def _load_inverse_variance_map(self,
tube,
output_units="uK_CMB",
band=None):
""" Internal function to return a preloaded inverse var map or load one from a from file.
By default this just returns None so an inv_var map is computed from a white noise level
and a hits map
"""
survey = self.get_survey(tube)
noise_indices = self.get_noise_indices(tube, band)
# If the survey has a set of preloaded invariance maps use them
if hasattr(survey,
"get_ivar_maps") and survey.get_ivar_maps() is not None:
ret = np.array(survey.get_ivar_maps())[noise_indices]
elif (hasattr(survey, "get_ivar_map_filenames")
and survey.get_ivar_map_filenames() is not None):
ivar_map_filenames = survey.get_ivar_map_filenames()
if ivar_map_filenames is None:
return None
ivar_map_filenames = [ivar_map_filenames[i] for i in noise_indices]
ivar_maps = []
for ivar_map_filename in ivar_map_filenames:
ivar_maps.append(self._load_map(ivar_map_filename))
ret = np.array(ivar_maps)
else:
return None
for i in range(self.channel_per_tube):
freq = self.tubes[tube][i].center_frequency
unit_conv = (1 * u.uK_CMB).to_value(
u.Unit(output_units), equivalencies=u.cmb_equivalencies(freq))
ret[i] /= unit_conv**2.0 # divide by square since the default is 1/uK^2
return ret
def get_emission(
self,
freqs: u.GHz,
fwhm: [u.arcmin, None] = None,
weights=None,
output_units=u.uK_RJ,
):
"""Return map in uK_RJ at given frequency or array of frequencies
Parameters
----------
freqs : list or ndarray
Frequency or frequencies in GHz at which compute the signal
fwhm : float (optional)
Smooth the input alms before computing the signal, this can only be used
if the class was initialized with `precompute_output_map` to False.
output_units : str
Output units, as defined in `pysm.convert_units`, by default this is
"uK_RJ" as expected by PySM.
Returns
-------
output_maps : ndarray
Output maps array with the shape (num_freqs, 1 or 3 (I or IQU), npix)
"""
freqs = pysm.utils.check_freq_input(freqs)
weights = pysm.utils.normalize_weights(freqs, weights)
try:
output_map = self.output_map
except AttributeError:
if fwhm is None:
alm = self.alm
else:
alm = hp.smoothalm(self.alm,
fwhm=fwhm.to_value(u.radian),
pol=True,
inplace=False)
output_map = self.compute_output_map(alm)
output_units = u.Unit(output_units)
assert output_units in [u.uK_RJ, u.uK_CMB]
if output_units == u.uK_RJ:
convert_to_uK_RJ = (np.ones(len(freqs), dtype=np.double) *
u.uK_CMB).to_value(
u.uK_RJ,
equivalencies=u.cmb_equivalencies(freqs *
u.GHz))
if len(freqs) == 1:
scaling_factor = convert_to_uK_RJ[0]
else:
scaling_factor = np.trapz(convert_to_uK_RJ * weights, x=freqs)
return output_map.value * scaling_factor << u.uK_RJ
elif output_units == output_map.unit:
return output_map
def __init__(
self,
simulation,
parameters: Union[Dict[str, Any], str,
MbsParameters] = MbsParameters(),
instrument=None,
detector_list=None,
channel_list=None,
):
self.sim = simulation
self.imo = self.sim.imo
if isinstance(parameters, MbsParameters):
self.params = parameters
elif isinstance(parameters, str):
self.params = MbsParameters.from_dict(
simulation.parameters[parameters])
else:
self.params = MbsParameters.from_dict(parameters)
self.instrument = instrument
self.det_list = detector_list
self.ch_list = channel_list
self.pysm_units = u.Unit(self.params.units)
def simulate(
self,
tube,
output_units="uK_CMB",
seed=None,
nsplits=1,
mask_value=None,
atmosphere=True,
hitmap=None,
white_noise_rms=None,
):
"""Create a random realization of the noise power spectrum
Parameters
----------
tube : str
Specify a tube (for SO: ST0-ST3, LT0-LT6) see the `tubes` attribute
output_units : str
Output unit supported by PySM.units, e.g. uK_CMB or K_RJ
seed : integer or tuple of integers, optional
Specify a seed. The seed is converted to a tuple if not already
one and appended to (0,0,6,tube_id) to avoid collisions between
tubes, with the signal sims and with ACT noise sims, where
tube_id is the integer ID of the tube.
