def angular_distance_from_mask(mask):
"""
For each pixel of a Healpix map, return the smallest angular distance
to a set of masked pixels (of value True), in degrees.
Parameter
---------
maskok : boolean Healpix map
The Healpix mask that defines the set of masked pixels (of value True)
whose smallest angular distance to each pixel of a Healpix map of same
nside is computed.
"""
nside = hp.npix2nside(len(mask))
# get the list of pixels on the external border of the mask
ip = np.arange(12*nside**2)[~mask]
neigh = hp.get_all_neighbours(nside, ip)
nn = np.unique(neigh.ravel())
if nn[0] == -1:
nn = nn[1:]
nn = nn[mask[nn]]
# get unit vectors for border and inner pixels
vecpix_inner = np.array(hp.pix2vec(nside, ip))
vecpix_outer = np.array(hp.pix2vec(nside, nn))
# get angles between the border pixels and inner pixels
cosang = np.dot(vecpix_inner.T, vecpix_outer)
mapang = np.zeros(12*nside**2)
mapang[~mask] = np.degrees(np.arccos(np.max(cosang, axis=1)))
return mapang
def correlation(self, k, skymap, skymask):
#{{{
# en la version paralela hace un solo centro cada vez
# que estra a esta funcion
import numpy as np
import healpy as hp
import astropy.units as u
import time
import random
random.seed((k + 42) * 3)
# draw a set of nran pixel pairs
x = np.array([random.random() for _ in range(self.nran * 2)])
x = x * self.N_ma_IDs
x = x.astype(int)
x = x.reshape((-1, 2))
# compute frequency
coso = np.zeros(self.nran)
tt = np.zeros(self.nran)
for j, idxs in enumerate(x):
v1 = hp.pix2vec(self.nside, self.masked_indices[idxs[0]])
v2 = hp.pix2vec(self.nside, self.masked_indices[idxs[1]])
coso[j] = np.dot(v1, v2)
tt[j] = skymap.data[idxs[0]] * skymap.data[idxs[1]]
H = np.histogram(coso, bins=self.breaks, weights=tt, density=False)[0]
K = np.histogram(coso, bins=self.breaks, density=False)[0]
return (H, K)
def angular_distance_from_mask(mask):
"""
For each pixel of a Healpix map, return the smallest angular distance
to a set of masked pixels (of value True), in degrees.
Parameter
---------
maskok : boolean Healpix map
The Healpix mask that defines the set of masked pixels (of value True)
whose smallest angular distance to each pixel of a Healpix map of same
nside is computed.
"""
nside = hp.npix2nside(len(mask))
# get the list of pixels on the external border of the mask
ip = np.arange(12 * nside**2)[~mask]
neigh = hp.get_all_neighbours(nside, ip)
nn = np.unique(neigh.ravel())
if nn[0] == -1:
nn = nn[1:]
nn = nn[mask[nn]]
# get unit vectors for border and inner pixels
vecpix_inner = np.array(hp.pix2vec(nside, ip))
vecpix_outer = np.array(hp.pix2vec(nside, nn))
# get angles between the border pixels and inner pixels
cosang = np.dot(vecpix_inner.T, vecpix_outer)
mapang = np.zeros(12 * nside**2)
mapang[~mask] = np.degrees(np.arccos(np.max(cosang, axis=1)))
return mapang
def main_loop(ar_map, ar_map_unc, max_bin_angle, max_angular_separation, outer_disc_mean, outer_disc):
ar_product = np.zeros(shape=num_bins)
ar_weights = np.zeros(shape=num_bins)
ar_counts = np.zeros(shape=num_bins)
chosen_indices = np.random.choice(outer_disc, size=100, replace=False)
for index in chosen_indices:
vec_a = hp.pix2vec(ar_map_nside, index)
inner_disc = hp.query_disc(ar_map_nside, vec=vec_a, radius=max_angular_separation.to(u.rad).value)
if enable_intersection:
inner_disc = np.intersect1d(inner_disc, outer_disc, assume_unique=True)
vec_b = hp.pix2vec(ar_map_nside, inner_disc)
ar_ang_dist_with_zero = hp.rotator.angdist(vec_b, vec_a)
a = index
b = inner_disc[ar_ang_dist_with_zero > 0]
ar_ang_dist = ar_ang_dist_with_zero[ar_ang_dist_with_zero > 0]
ar_bins_float = ar_ang_dist / max_bin_angle * num_bins # type: np.ndarray
ar_bins = ar_bins_float.astype(int)
# TODO: filter NaNs earlier so that they don't decrease the correlation
ar_pair_product = np.nan_to_num((ar_map[a] - outer_disc_mean) * (ar_map[b] - outer_disc_mean))
ar_pair_weights = (ar_map_unc[a] * ar_map_unc[b]) ** (-2) # type: np.ndarray
ar_product += np.bincount(ar_bins, weights=ar_pair_product * ar_pair_weights, minlength=num_bins)
ar_weights += np.bincount(ar_bins, weights=ar_pair_weights, minlength=num_bins)
ar_counts += np.bincount(ar_bins, minlength=num_bins)
return ar_product, ar_weights, ar_counts
def compute_luminosity(self, SZ_map):
self.compute_FWHM_in_degrees(SZ_map)
NSIDE = hp.get_nside(SZ_map)
pixels_in_disk = hp.query_disc(NSIDE,
hp.pix2vec(NSIDE, self.peak_index),
np.radians(self.FWHM * 1.5))
nb_pixels_disk = len(pixels_in_disk)
vania_luminosity = 0
for pixel in pixels_in_disk:
vania_luminosity += SZ_map[pixel]
inner_ring = hp.query_disc(NSIDE, hp.pix2vec(NSIDE, self.peak_index),
np.radians(self.FWHM * 3.5))
outer_ring = hp.query_disc(NSIDE, hp.pix2vec(NSIDE, self.peak_index),
np.radians(self.FWHM * 5.5))
pixels_values_ring = list()
nb_pixels_background = len(outer_ring) - len(inner_ring)
for pixel in outer_ring:
if not (pixel in inner_ring):
pixels_values_ring.append(SZ_map[pixel])
self.luminosity_error = np.std(pixels_values_ring)
local_noise_ring = sum(pixels_values_ring)
self.luminosity = vania_luminosity - local_noise_ring * (
nb_pixels_disk / nb_pixels_background)
print 'luminosity = %s \pm %s' % (self.luminosity,
self.luminosity_error)
def alpha_mat():
npix = hp.nside2npix(8)
alphas = np.zeros((npix, npix))
for i in range(npix):
for j in range(i):
d1 = hp.pix2vec(8, i)
d2 = hp.pix2vec(8, j)
alphas[i, j] = get_alpha(d1, d2)
alphas[j, i] = -alphas[i, j]
return alphas
def make_ring_mask(inner, outer, ring_b, ring_l, nside):
""" Masks outside inner < r < outer, of a ring centred at (ring_b,ring_l)
"""
mask_none = np.arange(hp.nside2npix(nside))
return np.logical_not(
(np.cos(np.radians(inner)) >= np.dot(
hp.ang2vec(np.radians(90 - ring_b), np.radians(ring_l)),
hp.pix2vec(nside, mask_none))) *
(np.dot(hp.ang2vec(np.radians(90 - ring_b), np.radians(ring_l)),
hp.pix2vec(nside, mask_none)) >= np.cos(np.radians(outer))))
def alpha_test():
d1 = hp.pix2vec(8, 700)
d2 = hp.pix2vec(8, 600)
alpha = get_alpha(d1, d2)
print(alpha)
alphas = alpha_mat()
plt.imshow(alphas)
plt.colorbar()
plt.show()
return
def create_pixel_list(nside,
area_center_nside=None,
area_center_pixel=None,
area_num_pixels=None):
if (area_center_nside is not None or area_center_pixel is not None or area_num_pixels is not None) and \
(area_center_nside is None or area_center_pixel is None or area_num_pixels is None):
raise RuntimeError(
"You have to either set none of the three options area_center_nside,area_center_pixel,area_num_pixels or all of them"
)
npixel_max = healpy.nside2npix(nside)
# just return all pixels if no specific area is requested or the area covers the entire map
if (area_center_nside is None) or (area_num_pixels >= npixel_max):
return range(npixel_max)
# otherwise, build the area iteratively
pixel_area_sqdeg = healpy.nside2pixarea(nside, degrees=True)
area_for_requested_pixels_sqdeg = pixel_area_sqdeg * float(area_num_pixels)
approx_radius = numpy.sqrt(area_for_requested_pixels_sqdeg) / numpy.pi
print(
"Building healpix pixel list for nside {} with an area of {} (out of {}) pixels (=={:.2f}sqdeg; radius={:.2f}deg)"
.format(nside, area_num_pixels, npixel_max,
area_for_requested_pixels_sqdeg, approx_radius))
# get the center coordinate
c_x, c_y, c_z = healpy.pix2vec(area_center_nside, area_center_pixel)
start_pixel = healpy.vec2pix(nside, c_x, c_y, c_z)
c_x, c_y, c_z = healpy.pix2vec(nside, start_pixel)
pixel_set = set([start_pixel])
print("start pixel:", start_pixel)
