def query_disc(nside, vec, radius, inclusive=False, fact=4, nest=False):
"""
Wrapper around healpy.query_disc to deal with old healpy implementation.
nside : int
The nside of the Healpix map.
vec : float, sequence of 3 elements
The coordinates of unit vector defining the disk center.
radius : float
The radius (in degrees) of the disc
inclusive : bool, optional
If False, return the exact set of pixels whose pixel centers lie
within the disk; if True, return all pixels that overlap with the disk,
and maybe a few more. Default: False
fact : int, optional
Only used when inclusive=True. The overlapping test will be done at
the resolution fact*nside. For NESTED ordering, fact must be a power of 2,
else it can be any positive integer. Default: 4.
nest: bool, optional
if True, assume NESTED pixel ordering, otherwise, RING pixel ordering
"""
try:
# New-style call (healpy 1.6.3)
return hp.query_disc(nside, vec, np.radians(radius), inclusive, fact, nest)
except Exception as e:
print(e)
# Old-style call (healpy 0.10.2)
return hp.query_disc(nside, vec, np.radians(radius), nest, deg=False)
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 test_combine(tmpdir):
"""Test ligo-skymap-combine."""
fn1 = str(tmpdir / 'skymap1.fits.gz')
fn2 = str(tmpdir / 'skymap2.fits.gz')
fn3 = str(tmpdir / 'joint_skymap.fits.gz')
# generate a hemisphere of constant probability
nside1 = 32
npix1 = ah.nside_to_npix(nside1)
m1 = np.zeros(npix1)
disc_idx = hp.query_disc(nside1, (1, 0, 0), np.pi / 2)
m1[disc_idx] = 1
m1 /= m1.sum()
hp.write_map(fn1,
m1,
column_names=['PROBABILITY'],
extra_header=[('INSTRUME', 'X1')])
# generate another hemisphere of constant probability
# but with higher resolution and rotated 90 degrees
nside2 = 64
npix2 = ah.nside_to_npix(nside2)
m2 = np.zeros(npix2)
disc_idx = hp.query_disc(nside2, (0, 1, 0), np.pi / 2)
m2[disc_idx] = 1
m2 /= m2.sum()
hp.write_map(fn2,
m2,
column_names=['PROBABILITY'],
extra_header=[('INSTRUME', 'Y1')])
run_entry_point('ligo-skymap-combine', fn1, fn2, fn3)
m3 = hp.read_map(fn3, nest=True)
npix3 = len(m3)
nside3 = ah.npix_to_nside(npix3)
pix_area3 = ah.nside_to_pixel_area(nside3).to_value(u.sr)
# resolution must match the highest original resolution
assert npix3 == npix2
# probability must be normalized to 1
assert m3.sum() == pytest.approx(1)
# support must be ¼ of the sphere
tolerance = 10 * ah.nside_to_pixel_area(nside1).to_value(u.sr)
assert sum(m3 > 0) * pix_area3 == pytest.approx(np.pi, abs=tolerance)
# generate a BAYESTAR-like map with mock distance information
d_mu = np.zeros_like(m1)
d_sigma = np.ones_like(m1)
d_norm = np.ones_like(m1)
io.write_sky_map(fn1, [m1, d_mu, d_sigma, d_norm])
run_entry_point('ligo-skymap-combine', fn1, fn2, fn3)
m3, meta3 = io.read_sky_map(fn3, nest=True, distances=True)
# check that marginal distance moments match what was simulated
mean, std, _ = distance.parameters_to_moments(d_mu[0], d_sigma[0])
assert meta3['distmean'] == pytest.approx(mean)
assert meta3['diststd'] == pytest.approx(std)
def get_hem_Cls(skymap, direction, LMAX=256, deg=90.):
"""
from the given healpix skymap, return Cls for two hemispheres defined by the
direction given, useful to study the possible scale dependence of power modulation
direction should be a unit vector
"""
# generate hemispherical mask
NPIX = len(skymap)
NSIDE = hp.npix2nside(NPIX)
maskp = np.array([0.] * NPIX)
disc = hp.query_disc(nside=NSIDE, vec=direction, radius=0.0174532925 * deg)
maskp[disc] = 1.
#skymap=hp.remove_monopole(skymap)
map1 = hp.ma(skymap)
map1.mask = maskp
Clsp = hp.anafast(map1, lmax=LMAX * 2.0)
if (deg < 90.):
maskm = np.array([0.] * NPIX)
disc = hp.query_disc(nside=NSIDE,
vec=-direction,
radius=0.0174532925 * deg)
maskm[disc] = 1.
map1.mask = maskm
else:
map1.mask = np.logical_not(maskp)
Clsm = hp.anafast(map1, lmax=LMAX * 2.0)
return [Clsp[0:LMAX + 1], Clsm[0:LMAX + 1]]
def csi_compute(param):
"""worker function"""
get_var_from_file(os.path.join(GRATOOLS_CONFIG, 'Csi_config.py'))
th_bins = data.TH_BINNING
i, veci, dI, R, nside = param
if i%10000 == 0:
print i
dIi = dI[i]
Ri = R[i]
dIij_list = [[] for l in range(0, len(th_bins)-1)]
counts_list = [[] for l in range(0, len(th_bins)-1)]
Rij_list = [[] for l in range(0, len(th_bins)-1)]
for th, (thmin, thmax) in enumerate(zip(th_bins[:-1], th_bins[1:])):
pixintorad_min = hp.query_disc(nside, veci, thmin)
pixintorad_max = hp.query_disc(nside, veci, thmax)
pixintoring = np.setxor1d(pixintorad_max, pixintorad_min)
Rj = R[pixintoring]
Rj = Rj[Rj > hp.UNSEEN]
dIj = dI[pixintoring]
dIj = dIj[dIj > hp.UNSEEN]
dIij = np.sum(dIi*dIj)#-Imean**2)
Rij = np.sum(Ri*Rj)
counts = len(dIj)
dIij_list[th].append(dIij)
counts_list[th].append(counts)
Rij_list[th].append(Rij)
return dIij_list, counts_list, Rij_list
def get_index_list(nside, nest, region):
""" Returns the list of pixels indices for all the pixels in a region
nside : HEALPix nside parameter
nest : True for 'NESTED', False = 'RING'
region : HEALPix region string
"""
tokens = parse_hpxregion(region)
if tokens[0] == 'DISK':
vec = coords_to_vec(float(tokens[1]), float(tokens[2]))
ilist = hp.query_disc(nside, vec[0], np.radians(float(tokens[3])),
inclusive=False, nest=nest)
elif tokens[0] == 'DISK_INC':
vec = coords_to_vec(float(tokens[1]), float(tokens[2]))
ilist = hp.query_disc(nside, vec[0], np.radians(float(tokens[3])),
inclusive=True, fact=int(tokens[4]),
nest=nest)
elif tokens[0] == 'HPX_PIXEL':
nside_pix = int(tokens[2])
if tokens[1] == 'NESTED':
ipix_ring = hp.nest2ring(nside_pix, int(tokens[3]))
elif tokens[1] == 'RING':
ipix_ring = int(tokens[3])
else:
raise Exception(
"Did not recognize ordering scheme %s" % tokens[1])
ilist = match_hpx_pixel(nside, nest, nside_pix, ipix_ring)
else:
raise Exception(
"HPX.get_index_list did not recognize region type %s" % tokens[0])
return ilist
def mask_extsrc(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 extended sources activated')
src_cat = pf.open(cat_file)
NPIX = hp.pixelfunc.nside2npix(NSIDE)
CAT_EXTENDED = src_cat['ExtendedSources']
BAD_PIX_SRC = []
EXT_SOURCES = CAT_EXTENDED.data
src_cat.close()
for i, src in enumerate(EXT_SOURCES):
NAME = EXT_SOURCES.field('Source_Name')[i]
GLON = EXT_SOURCES.field('GLON')[i]
GLAT = EXT_SOURCES.field('GLAT')[i]
if 'LMC' in NAME or 'CenA Lobes' in NAME:
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)
radintpix = hp.query_disc(NSIDE, (x, y, z), np.radians(10))
BAD_PIX_SRC.extend(radintpix)
else:
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)
radintpix = hp.query_disc(NSIDE, (x, y, z), np.radians(5))
BAD_PIX_SRC.extend(radintpix)
return BAD_PIX_SRC
def get_disk(mask, pos_src, out_edge, in_edge, tol=1):
'''
Return unmasked pixel indices of disks centred at a source.
