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Potential (#13)

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* add basic density field

* Add TODO

* add field smoothing

* update how pos are calculated

* add transforms both ways

* add import

* add sky density

* add make skymap func

* update TODO

* update gitignore

* add potential field calculation

* delete boxsize setter

* add tidal tensor
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Richard Stiskalek 2022-11-27 07:53:38 +00:00 committed by GitHub
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1
.gitignore vendored
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@ -16,3 +16,4 @@ build/*
csiborgtools.egg-info/*
scripts/playground_*
scripts/playground.ipynb
Pylians3/*

2
csiborgtools/__init__.py
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@ -13,4 +13,4 @@
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
from csiborgtools import (read, match, utils, units, fits) # noqa
from csiborgtools import (read, match, utils, units, fits, field) # noqa

16
csiborgtools/field/__init__.py Normal file
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@ -0,0 +1,16 @@
# 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.
from .density import DensityField # noqa

323
csiborgtools/field/density.py Normal file
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@ -0,0 +1,323 @@
# 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.
import numpy
import MAS_library as MASL
import smoothing_library as SL
from warnings import warn
from tqdm import trange
from ..units import (BoxUnits, radec_to_cartesian)
class DensityField:
"""
Density field calculations. Based primarily on routines of Pylians [1].
Parameters
----------
particles : structured array
Particle array. Must contain keys `['x', 'y', 'z', 'M']`.
box : :py:class:`csiborgtools.units.BoxUnits`
The simulation box information and transformations.
References
----------
[1] https://pylians3.readthedocs.io/
"""
_particles = None
_boxsize = None
_box = None
def __init__(self, particles, box):
self.particles = particles
self.box = box
self._boxsize = 1.
@property
def particles(self):
"""
Particles structured array.
Returns
-------
particles : structured array
"""
return self._particles
@particles.setter
def particles(self, particles):
"""Set `particles`, checking it has the right columns."""
if any(p not in particles.dtype.names for p in ('x', 'y', 'z', 'M')):
raise ValueError("`particles` must be a structured array "
"containing `['x', 'y', 'z', 'M']`.")
self._particles = particles
@property
def box(self):
"""
The simulation box information and transformations.
Returns
-------
box : :py:class:`csiborgtools.units.BoxUnits`
"""
return self._box
@box.setter
def box(self, box):
"""Set the simulation box."""
if not isinstance(box, BoxUnits):
raise TypeError("`box` must be `BoxUnits` instance.")
self._box = box
@property
def boxsize(self):
"""
Boxsize.
Returns
-------
boxsize : float
"""
return self._boxsize
@staticmethod
def _force_f32(x, name):
if x.dtype != numpy.float32:
warn("Converting `{}` to float32.".format(name))
x = x.astype(numpy.float32)
return x
def density_field(self, grid, verbose=True):
"""
Calculate the density field using a Pylians routine [1, 2]. Enforces
float32 precision.
Parameters
----------
grid : int
The grid size.
verbose : float, optional
A verbosity flag. By default `True`.
Returns
-------
rho : 3-dimensional array of shape `(grid, grid, grid)`.
Density field.
References
----------
[1] https://pylians3.readthedocs.io/
[2] https://github.com/franciscovillaescusa/Pylians3/blob/master
/library/MAS_library/MAS_library.pyx
"""
pos = numpy.vstack([self.particles[p] for p in ('x', 'y', 'z')]).T
pos *= self.boxsize
pos = self._force_f32(pos, "pos")
weights = self._force_f32(self.particles['M'], 'M')
MAS = "CIC" # Cloud in cell
# Pre-allocate and do calculations
rho = numpy.zeros((grid, grid, grid), dtype=numpy.float32)
MASL.MA(pos, rho, self.boxsize, MAS, W=weights, verbose=verbose)
return rho
def overdensity_field(self, grid, verbose=True):
r"""
Calculate the overdensity field using Pylians routines.
Defined as :math:`\rho/ <\rho> - 1`.
Parameters
----------
grid : int
The grid size.
verbose : float, optional
A verbosity flag. By default `True`.
Returns
-------
overdensity : 3-dimensional array of shape `(grid, grid, grid)`.
Overdensity field.
"""
# Get the overdensity
delta = self.density_field(grid, verbose)
delta /= delta.mean()
delta -= 1
return delta
def potential_field(self, grid, verbose=True):
"""
Calculate the potential field using Pylians routines.
Parameters
----------
grid : int
The grid size.
verbose : float, optional
