(ABC):
_box = None
_MAS = None
@property
def boxsize(self):
"""
Box size. Particle positions are always assumed to be in box units,
therefore this is 1.
Returns
-------
boxsize : float
"""
return 1.
@property
def box(self):
"""
@ -51,7 +38,7 @@ class BaseField(ABC):
Returns
-------
box : :py:class:`csiborgtools.units.CSiBORGBox`
:py:class:`csiborgtools.units.CSiBORGBox`
"""
return self._box
@ -70,10 +57,10 @@ class BaseField(ABC):
Returns
-------
MAS : str
str
"""
if self._MAS is None:
raise ValueError("`mas` is not set.")
raise ValueError("`MAS` is not set.")
return self._MAS
@MAS.setter
@ -99,6 +86,8 @@ class DensityField(BaseField):
Mass assignment scheme. Options are Options are: 'NGP' (nearest grid
point), 'CIC' (cloud-in-cell), 'TSC' (triangular-shape cloud), 'PCS'
(piecewise cubic spline).
paths : :py:class:`csiborgtools.read.Paths`
The simulation paths.
References
----------
@ -128,13 +117,12 @@ class DensityField(BaseField):
delta -= 1
return delta
def __call__(self, parts, grid, in_rsp, flip_xz=True, nbatch=30,
verbose=True):
def __call__(self, parts, grid, flip_xz=True, nbatch=30, verbose=True):
"""
Calculate the density field using a Pylians routine [1, 2].
Iteratively loads the particles into memory, flips their `x` and `z`
coordinates. Particles are assumed to be in box units, with positions
in [0, 1] and observer in the centre of the box if RSP is applied.
in [0, 1]
Parameters
----------
@ -143,8 +131,6 @@ class DensityField(BaseField):
Columns are: `x`, `y`, `z`, `vx`, `vy`, `vz`, `M`.
grid : int
Grid size.
in_rsp : bool
Whether to calculate the density field in redshift space.
flip_xz : bool, optional
Whether to flip the `x` and `z` coordinates.
nbatch : int, optional
@ -173,21 +159,14 @@ class DensityField(BaseField):
pos = parts[start:end]
pos, vel, mass = pos[:, :3], pos[:, 3:6], pos[:, 6]
pos = force_single_precision(pos, "particle_position")
vel = force_single_precision(vel, "particle_velocity")
mass = force_single_precision(mass, "particle_mass")
pos = force_single_precision(pos)
vel = force_single_precision(vel)
mass = force_single_precision(mass)
if flip_xz:
pos[:, [0, 2]] = pos[:, [2, 0]]
vel[:, [0, 2]] = vel[:, [2, 0]]
if in_rsp:
raise NotImplementedError("Redshift space needs to be fixed.")
# TODO change how called + units.
pos = real2redshift(pos, vel, [0.5, 0.5, 0.5], self.box,
in_box_units=True, periodic_wrap=True,
make_copy=False)
MASL.MA(pos, rho, self.boxsize, self.MAS, W=mass, verbose=False)
MASL.MA(pos, rho, 1., self.MAS, W=mass, verbose=False)
if end == nparts:
break
start = end
@ -223,7 +202,7 @@ class VelocityField(BaseField):
@staticmethod
@jit(nopython=True)
def radial_velocity(rho_vel):
def radial_velocity(rho_vel, observer_velocity):
"""
Calculate the radial velocity field around the observer in the centre
of the box.
@ -232,6 +211,8 @@ class VelocityField(BaseField):
----------
rho_vel : 4-dimensional array of shape `(3, grid, grid, grid)`.
Velocity field along each axis.
observer_velocity : 3-dimensional array of shape `(3,)`
Observer velocity.
Returns
-------
@ -240,13 +221,19 @@ class VelocityField(BaseField):
"""
grid = rho_vel.shape[1]
radvel = numpy.zeros((grid, grid, grid), dtype=numpy.float32)
vx0, vy0, vz0 = observer_velocity
for i in range(grid):
px = i - 0.5 * (grid - 1)
for j in range(grid):
py = j - 0.5 * (grid - 1)
for k in range(grid):
pz = k - 0.5 * (grid - 1)
vx, vy, vz = rho_vel[:, i, j, k]
vx = rho_vel[0, i, j, k] - vx0
vy = rho_vel[1, i, j, k] - vy0
vz = rho_vel[2, i, j, k] - vz0
radvel[i, j, k] = ((px * vx + py * vy + pz * vz)
/ numpy.sqrt(px**2 + py**2 + pz**2))
return radvel
@ -297,19 +284,19 @@ class VelocityField(BaseField):
pos = parts[start:end]
pos, vel, mass = pos[:, :3], pos[:, 3:6], pos[:, 6]
pos = force_single_precision(pos, "particle_position")
vel = force_single_precision(vel, "particle_velocity")
mass = force_single_precision(mass, "particle_mass")
pos = force_single_precision(pos)
vel = force_single_precision(vel)
mass = force_single_precision(mass)
if flip_xz:
pos[:, [0, 2]] = pos[:, [2, 0]]
vel[:, [0, 2]] = vel[:, [2, 0]]
vel *= mass.reshape(-1, 1)
for i in range(3):
MASL.MA(pos, rho_vel[i], self.boxsize, self.MAS, W=vel[:, i],
MASL.MA(pos, rho_vel[i], 1., self.MAS, W=vel[:, i],
verbose=False)
MASL.MA(pos, cellcounts, self.boxsize, self.MAS, W=mass,
MASL.MA(pos, cellcounts, 1., self.MAS, W=mass,
verbose=False)
if end == nparts:
break

