def compute_subcovmat(self, spins):
cw = nmt.NmtCovarianceWorkspace()
cw.compute_coupling_coefficients(
self.get_field(self.namap1, spins[0]),
self.get_field(self.namap2, spins[1]),
self.get_field(self.namap1, spins[2]),
self.get_field(self.namap2, spins[3]),
lmax=self.lmax,
)
a1b1, a1b2, a2b1, a2b2 = self.get_cov_input_spectra(spins)
ordering_a = self.ordering[(spins[0], spins[1])]
ordering_b = self.ordering[(spins[2], spins[3])]
covar = nmt.gaussian_covariance(
cw,
spins[0],
spins[1],
spins[2],
spins[3],
a1b1,
a1b2,
a2b1,
a2b2,
self.mc_12.workspace_dict[(spins[0], spins[1])],
wb=self.mc_12.workspace_dict[(spins[2], spins[3])],
).reshape(
[self.num_ell,
len(ordering_a), self.num_ell,
len(ordering_b)])
for i, AB in enumerate(ordering_a):
for j, CD in enumerate(ordering_b):
self.covmat[AB + CD] = covar[:, i, :, j]
def get_cov(self, cosmo, fields, cls):
cw = self.get_workspace(fields)
cla1b1 = self._search_cl(cls, self.tracers_1[0],
self.tracers_2[0]).get_cl_theory(
cosmo, fields, return_decoupled=False)
cla1b2 = self._search_cl(cls, self.tracers_1[0],
self.tracers_2[1]).get_cl_theory(
cosmo, fields, return_decoupled=False)
cla2b1 = self._search_cl(cls, self.tracers_1[1],
self.tracers_2[0]).get_cl_theory(
cosmo, fields, return_decoupled=False)
cla2b2 = self._search_cl(cls, self.tracers_1[1],
self.tracers_2[1]).get_cl_theory(
cosmo, fields, return_decoupled=False)
cla = self._search_cl(cls, self.tracers_1[0], self.tracers_1[1])
wa = cla.get_workspace(fields)
ncla = cla.ncls
nl = cla.nl
clb = self._search_cl(cls, self.tracers_2[0], self.tracers_2[1])
wb = clb.get_workspace(fields)
nclb = clb.ncls
cov = nmt.gaussian_covariance(cw, fields[self.tracers_1[0]].get_spin(),
fields[self.tracers_1[1]].get_spin(),
fields[self.tracers_2[0]].get_spin(),
fields[self.tracers_2[1]].get_spin(),
cla1b1, cla1b2, cla2b1, cla2b2, wa, wb)
cov = cov.reshape([nl, ncla, nl, nclb])
return cov
def get_covariance(self, typ1, typ2):
tttt = typ1 + typ2
if self.cov[tttt] is None:
fname = self.get_clfile_name(tttt, 'cov', 'npz')
if not os.path.isfile(fname):
t1, t2, t3, t4 = tttt
clt = {}
cwsp = self.get_covariance_workspace(typ1, typ2)
w1 = self.get_workspace(typ1)
w2 = self.get_workspace(typ2)
for tt in [t1 + t3, t1 + t4, t2 + t3, t2 + t4]:
clt[tt] = self.get_interpolated_cl(tt)
self.cov[tttt] = nmt.gaussian_covariance(cwsp,
0,
0,
0,
0,
clt[t1 + t3],
clt[t1 + t4],
clt[t2 + t3],
clt[t2 + t4],
w1,
wb=w2)
np.savez(fname, cov=self.cov[tttt])
else:
d = np.load(fname)
self.cov[tttt] = d['cov']
return self.cov[tttt]
def get_covariance_TE_TE(self, cl_te):
self.get_covariance_coeff()
w02 = self.w[2]
n_ell = len(cl_te)
cl_tt = np.zeros(n_ell)
cl_bb = np.zeros(n_ell)
cl_ee = np.zeros(n_ell)
cl_eb = np.zeros(n_ell)
cl_tb = np.zeros(n_ell)
covar_02_02 = nmt.gaussian_covariance(
self.cw,
0,
2,
0,
2, # Spins of the 4 fields
[cl_tt], # TT
[cl_te, cl_tb], # TE, TB
[cl_te, cl_tb], # ET, BT
[cl_ee, cl_eb, cl_eb, cl_bb], # EE, EB, BE, BB
w02,
wb=w02)
covar_02_02 = np.reshape(
covar_02_02, (len(self.ell_binned), 2, len(self.ell_binned), 2))
covar_TE_TE = covar_02_02[:, 0, :, 0]
# covar_TE_TB = covar_02_02[:, 0, :, 1]
# covar_TB_TE = covar_02_02[:, 1, :, 0]
# covar_TB_TB = covar_02_02[:, 1, :, 1]
return covar_TE_TE
def compute_covariance(w,clpred,binning,t1,t2,t3,t4,nz1,nz2,cw):
"""Routine to compute the covariance matrix using NaMaster
needs a NaMaster workspace w, the 4 tracers considered, and an array with the predicted cls
cl_t1t3, cl_t1t4, cl_t2t3, cl_t2t4.
