def test_upgrade_healpix(self):
"""Test correctness of healpix upgrading
"""
nside_in = 2
nside_out = nside_in * 2 # must differ by 1 order for this test
npix_in = hp.nside2npix(nside_in)
npix_out = hp.nside2npix(nside_out)
pix_i = 5
# Upgrade pix_i in NSIDE=1 using cu
# Downgrade all pixels in NSIDE=2 to NSIDE=1
# Check if mappings from NSIDE=1 to NSIDE=2 match
# Output is always NESTED
# Test 1: Input pix_i is in NESTED
# "visual" checks with https://healpix.jpl.nasa.gov/html/intronode4.htm
actual = obs_utils.upgrade_healpix(pix_i, True, nside_in, nside_out)
desired_all = np.arange(npix_out).reshape((npix_in, 4))
desired = np.sort(desired_all[pix_i, :]) # NESTED
np.testing.assert_array_equal(desired, [20, 21, 22, 23], "visual")
np.testing.assert_array_equal(actual, desired, "input in NESTED")
# Test 2: Input pix_i is in RING
actual = obs_utils.upgrade_healpix(pix_i, False, nside_in, nside_out)
# See https://stackoverflow.com/a/56675901
# `reorder` reorders RING IDs in NESTED order
# `reshape` is possible because the ordering is NESTED
# indexing should be done with a NESTED ID because ordering is NESTED
# but the output is in RING ID, which was reordered in the first place
desired_all = hp.reorder(np.arange(npix_out), r2n=True).reshape(
(npix_in, 4))
desired_ring = desired_all[hp.ring2nest(nside_in, pix_i), :]
np.testing.assert_array_equal(np.sort(desired_ring), [14, 26, 27, 43],
"visual")
desired_nest = hp.ring2nest(nside_out, desired_ring)
np.testing.assert_array_equal(np.sort(actual), np.sort(desired_nest),
"input in RING")
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 patches(ind, NSIDEin, NSIDEout, nest=False):
"""Daughter pixel indices in a low resolution HEALPix patch.
Return HEALPix indices for all pixels of a higher resolution map
contained inside the pixel(s) of a lower resolution map. Output pixels
are always in the RING ordering scheme.
Parameters
----------
ind: int or array of ints
Index of the parent HEALPix patch(es).
NSIDEin: int
NSIDE resolution of the parent HEALPix patch(es).
NSIDEout: int
NSIDE resolution of the daughter HEALPix pixels.
nest: bool, optional
If True, assume ``ind`` are given in NESTED pixel ordering.
Otherwise, assume RING ordering. Default: False.
Returns
-------
ipix: 1d-array of int
Indices of all pixels contained with the parent patch(es). Output
is always in RING ordering.
"""
if NSIDEout/2 == NSIDEin: # Base case
inds = np.array(ind)
if nest:
return hp.nest2ring(NSIDEout, np.tile(np.arange(4), inds.size) + \
4*inds.repeat(4))
else:
return hp.nest2ring(NSIDEout, np.tile(np.arange(4), inds.size) + \
4*hp.ring2nest(NSIDEin, inds).repeat(4))
else:
inds = np.array(ind)
s = inds.size
if nest:
ipix = np.tile(np.arange(4), s) + 4*inds.repeat(4)
else:
ipix = np.tile(np.arange(4), s) + \
4*hp.ring2nest(NSIDEin, inds).repeat(4)
return np.concatenate((patches(ipix[:s], NSIDEin*2, NSIDEout, True),
patches(ipix[s:2*s], NSIDEin*2, \
NSIDEout, True),
patches(ipix[2*s:3*s], NSIDEin*2, \
NSIDEout, True),
patches(ipix[3*s:], NSIDEin*2, \
NSIDEout, True),
))
def gen_random_fast(nrandom, mask):
""" This method approximates using a higher resolution healpix map
to place the random points. It should be fine for measurements larger
than the mask pixel scale. We take advantage of the equal area nature
of the healpixels. The downside of this method is that it needs a lot
of memory for large masks"""
nside = hp.get_nside(mask)
nside2 = 4 * nside
ra = []
th = []
filled_pixels = np.where((mask > 0) & (np.isnan(mask) == False))[0]
densities = mask[filled_pixels]
kpix = np.random.choice(filled_pixels,
size=nrandom,
p=densities / np.sum(densities))
bincounts = np.bincount(kpix)
kpix2 = np.unique(kpix)
counts = bincounts[bincounts > 0]
hh = nside2**2 / nside**2
i = 0
for i, c in enumerate(counts):
rpix = np.random.randint(0, high=hh, size=c)
nestpix = hp.ring2nest(nside, kpix2[i])
theta, phi = hp.pix2ang(nside2, hh * nestpix + rpix, nest=True)
theta = 90. - theta * 180. / np.pi
phi = phi * 180. / np.pi
for j in range(0, len(theta)):
ra.append(phi[j])
th.append(theta[j])
ra = np.array(ra)
dec = np.array(th)
return ra, dec
def u_grade_ipix(ipix, nside_in, nside_out, nest=False):
"""
Return the indices of sub-pixels (resolution nside_subpix) within
the super-pixel(s) (resolution nside_superpix).
Parameters:
-----------
ipix : index of the input superpixel(s)
nside_in : nside of the input superpixel
nside_out : nside of the desired subpixels
Returns:
--------
ipix_out : subpixels for each superpixel
"""
if nside_in == nside_out: return ipix
if not (nside_in < nside_out):
raise ValueError("nside_in must be less than nside_out")
if nest: nest_ipix = ipix
else: nest_ipix = hp.ring2nest(nside_in, ipix)
factor = (nside_out // nside_in)**2
if np.isscalar(ipix):
nest_ipix_out = factor * nest_ipix + np.arange(factor)
else:
nest_ipix_out = factor * np.asarray(
nest_ipix)[:, np.newaxis] + np.arange(factor)
if nest: return nest_ipix_out
else: return hp.nest2ring(nside_out, nest_ipix_out)
def _get_converted_data(self, scheme):
"""
internal routine to get the data converted to the requested
scheme
If the scheme would be unchanged, a reference to the data is returned
"""
import healpy
scheme_num = get_scheme_num(scheme)
if scheme_num == self.hpix.scheme_num:
return self.data
if scheme_num==NESTED:
ipring=numpy.arange(self.hpix.npix,dtype='i8')
ipnest=healpy.ring2nest(self.hpix.nside, ipring)
newdata=self.data.copy()
newdata[ipnest]=self.data
else:
ipnest=numpy.arange(self.hpix.npix,dtype='i8')
ipring=healpy.nest2ring(self.hpix.nside, ipnest)
newdata=self.data.copy()
newdata[ipring]=self.data
return newdata
def random_u_grade_ang(m_inds, nside_in=0, nside_out=16384, is_nest=False):
"""
Random upscaling of the PS positions, given the pixel centres at resolution nside_in.
Each PS is moved to one of the high-resolution pixel centres at resolution nside_out.
For example, for nside_in = 128 and nside_out = 16384, there are npix_out / npix_in = 16384
possible PS locations within each pixel.
