def test_cls_raise_ell_reversed(ells):
z = np.linspace(0., 1., 200)
n = np.exp(-((z - 0.5) / 0.1)**2)
lens = ccl.WeakLensingTracer(COSMO, (z, n))
with pytest.raises(ValueError):
ccl.angular_cl(COSMO, lens, lens, ells)
def test_pk2d_cls():
"""
Test interplay between Pk2D and the Limber integrator
"""
cosmo = ccl.Cosmology(Omega_c=0.27,
Omega_b=0.045,
h=0.67,
A_s=1e-10,
n_s=0.96)
z = np.linspace(0., 1., 200)
n = np.exp(-((z - 0.5) / 0.1)**2)
lens1 = ccl.WeakLensingTracer(cosmo, (z, n))
ells = np.arange(2, 10)
# Check that passing no power spectrum is fine
cells = ccl.angular_cl(cosmo, lens1, lens1, ells)
assert all_finite(cells)
# Check that passing a bogus power spectrum fails as expected
assert_raises(ValueError,
ccl.angular_cl,
cosmo,
lens1,
lens1,
ells,
p_of_k_a=1)
# Check that passing a correct power spectrum runs as expected
psp = ccl.Pk2D(pkfunc=lpk2d, cosmo=cosmo)
cells = ccl.angular_cl(cosmo, lens1, lens1, ells, p_of_k_a=psp)
assert all_finite(cells)
def get_cl_ccl(pars, ell_bp):
cosmo = get_cosmo_ccl(pars)
clust = ccl.NumberCountsTracer(cosmo,
has_rsd=False,
dndz=(z, pz),
bias=(z, bz))
lens = ccl.WeakLensingTracer(cosmo, dndz=(z, pz))
ell = np.arange(nell)
cl0 = np.zeros(nell) * 0.
cls = np.zeros([3, 3, nell])
cls[0, 0, :] = ccl.angular_cl(cosmo, clust, clust, ell)
cls[0, 1, :] = ccl.angular_cl(cosmo, clust, lens, ell)
cls[0, 2, :] = cl0
cls[1, 0, :] = cls[0, 1, :]
cls[1, 1, :] = ccl.angular_cl(cosmo, lens, lens, ell)
cls[1, 2, :] = cl0
cls[2, 0, :] = cls[0, 2, :]
cls[2, 1, :] = cls[1, 2, :]
cls[2, 2, :] = cl0
cl_flat = np.concatenate(
[cls[0, 0, ell_bp], cls[0, 1, ell_bp], cls[1, 1, ell_bp]])
return cl_flat
def test_cls_smoke(p_of_k_a):
# make a set of tracers to test with
z = np.linspace(0., 1., 200)
n = np.exp(-((z - 0.5) / 0.1)**2)
b = np.sqrt(1. + z)
lens1 = ccl.WeakLensingTracer(COSMO, (z, n))
lens2 = ccl.WeakLensingTracer(COSMO, dndz=(z, n), ia_bias=(z, n))
nc1 = ccl.NumberCountsTracer(COSMO, False, dndz=(z, n), bias=(z, b))
nc2 = ccl.NumberCountsTracer(COSMO, True, dndz=(z, n), bias=(z, b))
nc3 = ccl.NumberCountsTracer(COSMO,
True,
dndz=(z, n),
bias=(z, b),
mag_bias=(z, b))
cmbl = ccl.CMBLensingTracer(COSMO, 1100.)
tracers = [lens1, lens2, nc1, nc2, nc3, cmbl]
ell_scl = 4.