"""
t1t3 = np.logical_and(binning.binar['T1']==min(t1,t3),binning.binar['T2']==max(t3,t1))
t1t4 = np.logical_and(binning.binar['T1']==min(t1,t4),binning.binar['T2']==max(t4,t1))
t2t3 = np.logical_and(binning.binar['T1']==min(t2,t3),binning.binar['T2']==max(t2,t3))
t2t4 = np.logical_and(binning.binar['T1']==min(t2,t4),binning.binar['T2']==max(t4,t2))
if t1==t3:
c13 = clpred[t1t3]+1./nz1
else:
c13 = clpred[t1t3]
if t1==t4:
c14 = clpred[t1t4]+1./nz1
else:
c14 = clpred[t1t4]
if t2==t3:
c23 = clpred[t2t3]+1./nz2
else:
c23 = clpred[t2t3]
if t2==t4:
c24 = clpred[t2t4]+1./nz2
else:
c24 = clpred[t2t4]
return nmt.gaussian_covariance(cw,c13,c14,c23,c24)
def test_workspace_covar_spin0():
# Compute all coefficients
cw1 = nmt.NmtCovarianceWorkspace()
cw1.compute_coupling_coefficients(CT.f0, CT.f2)
# Write to file
cw1.write_to("cwsp_test.fits")
# Only spin-0
cw2 = nmt.NmtCovarianceWorkspace()
cw2.compute_coupling_coefficients(CT.f0, CT.f2, spin0_only=True)
# Read only spin-0 from file
cw3 = nmt.NmtCovarianceWorkspace()
cw3.read_from("cwsp_test.fits", force_spin0_only=True)
# Spin-0 matrices
c1 = nmt.gaussian_covariance(cw1, 0, 0, 0, 0, [CT.cltt], [CT.cltt],
[CT.cltt], [CT.cltt], CT.w)
c2 = nmt.gaussian_covariance(cw2, 0, 0, 0, 0, [CT.cltt], [CT.cltt],
[CT.cltt], [CT.cltt], CT.w)
c3 = nmt.gaussian_covariance(cw3, 0, 0, 0, 0, [CT.cltt], [CT.cltt],
[CT.cltt], [CT.cltt], CT.w)
assert np.all(c1 == c2)
assert np.all(c1 == c3)
# Errors thrown otherwise
# This should be fine
c1 = nmt.gaussian_covariance(cw1,
0,
2,
0,
2, [CT.cltt], [CT.clte, 0 * CT.clte],
[CT.clte, 0 * CT.clte],
[CT.clee, 0 * CT.clee, 0 * CT.clee, CT.clbb],
CT.w02,
wb=CT.w02)
# These shouldn't
with pytest.raises(RuntimeError):
nmt.gaussian_covariance(cw2,
0,
2,
0,
2, [CT.cltt], [CT.clte, 0 * CT.clte],
[CT.clte, 0 * CT.clte],
[CT.clee, 0 * CT.clee, 0 * CT.clee, CT.clbb],
CT.w02,
wb=CT.w02)
with pytest.raises(RuntimeError):
nmt.gaussian_covariance(cw3,
0,
2,
0,
2, [CT.cltt], [CT.clte, 0 * CT.clte],
[CT.clte, 0 * CT.clte],
[CT.clee, 0 * CT.clee, 0 * CT.clee, CT.clbb],
CT.w02,
wb=CT.w02)
def test_workspace_covar_benchmark(self):
cw = nmt.NmtCovarianceWorkspace()
cw.compute_coupling_coefficients(self.w, self.w)
covar = nmt.gaussian_covariance(cw, self.cltt, self.cltt, self.cltt,
self.cltt)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov.txt",
unpack=True)
self.assertTrue(
(np.fabs(covar - covar_bench) <=
np.fmin(np.fabs(covar), np.fabs(covar_bench)) * 1E-5).all())
def test_workspace_covar_errors():
cw = nmt.NmtCovarianceWorkspace()
with pytest.raises(ValueError): # Write uninitialized
cw.write_to("wsp.fits")
cw.compute_coupling_coefficients(CT.f0, CT.f0) # All good
assert cw.wsp.lmax == CT.w.wsp.lmax
assert cw.wsp.lmax == CT.w.wsp.lmax
cw.read_from('test/benchmarks/bm_nc_np_cw00.fits') # Correct reading
assert cw.wsp.lmax == CT.w.wsp.lmax
assert cw.wsp.lmax == CT.w.wsp.lmax
# gaussian_covariance
with pytest.raises(ValueError): # Wrong input cl size
nmt.gaussian_covariance(cw, 0, 0, 0, 0, [CT.cltt], [CT.cltt],
[CT.cltt], [CT.cltt[:15]], CT.w)
with pytest.raises(ValueError): # Wrong input cl shapes
nmt.gaussian_covariance(cw, 0, 0, 0, 0, [CT.cltt], [CT.cltt],
[CT.cltt], [CT.cltt, CT.cltt], CT.w)
with pytest.raises(ValueError): # Wrong input spins
nmt.gaussian_covariance(cw, 0, 2, 0, 0, [CT.cltt], [CT.cltt],
[CT.cltt], [CT.cltt, CT.cltt], CT.w)
with pytest.raises(RuntimeError): # Incorrect reading
cw.read_from('none')
with pytest.raises(ValueError): # Incompatible resolutions
cw.compute_coupling_coefficients(CT.f0, CT.f0_half)
def test_workspace_covar_errors(self):
cw = nmt.NmtCovarianceWorkspace()
with self.assertRaises(ValueError): #Write uninitialized
cw.write_to("wsp.dat")
cw.compute_coupling_coefficients(self.w, self.w) #All good
self.assertEqual(cw.wsp.cs.n_eq, self.w.wsp.cs.n_eq)
self.assertEqual(cw.wsp.lmax_a, self.w.wsp.lmax)
self.assertEqual(cw.wsp.lmax_b, self.w.wsp.lmax)
with self.assertRaises(RuntimeError): #Write uninitialized
cw.write_to("tests/wsp.dat")
cw.read_from('test/benchmarks/bm_nc_np_cw00.dat') #Correct reading
self.assertEqual(cw.wsp.cs.n_eq, self.w.wsp.cs.n_eq)
self.assertEqual(cw.wsp.lmax_a, self.w.wsp.lmax)
self.assertEqual(cw.wsp.lmax_b, self.w.wsp.lmax)
#gaussian_covariance
with self.assertRaises(ValueError): #Wrong input power spectra
nmt.gaussian_covariance(cw, self.cltt, self.cltt, self.cltt,
self.cltt[:15])
with self.assertRaises(RuntimeError): #Incorrect reading
cw.read_from('none')
w2 = nmt.NmtWorkspace()