:param m_inds: indices of the PSs w.r.t. nside_in, in RING ordering
:param nside_in: nside in
:param nside_out: nside to use for upscaling
:param is_nest: if True: indices are assumed to correspond to NEST format instead of RING
:return: theta, phi of randomly placed PSs within each pixel
"""
if len(m_inds) == 0:
return m_inds
n_ps = len(m_inds) # number of point sources
if is_nest:
m_inds_nest = m_inds
else:
m_inds_nest = hp.ring2nest(nside_in,
m_inds) # convert to NEST ordering
hp.isnsideok(nside_out, nest=True) # check that nside_out is okay
npix_in = hp.nside2npix(nside_in)
npix_out = hp.nside2npix(nside_out)
rat2 = npix_out // npix_in
# For each PS, draw a random fine pixel within the coarse pixel
inds_fine = np.random.choice(rat2, size=n_ps)
# Set indices w.r.t. upscaled nside (NEST): rat2 * m_inds_nest -> high-res. pixel 0, inds_fine adds 0 ... rat2 - 1
inds_out = rat2 * m_inds_nest + inds_fine
# Calculate angles
th_out, ph_out = hp.pix2ang(nside_out, inds_out, nest=True, lonlat=False)
# Note: for rat2 = 16384 and 150 PSs, the chance that there exists at least a pair of equal th/ph_out is > 50%!
return th_out, ph_out
def _get_nz(self):
c_p = self.get_catalog()
c_s = self._get_specsample(c_p)
# Sort spec sample by nested pixel index so jackknife
# samples are spatially correlated.
ip_s = hp.ring2nest(
self.nside,
hp.ang2pix(self.nside,
c_s[self.ra_name],
c_s[self.dec_name],
lonlat=True))
idsort = np.argsort(ip_s)
c_s = c_s[idsort]
# Compute DIR N(z)
z, nz, nz_jk = get_DIR_Nz(
c_s,
c_p, [
'JCORR', 'KCORR', 'HCORR', 'W1MCORR', 'W2MCORR', 'BCALCORR',
'RCALCORR', 'ICALCORR'
],
zflag='ZSPEC',
zrange=[0, 0.4],
nz=100,
njk=self.config.get('n_jk_dir', 100))
zm = 0.5 * (z[1:] + z[:-1])
return {'z_mid': zm, 'nz': nz, 'nz_jk': nz_jk}
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_converted_data(self, scheme):
"""
internal routine to get the data converted to the requested
scheme
If the scheme would be unchanged, a reference to the data is returned
"""
import healpy
scheme_num = get_scheme_num(scheme)
if scheme_num == self.hpix.scheme_num:
return self.data
if scheme_num == NESTED:
ipring = numpy.arange(self.hpix.npix, dtype='i8')
ipnest = healpy.ring2nest(self.hpix.nside, ipring)
newdata = self.data.copy()
newdata[ipnest] = self.data
else:
ipnest = numpy.arange(self.hpix.npix, dtype='i8')
ipring = healpy.nest2ring(self.hpix.nside, ipnest)
newdata = self.data.copy()
newdata[ipring] = self.data
return newdata
def upgrade_healpix(pix_id, nested, nside_in, nside_out):
"""Upgrade (superresolve) a healpix into finer ones
Parameters
----------
pix_id : int
coarse healpix ID to upgrade
nested : bool
whether `pix_id` is given in NESTED scheme
nside_in : int
NSIDE of `pix_id`
nside_out : int
desired NSIDE of finer healpix
Returns
-------
np.array
the upgraded healpix IDs in the NESTED scheme
"""
if not nested:
pix_id = hp.ring2nest(nside_in, pix_id)
order_diff = np.log2(nside_out) - np.log2(nside_in)
factor = 4**order_diff
upgraded_ids = pix_id * factor + np.arange(factor)
return upgraded_ids.astype(int)
def patchToPixels(nsidePat, nsidePix, patch, nest=False, sort=False):
"""
Return all pixel ring or nest numbers related to a given patch.
Parameters
----------
nsidePat : int
nside of the patch
nsidePix : int
nside of the child patch
patch : int
ring or nest number of the patch
nest : bool, optional
consider nest
sort : bool, optional
sort the returned array
Returns
-------
pix : int array
ring or nest numbers of all pixels
"""
patch = patch if nest == True else hp.ring2nest(nsidePat, patch)
length = (nsidePix // nsidePat)**2
pix = np.arange(patch * length, (patch + 1) * length)
pix = pix if nest == True else hp.nest2ring(nsidePix, pix)
if sort == True:
pix.sort()
return pix
def hp_in_dec_range(nside, decmin, decmax, inclusive=True):
"""HEALPixels in a specified range of Declination.
Parameters
----------
nside : :class:`int`
(NESTED) HEALPixel nside.
decmin, decmax : :class:`float`
Declination range (degrees).
inclusive : :class:`bool`, optional, defaults to ``True``
see documentation for `healpy.query_strip()`.
Returns
-------
:class:`list`
(Nested) HEALPixels at `nside` in the specified Dec range.
Notes
-----
- Just syntactic sugar around `healpy.query_strip()`.
- `healpy.query_strip()` isn't implemented for the NESTED scheme
in early healpy versions, so this queries in the RING scheme
and then converts to the NESTED scheme.
"""
# ADM convert Dec to co-latitude in radians.
# ADM remember that, min/max swap because of the -ve sign.
thetamin = np.radians(90.-decmax)
thetamax = np.radians(90.-decmin)
# ADM determine the pixels that touch the box.
pixring = hp.query_strip(nside, thetamin, thetamax,
inclusive=inclusive, nest=False)
pixnest = hp.ring2nest(nside, pixring)
return pixnest
def read_map2(filename,field=0,dtype=np.float64,nest=False,hdu=1,h=False,verbose=True,memmap=False):
hdr=fitsio.read_header(filename,ext=hdu)
fullsky = False
try:
if (hdr['OBJECT'].strip() == 'PARTIAL') :
# partial sky format
fullsky=False
else:
fullsky=True
except:
# if no OBJECT in header, assume full sky
fullsky=True
if fullsky:
m=hp.read_map(filename,field=field,dtype=dtype,nest=nest,hdu=hdu,h=h,verbose=verbose,memmap=memmap)
else:
# partial sky
st=fitsio.read(filename,ext=1)
nside=hdr['NSIDE']
m=np.zeros(12*nside*nside,dtype=dtype) + hp.UNSEEN
if ((hdr['ORDERING'].strip() == 'NESTED') and (not nest)) :
# change from nest to ring...
m[hp.nest2ring(nside,st['PIXEL'])] = st['SIGNAL']
elif ((hdr['ORDERING'].strip() == 'RING') and (nest)):
# change from ring to nest...
m[hp.ring2nest(nside,st['PIXEL'])] = st['SIGNAL']
else :
# straight up
m[st['PIXEL']] = st['SIGNAL']
return m
def get_subpixels(idx, nside_superpix, nside_subpix, nest=True):
"""Compute the indices of subpixels contained within superpixels.
This function returns an output array with one additional
dimension of size N for subpixel indices where N is the maximum
number of subpixels for any pair of ``nside_superpix`` and
``nside_subpix``. If the number of subpixels is less than N the
remaining subpixel indices will be set to -1.
Parameters
----------
idx : `~numpy.ndarray`
Array of HEALPix pixel indices for superpixels of NSIDE
``nside_superpix``.
nside_superpix : int or `~numpy.ndarray`
NSIDE of superpixel.
nside_subpix : int or `~numpy.ndarray`
NSIDE of subpixel.
nest : bool
If True, assume NESTED pixel ordering, otherwise, RING pixel
ordering.
Returns
-------
idx_sub : `~numpy.ndarray`
Indices of HEALpix pixels of nside ``nside_subpix`` contained
within pixel indices ``idx`` of nside ``nside_superpix``.
"""
import healpy as hp
if not nest:
idx = hp.ring2nest(nside_superpix, idx)
idx = np.asarray(idx)
nside_superpix = np.asarray(nside_superpix)
nside_subpix = np.asarray(nside_subpix)
if np.any(~is_power2(nside_superpix)) or np.any(~is_power2(nside_subpix)):
raise ValueError("NSIDE must be a power of 2.")