ell_int = 4
ell_lst = [2, 3, 4, 5]
ell_arr = np.arange(2, 5)
ells = [ell_int, ell_scl, ell_lst, ell_arr]
for i in range(len(tracers)):
for j in range(i, len(tracers)):
for ell in ells:
corr = ccl.angular_cl(COSMO,
tracers[i],
tracers[j],
ell,
p_of_k_a=p_of_k_a)
assert np.all(np.isfinite(corr))
assert np.shape(corr) == np.shape(ell)
# reversing should be fine
corr_rev = ccl.angular_cl(COSMO,
tracers[j],
tracers[i],
ell,
p_of_k_a=p_of_k_a)
assert np.allclose(corr, corr_rev)
# Check invalid dndz
with assert_raises(ValueError):
ccl.NumberCountsTracer(COSMO, False, dndz=z, bias=(z, b))
with assert_raises(ValueError):
ccl.NumberCountsTracer(COSMO, False, dndz=(z, n, n), bias=(z, b))
with assert_raises(ValueError):
ccl.NumberCountsTracer(COSMO, False, dndz=(z, ), bias=(z, b))
with assert_raises(ValueError):
ccl.NumberCountsTracer(COSMO, False, dndz=(1, 2), bias=(z, b))
with assert_raises(ValueError):
ccl.WeakLensingTracer(COSMO, dndz=z)
with assert_raises(ValueError):
ccl.WeakLensingTracer(COSMO, dndz=(z, n, n))
with assert_raises(ValueError):
ccl.WeakLensingTracer(COSMO, dndz=(z, ))
with assert_raises(ValueError):
ccl.WeakLensingTracer(COSMO, dndz=(1, 2))
def test_cls_raise_weird_pk():
z = np.linspace(0., 1., 200)
n = np.exp(-((z - 0.5) / 0.1)**2)
lens = ccl.WeakLensingTracer(COSMO, (z, n))
ells = [10, 11]
with pytest.raises(ValueError):
ccl.angular_cl(COSMO, lens, lens, ells, p_of_k_a=lambda k, a: 10)
def test_cls_raise_integ_method():
ells = [10, 11]
with pytest.raises(ValueError):
ccl.angular_cl(COSMO,
LENS,
LENS,
ells,
limber_integration_method='guad')
def get_tomo_xi_ccl_2(sigma8, Omega_cm0, Omega_bm0, h, zpts, zhist, theta_deg, theta_num_per_bin, ell, used_zbins, xi_pm="xi_p"):
"""
for the MCMC
:param sigma8:
:param Omega_cm0:
:param Omega_bm0:
:param h:
:param zpts: the center of the Z bins
:param zhist: Z histogram, (n,m), n is the tomographic bin num,
includes the histograms of all bins, the used_zbins will determine which bins are used
:param theta_deg: where the signals are measured, (n,)
:param ell: \ell of C(\ell), the angular power spectrum
:param uesd_zbins: numpy array,(n,), labels, 1 for used, 0 for not used
:return:
"""
# tomo panel num
tomo_bin_num, zbin_num = used_zbins.shape[0],used_zbins.sum()
cosmo = pyccl.Cosmology(Omega_c=Omega_cm0, Omega_b=Omega_bm0, h=h, n_s=0.965, sigma8=sigma8,
transfer_function="boltzmann_camb")
ccl_lens_trs = []
for i in range(tomo_bin_num):
if used_zbins[i] == 1:
lens_tr = pyccl.WeakLensingTracer(cosmo, dndz=(zpts, zhist[i]))
ccl_lens_trs.append(lens_tr)
if xi_pm == "all":
pts_num = int(2*theta_deg.shape[0])
ccl_xipm = numpy.zeros((pts_num,))
tag = 0
for i in range(zbin_num):
for j in range(i, zbin_num):
st, ed = int(tag * theta_num_per_bin), int((tag + 1) * theta_num_per_bin)
ccl_cls = pyccl.angular_cl(cosmo, ccl_lens_trs[i], ccl_lens_trs[j], ell)
ccl_xipm[st:ed] = pyccl.correlation(cosmo, ell, ccl_cls, theta_deg[st:ed], type='GG+', method='FFTLog')
ccl_xipm[pts_num+st:pts_num+ed] = pyccl.correlation(cosmo, ell, ccl_cls, theta_deg[st:ed], type='GG-', method='FFTLog')
tag += 1
return ccl_xipm
if xi_pm == "xi_p":
corr_type = "GG+"
elif xi_pm == "xi_m":
corr_type = "GG-"
else:
print("xi_pm must be one of [\"xi_p\", \"xi_m\",\"all\"]")
return None
ccl_xi = numpy.zeros_like(theta_deg)
tag = 0
for i in range(zbin_num):
for j in range(i, zbin_num):
st, ed = int(tag*theta_num_per_bin), int((tag+1)*theta_num_per_bin)
ccl_cls = pyccl.angular_cl(cosmo, ccl_lens_trs[i], ccl_lens_trs[j], ell)
ccl_xi[st:ed] = pyccl.correlation(cosmo, ell, ccl_cls, theta_deg[st:ed], type=corr_type, method='FFTLog')
tag += 1
return ccl_xi
def test_two_point_some(kind, tmpdir):
cosmo = ccl.Cosmology(Omega_c=0.27,
Omega_b=0.045,
Omega_k=0.0,
w0=-1.0,
wa=0.0,
sigma8=0.8,
n_s=0.96,
h=0.67)
sources = {}
for i, mn in enumerate([0.25, 0.75]):
sources['src%d' % i] = DummySource()
z = np.linspace(0, 2, 50)
nz = np.exp(-0.5 * (z - mn)**2 / 0.25 / 0.25)
if ('g' in kind and i == 0) or kind == 'gg':
sources['src%d' % i].tracer_ = ccl.ClTracerNumberCounts(
cosmo,
has_rsd=False,
has_magnification=False,
z=z,
n=nz,
bias=np.ones_like(z) * 2.0)
else:
sources['src%d' % i].tracer_ = ccl.ClTracerLensing(
cosmo, has_intrinsic_alignment=False, z=z, n=nz)
sources['src%d' % i].scale_ = i / 2.0 + 1.0
# compute the statistic
tracers = [v.tracer_ for k, v in sources.items()]
scale = np.prod([v.scale_ for k, v in sources.items()])
data = os.path.join(tmpdir, 'stat.csv')
if kind == 'cl':
ell = np.logspace(1, 3, 10)
cell = ccl.angular_cl(cosmo, *tracers, ell) * scale
pd.DataFrame({'l': ell, 'cl': cell}).to_csv(data, index=False)
else:
theta = np.logspace(1, 2, 100)
ell = _ell_for_xi()
cell = ccl.angular_cl(cosmo, *tracers, ell)
xi = ccl.correlation(cosmo, ell, cell, theta / 60.0,
corr_type=kind) * scale
pd.DataFrame({'t': theta, 'xi': xi}).to_csv(data, index=False)
stat = TwoPointStatistic(data=data, kind=kind, sources=['src0', 'src1'])
stat.compute(cosmo, {}, sources, systematics=None)
if kind == 'cl':
assert np.allclose(stat.measured_statistic_, cell)
else:
assert np.allclose(stat.measured_statistic_, xi)
assert np.allclose(stat.measured_statistic_, stat.predicted_statistic_)
def get_log_prob(self, theta):
# Check the priors
log_prior = self.get_log_prior(theta)
if not np.isfinite(log_prior):
return -np.inf
# Update default cosmological parameters with new sampled parameters
params = self.cosmology_params.copy()
for param_name in self.arg_names:
if param_name in params:
params[param_name] = theta[self.arg_names.index(param_name)]
cosmo = ccl.Cosmology(**params)
# Update data parameters
z_tail = theta[self.arg_names.index(
'z_tail')] if 'z_tail' in self.arg_names else self.z_tail
bias = theta[self.arg_names.index(
'bias')] if 'bias' in self.arg_names else self.bias
# Get redshift distribution
z_arr, n_arr = get_lotss_redshift_distribution(z_tail=z_tail)
bias_arr = bias * np.ones(len(z_arr))
bias_arr = bias_arr / ccl.growth_factor(cosmo, 1. / (1 + z_arr))
# Get correlations
number_counts_tracer = ccl.NumberCountsTracer(cosmo,
has_rsd=False,
dndz=(z_arr, n_arr),
bias=(z_arr, bias_arr))
cmb_lensing_tracer = ccl.CMBLensingTracer(cosmo, 1091)
correlations = {}
if 'gg' in self.correlation_symbols:
correlations['gg'] = ccl.angular_cl(cosmo, number_counts_tracer,
number_counts_tracer,
self.l_arr)
if 'gk' in self.correlation_symbols:
correlations['gk'] = ccl.angular_cl(cosmo, number_counts_tracer,
cmb_lensing_tracer, self.l_arr)
# Bin spectra using coupling matrices in workspaces
for correlation_symbol in self.correlation_symbols:
correlations[correlation_symbol] = decouple_correlation(
self.workspaces[correlation_symbol],
correlations[correlation_symbol])
# Calculate log prob
model = np.concatenate([
correlations[correlation_symbol][:self.n_ells[correlation_symbol]]
for correlation_symbol in self.correlation_symbols
])
diff = self.data_vector - model
log_prob = log_prior - np.dot(
diff, np.dot(self.inverted_covariance, diff)) / 2.0
return log_prob
def getLensingCRmatrix(lenses, ell, cosmo):
"""This function calculats auto- and cross-power spectra for given lensing objects in tomographic bins. Input the lensing objects and ls' to integrate over. It returns a matrix that stores the cross power spectra between different bins"""
n = len(lenses)
lensCL = np.zeros([n, n, len(ell)])
#create an empty n-by-n array that stores the lensing cross power spectrum between the ith and jth bin
for i in range(n):
lensCL[i, i, :] = ccl.angular_cl(cosmo, lenses[i], lenses[i], ell)
for j in range(n - 1):
for k in range(j + 1, n):
lensCL[j, k, :] = ccl.angular_cl(cosmo, lenses[j], lenses[k], ell)
lensCL[k, j, :] = lensCL[j, k, :]
return lensCL
def getTheories(ccl_cosmo,s,ctracers) :
theo={}
for t1i,t2i,ells,_ in s.sortTracers():
cls=ccl.angular_cl(ccl_cosmo,ctracers[t1i],ctracers[t2i],ells)
theo[(t1i,t2i)]=cls
theo[(t2i,t1i)]=cls
return theo
def theory_corr(self, n_z2, xvals, lmax2, chi_max, zlo2, zhi2, cosmo_cat):
'''compute the correlation function from limber integration over the CAMB power spectrum'''
nz_int = self.compute_nz(n_z2)
z_vals = np.linspace(zlo2, zhi2, 1000)
n_vals = nz_int(z_vals)
ns = getattr(cosmo_cat, 'n_s', 0.963)
s8 = getattr(cosmo_cat, 'sigma8', 0.8)
Omega_c = (cosmo_cat.Om0 - cosmo_cat.Ob0)
Omega_b = cosmo_cat.Ob0
h = cosmo_cat.H0.value / 100.