244
csiborgtools/field/interp.py
View File

@ -20,23 +20,22 @@ import numpy
from numba import jit
from tqdm import trange
from ..read.utils import radec_to_cartesian, real2redshift
from .utils import force_single_precision
from ..utils import periodic_wrap_grid, radec_to_cartesian
def evaluate_cartesian(*fields, pos, interp="CIC"):
"""
Evaluate a scalar field at Cartesian coordinates.
Evaluate a scalar field(s) at Cartesian coordinates `pos`.
Parameters
----------
field : (list of) 3-dimensional array of shape `(grid, grid, grid)`
Fields to be interpolated.
pos : 2-dimensional array of shape `(n_samples, 3)`
Positions to evaluate the density field. Assumed to be in box
units.
Query positions in box units.
interp : str, optional
Interpolation method. Can be either `CIC` or `NGP`.
Interpolation method, `NGP` or `CIC`.
Returns
-------
@ -44,7 +43,7 @@ def evaluate_cartesian(*fields, pos, interp="CIC"):
"""
assert interp in ["CIC", "NGP"]
boxsize = 1.
pos = force_single_precision(pos, "pos")
pos = force_single_precision(pos)
nsamples = pos.shape[0]
interp_fields = [numpy.full(nsamples, numpy.nan, dtype=numpy.float32)
@ -64,60 +63,71 @@ def evaluate_cartesian(*fields, pos, interp="CIC"):
return interp_fields
def evaluate_sky(*fields, pos, box, isdeg=True):
def evaluate_sky(*fields, pos, box):
"""
Evaluate the scalar fields at given distance, right ascension and
declination. Assumes an observed in the centre of the box, with
distance being in :math:`Mpc`. Uses CIC interpolation.
Evaluate a scalar field(s) at radial distance `Mpc / h`, right ascensions
[0, 360) deg and declinations [-90, 90] deg.
Parameters
----------
fields : (list of) 3-dimensional array of shape `(grid, grid, grid)`
Field to be interpolated.
pos : 2-dimensional array of shape `(n_samples, 3)`
Spherical coordinates to evaluate the field. Columns are distance,
right ascension, declination, respectively.
Query spherical coordinates.
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`.
Returns
-------
interp_fields : (list of) 1-dimensional array of shape `(n_samples,).
"""
pos = force_single_precision(pos, "pos")
# We first calculate convert the distance to box coordinates and then
# convert to Cartesian coordinates.
pos = force_single_precision(pos)
pos[:, 0] = box.mpc2box(pos[:, 0])
X = radec_to_cartesian(pos, isdeg)
# Then we move the origin to match the box coordinates
X += 0.5
return evaluate_cartesian(*fields, pos=X)
cart_pos = radec_to_cartesian(pos) + 0.5
return evaluate_cartesian(*fields, pos=cart_pos)
def observer_vobs(velocity_field):
"""
Calculate the observer velocity from a velocity field. Assumes an observer
in the centre of the box.
Parameters
----------
velocity_field : 4-dimensional array of shape `(3, grid, grid, grid)`
Returns
-------
1-dimensional array of shape `(3,)`
"""
pos = numpy.asanyarray([0.5, 0.5, 0.5]).reshape(1, 3)
vobs = numpy.full(3, numpy.nan, dtype=numpy.float32)
for i in range(3):
vobs[i] = evaluate_cartesian(velocity_field[i, ...], pos=pos)[0]
return vobs
def make_sky(field, angpos, dist, box, volume_weight=True, verbose=True):
r"""
Make a sky map of a scalar field. The observer is in the centre of the
box the field is evaluated along directions `angpos`. Along each
direction, the field is evaluated distances `dist_marg` and summed.
Uses CIC interpolation.
box the field is evaluated along directions `angpos` (RA [0, 360) deg,
dec [-90, 90] deg). Along each direction, the field is evaluated distances
`dist` (`Mpc / h`) and summed. Uses CIC interpolation.
Parameters
----------
field : 3-dimensional array of shape `(grid, grid, grid)`
Field to be interpolated
angpos : 2-dimensional arrays of shape `(ndir, 2)`
Directions to evaluate the field. Assumed to be RA
:math:`\in [0, 360]` and dec :math:`\in [-90, 90]` degrees,
respectively.
Directions to evaluate the field.
dist : 1-dimensional array
Uniformly spaced radial distances to evaluate the field.
box : :py:class:`csiborgtools.read.CSiBORGBox`
The simulation box information and transformations.
volume_weight : bool, optional
Whether to weight the field by the volume of the pixel, i.e. a
:math:`r^2` correction.
Whether to weight the field by the volume of the pixel.
verbose : bool, optional
Verbosity flag.
@ -152,22 +162,9 @@ def make_sky(field, angpos, dist, box, volume_weight=True, verbose=True):
@jit(nopython=True)
def divide_nonzero(field0, field1):
"""
Divide two fields where the second one is not zero. If the second field
is zero, the first one is left unchanged. Operates in-place.
Parameters
----------
field0 : 3-dimensional array of shape `(grid, grid, grid)`
Field to be divided.
field1 : 3-dimensional array of shape `(grid, grid, grid)`
Field to divide by.
Returns
-------
field0 : 3-dimensional array of shape `(grid, grid, grid)`
Field divided by the second one.
Perform in-place `field0 /= field1` but only where `field1 != 0`.
"""
assert field0.shape == field1.shape
assert field0.shape == field1.shape, "Field shapes must match."
imax, jmax, kmax = field0.shape
for i in range(imax):
@ -177,134 +174,89 @@ def divide_nonzero(field0, field1):
field0[i, j, k] /= field1[i, j, k]
def observer_vobs(velocity_field):
@jit(nopython=True)
def make_gridpos(grid_size):
"""Make a regular grid of positions and distances from the center."""
grid_pos = numpy.full((grid_size**3, 3), numpy.nan, dtype=numpy.float32)
grid_dist = numpy.full(grid_size**3, numpy.nan, dtype=numpy.float32)
n = 0
for i in range(grid_size):
px = (i - 0.5 * (grid_size - 1)) / grid_size
px2 = px**2
for j in range(grid_size):
py = (j - 0.5 * (grid_size - 1)) / grid_size
py2 = py**2
for k in range(grid_size):
pz = (k - 0.5 * (grid_size - 1)) / grid_size
pz2 = pz**2
grid_pos[n, 0] = px
grid_pos[n, 1] = py
grid_pos[n, 2] = pz
grid_dist[n] = (px2 + py2 + pz2)**0.5
n += 1
return grid_pos, grid_dist
def field2rsp(field, radvel_field, box, MAS, init_value=0.):
"""
Calculate the observer velocity from a velocity field. Assumes the observer
is in the centre of the box.
Forward model a real space scalar field to redshift space.
Parameters
----------
velocity_field : 4-dimensional array of shape `(3, grid, grid, grid)`
Velocity field to calculate the observer velocity from.
Returns
-------
vobs : 1-dimensional array of shape `(3,)`
Observer velocity in units of `velocity_field`.
"""
pos = numpy.asanyarray([0.5, 0.5, 0.5]).reshape(1, 3)
vobs = numpy.full(3, numpy.nan, dtype=numpy.float32)
for i in range(3):
vobs[i] = evaluate_cartesian(velocity_field[i, ...], pos=pos)[0]
return vobs
def field2rsp(*fields, parts, vobs, box, nbatch=30, flip_partsxz=True,
init_value=0., verbose=True):
"""
Forward model real space scalar fields to redshift space. Attaches field
values to particles, those are then moved to redshift space and from their
positions reconstructs back the field on a grid by NGP interpolation.
Parameters
----------
fields : (list of) 3-dimensional array of shape `(grid, grid, grid)`
Real space fields to be evolved to redshift space.
parts : 2-dimensional array of shape `(n_parts, 6)`
Particle positions and velocities in real space. Must be organised as
`x, y, z, vx, vy, vz`.
vobs : 1-dimensional array of shape `(3,)`
Observer velocity in units matching `parts`.
field : 3-dimensional array of shape `(grid, grid, grid)`
Real space field to be evolved to redshift space.
radvel_field : 3-dimensional array of shape `(grid, grid, grid)`
Radial velocity field in `km / s`. Expected to account for the observer
velocity.
box : :py:class:`csiborgtools.read.CSiBORGBox`
The simulation box information and transformations.
nbatch : int, optional
Number of batches to use when moving particles to redshift space.
Particles are assumed to be lazily loaded to memory.
flip_partsxz : bool, optional
Whether to flip the x and z coordinates of the particles. This is
because of a RAMSES bug.
MAS : str
Mass assignment. Must be one of `NGP`, `CIC`, `TSC` or `PCS`.
init_value : float, optional
Initial value of the RSP field on the grid.
verbose : bool, optional
Verbosity flag.
Returns
-------
rsp_fields : (list of) 3-dimensional array of shape `(grid, grid, grid)`
3-dimensional array of shape `(grid, grid, grid)`
"""
raise NotImplementedError("Figure out what to do with Vobs.")
nfields = len(fields)
# Check that all fields have the same shape.
if nfields > 1:
assert all(fields[0].shape == fields[i].shape
for i in range(1, nfields))
grid = field.shape[0]
H0_inv = 1. / 100 / box.box2mpc(1.)
rsp_fields = [numpy.full(field.shape, init_value, dtype=numpy.float32)
for field in fields]
cellcounts = numpy.zeros(rsp_fields[0].shape, dtype=numpy.float32)
# Calculate the regular grid positions and distances from the center.
grid_pos, grid_dist = make_gridpos(grid)
grid_dist = grid_dist.reshape(-1, 1)
nparts = parts.shape[0]
batch_size = nparts // nbatch
start = 0
for __ in trange(nbatch + 1) if verbose else range(nbatch + 1):
# We first load the batch of particles into memory and flip x and z.
end = min(start + batch_size, nparts)
pos = parts[start:end]
pos, vel = pos[:, :3], pos[:, 3:6]
if flip_partsxz:
pos[:, [0, 2]] = pos[:, [2, 0]]
vel[:, [0, 2]] = vel[:, [2, 0]]
# Then move the particles to redshift space.
# TODO here the function is now called differently and pos assumes
# different units.
rsp_pos = real2redshift(pos, vel, [0.5, 0.5, 0.5], box,
in_box_units=True, periodic_wrap=True,
make_copy=True)
# ... and count the number of particles in each grid cell.
MASL.MA(rsp_pos, cellcounts, 1., "NGP")
# Move the grid positions to redshift space.
grid_pos *= (1 + H0_inv * radvel_field.reshape(-1, 1) / grid_dist)
grid_pos += 0.5
grid_pos = periodic_wrap_grid(grid_pos)
# Now finally we evaluate the field at the particle positions in real
# space and then assign the values to the grid in redshift space.
for i in range(nfields):
values = evaluate_cartesian(fields[i], pos=pos)
MASL.MA(rsp_pos, rsp_fields[i], 1., "NGP", W=values)
if end == nparts:
break
start = end
rsp_field = numpy.full(field.shape, init_value, dtype=numpy.float32)
cell_counts = numpy.zeros(rsp_field.shape, dtype=numpy.float32)
# We divide by the number of particles in each cell.
for i in range(len(fields)):
divide_nonzero(rsp_fields[i], cellcounts)
# Interpolate the field to the grid positions.
MASL.MA(grid_pos, rsp_field, 1., MAS, W=field.reshape(-1,))
MASL.MA(grid_pos, cell_counts, 1., MAS)
divide_nonzero(rsp_field, cell_counts)
if len(fields) == 1:
return rsp_fields[0]
return rsp_fields
return rsp_field
@jit(nopython=True)
def fill_outside(field, fill_value, rmax, boxsize):
"""
Fill cells outside of a sphere of radius `rmax` with `fill_value`. Centered
in the middle of the box.
Parameters
----------
field : 3-dimensional array of shape `(grid, grid, grid)`
Field to be filled.
fill_value : float
Value to fill the field with.
rmax : float
Radius outside of which to fill the field..
boxsize : float
Size of the box.
Returns
-------
field : 3-dimensional array of shape `(grid, grid, grid)`
Fill cells outside of a sphere of radius `rmax` around the box centre with
`fill_value`.
"""
imax, jmax, kmax = field.shape
assert imax == jmax == kmax
N = imax
# Squared radial distance from the center of the box in box units.
rmax_box2 = (N * rmax / boxsize)**2

49
csiborgtools/field/utils.py
View File

@ -15,31 +15,16 @@
"""
Utility functions for the field module.
"""
from warnings import warn
import healpy
import numpy
import smoothing_library as SL
def force_single_precision(x, name):
def force_single_precision(x):
"""
Convert `x` to float32 if it is not already.
Parameters
----------
x : array
Array to convert.
name : str
Name of the array.
Returns
-------
x : array
Converted array.
Attempt to convert an array `x` to float 32.
"""
if x.dtype != numpy.float32:
warn(f"Converting `{name}` to float32.", UserWarning, stacklevel=1)
x = x.astype(numpy.float32)
return x
@ -47,21 +32,6 @@ def force_single_precision(x, name):
def smoothen_field(field, smooth_scale, boxsize, threads=1):
"""
Smooth a field with a Gaussian filter.
Parameters
----------
field : 3-dimensional array of shape `(grid, grid, grid)`
Field to be smoothed.
smooth_scale : float, optional
Gaussian kernal scale to smoothen the density field, in box units.
boxsize : float
Size of the box.
threads : int, optional
Number of threads. By default 1.
Returns
-------
smoothed_field : 3-dimensional array of shape `(grid, grid, grid)`
"""
W_k = SL.FT_filter(boxsize, smooth_scale, field.shape[0], "Gaussian",
threads)
@ -70,19 +40,10 @@ def smoothen_field(field, smooth_scale, boxsize, threads=1):
def nside2radec(nside):
"""
Generate RA and declination for HEALPix pixel centres.
Parameters
----------
nside : int
HEALPix nside parameter.
Returns
-------
radec : array of shape `(npix, 2)`
RA and declination in degrees.
Generate RA [0, 360] deg. and declination [-90, 90] deg. for HEALPix pixel
centres at a given nside.
"""
pixs = numpy.arange(healpy.nside2npix(nside))
theta, phi = healpy.pix2ang(nside, pixs)
theta -= numpy.pi / 2
return numpy.rad2deg(numpy.vstack([phi, theta]).T)
return 180 / numpy.pi * numpy.vstack([phi, theta]).T