# number of subpixels in each superpixel
npix = np.array((nside_subpix // nside_superpix)**2, ndmin=1)
x = np.arange(np.max(npix), dtype=int)
idx = idx * npix
if not np.all(npix[0] == npix):
x = np.broadcast_to(x, idx.shape + x.shape)
idx = idx[..., None] + x
idx[x >= np.broadcast_to(npix[..., None], x.shape)] = INVALID_INDEX.int
else:
idx = idx[..., None] + x
if not nest:
m = idx == INVALID_INDEX.int
idx[m] = 0
idx = hp.nest2ring(nside_subpix[..., None], idx)
idx[m] = INVALID_INDEX.int
return idx
def calc_areas(self, mags):
"""
Calculate total area from the depth map as a function of magnitude.
Parameters
----------
mags: `np.array`
Float array of magnitudes at which to compute area
Returns
-------
areas: `np.array`
Float array of total areas for each of the mags
"""
pixsize = hp.nside2pixarea(self.nside, degrees=True)
if (self.w < 0.0):
# This is just constant area
areas = np.zeros(mags.size) + self.config_area
return areas
if self.subpix_hpix > 0:
# for the subregion, we need the area covered in the main pixel
# I'm not sure what to do about border...but you shouldn't
# be running this with a subregion with a border
if self.subpix_border > 0.0:
raise RuntimeError(
"Cannot run calc_areas() with a subregion with a border")
bitShift = 2 * int(
np.round(np.log(self.nside / self.subpix_nside) / np.log(2)))
nFinePerSub = 2**bitShift
ipnest = np.left_shift(
hp.ring2nest(self.subpix_nside, self.subpix_hpix),
bitShift) + np.arange(nFinePerSub)
else:
ipnest = self.sparse_depthmap.validPixels
areas = np.zeros(mags.size)
values = self.sparse_depthmap.getValuePixel(ipnest)
gd, = np.where(values['m50'] > 0.0)
depths = values['m50'][gd]
st = np.argsort(depths)
depths = depths[st]
fracgoods = values['fracgood'][gd[st]]
inds = np.clip(np.searchsorted(depths, mags) - 1, 1, depths.size - 1)
lo = (inds < 0)
areas[lo] = np.sum(fracgoods) * pixsize
carea = pixsize * np.cumsum(fracgoods)
areas[~lo] = carea[carea.size - inds[~lo]]
return areas
def getFilePixels(self, r):
"""Given a healpix cell and radius for a given nside, figure out which
lightcone pixels we need to read
Parameters
----------
r : int
radial bin to read
Returns
-------
pix_file : list
List of the lightcone file pixels that need to be read
peano_idx : list
List of the peano indices of particles that need to be read
"""
partpath = self.nbody.partpath[self.nbody.boxnum]
nside = self.nbody.domain.nside
pix = self.nbody.domain.pix
header_fmt = ['Np', 'nside_index', 'nside_file', 'box_rmin',
'box_rmax', 'void', 'Lbox', 'Mpart', 'Omega_m', 'Omega_l', 'h']
f = '{}/snapshot_Lightcone_{}_0'.format(partpath, r)
hdr, idx = read_radial_bin(f)
hdr = dict(zip(header_fmt, hdr))
self.part_mass = hdr['Mpart'] * 1e10
if not self.nbody.domain.nest:
pix = hp.ring2nest(nside, pix)
# this assumes that nside < nside_index which should always be true
idxmap = hp.ud_grade(np.arange(12 * nside**2), hdr['nside_index'],
order_in='NESTED', order_out='NESTED')
# get peano cells corresponding to pix
# first get nside=nside_index, nest ordered cells corresponding to pix
peano_idx = nest2peano(np.where(idxmap == pix)[0],
int(np.log2(hdr['nside_index'])))
if nside < hdr['nside_file']:
udmap = hp.ud_grade(np.arange(12 * nside**2), hdr['nside_file'],
order_in='NESTED', order_out='NESTED')
pix_file, = np.where(udmap == pix)
elif nside > hdr['nside_file']:
udmap = hp.ud_grade(np.arange(12 * hdr['nside_file']**2), nside,
order_in='NESTED', order_out='NESTED')
pix_file = [udmap[pix]]
else:
pix_file = [pix]
return pix_file, peano_idx
def ring2nest(testcase):
cs = []
for norder in range(16):
nside = 1 << norder
for i in range(1000):
ipix = random.randrange(12 * nside * nside)
args = (nside, ipix)
cs.append(
dict(args=args, expected=healpy.ring2nest(*args).tolist()))
testcase['ring2nest'] = cs
def downsize(a):
"""For an HEAPix RING array with nside a power of two,
return an nside/2 array of the average for each group of pixels
"""
import healpy
nside = int(np.sqrt(len(a)/12.))
a1 =a[healpy.nest2ring(nside, range(len(a)))]
t=a1.reshape(len(a)/4,4)
a2=t.mean(axis=1)
return a2[healpy.ring2nest(nside/2, range(len(a2)))]
def calc_areas(self, mags):
"""
Calculate total area from the depth map as a function of magnitude.
Parameters
----------
mags: `np.array`
Float array of magnitudes at which to compute area
Returns
-------
areas: `np.array`
Float array of total areas for each of the mags
"""
pixsize = hp.nside2pixarea(self.nside, degrees=True)
if (self.w < 0.0):
# This is just constant area
areas = np.zeros(mags.size) + self.config_area
return areas
if self.subpix_hpix > 0:
# for the subregion, we need the area covered in the main pixel
# I'm not sure what to do about border...but you shouldn't
# be running this with a subregion with a border
if self.subpix_border > 0.0:
raise RuntimeError("Cannot run calc_areas() with a subregion with a border")
bitShift = 2 * int(np.round(np.log(self.nside / self.subpix_nside) / np.log(2)))
nFinePerSub = 2**bitShift
ipnest = np.left_shift(hp.ring2nest(self.subpix_nside, self.subpix_hpix), bitShift) + np.arange(nFinePerSub)
else:
ipnest = self.sparse_depthmap.validPixels
areas = np.zeros(mags.size)
values = self.sparse_depthmap.getValuePixel(ipnest)
gd, = np.where(values['m50'] > 0.0)
depths = values['m50'][gd]
st = np.argsort(depths)
depths = depths[st]
fracgoods = values['fracgood'][gd[st]]
inds = np.clip(np.searchsorted(depths, mags) - 1, 1, depths.size - 1)
lo = (inds < 0)
areas[lo] = np.sum(fracgoods) * pixsize
carea = pixsize * np.cumsum(fracgoods)
areas[~lo] = carea[carea.size - inds[~lo]]
return areas
def build_cov(cl,
nside,
mask=None,
tree_depth=0,
lmax=None,
apply_pixwin=False,
ninterp=10000,
log=False,
shift=None):
tree_depth = 2**(tree_depth)
if mask is None:
mask = np.ones(hp.nside2npix(nside), dtype=bool)
if lmax is not None and lmax > len(cl) - 1:
lmax = len(cl) - 1
cl = cl[:lmax + 1]
if apply_pixwin:
pw = hp.pixwin(nside * tree_depth, lmax=lmax)
cl = cl[:len(pw)] * (pw**2)
npix = int(mask.sum())
mask_inds = hp.ring2nest(nside, np.arange(hp.nside2npix(nside))[mask])
thetas = np.linspace(0, np.pi, ninterp)
xis = cl2xi_theta(cl, thetas)
exe_path = os.path.join(os.path.dirname(__file__), 'healcov')
proc = subprocess.Popen(exe_path,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
proc.stdin.write(nside.to_bytes(8, 'little'))
proc.stdin.write(npix.to_bytes(8, 'little'))
proc.stdin.write(mask_inds.tobytes())
proc.stdin.write(tree_depth.to_bytes(8, 'little'))
proc.stdin.write(ninterp.to_bytes(8, 'little'))
proc.stdin.write(thetas.tobytes())
proc.stdin.write(xis.tobytes())
proc.stdin.close()
cov = np.frombuffer(proc.stdout.read()).reshape([npix, npix])
info = proc.wait()
if info != 0:
raise Exception()
if log is True:
cov = np.log(cov / (shift**2) + 1)
return cov
def compute_cl(m, nside=1024, nest=True, lmax=1500):
logging.info('compute_cl -> lmax=%d' % lmax)
if nest:
npix = hp.nside2npix(nside)
mm = np.zeros(npix)
i = np.arange(npix)
mm[:] = m[hp.ring2nest(nside, i)]
else:
mm = m
c = hp.anafast(mm, lmax=lmax)
return c
def read_skymap_rotate(skymap_filename, theta=0, phi=0):
'''Read the healpix skymap'''
skymap, metadata = fits.read_sky_map(skymap_filename, nest=True)
nside = hp.get_nside(skymap)
npix = hp.nside2npix(nside)
skymap = skymap[hp.ring2nest(nside, np.arange(npix))]
if (not theta == 0) or (not phi == 0):
skymap = rotate_map(skymap, np.deg2rad(theta), np.deg2rad(phi))
return skymap
def pix_in_pix(nside_low, nside_high, ipix, ord_in='Ring', ord_out='Ring'):
rat = int(nside_high // nside_low)**2
if ord_in is 'Ring':
ipix = hp.ring2nest(nside_low, ipix)
ipix *= rat
liste = np.arange(ipix, ipix + rat)
if ord_out is 'Ring':
liste = hp.nest2ring(nside_high, liste)
return liste
def anafast_patch(i, ps, kap):
t = time.time()
#print "Starting " +str(i+1)+ " / " +str(N)
n1 = hp.get_nside(kap_down)
n2 = hp.npix2nside(len(cib))
r = n2 / n1
pixn = hp.ring2nest(n1, i)
ind = np.arange(r**2 * pixn, r**2 * (pixn + 1))
ind = hp.nest2ring(n2, ind)
ps[i] = np.mean(cib[ind]**power) - (np.mean(cib[ind]))**power
kap[i] = np.mean(kappa[ind])
def inpaint(m,num_degrades=1,nside_in=2048):
"""
Inpaints missing pixels by degrading the map (while ignoring missing pixels),
then setting the missing values correpsonding to their value in the degraded map.