# Create a full list of pixels ordered so that the center pixel is first and the distance to the center is growing.
# Then crop the list to return the number of requested pixels. This makes sure that we can extend the list later.
pixels = numpy.array(range(npixel_max))
p_x, p_y, p_z = healpy.pix2vec(nside, pixels)
pixel_space_angles = numpy.arccos(
numpy.clip(c_x * p_x + c_y * p_y + c_z * p_z, -1., 1.))
pixel_num = numpy.array(range(len(pixel_space_angles)), dtype=numpy.float)
# pixels, sorted by distance from the requested pixel; secondary sort key is just the healpix pixel index
pixel_list_sorted = pixels[numpy.lexsort(
(pixel_num, pixel_space_angles))].tolist()
return_list = pixel_list_sorted[:area_num_pixels]
print("Pixel set created. It has {} entries (requested entries were {})".
format(len(return_list), area_num_pixels))
return return_list
def _get_mask(tag, nside):
if tag == 'nomask':
return np.zeros(hp.nside2npix(nside)).astype(bool)
elif 'gal' in tag:
gal_cut = int(tag.split('gal')[-1])
pix = np.arange(hp.nside2npix(nside))
return np.abs(hp.pix2vec(nside, pix)[2]) < np.sin(np.radians(gal_cut))
elif 'pole' in tag:
pix = np.arange(hp.nside2npix(nside))
return hp.pix2vec(nside, pix)[2] < 0
else:
raise ValueError('Unsupported tag: %s' % tag)
def my_query_disk(nside, x0, radius):
# Avoid the stupid nside limit of powers of two.
ret = []
npix = hp.nside2npix(nside)
all_pixels = np.array(range(npix))
all_vec = hp.pix2vec(nside, all_pixels)
for i in all_pixels:
x1 = hp.pix2vec(nside, i)
angle = np.arccos(np.dot(x1, x0))
if angle <= radius:
ret.append(i)
return np.array(ret)
def _setup(nside):
self.cov = np.diag([self.unc_x**2, self.unc_y**2, self.unc_z**2])
# compute pdf for each pixel
self.nside = nside
self._n_order = self._nside2norder()
self.npix = hp.nside2npix(nside)
self.dir_x_s, self.dir_y_s, self.dir_z_s = \
hp.pix2vec(nside, range(self.npix))
self.neg_llh_values = -self.log_prob_dir(
self.dir_x_s, self.dir_y_s, self.dir_z_s)
# sort directions according to neg llh
sorted_indices = np.argsort(self.neg_llh_values)
self.dir_x_s = self.dir_x_s[sorted_indices]
self.dir_y_s = self.dir_y_s[sorted_indices]
self.dir_z_s = self.dir_z_s[sorted_indices]
self.neg_llh_values = self.neg_llh_values[sorted_indices]
self.ipix_list = sorted_indices
# get zenith and azimuth
self.zenith_s, self.azimuth_s = self.get_zenith_azimuth(
self.dir_x_s, self.dir_y_s, self.dir_z_s)
# get normalized probabilities and cdf
prob = np.exp(-self.neg_llh_values)
self.prob_values = prob / np.sum(prob)
self.cdf_values = np.cumsum(self.prob_values)
def contour_area(self, levels, nside):
"""Get the area inside a contour of a given level in square degrees.
Parameters
----------
levels : float or array_like
The level or levels for which to compute the contained area.
Must be a value in (0, 1).
nside : int
The nside parameter of the HEALpix.
The higher nside, the more accurate, but also slower to compute.
Returns
-------
array_like
The contained area in square degrees for each specified level
"""
if isinstance(levels, float):
levels = [levels]
# area of one HEALPix with given nside in square degrees
pix_area = hp.nside2pixarea(nside, degrees=True)
npix = hp.nside2npix(nside)
cdf_values = self.cdf_dir(*hp.pix2vec(nside, range(npix)))
# number of HEALPix pixels within contour
contour_areas = []
for level in levels:
num_pixels_inside = np.sum(cdf_values <= level)
contour_areas.append(num_pixels_inside * pix_area)
return contour_areas
def as_healpix(self, nside, nest=True):
r"""Returns a healpix map with the mean and standard deviations
of :math:`d` for any pixel containing at least one posterior
sample.