43
csiborgtools/match/match.py
View File

@ -151,7 +151,7 @@ class RealisationsMatcher(BaseMatcher):
Returns
-------
dlogmass : float
float
"""
return self._dlogmass
@ -169,7 +169,7 @@ class RealisationsMatcher(BaseMatcher):
Returns
-------
mass_kind : str
str
"""
return self._mass_kind
@ -186,7 +186,7 @@ class RealisationsMatcher(BaseMatcher):
Returns
-------
overlapper : :py:class:`csiborgtools.match.ParticleOverlap`
:py:class:`csiborgtools.match.ParticleOverlap`
"""
return self._overlapper
@ -661,20 +661,7 @@ class ParticleOverlap(BaseMatcher):
def pos2cell(pos, ncells):
"""
Convert position to cell number. If `pos` is in
`numpy.typecodes["AllInteger"]` assumes it to already be the cell
number.
Parameters
----------
pos : 1-dimensional array
Array of positions along an axis in the box.
ncells : int
Number of cells along the axis.
Returns
-------
cells : 1-dimensional array
Convert position to cell number if there are `ncells` cells along the axis.
"""
if pos.dtype.char in numpy.typecodes["AllInteger"]:
return pos
@ -684,17 +671,7 @@ def pos2cell(pos, ncells):
def read_nshift(smooth_kwargs):
"""
Determine the number of cells to pad the density field if smoothing is
applied. It defaults to the ceiling of three times the smoothing scale.
Parameters
----------
smooth_kwargs : dict or None
Arguments to be passed to :py:func:`scipy.ndimage.gaussian_filter`.
If `None`, no smoothing is applied.
Returns
-------
nshift : int
applied. Defaults to the ceiling of three times the smoothing scale.
"""
return 0 if smooth_kwargs is None else ceil(3 * smooth_kwargs["sigma"])
@ -702,8 +679,7 @@ def read_nshift(smooth_kwargs):
@jit(nopython=True)
def fill_delta(delta, xcell, ycell, zcell, xmin, ymin, zmin, weights):
"""
Fill array `delta` by adding `weights` to the specified cells. This is a
JIT implementation.
Fill array `delta` by adding `weights` to the specified cells.
Parameters
----------
@ -730,8 +706,8 @@ def fill_delta(delta, xcell, ycell, zcell, xmin, ymin, zmin, weights):
@jit(nopython=True)
def fill_delta_indxs(delta, xcell, ycell, zcell, xmin, ymin, zmin, weights):
"""
Fill array `delta` by adding `weights` to the specified cells and return
indices where `delta` was assigned a value. This is a JIT implementation.
Fill array `delta` by adding `weights` to the specified cells. Returns
the indices where `delta` was assigned a value.
Parameters
----------
@ -1161,6 +1137,9 @@ def matching_max(cat0, catx, mass_kind, mult, periodic, overlap=None,
out[i]["hid0"] = hid0
out[i]["mass0"] = 10**mass0[i]
if not numpy.isfinite(rad0[i]):
continue
neigh_dists, neigh_inds = knnx.radius_neighbors(pos0[i].reshape(1, -1),
mult * rad0[i])
neigh_dists, neigh_inds = neigh_dists[0], neigh_inds[0]

3
csiborgtools/read/__init__.py
View File

@ -26,5 +26,4 @@ from .pk_summary import PKReader # noqa
from .readsim import (MmainReader, CSiBORGReader, QuijoteReader, halfwidth_mask, # noqa
load_halo_particles) # noqa
from .tpcf_summary import TPCFReader # noqa
from .utils import (cartesian_to_radec, cols_to_structured, radec_to_cartesian, # noqa
read_h5, real2redshift) # noqa
from .utils import (cols_to_structured, read_h5) # noqa

20
csiborgtools/read/halo_cat.py
View File

@ -31,9 +31,9 @@ from sklearn.neighbors import NearestNeighbors
from .box_units import CSiBORGBox, QuijoteBox
from .paths import Paths
from .readsim import CSiBORGReader
from .utils import (add_columns, cartesian_to_radec, cols_to_structured,
flip_cols, radec_to_cartesian, real2redshift)
from ..utils import periodic_distance_two_points
from .utils import add_columns, cols_to_structured, flip_cols
from ..utils import (periodic_distance_two_points, real2redshift,
cartesian_to_radec, radec_to_cartesian)
class BaseCatalogue(ABC):
@ -631,6 +631,9 @@ class QuijoteHaloCatalogue(BaseCatalogue):
Load initial positions from `fit_init.py`.
with_lagpatch : bool, optional
Load halos with a resolved Lagrangian patch.
load_backup : bool, optional
Load halos from the backup catalogue that do not have corresponding
snapshots.
"""
_nsnap = None
_origin = None
@ -638,14 +641,15 @@ class QuijoteHaloCatalogue(BaseCatalogue):
def __init__(self, nsim, paths, nsnap,
observer_location=[500., 500., 500.],
bounds=None, load_fitted=True, load_initial=True,
with_lagpatch=False):
with_lagpatch=False, load_backup=False):
self.nsim = nsim
self.paths = paths
self.nsnap = nsnap
self.observer_location = observer_location
self._box = QuijoteBox(nsnap, nsim, paths)
# NOTE watch out about here setting nsim = 0
self._box = QuijoteBox(nsnap, 0, paths)
fpath = self.paths.fof_cat(nsim, "quijote")
fpath = self.paths.fof_cat(nsim, "quijote", load_backup)
fof = FoF_catalog(fpath, self.nsnap, long_ids=False, swap=False,
SFR=False, read_IDs=False)
@ -667,6 +671,10 @@ class QuijoteHaloCatalogue(BaseCatalogue):
# particles unassigned to any FoF group.
data["index"] = 1 + numpy.arange(data.size, dtype=numpy.int32)
if load_backup and (load_initial or load_fitted):
raise ValueError("Cannot load initial/fitted data for the backup "
"catalogues.")
if load_initial:
data = self.load_initial(data, paths, "quijote")
if load_fitted:

65
csiborgtools/read/paths.py
View File

@ -214,7 +214,7 @@ class Paths:
fout = fout.replace(".npy", "_sorted.npy")
return fout
def fof_cat(self, nsim, simname):
def fof_cat(self, nsim, simname, from_quijote_backup=False):
r"""
Path to the :math:`z = 0` FoF halo catalogue.
@ -224,13 +224,24 @@ class Paths:
IC realisation index.
simname : str
Simulation name. Must be one of `csiborg` or `quijote`.
from_quijote_backup : bool, optional
Whether to return the path to the Quijote FoF catalogue from the
backup.
Returns
-------
path : str
"""
if simname == "csiborg":
fdir = join(self.postdir, "FoF_membership", )
try_create_directory(fdir)
return join(fdir, f"halo_catalog_{nsim}_FOF.txt")
elif simname == "quijote":
return join(self.quijote_dir, "Halos_fiducial", str(nsim))
if from_quijote_backup:
return join(self.quijote_dir, "halos_backup", str(nsim))
else:
return join(self.quijote_dir, "Halos_fiducial", str(nsim))
else:
raise ValueError(f"Unknown simulation name `{simname}`.")
@ -285,7 +296,7 @@ class Paths:
try_create_directory(fdir)
return join(fdir, f"{kind}_{str(nsim).zfill(5)}.{ftype}")
def get_ics(self, simname):
def get_ics(self, simname, from_quijote_backup=False):
"""
Get available IC realisation IDs for either the CSiBORG or Quijote
simulation suite.
@ -294,6 +305,8 @@ class Paths:
----------
simname : str
Simulation name. Must be `csiborg` or `quijote`.
from_quijote_backup : bool, optional
Whether to return the ICs from the Quijote backup.
Returns
-------
@ -311,10 +324,13 @@ class Paths:
except ValueError:
pass
elif simname == "quijote" or simname == "quijote_full":
files = glob(
"/mnt/extraspace/rstiskalek/Quijote/Snapshots_fiducial/*")
if from_quijote_backup:
files = glob(join(self.quijote_dir, "halos_backup", "*"))
else:
warn(("Taking only the snapshots that also have "
"a FoF catalogue!"))
files = glob(join(self.quijote_dir, "Snapshots_fiducial", "*"))
files = [int(f.split("/")[-1]) for f in files]
warn("Taking only the snapshots that also have a FoF catalogue!")
files = [f for f in files if f < 100]
else:
raise ValueError(f"Unknown simulation name `{simname}`.")
@ -545,7 +561,7 @@ class Paths:
return join(fdir, fname)
def field(self, kind, MAS, grid, nsim, in_rsp, smooth_scale=None):
def field(self, kind, MAS, grid, nsim, in_rsp):
r"""
Path to the files containing the calculated density fields in CSiBORG.
@ -562,8 +578,6 @@ class Paths:
IC realisation index.
in_rsp : bool
Whether the calculation is performed in redshift space.
smooth_scale : float, optional
Smoothing scale in :math:`\mathrm{Mpc}/h`
Returns
-------
@ -579,12 +593,32 @@ class Paths:
kind = kind + "_rsp"
fname = f"{kind}_{MAS}_{str(nsim).zfill(5)}_grid{grid}.npy"
if smooth_scale is not None and smooth_scale > 0:
smooth_scale = float(smooth_scale)
fname = fname.replace(".npy", f"smooth{smooth_scale}.npy")
return join(fdir, fname)
def halo_counts(self, simname, nsim):
def observer_peculiar_velocity(self, MAS, grid, nsim):
"""
Path to the files containing the observer peculiar velocity.
Parameters
----------
MAS : str
Mass-assignment scheme.
grid : int
Grid size.
nsim : int
IC realisation index.
Returns
-------
path : str
"""
fdir = join(self.postdir, "environment")
try_create_directory(fdir)
fname = f"obs_vp_{MAS}_{str(nsim).zfill(5)}_{grid}.npz"
return join(fdir, fname)
def halo_counts(self, simname, nsim, from_quijote_backup=False):
"""
Path to the files containing the binned halo counts.
@ -594,6 +628,9 @@ class Paths:
Simulation name. Must be `csiborg`, `quijote` or `quijote_full`.
nsim : int
IC realisation index.
from_quijote_backup : bool, optional
Whether to return the path to the Quijote halo counts from the
backup catalogues.
Returns
-------
@ -602,6 +639,8 @@ class Paths:
fdir = join(self.postdir, "HMF")
try_create_directory(fdir)
fname = f"halo_counts_{simname}_{str(nsim).zfill(5)}.npz"
if from_quijote_backup:
fname = fname.replace("halo_counts", "halo_counts_backup")
return join(fdir, fname)
def cross_nearest(self, simname, run, kind, nsim=None, nobs=None):