For usage purpose the input includes two disks.
Input: mask: mask healpix map;
pos_src: position of source (with shape=3);
out_edge: outer disk centred at each source(in arcmin);
in_edge: inner disk centred at each source(in arcmin);
tol: tolerance between 0 and 1 indicating a threshold of fraction of
unmasked pixels in a disk
Output: pixel indices of both disks.
'''
Ns = hp.npix2nside(mask.size)
list_out = hp.query_disc(Ns, pos_src, np.radians(out_edge / 60.))
npix_out = len(list_out)
list_out_unmasked = list_out[mask[list_out] > 0]
if (list_out_unmasked.size < tol * npix_out):
return [0, 0]
lon, lat = hp.vec2dir(pos_src, lonlat=True)
list_in = hp.query_disc(Ns, pos_src, np.radians(in_edge / 60.))
list_in_unmasked = list_in[mask[list_in] > 0]
return list_out_unmasked, list_in_unmasked
def query_disc(nside, vec, radius, inclusive=False, fact=4, nest=False):
"""
Wrapper around healpy.query_disc to deal with old healpy implementation.
nside : int
The nside of the Healpix map.
vec : float, sequence of 3 elements
The coordinates of unit vector defining the disk center.
radius : float
The radius (in degrees) of the disc
inclusive : bool, optional
If False, return the exact set of pixels whose pixel centers lie
within the disk; if True, return all pixels that overlap with the disk,
and maybe a few more. Default: False
fact : int, optional
Only used when inclusive=True. The overlapping test will be done at
the resolution fact*nside. For NESTED ordering, fact must be a power of 2,
else it can be any positive integer. Default: 4.
nest: bool, optional
if True, assume NESTED pixel ordering, otherwise, RING pixel ordering
"""
try:
# New-style call (healpy 1.6.3)
return hp.query_disc(nside, vec, np.radians(radius), inclusive, fact, nest)
except Exception as e:
print(e)
# Old-style call (healpy 0.10.2)
return hp.query_disc(nside, vec, np.radians(radius), nest, deg=False)
def get_index_list(nside, nest, region):
""" Returns the list of pixels indices for all the pixels in a region
nside : HEALPix nside parameter
nest : True for 'NESTED', False = 'RING'
region : HEALPix region string
"""
import healpy as hp
tokens = re.split('\(|\)|,', region)
if tokens[0] == 'DISK':
vec = coords_to_vec(float(tokens[1]), float(tokens[2]))
ilist = hp.query_disc(nside, vec[0], np.radians(float(tokens[3])),
inclusive=False, nest=nest)
elif tokens[0] == 'DISK_INC':
vec = coords_to_vec(float(tokens[1]), float(tokens[2]))
ilist = hp.query_disc(nside, vec[0], np.radians(float(tokens[3])),
inclusive=True, fact=int(tokens[4]),
nest=nest)
elif tokens[0] == 'HPX_PIXEL':
nside_pix = int(tokens[2])
if tokens[1] == 'NESTED':
ipix_ring = hp.nest2ring(nside_pix, int(tokens[3]))
elif tokens[1] == 'RING':
ipix_ring = int(tokens[3])
else:
raise Exception(
"Did not recognize ordering scheme %s" % tokens[1])
ilist = match_hpx_pixel(nside, nest, nside_pix, ipix_ring)
else:
raise Exception(
"HPX.get_index_list did not recognize region type %s" % tokens[0])
return ilist
def get_hem_Cls(skymap, direction, LMAX=256, deg=90.):
"""
from the given healpix skymap, return Cls for two hemispheres defined by the
direction given, useful to study the possible scale dependence of power modulation
direction should be a unit vector
"""
# generate hemispherical mask
NPIX=len(skymap)
NSIDE=hp.npix2nside(NPIX)
maskp=np.array([0.]*NPIX)
disc=hp.query_disc(nside=NSIDE, vec=direction, radius=0.0174532925*deg)
maskp[disc]=1.
#skymap=hp.remove_monopole(skymap)
map1=hp.ma(skymap)
map1.mask=maskp
Clsp=hp.anafast(map1, lmax=LMAX)
if (deg<90.):
maskm=np.array([0.]*NPIX)
disc=hp.query_disc(nside=NSIDE, vec=-direction, radius=0.0174532925*deg)
maskm[disc]=1.
map1.mask=maskm
else:
map1.mask=np.logical_not(maskp)
Clsm=hp.anafast(map1, lmax=LMAX)
return [Clsp, Clsm]
def csi_compute(param):
"""worker function"""
get_var_from_file(os.path.join(GRATOOLS_CONFIG, 'Csi_config.py'))
th_bins = data.TH_BINNING
i, veci, dI, R, nside = param
if i % 10000 == 0:
print i
dIi = dI[i]
Ri = R[i]
dIij_list = [[] for l in range(0, len(th_bins) - 1)]
counts_list = [[] for l in range(0, len(th_bins) - 1)]
Rij_list = [[] for l in range(0, len(th_bins) - 1)]
for th, (thmin, thmax) in enumerate(zip(th_bins[:-1], th_bins[1:])):
pixintorad_min = hp.query_disc(nside, veci, thmin)
pixintorad_max = hp.query_disc(nside, veci, thmax)
pixintoring = np.setxor1d(pixintorad_max, pixintorad_min)
Rj = R[pixintoring]
Rj = Rj[Rj > hp.UNSEEN]
dIj = dI[pixintoring]
dIj = dIj[dIj > hp.UNSEEN]
dIij = np.sum(dIi * dIj) #-Imean**2)
Rij = np.sum(Ri * Rj)
counts = len(dIj)
dIij_list[th].append(dIij)
counts_list[th].append(counts)
Rij_list[th].append(Rij)
return dIij_list, counts_list, Rij_list
def get_disk(self, src_ind, out_edge, in_edge, tol=1):
'''
Return unmasked pixel indices of disks centred at a source.
For usage purpose the input includes two disks.
Input: src_ind: index of source;
out_edge: outer disk centred at each source(in arcmin);
in_edge: inner disk centred at each source(in arcmin);
tol: tolerance between 0 and 1 indicating a threshold of
fraction of unmasked pixels in a disk
Output: pixel indices of both disks.