"""
from lalinference.bayestar import distance
npix = hp.nside2npix(nside)
datasets = [kde.dataset for kde in self.kdes]
inverse_covariances = [kde.inv_cov for kde in self.kdes]
weights = self.weights
# Compute marginal probability, conditional mean, and conditional
# standard deviation in all directions.
prob, mean, std = np.transpose([distance.cartesian_kde_to_moments(
np.asarray(hp.pix2vec(nside, ipix, nest=nest)),
datasets, inverse_covariances, weights)
for ipix in range(npix)])
# Normalize marginal probability...
# just to be safe. It should be marginalized already.
prob /= prob.sum()
# Apply method of moments to find location parameter, scale parameter,
# and normalization.
distmu, distsigma, distnorm = distance.moments_to_parameters(mean, std)
# Done!
return prob, distmu, distsigma, distnorm
def distance_to_mask(mask, maxdist=None, deg=True):
nside = hp.npix2nside(len(mask))
if maxdist == None:
if deg:
maxdist = 180.
else:
maxdist = np.pi
p0, p1 = border_of_mask(mask)
dist = maxdist * mask
if len(p0):
for p in range(len(p0)):
vec = np.array(hp.pix2vec(nside, p0[p]))
listpix, d = query_dist(nside, vec, maxdist, deg=deg)
if len(listpix):
tmpdist = dist[listpix]
wh, = np.where(d < tmpdist)
tmpdist[wh] = d[wh]
dist[listpix] = tmpdist
return dist * mask
def rotate_QU_frame(q, u, rot):
"""
Rotate coordinate from of QU angles on a HEALPIX map
Parameters
----------
q, u: healpy map for stoke parameters Q and U
rot: Rotator object
"""
nside = int(np.sqrt(q.size/12.))
pix = np.arange(12*nside**2).astype(int)
vecs = np.array(hp.pix2vec(nside, pix))
# First rotate the map pixels
qp = rot.rotate_map_pixel(q)
up = rot.rotate_map_pixel(u)
qp[qp < -1e25] = hp.UNSEEN
up[up < -1e25] = hp.UNSEEN
# Then caculate the reference angles in the rotated frame
vecs_r = rot(vecs,inv=True)
angles = rot.angle_ref(vecs_r)
L_map = (qp + 1j * up)*np.exp(1j*2*angles)
return np.real(L_map), np.imag(L_map)
def min_all_cos_dtheta_fast(pix, nside, nest=False, safe=False):
"""
computes the maximum angular separation between any two pixels within pix=[ipix,ipix,...]
does this with a boarder-to-boarder search after checking some other things
this could be in error up to the pixel size (hopefully small)
This algorithm is due in part to Antonios Kontos, who helped Reed Essick think through the details
"""
Npix = len(pix)
### check to see if more than half the sky is filled
if Npix * hp.nside2pixarea(nside) > 2 * np.pi:
return -1
### check to see if the antipode of any point is in the set
npix = hp.nside2npix(nside)
selected = np.zeros(npix, dtype=bool)
selected[pix] = True
antipodes = np.zeros_like(selected)
vec = -np.array(hp.pix2vec(nside, pix, nest=nest)) ### reflect vectors
antipodes[hp.vec2pix(nside, vec[0], vec[1], vec[2],
nest=nest)] = True ### reflection -> antipode
### reflection accomplished in cartesian coords
if np.sum(selected *
antipodes): ### point and it's antipode are in the set
return -1 ### could be in error by the pixel size...
### boarder-to-boarder search
boarder_pix = []
for bpix in __into_boarders(nside, pix, nest=nest):
boarder_pix += bpix
return min_all_cos_dtheta(boarder_pix, nside, nest=nest, safe=False)
def cartesian_gaussian_to_skymap(level, mean, cov):
"""Convert a 3D Cartesian Gaussian to a 3D sky map."""
# Set up HEALPix grid.
nside = 2**level
npix = ah.nside_to_npix(nside)
ipix = np.arange(npix)
coords = np.column_stack(hp.pix2vec(nside, ipix, nest=True))
# Create sky map using same method as KDE to convert from Cartesian
# to spherical representation. This is just a special case where there
# is only a single cluster and a single KDE sample.
means = mean[np.newaxis, ..., np.newaxis]
inv_covs = np.linalg.inv(cov)[np.newaxis, ...]
weights = np.ones(1)
probdensity, distmean, diststd = np.transpose([
cartesian_kde_to_moments(n, means, inv_covs, weights) for n in coords
])
# Create 3D, multi-order sky map.
uniq = nest2uniq(level, ipix)
distmu, distsigma, distnorm = moments_to_parameters(distmean, diststd)
return Table({
'UNIQ': uniq,
'PROBDENSITY': probdensity,
'DISTMU': distmu,
'DISTSIGMA': distsigma,
'DISTNORM': distnorm
})
def get_npix(self, rbins, src_ind, out_edge, tol=1):
'''
Return the number of sources within each r bins around a source.
Input: rbins: r bins specified by the user. Need to be an int or an array
src_ind: index of source;
out_edge: radius of the disk that is taken into account. in arcmin;
tol: tolerance between 0 and 1 indicating a threshold of fraction of
unmasked pixels in a disk
Output: number of sources within each r bins around a source.
'''
mask = self.mask
pos_src = self.pos_src_all[src_ind]
list_out_unmasked, list_in_unmasked = self.get_disk(mask, pos_src,
out_edge, 0,
tol)
if np.asarray(list_out_unmasked).sum() == 0:
return np.zeros(rbins.size-1)
Ns = hp.npix2nside(mask.size)
vector_disc = np.array(hp.pix2vec(Ns, list_out_unmasked))
# Get the unit vector of each pixels within the out disc
innprod = np.round(np.dot(pos_src, vector_disc), 15)
innprod[innprod > 1] = 1
rtheta = np.degrees(np.arccos(innprod)) * 60.
normal = np.histogram(rtheta, bins=rbins)[0]
return normal
def healpix_graph(nside=16,
nest=True,
lap_type='normalized',
indexes=None,
use_4=False,
dtype=np.float32):
"""Build a healpix graph using the pygsp from NSIDE."""
from pygsp import graphs
if indexes is None:
indexes = range(nside**2 * 12)
# 1) get the coordinates
npix = hp.nside2npix(nside) # number of pixels: 12 * nside**2
pix = range(npix)
x, y, z = hp.pix2vec(nside, pix, nest=nest)
coords = np.vstack([x, y, z]).transpose()[indexes]
# 2) computing the weight matrix
if use_4:
raise NotImplementedError()
W = build_matrix_4_neighboors(nside, indexes, nest=nest, dtype=dtype)
else:
W = healpix_weightmatrix(nside=nside,
nest=nest,
indexes=indexes,
dtype=dtype)
# 3) building the graph
G = graphs.Graph(W, lap_type=lap_type, coords=coords)
return G
def calc_azza(self, Nside, center, return_inds=False):
"""
Set the az/za arrays.
Center = lon/lat in degrees
radius = selection radius in degrees
return_inds = Return the healpix indices too
"""
if self.fov is None:
raise AttributeError("Need to set a field of view in degrees")
radius = self.fov * np.pi / 180. * 1 / 2.
cvec = hp.ang2vec(center[0], center[1], lonlat=True)
pix = hp.query_disc(Nside, cvec, radius)
vecs = hp.pix2vec(Nside, pix)
vecs = np.array(vecs).T # Shape (Npix_use, 3)
colat = np.radians(90. - center[1]) # Colatitude, radians.
xvec = [-cvec[1], cvec[0], 0] * 1 / np.sin(colat) # From cross product
yvec = np.cross(cvec, xvec)
sdotx = np.tensordot(vecs, xvec, 1)
sdotz = np.tensordot(vecs, cvec, 1)
sdoty = np.tensordot(vecs, yvec, 1)
za_arr = np.arccos(sdotz)
az_arr = (np.arctan2(sdotx, sdoty) + np.pi) % (
2 * np.pi
) # xy plane is tangent. Increasing azimuthal angle eastward, zero at North (y axis)
if return_inds:
return za_arr, az_arr, pix
return za_arr, az_arr
def match_hpx_pixel(nside, nest, nside_pix, ipix_ring):
"""
"""
ipix_in = np.arange(12 * nside * nside)
vecs = hp.pix2vec(nside, ipix_in, nest)
pix_match = hp.vec2pix(nside_pix, vecs[0], vecs[1], vecs[2]) == ipix_ring
return ipix_in[pix_match]
def _sample_from_ipix(self, ipix, nest=False):
"""
Sample vectors from a uniform distribution within a HEALpixel.