164
csiborgtools/read/utils.py
View File

@ -12,126 +12,11 @@
# 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.
"""
Various coordinate transformations.
"""
from os.path import isfile
import numpy
from h5py import File
###############################################################################
# Coordinate transforms #
###############################################################################
def cartesian_to_radec(X, indeg=True):
"""
Calculate the radial distance, RA, dec from Cartesian coordinates. Note,
RA is in range [0, 360) degrees and dec in range [-90, 90] degrees.
Parameters
----------
X : 2-dimensional array `(nsamples, 3)`
Cartesian coordinates.
indeg : bool, optional
Whether to return RA and DEC in degrees.
Returns
-------
out : 2-dimensional array `(nsamples, 3)`
Radial distance, RA and dec.
"""
x, y, z = X[:, 0], X[:, 1], X[:, 2]
dist = numpy.linalg.norm(X, axis=1)
dec = numpy.arcsin(z / dist)
ra = numpy.arctan2(y, x)
ra[ra < 0] += 2 * numpy.pi # Wrap RA to [0, 2pi)
if indeg:
ra = numpy.rad2deg(ra)
dec = numpy.rad2deg(dec)
return numpy.vstack([dist, ra, dec]).T
def radec_to_cartesian(X, isdeg=True):
"""
Calculate Cartesian coordinates from radial distance, RA, dec. Note, RA is
expected in range [0, 360) degrees and dec in range [-90, 90] degrees.
Parameters
----------
X : 2-dimensional array `(nsamples, 3)`
Radial distance, RA and dec.
isdeg : bool, optional
Whether to return RA and DEC in degrees.
Returns
-------
out : 2-dimensional array `(nsamples, 3)`
Cartesian coordinates.
"""
dist, ra, dec = X[:, 0], X[:, 1], X[:, 2]
if isdeg:
ra = numpy.deg2rad(ra)
dec = numpy.deg2rad(dec)
x = dist * numpy.cos(dec) * numpy.cos(ra)
y = dist * numpy.cos(dec) * numpy.sin(ra)
z = dist * numpy.sin(dec)
return numpy.vstack([x, y, z]).T
def real2redshift(pos, vel, observer_location, box, periodic_wrap=True,
subtract_observer=False, make_copy=True):
r"""
Convert real-space position to redshift space position.
Parameters
----------
pos : 2-dimensional array `(nsamples, 3)`
Real-space Cartesian components in :math:`\mathrm{cMpc} / h`.
vel : 2-dimensional array `(nsamples, 3)`
Cartesian velocity in :math:`\mathrm{km} \mathrm{s}^{-1}`.
observer_location: 1-dimensional array `(3,)`
Observer location in :math:`\mathrm{cMpc} / h`.
box : py:class:`csiborg.read.CSiBORGBox`
Box units.
periodic_wrap : bool, optional
Whether to wrap around the box, particles may be outside the default
bounds once RSD is applied.
subtract_observer : bool, optional
If True, subtract the observer's location from the returned
positions.
make_copy : bool, optional
Whether to make a copy of `pos` before modifying it.
Returns
-------
pos : 2-dimensional array `(nsamples, 3)`
Redshift-space Cartesian position in :math:`\mathrm{cMpc} / h`.
"""
if make_copy:
pos = numpy.copy(pos)
# Place the observer at the origin
pos -= observer_location
# Dot product of position vector and velocity
vr_dot = numpy.sum(pos * vel, axis=1)
# Compute the norm squared of the displacement
norm2 = numpy.sum(pos**2, axis=1)
pos *= (1 + box._aexp / box.H0 * vr_dot / norm2).reshape(-1, 1)
# Place the observer back at the original location
if not subtract_observer:
pos += observer_location
if periodic_wrap:
boxsize = box.box2mpc(1.)
# Wrap around the box.
pos = numpy.where(pos > boxsize, pos - boxsize, pos)
pos = numpy.where(pos < 0, pos + boxsize, pos)
return pos
###############################################################################
# Array manipulation #
@ -140,19 +25,7 @@ def real2redshift(pos, vel, observer_location, box, periodic_wrap=True,
def cols_to_structured(N, cols):
"""
Allocate a structured array from `cols`.
Parameters
----------
N : int
Structured array size.
cols: list of tuples
Column names and dtypes. Each tuple must be written as `(name, dtype)`.
Returns
-------
out : structured array
Initialized structured array.
Allocate a structured array from `cols`, a list of (name, dtype) tuples.
"""
if not (isinstance(cols, list)
and all(isinstance(c, tuple) and len(c) == 2 for c in cols)):
@ -167,19 +40,6 @@ def cols_to_structured(N, cols):
def add_columns(arr, X, cols):
"""
Add new columns `X` to a record array `arr`. Creates a new array.
Parameters
----------
arr : structured array
Structured array to add columns to.
X : (list of) 1-dimensional array(s)
Columns to be added.
cols : str or list of str
Column names to be added.
Returns
-------
out : structured array
"""
cols = [cols] if isinstance(cols, str) else cols
@ -214,17 +74,6 @@ def add_columns(arr, X, cols):
def rm_columns(arr, cols):
"""
Remove columns `cols` from a structured array `arr`. Allocates a new array.
Parameters
----------
arr : structured array
Structured array to remove columns from.
cols : str or list of str
Column names to be removed.
Returns
-------
out : structured array
"""
# Ensure cols is a list
cols = [cols] if isinstance(cols, str) else cols
@ -247,16 +96,7 @@ def rm_columns(arr, cols):
def flip_cols(arr, col1, col2):
"""
Flip values in columns `col1` and `col2`. `arr` is modified in place.
Parameters
----------
arr : structured array
Array whose columns are to be flipped.
col1 : str
First column name.
col2 : str
Second column name.
Flip values in columns `col1` and `col2` of a structured array `arr`.
"""
if col1 not in arr.dtype.names or col2 not in arr.dtype.names:
raise ValueError(f"Both `{col1}` and `{col2}` must exist in `arr`.")