"""
import healpy as H
nside_deg = nside_in/(2**num_degrades)
badpix = arange(12*nside_in**2)[m==H.UNSEEN]
badpix_deg = H.nest2ring(nside_deg,H.ring2nest(nside_in,badpix) >> 2*num_degrades)
m_deg = H.ud_grade(m,nside_deg)
m2=m.copy()
m2[badpix]=m_deg[badpix_deg]
return m2
def crosscheck_prob(self):
try:
nside = self.ligo_nside
except AttributeError:
nside = self.nside
class MNS:
def __init__(self, data):
self.data = pandas.DataFrame(
data, columns=["field", "ra", "dec", "datetime"])
data = []
for f in self.overlap_fields:
ra, dec = ztfquery_fields.field_to_coords(float(f))[0]
t = Time(self.t_min.jd, format="jd").utc
t.format = "isot"
t = t.value
data.append([f, ra, dec, t])
mns = MNS(data)
data = mns.data.copy()
self.logger.info("Unpacking observations")
field_prob = 0.0
ps = []
for index, row in tqdm(data.iterrows()):
pix = get_quadrant_ipix(nside, row["ra"], row["dec"])
flat_pix = []
for sub_list in pix:
for p in sub_list:
flat_pix.append(p)
flat_pix = list(set(flat_pix))
ps += flat_pix
ps = list(set(ps))
for p in hp.ring2nest(nside, ps):
field_prob += self.data[self.key][int(p)]
self.logger.info(
f"Intergrating all fields overlapping 90% contour gives {100*field_prob:.2g}%"
)
def add_weights(self, filename):
"""Add weights to the photon data
"""
# load a pickle containing weights, generated by pointlike
assert os.path.exists(filename),f'File {filename} not found.'
with open(filename, 'rb') as file:
wtd = pickle.load(file, encoding='latin1')
assert type(wtd)==dict, 'Expect a dictionary'
test_elements = 'energy_bins pixels weights nside model_name radius order roi_name'.split()
assert np.all([x in wtd.keys() for x in test_elements]),f'Dict missing one of the keys {test_elements}'
pos = wtd['source_lb']
if self.verbose>0:
print(f'Adding weights from file {os.path.realpath(filename)}')
print(f'Found weights for {wtd["source_name"]} at ({pos[0]:.2f}, {pos[1]:.2f})')
# extract pixel ids and nside used
wt_pix = wtd['pixels']
nside_wt = wtd['nside']
# merge the weights into a table, with default nans
# indexing is band id rows by weight pixel columns
# append one empty column for photons not in a weight pixel
# calculated weights are in a dict with band id keys
wts = np.full((32, len(wt_pix)+1), np.nan, dtype=np.float32)
weight_dict = wtd['weights']
for k in weight_dict.keys():
wts[k,:-1] = weight_dict[k]
# get the photon pixel ids, convert to NEST and right shift them
photons = self.photon_data
photon_pix = healpy.ring2nest(self.nside, photons.pixel.values)
to_shift = 2*int(np.log2(self.nside/nside_wt));
shifted_pix = np.right_shift(photon_pix, to_shift)
bad = np.logical_not(np.isin(shifted_pix, wt_pix))
if self.verbose>0:
print(f'\t{sum(bad)} / {len(bad)} photon pixels are outside weight region')
if sum(bad)==len(bad):
raise Exception('No weights found')
shifted_pix[bad] = 12*nside_wt**2 # set index to be beyond pixel indices
# find indices with search and add a "weights" column
# (expect that wt_pix are NEST ordering and sorted)
weight_index = np.searchsorted(wt_pix,shifted_pix)
band_index = photons.band.values
# final grand lookup -- isn't numpy wonderful!
photons.loc[:,'weight'] = wts[tuple([band_index, weight_index])]
if self.verbose>0:
print(f'\t{sum(np.isnan(photons.weight.values))} weights set to NaN')
return wtd # for reference
def test_get_healpix_centers(self):
"""Test if correct sky locations are returned in the cosmoDC2 convention
"""
# Correct answers hardcoded with known cosmoDC2 catalog values
# Input i_pix is in nested scheme
ra, dec = obs_utils.get_healpix_centers(hp.ring2nest(32, 10450),
32,
nest=True)
np.testing.assert_array_almost_equal(ra, [67.5], decimal=1)
np.testing.assert_array_almost_equal(dec, [-45.0], decimal=1)
# Input i_pix is in ring scheme
ra, dec = obs_utils.get_healpix_centers(10450, 32, nest=False)
np.testing.assert_array_almost_equal(ra, [67.5], decimal=1)
np.testing.assert_array_almost_equal(dec, [-45.0], decimal=1)
def ncmap_sample_positions(nc_map, ip_good, nside, fgoodmap, nside_up=4):
"""
Samples positions of galaxies inside a footprint from a number counts map
"""
ip_good_nest = hp.ring2nest(nside, ip_good)
ipix_nest = [
rd.sample(
range(ip_good_nest[i] * 4**nside_up,
(ip_good_nest[i] + 1) * 4**nside_up), nc_map[i])
for i in range(len(ip_good))
]
ipix_nest = [ip for sub in ipix_nest for ip in sub]
hpix = hu.HealPix('nest', nside * 2**nside_up)
ra, dec = hpix.pix2eq(ipix_nest)
return ra, dec
def rand_exposure_vec_in_pix(nside,
ipix,
a0=-35.25,
zmax=60,
coord_system='gal',
deviation=0.5,
nest=False):
"""
Draw vectors from a distribution within a HEALpixel that follow the exposure
distribution within the pixel. It is much slower than rand_vec_in_pix() and
should therefore only be used for problematic pixels (close to zero exposure).