cosmo_ccl = ccl.Cosmology(
Omega_c=Omega_c, Omega_b=Omega_b, h=h, sigma8=s8, n_s=ns
) #, transfer_function='boltzmann_class', matter_power_spectrum='emu')
ll = np.arange(0, 15000)
lens1 = ccl.WeakLensingTracer(cosmo_ccl, dndz=(z_vals, n_vals))
pp = ccl.angular_cl(cosmo_ccl, lens1, lens1, ll)
pp3_2 = np.zeros((lmax2, 4))
pp3_2[:, 1] = pp[:] * (ll * (ll + 1.)) / (2. * np.pi)
cxvals = np.cos(xvals / (60.) / (180. / np.pi))
vals = camb.correlations.cl2corr(pp3_2, cxvals)
return xvals, vals[:, 1], vals[:, 2]
def get_cl(trs, b1, b2):
nl = np.zeros(3*o.nside)
if (b1 == b2) and (not o.full_noise):
fname_nl = predir + "maps_metacal_bin%d_ns%d_nells.npz" % (b1, o.nside)
d = np.load(fname_nl)
nl[2:] = d['nl_cov']
sl = ccl.angular_cl(cosmo, trs[b1], trs[b2], ls)
if o.old_nka:
return np.array([sl + nl, cl0, cl0, nl])
else:
w = nmt.NmtWorkspace()
predir_mcm = predir + 'cls_metacal_mcm_bins_'
fname_mcm = predir_mcm + '%d%d_ns%d.fits' % (b1, b2, o.nside)
if os.path.isfile(fname_mcm):
w.read_from(fname_mcm)
else:
fname_mcm = predir_mcm + '%d%d_ns%d.fits' % (b2, b1, o.nside)
if os.path.isfile(fname_mcm):
w.read_from(fname_mcm)
else:
raise ValueError("Can't find MCM " + fname_mcm)
mskprod = get_field(b1, return_mask=True)
if b1 == b2:
mskprod *= mskprod
else:
mskprod *= get_field(b2, return_mask=True)
fsky = np.mean(mskprod)
return w.couple_cell([sl, cl0, cl0, cl0])/fsky + np.array([nl, cl0, cl0, nl])
def test_xi(set_up, corr_method, t1, t2, bm, er, kind, pref):
cosmo, trcs, bms, ers, fls = set_up
method, errfac = corr_method
# Debugging - define the same cosmology but in GR
cl = ccl.angular_cl(cosmo, trcs[t1], trcs[t2], fls['ells'])
ell = np.arange(fls['lmax'])
cli = interp1d(fls['ells'], cl, kind='cubic')(ell)
# Our benchmarks have theta in arcmin
# but CCL requires it in degrees:
theta_deg = bms['theta'] / 60.