w2.read_from("test/benchmarks/bm_nc_np_w00.dat")
w2.wsp.cs.n_eq = self.w.wsp.cs.n_eq // 2
with self.assertRaises(ValueError): #Incompatible resolutions
cw.compute_coupling_coefficients(self.w, w2)
w2.wsp.cs.n_eq = self.w.wsp.cs.n_eq
w2.wsp.lmax = self.w.wsp.lmax // 2
with self.assertRaises(RuntimeError): #Incompatible resolutions
cw.compute_coupling_coefficients(self.w, w2)
w2.wsp.lmax = self.w.wsp.lmax
w2.read_from("test/benchmarks/bm_nc_np_w02.dat")
with self.assertRaises(ValueError): #Spin-2
cw.compute_coupling_coefficients(self.w, w2)
def test_workspace_covar_errors(self):
cw = nmt.NmtCovarianceWorkspace()
with self.assertRaises(ValueError): # Write uninitialized
cw.write_to("wsp.fits")
cw.compute_coupling_coefficients(self.f0, self.f0) # All good
self.assertEqual(cw.wsp.lmax, self.w.wsp.lmax)
self.assertEqual(cw.wsp.lmax, self.w.wsp.lmax)
with self.assertRaises(RuntimeError): # Write uninitialized
cw.write_to("tests/wsp.fits")
cw.read_from('test/benchmarks/bm_nc_np_cw00.fits') # Correct reading
self.assertEqual(cw.wsp.lmax, self.w.wsp.lmax)
self.assertEqual(cw.wsp.lmax, self.w.wsp.lmax)
# gaussian_covariance
with self.assertRaises(ValueError): # Wrong input cl size
nmt.gaussian_covariance(cw, 0, 0, 0, 0, [self.cltt], [self.cltt],
[self.cltt], [self.cltt[:15]], self.w)
with self.assertRaises(ValueError): # Wrong input cl shapes
nmt.gaussian_covariance(cw, 0, 0, 0, 0, [self.cltt], [self.cltt],
[self.cltt], [self.cltt, self.cltt],
self.w)
with self.assertRaises(ValueError): # Wrong input spins
nmt.gaussian_covariance(cw, 0, 2, 0, 0, [self.cltt], [self.cltt],
[self.cltt], [self.cltt, self.cltt],
self.w)
with self.assertRaises(RuntimeError): # Incorrect reading
cw.read_from('none')
with self.assertRaises(ValueError): # Incompatible resolutions
cw.compute_coupling_coefficients(self.f0, self.f0_half)
def get_covariance_TT_TT(self, cl_tt):
self.get_covariance_coeff()
w00 = self.w[0]
covar_00_00 = nmt.gaussian_covariance(self.cw,
0, 0, 0, 0, # Spins of the 4 fields
[cl_tt * 0], # TT
[cl_tt * 0], # TT
[cl_tt * 0], # TT
[cl_tt * 0], # TT
w00, wb=w00).reshape([len(self.ell_binned), 1,
len(self.ell_binned), 1])
covar_TT_TT = covar_00_00[:, 0, :, 0]
return covar_TT_TT
def get_covariance(self):
fname = os.path.join(
self.outdir, 'cov_{}_{}_{}_{}.npz'.format(self.trA1, self.trA2,
self.trB1, self.trB2))
if os.path.isfile(fname):
return np.load(fname)['cov']
self.load_cls()
wa1b1 = self.clA1B1.get_workspace()
wa1b2 = self.clA1B2.get_workspace()
wa2b1 = self.clA2B1.get_workspace()
wa2b2 = self.clA2B2.get_workspace()
# Couple Theory Cls
cla1b1 = wa1b1.couple_cell(self.clfid_A1B1.cl)
cla1b2 = wa1b2.couple_cell(self.clfid_A1B2.cl)
cla2b1 = wa2b1.couple_cell(self.clfid_A2B1.cl)
cla2b2 = wa2b2.couple_cell(self.clfid_A2B2.cl)
#####
nla1b1 = self.clA1B1.nl_cp
nla1b2 = self.clA1B2.nl_cp
nla2b1 = self.clA2B1.nl_cp
nla2b2 = self.clA2B2.nl_cp
#####
m_a1, m_b1 = self.clA1B1.get_masks()
m_a2, m_b2 = self.clA2B2.get_masks()
##### Weight the Cls
cla1b1 = (cla1b1 + nla1b1) / np.mean(m_a1 * m_b1)
cla1b2 = (cla1b2 + nla1b2) / np.mean(m_a1 * m_b2)
cla2b1 = (cla2b1 + nla2b1) / np.mean(m_a2 * m_b1)
cla2b2 = (cla2b2 + nla2b2) / np.mean(m_a2 * m_b2)
#####
wa = self.clA1A2.get_workspace()
wb = self.clB1B2.get_workspace()
cw = self.get_covariance_workspace()
s_a1, s_a2 = self.clA1A2.get_spins()
s_b1, s_b2 = self.clB1B2.get_spins()
cov = nmt.gaussian_covariance(cw, s_a1, s_a2, s_b1, s_b2, cla1b1,
cla1b2, cla2b1, cla2b2, wa, wb)
np.savez_compressed(fname, cov=cov)
return cov
def from_fields(Covariance,
field_a1,
field_a2,
field_b1,
field_b2,
wsp_a,
wsp_b,
cla1b1,
cla1b2,
cla2b1,
cla2b2,
cwsp=None):
"""Creator from a set of fields.
Args:
field_a1, field_a2 (:obj:`Field`): the two fields
contributing to the first power spectrum we want
the covariance of.
field_b1, field_b2 (:obj:`Field`): the two fields
contributing to the second power spectrum we want
the covariance of.
wsp_a, wsp_b (:obj:`NmtWorkspace`): mode-coupling matrix
for the two different power spectra.
cla1b1 (array): power spectrum between `field_a1` and
`field_b1`. Must be sampled at all multipoles between
0 and 3*nside-1.
cla1b2 (array): same as cla1b1 for field_a1 and field_b2.
cla2b1 (array): same as cla2b1 for field_a2 and field_b1.
cla2b2 (array): same as cla2b2 for field_a2 and field_b2.
cwsp (:obj:`NmtCovarianceWorkspace`): container for the
mode-coupling coefficients used to compute the
covariance matrix. If `None`, a new one will be
generated from the inputs.
