def test_complex_apply(comm):
pm = ParticleMesh(BoxSize=8.0, Nmesh=[8, 8], comm=comm, dtype='f8')
complex = ComplexField(pm)
def filter(k, v):
return k[0] + k[1] * 1j
complex.apply(filter, out=Ellipsis)
for i, x, slab in zip(complex.slabs.i, complex.slabs.x, complex.slabs):
assert_array_equal(slab, x[0] + x[1] * 1j)
def test_complex_apply(comm):
pm = ParticleMesh(BoxSize=8.0, Nmesh=[8, 8], comm=comm, dtype='f8')
complex = ComplexField(pm)
def filter(k, v):
knormp = k.normp()
assert_allclose(knormp, sum(ki ** 2 for ki in k))
return k[0] + k[1] * 1j
complex.apply(filter, out=Ellipsis)
for i, x, slab in zip(complex.slabs.i, complex.slabs.x, complex.slabs):
assert_array_equal(slab, x[0] + x[1] * 1j)
def _compute_multipoles(self, kedges):
"""
Compute the window-convoled power spectrum multipoles, for a data set
with non-trivial survey geometry.
This estimator builds upon the work presented in Bianchi et al. 2015
and Scoccimarro et al. 2015, but differs in the implementation. This
class uses the spherical harmonic addition theorem such that
only :math:`2\ell+1` FFTs are required per multipole, rather than the
:math:`(\ell+1)(\ell+2)/2` FFTs in the implementation presented by
Bianchi et al. and Scoccimarro et al.
References
----------
* Bianchi, Davide et al., `Measuring line-of-sight-dependent Fourier-space clustering using FFTs`,
MNRAS, 2015
* Scoccimarro, Roman, `Fast estimators for redshift-space clustering`, Phys. Review D, 2015
"""
# clear compensation from the actions
for source in [self.first, self.second]:
source.actions[:] = []
source.compensated = False
assert len(source.actions) == 0
# compute the compensations
compensation = {}
for name, mesh in zip(['first', 'second'], [self.first, self.second]):
compensation[name] = get_compensation(mesh)
if self.comm.rank == 0:
if compensation[name] is not None:
args = (compensation[name]['func'].__name__, name)
self.logger.info(
"using compensation function %s for source '%s'" %
args)
else:
self.logger.warning(
"no compensation applied for source '%s'" % name)
rank = self.comm.rank
pm = self.first.pm
# setup the 1D-binning
muedges = numpy.linspace(-1, 1, 2, endpoint=True)
edges = [kedges, muedges]
# make a structured array to hold the results
cols = ['k'] + ['power_%d' % l
for l in sorted(self.attrs['poles'])] + ['modes']
dtype = ['f8'] + ['c8'] * len(self.attrs['poles']) + ['i8']
dtype = numpy.dtype(list(zip(cols, dtype)))
result = numpy.empty(len(kedges) - 1, dtype=dtype)
# offset the box coordinate mesh ([-BoxSize/2, BoxSize]) back to
# the original (x,y,z) coords
offset = self.attrs['BoxCenter'] + 0.5 * pm.BoxSize / pm.Nmesh
# always need to compute ell=0
poles = sorted(self.attrs['poles'])
if 0 not in poles:
poles = [0] + poles
assert poles[0] == 0
# spherical harmonic kernels (for ell > 0)
Ylms = [[get_real_Ylm(l, m) for m in range(-l, l + 1)]
for l in poles[1:]]
# paint the 1st FKP density field to the mesh (paints: data - alpha*randoms, essentially)
rfield1 = self.first.compute(Nmesh=self.attrs['Nmesh'])
meta1 = rfield1.attrs.copy()
if rank == 0:
self.logger.info("%s painting of 'first' done" %
self.first.resampler)
# store alpha: ratio of data to randoms
self.attrs['alpha'] = meta1['alpha']
# FFT 1st density field and apply the resampler transfer kernel
cfield = rfield1.r2c()
if compensation['first'] is not None:
cfield.apply(out=Ellipsis, **compensation['first'])
if rank == 0: self.logger.info('ell = 0 done; 1 r2c completed')
# monopole A0 is just the FFT of the FKP density field
# NOTE: this holds FFT of density field #1
volume = pm.BoxSize.prod()
A0_1 = ComplexField(pm)