# We cut the largest theta value for xi+ because of issues with the
# benchmarks.
if kind == 'GG+':
xi = ccl.correlation(cosmo,
ell,
cli,
theta_deg[0:14],
type=kind,
method=method)
else:
xi = ccl.correlation(cosmo,
ell,
cli,
theta_deg,
type=kind,
method=method)
xi *= pref
assert np.all(np.fabs(xi - bms[bm]) < ers[er] * errfac)
def get_cl(dtype):
config = get_config(dtype)
cosmo_pars = config['cosmo']
cosmo = ccl.Cosmology(**cosmo_pars)
if config['dtype'] == 'generic':
return np.ones(3 * config['nside'])
if config['dtype'] == 'galaxy_density':
z, nz = np.loadtxt('xcell/tests/data/DESY1gc_dndz_bin0.txt',
usecols=(1, 3),
unpack=True)
b = np.ones_like(z)
tracer = ccl.NumberCountsTracer(cosmo,
dndz=(z, nz),
bias=(z, b),
has_rsd=None)
elif config['dtype'] == 'galaxy_shear':
z, nz = np.loadtxt('xcell/tests/data/Nz_DIR_z0.1t0.3.asc',
usecols=(0, 1),
unpack=True)
tracer = ccl.WeakLensingTracer(cosmo, dndz=(z, nz))
elif config['dtype'] == 'cmb_convergence':
tracer = ccl.CMBLensingTracer(cosmo, z_source=1100)
elif config['dtype'] == 'cmb_tSZ':
tracer = ccl.tSZTracer(cosmo, z_max=3.)
cl = ccl.angular_cl(cosmo, tracer, tracer, np.arange(3 * config['nside']))
return cl
def get_cl_file(self):
nside = self.data['healpy']['nside']
if self.read_symm:
tr1 = self.tr2
tr2 = self.tr1
else:
tr1 = self.tr1
tr2 = self.tr2
fname = os.path.join(self.outdir, 'cl_{}_{}.npz'.format(tr1, tr2))
ell = np.arange(3 * nside)
if not os.path.isfile(fname):
ccl_tr1, ccl_tr2 = self.get_tracers_ccl()
cl = ccl.angular_cl(self.cosmo, ccl_tr1, ccl_tr2, ell)
tracers = self.data['tracers']
fiducial = self.data['cov']['fiducial']
for tr in [self.tr1, self.tr2]:
if (tracers[tr]['type'] == 'wl') and fiducial['wl_m']:
cl = (1 + tracers[tr]['m']) * cl
s1, s2 = self.get_spins()
size = s1 + s2
if size == 0:
size = 1
cl_vector = np.zeros((size, cl.size))
cl_vector[0] = cl
np.savez_compressed(fname, cl=cl_vector, ell=ell)
cl_file = np.load(fname)
if np.any(cl_file['ell'] != ell):
raise ValueError(
'The ell in {} does not match the ell from nside={}'.format(
fname, nside))
return cl_file
def check_corr(cosmo):
# Number density input
z = np.linspace(0., 1., 200)
n = np.ones(z.shape)
# ClTracer test objects
lens1 = ccl.ClTracerLensing(cosmo, False, n=n, z=z)
lens2 = ccl.ClTracerLensing(cosmo,
True,
n=(z, n),
bias_ia=(z, n),
f_red=(z, n))
ells = np.arange(3000)
cls = ccl.angular_cl(cosmo, lens1, lens2, ells)
t = np.logspace(-2, np.log10(5.), 20) #degrees
corrfunc = ccl.correlation(cosmo,
ells,
cls,
t,
corr_type='L+',
method='FFTLog')
assert_(all_finite(corrfunc))
def compute_cls(oc,ob,h,s8,ns,w,fname_out=False) :
#Fiducial cosmological parameters
cosmo=ccl.Cosmology(Omega_c=oc,Omega_b=ob,h=h,sigma8=s8,n_s=ns,w0=w,
transfer_function='eisenstein_hu')
print ccl.sigma8(cosmo)
#Tracers
tracers=[]
for i in np.arange(nbins) :
print i
# tracers.append(ccl.ClTracer(cosmo,tracer_type='nc',z=zarr,n=nz_bins[i],bias=bzarr))
tracers.append(ccl.ClTracer(cosmo,tracer_type='wl',z=zarr,n=nz_bins[i]))#,bias=bzarr))
#Power spectra
c_ij=np.zeros([LMAX+1,nbins,nbins])