"""
if cwsp is None: # Generate coupling coefficients if needed.
cwsp = nmt.NmtCovarianceWorskpace()
cwsp.compute_coupling_coefficients(field_a1.field, field_a2.field,
field_b1.field, field_b2.field)
# Compute covariance matrix
covar = nmt.gaussian_covariance(cwsp, 0, 0, 0, 0, [cla1b1], [cla1b2],
[cla2b1], [cla2b2], wsp_a, wsp_b)
return Covariance(field_a1.name, field_a2.name, field_b1.name,
field_b2.name, covar)
def compute_covariance_full_spin0(nmaps, nbins, maps_bins, maps_spins, w00):
cl_indices = []
cl_modes = []
cl_bins = []
for i in range(nmaps):
si = maps_modes[i]
for j in range(i, nmaps):
sj = maps_modes[j]
cl_indices.append([i, j])
cl_modes.append([si, sj])
cl_bins.append([maps_bins[i], maps_bins[j]])
cov_indices = []
cov_modes = []
cov_bins = []
for i, clij in enumerate(cl_indices):
for j, clkl in enumerate(cl_indices[i:]):
cov_indices.append(cl_indices[i] + cl_indices[i + j])
cov_modes.append(cl_modes[i] + cl_modes[i + j])
cov_bins.append(cl_bins[i] + cl_bins[i + j])
cov_indices = np.array(cov_indices)
cov_modes = np.array(cov_modes)
cov_bins = np.array(cov_bins)
for i, indices in enumerate(cov_indices):
fname = out_run_path + '_cov_c{}{}{}{}_{}{}{}{}.npz'.format(
*cov_modes[i], *cov_bins[i])
if os.path.isfile(fname):
continue
ibin_a1, ibin_a2, ibin_b1, ibin_b2 = indices
cla1b1 = [clTh[ibin_a1, ibin_b1]]
cla1b2 = [clTh[ibin_a1, ibin_b2]]
cla2b1 = [clTh[ibin_a2, ibin_b1]]
cla2b2 = [clTh[ibin_a2, ibin_b2]]
cov = nmt.gaussian_covariance(cw, 0, 0, 0, 0, cla1b1, cla1b2, cla2b1,
cla2b2, w00)
np.savez_compressed(fname, cov)
def gcov_make(fa1, fa2, fb1, fb2, wa, wb, cla1b1, cla1b2, cla2b1, cla2b2,
n_ell):
"""Returns the Gaussian covariance matrix fa1fa2_fb1fb2
"""
cw = nmt.NmtCovarianceWorkspace()
cw.compute_coupling_coefficients(fa1, fb1, fa2, fb2)
cov = nmt.gaussian_covariance(
cw,
2,
2,
2,
2, # Spins of the 4 fields
# EE, EB, BE, BB
cla1b1,
cla1b2,
cla2b1,
cla2b2,
wa,
wb=wb).reshape([n_ell, 4, n_ell, 4])
return cov
def get_covariance_BB_BB(self, cl_bb):
w22 = self.w[1]
n_ell = len(cl_bb)
cl_eb = np.zeros(n_ell)
cl_ee = np.zeros(n_ell)
covar_22_22 = nmt.gaussian_covariance(
self.cw,
2,
2,
2,
2, # Spins of the 4 fields
[cl_ee, cl_eb, cl_eb, cl_bb], # EE, EB, BE, BB
[cl_ee, cl_eb, cl_eb, cl_bb], # EE, EB, BE, BB
[cl_ee, cl_eb, cl_eb, cl_bb], # EE, EB, BE, BB
[cl_ee, cl_eb, cl_eb, cl_bb], # EE, EB, BE, BB
w22,
wb=w22)
covar_22_22 = np.reshape(
covar_22_22, (len(self.ell_binned), 4, len(self.ell_binned), 4))
# covar_EE_EE = covar_22_22[:, 0, :, 0]
# covar_EE_EB = covar_22_22[:, 0, :, 1]
# covar_EE_BE = covar_22_22[:, 0, :, 2]
# covar_EE_BB = covar_22_22[:, 0, :, 3]
# covar_EB_EE = covar_22_22[:, 1, :, 0]
# covar_EB_EB = covar_22_22[:, 1, :, 1]
# covar_EB_BE = covar_22_22[:, 1, :, 2]
# covar_EB_BB = covar_22_22[:, 1, :, 3]
# covar_BE_EE = covar_22_22[:, 2, :, 0]
# covar_BE_EB = covar_22_22[:, 2, :, 1]
# covar_BE_BE = covar_22_22[:, 2, :, 2]
# covar_BE_BB = covar_22_22[:, 2, :, 3]
# covar_BB_EE = covar_22_22[:, 3, :, 0]
# covar_BB_EB = covar_22_22[:, 3, :, 1]
# covar_BB_BE = covar_22_22[:, 3, :, 2]
covar_BB_BB = covar_22_22[:, 3, :, 3]
return covar_BB_BB
def set_covariance_matrices(self):
correlation_pairs = get_pairs(self.correlation_symbols, join_with='-')
for correlation_pair in tqdm(correlation_pairs,
desc='covariance matrices'):
a1 = correlation_pair[0]
a2 = correlation_pair[1]
b1 = correlation_pair[3]
b2 = correlation_pair[4]
covariance_workspace = nmt.NmtCovarianceWorkspace()
covariance_workspace.compute_coupling_coefficients(
self.fields[a1], self.fields[a2], self.fields[b1],
self.fields[b2])
self.covariance_matrices[
correlation_pair] = nmt.gaussian_covariance(
covariance_workspace,
0,
0,
0,
0,
[self.theory_correlations[''.join(sorted([a1, b1]))]],
[self.theory_correlations[''.join(sorted([a1, b2]))]],
[self.theory_correlations[''.join(sorted([a2, b1]))]],
[self.theory_correlations[''.join(sorted([a2, b2]))]],
wa=self.workspaces[a1 + a2],
wb=self.workspaces[b1 + b2],
)
transpose_corr_symbol = b1 + b2 + '-' + a1 + a2
self.covariance_matrices[transpose_corr_symbol] = np.transpose(
self.covariance_matrices[correlation_pair])
if a1 + a2 == b1 + b2:
self.correlation_matrices[
correlation_pair] = get_correlation_matrix(