Credit goes to
https://git.rwth-aachen.de/astro/astrotools/blob/master/
astrotools/healpytools.py
:param ipix: pixel number(s)
:param nest: set True in case you work with healpy's nested scheme
:return: vectors containing events from the pixel(s) specified in ipix
Parameters
----------
ipix : int, list of int
Healpy pixels.
nest : bool, optional
Set to True in case healpy's nested scheme is used.
Returns
-------
np.array, np.array, np.array
The sampled direction vector components.
"""
if not nest:
ipix = hp.ring2nest(self.nside, ipix=ipix)
n_up = 29 - self._n_order
i_up = ipix * 4**n_up
i_up += self._random_state.randint(0, 4**n_up, size=np.size(ipix))
return hp.pix2vec(nside=2**29, ipix=i_up, nest=True)
def get_vertices(m):
m = np.copy(m)
top_npix = len(m)
top_nside = hp.npix2nside(top_npix)
top_order = int(np.log2(top_nside))
for order in range(top_order + 1):
nside = 1 << order
npix = hp.nside2npix(nside)
stride = 1 << (2 * (top_order - order))
keep = (hp.pix2vec(nside, np.arange(npix), nest=True) *
np.expand_dims(xyz0, 1)).sum(0) >= np.cos(np.deg2rad(30))
if order < top_order:
mm = m.reshape((-1, stride))
keep &= (mm[:, :-1] == mm[:, 1:]).all(axis=1)
m += hp.ud_grade(np.where(keep, np.nan, 0),
nside_out=top_nside,
order_in='NEST',
order_out='NEST')
else:
keep &= ~np.isnan(m)
for ipix in np.flatnonzero(keep):
boundaries = hp.boundaries(nside, ipix, nest=True, step=1).T
theta, phi = hp.vec2ang(boundaries)
ra = np.rad2deg(phi)
dec = np.rad2deg(0.5 * np.pi - theta)
vertices = np.column_stack((ra, dec))
yield vertices
def calc_beam(cal, nside, inttime, freq):
"""Calculate Effective Omega from Beam integral."""
from scipy.interpolate import interp1d
from capo import fringe
aa1 = ap.cal.get_aa(cal, np.array([freq]))
npix = hp.nside2npix(nside)
pix = np.arange(npix)
theta, phi = hp.pix2ang(nside, pix)
# only keep points above the horizon
phi = phi[theta < np.pi/2.]
theta = theta[theta < np.pi/2.]
intpix = hp.ang2pix(nside, theta, phi)
x, y, z = hp.pix2vec(nside, intpix)
# need xyz in eq coords to make fringe weights
xyz_eq = np.dot(np.linalg.inv(aa1._eq2zen), np.array([x, y, z]))
# A is defined as the power
A = aa1[0].bm_response((x, y, z), pol=args.pol)[0]**2
# calculate the fringe weights for FRF'd data
bins = fringe.gen_frbins(inttime)
frp, bins = fringe.aa_to_fr_profile(aa1, (1, 4), 0, bins=bins)
bl = aa1.get_baseline(1, 4, 'r') * freq
fng = fringe.mk_fng(bl, xyz_eq)
wgts = interp1d(bins, frp, kind='linear')
fng_wgt = wgts(fng)
fng_bm = A * fng_wgt
return A, fng_wgt
def mask_src(cat_file, MASK_S_RAD, NSIDE):
"""Returns the 'bad pixels' defined by the position of a source and a
certain radius away from that point.
SOURCE_CAT: str
opened fits file with the sorce catalog
MASK_S_RAD: float
radius around each source definig bad pixels to mask
NSIDE: int
healpix nside parameter
"""
logger.info('Mask for sources activated')
src_cat = pf.open(cat_file)
NPIX = hp.pixelfunc.nside2npix(NSIDE)
CAT = src_cat['LAT_Point_Source_Catalog']
BAD_PIX_SRC = []
SOURCES = CAT.data
RADrad = MASK_S_RAD * np.pi / 180.
for i in range(0, len(SOURCES) - 1):
GLON = SOURCES[i][3]
GLAT = SOURCES[i][4]
x, y, z = hp.rotator.dir2vec(GLON, GLAT, lonlat=True)
b_pix = hp.pixelfunc.vec2pix(NSIDE, x, y, z)
BAD_PIX_SRC.append(b_pix)
BAD_PIX_inrad = []
for bn in BAD_PIX_SRC:
pixVec = hp.pix2vec(NSIDE, bn)
radintpix = hp.query_disc(NSIDE, pixVec, RADrad)
BAD_PIX_inrad.extend(radintpix)
BAD_PIX_SRC.extend(BAD_PIX_inrad)
src_cat.close()
return BAD_PIX_SRC
def get_mask(self):
if self.mask is None:
if self.fsky >= 1:
self.mask = np.ones(hp.nside2npix(self.nside))
else:
# This generates a correctly-apodized mask
v0 = np.array([np.sin(np.radians(90-self.dec0)) *
np.cos(np.radians(self.ra0)),
np.sin(np.radians(90-self.dec0)) *
np.sin(np.radians(self.ra0)),
np.cos(np.radians(90-self.dec0))])
vv = np.array(hp.pix2vec(self.nside,
np.arange(hp.nside2npix(self.nside))))
cth = np.sum(v0[:, None]*vv, axis=0)
th = np.arccos(cth)
th0 = np.arccos(1-2*self.fsky)
th_apo = np.radians(self.aposize)
id0 = np.where(th >= th0)[0]
id1 = np.where(th <= th0-th_apo)[0]
idb = np.where((th > th0-th_apo) & (th < th0))[0]
x = np.sqrt((1 - np.cos(th[idb] - th0)) / (1 - np.cos(th_apo)))
mask_apo = np.zeros(hp.nside2npix(self.nside))
mask_apo[id0] = 0.
mask_apo[id1] = 1.