206
csiborgtools/utils.py
View File

@ -16,34 +16,25 @@
import numpy
from numba import jit
###############################################################################
# Positions #
###############################################################################
@jit(nopython=True, fastmath=True, boundscheck=False)
def center_of_mass(points, mass, boxsize):
def center_of_mass(particle_positions, particles_mass, boxsize):
"""
Calculate the center of mass of a halo while assuming periodic boundary
conditions of a cubical box. Assuming that particle positions are in
`[0, boxsize)` range. This is a JIT implementation.
Parameters
----------
points : 2-dimensional array of shape (n_particles, 3)
Particle position array.
mass : 1-dimensional array of shape `(n_particles, )`
Particle mass array.
boxsize : float
Box size in the same units as `parts` coordinates.
Returns
-------
cm : 1-dimensional array of shape `(3, )`
conditions of a cubical box.
"""
cm = numpy.zeros(3, dtype=points.dtype)
totmass = sum(mass)
cm = numpy.zeros(3, dtype=particle_positions.dtype)
totmass = sum(particles_mass)
# Convert positions to unit circle coordinates in the complex plane,
# calculate the weighted average and convert it back to box coordinates.
for i in range(3):
cm_i = sum(mass * numpy.exp(2j * numpy.pi * points[:, i] / boxsize))
cm_i = sum(particles_mass * numpy.exp(
2j * numpy.pi * particle_positions[:, i] / boxsize))
cm_i /= totmass
cm_i = numpy.arctan2(cm_i.imag, cm_i.real) * boxsize / (2 * numpy.pi)
@ -55,24 +46,11 @@ def center_of_mass(points, mass, boxsize):
return cm
@jit(nopython=True)
def periodic_distance(points, reference, boxsize):
@jit(nopython=True, fastmath=True, boundscheck=False)
def periodic_distance(points, reference_point, boxsize):
"""
Compute the 3D distance between multiple points and a reference point using
periodic boundary conditions. This is an optimized JIT implementation.
Parameters
----------
points : 2-dimensional array of shape `(n_points, 3)`
Points to calculate the distance from the reference point.
reference : 1-dimensional array of shape `(3, )`
Reference point.
boxsize : float
Box size.
Returns
-------
dist : 1-dimensional array of shape `(n_points, )`
periodic boundary conditions.
"""
npoints = len(points)
half_box = boxsize / 2
@ -80,7 +58,7 @@ def periodic_distance(points, reference, boxsize):
dist = numpy.zeros(npoints, dtype=points.dtype)
for i in range(npoints):
for j in range(3):
dist_1d = abs(points[i, j] - reference[j])
dist_1d = abs(points[i, j] - reference_point[j])
if dist_1d > (half_box):
dist_1d = boxsize - dist_1d
@ -94,23 +72,7 @@ def periodic_distance(points, reference, boxsize):
@jit(nopython=True, fastmath=True, boundscheck=False)
def periodic_distance_two_points(p1, p2, boxsize):
"""
Compute the 3D distance between two points using periodic boundary
conditions. This is an optimized JIT implementation.
Parameters
----------
p1 : 1-dimensional array of shape `(3, )`
First point.
p2 : 1-dimensional array of shape `(3, )`
Second point.
boxsize : float
Box size.
Returns
-------
dist : 1-dimensional array of shape `(n_points, )`
"""
"""Compute the 3D distance between two points in a periodic box."""
half_box = boxsize / 2
dist = 0
@ -125,47 +87,133 @@ def periodic_distance_two_points(p1, p2, boxsize):
return dist**0.5
@jit(nopython=True)
def periodic_wrap_grid(pos, boxsize=1):
"""Wrap positions in a periodic box."""
for n in range(pos.shape[0]):
for i in range(3):
if pos[n, i] > boxsize:
pos[n, i] -= boxsize
elif pos[n, i] < 0:
pos[n, i] += boxsize
return pos
@jit(nopython=True, fastmath=True, boundscheck=False)
def delta2ncells(delta):
def delta2ncells(field):
"""
Calculate the number of cells in `delta` that are non-zero.
Parameters
----------
delta : 3-dimensional array
Halo density field.
Returns
-------
ncells : int
Number of non-zero cells.
Calculate the number of cells in `field` that are non-zero.
"""
tot = 0
imax, jmax, kmax = delta.shape
imax, jmax, kmax = field.shape
for i in range(imax):
for j in range(jmax):
for k in range(kmax):
if delta[i, j, k] > 0:
if field[i, j, k] > 0:
tot += 1
return tot
def cartesian_to_radec(X):
"""
Calculate the radial distance, RA [0, 360) deg and dec [-90, 90] deg.
"""
x, y, z = X[:, 0], X[:, 1], X[:, 2]
dist = numpy.linalg.norm(X, axis=1)
dec = numpy.arcsin(z / dist)
ra = numpy.arctan2(y, x)
ra[ra < 0] += 2 * numpy.pi
ra *= 180 / numpy.pi
dec *= 180 / numpy.pi
return numpy.vstack([dist, ra, dec]).T
def radec_to_cartesian(X):
"""
Calculate Cartesian coordinates from radial distance, RA [0, 360) deg and
dec [-90, 90] deg.
"""
dist, ra, dec = X[:, 0], X[:, 1], X[:, 2]
ra *= numpy.pi / 180
dec *= numpy.pi / 180
cdec = numpy.cos(dec)
return numpy.vstack([
dist * cdec * numpy.cos(ra),
dist * cdec * numpy.sin(ra),
dist * numpy.sin(dec)
]).T
def real2redshift(pos, vel, observer_location, observer_velocity, box,
periodic_wrap=True, make_copy=True):
r"""
Convert real-space position to redshift space position.
Parameters
----------
pos : 2-dimensional array `(nsamples, 3)`
Real-space Cartesian components in `Mpc / h`.
vel : 2-dimensional array `(nsamples, 3)`
Cartesian velocity in `km / s`.
observer_location: 1-dimensional array `(3,)`
Observer location in `Mpc / h`.
observer_velocity: 1-dimensional array `(3,)`
Observer velocity in `km / s`.
box : py:class:`csiborg.read.CSiBORGBox`
Box units.
periodic_wrap : bool, optional
Whether to wrap around the box, particles may be outside the default
bounds once RSD is applied.
make_copy : bool, optional
Whether to make a copy of `pos` before modifying it.
Returns
-------
pos : 2-dimensional array `(nsamples, 3)`
Redshift-space Cartesian position in `Mpc / h`.
"""
if make_copy:
pos = numpy.copy(pos)
vel = numpy.copy(vel)
H0_inv = 1. / 100
# Place the observer at the origin
pos -= observer_location
vel -= observer_velocity
vr_dot = numpy.einsum('ij,ij->i', pos, vel)
norm2 = numpy.einsum('ij,ij->i', pos, pos)
pos *= (1 + H0_inv * vr_dot / norm2).reshape(-1, 1)
# Place the observer back
pos += observer_location
if not make_copy:
vel += observer_velocity
if periodic_wrap:
boxsize = box.box2mpc(1.)
pos = periodic_wrap_grid(pos, boxsize)
return pos
###############################################################################
# Statistics #
###############################################################################
@jit(nopython=True, fastmath=True, boundscheck=False)
def number_counts(x, bin_edges):
"""
Calculate counts of samples in bins.
Parameters
----------
x : 1-dimensional array
Samples' values.
bin_edges : 1-dimensional array
Bin edges.
Returns
-------
counts : 1-dimensional array
Bin counts.
"""
out = numpy.full(bin_edges.size - 1, numpy.nan, dtype=numpy.float32)
for i in range(bin_edges.size - 1):

108
scripts/field_obs_vp.py Normal file
View File

@ -0,0 +1,108 @@
# Copyright (C) 2022 Richard Stiskalek
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
"""
Script to calculate the peculiar velocity of an observer in the centre of the
CSiBORG box.
"""
from argparse import ArgumentParser
from distutils.util import strtobool
import numpy
from mpi4py import MPI
from taskmaster import work_delegation
from tqdm import tqdm
from utils import get_nsims
try:
import csiborgtools
except ModuleNotFoundError:
import sys
sys.path.append("../")
import csiborgtools
def observer_peculiar_velocity(nsim, parser_args):
"""
Calculate the peculiar velocity of an observer in the centre of the box
for several smoothing scales.
"""
pos = numpy.array([0.5, 0.5, 0.5]).reshape(-1, 3)
boxsize = 677.7
smooth_scales = [0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0]
observer_vp = numpy.full((len(smooth_scales), 3), numpy.nan,
dtype=numpy.float32)
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
field_path = paths.field("velocity", parser_args.MAS, parser_args.grid,
nsim, in_rsp=False)
field0 = numpy.load(field_path)
for j, smooth_scale in enumerate(tqdm(smooth_scales,
desc="Smoothing the fields",
disable=not parser_args.verbose)):
if smooth_scale > 0:
field = [None, None, None]
for k in range(3):
field[k] = csiborgtools.field.smoothen_field(
field0[k], smooth_scale, boxsize)
else:
field = field0
v = csiborgtools.field.evaluate_cartesian(
field[0], field[1], field[2], pos=pos)
observer_vp[j, 0] = v[0][0]
observer_vp[j, 1] = v[1][0]
observer_vp[j, 2] = v[2][0]
fout = paths.observer_peculiar_velocity(parser_args.MAS, parser_args.grid,
nsim)
if parser_args.verbose:
print(f"Saving to ... `{fout}`")
numpy.savez(fout, smooth_scales=smooth_scales, observer_vp=observer_vp)
return observer_vp
###############################################################################
# Command line interface #
###############################################################################
if __name__ == "__main__":
parser = ArgumentParser()
parser.add_argument("--nsims", type=int, nargs="+", default=None,
help="IC realisations. `-1` for all simulations.")
parser.add_argument("--kind", type=str,
choices=["density", "rspdensity", "velocity", "radvel",
"potential", "environment"],
help="What derived field to calculate?")
parser.add_argument("--MAS", type=str,
choices=["NGP", "CIC", "TSC", "PCS"])
parser.add_argument("--grid", type=int, help="Grid resolution.")
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
help="Verbosity flag for reading in particles.")
parser.add_argument("--simname", type=str, default="csiborg",
help="Verbosity flag for reading in particles.")
parser_args = parser.parse_args()
comm = MPI.COMM_WORLD
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsims = get_nsims(parser_args, paths)
def main(nsim):
return observer_peculiar_velocity(nsim, parser_args)
work_delegation(main, nsims, comm, master_verbose=True)