self.covariance_matrices[correlation_pair])
def test_workspace_covar_benchmark(self):
def compare_covars(c, cb):
# Check first and second diagonals
for k in [0, 1]:
d = np.diag(c, k=k)
db = np.diag(cb, k=k)
self.assertTrue(
(np.fabs(d - db) <=
np.fmin(np.fabs(d), np.fabs(db)) * 1E-4).all())
# Check against a benchmark
cw = nmt.NmtCovarianceWorkspace()
cw.compute_coupling_coefficients(self.f0, self.f0)
# [0,0 ; 0,0]
covar = nmt.gaussian_covariance(cw, 0, 0, 0, 0, [self.cltt],
[self.cltt], [self.cltt], [self.cltt],
self.w)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov.txt",
unpack=True)
compare_covars(covar, covar_bench)
# [0,2 ; 0,2]
covar = nmt.gaussian_covariance(
cw,
0,
2,
0,
2, [self.cltt], [self.clte, 0 * self.clte],
[self.clte, 0 * self.clte],
[self.clee, 0 * self.clee, 0 * self.clee, self.clbb],
self.w02,
wb=self.w02)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov0202.txt")
compare_covars(covar, covar_bench)
# [0,0 ; 0,2]
covar = nmt.gaussian_covariance(cw,
0,
0,
0,
2, [self.cltt],
[self.clte, 0 * self.clte],
[self.cltt],
[self.clte, 0 * self.clte],
self.w,
wb=self.w02)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov0002.txt")
compare_covars(covar, covar_bench)
# [0,0 ; 2,2]
covar = nmt.gaussian_covariance(cw,
0,
0,
2,
2, [self.clte, 0 * self.clte],
[self.clte, 0 * self.clte],
[self.clte, 0 * self.clte],
[self.clte, 0 * self.clte],
self.w,
wb=self.w22)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov0022.txt")
compare_covars(covar, covar_bench)
# [2,2 ; 2,2]
covar = nmt.gaussian_covariance(
cw,
2,
2,
2,
2, [self.clee, 0 * self.clee, 0 * self.clee, self.clbb],
[self.clee, 0 * self.clee, 0 * self.clee, self.clbb],
[self.clee, 0 * self.clee, 0 * self.clee, self.clbb],
[self.clee, 0 * self.clee, 0 * self.clee, self.clbb],
self.w22,
wb=self.w22)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov2222.txt")
compare_covars(covar, covar_bench)
wa = nmt.NmtWorkspace()
wa.read_from(fname_mcm_a)
if (o.bin_a1 == o.bin_b1) and (o.bin_a2 == o.bin_b2):
wb = wa
else:
fname_mcm_b = predir + 'cls_metacal_mcm_bins_'
fname_mcm_b += '%d%d_ns%d.fits' % (o.bin_b1, o.bin_b2, o.nside)
wb = nmt.NmtWorkspace()
wb.read_from(fname_mcm_b)
nbpw = wa.wsp.bin.n_bands
printflush("Covariance")
cov = nmt.gaussian_covariance(cw, 2, 2, 2, 2,
clt['%d%d' % (o.bin_a1, o.bin_b1)],
clt['%d%d' % (o.bin_a1, o.bin_b2)],
clt['%d%d' % (o.bin_a2, o.bin_b1)],
clt['%d%d' % (o.bin_a2, o.bin_b2)],
wa, wb).reshape([nbpw, 4, nbpw, 4])
if o.full_noise:
name = '%d%d_%d%d' % (o.bin_a1, o.bin_a2, o.bin_b1, o.bin_b2)
cl_ones = np.array([cl1, cl0, cl0, cl1])
cl_zeros = np.array([cl0, cl0, cl0, cl0])
if o.bin_a1 == o.bin_b1:
cov += nmt.gaussian_covariance(cw_sn[name + '_10_10'], 2, 2, 2, 2,
cl_ones,
cl_zeros,
cl_zeros,
clt['%d%d' % (o.bin_a2, o.bin_b2)],
wa, wb).reshape([nbpw, 4, nbpw, 4])*pix_area
if o.bin_a2 == o.bin_b2:
cov += nmt.gaussian_covariance(cw_nn[name], 2, 2, 2, 2,
def compute_covariance_full(nmaps, nbins, maps_bins, maps_spins):
cl_indices = []
cl_spins = []
cl_bins = []
for i in range(nmaps):
si = maps_spins[i]
for j in range(i, nmaps):
sj = maps_spins[j]
cl_indices.append([i, j])
cl_spins.append([si, sj])
cl_bins.append([maps_bins[i], maps_bins[j]])
cov_indices = []
cov_spins = []
cov_bins = []
for i, clij in enumerate(cl_indices):
for j, clkl in enumerate(cl_indices[i:]):
cov_indices.append(cl_indices[i] + cl_indices[i + j])
cov_spins.append(cl_spins[i] + cl_spins[i + j])
cov_bins.append(cl_bins[i] + cl_bins[i + j])
cov_indices = np.array(cov_indices)
cov_spins = np.array(cov_spins)
cov_bins = np.array(cov_bins)
fname_cw_old = ''
for i, indices in enumerate(cov_indices):
s_a1, s_a2, s_b1, s_b2 = cov_spins[i]
na1 = get_nelems_spin(s_a1)
na2 = get_nelems_spin(s_a2)
nb1 = get_nelems_spin(s_b1)
nb2 = get_nelems_spin(s_b2)
bin_a1, bin_a2, bin_b1, bin_b2 = cov_bins[i]
fname = out_run_path + '_cov_c{}{}{}{}_{}{}{}{}.npz'.format(
*cov_spins[i], *cov_bins[i])
if os.path.isfile(fname):
continue
ibin_a1, ibin_a2, ibin_b1, ibin_b2 = indices
cla1b1 = [clTh[ibin_a1, ibin_b1]]
cla1b2 = [clTh[ibin_a1, ibin_b2]]
cla2b1 = [clTh[ibin_a2, ibin_b1]]
cla2b2 = [clTh[ibin_a2, ibin_b2]]
wa = get_workspace_from_spins_masks(0, 0, bin_a1, bin_a2)