mask_apo[idb] = x-np.sin(2 * np.pi * x) / (2 * np.pi)
self.mask = mask_apo
return self.mask
def main(args):
log = logging.getLogger('root')
hdlr = logging.StreamHandler(sys.stdout)
log.addHandler(hdlr)
log.setLevel(logging.getLevelName(args.loglevel.upper()))
pyfftw.interfaces.cache.enable()
vol1 = mrc.read(args.volume1, inc_header=False, compat="relion")
vol2 = mrc.read(args.volume2, inc_header=False, compat="relion")
if args.mask is not None:
mask = mrc.read(args.mask, inc_header=False, compat="relion")
vol1 *= mask
vol2 *= mask
f3d1 = fft.rfftn(vol1, threads=args.threads)
f3d2 = fft.rfftn(vol2, threads=args.threads)
nside = 2**args.healpix_order
x, y, z = pix2vec(nside, np.arange(12 * nside ** 2))
xhalf = x >= 0
hp = np.column_stack([x[xhalf], y[xhalf], z[xhalf]])
t0 = time.time()
fcor = calc_dfsc(f3d1, f3d2, hp, np.deg2rad(args.arc))
log.info("Computed CFSC in %0.2f s" % (time.time() - t0))
fsc = calc_fsc(f3d1, f3d2)
t0 = time.time()
log.info("Computed GFSC in %0.2f s" % (time.time() - t0))
freqs = np.fft.rfftfreq(f3d1.shape[0])
np.save(args.output, np.row_stack([freqs, fsc, fcor]))
return 0
def gsr_files(infilenames,
pixel,
nside,
n,
angDeg=5.5,
g=0.4,
gdot=0.0,
cluster_id_dict={}):
""" This function was supposed to help create a meta cluster plot, but the healpix vector
format was too difficult to manipulate in the time we had, so this file is in misc.py"""
hp_dicts = []
for infn in infilenames:
hp_dicts.append(util.get_hpdict(infn))
vec = hp.pix2vec(nside, pixel, nest=True)
neighbors = hp.query_disc(nside,
vec,
angDeg * np.pi / 180.,
inclusive=True,
nest=True)
lines = []
for pix in neighbors:
for hp_dict in hp_dicts:
for line in hp_dict[pix]:
lines.append(line)
outfilename = 'demo_train/training_quiver_meta'
if len(lines) > 0:
transform_to_arrows(util.lunation_center(n), [(g, gdot)],
vec,
lines,
outfilename,
makefiles=True,
cluster_id_dict=cluster_id_dict)
def mask_src(cat_file, MASK_S_RAD, NSIDE):
"""Returns the 'bad pixels' defined by the position of a source and a
certain radius away from that point.
cat_file: str
.fits file of the sorce catalog
MASK_S_RAD: float
radius around each source definig bad pixels to mask
NSIDE: int
healpix nside parameter
"""
logger.info('Mask for sources activated')
src_cat = pf.open(cat_file)
NPIX = hp.pixelfunc.nside2npix(NSIDE)
CAT = src_cat['LAT_Point_Source_Catalog']
BAD_PIX_SRC = []
SOURCES = CAT.data
RADrad = MASK_S_RAD*np.pi/180.
for i in range (0,len(SOURCES)-1):
GLON = SOURCES.field('GLON')[i]
GLAT = SOURCES.field('GLAT')[i]
x, y, z = hp.rotator.dir2vec(GLON,GLAT,lonlat=True)
b_pix= hp.pixelfunc.vec2pix(NSIDE, x, y, z)
BAD_PIX_SRC.append(b_pix)
BAD_PIX_inrad = []
for bn in BAD_PIX_SRC:
pixVec = hp.pix2vec(NSIDE,bn)
radintpix = hp.query_disc(NSIDE, pixVec, RADrad)
BAD_PIX_inrad.extend(radintpix)
BAD_PIX_SRC.extend(BAD_PIX_inrad)
src_cat.close()
return BAD_PIX_SRC
def build_adjacency_from_heat_kernel(nside,
comm,
stopping_threshold=1e-7,
KS_weighted=False,
Q=None,
alpha=0.5):
if comm is None:
rank = 0
nprocs = 1
else:
rank = comm.Get_rank()
nprocs = comm.Get_size()
p = np.arange(hp.nside2npix(nside))
V = np.array(hp.pix2vec(ipix=p, nside=hp.get_nside(p))).T
scalprod = minmaxrescale(V.dot(V.T), a=-1, b=1)
if KS_weighted:
Theta = np.arccos(scalprod)
Psi = Theta + alpha * (1 - Q) * np.pi / 2
scalprod = np.cos(Psi)
lmax, sigmabeam = get_lmax(nside, stopping_threshold)
Gloc = np.zeros_like(scalprod)
start_ell, stop_ell = split_data_among_processors(lmax, rank, nprocs)
for l in np.arange(start_ell, stop_ell):
Gloc += heat_kernel(scalprod, l, sigmabeam)
Gloc = comm.allreduce(Gloc, op=MPI.SUM)
return Gloc
def match_hpx_pixel(nside, nest, nside_pix, ipix_ring):
"""
"""
ipix_in = np.arange(12 * nside * nside)
vecs = hp.pix2vec(nside, ipix_in, nest)
pix_match = hp.vec2pix(nside_pix, vecs[0], vecs[1], vecs[2]) == ipix_ring
return ipix_in[pix_match]
def map_ang_from_edges(maskok):
print('Calculating Angle Mask Map')
nsmask = hp.npix2nside(len(maskok))
### Get the list of pixels on the external border of the mask
ip = np.arange(12*nsmask**2)
neigh = hp.get_all_neighbours(nsmask, ip[maskok])
nn = np.unique(np.sort(neigh.ravel()))
nn = nn[maskok[nn] == False]
### Get unit vectors for border and inner pixels
vecpixarray_inner = np.array(hp.pix2vec(nsmask,ip[maskok]))
vecpixarray_outer = np.array(hp.pix2vec(nsmask,nn))
### get angles between the border pixels and inner pixels
cosang = np.dot(np.transpose(vecpixarray_inner),vecpixarray_outer)
mapang = np.zeros(12*nsmask**2)
mapang[maskok] = np.degrees(np.arccos(np.max(cosang,axis=1)))
return mapang
def make_window(window, mask):
nside = hp.npix2nside(len(mask))
valid_sky = np.where(mask==1)[0]
edge = get_edge(mask)
interior = np.setdiff1d(valid_sky, edge)
distance = np.zeros(len(mask))
i = 0
for pixel in interior:
# min_distance = 1000
# vec = hp.pix2vec(nside, pixel)
# for edge_pixel in edge:
# dist = np.arccos(np.dot(vec, hp.pix2vec(nside, edge_pixel)))
# if dist < min_distance:
# min_distance = dist
# distance[pixel] = min_distance
vec = hp.pix2vec(nside, pixel)
distance[pixel] = 47.41*np.pi/180.0 - np.arccos(np.dot(vec, hp.ang2vec(np.pi/2, 0.0)))
#i = i + 1
#print "%d/%d\r" % (i, len(interior)),
max_distance = np.max(distance)
map_window = np.zeros(len(mask))
for pixel in interior:
arg = int((distance[pixel] / (2.0 * max_distance)) * len(window))
map_window[pixel] = window[arg]
return map_window
def exec(self, data):
"""
Create the gradient timestreams.
This pixelizes each detector's pointing and then assigns a
timestream value based on the cartesian Z coordinate of the pixel
center.
Args:
data (toast.Data): The distributed data.