nsplits : integer, optional
Number of splits to generate. The splits will have independent noise
realizations, with noise power scaled by a factor of nsplits, i.e. atmospheric
noise is assumed to average down with observing time the same way
the white noise does. By default, only one split (the coadd) is generated.
mask_value : float, optional
The value to set in masked (unobserved) regions. By default, it uses
the value in default_mask_value, which for healpix is healpy.UNSEEN
and for CAR is numpy.nan.
atmosphere : bool, optional
Whether to include the correlated 1/f from the noise model. This is
True by default. If it is set to False, then a pure white noise map
is generated from the white noise power in the noise model, and
the covariance between arrays is ignored.
hitmap : string or map, optional
Provide the path to a hitmap to override the default used for
the tube. You could also provide the hitmap as an array
directly.
white_noise_rms : float or tuple of floats, optional
Optionally scale the simulation so that the small-scale limit white noise
level is white_noise_rms in uK-arcmin (either a single number or
a pair for the dichroic array).
Returns
-------
output_map : ndarray or ndmap
Numpy array with the HEALPix or CAR map realization of noise.
The shape of the returned array is (2,3,nsplits,)+oshape, where
oshape is (npix,) for HEALPix and (Ny,Nx) for CAR.
The first dimension of size 2 corresponds to the two different
bands within a dichroic tube.
See the `band_id` attribute of the Channel class
to identify which is the index of a Channel in the array.
The second dimension corresponds to independent split realizations
of the noise, e.g. it is 1 for full mission.
The third dimension corresponds to the three polarization
Stokes components I,Q,U
The last dimension is the number of pixels
"""
assert nsplits >= 1
if mask_value is None:
mask_value = (default_mask_value["healpix"]
if self.healpix else default_mask_value["car"])
# This seed tuple prevents collisions with the signal sims
# but we should eventually switch to centralized seed
# tracking.
if seed is not None:
try:
iter(seed)
except:
seed = (seed, )
tube_id = self.tubes[tube][0].tube_id
seed = (0, 0, 6, tube_id) + seed
np.random.seed(seed)
# In the third row we return the correlation coefficient P12/sqrt(P11*P22)
# since that can be used straightforwardly when the auto-correlations are re-scaled.
ell, ps_T, ps_P, fsky, wnoise_power, weightsMap = self.get_noise_properties(
tube,
nsplits=nsplits,
hitmap=hitmap,
white_noise_rms=white_noise_rms,
atmosphere=atmosphere,
)
if not (atmosphere):
if self.apply_beam_correction:
raise NotImplementedError(
"Beam correction is not currently implemented for pure-white-noise sims."
)
# If no atmosphere is requested, we use a simpler/faster method
# that generates white noise in real-space.
if self.healpix:
ashape = (hp.nside2npix(self.nside), )
sel = np.s_[:, None, None, None]
pmap = self.pixarea_map
else:
ashape = self.shape[-2:]
sel = np.s_[:, None, None, None, None]
pmap = pixell.enmap.enmap(self.pixarea_map, self.wcs)
spowr = np.sqrt(wnoise_power[sel] / pmap)
output_map = spowr * np.random.standard_normal(
(self.channel_per_tube, nsplits, 3) + ashape)
output_map[:, :, 1:, :] = output_map[:, :, 1:, :] * np.sqrt(2.0)
else:
if self.healpix:
npix = hp.nside2npix(self.nside)
output_map = np.zeros(
(self.channel_per_tube, nsplits, 3, npix))
for i in range(nsplits):
for i_pol in range(3):
output_map[:, i, i_pol] = np.array(
hp.synfast(
ps_T if i_pol == 0 else ps_P,
nside=self.nside,
pol=False,
new=True,
verbose=False,
))
else:
output_map = pixell.enmap.zeros((2, nsplits, 3) + self.shape,
self.wcs)
ps_T = pixell.powspec.sym_expand(np.asarray(ps_T),
scheme="diag")
ps_P = pixell.powspec.sym_expand(np.asarray(ps_P),
scheme="diag")
# TODO: These loops can probably be vectorized
for i in range(nsplits):
for i_pol in range(3):
output_map[:, i, i_pol] = pixell.curvedsky.rand_map(
(self.channel_per_tube, ) + self.shape,
self.wcs,
ps_T if i_pol == 0 else ps_P,
spin=0,
)
for i in range(self.channel_per_tube):
freq = self.tubes[tube][i].center_frequency
if not (self.homogeneous):
good = weightsMap[i] != 0
# Normalize on the Effective sky fraction, see discussion in:
# https://github.com/simonsobs/mapsims/pull/5#discussion_r244939311
output_map[i, :, :,
good] /= np.sqrt(weightsMap[i][good][..., None,
None])
output_map[i, :, :, np.logical_not(good)] = mask_value
unit_conv = (1 * u.uK_CMB).to_value(
u.Unit(output_units), equivalencies=u.cmb_equivalencies(freq))
output_map[i] *= unit_conv
return output_map
def get_inverse_variance(self,
tube,
output_units="uK_CMB",
hitmap=None,
white_noise_rms=None):
"""Get the inverse noise variance in each pixel for the requested tube.