'''
mask = self.mask
Ns = self.Nside
pos_src = self.pos_src_all[src_ind]
list_out = hp.query_disc(Ns, pos_src, np.radians(out_edge / 60.))
npix_out = len(list_out)
list_out_unmasked = list_out[mask[list_out] > 0]
if(list_out_unmasked.size < tol * npix_out):
return [0, 0]
lon, lat = hp.vec2dir(pos_src, lonlat=True)
list_in = hp.query_disc(Ns, pos_src, np.radians(in_edge / 60.))
list_in_unmasked = list_in[mask[list_in] > 0]
return list_out_unmasked, list_in_unmasked
def find_biggest_pixel(ra, dec, radius, root_nside=1, max_nside=32):
from astropy.coordinates import SkyCoord
from astropy import units as u
import healpy as hp
import numpy as np
nside = root_nside
radius = np.radians(radius)
sc = SkyCoord(ra=ra * u.degree, dec=dec * u.degree, frame='icrs')
theta = sc.galactic.l.degree
phi = sc.galactic.b.degree
vec = hp.ang2vec(theta=theta, phi=phi, lonlat=True)
pixels = hp.query_disc(vec=vec,
nside=nside,
radius=radius,
inclusive=False,
nest=True)
while len(pixels) <= 1:
if nside == max_nside:
break
nside *= 2
pixels = hp.query_disc(vec=vec,
nside=nside,
radius=radius,
inclusive=False,
nest=True)
if nside > 1:
nside //= 2
return nside, hp.vec2pix(nside, *vec, nest=True)
def CreateAnafastPartialSky_(cl,
nside,
lmin,
lmax,
delta_ell,
f_sky=2 / 100,
plot_results=False,
noise_rms=200):
import NamasterLib as nam
# Determine SEEN pixels from f_sky using query_disc
vec = hp.pixelfunc.ang2vec(np.pi / 2, np.pi * 3 / 4)
radius = f_sky * np.pi
#print(np.array([cl.T[0,:]]).shape)
ipix_disc = hp.query_disc(nside=nside, vec=vec, radius=radius, nest=False)
while len(ipix_disc) < f_sky * 12 * nside**2:
radius += 0.01 * np.pi
ipix_disc = hp.query_disc(nside=nside,
vec=vec,
radius=radius,
nest=False)
#print("npix_partial_sky: ", len(ipix_disc))
m = np.arange(12 * nside**2)
m = np.delete(m, ipix_disc, axis=None)
# Define the seen pixels
seenpix = ipix_disc
### Making mask - it will be automaticall apodized when instanciating the object with default (tunable) parameters
mask = np.zeros(12 * nside**2)
mask[seenpix] = 1
Namaster = nam.Namaster(mask, lmin=lmin, lmax=lmax, delta_ell=delta_ell)
ell_binned, b = Namaster.get_binning(nside)
# Get binned input spectra
cl_theo_binned = np.zeros(shape=(4, ell_binned.shape[0]))
for i in range(4):
cl_theo_binned[i, :] = Namaster.bin_spectra(np.array([cl.T[i, :]]),
nside)
map_ = hp.synfast(cl.T, nside, pixwin=False, verbose=False, new=True)
npix = 12 * nside**2
noise = np.random.randn(npix) * noise_rms
map_partial = map_ + noise
# Anafast spectrum of this map
# Set UNSEEN pixels to hp.UNSEEN for Anafast
map_partial[:, m] = hp.UNSEEN
cl_ana, alm_ana = hp.anafast(map_partial, alm=True, lmax=lmax)
# Get binned input spectra
cl_ana_binned = np.zeros(shape=(4, ell_binned.shape[0]))
for i in range(4):
cl_ana_binned[i, :] = Namaster.bin_spectra(np.array([cl_ana[i, :]]),
nside)
return alm_ana, cl_ana_binned, cl_theo_binned
def getAMatrix(self):
# A = lil_matrix((self.Nd, self.Np), dtype=np.float32)
data = []
rows = []
columns = []
start = time.time()
pixarea = hp.nside2pixarea(self.Nside, False)
# get relevant pair of pixels
# for j in range(1000):
for j in range(self.Nd):
qtheta1=self.q.theta[self.d.i1[j]]
qphi1=self.q.phi[self.d.i1[j]]
qtheta2=self.q.theta[self.d.i2[j]]
qphi2=self.q.phi[self.d.i2[j]]
q1 = self.Ang2Vec(qtheta1, qphi1)
q2 = self.Ang2Vec(qtheta2, qphi2)
# rad = np.arccos(np.dot(q1,q2))
# if(rad <= self.resolution):
# s = np.array([self.d.hi1[j]])
# else:
neipixels1=hp.query_disc(self.Nside, q1, self.sradius)
neipixels2=hp.query_disc(self.Nside, q2, self.sradius)
s = np.union1d(neipixels1, neipixels2)
ss = set(s)
smols = np.array([*ss.intersection(self.setpix)])
jthrow = [self.pixdict[l] for l in smols]
if (smols.shape[0] == 0):
continue
ms = np.array([self.hpix[x] for x in smols])
d1 = q1 - ms
d2 = q2 - ms
norm1 = np.sqrt(np.einsum('ij,ij->i', d1, d1)) #Faster way to calculate norms
norm2 = np.sqrt(np.einsum('ij,ij->i', d2, d2))
resp1=1/norm1*(1-np.exp(-norm1**2/(self.sigweight)))
resp2=1/norm2*(1-np.exp(-norm2**2/(self.sigweight)))
drr = (d1.T*resp1).T - (d2.T*resp2).T
dr = d1 - d2
totresponse = 2*pixarea*np.einsum('ij,ij->i', drr, drr)/np.einsum('ij,ij->i',dr,dr)
totresponse *= np.sqrt(self.d.weight[j])
data += list(totresponse)
rows += [j]*len(jthrow)
columns += jthrow
# A[j,jthrow] = totresponse
if(j%1000==0):
iteration = time.time()
print("%i/%i with time: %f" % (j,self.Nd, iteration - start))
print("Creating A matrix...")
# A = scipy.sparse.csr_matrix((data, (rows, columns)), shape=(self.Nd, self.Np))
A = csr_matrix((data, (rows, columns)), shape=(self.Nd, self.Np))
return A
def get_index_list(nside, nest, region):
"""Get list of pixels indices for all the pixels in a region.
Parameters
----------
nside : int
HEALPIX nside parameter
nest : bool
True for 'NESTED', False = 'RING'
region : str
HEALPIX region string
Returns
-------
ilist : `~numpy.ndarray`
List of pixel indices.