:param nside: nside of the healpy pixelization
:param ipix: pixel number(s)
:param a0: latitude of detector (-90, 90) in degrees (default: Auger)
:param zmax: maximum acceptance zenith angle (0, 90) degrees
:param coord_system: choose between different coordinate systems - gal, eq, sgal, ecl
:param deviation: maximum relative deviation between exposure values in pixel corners
:param nest: set True in case you work with healpy's nested scheme
:return: vectors containing events from the pixel(s) specified in ipix
"""
ipix = np.atleast_1d(ipix)
vecs = np.zeros((3, ipix.size))
mask = check_problematic_pixel(nside, ipix, a0, zmax, deviation)
vecs[:, ~mask] = rand_vec_in_pix(nside, ipix[~mask], nest)
if not nest:
ipix = hp.ring2nest(nside, ipix=ipix)
for pix in np.unique(ipix[mask]):
n = np.sum(ipix == pix)
# increase resolution of healpy schemes cooresponding to number of crs per pixel
n_up = max(3, int(np.ceil(np.log10(10 * n) / np.log10(4))))
pix_new = pix * 4**n_up + np.arange(4**n_up)
v = pix2vec(nside=nside * 2**n_up, ipix=pix_new, nest=True)
if coord_system != 'eq':
v = getattr(coord, '%s2eq' % coord_system)(v)
p = coord.exposure_equatorial(coord.vec2ang(v)[1], a0, zmax)
pixel = np.random.choice(pix_new,
size=n,
replace=False,
p=p / np.sum(p))
vecs[:, ipix == pix] = pix2vec(nside=nside * 2**n_up,
ipix=pixel,
nest=True)
return np.array(vecs)
def multiply(a, b):
""" multiply HEALPix array a by b, element by element. Both must have power-of-2 nside.
b must have smaller of equal nside. Return the new array, with dimension of a.
"""
alen=len(a); blen=len(b)
if alen==blen: return a*b
assert alen>blen, 'Expect len(a)>len(b)'
anside = int(np.sqrt(alen/12.))
bnside = int(np.sqrt(blen/12.))
#reorder a and b to NEST order, reshape a, b to 2D with first dimension blen
anest = a[healpy.nest2ring(anside, range(alen))].reshape(blen, alen/blen)
bnest = b[healpy.nest2ring(bnside, range(blen))].reshape(blen, 1)
# broadcast the multiply, back to 1D
cnest = (anest * bnest).reshape(alen)
# back to RING
c = cnest[healpy.ring2nest(anside, range(alen))]
return c
def _add_weights(config, wts, wt_pix, nside_wt, photon_data):
""" get the photon pixel ids, convert to NEST (if not already) and right shift them
add 'weight', remove 'band', 'pixel'
"""
if not config.nest:
# data are RING
photon_pix = healpy.ring2nest(config.nside,
photon_data.nest_index.values)
else:
photon_pix = photon_data.nest_index.values
to_shift = 2 * int(np.log2(config.nside / nside_wt))
shifted_pix = np.right_shift(photon_pix, to_shift)
bad = np.logical_not(np.isin(shifted_pix, wt_pix))
if config.verbose > 0 & sum(bad) > 0:
print(
f'\tApplying weights: {sum(bad)} / {len(bad)} photon pixels are outside weight region'
)
if sum(bad) == len(bad):
a = np.array(healpy.pix2ang(nside_wt, wt_pix, nest=True,
lonlat=True)).mean(axis=1).round(1)
b = np.array(
healpy.pix2ang(nside_wt, shifted_pix, nest=True,
lonlat=True)).mean(axis=1).round(1)
raise Exception(
f'There was no overlap of the photon data at {b} and the weights at {a}'
)
shifted_pix[bad] = 12 * nside_wt**2 # set index to be beyond pixel indices
# find indices with search and add a "weights" column
# (expect that wt_pix are NEST ordering and sorted)
weight_index = np.searchsorted(wt_pix, shifted_pix)
band_index = np.fmin(
31, photon_data.band.values) #all above 1 TeV into last bin
# final grand lookup -- isn't numpy wonderful!
photon_data.loc[:, 'weight'] = self.wts[tuple([band_index, weight_index])]
# don't need these columns now (add flag to config to control??)
# photon_data.drop(['band', 'pixel'], axis=1)
if config.verbose > 1:
print(
f'\t{sum(np.isnan(photon_data.weight.values))} events without weight'
)
def to_swapped(self):
import healpy as hp
hpx_out = self.geom.to_swapped()
map_out = self.__class__(hpx_out, meta=copy.deepcopy(self.meta))
idx = self.geom.get_idx(flat=True)
vals = self.get_by_idx(idx)
if self.geom.nside.size > 1:
nside = self.geom.nside[idx[1:]]
else:
nside = self.geom.nside
if self.geom.nest:
idx_new = tuple([hp.nest2ring(nside, idx[0])]) + idx[1:]
else:
idx_new = tuple([hp.ring2nest(nside, idx[0])]) + idx[1:]
map_out.set_by_idx(idx_new, vals)
return map_out
def randVecInPix(nside, ipix, nest=False):
"""
Draw vectors from a uniform distribution within a HEALpixel.
nside : healpix nside parameter
ipix : pixel number(s)
"""
if not(nest):
ipix = healpy.ring2nest(nside, ipix=ipix)
norder = nside2norder(nside)
nUp = 29 - norder
iUp = ipix * 4**nUp
if np.iterable(ipix):
iUp += np.random.randint(0, 4**nUp, size=np.size(ipix))
else:
iUp += np.random.randint(0, 4**nUp)
vec = healpy.pix2vec(nside=2**29, ipix=iUp, nest=True)
return vec
def to_swapped(self):
import healpy as hp
hpx_out = self.geom.to_swapped()
map_out = self._init_copy(geom=hpx_out, data=None)
idx = self.geom.get_idx(flat=True)
vals = self.get_by_idx(idx)
if self.geom.nside.size > 1:
nside = self.geom.nside[idx[1:]]
else:
nside = self.geom.nside
if self.geom.nest:
idx_new = tuple([hp.nest2ring(nside, idx[0])]) + idx[1:]
else:
idx_new = tuple([hp.ring2nest(nside, idx[0])]) + idx[1:]
map_out.set_by_idx(idx_new, vals)
return map_out
def read_map(filename, HDU=0, field=0, nest=False):
"""Read Healpix map
all columns of the specified HDU are read into a compound numpy MASKED array
if nest is not None, the map is converted if need to NEST or RING ordering.
this function requires healpy"""
m, h = read(filename, HDU=HDU, return_header=True)
try:
m = m[field]
except exceptions.KeyError:
m = m.values()[field]
nside = healpy.npix2nside(m.size)
if not nest is None:
if h.get('ORDERING', False):
if h['ORDERING'] == 'NESTED' and not nest:
idx = healpy.ring2nest(nside,np.arange(m.size,dtype=np.int32))
m = m[idx]
elif h['ORDERING'] == 'RING' and nest:
idx = healpy.nest2ring(nside,np.arange(m.size,dtype=np.int32))
m = m[idx]
return healpy.ma(m)
def generateStarCatalog(self, nstars,nside2=65536):
"""
Generates star catalog by sampling from healpix map.
nstars : number of stars to generate
nside2 : healpix grid use to subsample pixels
note that since nside2 is never allocated it can be arbitrarily large.