"""
autotimer = timing.auto_timer(type(self).__name__)
comm = data.comm
zaxis = np.array([0, 0, 1], dtype=np.float64)
nullquat = np.array([0, 0, 0, 1], dtype=np.float64)
range = self._max - self._min
for obs in data.obs:
tod = obs['tod']
offset, nsamp = tod.local_samples
common = tod.local_common_flags() & self._common_flag_mask
for det in tod.local_dets:
flags = tod.local_flags(det) & self._flag_mask
totflags = (flags | common)
del flags
pdata = tod.local_pointing(det).copy()
pdata[totflags != 0, :] = nullquat
dir = qa.rotate(pdata, zaxis)
pixels = hp.vec2pix(self._nside,
dir[:, 0],
dir[:, 1],
dir[:, 2],
nest=self._nest)
x, y, z = hp.pix2vec(self._nside, pixels, nest=self._nest)
z += 1.0
z *= 0.5
z *= range
z += self._min
z[totflags != 0] = 0.0
cachename = "{}_{}".format(self._out, det)
if not tod.cache.exists(cachename):
tod.cache.create(cachename, np.float64, (nsamp, ))
ref = tod.cache.reference(cachename)
ref[:] += z
del ref
if not self._keep_quats:
cachename = 'quat_{}'.format(det)
tod.cache.destroy(cachename)
del common
return
def calc_beam(cal, nside, inttime, freq):
"""Calculate Effective Omega from Beam integral."""
from scipy.interpolate import interp1d
from capo import fringe
aa1 = ap.cal.get_aa(cal, np.array([freq]))
npix = hp.nside2npix(nside)
pix = np.arange(npix)
theta, phi = hp.pix2ang(nside, pix)
# only keep points above the horizon
phi = phi[theta < np.pi / 2.]
theta = theta[theta < np.pi / 2.]
intpix = hp.ang2pix(nside, theta, phi)
x, y, z = hp.pix2vec(nside, intpix)
# need xyz in eq coords to make fringe weights
xyz_eq = np.dot(np.linalg.inv(aa1._eq2zen), np.array([x, y, z]))
# A is defined as the power
A = aa1[0].bm_response((x, y, z), pol=args.pol)[0]**2
# calculate the fringe weights for FRF'd data
bins = fringe.gen_frbins(inttime)
frp, bins = fringe.aa_to_fr_profile(aa1, (1, 4), 0, bins=bins)
bl = aa1.get_baseline(1, 4, 'r') * freq
fng = fringe.mk_fng(bl, xyz_eq)
wgts = interp1d(bins, frp, kind='linear')
fng_wgt = wgts(fng)
fng_bm = A * fng_wgt
return A, fng_wgt
def compute_ds_dcb_line_par(map,mask,ellmin,ellmax,fwhmrad,nthreads):
npix=np.size(np.where(mask))
ellbins=ellmin.size
ellval=(ellmin+ellmax)/2
print(' Calculating dS/dCb')
pixwin=hp.pixwin(hp.npix2nside(len(map)))
maxell=np.max(ellmax)
ll=np.arange(int(maxell)+1)
bl=np.exp(-0.5*ll**2*(fwhmrad/2.35)**2)
nside=np.sqrt(map.size/12)
iprings=np.arange(map.size)
vecs=hp.pix2vec(int(nside),iprings[mask])
cosangles=np.dot(np.transpose(vecs),vecs)
nshots=npix//nthreads+1
ntot=nshots*nthreads
indices=np.arange(ntot)
indices[indices>npix-1]=npix-1
lines=np.reshape(indices,(nshots,nthreads))
ds_dcb=np.zeros((ellbins,npix,npix))
for num in np.arange(nshots):
# initiate multithreading
tasks=multiprocessing.JoinableQueue()
results = multiprocessing.Queue()
# start consumers
num_consumers = nthreads
#print 'Creating %d consumers' % num_consumers
consumers = [ Consumer(tasks, results)
for i in xrange(num_consumers) ]
for w in consumers:
w.start()
# Enqueue jobs
num_jobs = nthreads
for i in np.arange(num_jobs):
#print('Calling task ',lines[num,i])
tasks.put(Task(cosangles[lines[num,i],:],lines[num,i],ll,bl,pixwin,ellmin,ellmax,ellval))
# poison them when finished
for i in np.arange(num_jobs):
#print 'Killing Task %d ' % i
tasks.put(None)
#print('****** Now ready to join tasks ******')
tasks.join()
#print('###### Tasks were joined ######')
while num_jobs:
#print('Getting result for task %d' % num_jobs)
result = results.get()
bla=result[0]
num=result[1]
ds_dcb[:,num,num:]=bla[:,num:]
ds_dcb[:,num:,num]=bla[:,num:]
num_jobs -= 1
return(ds_dcb)
def solar_system_dipole_map(nside=16, nest=False, dipole_vector_galactic=None):
pix = np.arange(healpy.nside2npix(nside),dtype=np.int)
vec = np.zeros([len(pix),3])
vec[:,0], vec[:,1], vec[:,2] = healpy.pix2vec(nside, pix, nest=nest)
dip = Dipole(type='solar_system', coord='G', lowmem=False, dipole_vector_galactic=dipole_vector_galactic)
dipole_tod = dip.get(None, vec)
m = np.zeros(len(pix))
m[pix] = dipole_tod
return m
def sample_dpgmm(args):
print 'sampling component ..'
# parse the arguments
((w, p), (d_grid, npix)) = args
# get the number of pixels for the healpy nside
# calculate the log probablity at the cartesian coordinates
logp = np.array([[p.logProb(d*np.array(hp.pix2vec(np.int(nside), pix, nest=True))) for pix in xrange(npix)] for d in d_grid])
# multiply by weight of component and return
return np.log(w) + logp
def get_disc(pix, disc_size, nside):
vec = hp.pix2vec(nside, pix, nest=False)
in_disc = hp.query_disc(
nside=nside,
vec=vec,
radius=np.deg2rad(disc_size),
nest=False)
return in_disc
def exec(self, data):
"""
Create the gradient timestreams.
This pixelizes each detector's pointing and then assigns a
timestream value based on the cartesian Z coordinate of the pixel
center.
Args:
data (toast.Data): The distributed data.
"""
autotimer = timing.auto_timer(type(self).__name__)
comm = data.comm
zaxis = np.array([0, 0, 1], dtype=np.float64)
nullquat = np.array([0, 0, 0, 1], dtype=np.float64)
range = self._max - self._min
for obs in data.obs:
tod = obs['tod']
offset, nsamp = tod.local_samples
common = tod.local_common_flags() & self._common_flag_mask
for det in tod.local_dets:
flags = tod.local_flags(det) & self._flag_mask
totflags = (flags | common)
del flags
pdata = tod.local_pointing(det).copy()
pdata[totflags != 0, :] = nullquat
dir = qa.rotate(pdata, zaxis)
pixels = hp.vec2pix(self._nside, dir[:, 0], dir[:, 1], dir[:, 2],
nest=self._nest)
x, y, z = hp.pix2vec(self._nside, pixels, nest=self._nest)
z += 1.0
z *= 0.5
z *= range
z += self._min
z[totflags != 0] = 0.0
cachename = "{}_{}".format(self._out, det)
if not tod.cache.exists(cachename):
tod.cache.create(cachename, np.float64, (nsamp,))
ref = tod.cache.reference(cachename)
ref[:] += z
del ref
if not self._keep_quats:
cachename = 'quat_{}'.format(det)
tod.cache.destroy(cachename)
del common
return
def make_gauss_map(nside=64,fwhm=1.0,cpix=0):
"""
produce healpix map nside=nside with gaussian fwhm=fwhm (degrees) centered on cpix
"""
npix=hp.nside2npix(nside)
gmap=np.zeros(npix)
vcen=hp.pix2vec(nside,cpix)
sigma=np.radians(fwhm)/(2*np.sqrt(2*log(2.)))
twosigmasquared=2*sigma**2
print fwhm/sigma
for p in arange(npix):
v=hp.pix2vec(nside,p)
ang=np.arccos(np.dot(vcen,v))
gmap[p]=exp(-ang**2/twosigmasquared)
return gmap
def add_doppler(map1, A, dvec):
""" return a map that has the doppler dipole added to the temperature map given by the amplitude A and direction (angle); the amplitdue A should inlclude the frequency dependent boost factor b_nu.