A verbosity flag. By default `True`.
Returns
-------
potential : 3-dimensional array of shape `(grid, grid, grid)`.
Potential field.
"""
delta = self.overdensity_field(grid, verbose)
if verbose:
print("Calculating potential from the overdensity..")
return MASL.potential(delta, self.box._omega_m, self.box._aexp, "CIC")
def tensor_field(self, grid, verbose=True):
"""
Calculate the tidal tensor field.
Parameters
----------
grid : int
The grid size.
verbose : float, optional
A verbosity flag. By default `True`.
Returns
-------
tidal_tensor : :py:class:`MAS_library.tidal_tensor`
Tidal tensor object, whose attributes `tidal_tensor.Tij` contain
the relevant tensor components.
"""
delta = self.overdensity_field(grid, verbose)
return MASL.tidal_tensor(delta, self.box._omega_m, self.box._aexp,
"CIC")
def smooth_field(self, field, scale, threads=1):
"""
Smooth a field with a Gaussian filter.
Parameters
----------
field : 3-dimensional array of shape `(grid, grid, grid)`
The field to be smoothed.
scale : float
The smoothing scale of the Gaussian filter. Units must match that
of `self.boxsize`.
threads : int, optional
Number of threads. By default 1.
Returns
-------
smoothed_field : 3-dimensional array of shape `(grid, grid, grid)`
"""
Filter = "Gaussian"
grid = field.shape[0]
# FFT of the filter
W_k = SL.FT_filter(self.boxsize, scale, grid, Filter, threads)
return SL.field_smoothing(field, W_k, threads)
def evaluate_field(self, pos, field):
"""
Evaluate the field at Cartesian coordinates.
Parameters
----------
pos : 2-dimensional array of shape `(n_samples, 3)`
Positions to evaluate the density field. The coordinates span range
of [0, boxsize].
field : 3-dimensional array of shape `(grid, grid, grid)`
The density field that is to be interpolated.
Returns
-------
interp_field : 1-dimensional array of shape `(n_samples,).
Interpolated field at `pos`.
"""
self._force_f32(pos, "pos")
density_interpolated = numpy.zeros(pos.shape[0], dtype=numpy.float32)
MASL.CIC_interp(field, self.boxsize, pos, density_interpolated)
return density_interpolated
def evaluate_sky(self, pos, field, isdeg=True):
"""
Evaluate the field at given distance, right ascension and declination.
Assumes that the observed is in the centre of the box.
Parameters
----------
pos : 2-dimensional array of shape `(n_samples, 3)`
Spherical coordinates to evaluate the field. Should be distance,
right ascension, declination, respectively.
field : 3-dimensional array of shape `(grid, grid, grid)`
The density field that is to be interpolated. Assumed to be defined
on a Cartesian grid.
isdeg : bool, optional
Whether `ra` and `dec` are in degres. By default `True`.
Returns
-------
interp_field : 1-dimensional array of shape `(n_samples,).
Interpolated field at `pos`.
"""
self._force_f32(pos, "pos")
X = numpy.vstack(
radec_to_cartesian(*(pos[:, i] for i in range(3)), isdeg)).T
X = X.astype(numpy.float32)
# Place the observer at the center of the box
X += 0.5 * self.boxsize
return self.evaluate_field(X, field)
def make_sky_map(self, ra, dec, field, dist_marg, isdeg=True,
verbose=True):
"""
Make a sky map of a density field. Places the observed in the center of
the box and evaluates the field in directions `ra`, `dec`. At each such
position evaluates the field at distances `dist_marg` and sums these
interpolated values of the field.
Parameters
----------
ra, dec : 1-dimensional arrays of shape `(n_pos, )`
Directions to evaluate the field. Assumes `dec` is in [-90, 90]
degrees (or equivalently in radians).
field : 3-dimensional array of shape `(grid, grid, grid)`
The density field that is to be interpolated. Assumed to be defined
on a Cartesian grid `[0, self.boxsize]^3`.
dist_marg : 1-dimensional array
Radial distances to evaluate the field.
isdeg : bool, optional
Whether `ra` and `dec` are in degres. By default `True`.
verbose : bool, optional
Verbosity flag. By default `True`.
Returns
-------
interp_field : 1-dimensional array of shape `(n_pos, )`.
"""
# Angular positions at which to evaluate the field
Nang = ra.size
pos = numpy.vstack([ra, dec]).T
# Now loop over the angular positions, each time evaluating a vector
# of distances. Pre-allocate arrays for speed
ra_loop = numpy.ones_like(dist_marg)
dec_loop = numpy.ones_like(dist_marg)
pos_loop = numpy.ones((dist_marg.size, 3), dtype=numpy.float32)
out = numpy.zeros(Nang, dtype=numpy.float32)
for i in trange(Nang) if verbose else range(Nang):
# Get the position vector for this choice of theta, phi
ra_loop[:] = pos[i, 0]
dec_loop[:] = pos[i, 1]
pos_loop[:] = numpy.vstack([dist_marg, ra_loop, dec_loop]).T
# Evaluate and sum it up
out[i] = numpy.sum(self.evaluate_sky(pos_loop, field, isdeg))
return out