"""
import healpy as hp
# TODO: this should return something more friendly than a tuple
# e.g. a namedtuple or a dict
tokens = parse_hpxregion(region)
reg_type = tokens[0]
if reg_type == "DISK":
lon, lat = float(tokens[1]), float(tokens[2])
radius = np.radians(float(tokens[3]))
vec = coords_to_vec(lon, lat)[0]
ilist = hp.query_disc(nside,
vec,
radius,
inclusive=False,
nest=nest)
elif reg_type == "DISK_INC":
lon, lat = float(tokens[1]), float(tokens[2])
radius = np.radians(float(tokens[3]))
vec = coords_to_vec(lon, lat)[0]
fact = int(tokens[4])
ilist = hp.query_disc(nside,
vec,
radius,
inclusive=True,
nest=nest,
fact=fact)
elif reg_type == "HPX_PIXEL":
nside_pix = int(tokens[2])
if tokens[1] == "NESTED":
ipix_ring = hp.nest2ring(nside_pix, int(tokens[3]))
elif tokens[1] == "RING":
ipix_ring = int(tokens[3])
else:
raise ValueError(f"Invalid ordering scheme: {tokens[1]!r}")
ilist = match_hpx_pix(nside, nest, nside_pix, ipix_ring)
else:
raise ValueError(f"Invalid region type: {reg_type!r}")
return ilist
def get_annulus_galactic(phi,theta,R,hp_map,nside):
vec = hp.ang2vec(theta,phi)
R_rad_inner = (np.pi/180.)*R
R_rad_outer = R_rad_inner*np.sqrt(2)
pix_disc_out = hp.query_disc(nside,vec,R_rad_outer,inclusive = True)
pix_disc_inner = hp.query_disc(nside,vec,R_rad_inner, inclusive = True)
pix_annulus = np.setdiff1d(pix_disc_out,pix_disc_inner)
vals_annulus = hp_map[pix_annulus]
return pix_annulus, vals_annulus
def get_annulus(RA, Dec, R, hp_map, nside):
theta, phi = DeclRaToThetaPhi(Dec, RA)
vec = hp.ang2vec(theta, phi)
R_rad_inner = (np.pi / 180.) * R
R_rad_outer = R_rad_inner * np.sqrt(2)
pix_disc_out = hp.query_disc(nside, vec, R_rad_outer, inclusive=True)
pix_disc_inner = hp.query_disc(nside, vec, R_rad_inner, inclusive=True)
pix_annulus = np.setdiff1d(pix_disc_out, pix_disc_inner)
vals_annulus = hp_map[pix_annulus]
return pix_annulus, vals_annulus
def get_probability_coverage(ft2file, ligo_map_file, met_t1, met_t2, theta_cut,
zenith_cut):
ft2data = pyfits.getdata(ft2file)
ligo_map = hp.read_map(ligo_map_file)
# Probe NSIDE
nside = hp.get_nside(ligo_map)
# Get entries from the FT2 file every 10 s (cadence)
start, ra_scz, dec_scz, ra_zenith, dec_zenith = _gtmktime(ft2data,
met_t1,
met_t2,
cadence=30)
coverage = np.zeros_like(start)
for i, (t, rz, dz, rz2, dz2) in enumerate(
zip(start, ra_scz, dec_scz, ra_zenith, dec_zenith)):
# Find the pixels inside the LAT FoV (theta < theta_cut)
vec = hp.rotator.dir2vec(rz, dz, lonlat=True)
idx_z = hp.query_disc(nside,
vec,
np.deg2rad(theta_cut),
inclusive=False)
# Find the pixels at Zenith angles less
# than zenith_cut
vec = hp.rotator.dir2vec(rz2, dz2, lonlat=True)
idx_z2 = hp.query_disc(nside,
vec,
np.deg2rad(zenith_cut),
inclusive=False)
# Intersect the two lists of pixels to find pixels which are at the same time
# inside the FoV and at Zenith < zenith_cut
idx = np.intersect1d(idx_z, idx_z2)
# Compute the incremental probability coverage
coverage[i] = np.sum(ligo_map[idx])
# Now put the pixel I counted to zero so I don't count them twice
ligo_map[idx] = 0
sys.stdout.write("\r%.1f percent completed" %
((i + 1) / float(coverage.shape[0]) * 100.0))
return start, coverage
def makeMasks(nside=64, nested=False, ISWDir='/Data/PSG/hundred_point/'):
"""
Purpose:
Makes a set of masks around GNS coordinates of various apertures
Args:
nside:
nested:
ISWDir:
Returns:
writes healpix files to ISWDir containing masks
"""
# load HEALpix coordinates file
print 'NSIDE=', nside, ' NESTED=', nested
longitudes, latitudes = getMapCoords(nside, nested)
# load GNS catalog coordinates
cgl, cgb, vgl, vgb = getGNScoords()
# set radii for apertures around coordinate locations
radiiDeg = np.array([
4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 11.5, 12
]) #degrees
#radiiDeg = np.array([5.0])
radii = radiiDeg * np.pi / 180. # converted to radians
numCV = 50 # number of clusters and voids in catalog
for radNum, radius in enumerate(radii):
print 'starting radius ', radiiDeg[radNum], ' degrees: '
mask = np.zeros(hp.nside2npix(nside))
cCentralVec = glgb2vec(cgl, cgb) #returns array of unit vectors
vCentralVec = glgb2vec(vgl, vgb) #returns array of unit vectors
for cvNum in np.arange(numCV):
#print 'starting (cluster,void) number ',cvNum+1
# cluster
myPixels = hp.query_disc(nside,
cCentralVec[cvNum],
radius,
nest=nested)
mask[myPixels] = 1
# void
myPixels = hp.query_disc(nside,
vCentralVec[cvNum],
radius,
nest=nested)
mask[myPixels] = 1
radString = str("%04.1f" % radiiDeg[radNum])
pixNumStr = str(int(np.sum(mask)))
print 'number of pixels for radius ' + radString + ': ' + pixNumStr
maskFile = 'ISWmask_' + radString + 'deg_' + pixNumStr + 'pix.fits'
hp.write_map(ISWDir + maskFile, mask, nest=nested, coord='GALACTIC')
def plot_exposures(pointings,
Aeff_fact,
index=1,
lat=0.,
lon=np.radians(260.),
Earth=True,
antiEarth=False,
NSIDE=32,
doplot=True):
npointings = len(pointings)
sc = Spacecraft(pointings, lat=lat, lon=lon)
exposure_positions_hp = np.arange(hp.nside2npix(NSIDE))
exposure_positions_pix = hp.pix2ang(NSIDE,
exposure_positions_hp,
lonlat=True)
exposure_positions = np.vstack(exposure_positions_pix)
exposures = np.array([[
detector.exposure(position[0], position[1], alt=-90., index=index)
for position in exposure_positions.T
] for detector in sc.detectors])
exps = exposures.sum(axis=0) * Aeff_fact
fs = exps #-min(gbm_exps))/max(gbm_exps)
if Earth:
vec = hp.ang2vec(180, 0, lonlat=True)
i = hp.query_disc(NSIDE, vec, 67 * np.pi / 180.)
fs[i] = 0
exposures[:, i] = 0
if antiEarth:
vec = hp.ang2vec(np.degrees(lon) - 260. + 180., 0, lonlat=True)
i = hp.query_disc(NSIDE, vec, 67 * np.pi / 180.)
fs[i] = 0
exposures[:, i] = 0
if doplot:
plot.figure(figsize=(20, npointings))
s = np.argsort(pointings.keys())
for j in range(npointings):
i = s[j]
hp.mollview(exposures[i]/max(exposures[i])*Aeff_fact,title='Detector ',\
sub = [np.round(npointings/3.+0.5),3,int(str(j+1))])
#+pointings.keys()[i],\
hp.mollview(fs, title='Sum of All Detectors')
# plot.savefig(biadir+'exposure_maps_'+str(ang)+'.png')
return sc, fs, exposure_positions, pointings, exposures
def addring(nside, ra, dec, anga, angb):
"""
take a map, and add 1 to elements between anga and angb from ra, dec
"""
theta = np.deg2rad(90-dec)
phi = np.deg2rad(ra)
temp_map = np.zeros(hp.nside2npix(nside))
assert angb > anga # else error
# Everything from 0 to angb = 1
pixlist = hp.query_disc(nside, hp.ang2vec(theta, phi), np.deg2rad(angb))
temp_map[pixlist] += 1
# now delete everything from 0 to anga
pixlist = hp.query_disc(nside, hp.ang2vec(theta, phi), np.deg2rad(anga))
temp_map[pixlist] -= 1
return temp_map
def gen_map_disc(radec_cen, rad, nside):
'''Generates a Healpix map with the only non-zero values in the
pixels inside the input disc.