"""
nside=hp.get_nside(self.smap.data)
ra=[]
th=[]
filled_pixels = np.where(self.smap>0)[0]
densities = self.smap[filled_pixels]
kpix = np.random.choice(filled_pixels,size=nstars,p=densities/np.sum(densities))
bincounts = np.bincount(kpix)
kpix2 = np.unique(kpix)
counts=bincounts[bincounts>0]
hh=nside2**2/nside**2
i=0
for i,c in enumerate(counts):
rpix=np.random.randint(0,high=hh,size=c)
nestpix=hp.ring2nest(nside,kpix2[i])
theta, phi = hp.pix2ang(nside2,hh*nestpix+rpix,nest=True)
theta=90.-theta*180./np.pi
phi=phi*180./np.pi
for j in range(0,len(theta)):
ra.append(phi[j])
th.append(theta[j])
ra=np.array(ra)
dec=np.array(th)
z=np.random.normal(self.zmean, self.zsigma, nstars)
catalog=cat.Catalog(nstars)
catalog['ra']=ra
catalog['dec']=dec
catalog['z']=z
return catalog
map_cmb_true[:,ipol]=hp.read_map("../../r0p00s4321/cmb_r0p00_ns256s4321.fits",field=ipol)
maps_obs=np.zeros([par.n_pix,par.n_pol,par.n_nu])
for inu in np.arange(par.n_nu) :
for ipol in np.arange(par.n_pol) :
maps_obs[:,ipol,inu]=hp.read_map("../../r0p00s4321/obs_r0p00_nu%03d.fits"%(inu+1),field=ipol)
amin2_per_pix=4*np.pi*(180*60/np.pi)**2/par.n_pix
sigma2_per_pix=par.noise_list**2/amin2_per_pix
maps_s2_noise=np.ones([par.n_pix,par.n_pol,par.n_nu])*sigma2_per_pix[np.newaxis,np.newaxis,:]
if par.include_polarization :
maps_s2_noise[:,1:,:]*=2
maps_noise_weights=1./maps_s2_noise
npix_spec=hp.nside2npix(nside_spec)
ipix0=hp.ring2nest(par.nside_spec,hp.ang2pix(par.nside_spec,theta_patch*np.pi/180,phi_patch*np.pi/180))
print "pixel", ipix0
map_mean=np.zeros([par.n_pix,par.n_pol,par.n_comp])
map_sigma=np.zeros([par.n_pix,par.n_pol,par.n_comp])
map_xspec_mean=np.zeros([npix_spec,par.n_spec_vary])
map_xspec_sigma=np.zeros([npix_spec,par.n_spec_vary])
#for ipix in [ipix0] :
for ipix in np.arange(npix_spec) :
if ipix!=ipix0 :
continue
ipix_list=hp.nest2ring(par.nside,ipix*par.n_sub+np.arange(par.n_sub))
if plot_stuff :
map_show=np.zeros(par.n_pix); map_show[ipix_list]=1.0; hp.mollview(map_show); plt.show()
def computeHPXpix_sequ_new(nside, propertyArray, pixoffset=0, ratiores=4, coadd_cut=False):
#return 'ERROR'
#img_ras, img_decs = [propertyArray[v] for v in ['ra0', 'ra1', 'ra2','ra3']],[propertyArray[v] for v in ['dec0', 'dec1', 'dec2','dec3']]
#x = [1+pixoffset, propertyArray['NAXIS1']-pixoffset, propertyArray['NAXIS1']-pixoffset, 1+pixoffset, 1+pixoffset]
#y = [1+pixoffset, 1+pixoffset, propertyArray['NAXIS2']-pixoffset, propertyArray['NAXIS2']-pixoffset, 1+pixoffset]
#if np.any(img_ras > 360.0):
# img_ras[img_ras > 360.0] -= 360.0
#if np.any(img_ras < 0.0):
# img_ras[img_ras < 0.0] += 360.0
#print 'in here'
#print len(img_ras)#,len(img_ras[0])
#plt.plot(img_ras[0],img_decs[0],'k,')
#plt.show()
img_ras, img_decs = computeCorners_WCS_TPV(propertyArray, pixoffset)
# Coordinates of coadd corners
# RALL, t.DECLL, t.RAUL, t.DECUL, t.RAUR, t.DECUR, t.RALR, t.DECLR, t.URALL, t.UDECLL, t.URAUR, t.UDECUR
if coadd_cut:
#coadd_ras = [propertyArray[v] for v in ['URAUL', 'URALL', 'URALR', 'URAUR']]
#coadd_decs = [propertyArray[v] for v in ['UDECUL', 'UDECLL', 'UDECLR', 'UDECUR']]
coadd_ras = [propertyArray[v] for v in ['ra0', 'ra1', 'ra2', 'ra3']]
coadd_decs = [propertyArray[v] for v in ['dec0', 'dec1', 'dec2', 'dec3']]
coadd_phis = np.multiply(coadd_ras, np.pi/180)
coadd_thetas = np.pi/2 - np.multiply(coadd_decs, np.pi/180)
else:
coadd_phis = 0.0
coadd_thetas = 0.0
# Coordinates of image corners
#print img_ras
img_phis = np.multiply(img_ras , np.pi/180)
img_thetas = np.pi/2 - np.multiply(img_decs , np.pi/180)
img_pix = hp.ang2pix(nside, img_thetas, img_phis, nest=False)
pix_thetas, pix_phis = hp.pix2ang(nside, img_pix, nest=False)
#img_phis = np.mod( img_phis + np.pi, 2*np.pi ) # Enable these two lines to rotate everything by 180 degrees
#coadd_phis = np.mod( coadd_phis + np.pi, 2*np.pi ) # Enable these two lines to rotate everything by 180 degrees
ind_U = 0
ind_L = 2
ind_R = 3
ind_B = 1
ipix_list = np.zeros(0, dtype=long)
weight_list = np.zeros(0, dtype=float)
# loop over rings until reached bottom
iring_U = ring_num(nside, np.cos(img_thetas.min()), shift=0)
iring_B = ring_num(nside, np.cos(img_thetas.max()), shift=0)
ipixs_ring = []
pmax = np.max(img_phis)
pmin = np.min(img_phis)
if (pmax - pmin > np.pi):
ipixs_ring = np.int64(np.concatenate([in_ring(nside, iring, pmax, pmin, conservative=True) for iring in range(iring_U-1, iring_B+1)]))
else:
ipixs_ring = np.int64(np.concatenate([in_ring(nside, iring, pmin, pmax, conservative=True) for iring in range(iring_U-1, iring_B+1)]))
ipixs_nest = hp.ring2nest(nside, ipixs_ring)
npixtot = hp.nside2npix(nside)
if ratiores > 1:
subipixs_nest = np.concatenate([np.arange(ipix*ratiores**2, ipix*ratiores**2+ratiores**2, dtype=np.int64) for ipix in ipixs_nest])
nsubpixperpix = ratiores**2
else:
subipixs_nest = ipixs_nest
nsubpixperpix = 1
rangepix_thetas, rangepix_phis = hp.pix2ang(nside*ratiores, subipixs_nest, nest=True)
#subipixs_ring = hp.ang2pix(nside*ratiores, rangepix_thetas, rangepix_phis, nest=False).reshape(-1, nsubpixperpix)
if (pmax - pmin > np.pi) or (np.max(coadd_phis) - np.min(coadd_phis) > np.pi):
img_phis= np.mod( img_phis + np.pi, 2*np.pi )
coadd_phis= np.mod( coadd_phis + np.pi, 2*np.pi )
rangepix_phis = np.mod( rangepix_phis + np.pi, 2*np.pi )
subweights = in_region(rangepix_thetas, rangepix_phis,
img_thetas[ind_U], img_phis[ind_U], img_thetas[ind_L], img_phis[ind_L],
img_thetas[ind_R], img_phis[ind_R], img_thetas[ind_B], img_phis[ind_B])
if coadd_cut:
subweights_coadd = in_region(rangepix_thetas, rangepix_phis,
coadd_thetas[ind_U], coadd_phis[ind_U], coadd_thetas[ind_L], coadd_phis[ind_L],
coadd_thetas[ind_R], coadd_phis[ind_R], coadd_thetas[ind_B], coadd_phis[ind_B])
resubweights = np.logical_and(subweights, subweights_coadd).reshape(-1, nsubpixperpix)
else:
resubweights = subweights.reshape(-1, nsubpixperpix)
sweights = resubweights.sum(axis=1) / float(nsubpixperpix)
ind = (sweights > 0.0)
return ipixs_ring[ind], sweights[ind], img_thetas, img_phis, resubweights[ind,:]
)
elif targetsys == 'MS':
correctallhpxindices_ring = healpy.ang2pix(
targetnside, np.pi / 2 - mlat, mlon, nest=False
)
else:
print 'not implemented'
sys.exit(1)
# if targetnside<2048:
# print "removing duplicate pixels for targetnside",targetnside,"<",2048
# print "size before",len(correctallhpxindices_ring)
# correctallhpxindices_ring=np.unique(correctallhpxindices_ring)
# print "size after",len(correctallhpxindices_ring)
correctallhpxindices = healpy.ring2nest(targetnside, correctallhpxindices_ring)
print 'done'
# print infodict.keys()
print "I'm pretty sure it's datetime.now()..."