wb = get_workspace_from_spins_masks(0, 0, bin_b1, bin_b2)
print('Computing ', fname)
print('spins: ', s_a1, s_a2, s_b1, s_b2)
print('cla1b1', (s_a1, s_b1), ibin_a1)
print('cla1b2', (s_a1, s_b2), ibin_a1)
print('cla2b1', (s_a2, s_b1), ibin_a2)
print('cla2b2', (s_a2, s_b2), ibin_a2)
fname_cw = out_run_path_NKA + '_cw{}{}{}{}.dat'.format(*cov_bins[i])
if fname_cw != fname_cw_old:
cw = nmt.NmtCovarianceWorkspace()
cw.read_from(fname_cw)
fname_cw_old = fname_cw
cov = nmt.gaussian_covariance(cw, 0, 0, 0, 0, cla1b1, cla1b2, cla2b1,
cla2b2, wa, wb)
np.savez_compressed(fname, cov)
if not os.path.isfile(prefix_out + "_cw2222.dat"): #spin0-spin2
print("Computing cw2222")
cw.compute_coupling_coefficients(f2, f2, f2, f2, n_iter=0)
cw.write_to(prefix_out + "_cw2222.dat")
else:
cw.read_from(prefix_out + '_cw2222.dat')
cla1b1 = cla2b2 = cla1b2 = cla2b1 = [(clee + nlee), cleb, clbe,
clbb + nlbb]
s_a1 = s_b1 = 2
s_a2 = s_b2 = 2
###
wa = wb = w22
C = nmt.gaussian_covariance(cw, int(s_a1), int(s_a2), int(s_b1), int(s_b2),
cla1b1, cla1b2, cla2b1, cla2b2, wa, wb)
fname = prefix_out + '_covTh.npz'
np.savez_compressed(fname, C)
#Generate theory prediction
if not os.path.isfile(prefix_out + '_cl_th.txt'):
print("Computing theory prediction")
cl00_th = w22.decouple_cell(
w22.couple_cell(np.array([clee, cleb, clbe, clbb])))
np.savetxt(prefix_out + "_cl_th.txt", np.transpose([lbpw, cl00_th[0]]))
#Compute mean and variance over nsims simulations
cl00_all = []
for i in np.arange(nsims):
#if i%100==0 :
print("%d-th sim" % (i + o.isim_ini))
[mp_t]), nmt.NmtField(window.data, [mp_q, mp_u])
b = nmt.NmtBin(nside, nlb=nlb)
lb = b.get_effective_ells()
w00 = nmt.NmtWorkspace()
w00.compute_coupling_matrix(f0, f0, b)
cl_00 = compute_master(f0, f0, w00)
n_ell = len(cl_00[0])
cw = nmt.NmtCovarianceWorkspace()
cw.compute_coupling_coefficients(f0, f0, f0, f0)
covar_00_00 = nmt.gaussian_covariance(cw,
0,
0,
0,
0, [cl_tt], [cl_tt], [cl_tt], [cl_tt],
w00,
wb=w00).reshape([n_ell, 1, n_ell, 1])
cov_namaster = covar_00_00[:, 0, :, 0]
corr_pspy = so_cov.cov2corr(cov_pspy)
plt.matshow(corr_pspy, vmin=-0.3, vmax=0.3)
plt.savefig("%s/corr_pspsy.png" % (test_dir))
plt.clf()
plt.close()
corr_namaster = so_cov.cov2corr(cov_namaster)
plt.matshow(corr_namaster, vmin=-0.3, vmax=0.3)
plt.savefig("%s/corr_namaster.png" % (test_dir))
b = nmt.NmtBin(nside_out, nlb=16)
leff = b.get_effective_ells()
lfull = np.arange(3 * nside_out)
#No contaminants
prefix = 'bm_nc_np'
f0 = nmt.NmtField(mask, [dl])
f2 = nmt.NmtField(mask, [dw_q, dw_u])
w00 = nmt.NmtWorkspace()
w00.compute_coupling_matrix(f0, f0, b)
cw00 = nmt.NmtCovarianceWorkspace()
cw00.compute_coupling_coefficients(w00, w00)
cw00.write_to(prefix + '_cw00.dat')
cov = nmt.gaussian_covariance(cw00, (cltt + nltt)[:3 * nside_out],
(cltt + nltt)[:3 * nside_out],
(cltt + nltt)[:3 * nside_out],
(cltt + nltt)[:3 * nside_out])
np.savetxt(prefix + "_cov.txt", cov)
clb00 = np.array([nltt[:3 * nside_out]])
c00 = w00.decouple_cell(nmt.compute_coupled_cell(f0, f0), cl_bias=clb00)
w00.write_to(prefix + '_w00.dat')
np.savetxt(prefix + "_c00.txt", np.transpose([leff, c00[0]]))
w02 = nmt.NmtWorkspace()
w02.compute_coupling_matrix(f0, f2, b)
clb02 = np.array([nlte[:3 * nside_out], 0 * nlte[:3 * nside_out]])
c02 = w02.decouple_cell(nmt.compute_coupled_cell(f0, f2), cl_bias=clb02)
w02.write_to(prefix + '_w02.dat')
np.savetxt(prefix + "_c02.txt", np.transpose([leff, c02[0], c02[1]]))
w22 = nmt.NmtWorkspace()
w22.compute_coupling_matrix(f2, f2, b)
clb22 = np.array([
cwsp = nmt.NmtCovarianceWorkspace()
path2cwsp = output + 'cw.fits'
if os.path.isfile(path2cwsp):
cwsp.read_from(path2cwsp)
else:
cwsp.compute_coupling_coefficients(f, f)
cwsp.write_to(path2cwsp)
# Clfid #
clfid = np.load(
f'/mnt/extraspace/gravityls_3/S8z/Cls_2/4096_asDavid/fiducial/DESgc_DESgc/cl_DESgc{ibin}_DESgc{ibin}.npz'
)['cl']
clfid_cp = wsp.couple_cell(clfid)
cla1b1 = cla1b2 = cla2b1 = cla2b2 = (clfid_cp + nl_cp) / np.mean(mask * mask)
cov = nmt.gaussian_covariance(cwsp,
0,
0,
0,
0,
cla1b1,
cla1b2,
cla2b1,
cla2b2,
wa=wsp,
wb=wsp)
np.savez_compressed(
output +
f'cov_DESgc{ibin}_DESgc{ibin}_DESgc{ibin}_DESgc{ibin}{corr_suffix}.npz',
cov)
#Let's generate one particular sample and its power spectrum.