A0_1[:] = cfield[:] * volume # normalize with a factor of volume
# paint second mesh too?
if self.first is not self.second:
# paint the second field
rfield2 = self.second.compute(Nmesh=self.attrs['Nmesh'])
meta2 = rfield2.attrs.copy()
if rank == 0:
self.logger.info("%s painting of 'second' done" %
self.second.resampler)
# need monopole of second field
if 0 in self.attrs['poles']:
# FFT density field and apply the resampler transfer kernel
A0_2 = rfield2.r2c()
A0_2[:] *= volume
if compensation['second'] is not None:
A0_2.apply(out=Ellipsis, **compensation['second'])
else:
rfield2 = rfield1
meta2 = meta1
# monopole of second field is first field
if 0 in self.attrs['poles']:
A0_2 = A0_1
# ensure alpha from first mesh is equal to alpha from second mesh
# NOTE: this is mostly just a sanity check, and should always be true if
# we made it this far already
if not numpy.allclose(
rfield1.attrs['alpha'], rfield2.attrs['alpha'], rtol=1e-3):
msg = (
"ConvolvedFFTPower cross-correlations currently require the same"
" FKPCatalog (data/randoms), such that only the weight column can vary;"
" different ``alpha`` values found for first/second meshes")
raise ValueError(msg)
# save the painted density field #2 for later
density2 = rfield2.copy()
# initialize the memory holding the Aell terms for
# higher multipoles (this holds sum of m for fixed ell)
# NOTE: this will hold FFTs of density field #2
Aell = ComplexField(pm)
# the real-space grid
xgrid = [
xx.astype('f8') + offset[ii]
for ii, xx in enumerate(density2.slabs.optx)
]
xnorm = numpy.sqrt(sum(xx**2 for xx in xgrid))
xgrid = [x / xnorm for x in xgrid]
# the Fourier-space grid
kgrid = [kk.astype('f8') for kk in cfield.slabs.optx]
knorm = numpy.sqrt(sum(kk**2 for kk in kgrid))
knorm[knorm == 0.] = numpy.inf
kgrid = [k / knorm for k in kgrid]
# proper normalization: same as equation 49 of Scoccimarro et al. 2015
for name in ['data', 'randoms']:
self.attrs[name + '.norm'] = self.normalization(
name, self.attrs['alpha'])
if self.attrs['randoms.norm'] > 0:
norm = 1.0 / self.attrs['randoms.norm']
# check normalization
Adata = self.attrs['data.norm']
Aran = self.attrs['randoms.norm']
if not numpy.allclose(Adata, Aran, rtol=0.05):
msg = "normalization in ConvolvedFFTPower different by more than 5%; "
msg += ",algorithm requires they must be similar\n"
msg += "\trandoms.norm = %.6f, data.norm = %.6f\n" % (Aran,
Adata)
msg += "\tpossible discrepancies could be related to normalization "
msg += "of n(z) column ('%s')\n" % self.first.nbar
msg += "\tor the consistency of the FKP weight column for 'data' "
msg += "and 'randoms';\n"
msg += "\tn(z) columns for 'data' and 'randoms' should be "
msg += "normalized to represent n(z) of the data catalog"
raise ValueError(msg)
if rank == 0:
self.logger.info(
"normalized power spectrum with `randoms.norm = %.6f`" %
Aran)
else:
# an empty random catalog is provides, so we will ignore the normalization.
norm = 1.0
if rank == 0:
self.logger.info(
"normalization of power spectrum is neglected, as no random is provided."
)
# loop over the higher order multipoles (ell > 0)
start = time.time()
for iell, ell in enumerate(poles[1:]):
# clear 2D workspace
Aell[:] = 0.
# iterate from m=-l to m=l and apply Ylm
substart = time.time()
for Ylm in Ylms[iell]:
# reset the real-space mesh to the original density #2
rfield2[:] = density2[:]
# apply the config-space Ylm
for islab, slab in enumerate(rfield2.slabs):
slab[:] *= Ylm(xgrid[0][islab], xgrid[1][islab],
xgrid[2][islab])
# real to complex of field #2
rfield2.r2c(out=cfield)
# apply the Fourier-space Ylm
for islab, slab in enumerate(cfield.slabs):
slab[:] *= Ylm(kgrid[0][islab], kgrid[1][islab],
kgrid[2][islab])
# add to the total sum
Aell[:] += cfield[:]
# and this contribution to the total sum
substop = time.time()
if rank == 0:
self.logger.debug("done term for Y(l=%d, m=%d) in %s" %
(Ylm.l, Ylm.m, timer(substart, substop)))
# apply the compensation transfer function
if compensation['second'] is not None:
Aell.apply(out=Ellipsis, **compensation['second'])
# factor of 4*pi from spherical harmonic addition theorem + volume factor
Aell[:] *= 4 * numpy.pi * volume
# log the total number of FFTs computed for each ell
if rank == 0:
args = (ell, len(Ylms[iell]))
self.logger.info('ell = %d done; %s r2c completed' % args)
# calculate the power spectrum multipoles, slab-by-slab to save memory
# NOTE: this computes (A0 of field #1) * (Aell of field #2).conj()
for islab in range(A0_1.shape[0]):
Aell[islab, ...] = norm * A0_1[islab] * Aell[islab].conj()
# project on to 1d k-basis (averaging over mu=[0,1])
proj_result, _ = project_to_basis(Aell, edges)
result['power_%d' % ell][:] = numpy.squeeze(proj_result[2])
# summarize how long it took
stop = time.time()
if rank == 0:
self.logger.info(
"higher order multipoles computed in elapsed time %s" %
timer(start, stop))
# also compute ell=0
if 0 in self.attrs['poles']:
# the 3D monopole
for islab in range(A0_1.shape[0]):
A0_1[islab, ...] = norm * A0_1[islab] * A0_2[islab].conj()
# the 1D monopole
proj_result, _ = project_to_basis(A0_1, edges)
result['power_0'][:] = numpy.squeeze(proj_result[2])
# save the number of modes and k
result['k'][:] = numpy.squeeze(proj_result[0])
result['modes'][:] = numpy.squeeze(proj_result[-1])
# compute shot noise
self.attrs['shotnoise'] = self.shotnoise(self.attrs['alpha'])
# copy over any painting meta data
if self.first is self.second:
copy_meta(self.attrs, meta1)
else:
copy_meta(self.attrs, meta1, prefix='first')
copy_meta(self.attrs, meta2, prefix='second')
return result
def _compute_multipoles(self):
"""
Compute the window-convoled power spectrum multipoles, for a data set
with non-trivial survey geometry.