250
scripts/field_prop.py
View File

@ -43,44 +43,29 @@ from utils import get_nsims
def density_field(nsim, parser_args, to_save=True):
"""
Calculate the density field in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
field : 3-dimensional array
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
gen = csiborgtools.field.DensityField(box, parser_args.MAS)
if parser_args.kind == "density":
field = gen(parts, parser_args.grid, in_rsp=False,
verbose=parser_args.verbose)
if parser_args.in_rsp:
field = csiborgtools.field.field2rsp(*field, parts=parts, box=box,
verbose=parser_args.verbose)
if not parser_args.in_rsp:
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
gen = csiborgtools.field.DensityField(box, parser_args.MAS)
field = gen(parts, parser_args.grid, verbose=parser_args.verbose)
else:
field = gen(parts, parser_args.grid, in_rsp=parser_args.in_rsp,
verbose=parser_args.verbose)
field = numpy.load(paths.field(
"density", parser_args.MAS, parser_args.grid, nsim, False))
radvel_field = numpy.load(paths.field(
"radvel", parser_args.MAS, parser_args.grid, nsim, False))
if parser_args.smooth_scale > 0:
field = csiborgtools.field.smoothen_field(
field, parser_args.smooth_scale, box.boxsize * box.h, threads=1)
field = csiborgtools.field.field2rsp(field, radvel_field, box,
parser_args.MAS)
if to_save:
fout = paths.field(parser_args.kind, parser_args.MAS, parser_args.grid,
nsim, parser_args.in_rsp, parser_args.smooth_scale)
nsim, parser_args.in_rsp)
print(f"{datetime.now()}: saving output to `{fout}`.")
numpy.save(fout, field)
return field
@ -93,35 +78,20 @@ def density_field(nsim, parser_args, to_save=True):
def velocity_field(nsim, parser_args, to_save=True):
"""
Calculate the velocity field in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
velfield : 4-dimensional array
Calculate the velocity field in a CSiBORG simulation.
"""
if parser_args.in_rsp:
raise NotImplementedError("Velocity field in RSP is not implemented.")
if parser_args.smooth_scale > 0:
raise NotImplementedError(
"Smoothed velocity field is not implemented.")
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
mpart = 1.1641532e-10 # Particle mass in CSiBORG simulations.
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
field = gen(parts, parser_args.grid, mpart, verbose=parser_args.verbose)
field = gen(parts, parser_args.grid, verbose=parser_args.verbose)
if to_save:
fout = paths.field("velocity", parser_args.MAS, parser_args.grid,
@ -131,57 +101,6 @@ def velocity_field(nsim, parser_args, to_save=True):
return field
###############################################################################
# Potential field #
###############################################################################
def potential_field(nsim, parser_args, to_save=True):
"""
Calculate the potential field in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
potential : 3-dimensional array
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
# Load the real space overdensity field
density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
rho = numpy.load(paths.field("density", parser_args.MAS, parser_args.grid,
nsim, in_rsp=False))
if parser_args.smooth_scale > 0:
rho = csiborgtools.field.smoothen_field(rho, parser_args.smooth_scale,
box.boxsize * box.h, threads=1)
rho = density_gen.overdensity_field(rho)
# Calculate the real space potentiel field
gen = csiborgtools.field.PotentialField(box, parser_args.MAS)
field = gen(rho)
if parser_args.in_rsp:
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
field = csiborgtools.field.field2rsp(*field, parts=parts, box=box,
verbose=parser_args.verbose)
if to_save:
fout = paths.field(parser_args.kind, parser_args.MAS, parser_args.grid,
nsim, parser_args.in_rsp, parser_args.smooth_scale)
print(f"{datetime.now()}: saving output to `{fout}`.")
numpy.save(fout, field)
return field
###############################################################################
# Radial velocity field #
###############################################################################
@ -190,33 +109,21 @@ def potential_field(nsim, parser_args, to_save=True):
def radvel_field(nsim, parser_args, to_save=True):
"""
Calculate the radial velocity field in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
radvel : 3-dimensional array
"""
if parser_args.in_rsp:
raise NotImplementedError("Radial vel. field in RSP not implemented.")
if parser_args.smooth_scale > 0:
raise NotImplementedError(
"Smoothed radial vel. field not implemented.")
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
vel = numpy.load(paths.field("velocity", parser_args.MAS, parser_args.grid,
nsim, parser_args.in_rsp))
observer_velocity = csiborgtools.field.observer_vobs(vel)
gen = csiborgtools.field.VelocityField(box, parser_args.MAS)
field = gen.radial_velocity(vel)
field = gen.radial_velocity(vel, observer_velocity)
if to_save:
fout = paths.field("radvel", parser_args.MAS, parser_args.grid,
nsim, parser_args.in_rsp)
@ -224,6 +131,43 @@ def radvel_field(nsim, parser_args, to_save=True):
numpy.save(fout, field)
return field
###############################################################################
# Potential field #
###############################################################################
def potential_field(nsim, parser_args, to_save=True):
"""
Calculate the potential field in the CSiBORG simulation.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
if not parser_args.in_rsp:
rho = numpy.load(paths.field(
"density", parser_args.MAS, parser_args.grid, nsim, in_rsp=False))
density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
rho = density_gen.overdensity_field(rho)
gen = csiborgtools.field.PotentialField(box, parser_args.MAS)
field = gen(rho)
else:
field = numpy.load(paths.field(
"potential", parser_args.MAS, parser_args.grid, nsim, False))
radvel_field = numpy.load(paths.field(
"radvel", parser_args.MAS, parser_args.grid, nsim, False))
field = csiborgtools.field.field2rsp(field, radvel_field, box,
parser_args.MAS)
if to_save:
fout = paths.field(parser_args.kind, parser_args.MAS, parser_args.grid,
nsim, parser_args.in_rsp)
print(f"{datetime.now()}: saving output to `{fout}`.")
numpy.save(fout, field)
return field
###############################################################################
# Environment classification #
@ -233,77 +177,47 @@ def radvel_field(nsim, parser_args, to_save=True):
def environment_field(nsim, parser_args, to_save=True):
"""
Calculate the environmental classification in the CSiBORG simulation.
Parameters
----------
nsim : int
Simulation index.
parser_args : argparse.Namespace
Parsed arguments.
to_save : bool, optional
Whether to save the output to disk.
Returns
-------
env : 3-dimensional array
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
gen = csiborgtools.field.TidalTensorField(box, parser_args.MAS)
# Load the real space overdensity field
if parser_args.verbose:
print(f"{datetime.now()}: loading density field.")
rho = numpy.load(paths.field("density", parser_args.MAS, parser_args.grid,
nsim, in_rsp=False))
if parser_args.smooth_scale > 0:
rho = csiborgtools.field.smoothen_field(rho, parser_args.smooth_scale,
box.boxsize * box.h, threads=1)
rho = numpy.load(paths.field(
"density", parser_args.MAS, parser_args.grid, nsim, in_rsp=False))
density_gen = csiborgtools.field.DensityField(box, parser_args.MAS)
rho = density_gen.overdensity_field(rho)
# Calculate the real space tidal tensor field, delete overdensity.
if parser_args.verbose:
print(f"{datetime.now()}: calculating tidal tensor field.")
tensor_field = gen(rho)
gen = csiborgtools.field.TidalTensorField(box, parser_args.MAS)
field = gen(rho)
del rho
collect()
# Optionally drag the field to RSP.
if parser_args.in_rsp:
parts = csiborgtools.read.read_h5(paths.particles(nsim, "csiborg"))
parts = parts["particles"]
fields = (tensor_field.T00, tensor_field.T11, tensor_field.T22,
tensor_field.T01, tensor_field.T02, tensor_field.T12)
radvel_field = numpy.load(paths.field(
"radvel", parser_args.MAS, parser_args.grid, nsim, False))
args = (radvel_field, box, parser_args.MAS)
T00, T11, T22, T01, T02, T12 = csiborgtools.field.field2rsp(
*fields, parts=parts, box=box, verbose=parser_args.verbose)
tensor_field.T00[...] = T00
tensor_field.T11[...] = T11
tensor_field.T22[...] = T22
tensor_field.T01[...] = T01
tensor_field.T02[...] = T02
tensor_field.T12[...] = T12
del T00, T11, T22, T01, T02, T12
field.T00 = csiborgtools.field.field2rsp(field.T00, *args)
field.T11 = csiborgtools.field.field2rsp(field.T11, *args)
field.T22 = csiborgtools.field.field2rsp(field.T22, *args)
field.T01 = csiborgtools.field.field2rsp(field.T01, *args)
field.T02 = csiborgtools.field.field2rsp(field.T02, *args)
field.T12 = csiborgtools.field.field2rsp(field.T12, *args)
del radvel_field
collect()
# Calculate the eigenvalues of the tidal tensor field, delete tensor field.
if parser_args.verbose:
print(f"{datetime.now()}: calculating eigenvalues.")
eigvals = gen.tensor_field_eigvals(tensor_field)
del tensor_field
eigvals = gen.tensor_field_eigvals(field)
del field
collect()
# Classify the environment based on the eigenvalues.
if parser_args.verbose:
print(f"{datetime.now()}: classifying environment.")
env = gen.eigvals_to_environment(eigvals)
del eigvals
collect()
if to_save:
fout = paths.field("environment", parser_args.MAS, parser_args.grid,
nsim, parser_args.in_rsp, parser_args.smooth_scale)
nsim, parser_args.in_rsp)
print(f"{datetime.now()}: saving output to `{fout}`.")
numpy.save(fout, env)
return env
@ -327,8 +241,6 @@ if __name__ == "__main__":
parser.add_argument("--grid", type=int, help="Grid resolution.")
parser.add_argument("--in_rsp", type=lambda x: bool(strtobool(x)),
help="Calculate in RSP?")
parser.add_argument("--smooth_scale", type=float, default=0,
help="Smoothing scale in Mpc/h.")
parser.add_argument("--verbose", type=lambda x: bool(strtobool(x)),
help="Verbosity flag for reading in particles.")
parser.add_argument("--simname", type=str, default="csiborg",