starttime = datetime.datetime.now()
print starttime.isoformat()
hpx4indices = range(healpy.nside2npix(4))
# we want to split the 2048 final (gridded) hpx db to be split into pieces
# according to the 192 hpx indices of nside=4
# using the lookup, we can easily find out, which files contribute, however,
# we need to include adjacent pixels
# idea: for each of the 192 pixels, take all 49152/192 subpixels
def getchildren(ipix,nside):
ipixnest = healpy.ring2nest(ipix,nside)
# regardless of resolution the next children are always the same: 4 * ipix + 0,1,2,3
children = [ipixnest*4, ipixnest*4+1, ipixnest*4+2, ipixnest*4+3]
return children
def radec2healpix(ra,dec,nside):
(theta,phi) = radec2polar(ra,dec)
healpixring = polar2healpix(theta,phi,nside)
return healpy.ring2nest(nside,healpixring)
def ipix2tuple(pixelring,nside):
ipixnest = healpy.ring2nest(nside,pixelring)
npix = healpy.nside2npix(nside)
return (ipixnest / (npix/12) ,ipixnest % (npix/12))
def project_and_write_maps(mode, propertiesweightsoperations, tbdata, catalogue_name, outrootdir, sample_names, inds, nside, ratiores, pixoffset, nsidesout=None):
resol_prefix = 'nside'+str(nside)+'_oversamp'+str(ratiores)
outroot = outrootdir + '/' + catalogue_name + '/' + resol_prefix + '/'
mkdir_p(outroot)
if mode == 1: # Fully sequential
for sample_name, ind in zip(sample_names, inds):
#print len(tbdata[ind]['ra1'])
#plt.plot(tbdata[ind]['ra1'],tbdata[ind]['dec1'],'k,')
#plt.show()
treemap = makeHealTree( (catalogue_name+'_'+sample_name, nside, ratiores, pixoffset, np.array(tbdata[ind])) )
for property, weights, operation in propertiesweightsoperations:
cutmap_indices, cutmap_signal = makeHpxMap_partial( (treemap, property, weights, operation) )
if nsidesout is None:
fname = outroot + '_'.join([catalogue_name, sample_name, resol_prefix, property, weights, operation]) + '.fits'
print 'Creating and writing', fname
write_partial_map(fname, cutmap_indices, cutmap_signal, nside, nest=False)
else:
cutmap_indices_nest = hp.ring2nest(nside, cutmap_indices)
outmap_hi = np.zeros(hp.nside2npix(nside))
outmap_hi.fill(0.0) #outmap_hi.fill(hp.UNSEEN)
outmap_hi[cutmap_indices_nest] = cutmap_signal
for nside_out in nsidesout:
if nside_out == nside:
outmap_lo = outmap_hi
else:
outmap_lo = hp.ud_grade(outmap_hi, nside_out, order_in='NESTED', order_out='NESTED')
resol_prefix2 = 'nside'+str(nside_out)+'from'+str(nside)+'o'+str(ratiores)
outroot2 = outrootdir + '/' + catalogue_name + '/' + resol_prefix2 + '/'
mkdir_p(outroot2)
fname = outroot2 + '_'.join([catalogue_name, sample_name, resol_prefix2, property, weights, operation]) + '.fits'
print 'Writing', fname
hp.write_map(fname, outmap_lo, nest=True)
subprocess.call("gzip "+fname,shell=True)
if mode == 3: # Fully parallel
pool = Pool(len(inds))
print 'Creating HealTrees'
treemaps = pool.map( makeHealTree,
[ (catalogue_name+'_'+samplename, nside, ratiores, pixoffset, np.array(tbdata[ind]))
for samplename, ind in zip(sample_names, inds) ] )
for property, weights, operation in propertiesweightsoperations:
print 'Making maps for', property, weights, operation
outmaps = pool.map( makeHpxMap_partial,
[ (treemap, property, weights, operation) for treemap in treemaps ] )
for sample_name, outmap in zip(sample_names, outmaps):
fname = outroot + '_'.join([catalogue_name, sample_name, resol_prefix, property, weights, operation]) + '.fits'
print 'Writing', fname
cutmap_indices, cutmap_signal = outmap
write_partial_map(fname, cutmap_indices, cutmap_signal, nside, nest=False)
if mode == 2: # Parallel tree making and sequential writing
pool = Pool(len(inds))
print 'Creating HealTrees'
treemaps = pool.map( makeHealTree,
[ (catalogue_name+'_'+samplename, nside, ratiores, pixoffset, np.array(tbdata[ind]))
for samplename, ind in zip(sample_names, inds) ] )
for property, weights, operation in propertiesweightsoperations:
for sample_name, treemap in zip(sample_names, treemaps):
fname = outroot + '_'.join([catalogue_name, sample_name, resol_prefix, property, weights, operation]) + '.fits'
print 'Writing', fname
#outmap = makeHpxMap( (treemap, property, weights, operation) )
#hp.write_map(fname, outmap, nest=False)
cutmap_indices, cutmap_signal = makeHpxMap_partial( (treemap, property, weights, operation) )
write_partial_map(fname, cutmap_indices, cutmap_signal, nside, nest=False)
def _stage_pixels(self, data, detectors, nsamp, ndet, obs_period_ranges, nside):
""" Stage pixels
"""
auto_timer = timing.auto_timer(type(self).__name__)
self._madam_pixels = self._cache.create(
"pixels", madam.PIXEL_TYPE, (nsamp * ndet,)
)
self._madam_pixels[:] = -1
global_offset = 0
for iobs, obs in enumerate(data.obs):
tod = obs["tod"]
period_ranges = obs_period_ranges[iobs]
commonflags = None
for idet, det in enumerate(detectors):