for i1 in np.arange(nbins) :
for i2 in np.arange(i1,nbins) :
print i1,i2
if xcorr[i1,i2]<-1:#1E-6 :
c_ij[:,i1,i2]=0
else :
c_ij[:,i1,i2]=ccl.angular_cl(cosmo,tracers[i1],tracers[i2],np.arange(LMAX+1))#,l_limber=100)
if i1!=i2 :
c_ij[:,i2,i1]=c_ij[:,i1,i2]
if fname_out!=False :
np.save(fname_out,c_ij)
return c_ij
def get_tomo_xi_ccl(sigma8, Omega_cm0, Omega_bm0, h, zpts, zhist, theta_deg, ell):
ns = 0.965
ell_num = len(ell)
# tomo panel num
tomo_bin_num, zpts_num = zhist.shape
tomo_panel_num = int((tomo_bin_num * tomo_bin_num + tomo_bin_num) / 2)
cosmo = pyccl.Cosmology(Omega_c=Omega_cm0, Omega_b=Omega_bm0, h=h, n_s=ns, sigma8=sigma8,
transfer_function="boltzmann_camb")
ccl_lens_trs = []
ccl_PL = numpy.zeros((tomo_panel_num, ell_num))
ccl_xip = numpy.zeros_like(theta_deg)
ccl_xim = numpy.zeros_like(theta_deg)
for i in range(tomo_bin_num):
lens_tr = pyccl.WeakLensingTracer(cosmo, dndz=(zpts, zhist[i]))
ccl_lens_trs.append(lens_tr)
tag = 0
for i in range(tomo_bin_num):
for j in range(i, tomo_bin_num):
ccl_PL[tag] = pyccl.angular_cl(cosmo, ccl_lens_trs[i], ccl_lens_trs[j], ell)
ccl_xip[tag] = pyccl.correlation(cosmo, ell, ccl_PL[tag], theta_deg[tag], type='GG+', method='FFTLog')
ccl_xim[tag] = pyccl.correlation(cosmo, ell, ccl_PL[tag], theta_deg[tag], type='GG-', method='FFTLog')
tag += 1
return ccl_xip, ccl_xim, ccl_PL
def test_cls(set_up, t1, t2, bm,
a1b1, a1b2, a2b1, a2b2, fl):
cosmo, trcs, lfc, bmk = set_up
cl = ccl.angular_cl(cosmo, trcs[t1], trcs[t2], lfc['ells']) * lfc[fl]
el = np.sqrt((bmk[a1b1] * bmk[a2b2] + bmk[a1b2] * bmk[a2b1]) /
(2 * lfc['ells'] + 1.))
assert np.all(np.fabs(cl - bmk[bm]) < 0.1 * el)
def getcorrCCL(theta, data, centers):
Nz, be = np.histogram(data['z'], bins=8, range=(0.05, 0.15))
z = 0.5 * (be[1:] + be[:-1])
h = 0.675 # Planck value for h (Hubble parameter)
Ob = 0.044 # Planck value for Omega_b (Baryon energy density)
Om = theta[1] # Planck value for Omega_m (Matter energy density)
Oc = Om - Ob # Value for Omega_c (Cold dark matter energy density)
ns = 0.965 # Scalar index
cosmo = ccl.Cosmology(Omega_c=Oc,
Omega_b=Ob,
h=h,
sigma8=0.8,
n_s=ns,
matter_power_spectrum='linear')
tracer = ccl.NumberCountsTracer(cosmo,
has_rsd=False,
dndz=(z, Nz),
bias=(z, np.ones_like(z)))
ell = np.arange(1, 7500) # is this the same as lmax?
angular_power_spectrum = ccl.angular_cl(cosmo, tracer, tracer, ell)
th = centers #np.linspace(0,0.2, num = 15)
ang_corr_func = ccl.correlation(cosmo, ell, angular_power_spectrum, th)
return ang_corr_func
def test_xi(set_up, corr_method, t1, t2, bm, er, kind, pref):
cosmo, trcs, bms, ers, fls = set_up
method, errfac = corr_method
global T0_CLS
t0 = time.time()
cl = ccl.angular_cl(cosmo, trcs[t1], trcs[t2], fls['ells'])
T0_CLS += (time.time() - t0)
ell = np.arange(fls['lmax'])
cli = interp1d(fls['ells'], cl, kind='cubic')(ell)
global T0
t0 = time.time()
xi = ccl.correlation(cosmo,
ell,
cli,
bms['theta'],
corr_type=kind,
method=method)
T0 += (time.time() - t0)
xi *= pref
assert np.all(np.fabs(xi - bms[bm]) < ers[er] * errfac)
print("time:", T0)