Parameters
----------
radec_cen : array-like with shape (2,)
The center ra,dec of the disc in degrees
rad : float
The radius of the disc in degrees
nside : int
The nside of the output Healpix map
Returns
-------
hpx_map : array-like
A Healpix map with non-zero values inside the disc
'''
theta = np.pi / 2 - np.radians(radec_cen[1])
phi = np.radians(radec_cen[0])
vec = H.ang2vec(theta, phi)
ipix = H.query_disc(nside, vec, np.radians(rad))
hpx_map = np.zeros(H.nside2npix(nside))
hpx_map[ipix] = 1.0
return hpx_map
def grow_hp(inmap, hpids, radius=1.75, replace_val=np.nan):
"""
grow a healpix mask
Parameters
----------
inmap : np.array
A HEALpix map
hpids : array
The healpixel values to grow around
radius : float (1.75)
The radius to grow around each point (degrees)
replace_val : float (np.nan)
The value to plug into the grown areas
"""
nside = hp.npix2nside(np.size(inmap))
theta, phi = hp.pix2ang(nside=nside, ipix=hpids)
vec = hp.ang2vec(theta, phi)
ipix_disc = [
hp.query_disc(nside=nside, vec=vector, radius=np.radians(radius))
for vector in vec
]
ipix_disc = np.unique(np.concatenate(ipix_disc))
outmap = inmap + 0
outmap[ipix_disc] = replace_val
return outmap
def query_disc(self, lon, lat, radius, fact=4): """ Find pixels that overlap with discs centered at (lon,lat) Inputs ------ lon : float, ndarray longitude (degr) lat : float, ndarray latitude (degr) radius : float, ndarray radius of disk (degrees) fact : float supersampling factor to find overlapping pixels (see healpy.query_disc doc) Returns ------ ndarray : pixel indices """ phi = np.array(lon) * self.deg2rad theta = (90 - np.array(lat)) * self.deg2rad vec = healpy.ang2vec(theta, phi) pix = healpy.query_disc(self.nside, vec, radius * self.deg2rad, inclusive=True, fact=fact, nest=self.nest) return pix
def find_field_visits(visits, ra, decl, nside=512, field_radius_deg=1.75):
"""Return visits centered near a pointing
Parameters
----------
visits : `pandas.DataFrame`
The visits in which to look for fields
ra : `float`
The RA around which to search.
decl : `float`
The declination around which to search
nside : `int`
The nside for the healpix search
field_radious_deg : `float`
The radious round which to search, in degrees
Returns
-------
field_visits : `pandas.DataFrame`
The visits on the field.
"""
field_hpxs = healpy.query_disc(
nside,
healpy.ang2vec(ra, decl, lonlat=True),
np.radians(field_radius_deg),
)
visit_hpxs = healpy.ang2pix(nside,
visits["fieldRA"].values,
visits["fieldDec"].values,
lonlat=True)
field_visits = visits.loc[np.isin(visit_hpxs, field_hpxs)]
return field_visits
def pencil(self, theta, phi, angrad, **kwargs):
"""Query a pencil beam from this `SkyMap`
Returns the subset of this `SkyMap` that covers an angular disc on
the sky (i.e., a pencil beam)
Parameters
----------
theta : `float`
zenith angle (radians) at the center of the disc
phi : `float`
azimuth angle (radians) at the center of the disc
angrad : `float` or `~astropy.units.Quantity`
angular radius (radians) subtended by the disc
**kwargs : `dict`, optional
additional keyword arguments to `~healpy.query_disc`
Returns
-------
out : `SkyMap`
the subset of `SkyMap` subtended by this pencil beam
"""
if isinstance(angrad, units.Quantity):
angrad = angrad.to("rad").value
direction = healpy.ang2vec(theta, phi)
indices = healpy.query_disc(self.nside,
direction,
angrad,
nest=self.nest,
**kwargs)
return self[indices]
def handling_exception(params, constraints):
NSIDEmax = params['NSIDE max']
vec = hp.ang2vec(params["ang"][0], params["ang"][1], lonlat=True)
pixels = hp.query_disc(NSIDEmax,
vec,
np.radians(params['r'] / 3600.),
inclusive=True)
subjobs = mastcasjobs.MastCasJobs(context="PanSTARRS_DR2")
for pixel in pixels:
ang, r = qr.parameters(NSIDEmax, pixel)
subquery = sub_query_string(ang[0], ang[1], r)
accept = True
while accept:
try:
subtab = subjobs.quick(subquery,
task_name="python cone search")
accept = False
except Exception:
from time import sleep
sleep(60)
pass
subtab = qr.fixcolnames(ascii.read(subtab))
subtab = qr.query_constraints(subtab, constraints)
if pixel == pixels[0]:
table = subtab
else:
table = vstack([table, subtab])
return table
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 generate_inmaskcat(self, out_edge, tol=1):
'''
Return unmasked sources.
Input: out_edge: out edge of the disk centred at each source(in arcmin);
tol: tolerance between 0 and 1 indicating a threshold of fraction of
unmasked pixels in a disk
Output: indices of unmasked sources.
'''
mask = self.mask
Ns = self.Nside
Nsource = self.Nsource
pos_src_all = self.pos_src_all
inmask_ind = np.zeros(Nsource)
for i in range(Nsource):
if i % 10000 == 0:
print i
list_out = hp.query_disc(Ns, pos_src_all[i], np.radians(out_edge / 60.))
npix_out = list_out.size
neff_out = np.sum(mask[list_out])
if(neff_out < tol * npix_out):
continue
else:
inmask_ind[i] = 1
print str(inmask_ind.sum()) + ' sources in mask.'
return inmask_ind
def get_hpmask_subpix_indices(submask_nside, submask_hpix, submask_border, nside_mask, hpix):
"""
"""
nside_cutref = np.clip(submask_nside * 4, 256, nside_mask)
# Find out which cutref pixels are inside the main pixel
theta, phi = hp.pix2ang(nside_cutref, np.arange(hp.nside2npix(nside_cutref)))
ipring_coarse = hp.ang2pix(submask_nside, theta, phi)
inhpix, = np.where(ipring_coarse == submask_hpix)
# If there is a border, we need to find the boundary pixels
if submask_border > 0.0:
boundaries = hp.boundaries(submask_nside, submask_hpix, step=nside_cutref/submask_nside)
# These are all the pixels that touch the boundary
for i in xrange(boundaries.shape[1]):
pixint = hp.query_disc(nside_cutref, boundaries[:, i],
np.radians(submask_border), inclusive=True, fact=8)
inhpix = np.append(inhpix, pixint)
# Need to uniqify here because of overlapping pixels
inhpix = np.unique(inhpix)
# And now choose just those depthmap pixels that are in the inhpix region
theta, phi = hp.pix2ang(nside_mask, hpix)
ipring = hp.ang2pix(nside_cutref, theta, phi)
_, use = esutil.numpy_util.match(inhpix, ipring)
return use
def calculate_efficiency(hpx, d0, s0, s1, nfields, fieldop):
'''This function determines the score of a given set of tiling parameters for the optimization.
The figure of merit is the sum value of the for the <nfields> higher fields of the tiling'''
nside = hp.npix2nside(len(hpx))
keptfields = build_fields(hpx, d0, s0, s1, nfields, fieldop)
# totaldots = np.sum(keptfields["prob"])
total = 0
prob_integral = []
for indec in range(0, len(keptfields)):
# cornerra, cornerdec = getcorners(keptfields["ra"][indec],keptfields["dec"][indec],field=4.2)
# xyz = hp.ang2vec(checktheta(dectotheta(cornerdec)),checkphi(ratophi(cornerdec)))
# hp.query_polygon(nside,xyz)
xyz = hp.ang2vec(dectotheta(keptfields["dec"][indec]),
ratophi(keptfields["ra"][indec]))
ipix_disc = hp.query_disc(nside, xyz, np.deg2rad(
fieldop)) #here radius seems to be a diameter instead * (sq2+1)/4)
totdisc = hpx[ipix_disc].sum()
prob_integral.append(totdisc)
total += totdisc
# efficiency = total / nfields
#print (total)
return total, prob_integral
def disk_plot(value, dir_vec, ang_size, nside_var):
coord = hp.query_disc(nside=nside_var,
vec=dir_vec,
radius=np.deg2rad(ang_size),
inclusive=True,
fact=16)
m[coord] = value
def label_visits(visits, wfd_footprint, nside=64):
# Set up DD names.
d = set()
for p in visits['note'].unique():
if p.startswith('DD'):
d.add(define_ddname(p))
# Define dictionary of proposal tags.
propTags = {'Other': 0, 'WFD': 1}
for i, field in enumerate(d):