In the noise model, all the splits and all the I,Q,U components have the
same position dependence of the noise variance. Each split just has `nsplits`
times the noise power (or `1/nsplits` the inverse noise variance) and the
Q,U components have 2x times the noise power (or 1/2 times the inverse
noise variance) of the intensity components. The inverse noise variance
provided by this function is for the `nsplits=1` intensity component.
Two maps are stored in the leading dimension, one for each of the
two correlated arrays in the dichroic tube.
Parameters
----------
tube : str
Specify a tube (for SO: ST0-ST3, LT0-LT6) see the `tubes` attribute
output_units : str
Output unit supported by PySM.units, e.g. uK_CMB or K_RJ
hitmap : string or map, optional
Provide the path to a hitmap to override the default used for
the tube. You could also provide the hitmap as an array
directly.
white_noise_rms : float or tuple of floats, optional
Optionally scale the simulation so that the small-scale limit white noise
level is white_noise_rms in uK-arcmin (either a single number or
a pair for the dichroic array).
Returns
-------
ivar_map : ndarray or ndmap
Numpy array with the HEALPix or CAR map of the inverse variance
in each pixel. The default units are uK^(-2). This is an extensive
quantity that depends on the size of pixels.
See the `band_id` attribute of the Channel class
to identify which is the index of a Channel in the array.
"""
ret = self._load_inverse_variance_map(tube, output_units=output_units)
if ret is not None:
return ret
fsky, hitmaps = self._get_requested_hitmaps(tube, hitmap)
wnoise_scale = self._get_wscale_factor(white_noise_rms, tube, fsky)
sel = np.s_[:, None] if self.healpix else np.s_[:, None, None]
whiteNoise = self.get_white_noise_power(tube,
sky_fraction=1,
units="sr")
if whiteNoise is None:
raise AssertionError(
" Survey white noise level not specified. Cannot generate ivar_map"
)
power = whiteNoise[sel] * fsky[sel] * wnoise_scale[:, 0][sel]
"""
We now have the physical white noise power uK^2-sr
and the hitmap
ivar = hitmap * pixel_area * fsky / <hitmap> / power
"""
avgNhits = np.asarray(
[self._average(hitmaps[i]) for i in range(self.channel_per_tube)])
ret = hitmaps * self.pixarea_map * fsky[sel] / avgNhits[sel] / power
# Convert to desired units
for i in range(self.channel_per_tube):
freq = self.tubes[tube][i].center_frequency
unit_conv = (1 * u.uK_CMB).to_value(
u.Unit(output_units), equivalencies=u.cmb_equivalencies(freq))
ret[i] /= unit_conv**2.0 # divide by square since the default is 1/uK^2
return ret
def __init__(
self,
target_nside,
output_units,
has_polarization=True,
line="10",
include_high_galactic_latitude_clouds=False,
polarization_fraction=0.001,
theta_high_galactic_latitude_deg=20.0,
random_seed=1234567,
verbose=False,
run_mcmole3d=False,
map_dist=None,
coord="C",
):
"""Class defining attributes for CO line emission.