print("time cls:", T0_CLS)
def getTheories(ccl_cosmo,s,ctracers) :
theo={}
for t1i,t2i,ells,_ in s.sortTracers():
cls=ccl.angular_cl(ccl_cosmo,ctracers[t1i],ctracers[t2i],ells)
theo[(t1i,t2i)]=cls
theo[(t2i,t1i)]=cls
return theo
def get_power_spectrum(self, cosmo, nz1, nz2):
"""
Compute power spectrum between two redshift distributions
"""
t1 = ccl.WeakLensingTracer(cosmo, nz1)
t2 = ccl.WeakLensingTracer(cosmo, nz2)
return ccl.angular_cl(cosmo, t1, t2, self.ells)
def compute_cls(cosmo, tracers_info, ells, outdir):
# Get the Tracer instaces
print('Get tracer instances')
get_tracers_ccl(cosmo, tracers_info)
cls_ar = np.zeros((len(tracers_info['data_vectors']), ells.size))
# Get theory Cls
print('Computing theory Cls')
for i, dv in enumerate(tracers_info['data_vectors']):
tracer1 = next(x['tracer'] for x in tracers_info['maps']
if x['name'] == dv['tracers'][0])
tracer2 = next(x['tracer'] for x in tracers_info['maps']
if x['name'] == dv['tracers'][1])
cls = ccl.angular_cl(cosmo, tracer1, tracer2, ells)
# # Add multiplicative bias to WL
# type1 = next(x['type'] for x in tracers_info['maps'] if x['name']==dv['tracers'][0])
# type2 = next(x['type'] for x in tracers_info['maps'] if x['name']==dv['tracers'][1])
# if type1 == 'wl':
# bin = next(x['bin'] for x in tracers_info['maps'] if x['name']==dv['tracers'][0])
# m =
# cls = (1.+m)*cls
# if type2 == 'wl':
# bin = next(x['bin'] for x in tracers_info['maps'] if x['name']==dv['tracers'][1])
# m =
# cls = (1.+m)*cls
fname = os.path.join(outdir, 'cls_{}_{}.npz'.format(*dv['tracers']))
print('Saving {}'.format(fname))
np.savez_compressed(fname, cls=cls, ells=ells)
cls_ar[i] = cls
return cls_ar
def test_clfid_halomod(tr1, tr2):
data = get_config(dtype0=tr1, dtype1=tr2, inc_hm=True)
cosmo = ccl.Cosmology(**data['cov']['fiducial']['cosmo'])
md = ccl.halos.MassDef200m()
mf = ccl.halos.MassFuncTinker10(cosmo, mass_def=md)
hb = ccl.halos.HaloBiasTinker10(cosmo, mass_def=md)
cm = ccl.halos.ConcentrationDuffy08(mdef=md)
hmc = ccl.halos.HMCalculator(cosmo, mf, hb, md)
pNFW = ccl.halos.HaloProfileNFW(cm)
profs = {}
ccltr = {}
normed = {}
for tr, lab in [(tr1, 'Dummy__0'), (tr2, 'Dummy__1')]:
if tr == 'galaxy_density':
data['tracers'][lab]['hod_params'] = {'lMmin_0': 12.1,
'lM1_p': 0.1,
'bg_0': 1.2}
profs[tr] = ccl.halos.HaloProfileHOD(cm, lMmin_0=12.1,
lM1_p=0.1, bg_0=1.2)
z, nz = np.loadtxt('xcell/tests/data/DESY1gc_dndz_bin0.txt',
usecols=(1, 3), unpack=True)
ccltr[tr] = ccl.NumberCountsTracer(cosmo, False, dndz=(z, nz),
bias=(z, np.ones_like(z)))
normed[tr] = True
elif tr == 'cmb_tSZ':
data['tracers'][lab]['gnfw_params'] = {'mass_bias': 0.9}
profs[tr] = ccl.halos.HaloProfilePressureGNFW(mass_bias=0.9)
ccltr[tr] = ccl.tSZTracer(cosmo, z_max=3.)
normed[tr] = False
elif tr == 'galaxy_shear':
profs[tr] = pNFW
z, nz = np.loadtxt('xcell/tests/data/Nz_DIR_z0.1t0.3.asc',
usecols=(0, 1), unpack=True)
ccltr[tr] = ccl.WeakLensingTracer(cosmo, dndz=(z, nz))
normed[tr] = True
elif tr == 'cmb_convergence':
profs[tr] = pNFW
ccltr[tr] = ccl.CMBLensingTracer(cosmo, z_source=1100.)