propTags[field] = i + 2
# Identify Healpixels associated with each visit.
vec = hp.dir2vec(visits['fieldRA'], visits['fieldDec'], lonlat=True)
vec = vec.swapaxes(0, 1)
radius = np.radians(1.75) # fov radius
#pointings = []
propId = np.zeros(len(visits), int)
for i, (v, note) in enumerate(zip(vec, visits['note'])):
# Identify the healpixels which would be inside this pointing
pointing_healpix = hp.query_disc(nside, v, radius, inclusive=False)
# This can be useful for debugging/plotting
#pointings.append(pointing_healpix)
# The wfd_footprint consists of values of 0/1 if out/in WFD footprint
in_wfd = wfd_footprint[pointing_healpix].sum()
# So in_wfd = the number of healpixels which were in the WFD footprint
# .. in the # in / total # > limit (0.4) then "yes" it's in WFD
propId[i] = np.where(in_wfd / len(pointing_healpix) > 0.4,
propTags['WFD'], 0)
# BUT override - if the visit was taken for DD, use that flag instead.
if note.startswith('DD'):
propId[i] = propTags[define_ddname(note)]
return visits, propTags, propId
def dust_vals_disk(self,lcen,bcen,dist,radius):
"""
NAME:
dust_vals_disk
PURPOSE:
return the distribution of extinction within a small disk as samples
INPUT:
lcen, bcen - Galactic longitude and latitude of the center of the disk (deg)
dist - distance in kpc
radius - radius of the disk (deg)
OUTPUT:
(pixarea,extinction) - arrays of pixel-area in sq rad and extinction value
HISTORY:
2015-03-07 - Written - Bovy (IAS)
"""
# Convert the disk center to a HEALPIX vector
vec= healpy.pixelfunc.ang2vec((90.-bcen)*_DEGTORAD,lcen*_DEGTORAD)
# We pixelize the map with a HEALPIX grid with nside=256, to somewhat
# oversample the Drimmel resolution
nside= 256
# Find the pixels at this resolution that fall within the disk
ipixs= healpy.query_disc(nside,vec,radius*_DEGTORAD,
inclusive=False,nest=False)
# Query the HEALPIX map for pixels that lie within the disk
pixarea= healpy.pixelfunc.nside2pixarea(nside)+numpy.zeros(len(ipixs))
extinction= []
for ii, ipix in enumerate(ipixs):
# Get glon and glat
b9, l= healpy.pixelfunc.pix2ang(nside,ipix,nest=False)
b= 90.-b9/_DEGTORAD
l/= _DEGTORAD
# Now evaluate
extinction.append(self._evaluate(l,b,dist))
extinction= numpy.array(extinction)
return (pixarea,extinction)
def gen_map_disc(radec_cen, rad, nside):
'''Generates a Healpix map with the only non-zero values in the
pixels inside the input disc.
Parameters
----------
radec_cen : array-like with shape (2,)
The center ra,dec of the disc in degrees
rad : float
The radius of the disc in degrees
nside : int
The nside of the output Healpix map
Returns
-------
hpx_map : array-like
A Healpix map with non-zero values inside the disc
'''
theta = np.pi/2 - np.radians(radec_cen[1])
phi = np.radians(radec_cen[0])
vec = H.ang2vec(theta, phi)
ipix = H.query_disc(nside, vec, np.radians(rad))
hpx_map = np.zeros(H.nside2npix(nside))
hpx_map[ipix] = 1.0
return hpx_map
def _get_mask(self):
if self.config.get('mask_file', None) is not None:
mask = hp.read_map(self.config['mask_file'])
mask = hp.ud_grade(rotate_mask(mask, self.rot),
nside_out=self.nside)
mask[mask > 0.5] = 1.
mask[mask <= 0.5] = 0.
else:
mask = np.ones(self.npix)
r = hp.Rotator(coord=['C', 'G'])
RApix, DEpix = hp.pix2ang(self.nside,
np.arange(self.npix),
lonlat=True)
lpix, bpix = r(RApix, DEpix, lonlat=True)
# angular conditions
mask[(DEpix < self.config.get('DEC_min_deg', -40)) |
(np.fabs(bpix) < self.config.get('GLAT_max_deg', 5))] = 0
if self.file_sourcemask is not None:
# holes catalog
RAmask, DEmask, radmask = np.loadtxt(self.file_sourcemask,
unpack=True)
vecmask = hp.ang2vec(RAmask, DEmask, lonlat=True)
for vec, radius in zip(vecmask, radmask):
ipix_hole = hp.query_disc(self.nside,
vec,
np.radians(radius),
inclusive=True)
mask[ipix_hole] = 0
mask = rotate_mask(mask, self.rot, binarize=True)
return mask
def compute_circle(N, t, p, r, r_in):
# Compute query (outer circle) and query_in (inner circle)
query = hp.query_disc(nside=N,
vec=hp.ang2vec(np.pi / 2 - t, p),
radius=r,
inclusive=False,
nest=False)
query_in = hp.query_disc(nside=N,
vec=hp.ang2vec(np.pi / 2 - t, p),
radius=r_in,
inclusive=False,
nest=False)
# Inverse intersection of query (outer circle) and query_in (inner circle)
inner = minus(query, query_in)
return inner
def test_inclusive(self):
#HIDL> query_disc, 8, [ 0.17101007, 0.03015369, 0.98480775],6,listpix,/DEG,NESTED=0,/inclusive
#HIDL> print,listpix
# 0 3 4 5 11 12 13 23
np.testing.assert_array_equal(
query_disc(self.NSIDE, self.vec, self.radius, inclusive=True),
np.array([ 0, 3, 4, 5, 11, 12, 13, 23 ])
)
def test_not_inclusive(self):
#HIDL> query_disc, 8, [ 0.17101007, 0.03015369, 0.98480775],6,listpix,/DEG,NESTED=0
#HIDL> print,listpix
# 4
np.testing.assert_array_equal(
query_disc(self.NSIDE, self.vec, self.radius, inclusive=False),
np.array([4])
)
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 get_pixels(centr_ra, centr_decl, fov_radius):
"""
Get a list of HEALPIX zones that contain a given image.
"""
vector = healpy.ang2vec(radians(90.0 - centr_decl),
radians(centr_ra))
pixels = healpy.query_disc(32, vector, radians(fov_radius),
inclusive=True, nest=True)
return str(pixels.tolist())[1:-1]
def gaussian_on_a_sphere(mean_th, mean_phi, sigma):
"""
This function returns a 2D normal pdf on a discretized healpy grid.
To chose the function values correctly in spherical coordinates,
the true angular distances to the mean are used.
Pixels farther away from the mean than clip * sigma are clipped
because the normal distribution falls quickly to zero. The error
made by this can be easily estimated and a discussion can be found
in [arXiv:1005.1929](https://arxiv.org/abs/1005.1929v2).
Parameters
----------
mean_th : float
Position of the mean in healpy coordinate `theta`. `theta` is in
[0, pi] going from north to south pole.
mean_phi : float
Position of the mean in healpy coordinate `phi`. `phi` is in [0, 2pi]
and is equivalent to the azimuth angle.
sigma : float
Standard deviation of the 2D normal distribution. Only symmetric
normal pdfs are used here.
Returns
-------
kernel : array
Values of the 2D normal distribution at the selected pixels. If clip
False, kernel is a valid healpy map with resolution NSIDE.
keep_idx : array
Pixel indices that are kept from the full healpy map after clipping.
If clip is False this is a sorted integer array with values
[0, 1, ..., NPIX-1] with NPIX tha number of pixels in the full healpy
map with resolution NSIDE.