# Optionally get the flags, otherwise they are
# assumed to have been applied to the pixel numbers.
if self._apply_flags:
detflags = tod.local_flags(det, self._flag_name)
commonflags = tod.local_common_flags(self._common_flag_name)
flags = np.logical_or(
(detflags & self._flag_mask) != 0,
(commonflags & self._common_flag_mask) != 0,
)
del detflags
# get the pixels for the valid intervals from the cache
pixelsname = "{}_{}".format(self._pixels, det)
pixels = tod.cache.reference(pixelsname)
pixels_dtype = pixels.dtype
if not self._pixels_nested:
# Madam expects the pixels to be in nested ordering
pixels = pixels.copy()
good = pixels >= 0
pixels[good] = hp.ring2nest(nside, pixels[good])
if self._apply_flags:
pixels = pixels.copy()
pixels[flags] = -1
offset = global_offset
for istart, istop in period_ranges:
nn = istop - istart
dslice = slice(idet * nsamp + offset, idet * nsamp + offset + nn)
self._madam_pixels[dslice] = pixels[istart:istop]
offset += nn
del pixels
if self._apply_flags:
del flags
# Always purge the pixels but restore them from the Madam
# buffers when purge_pixels=False
for idet, det in enumerate(detectors):
pixelsname = "{}_{}".format(self._pixels, det)
tod.cache.clear(pattern=pixelsname)
if self._name is not None and (
self._purge_tod or self._name == self._name_out
):
cachename = "{}_{}".format(self._name, det)
tod.cache.clear(pattern=cachename)
if self._purge_flags and self._flag_name is not None:
cacheflagname = "{}_{}".format(self._flag_name, det)
tod.cache.clear(pattern=cacheflagname)
del commonflags
if self._purge_flags and self._common_flag_name is not None:
tod.cache.clear(pattern=self._common_flag_name)
global_offset = offset
return pixels_dtype
def getFilePixels(self, nside):
"""
Get the healpix cells occupied by galaxies
in each file. Assumes files have already been
sorted correctly by parseFileStruct
"""
fpix = []
# BCC catalogs have pixels in filenames
if ("BCC" in self.__class__.__name__) & (self.filenside is not None) & (self.filenside >= self.groupnside):
fk = self.filestruct.keys()
for f in self.filestruct[fk[0]]:
p = int(f.split(".")[-2])
if self.filenside == self.groupnside:
fpix.append([p])
else:
if not self.nest:
while p > 12 * self.filenside ** 2:
p = p - 1000
p = hp.ring2nest(self.filenside, p)
o1 = int(np.log2(self.filenside))
o2 = int(np.log2(self.groupnside))
base = int(p >> 2 * o1)
hosubpix = int(p & ((1 << (2 * o1)) - 1))
losubpix = int(hosubpix // (1 << 2 * (o1 - o2)))
p = int(base * (1 << (2 * o2)) + losubpix)
fpix.append([p])
else:
ct = ["galaxycatalog"]
pmetric = PixMetric(self.ministry, self.groupnside, catalog_type=ct, nest=self.nest)
mg = self.ministry.genMetricGroups([pmetric])
ms = mg[0][1]
fm = mg[0][0]
mappables = self.ministry.genMappables(mg[0])
if self.ministry.parallel:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
mappables = mappables[rank::size]
for i, mappable in enumerate(mappables):
mapunit = self.ministry.readMappable(mappable, fm)
print("converting before getting file pixels")
if (not hasattr(ms, "__iter__")) and ("only" in ms.aschema):
mapunit = self.ministry.scListToDict(mapunit)
mapunit = self.ministry.convert(mapunit, ms)
mapunit = self.ministry.filter(mapunit)
elif "only" in ms[0].aschema:
mapunit = self.ministry.scListToDict(mapunit)
mapunit = self.ministry.convert(mapunit, ms)
mapunit = self.ministry.filter(mapunit)
if (ms[0].aschema == "galaxygalaxy") | (ms[0].aschema == "halohalo"):
mapunit = self.ministry.dcListToDict(mapunit)
mapunit = self.ministry.convert(mapunit, ms)
mapunit = self.ministry.filter(mapunit)
fpix.append(pmetric.map(mapunit))
del mapunit
if self.ministry.parallel:
gfpix = comm.allgather(fpix)
fpix = []
for fp in gfpix:
fpix.extend(fp)
return fpix
def read_sky_map(filename, nest=False, distances=False, moc=False, **kwargs):
"""
Read a LIGO/Virgo-type sky map and return a tuple of the HEALPix array
and a dictionary of metadata from the header.
Parameters
----------
filename: string
Path to the optionally gzip-compressed FITS file.
nest: bool, optional
If omitted or False, then detect the pixel ordering in the FITS file
and rearrange if necessary to RING indexing before returning.
If True, then detect the pixel ordering and rearrange if necessary to
NESTED indexing before returning.
If None, then preserve the ordering from the FITS file.
Regardless of the value of this option, the ordering used in the FITS
file is indicated as the value of the 'nest' key in the metadata
dictionary.
distances: bool, optional
If true, then read also read the additional HEALPix layers representing
the conditional mean and standard deviation of distance as a function
of sky location.
moc: bool, optional
If true, then preserve multi-order structure if present.
Example
-------
Test that we can read a legacy IDL-compatible file
(https://bugs.ligo.org/redmine/issues/5168):
>>> import tempfile
>>> with tempfile.NamedTemporaryFile(suffix='.fits') as f:
... nside = 512
... npix = hp.nside2npix(nside)
... ipix_nest = np.arange(npix)
... hp.write_map(f.name, ipix_nest, nest=True, column_names=['PROB'])
... m, meta = read_sky_map(f.name)
... np.testing.assert_array_equal(m, hp.ring2nest(nside, ipix_nest))
"""
m = Table.read(filename, format='fits', **kwargs)
# Remove some keys that we do not need
for key in (
'PIXTYPE', 'EXTNAME', 'NSIDE', 'FIRSTPIX', 'LASTPIX', 'INDXSCHM'):
m.meta.pop(key, None)
if m.meta.pop('COORDSYS', 'C') != 'C':
raise ValueError('LALInference only reads and writes sky maps in '
'equatorial coordinates.')
try:
value = m.meta.pop('ORDERING')
except KeyError:
pass
else:
if value == 'RING':
m.meta['nest'] = False
elif value == 'NESTED':
m.meta['nest'] = True
elif value == 'NUNIQ':
pass
else:
raise ValueError(
'ORDERING card in header has unknown value: {0}'.format(value))
for fits_key, rows in itertools.groupby(
FITS_META_MAPPING, lambda row: row[1]):
try:
value = m.meta.pop(fits_key)
except KeyError:
pass
else:
for row in rows:
key, _, _, _, from_fits = row
if from_fits is not None:
m.meta[key] = from_fits(value)
if 'UNIQ' not in m.colnames:
m = Table([col.ravel() for col in m.columns.values()], meta=m.meta)
if 'UNIQ' in m.colnames and not moc:
from ..bayestar.sky_map import rasterize
m = rasterize(m)
m.meta['nest'] = True
elif 'UNIQ' not in m.colnames and moc:
from ..bayestar.sky_map import derasterize
if not m.meta['nest']:
npix = len(m)
nside = hp.npix2nside(npix)
m = m[hp.nest2ring(nside, np.arange(npix))]
m = derasterize(m)
m.meta.pop('nest', None)
if 'UNIQ' not in m.colnames:
npix = len(m)
nside = hp.npix2nside(npix)
if nest is None:
pass
elif m.meta['nest'] and not nest:
m = m[hp.ring2nest(nside, np.arange(npix))]
elif not m.meta['nest'] and nest:
m = m[hp.nest2ring(nside, np.arange(npix))]
if moc:
return m
elif distances:
return tuple(
np.asarray(m[name]) for name in DEFAULT_NESTED_NAMES), m.meta
else:
return np.asarray(m[DEFAULT_NESTED_NAMES[0]]), m.meta
phiinc = 0.98 * (2.0 * np.pi / angperring)
theta = np.zeros(nring * angperring)
phi = np.zeros_like(theta)
n = 0
for t in range(nring):
for p in range(angperring):
theta[n] = t * thetainc
phi[n] = p * phiinc
n += 1
pixring = hp.ang2pix(nside, theta, phi)
pixnest = hp.ring2nest(nside, pixring)
ringtheta, ringphi = hp.pix2ang(nside, pixring)
print(" int64_t nside = {};".format(nside))
print("")
print(" int64_t ntest = {};".format(n))
print("")
print(" double theta[{}] = {{".format(n))
for i in range(n):
print(" {},".format(theta[i]))
print(" };")
print("")