"""
NPIX=len(map1)
NSIDE=hp.npix2nside(NPIX)
newmap=np.array([0.]*NPIX)
for i in range(NPIX):
pixvec=hp.pix2vec(NSIDE, i)
newmap[i]=map1[i]*(1+A*np.dot(pixvec, dvec))
return newmap
def weight(time):
"""
Weight of pixel at (lat_r, lon_r) assuming Lambertian surface
"""
EO_vec = latlon2cart(LAT_O, LON_O-OMEGA*time/deg2rad)
ES_vec = latlon2cart(LAT_S, LON_S-OMEGA*time/deg2rad)
ER_vec_array = np.array(hp.pix2vec(N_SIDE, np.arange(hp.nside2npix(N_SIDE))))
cosTH0_array = np.dot(ES_vec, ER_vec_array)
cosTH1_array = np.dot(EO_vec, ER_vec_array)
return np.clip(cosTH0_array, 0., 1.)*np.clip(cosTH1_array, 0., 1.)
def px2crd(self, px, ncrd=3):
"""Convert a 1 dimensional input array of pixel numbers to the type of coordinates specified by ncrd. If ncrd=3 (default), the returned array will have (x,y,z) for each pixel. Otherwise if ncrd=2, the returned array will have (theta,phi) for each pixel."""
is_nest = (self._scheme == 'NEST')
assert(ncrd in (2,3))
if ncrd == 2: # th/phi mode
th,phi = healpy.pix2ang(self._nside, px, nest=is_nest)
return th, phi
else: # ncrd == 3 -> vec mode
x,y,z = healpy.pix2vec(self._nside, px, nest=is_nest)
return x,y,z
def __init__(self, radius_mpc=r_cmb_mpc, n_side=2**4):
# FYI: n_side = 2**4 corresponds to
# 0.064 radians resolution = ~0.9 Mpc at z~1000.
from healpy import nside2npix, pix2vec
self.n_pix = nside2npix(n_side)
x, y, z = pix2vec(n_side, range(self.n_pix))
self.radius_mpc = radius_mpc
self.x = self.radius_mpc*x
self.y = self.radius_mpc*y
self.z = self.radius_mpc*z
self.update_xyz()
def weight_2(time, n_side, param_geometry):
"""
Weight of pixel at (lat_r, lon_r) assuming Lambertian surface
"""
lat_o, lon_o, lat_s, lon_s, omega = param_geometry
EO_vec = latlon2cart(lat_o, lon_o-omega*time/deg2rad)[0]
ES_vec = latlon2cart(lat_s, lon_s-omega*time/deg2rad)[0]
ER_vec_array = np.array(hp.pix2vec(n_side, np.arange(hp.nside2npix(n_side))))
cosTH0_array = np.dot(ES_vec, ER_vec_array)
cosTH1_array = np.dot(EO_vec, ER_vec_array)
return np.clip(cosTH0_array, 0., 1.)*np.clip(cosTH1_array, 0., 1.)
def map_generator():
#Constructing maps...............................
#if not os.path.exists('./map'):
# os.makedirs('./map')
#Star map
if(map_list['star'] == True): map['star'] = hp.read_map(star_map_file)[mpix2hpix]
#Galaxy map
if((map_list['gal'] == True) or (map_list['odds'] == True)):
for bin in zbin:
map['gal'][zbintag(bin)] = {}
i_eff = 0
for od in od_cut:
gal_map = np.zeros(N_mpix)
mask = cut(bin, od, cat['p']['val']['zp'], cat['p']['val']['od'])
mpix = cat['p']['val']['mpix'][mask]
for i in mpix:
if(i >= 0): gal_map[i] += 1
map['gal'][zbintag(bin)][odtag(eff_cut[i_eff])] = gal_map
if(map_list['gal'] == True): hp.write_map(folder_out + 'map/map_gal' + nside_tag + '_' + zbintag(bin) + '_' + odtag(eff_cut[i_eff]) + '.fits', np.append(gal_map, 0)[hpix2mpix])
i_eff += 1
#Odds map
if(map_list['odds'] == True):
for bin in zbin:
mask = cut(bin, 0., cat['p']['val']['zp'], cat['p']['val']['od'])
od_map = np.zeros(N_mpix)
n_map = map['gal'][zbintag(bin)][odtag(0.0)]
mpix = cat['p']['val']['mpix'][mask]
odds = cat['p']['val']['od'][mask]
for i in range(len(mpix)):
if(mpix[i] >= 0): od_map[mpix[i]] += odds[i]
for i in range(N_mpix):
if(n_map[i] != 0): od_map[i] /= n_map[i]
od_map_corr = np.copy(od_map)
for i in range(N_mpix):
if(n_map[i] == 0):
i_vec = hp.pix2vec(nside, mpix2hpix[i])
nest = hpix2mpix[hp.query_disc(nside, i_vec, 1 * (np.pi/ 180))]
nest = nest[nest >= 0]
o = 0
n = 0
for j in nest:
o += od_map[j]
if (od_map[j] > 0.00000001): n += 1
o /= float(n)
od_map_corr[i] = o
map['odds'][zbintag(bin)] = od_map_corr
hp.write_map(folder_out + 'Map/od_map' + nside_tag + zbintag(bin) + '.fits', np.append(od_map_corr,0)[hpix2mpix])
def subpixel(superpix, nside_superpix, nside_subpix):
"""
Return the indices of sub-pixels (resolution nside_subpix) within the super-pixel with (resolution nside_superpix).
"""
if nside_superpix == nside_subpix:
return superpix
vec = healpy.pix2vec(nside_superpix, superpix)
radius = np.degrees(2.0 * healpy.max_pixrad(nside_superpix))
subpix = query_disc(nside_subpix, vec, radius)
pix_for_subpix = superpixel(subpix, nside_subpix, nside_superpix)
# Might be able to speed up array indexing...
return subpix[pix_for_subpix == superpix]
def labelHealpix(pixels, values, nside, threshold=0, xsize=1000):
"""
Label contiguous regions of a (sparse) HEALPix map. Works by mapping
HEALPix array to a Mollweide projection and applying scipy.ndimage.label
Assumes non-nested HEALPix map.