"""
# Clip unneccessary pixels, just keep clip*sigma (radians)
# around the mean. Using inlusive=True to make sure at least
# one pixel gets returned.
# Always returns a list, so no manual np.array() required.
keep_idx = hp.query_disc(
self._nside, hp.ang2vec(mean_th, mean_phi),
self._clip * sigma, inclusive=True)
# Create only the needed the pixel healpy coordinates
th, phi = hp.pix2ang(self._nside, keep_idx)
sinTh = np.sin(th)
# For each pixel get the distance to (mean_th, mean_phi) direction
dist = angdist(mean_phi, mean_th, phi, sinTh)
# Get the 2D gaussian values at those distances -> kernel function
# Because the kernel is radial symmetric we use a simplified
# version -> 1D gaussian, properly normed
sigma2 = 2 * sigma**2
kernel = np.exp(-dist**2 / sigma2) / (np.pi * sigma2)
return kernel, keep_idx
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 dust_vals_disk(self,lcen,bcen,dist,radius):
"""
NAME:
dust_vals_disk
PURPOSE:
return the distribution of extinction within a small disk as samples
INPUT:
lcen, bcen - Galactic longitude and latitude of the center of the disk (deg)
dist - distance in kpc
radius - radius of the disk (deg)
OUTPUT:
(pixarea,extinction) - arrays of pixel-area in sq rad and extinction value
HISTORY:
2015-03-06 - Written - Bovy (IAS)
"""
# Convert the disk center to a HEALPIX vector
vec= healpy.pixelfunc.ang2vec((90.-bcen)*_DEGTORAD,lcen*_DEGTORAD)
distmod= 5.*numpy.log10(dist)+10.
# Query the HEALPIX map for pixels that lie within the disk
pixarea= []
extinction= []
for nside in self._nsides:
# Find the pixels at this resolution that fall within the disk
ipixs= healpy.query_disc(nside,vec,radius*_DEGTORAD,
inclusive=False,nest=True)
# Get indices of all pixels within the disk at current nside level
nsideindx= self._pix_info['nside'] == nside
potenIndxs= self._indexArray[nsideindx]
nsidepix= self._pix_info['healpix_index'][nsideindx]
# Loop through the pixels in the (small) disk
tout= []
for ii,ipix in enumerate(ipixs):
lbIndx= potenIndxs[ipix == nsidepix]
if numpy.sum(lbIndx) == 0: continue
if self._intps[lbIndx] != 0:
tout.append(self._intps[lbIndx][0](distmod))
else:
interpData=\
interpolate.InterpolatedUnivariateSpline(self._distmods,
self._best_fit[lbIndx],
k=self._interpk)
tout.append(interpData(distmod))
self._intps[lbIndx]= interpData
tarea= healpy.pixelfunc.nside2pixarea(nside)
tarea= [tarea for ii in range(len(tout))]
pixarea.extend(tarea)
extinction.extend(tout)
pixarea= numpy.array(pixarea)
extinction= numpy.array(extinction)
if not self._filter is None:
extinction= extinction*aebv(self._filter,sf10=self._sf10)
return (pixarea,extinction)
def get_healsparse_subpix_indices(subpix_nside, subpix_hpix, subpix_border, coverage_nside):
"""
Retrieve the coverage pixels that intersect the region, with a border.
Parameters
----------
subpix_nside: `int`
Nside for the subregion
subpix_hpix: `int`
Pixel number for the subregion (ring format)
subpix_border: `float`
Border radius to cover outside subpix_hpix
coverage_nside: `int`
Nside of the healsparse coverage map
"""
# First, we need to know which pixel(s) from nside_coverage are covered by
# subpix_hpix
if subpix_nside == coverage_nside:
# simply convert to nest
covpix = hp.ring2nest(subpix_nside, subpix_hpix)
elif subpix_nside > coverage_nside:
# what pixel is this contained in?
theta, phi = hp.pix2ang(subpix_nside, subpix_hpix, nest=False)
covpix = hp.ang2pix(coverage_nside, theta, phi, nest=True)
else:
# This is subpix_nside < coverage_nside
# what coverage pixels are contained in subpix_hpix?
subpix_hpix_nest = hp.ring2nest(subpix_nside, subpix_hpix)
bit_shift = 2 * int(np.round(np.log(coverage_nside / subpix_nside) / np.log(2)))
n_pix = 2**bit_shift
covpix = np.left_shift(subpix_hpix_nest, bit_shift) + np.arange(n_pix)
# And now if we have a border...
if subpix_border > 0.0:
nside_testing = max([coverage_nside * 4, subpix_nside * 4])
boundaries = hp.boundaries(subpix_nside, subpix_hpix, step=nside_testing/subpix_nside)
extrapix = np.zeros(0, dtype=np.int64)
# These are pixels that touch the boundary
for i in xrange(boundaries.shape[1]):
pixint = hp.query_disc(nside_testing, boundaries[:, i],
np.radians(subpix_border), inclusive=True, fact=8)
extrapix = np.append(extrapix, pixint)
extrapix = np.unique(extrapix)
theta, phi = hp.pix2ang(nside_testing, extrapix)
covpix = np.unique(np.append(covpix, hp.ang2pix(coverage_nside, theta, phi, nest=True)))
return covpix
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 find_available_galaxies(fiber_set, tile_set, object_set,
tile_ID, filename="available_galaxies"):
assert tile_set.healpix_n_side==object_set.healpix_n_side, "healpix n_side is different for tiles and objects"
assert tile_set.healpix_n_side>0, "healpix n_side is negative"
tile_theta = tile_set.theta[tile_ID]
tile_phi = tile_set.phi[tile_ID]
tile_center = np.array([tile_theta,tile_phi])
tile_vector = hp.rotator.dir2vec(tile_center)
pix = hp.query_disc(tile_set.healpix_n_side, tile_vector, fiber_set.plate_radius, inclusive=True)
# stores the galaxies that fall into the tile
objects_in_id = np.empty((0))
for i_pix in pix:
tmp_id_in = np.where(object_set.healpix_pixels==i_pix)
tmp_id_in = tmp_id_in[0]
objects_in_id = np.append(objects_in_id, tmp_id_in)
objects_in_id = np.int_(objects_in_id)
#if(not(i_tiling%(n_tilings/20))):
selected_objects = object_set.select(objects_in_id)
#these selected objects must have new a x,y coordinates in the focal plane
selected_x, selected_y = radec2xy(selected_objects.ra, selected_objects.dec, tile_set.ra[tile_ID], tile_set.dec[tile_ID])
n_fibers = np.size(fiber_set.x)
fiber_list = np.arange(n_fibers)
#np.random.shuffle(fiber_list)
#print fiber_list
out = open("tile_%d_%s.dat"%(tile_ID, filename), "w")
for fiber_i in fiber_list:
fiber_x = fiber_set.x[fiber_i]
fiber_y = fiber_set.y[fiber_i]
radius = np.sqrt((selected_x - fiber_x)**2 + (selected_y-fiber_y)**2)
inside = np.where((radius>fiber_set.patrol_radius_min) & (radius<fiber_set.patrol_radius_max))
inside = inside[0]
n_available = np.size(inside)
if(n_available):
out.write("%d %d %d "%(tile_ID, fiber_i, n_available))
id_available = ''.join('%d ' % i for i in selected_objects.ID[inside])
out.write("%s\n"%(id_available))
else:
out.write("%d %d %d \n"%(tile_ID, fiber_i, n_available))
out.close()
return selected_x, selected_y
def probability_inside_circle(self, ra, dec, radius):
"""Return the probability inside a circle."""