print("Field")
f0=get_sample_field()
b=nmt.NmtBin(nside,nlb=20) #We will use 20 multipoles per bandpower.
print("Workspace")
w=nmt.NmtWorkspace()
w.compute_coupling_matrix(f0,f0,b)
cl_0=compute_master(f0,f0,w)[0]
#Let's now compute the Gaussian estimate of the covariance!
print("Covariance")
#First we generate a NmtCovarianceWorkspace object to precompute
#and store the necessary coupling coefficients
cw=nmt.NmtCovarianceWorkspace()
cw.compute_coupling_coefficients(w,w) #<- This is the time-consuming operation
covar=nmt.gaussian_covariance(cw,clarr,clarr,clarr,clarr)
#Let's now compute the sample covariance
print("Sample covariance")
nsamp=100
covar_sample=np.zeros([len(cl_0),len(cl_0)])
mean_sample=np.zeros(len(cl_0))
for i in np.arange(nsamp) :
print(i)
f=get_sample_field()
cl=compute_master(f,f,w)[0]
covar_sample+=cl[None,:]*cl[:,None]
mean_sample+=cl
mean_sample/=nsamp
covar_sample=covar_sample/nsamp-mean_sample[None,:]*mean_sample[:,None]
# G-G
prefix = predir + "maps_metacal_bin%d_ns%d" % (o.bin_number, o.nside)
msk = np.load(prefix + '_w.npz')['w']
fsky = np.sum(msk**2) / npix
cl_gg = w.couple_cell([sl, cl0, cl0, cl0]) / fsky + np.array(
[nl, cl0, cl0, nl])
# PSF-PSF
fname_apsf = predir + "cls_metacal_cls_bins_%d%d_ns%d_apsf.npz" % (
o.bin_number, o.bin_number, o.nside)
dpsf = np.load(fname_apsf)
cl_pp = dpsf['cls_coupled'] / fsky
# G-PSF
cl_gp = np.array([cl0, cl0, cl0, cl0])
printflush("CMCM")
fname_cmcm = predir + 'cls_metacal_cmcm_bins_'
fname_cmcm += '%d%d_%d%d_ns%d.fits' % (o.bin_number, o.bin_number,
o.bin_number, o.bin_number, o.nside)
cw = nmt.NmtCovarianceWorkspace()
cw.read_from(fname_cmcm)
printflush("Covariance")
nbpw = w.wsp.bin.n_bands
cov = nmt.gaussian_covariance(cw, 2, 2, 2, 2, cl_gg, cl_gp, cl_gp, cl_pp, w,
w).reshape([nbpw, 4, nbpw, 4])
printflush("Writing")
fname_cov = predir + 'cls_metacal_covar_xpsf_bin'
fname_cov += '%d_ns%d.npz' % (o.bin_number, o.nside)
np.savez(fname_cov, cov=cov)
cl00_cov += nls_gc['cls_raw'][3]
cl00_cov /= np.mean(mask_gc**2)
#
cl02_cov = w02.couple_cell([clte, cltb]) / np.mean(mask_gc * mask_wl)
#
cl22_cov = w22.couple_cell([clee, cleb, clbe, clbb])
cl22_cov += nls_wl['cls_raw'][1].reshape(cl22_cov.shape)
cl22_cov /= np.mean(mask_wl**2)
#####
covar_00_00 = nmt.gaussian_covariance(
cw00_00,
0,
0,
0,
0, # Spins of the 4 fields
cl00_cov, # TT
cl00_cov, # TT
cl00_cov, # TT
cl00_cov, # TT
w00,
wb=w00).reshape([lbpw.size, 1, lbpw.size, 1])
covar_00_02 = nmt.gaussian_covariance(
cw00_02,
0,
0,
0,
2, # Spins of the 4 fields
cl00_cov, # TT
cl02_cov, # TE, TB
cl00_cov, # TT
# Let's now compute the Gaussian estimate of the covariance!
print("Covariance")
# First we generate a NmtCovarianceWorkspace object to precompute
# and store the necessary coupling coefficients
# This is the time-consuming operation
# Note that you only need to do this once,
# regardless of spin
cw = nmt.NmtCovarianceWorkspace()
cw.compute_coupling_coefficients(f0_1, f0_2, f0_1, f0_2)
covar_00_00 = nmt.gaussian_covariance(
cw,
0,
0,
0,
0, # Spins of the 4 fields
[cl_tt + nl_tt], # TT
[cl_tt], # TT
[cl_tt], # TT
[cl_tt + nl_tt], # TT
w00,
wb=w00,
coupled=True).reshape([n_ell, 1, n_ell, 1])
covar_TT_TT = covar_00_00[:, 0, :, 0]
np.save("covar_TT_TT", covar_TT_TT)
cw = nmt.NmtCovarianceWorkspace()
cw.compute_coupling_coefficients(f0_1, f0_2, f0_1, f2_2)
covar_00_02 = nmt.gaussian_covariance(
cw,
0,
0,
wt = nmt.NmtWorkspace()
wt.compute_coupling_matrix(f0,
f0,
b,
l_toeplitz=nside,
l_exact=nside // 2,
dl_band=40)
c_tpltz = wt.get_coupling_matrix() / (2 * ls[None, :] + 1.)