Parameters:
pixels : Pixel values associated to (sparse) HEALPix array
values : (Sparse) HEALPix array of data values
nside : HEALPix dimensionality
threshold : Threshold value for object detection
xsize : Size of Mollweide projection
Returns:
labels, nlabels
"""
proj = healpy.projector.MollweideProj(xsize=xsize)
vec = healpy.pix2vec(nside,pixels)
xy = proj.vec2xy(vec)
ij = proj.xy2ij(xy)
xx,yy = proj.ij2xy()
# Convert to Mollweide
searchims = []
if values.ndim < 2: iterate = [values]
else: iterate = values.T
for i,value in enumerate(iterate):
logger.debug("Labeling slice %i...")
searchim = numpy.zeros(xx.shape,dtype=bool)
select = (value > threshold)
yidx = ij[0][select]; xidx = ij[1][select]
searchim[yidx,xidx] |= True
searchims.append( searchim )
searchims = numpy.array(searchims)
# Full binary structure
s = ndimage.generate_binary_structure(searchims.ndim,searchims.ndim)
### # Dilate in the z-direction
logger.info(" Dilating image...")
searchims = ndimage.binary_dilation(searchims,s,1)
# Do the labeling
logger.info(" Labeling image...")
labels,nlabels = ndimage.label(searchims,structure=s)
# Convert back to healpix
pix_labels = labels[:,ij[0],ij[1]].T
pix_labels = pix_labels.reshape(values.shape)
pix_labels *= (values > threshold) # re-trim
return pix_labels, nlabels
def galmap2eqmap(map):
"""
function to rotate galactic coord map (healpix) to equatorial
"""
nside=np.int(np.sqrt(len(map)/12))
grot=hp.Rotator(coord='GC')
pixlist=range(len(map))
veclist=hp.pix2vec(nside,pixlist)
rveclist=grot(veclist)
rpixlist=hp.vec2pix(nside,rveclist[0,:],rveclist[1,:],rveclist[2,:])
outmap=np.zeros(len(map))
outmap[rpixlist]=map[pixlist]
return outmap
def sigmap(self):
"""
(array): Return the underlying signal map (full map on all processes).
"""
autotimer = timing.auto_timer(type(self).__name__)
range = self._max - self._min
pix = np.arange(0, 12 * self._nside * self._nside, dtype=np.int64)
x, y, z = hp.pix2vec(self._nside, pix, nest=self._nest)
z += 1.0
z *= 0.5
z *= range
z += self._min
return z
def local_mean_map(map1, mask1, deg):
""" return the local mean map for map1 with mask mask1
"""
mp1=hp.ma(map1)
mp1.mask=np.logical_not(mask1)
NSIDE1=hp.npix2nside(len(map1))
NSIDE2=nside(deg)
NPIX2=hp.nside2npix(NSIDE2)
mp2=np.array([0.]*NPIX2)
for pix2 in range(0, NPIX2):
disc1=hp.query_disc(nside=NSIDE1, vec=hp.pix2vec(NSIDE2, pix2), radius=deg2rad(deg))
mp2[pix2]=np.mean(mp1[disc1])
return mp2
def principal_axes(prob, distmu, distsigma, nest=False):
npix = len(prob)
nside = hp.npix2nside(npix)
good = np.isfinite(prob) & np.isfinite(distmu) & np.isfinite(distsigma)
ipix = np.flatnonzero(good)
distmean, diststd, _ = parameters_to_moments(distmu[good], distsigma[good])
mass = prob[good] * (np.square(diststd) + np.square(distmean))
xyz = np.asarray(hp.pix2vec(nside, ipix, nest=nest))
cov = np.dot(xyz * mass, xyz.T)
L, V = np.linalg.eigh(cov)
if np.linalg.det(V) < 0:
V = -V
return V
def principal_axes(prob, distmu, distsigma, nest=False):
npix = len(prob)
nside = hp.npix2nside(npix)
bad = ~(np.isfinite(prob) & np.isfinite(distmu) & np.isfinite(distsigma))
distmean, diststd, _ = parameters_to_moments(distmu, distsigma)
mass = prob * (np.square(diststd) + np.square(distmean))
mass[bad] = 0.0
xyz = np.asarray(hp.pix2vec(nside, np.arange(npix), nest=nest))
cov = np.dot(xyz * mass, xyz.T)
L, V = np.linalg.eigh(cov)
if np.linalg.det(V) < 0:
V = -V
return V
def aipy_beam(freq,theta,phi,efield=False):
# really only defined between 120 and 180 MHz
# theta, phi in radians
nside = 256
bm = prms['beam'](np.array([freq]),nside=nside,lmax=20,mmax=20,deg=7)
bm.set_params(prms['bm_prms'])
px = hp.ang2pix(nside,theta,phi)
xyz = hp.pix2vec(nside,px)
poly = np.array([h.map[px] for h in bm.hmap])
Axx = np.polyval(poly,freq)
Axx = np.where(xyz[-1] >= 0, Axx, 0)
Axx /= Axx.max()
if (not efield):
Axx = Axx*Axx
return Axx
def smoothMap(map, smooth=5.):
if smooth == 0:
return map
npix = len(map)
nside = hp.npix2nside(npix)
smooth_rad = smooth * np.pi/180.
smooth_map = np.zeros(map.shape)
vec = np.transpose(hp.pix2vec(nside, np.arange(npix)))
for i in range(npix):
neighbors = hp.query_disc(nside, vec[i], smooth_rad)
smooth_map[i] += np.sum(map[neighbors], axis=0)
return smooth_map
def hp_interpolator(map_, el, az, n_pix=4):
NSide = hp.pixelfunc.get_nside(map_)
direction = np.array([np.pi/2.-el.to_rad(),az.to_rad()])
steplength = hp.pixelfunc.max_pixrad(NSide)
for i, r in enumerate(np.arange(steplength, np.pi, steplength)):
pixels = np.array(hp.query_disc(NSide,hp.ang2vec(direction[0], direction[1]), r))
filled = np.where(map_[pixels] > -1.)[0]
l = len(filled)
if l >= n_pix:
# print(i, l)
filled_pixel = pixels[filled]
filled_pixel_directions = hp.pix2vec(NSide, filled_pixel)
angular_distance = hp.rotator.angdist(direction, filled_pixel_directions)
if angular_distance.min() == 0.: # do we really want this?
return map_[filled_pixel[angular_distance.argmin()]]
return np.average(map_[filled_pixel], weights=np.power(1./angular_distance, 2))
def local_variance_map(map1, mask1, deg):
""" return the local variance map for map1 with mask mask1, given the error tolerance tol for mask2
"""
mp1=hp.ma(map1)
mp1.mask=np.logical_not(mask1)
NSIDE1=hp.npix2nside(len(map1))
NSIDE2=nside(deg)
NPIX2=hp.nside2npix(NSIDE2)
#mask2=np.round(hp.ud_grade(mask1, nside_out=NSIDE2)+tol)
mp2=np.array([0.]*NPIX2)
for pix2 in range(0, NPIX2):
disc1=hp.query_disc(nside=NSIDE1, vec=hp.pix2vec(NSIDE2, pix2), radius=deg2rad(deg))
mp2[pix2]=np.var(mp1[disc1])
#varmp2.mask=np.logical_not(mask2)
return mp2
def mask_hemi_west(NSIDE):
"""Returns the 'bad pixels' in the westhern hemisphere.
NSIDE: int
healpix nside parameter
"""
logger.info('Masking westhern hemisphere...')
NPIX = hp.pixelfunc.nside2npix(NSIDE)
BAD_PIX_HEMI_W = []
iii = range(NPIX)
x,y,z = hp.pix2vec(NSIDE,iii)
lon,lat = hp.rotator.vec2dir(x,y,z,lonlat=True)
for i,b in enumerate(lon):
if 0 <= b <= 180:
BAD_PIX_HEMI_W.append(iii[i])
return BAD_PIX_HEMI_W