CO templates are extracted from Type 1 CO Planck maps.
See further details in https://www.aanda.org/articles/aa/abs/2014/11/aa21553-13/aa21553-13.html
Parameters
----------
target_nside : int
HEALPix NSIDE of the output maps
output_units : str
unit string as defined by `pysm.convert_units`, e.g. uK_RJ, K_CMB
has_polarization : bool
whether or not to simulate also polarization maps
line : string
CO rotational transitions.
Accepted values : 10, 21, 32
polarization_fraction: float
polarisation fraction for polarised CO emission.
include_high_galactic_latitude_clouds: bool
If True it includes a simulation from MCMole3D to include
high Galactic Latitude clouds.
(See more details at http://giuspugl.github.io/mcmole/index.html)
run_mcmole3d: bool
If True it simulates HGL cluds by running MCMole3D, otherwise it coadds
a map of HGL emission.
random_seed: int
set random seed for mcmole3d simulations.
theta_high_galactic_latitude_deg : float
Angle in degree to identify High Galactic Latitude clouds
(i.e. clouds whose latitude b is `|b|> theta_high_galactic_latitude_deg`).
map_dist : mpi4py communicator
Read inputs across a MPI communicator, see pysm.read_map
"""
self.line = line
self.line_index = {"10": 0, "21": 1, "32": 2}[line]
self.line_frequency = {
"10": 115.271 * u.GHz,
"21": 230.538 * u.GHz,
"32": 345.796 * u.GHz,
}[line]
self.target_nside = target_nside
self.template_nside = 512 if self.target_nside <= 512 else 2048
super().__init__(nside=target_nside, map_dist=map_dist)
self.remote_data = RemoteData(coord)
self.planck_templatemap_filename = "co/HFI_CompMap_CO-Type1_{}_R2.00_ring.fits".format(
self.template_nside
)
self.planck_templatemap = self.read_map(
self.remote_data.get(self.planck_templatemap_filename),
field=self.line_index,
unit=u.K_CMB,
)
self.include_high_galactic_latitude_clouds = (
include_high_galactic_latitude_clouds
)
self.has_polarization = has_polarization
self.polarization_fraction = polarization_fraction
self.theta_high_galactic_latitude_deg = theta_high_galactic_latitude_deg
self.random_seed = random_seed
self.run_mcmole3d = run_mcmole3d
self.output_units = u.Unit(output_units)
self.verbose = verbose
def test_convert_units(self):
a1 = 1 * u.uK_CMB.to(u.uK_RJ,
equivalencies=u.cmb_equivalencies(300.0 * u.GHz))
a2 = 1 * u.uK_RJ.to(u.uK_CMB,
equivalencies=u.cmb_equivalencies(300.0 * u.GHz))
self.assertAlmostEqual(1.0, a1 * a2)
a1 = 1 * u.uK_CMB.to(u.Unit("MJy/sr"),
equivalencies=u.cmb_equivalencies(300.0 * u.GHz))
a2 = 1 * u.Unit("MJy/sr").to(
u.uK_CMB, equivalencies=u.cmb_equivalencies(300.0 * u.GHz))
self.assertAlmostEqual(1.0, a1 * a2)
"""Validation against ECRSC tables.
https://irsasupport.ipac.caltech.edu/index.php?/Knowledgebase/
Article/View/181/20/what-are-the-intensity-units-of-the-planck
-all-sky-maps-and-how-do-i-convert-between-them
These tables are based on the following tables:
h = 6.626176e-26 erg*s
k = 1.380662e-16 erg/L
c = 2.997792458e1- cm/s
T_CMB = 2.726
The impact of the incorrect CMB temperature is especially impactful
and limits some comparison to only ~2/3 s.f.