cl_tpltz = wt.decouple_cell(nmt.compute_coupled_cell(f0, f0))
# You can also use the Toeplitz approximation to compute the
# Gaussian covariance matrix. Let's try that here:
# First, the exact calculation
cwe = nmt.NmtCovarianceWorkspace()
cwe.compute_coupling_coefficients(f0, f0)
cov_exact = nmt.gaussian_covariance(cwe, 0, 0, 0, 0, [cl_theory], [cl_theory],
[cl_theory], [cl_theory], we)
# Now using the Toeplitz approximation:
cwt = nmt.NmtCovarianceWorkspace()
cwt.compute_coupling_coefficients(f0,
f0,
l_toeplitz=nside,
l_exact=nside // 2,
dl_band=40)
cov_tpltz = nmt.gaussian_covariance(cwt, 0, 0, 0, 0, [cl_theory], [cl_theory],
[cl_theory], [cl_theory], wt)
# Let's compare the mode-coupling matrices themselves:
fig, (ax1, ax2, ax3) = plt.subplots(ncols=3, figsize=(14, 4))
ax1.set_title(r'Exact MCM ($\log_{10}$)')
ax1.imshow(np.log10(np.fabs(c_exact)), vmax=-1, vmin=-14)
ax1.set_xlabel(r'$\ell_1$', fontsize=15)
def test_workspace_covar_benchmark():
def compare_covars(c, cb):
# Check first and second diagonals
for k in [0, 1]:
d = np.diag(c, k=k)
db = np.diag(cb, k=k)
assert (np.fabs(d - db) <=
np.fmin(np.fabs(d), np.fabs(db)) * 1E-4).all()
# Check against a benchmark
cw = nmt.NmtCovarianceWorkspace()
cw.compute_coupling_coefficients(CT.f0, CT.f0)
# [0,0 ; 0,0]
covar = nmt.gaussian_covariance(cw, 0, 0, 0, 0, [CT.cltt], [CT.cltt],
[CT.cltt], [CT.cltt], CT.w)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov.txt", unpack=True)
compare_covars(covar, covar_bench)
# Check coupled
covar_rc = nmt.gaussian_covariance(cw,
0,
0,
0,
0, [CT.cltt], [CT.cltt], [CT.cltt],
[CT.cltt],
CT.w,
coupled=True) # [nl, nl]
covar_c = np.array([CT.w.decouple_cell([row])[0]
for row in covar_rc]) # [nl, nbpw]
covar = np.array([CT.w.decouple_cell([col])[0]
for col in covar_c.T]).T # [nbpw, nbpw]
compare_covars(covar, covar_bench)
# [0,2 ; 0,2]
covar = nmt.gaussian_covariance(
cw,
0,
2,
0,
2, [CT.cltt], [CT.clte, 0 * CT.clte], [CT.clte, 0 * CT.clte],
[CT.clee, 0 * CT.clee, 0 * CT.clee, CT.clbb],
CT.w02,
wb=CT.w02)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov0202.txt")
compare_covars(covar, covar_bench)
# [0,0 ; 0,2]
covar = nmt.gaussian_covariance(cw,
0,
0,
0,
2, [CT.cltt], [CT.clte, 0 * CT.clte],
[CT.cltt], [CT.clte, 0 * CT.clte],
CT.w,
wb=CT.w02)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov0002.txt")
compare_covars(covar, covar_bench)
# [0,0 ; 2,2]
covar = nmt.gaussian_covariance(cw,
0,
0,
2,
2, [CT.clte, 0 * CT.clte],
[CT.clte, 0 * CT.clte],
[CT.clte, 0 * CT.clte],
[CT.clte, 0 * CT.clte],
CT.w,
wb=CT.w22)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov0022.txt")
compare_covars(covar, covar_bench)
# [2,2 ; 2,2]
covar = nmt.gaussian_covariance(
cw,
2,
2,
2,
2, [CT.clee, 0 * CT.clee, 0 * CT.clee, CT.clbb],
[CT.clee, 0 * CT.clee, 0 * CT.clee, CT.clbb],
[CT.clee, 0 * CT.clee, 0 * CT.clee, CT.clbb],
[CT.clee, 0 * CT.clee, 0 * CT.clee, CT.clbb],
CT.w22,
wb=CT.w22)
covar_bench = np.loadtxt("test/benchmarks/bm_nc_np_cov2222.txt")
compare_covars(covar, covar_bench)
# wl1 - wl1
fname = '/mnt/extraspace/gravityls_3/S8z/Cls/fiducial/nobaryons/cls_DESwl{}_DESwl{}.npz'.format(
i, i)
clwlwl_ee = np.load(fname)['cls'][:3 * nside]
fname = os.path.join(output_folder,
'des_sh_{}_noise_ns{}.npz'.format(wltype, nside))
nls = np.load(fname)
cla2b2 = np.array(
[clwlwl_ee, 0 * clwlwl_ee, 0 * clwlwl_ee, 0 * clwlwl_ee])
cla2b2 = ws.couple_cell(cla2b2)
cla2b2 += nls['cls_raw'][i].reshape(cla2b2.shape)
cla2b2 /= np.mean(masks_gwl[i]**2)
covar = nmt.gaussian_covariance(
cw,
2,
2,
2,
2, # Spins of the 4 fields
cla1b1, # PP -> EE, EB, BE, BB
cla1b2, # Pe -> EE, EB, BE, BB
cla2b1, # eP -> EE, EB, BE, BB
cla2b2, # ee -> EE, EB, BE, BB
ws,
wb=ws).reshape([lbpw.size, 4, lbpw.size, 4])
covar_ar.append(covar)
np.savez(fname_cov, l=lbpw, cov=covar_ar)