4
csiborgtools/read/make_cat.py
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@ -163,7 +163,9 @@ class HaloCatalogue:
data = data[data["m500"] > min_m500]
# Now calculate spherical coordinates
d, ra, dec = cartesian_to_radec(data)
d, ra, dec = cartesian_to_radec(
data["peak_x"], data["peak_y"], data["peak_z"])
data = add_columns(data, [d, ra, dec], ["dist", "ra", "dec"])
# Cut on separation

2
csiborgtools/units/__init__.py
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@ -13,5 +13,5 @@
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
from .transforms import cartesian_to_radec # noqa
from .transforms import cartesian_to_radec, radec_to_cartesian # noqa
from .box_units import (BoxUnits) # noqa

58
csiborgtools/units/transforms.py
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@ -19,39 +19,49 @@ Various coordinate transformations.
import numpy
def cartesian_to_radec(arr, xpar="peak_x", ypar="peak_y", zpar="peak_z"):
r"""
Extract `x`, `y`, and `z` coordinates from a record array `arr` and
calculate the radial distance :math:`r` in coordinate units, right
ascension :math:`\mathrm{RA} \in [0, 360)` degrees and declination
:math:`\delta \in [-90, 90]` degrees.
def cartesian_to_radec(x, y, z):
"""
Calculate the radial distance, right ascension in [0, 360) degrees and
declination [-90, 90] degrees. Note, the observer should be placed in the
middle of the box.
Parameters
----------
arr : record array
Record array with the Cartesian coordinates.
xpar : str, optional
Name of the x coordinate in the record array.
ypar : str, optional
Name of the y coordinate in the record array.
zpar : str, optional
Name of the z coordinate in the record array.
x, y, z : 1-dimensional arrays
Cartesian coordinates.
Returns
-------
dist : 1-dimensional array
Radial distance.
ra : 1-dimensional array
Right ascension.
dec : 1-dimensional array
Declination.
dist, ra, dec : 1-dimensional arrays
Radial distance, right ascension and declination.
"""
x, y, z = arr[xpar], arr[ypar], arr[zpar]
dist = numpy.sqrt(x**2 + y**2 + z**2)
dec = numpy.rad2deg(numpy.arcsin(z/dist))
ra = numpy.rad2deg(numpy.arctan2(y, x))
# Make sure RA in the correct range
ra[ra < 0] += 360
return dist, ra, dec
def radec_to_cartesian(dist, ra, dec, isdeg=True):
"""
Convert distance, right ascension and declination to Cartesian coordinates.
Parameters
----------
dist, ra, dec : 1-dimensional arrays
The spherical coordinates.
isdeg : bool, optional
Whether `ra` and `dec` are in degres. By default `True`.
Returns
-------
x, y, z : 1-dimensional arrays
Cartesian coordinates.
"""
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 x, y, z