This estimator builds upon the work presented in Bianchi et al. 2015
and Scoccimarro et al. 2015, but differs in the implementation. This
class uses the spherical harmonic addition theorem such that
only :math:`2\ell+1` FFTs are required per multipole, rather than the
:math:`(\ell+1)(\ell+2)/2` FFTs in the implementation presented by
Bianchi et al. and Scoccimarro et al.
References
----------
* Bianchi, Davide et al., `Measuring line-of-sight-dependent Fourier-space clustering using FFTs`,
MNRAS, 2015
* Scoccimarro, Roman, `Fast estimators for redshift-space clustering`, Phys. Review D, 2015
"""
# clear compensation from the actions
for source in [self.first, self.second]:
source.actions[:] = []; source.compensated = False
assert len(source.actions) == 0
# compute the compensations
compensation = {}
for name, mesh in zip(['first', 'second'], [self.first, self.second]):
compensation[name] = get_compensation(mesh)
if self.comm.rank == 0:
if compensation[name] is not None:
args = (compensation[name]['func'].__name__, name)
self.logger.info("using compensation function %s for source '%s'" % args)
else:
self.logger.warning("no compensation applied for source '%s'" % name)
rank = self.comm.rank
pm = self.first.pm
# setup the 1D-binning
muedges = numpy.linspace(0, 1, 2, endpoint=True)
edges = [self.edges, muedges]
# make a structured array to hold the results
cols = ['k'] + ['power_%d' %l for l in sorted(self.attrs['poles'])] + ['A_%d' %l for l in sorted(self.attrs['poles'])] + ['modes']
dtype = ['f8'] + ['c8']*len(self.attrs['poles'])*2 + ['i8']
dtype = numpy.dtype(list(zip(cols, dtype)))
result = numpy.empty(len(self.edges)-1, dtype=dtype)
# offset the box coordinate mesh ([-BoxSize/2, BoxSize]) back to
# the original (x,y,z) coords
offset = self.attrs['BoxCenter'] + 0.5*pm.BoxSize / pm.Nmesh
# always need to compute ell=0
poles = sorted(self.attrs['poles'])
if 0 not in poles:
poles = [0] + poles
assert poles[0] == 0
# spherical harmonic kernels (for ell > 0)
Ylms = [[get_real_Ylm(l,m) for m in range(-l, l+1)] for l in poles[1:]]
# paint the 1st FKP density field to the mesh (paints: data - alpha*randoms, essentially)
rfield1 = self.first.paint(Nmesh=self.attrs['Nmesh'])
vol_per_cell = (pm.BoxSize/pm.Nmesh).prod()/rfield1.attrs['num_per_cell'] #to compensate the default normalization by num_per_cell
rfield1[:] /= vol_per_cell
meta1 = rfield1.attrs.copy()
if rank == 0: self.logger.info("%s painting of 'first' done" %self.first.window)
# FFT 1st density field and apply the paintbrush window transfer kernel
cfield = rfield1.r2c()
if compensation['first'] is not None:
cfield.apply(out=Ellipsis, **compensation['first'])
if rank == 0: self.logger.info('ell = 0 done; 1 r2c completed')
# monopole A0 is just the FFT of the FKP density field
# NOTE: this holds FFT of density field #1
volume = pm.BoxSize.prod()
A0_1 = ComplexField(pm)