23
scripts/fit_hmf.py
View File

@ -37,21 +37,6 @@ except ModuleNotFoundError:
def get_counts(nsim, bins, paths, parser_args):
"""
Calculate and save the number of haloes in each mass bin.
Parameters
----------
nsim : int
Simulation index.
bins : 1-dimensional array
Array of bin edges (in log10 mass).
paths : csiborgtools.read.Paths
Paths object.
parser_args : argparse.Namespace
Parsed command-line arguments.
Returns
-------
None
"""
simname = parser_args.simname
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
@ -75,13 +60,14 @@ def get_counts(nsim, bins, paths, parser_args):
counts[nobs, :] = csiborgtools.number_counts(logmass, bins)
elif simname == "quijote_full":
cat = csiborgtools.read.QuijoteHaloCatalogue(
nsim, paths, nsnap=4, load_fitted=False, load_initial=False)
nsim, paths, nsnap=4, load_fitted=False, load_initial=False,
load_backup=parser_args.from_quijote_backup)
logmass = numpy.log10(cat["group_mass"])
counts = csiborgtools.number_counts(logmass, bins)
else:
raise ValueError(f"Unknown simulation name `{simname}`.")
fout = paths.halo_counts(simname, nsim)
fout = paths.halo_counts(simname, nsim, parser_args.from_quijote_backup)
if parser_args.verbose:
print(f"{datetime.now()}: saving halo counts to `{fout}`.")
numpy.savez(fout, counts=counts, bins=bins, rmax=parser_args.Rmax)
@ -97,6 +83,9 @@ if __name__ == "__main__":
parser.add_argument(
"--Rmax", type=float, default=155,
help="High-res region radius in Mpc / h. Ignored for `quijote_full`.")
parser.add_argument("--from_quijote_backup",
type=lambda x: bool(strtobool(x)), default=False,
help="Flag to indicate Quijote backup data.")
parser.add_argument("--lims", type=float, nargs="+", default=[11., 16.],
help="Mass limits in Msun / h.")
parser.add_argument("--bw", type=float, default=0.2,

9
scripts/fit_init.py
View File

@ -41,15 +41,6 @@ def _main(nsim, simname, verbose):
"""
Calculate the Lagrangian halo centre of mass and Lagrangian patch size in
the initial snapshot.
Parameters
----------
nsim : int
IC realisation index.
simname : str
Simulation name.
verbose : bool
Verbosity flag.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
cols = [("index", numpy.int32),

31
scripts/match_all.py
View File

@ -29,16 +29,6 @@ def get_combs(simname):
"""
Get the list of all pairs of IC indices and permute them with a fixed
seed.
Parameters
----------
simname : str
Simulation name.
Returns
-------
combs : list
List of pairs of simulations.
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
combs = list(combinations(paths.get_ics(simname), 2))
@ -50,27 +40,6 @@ def get_combs(simname):
def main(comb, kind, simname, min_logmass, sigma, mult, verbose):
"""
Match a pair of simulations.
Parameters
----------
comb : tuple
Pair of simulation IC indices.
kind : str
Kind of matching.
simname : str
Simulation name.
min_logmass : float
Minimum log halo mass.
sigma : float
Smoothing scale in number of grid cells.
mult : float
Multiplicative factor for search radius.
verbose : bool
Verbosity flag.
Returns
-------
None
"""
nsim0, nsimx = comb
if kind == "overlap":

11
scripts/utils.py
View File

@ -52,7 +52,7 @@ def get_nsims(args, paths):
Simulation indices.
"""
if args.nsims is None or args.nsims[0] == -1:
nsims = paths.get_ics(args.simname)
nsims = paths.get_ics(args.simname, args.from_quijote_backup)
else:
nsims = args.nsims
return list(nsims)
@ -93,9 +93,14 @@ def read_single_catalogue(args, config, nsim, run, rmax, paths, nobs=None):
nsim, paths, load_fitted=True, load_inital=True,
with_lagpatch=False)
else:
if args.from_quijote_backup:
load_fitted = False
load_initial = False
cat = csiborgtools.read.QuijoteHaloCatalogue(
nsim, paths, nsnap=4, load_fitted=True, load_initial=True,
with_lagpatch=False)
nsim, paths, nsnap=4, load_fitted=load_fitted,
load_initial=load_initial, with_lagpatch=False,
load_backup=args.from_quijote_backup)
if nobs is not None:
# We may optionally already here pick a fiducial observer.
cat = cat.pick_fiducial_observer(nobs, args.Rmax)

40
scripts_plots/plot_data.py
View File

@ -305,7 +305,7 @@ def plot_hmf_quijote_full(pdf=False):
plt.close()
def load_field(kind, nsim, grid, MAS, in_rsp=False, smooth_scale=None):
def load_field(kind, nsim, grid, MAS, in_rsp=False):
r"""
Load a single field.
@ -321,16 +321,13 @@ def load_field(kind, nsim, grid, MAS, in_rsp=False, smooth_scale=None):
Mass assignment scheme.
in_rsp : bool, optional
Whether to load the field in redshift space.
smooth_scale : float, optional
Smoothing scale in :math:`\mathrm{Mpc} / h`.
Returns
-------
field : n-dimensional array
"""
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
return numpy.load(paths.field(kind, MAS, grid, nsim, in_rsp=in_rsp,
smooth_scale=smooth_scale))
return numpy.load(paths.field(kind, MAS, grid, nsim, in_rsp=in_rsp))
###############################################################################
@ -377,16 +374,16 @@ def plot_projected_field(kind, nsim, grid, in_rsp, smooth_scale, MAS="PCS",
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
if kind == "overdensity":
field = load_field("density", nsim, grid, MAS=MAS, in_rsp=in_rsp,
smooth_scale=smooth_scale)
field = load_field("density", nsim, grid, MAS=MAS, in_rsp=in_rsp)
density_gen = csiborgtools.field.DensityField(box, MAS)
field = density_gen.overdensity_field(field) + 1
field = density_gen.overdensity_field(field) + 2
field = numpy.log10(field)
elif kind == "borg_density":
field = File(paths.borg_mcmc(nsim), 'r')
field = field["scalars"]["BORG_final_density"][...]
else:
field = load_field(kind, nsim, grid, MAS=MAS, in_rsp=in_rsp,
smooth_scale=smooth_scale)
field = load_field(kind, nsim, grid, MAS=MAS, in_rsp=in_rsp)
if kind == "velocity":
field = field[vel_component, ...]
@ -423,6 +420,9 @@ def plot_projected_field(kind, nsim, grid, in_rsp, smooth_scale, MAS="PCS",
else:
ax[i].imshow(img, vmin=vmin, vmax=vmax, cmap=cmap)
k = img.shape[0] // 2
ax[i].scatter(k, k, marker="x", s=5, zorder=2, c="red")
frad = 155.5 / 677.7
R = 155.5 / 677.7 * grid
if slice_find is None:
@ -487,6 +487,7 @@ def plot_projected_field(kind, nsim, grid, in_rsp, smooth_scale, MAS="PCS",
else:
fig.colorbar(im, cax=cbar_ax, label=clabel)
fig.tight_layout(h_pad=0, w_pad=0)
for ext in ["png"] if pdf is False else ["png", "pdf"]:
fout = join(
@ -587,7 +588,7 @@ def plot_sky_distribution(field, nsim, grid, nside, smooth_scale=None,
nsnap = max(paths.get_snapshots(nsim, "csiborg"))
box = csiborgtools.read.CSiBORGBox(nsnap, nsim, paths)
if field== "overdensity":
if field == "overdensity":
field = load_field("density", nsim, grid, MAS=MAS, in_rsp=False,
smooth_scale=smooth_scale)
density_gen = csiborgtools.field.DensityField(box, MAS)
@ -652,7 +653,7 @@ if __name__ == "__main__":
if False:
plot_mass_vs_ncells(7444, pdf=False)
if True:
if False:
plot_hmf(pdf=False)
if False:
@ -665,16 +666,17 @@ if __name__ == "__main__":
plot_groups=False, dmin=45, dmax=60,
plot_halos=5e13, volume_weight=True)
if False:
kind = "overdensity"
grid = 256
if True:
kind = "potential"
grid = 512
smooth_scale = 0
# plot_projected_field("overdensity", 7444, grid, in_rsp=True,
# highres_only=False)
plot_projected_field(kind, 7444, grid, in_rsp=False,
smooth_scale=smooth_scale, slice_find=0.5,
MAS="PCS",
highres_only=True)
# for in_rsp in [True, False]:
for in_rsp in [True, False]:
plot_projected_field(kind, 7444, grid, in_rsp=in_rsp,
smooth_scale=smooth_scale, slice_find=0.5,
MAS="PCS", highres_only=True)
if False:
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)