prob = hp.read_map(self.skymap, verbose=False)
theta = 0.5 * np.pi - np.deg2rad(dec)
phi = np.deg2rad(ra)
radius = np.deg2rad(radius)
xyz = hp.ang2vec(theta, phi)
ipix_disc = hp.query_disc(self.nside, xyz, radius)
probability_inside_disc = prob[ipix_disc].sum()
return "%.1e" % probability_inside_disc
def correlations(i_ang): ang_low = (pi / 180) * (ang[i_ang] - (ang_res / 2)) ang_high = (pi / 180) * (ang[i_ang] + (ang_res / 2)) n = np.zeros(N_jkmpix) c = np.zeros((n_corr, N_jkmpix)) c_out = np.zeros((n_corr, N_jkmpix)) #c_gal = 0 #n_gal = 0 for i in range(N_mpix): i_vec = hp.pix2vec(nside, mpix2hpix[i]) disc_low = hp.query_disc(nside, i_vec, ang_low, inclusive = False) disc_high = hp.query_disc(nside, i_vec, ang_high, inclusive = False) disc = hpix2mpix[np.setdiff1d(disc_high, disc_low)] disc = disc[disc >= 0] k = hp.vec2pix(nside_jk, i_vec[0], i_vec[1], i_vec[2]) k = jkhpix2jkmpix[k] for l in range(n_corr): dmap1 = dmap[l][0] dmap2 = dmap[l][1] c[l][k] += dmap1[i] * dmap2[disc].sum() n[k] += len(disc) #c_gal += dmap[0][0][i] * dmap[0][1][disc].sum() #n_gal += len(disc) for l in range(n_corr): for k in range(N_jkmpix): c_out[l][k] = (c[l].sum() - c[l][k]) / (n.sum() - n[k]) print "theta = %.2f Done!" % ang[i_ang] return c_out
def make_dom_map(pmt_directions, values, nside=512, d=0.2, smoothing=0.1):
"""Create a mollweide projection of a DOM with given PMTs.
The output can be used to call the `healpy.mollview` function.
"""
import healpy as hp
discs = [hp.query_disc(nside, dir, 0.2) for dir in pmt_directions]
npix = hp.nside2npix(nside)
pixels = np.zeros(npix)
for disc, value in zip(discs, values):
for d in disc:
pixels[d] = value
if smoothing > 0:
return hp.sphtfunc.smoothing(pixels, fwhm=smoothing, iter=1)
return pixels
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 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 doPreCalcs(self):
"""
Perform the precalculations necessary to set up the sparse matrix.
"""
self.opsimdf['hids'] = [hp.query_disc(self.nside, vec, self._fieldRadius,
inclusive=self.inclusive,
fact=self.fact,
nest=self.nest)
for vec in self.opsimdf[self.vecColName]]
lens = map(len, self.opsimdf.hids.values)
rowdata = []
_ = list(rowdata.extend(repeat(i, lens[i]))
for i in xrange(len(self.opsimdf)))
coldata = np.concatenate(self.opsimdf.hids.values)
self._rowdata = rowdata
self._coldata = coldata
def mask_src_weighted_custom(cat_file, ENERGY, NSIDE):
"""Returns the 'bad pixels' defined by the position of a source and a
certain radius away from that point. The radii increase with the
brightness and rescaled by a factor between 1 and 0.3 shaped as the PSF.
cat_file: str
.fits file with the sorce catalog
ENERGY: float
Mean energy of the map to be masked
NSIDE: int
healpix nside parameter
"""
psf_ref_file = os.path.join(GRATOOLS_CONFIG, 'ascii/PSF_UCV_PSF1.txt')
src_cat = pf.open(cat_file)
NPIX = hp.pixelfunc.nside2npix(NSIDE)
CAT = src_cat[1]
BAD_PIX_SRC = []
SOURCES = CAT.data
src_cat.close()
psf_ref = get_psf_ref(psf_ref_file)
psf_en = psf_ref(ENERGY)
psf_min, psf_max = psf_ref.y[5], psf_ref.y[-1]
norm_min, norm_max = 1, 0.3
norm = norm_min + psf_en*((norm_max - norm_min)/(psf_max - psf_min)) -\
psf_min*((norm_max - norm_min)/(psf_max - psf_min))
logger.info('Normalization of radii due to energy: %.3f'%norm)
logger.info('Psf(%.2f)= %.2f'%(ENERGY, psf_en))
FLUX = np.log10(SOURCES.field('eflux1000'))
flux_min, flux_max = min(FLUX), max(FLUX)
rad_min, rad_max = 1, 5.
RADdeg = rad_min + FLUX*((rad_max - rad_min)/(flux_max - flux_min)) -\
flux_min*((rad_max - rad_min)/(flux_max - flux_min))
RADrad = np.radians(RADdeg)
logger.info('Flux-weighted mask for sources activated')
TS = SOURCES.field('ts')
indTS25 = TS > 25.
GLON = SOURCES.field('GLON')[indTS25]
GLAT = SOURCES.field('GLAT')[indTS25]
logger.info('Num Src: %i'%len(TS))
logger.info('Num Src TS>25: %i'%len(TS[indTS25]))
for i, src in enumerate(SOURCES[indTS25]):
x, y, z = hp.rotator.dir2vec(GLON[i],GLAT[i],lonlat=True)
b_pix= hp.pixelfunc.vec2pix(NSIDE, x, y, z)
BAD_PIX_SRC.append(b_pix)
radintpix = hp.query_disc(NSIDE, (x, y, z), RADrad[i]*norm)
BAD_PIX_SRC.extend(radintpix)
return BAD_PIX_SRC
def local_power_spectrum(map1, mask1, deg, LMAX=256):
""" return the local power spectrum for each disk given by the radius [deg]
"""
mp1=hp.ma(map1)
mp1.mask=np.logical_not(mask1)
NSIDE1=hp.npix2nside(len(map1))
NSIDE2=nside(deg)
NPIX2=hp.nside2npix(NSIDE2)
NPIX1=hp.nside2npix(NSIDE1)
mp2=[0]*NPIX2
for pix2 in range(0, NPIX2):
newmask=np.array([0.]*NPIX1)
disc1=hp.query_disc(nside=NSIDE1, vec=hp.pix2vec(NSIDE2, pix2), radius=deg2rad(deg))
newmask[disc1]=1.
newmask=newmask*mask1
mp1.mask=np.logical_not(mask1)
mp2[pix2]=hp.anafast(mp1, lmax=LMAX)
return mp2
def get_subpixel_indices(galtable, hpix=None, border=0.0, nside=0):
"""
Routine to get subpixel indices from a galaxy table.
Parameters
----------
galtable: `redmapper.Catalog`
A redmapper galaxy table master catalog
hpix: `int`, optional
Healpix number (ring format) of sub-region. Default is 0 (full catalog).
border: `float`, optional
Border around hpix (in degrees) to find pixels. Default is 0.0.
nside: `int`, optional
Nside of healpix subregion. Default is 0 (full catalog).
Returns
-------
indices: `np.array`
Integer array of indices of galaxy table pixels in the subregion.
"""
if hpix is None or nside == 0:
return np.arange(galtable.filenames.size)
theta, phi = hp.pix2ang(galtable.nside, galtable.hpix)
ipring_big = hp.ang2pix(nside, theta, phi)
indices, = np.where(ipring_big == hpix)
if border > 0.0:
# now we need to find the extra boundary...
boundaries = hp.boundaries(nside, hpix, step=galtable.nside/nside)
inhpix = galtable.hpix[indices]
for i in xrange(boundaries.shape[1]):
pixint = hp.query_disc(galtable.nside, boundaries[:, i],
border*np.pi/180., inclusive=True, fact=8)
inhpix = np.append(inhpix, pixint)
inhpix = np.unique(inhpix)
_, indices = esutil.numpy_util.match(inhpix, galtable.hpix)
return indices
def make_disc( nside, radius, direction=[1,0,0], radians=False, minus=False): import numpy as np import healpy as hp info_message( 'nside = ' + str(nside) ) info_message( 'radius = ' + str(radius) ) npix = 12l*nside**2 mask = np.zeros( npix ) d2r = np.pi / 180. if not radians: radius *= d2r listpix = hp.query_disc( nside, direction, radius ) mask[listpix] = 1. if minus: mask = 1. - mask return mask