A0_1[:] = cfield[:] * volume # normalize with a factor of volume
# paint second mesh too?
if self.first is not self.second:
# paint the second field
rfield2 = self.second.paint(Nmesh=self.attrs['Nmesh'],normalize=False)
rfield2[:] /= vol_per_cell
meta2 = rfield2.attrs.copy()
if rank == 0: self.logger.info("%s painting of 'second' done" %self.second.window)
# need monopole of second field
if 0 in self.attrs['poles']:
# FFT density field and apply the paintbrush window transfer kernel
A0_2 = rfield2.r2c()
A0_2[:] *= volume
if compensation['second'] is not None: A0_2.apply(out=Ellipsis, **compensation['second'])
else:
rfield2 = rfield1
meta2 = meta1
# monopole of second field is first field
if 0 in self.attrs['poles']:
A0_2 = A0_1
# save the painted density field #2 for later
density2 = rfield2.copy()
# initialize the memory holding the Aell terms for
# higher multipoles (this holds sum of m for fixed ell)
# NOTE: this will hold FFTs of density field #2
Aell = ComplexField(pm)
# the real-space grid
xgrid = [xx.astype('f8') + offset[ii] for ii, xx in enumerate(density2.slabs.optx)]
xnorm = numpy.sqrt(sum(xx**2 for xx in xgrid))
xgrid = [x/xnorm for x in xgrid]
# the Fourier-space grid
kgrid = [kk.astype('f8') for kk in cfield.slabs.optx]
knorm = numpy.sqrt(sum(kk**2 for kk in kgrid)); knorm[knorm==0.] = numpy.inf
kgrid = [k/knorm for k in kgrid]
# loop over the higher order multipoles (ell > 0)
start = time.time()
for iell, ell in enumerate(poles[1:]):
# clear 2D workspace
Aell[:] = 0.
# iterate from m=-l to m=l and apply Ylm
substart = time.time()
for Ylm in Ylms[iell]:
# reset the real-space mesh to the original density #2
rfield2[:] = density2[:]
# apply the config-space Ylm
for islab, slab in enumerate(rfield2.slabs):
slab[:] *= Ylm(xgrid[0][islab], xgrid[1][islab], xgrid[2][islab])
# real to complex of field #2
rfield2.r2c(out=cfield)
# apply the Fourier-space Ylm
for islab, slab in enumerate(cfield.slabs):
slab[:] *= Ylm(kgrid[0][islab], kgrid[1][islab], kgrid[2][islab])
# add to the total sum
Aell[:] += cfield[:]
# and this contribution to the total sum
substop = time.time()
if rank == 0:
self.logger.debug("done term for Y(l=%d, m=%d) in %s" %(Ylm.l, Ylm.m, timer(substart, substop)))
# apply the compensation transfer function
if compensation['second'] is not None:
Aell.apply(out=Ellipsis, **compensation['second'])
# factor of 4*pi from spherical harmonic addition theorem + volume factor
Aell[:] *= 4*numpy.pi*volume
# log the total number of FFTs computed for each ell
if rank == 0:
args = (ell, len(Ylms[iell]))
self.logger.info('ell = %d done; %s r2c completed' %args)
# project on to 1d k-basis (averaging over mu=[0,1])
proj_result, _ = project_to_basis(Aell, edges)
result['A_%d' %ell][:] = numpy.squeeze(proj_result[2])
# calculate the power spectrum multipoles, slab-by-slab to save memory
# NOTE: this computes (A0 of field #1) * (Aell of field #2).conj()
for islab in range(A0_1.shape[0]):
Aell[islab,...] = A0_1[islab] * Aell[islab].conj()
# project on to 1d k-basis (averaging over mu=[0,1])
proj_result, _ = project_to_basis(Aell, edges)
result['power_%d' %ell][:] = numpy.squeeze(proj_result[2])
# summarize how long it took
stop = time.time()
if rank == 0:
self.logger.info("higher order multipoles computed in elapsed time %s" %timer(start, stop))
# also compute ell=0
if 0 in self.attrs['poles']:
# the 1D monopole
proj_result, _ = project_to_basis(A0_2, edges)
result['A_0'][:] = numpy.squeeze(proj_result[2])
# the 3D monopole
for islab in range(A0_1.shape[0]):
A0_1[islab,...] = A0_1[islab]*A0_2[islab].conj()
# the 1D monopole
proj_result, _ = project_to_basis(A0_1, edges)
result['power_0'][:] = numpy.squeeze(proj_result[2])
# save the number of modes and k
result['k'][:] = numpy.squeeze(proj_result[0])
result['modes'][:] = numpy.squeeze(proj_result[-1])
# copy over any painting meta data
if self.first is self.second:
copy_meta(self.attrs, meta1)
else:
copy_meta(self.attrs, meta1, prefix='first')
copy_meta(self.attrs, meta2, prefix='second')
return result