129
scripts_plots/plot_match.py
View File

@ -191,7 +191,7 @@ def get_mtot_vs_maxpairoverlap(nsim0, simname, mass_kind, min_logmass,
def get_max(y_):
if len(y_) == 0:
return 0
return numpy.max(y_)
return numpy.nanmax(y_)
reader = csiborgtools.read.NPairsOverlap(cat0, catxs, paths, min_logmass)
@ -218,7 +218,6 @@ def mtot_vs_maxpairoverlap(nsim0, simname, mass_kind, min_logmass, smoothed,
x, y, xbins = get_mtot_vs_maxpairoverlap(nsim0, simname, mass_kind,
min_logmass, smoothed, nbins)
plt.close("all")
with plt.style.context(plt_utils.mplstyle):
plt.figure()
plt.hexbin(x, y, mincnt=1, gridsize=50, bins="log")
@ -252,6 +251,87 @@ def mtot_vs_maxpairoverlap(nsim0, simname, mass_kind, min_logmass, smoothed,
plt.close()
# --------------------------------------------------------------------------- #
###############################################################################
# Total DM halo mass vs maximum pair overlap consistency #
###############################################################################
# --------------------------------------------------------------------------- #
@cache_to_disk(120)
def get_mtot_vs_maxpairoverlap_consistency(nsim0, simname, mass_kind,
min_logmass, smoothed):
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsimxs = csiborgtools.read.get_cross_sims(simname, nsim0, paths,
min_logmass, smoothed=smoothed)
cat0 = open_cat(nsim0, simname)
catxs = open_cats(nsimxs, simname)
reader = csiborgtools.read.NPairsOverlap(cat0, catxs, paths, min_logmass)
x = numpy.log10(cat0[mass_kind])
mask = x > min_logmass
x = x[mask]
nhalos = len(x)
y = numpy.full((len(catxs), nhalos), numpy.nan)
for i in trange(len(catxs), desc="Stacking catalogues"):
overlaps = reader[i].overlap(smoothed)
for j in range(nhalos):
# if len(overlaps[j]) > 0:
y[i, j] = numpy.sum(overlaps[j])
return x, y
def mtot_vs_maxpairoverlap_consistency(nsim0, simname, mass_kind, min_logmass,
smoothed, ext="png"):
left_edges = numpy.arange(min_logmass, 15, 0.1)
# delete_disk_caches_for_function("get_mtot_vs_maxpairoverlap_consistency")
x, y0 = get_mtot_vs_maxpairoverlap_consistency(nsim0, simname, mass_kind,
min_logmass, smoothed)
nsims, nhalos = y0.shape
x_2, y0_2 = get_mtot_vs_maxpairoverlap_consistency(
0, "quijote", "group_mass", min_logmass, smoothed)
nsims2, nhalos = y0_2.shape
with plt.style.context(plt_utils.mplstyle):
plt.figure()
yplot = numpy.full(len(left_edges), numpy.nan)
yplot_2 = numpy.full(len(left_edges), numpy.nan)
for ymin in [0.3]:
y = numpy.sum(y0 > ymin, axis=0) / nsims
y_2 = numpy.sum(y0_2 > ymin, axis=0) / nsims2
for i, left_edge in enumerate(left_edges):
mask = x > left_edge
yplot[i] = numpy.mean(y[mask]) #/ nsims
mask = x_2 > left_edge
yplot_2[i] = numpy.mean(y_2[mask]) #/ nsims
plt.plot(left_edges, yplot, label="CSiBORG")
plt.plot(left_edges, yplot_2, label="Quijote")
plt.legend()
# y2 = numpy.concatenate(y0)
# y2 = y2[y2 > 0]
# m = y0 > 0
# plt.hist(y0[m], bins=30, density=True, histtype="step")
# m = y0_2 > 0
# plt.hist(y0_2[m], bins=30, density=True, histtype="step")
# plt.yscale("log")
plt.tight_layout()
fout = join(
plt_utils.fout,
f"mass_vs_max_pair_overlap_consistency_{simname}_{nsim0}.{ext}")
print(f"Saving to `{fout}`.")
plt.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
# --------------------------------------------------------------------------- #
###############################################################################
# Total DM halo mass vs summed pair overlaps #
@ -876,8 +956,7 @@ def get_matching_max_vs_overlap(simname, nsim0, min_logmass, mult):
def matching_max_vs_overlap(simname, nsim0, min_logmass):
left_edges = numpy.arange(min_logmass, 15, 0.1)
delete_disk_caches_for_function("get_matching_max_vs_overlap")
nsims = 100 if simname == "csiborg" else 9
with plt.style.context("science"):
fig, axs = plt.subplots(ncols=2, figsize=(3.5 * 2, 2.625))
@ -891,34 +970,36 @@ def matching_max_vs_overlap(simname, nsim0, min_logmass):
success = x["success"]
nbins = len(left_edges)
y = numpy.full((nbins, 100), numpy.nan)
y2 = numpy.full((nbins, 100), numpy.nan)
y = numpy.full((nbins, nsims), numpy.nan)
y2 = numpy.full(nbins, numpy.nan)
y2err = numpy.full(nbins, numpy.nan)
for i in range(nbins):
m = mass0 > left_edges[i]
for j in range(100):
for j in range(nsims):
y[i, j] = numpy.sum(
max_overlap[m, j] == match_overlap[m, j])
y[i, j] /= numpy.sum(success[m, j])
y2[i, j] = numpy.sum(success[m, j]) / numpy.sum(m)
offset = numpy.random.normal(0, 0.01)
y2[i] = numpy.mean(numpy.sum(success[m, :], axis=1) / nsims)
y2err[i] = numpy.std(numpy.sum(success[m, :], axis=1) / nsims)
offset = numpy.random.normal(0, 0.015)
ysummary = numpy.percentile(y, [16, 50, 84], axis=1)
axs[0].errorbar(
left_edges + offset, ysummary[1],
yerr=[ysummary[1] - ysummary[0], ysummary[2] - ysummary[1]],
capsize=3, c=cols[n],
capsize=4, c=cols[n], ls="dashed",
label=r"$\leq {}~R_{{\rm 200c}}$".format(mult), errorevery=2)
ysummary = numpy.percentile(y2, [16, 50, 84], axis=1)
axs[1].errorbar(
left_edges + offset, ysummary[1], ls="--",
yerr=[ysummary[1] - ysummary[0], ysummary[2] - ysummary[1]],
capsize=3, c=cols[n], errorevery=2)
axs[1].errorbar(left_edges + offset, y2, yerr=y2err,
capsize=4, errorevery=2, c=cols[n], ls="dashed")
axs[0].legend(ncols=2, fontsize="small")
for i in range(2):
axs[i].set_xlabel(r"$\log M_{\rm tot, min} ~ [M_\odot / h]$")
axs[1].set_ylim(0)
axs[0].set_ylabel(r"$f_{\rm agreement}$")
axs[1].set_ylabel(r"$f_{\rm match}$")
@ -1048,7 +1129,7 @@ if __name__ == "__main__":
smoothed = True
nbins = 10
ext = "png"
plot_quijote = False
plot_quijote = True
min_maxoverlap = 0.
funcs = [
@ -1128,5 +1209,19 @@ if __name__ == "__main__":
mtot_vs_maxoverlap_property(0, "quijote", min_logmass, key,
min_maxoverlap, smoothed)
if False:
matching_max_vs_overlap("csiborg", 7444, min_logmass)
if plot_quijote:
matching_max_vs_overlap("quijote", 0, min_logmass)
if True:
matching_max_vs_overlap(7444, min_logmass)
mtot_vs_maxpairoverlap_consistency(
7444, "csiborg", "fof_totpartmass", min_logmass, smoothed,
ext="png")
# if plot_quijote:
# mtot_vs_maxpairoverlap_consistency(
# 0, "quijote", "group_mass", min_logmass, smoothed,
# ext="png")

89
scripts_plots/plot_vobs.py Normal file
View File

@ -0,0 +1,89 @@
# 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.
from os.path import join
import matplotlib.pyplot as plt
import numpy
import scienceplots # noqa
from tqdm import tqdm
import csiborgtools
import plt_utils
def observer_peculiar_velocity(MAS, grid, ext="png"):
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
nsims = paths.get_ics("csiborg")
for n, nsim in enumerate(nsims):
fpath = paths.observer_peculiar_velocity(MAS, grid, nsim)
f = numpy.load(fpath)
if n == 0:
data = numpy.full((len(nsims), *f["observer_vp"].shape), numpy.nan)
smooth_scales = f["smooth_scales"]
data[n] = f["observer_vp"]
for n, smooth_scale in enumerate(tqdm(smooth_scales,
desc="Plotting smooth scales")):
with plt.style.context(plt_utils.mplstyle):
fig, axs = plt.subplots(ncols=3, figsize=(3.5 * 3, 2.625),
sharey=True)
fig.subplots_adjust(wspace=0)
for i, ax in enumerate(axs):
ax.hist(data[:, n, i], bins="auto", histtype="step")
mu, sigma = numpy.mean(data[:, n, i]), numpy.std(data[:, n, i])
ax.set_title(r"$V_{{\rm obs, i}} = {:.3f} \pm {:.3f} ~ \mathrm{{km}} / \mathrm{{s}}$".format(mu, sigma)) # noqa
axs[0].set_xlabel(r"$V_{\rm obs, x} ~ [\mathrm{km} / \mathrm{s}]$")
axs[1].set_xlabel(r"$V_{\rm obs, y} ~ [\mathrm{km} / \mathrm{s}]$")
axs[2].set_xlabel(r"$V_{\rm obs, z} ~ [\mathrm{km} / \mathrm{s}]$")
axs[0].set_ylabel(r"Counts")
fig.suptitle(r"$N_{{\rm grid}} = {}$, $\sigma_{{\rm smooth}} = {:.2f} ~ [\mathrm{{Mpc}} / h]$".format(grid, smooth_scale)) # noqa
fig.tight_layout(w_pad=0)
fout = join(plt_utils.fout,
f"observer_vp_{grid}_{smooth_scale}.{ext}")
fig.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
with plt.style.context(plt_utils.mplstyle):
fig, axs = plt.subplots(ncols=3, figsize=(3.5 * 3, 2.625))
for i, ax in enumerate(axs):
ymu = numpy.mean(data[..., i], axis=0)
ystd = numpy.std(data[..., i], axis=0)
ylow, yupp = ymu - ystd, ymu + ystd
ax.plot(smooth_scales, ymu, c="k")
ax.fill_between(smooth_scales, ylow, yupp, color="k", alpha=0.2)
ax.set_xlabel(r"$\sigma_{{\rm smooth}} ~ [\mathrm{{Mpc}} / h]$")
axs[0].set_ylabel(r"$V_{\rm obs, x} ~ [\mathrm{km} / \mathrm{s}]$")
axs[1].set_ylabel(r"$V_{\rm obs, y} ~ [\mathrm{km} / \mathrm{s}]$")
axs[2].set_ylabel(r"$V_{\rm obs, z} ~ [\mathrm{km} / \mathrm{s}]$")
fig.suptitle(r"$N_{{\rm grid}} = {}$".format(grid))
fig.tight_layout(w_pad=0)
fout = join(plt_utils.fout, f"observer_vp_summary_{grid}.{ext}")
fig.savefig(fout, dpi=plt_utils.dpi, bbox_inches="tight")
plt.close()
if __name__ == "__main__":
observer_peculiar_velocity("PCS", 512)