"""
freqs = [30, 143, 857]
uK_CMB_2_K_RJ = dict()
uK_CMB_2_K_RJ[30] = 9.77074e-7
uK_CMB_2_K_RJ[143] = 6.04833e-7
uK_CMB_2_K_RJ[857] = 6.37740e-11
for freq in freqs:
self.assertAlmostEqual(
uK_CMB_2_K_RJ[freq],
1 * u.uK_CMB.to(
u.K_RJ, equivalencies=u.cmb_equivalencies(freq * u.GHz)),
)
K_CMB_2_MJysr = dict()
K_CMB_2_MJysr[30] = 27.6515
K_CMB_2_MJysr[143] = 628.272
K_CMB_2_MJysr[857] = 22565.1
for freq in freqs:
self.assertAlmostEqual(
K_CMB_2_MJysr[freq] /
(1 *
u.K_RJ.to(u.MJy / u.sr,
equivalencies=u.cmb_equivalencies(freq * u.GHz))),
1.0,
places=4,
)
# Note that the MJysr definition seems to match comparatively poorly. The
# definitions of h, k, c in the document linked above are in cgs and differ
# from those on wikipedia. This may conflict with the scipy constants I use.
uK_CMB_2_MJysr = dict()
uK_CMB_2_MJysr[30] = 2.7e-5
uK_CMB_2_MJysr[143] = 0.0003800
uK_CMB_2_MJysr[857] = 1.43907e-6
for freq in freqs:
self.assertAlmostEqual(
uK_CMB_2_MJysr[freq] /
(1 *
u.uK_CMB.to(u.MJy / u.sr,
equivalencies=u.cmb_equivalencies(freq * u.GHz))),
1.0,
places=2,
)
def test_read_map_unit_dimensionless():
m = pysm3.read_map("pysm_2/dust_temp.fits", nside=8, field=0)
assert u.Unit("") == m.unit
def test_read_map_unit():
m = pysm3.read_map("pysm_2/dust_temp.fits", nside=8, field=0, unit="uK_RJ")
assert u.Unit("uK_RJ") == m.unit
def __init__(
self,
filename,
input_units="uK_CMB",
input_reference_frequency=None,
nside=None,
target_shape=None,
target_wcs=None,
from_cl=False,
from_cl_seed=None,
precompute_output_map=True,
has_polarization=True,
map_dist=None,
):
"""Generic component based on Precomputed Alms
Load a set of Alms from a FITS file and generate maps at the requested
resolution and frequency assuming the CMB black body spectrum.
A single set of Alms is used for all frequencies requested by PySM,
consider that PySM expects the output of components to be in uK_RJ.
See more details at https://so-pysm-models.readthedocs.io/en/latest/so_pysm_models/models.html
Also note that the Alms are clipped to 3*nside-1 to avoid
artifacts from high-ell components which cannot be properly represented
by a low-nside map.
Parameters
----------
filename : string
Path to the input Alms in FITS format
input_units : string
Input unit strings as defined by pysm.convert_units, e.g. K_CMB, uK_RJ, MJysr
input_reference_frequency: float
If input units are K_RJ or Jysr, the reference frequency
nside : int
HEALPix NSIDE of the output maps
from_cl : bool
If True, the input file contains C_ell instead of a_lm,
they should provided with the healpy old ordering TT, TE, TB, EE, EB, BB, sorry.
from_cl_seed : int
Seed set just before synalm to simulate the alms from the C_ell,
necessary to set it in order to get the same input map for different runs
only used if `from_cl` is True
precompute_output_map : bool
If True (default), Alms are transformed into a map in the constructor,
if False, the object only stores the Alms and generate the map at each
call of the signal method, this is useful to generate maps convolved
with different beams
has_polarization : bool
whether or not to simulate also polarization maps
Default: True
"""
self.nside = nside
self.shape = target_shape
self.wcs = target_wcs
self.filename = filename
self.input_units = u.Unit(input_units)
self.has_polarization = has_polarization
if from_cl:
np.random.seed(from_cl_seed)
cl = hp.read_cl(self.filename)
if not self.has_polarization and cl.ndim > 1:
cl = cl[0]
# using healpy old ordering TT, TE, TB, EE, EB, BB
alm = hp.synalm(cl, new=False, verbose=False)
else:
alm = np.complex128(
hp.read_alm(self.filename,
hdu=(1, 2, 3) if self.has_polarization else 1))
self.equivalencies = (None if input_reference_frequency is None else
u.cmb_equivalencies(input_reference_frequency))
if precompute_output_map:
self.output_map = self.compute_output_map(alm)
else:
self.alm = alm
def execute(self, write_outputs=False):
"""Run map simulations
Execute simulations for all channels and write to disk the maps,
unless `write_outputs` is False, then return them.