normed[tr] = True
clf = ClFid(data, 'Dummy__0', 'Dummy__1')
d = clf.get_cl_file()
shutil.rmtree(tmpdir1)
k_arr = np.geomspace(1E-4, 1E2, 512)
a_arr = 1./(1+np.linspace(0, 3, 15)[::-1])
pk = ccl.halos.halomod_Pk2D(cosmo, hmc, profs[tr1],
prof2=profs[tr2],
normprof1=normed[tr1],
normprof2=normed[tr2],
lk_arr=np.log(k_arr),
a_arr=a_arr)
# Commented out until these features are pushed to the pip release of CCL
# smooth_transition=(lambda a: 0.7),
# supress_1h=(lambda a: 0.01))
clb = ccl.angular_cl(cosmo, ccltr[tr1], ccltr[tr2], d['ell'], p_of_k_a=pk)
assert np.all(np.fabs(clb[2:]/d['cl'][0][2:]-1) < 1E-4)
def _get_cl(self, t1, t2, ls, dchi, lnl):
return ccl.angular_cl(self.cosmo,
t1,
t2,
ls,
l_limber=lnl,
limber_integration_method='spline',
dchi_nonlimber=dchi)
def project_Cl(cosmo, tracer, Pk_a_s, ks, a_s, want_plot=False):
# number of redshifts
num_zs = Pk_a_s.shape[0]
# hubble parameter
h = cosmo._params_init_kwargs['h']
# change the order cause that's what CCL prefers
i_sort = np.argsort(a_s)
a_s = a_s[i_sort]
Pk_a_s = Pk_a_s[i_sort, :]
assert num_zs == len(
a_s), "Different number of input spectra and redshifts"
# wave numbers
ells = np.geomspace(2, 1000, 20)
'''
# simple power spectrum for testing
lpk_array = np.log(np.array([ccl.nonlin_matter_power(cosmo, ks*h, a) for a in a_s]))
cl_tt = ccl.angular_cl(cosmo, tracer, tracer, ells)
# generating fake data
Cl_err = cl_tt*np.sqrt(2./(2*ells+1.))
cov = np.diag(Cl_err**2)
np.save("data_power/cl_gg_z%4.3f.npy"%a2z(a_s[0]),cl_tt)
np.save("data_power/ells.npy",ells)
np.save("data_power/cov_cl_gg_z%4.3f.npy"%a2z(a_s[0]),cov)
'''
# Create a Pk2D object, giving log k in Mpc^-1 and pk_arr in Mpc^3
#lpk_array = np.log(Pk_a_s/h**3)
#pk_tmp = ccl.Pk2D(a_arr=a_s, lk_arr=np.log(ks*h), pk_arr=lpk_array, is_logp=True)
pk_tmp = ccl.Pk2D(a_arr=a_s,
lk_arr=np.log(ks * h),
pk_arr=Pk_a_s / h**3,
is_logp=False)
# Compute power spectra with and without cutoff
cl_tt_tmp = ccl.angular_cl(cosmo, tracer, tracer, ells, p_of_k_a=pk_tmp)
if want_plot:
# plot the power spectra
plt.plot(np.log(ks * h), lpk_array[-1, :], label="ccl")
plt.plot(np.log(ks * h), np.log(Pk_a_s[-1, :] / h**3), label="buba")
plt.legend()
plt.show()
# plot the angular power spectra
plt.plot(ells, 1E4 * cl_tt, 'r-', label='built-in tracer')
plt.plot(ells, 1E4 * cl_tt_tmp, 'k--', label='custom tracer')
plt.xscale('log')
plt.xlabel('$\\ell$', fontsize=14)
plt.ylabel('$10^4\\times C_\\ell$', fontsize=14)
plt.legend(loc='upper right', fontsize=12, frameon=False)
plt.savefig("figs/Cls.png")
plt.show()
return ells, cl_tt_tmp
def get_ccl_cl(self, ccl_tr1, ccl_tr2, ell):
cosmo = self.get_cosmo_ccl()
pk = self.get_ccl_pk(ccl_tr1, ccl_tr2)
return ccl.angular_cl(cosmo,
ccl_tr1['ccl_tr'],
ccl_tr2['ccl_tr'],
ell,
p_of_k_a=pk)
def get_prediction(self, dic_par):
theory_out = np.zeros((self.s.size(), ))
cosmo = self.get_cosmo(dic_par)
tr = self.get_tracers(cosmo, dic_par)
for i1, i2, ells, ndx in self.s.sortTracers():
cls = ccl.angular_cl(cosmo, tr[i1], tr[i2], ells)
theory_out[ndx] = cls
return theory_out
def test_cls_spline(set_up, t1, t2, bm, a1b1, a1b2, a2b1, a2b2, fl):
cosmo, trcs, lfc, bmk = set_up
cl = ccl.angular_cl(cosmo,
trcs[t1],
trcs[t2],
lfc['ells'],
limber_integration_method='spline') * lfc[fl]
el = np.sqrt((bmk[a1b1] * bmk[a2b2] + bmk[a1b2] * bmk[a2b1]) /
(2 * lfc['ells'] + 1.))
assert np.all(np.fabs(cl - bmk[bm]) < 0.2 * el)