"""
if self.run_pysm:
sky_config = []
preset_strings = []
if self.pysm_components_string is not None:
for model in self.pysm_components_string.split(","):
if model.startswith("SO"):
sky_config.append(get_so_models(model, self.nside))
else:
preset_strings.append(model)
if len(preset_strings) > 0:
input_reference_frame = "G"
assert (
len(sky_config) == 0
), "Cannot mix PySM and SO models, they are defined in G and C frames"
else:
input_reference_frame = "C"
self.pysm_sky = pysm.Sky(
nside=self.nside,
preset_strings=preset_strings,
component_objects=sky_config,
output_unit=u.Unit(self.unit),
)
if self.pysm_custom_components is not None:
for comp_name, comp in self.pysm_custom_components.items():
self.pysm_sky.components.append(comp)
if not write_outputs:
output = {}
# ch can be single channel or tuple of 2 channels (tube dichroic)
for ch in self.channels:
if not isinstance(ch, tuple):
ch = [ch]
output_map_shape = (len(ch), 3) + self.shape
output_map = np.zeros(output_map_shape, dtype=np.float64)
if self.run_pysm:
for each, channel_map in zip(ch, output_map):
bandpass_integrated_map = self.pysm_sky.get_emission(
*each.bandpass).value
beam_width_arcmin = each.beam
# smoothing and coordinate rotation with 1 spherical harmonics transform
smoothed_map = hp.ma(
pysm.apply_smoothing_and_coord_transform(
bandpass_integrated_map,
fwhm=beam_width_arcmin,
lmax=3 * self.nside - 1,
rot=None if input_reference_frame
== self.pysm_output_reference_frame else
hp.Rotator(coord=(
input_reference_frame,
self.pysm_output_reference_frame,
)),
map_dist=None
if COMM_WORLD is None else pysm.MapDistribution(
nside=self.nside,
smoothing_lmax=3 * self.nside - 1,
mpi_comm=COMM_WORLD,
),
))
if smoothed_map.shape[0] == 1:
channel_map[0] += smoothed_map
else:
channel_map += smoothed_map
output_map = output_map.reshape((len(ch), 1, 3) + self.shape)
if self.other_components is not None:
for comp in self.other_components.values():
kwargs = dict(tube=ch[0].tube, output_units=self.unit)
if function_accepts_argument(comp.simulate, "ch"):
kwargs.pop("tube")
kwargs["ch"] = ch
if function_accepts_argument(comp.simulate, "nsplits"):
kwargs["nsplits"] = self.nsplits
if function_accepts_argument(comp.simulate, "seed"):
kwargs["seed"] = self.num
component_map = comp.simulate(**kwargs)
if self.nsplits == 1:
component_map = component_map.reshape((len(ch), 1, 3) +
self.shape)
component_map[hp.mask_bad(component_map)] = np.nan
output_map = output_map + component_map
for each, channel_map in zip(ch, output_map):
if write_outputs:
for split, each_split_channel_map in enumerate(
channel_map):
filename = self.output_filename_template.format(
telescope=each.telescope
if each.tube is None else each.tube,
band=each.band,
nside=self.nside,
tag=self.tag,
num=self.num,
nsplits=self.nsplits,
split=split + 1,
)
warnings.warn("Writing output map " + filename)
if self.car:
pixell.enmap.write_map(
os.path.join(self.output_folder, filename),
each_split_channel_map,
extra=dict(units=self.unit),
)
else:
each_split_channel_map[np.isnan(
each_split_channel_map)] = hp.UNSEEN
each_split_channel_map = hp.reorder(
each_split_channel_map, r2n=True)
hp.write_map(
os.path.join(self.output_folder, filename),
each_split_channel_map,
coord=self.pysm_output_reference_frame,
column_units=self.unit,
dtype=np.float32,
overwrite=True,
nest=True,
)
else:
if self.nsplits == 1:
channel_map = channel_map[0]
if not self.car:
channel_map[np.isnan(channel_map)] = hp.UNSEEN
output[each.tag] = channel_map
if not write_outputs:
return output
