def build_observations(Mr=21, b_normal=0.25, make=['data', 'covariance']):
''' Wrapper to build all the required fake observations and their
corresponding covariance matrices.
'''
# download the Multidark halo catalog if necessary
try:
halocat = CachedHaloCatalog(simname='multidark',
halo_finder='rockstar',
redshift=0.0)
except InvalidCacheLogEntry:
from halotools.sim_manager import DownloadManager
dman = DownloadManager()
dman.download_processed_halo_table('multidark', 'rockstar', 0.0)
if 'data' in make:
# xi, nbar, gmf
build_xi_bins(Mr=Mr)
print 'Building randoms and RRs for the subvolumes'
build_randoms_RR(Nr=5e5, box='md_sub')
print 'Building nbar, xi(r), GMF data vector... '
build_nbar_xi_gmf(Mr=Mr, b_normal=b_normal)
if 'covariance' in make:
print 'Computing covariance matrix of data...'
print 'building the sample covariance'
build_MCMC_cov_nbar_xi_gmf(Mr=Mr, b_normal=b_normal)
print 'building the poisson covariance'
build_ABC_cov_nbar_xi_gmf(Mr=Mr, b_normal=b_normal)
return None
def build_observations(Mr=21, b_normal=0.25, make=['data', 'covariance']):
''' Wrapper to build all the required fake observations and their
corresponding covariance matrices.
'''
# download the Multidark halo catalog if necessary
try:
halocat = CachedHaloCatalog(simname='multidark',
halo_finder='rockstar',
redshift=0.0)
except InvalidCacheLogEntry:
from halotools.sim_manager import DownloadManager
dman = DownloadManager()
dman.download_processed_halo_table('multidark', 'rockstar', 0.0)
if 'data' in make:
# xi, nbar, gmf
build_xi_bins(Mr=Mr)
print 'Building randoms and RRs for the subvolumes'
build_randoms_RR(Nr=5e5, box='md_sub')
print 'Building nbar, xi(r), GMF data vector... '
build_nbar_xi_gmf(Mr=Mr, b_normal=b_normal)
if 'covariance' in make:
print 'Computing covariance matrix of data...'
print 'building the sample covariance'
build_MCMC_cov_nbar_xi_gmf(Mr=Mr, b_normal=b_normal)
print 'building the poisson covariance'
build_ABC_cov_nbar_xi_gmf(Mr=Mr, b_normal=b_normal)
return None
ptcl_version_name = sim_defaults.default_ptcl_version_name
if args.ptcls_only is True:
download_halos = False
else:
download_halos = True
if args.halos_only is True:
download_ptcls = False
else:
download_ptcls = True
# Done parsing inputs
downman = DownloadManager()
##################################################################
# First check to see if the log has any matching entries before
# requesting the download
# This is technically redundant with the functionality in the downloading methods,
# but this makes it easier to issue the right error message
if args.overwrite == False:
if download_halos == True:
gen = downman.halo_table_cache.matching_log_entry_generator
matching_halocats = list(
gen(simname = simname, halo_finder = halo_finder,
version_name = version_name, redshift = redshift, dz_tol = 0.1))
def __init__(self, simname, halo_finder, redshift, comm=None):
from halotools.sim_manager import CachedHaloCatalog, DownloadManager
from halotools.sim_manager.supported_sims import supported_sim_dict
# do seme setup
self.comm = comm
meta_cols = ['Lbox', 'redshift', 'particle_mass']
# try to automatically load from the Halotools cache
exception = None
if self.comm.rank == 0:
kws = {'simname':simname, 'halo_finder':halo_finder, 'redshift':redshift}
try:
cached_halos = CachedHaloCatalog(dz_tol=0.1, **kws)
fname = cached_halos.fname # the filename to load
meta = {k:getattr(cached_halos, k) for k in meta_cols}
except Exception as e:
# try to download on the root rank
try:
# download
dl = DownloadManager()
dl.download_processed_halo_table(dz_tol=0.1, **kws)
# access the cached halo catalog and get fname attribute
# NOTE: this does not read the data
cached_halos = CachedHaloCatalog(dz_tol=0.1, **kws)
fname = cached_halos.fname
meta = {k:getattr(cached_halos, k) for k in meta_cols}
except Exception as e:
exception = e
else:
fname = None
meta = None
# re-raise a download error on all ranks if it occurred
exception = self.comm.bcast(exception, root=0)
if exception is not None:
raise exception
# broadcast the file we are loading
fname = self.comm.bcast(fname, root=0)
meta = self.comm.bcast(meta, root=0)
# initialize an HDF catalog and add Position/Velocity
cat = HDFCatalog(fname, comm=comm)
cat['Position'] = transform.StackColumns(cat['halo_x'], cat['halo_y'], cat['halo_z'])
cat['Velocity'] = transform.StackColumns(cat['halo_vx'], cat['halo_vy'], cat['halo_vz'])
# get the cosmology from Halotools
cosmo = supported_sim_dict[simname]().cosmology # this is astropy cosmology
cosmo = Cosmology.from_astropy(cosmo)
# initialize the HaloCatalog
HaloCatalog.__init__(self, cat, cosmo, meta['redshift'], mdef='vir', mass='halo_mvir')
# add some meta-data
# NOTE: all Halotools catalogs have to these attributes
self.attrs['BoxSize'] = meta['Lbox']
self.attrs['redshift'] = meta['redshift']
self.attrs['particle_mass'] = meta['particle_mass']
# save the cosmology
self.cosmo = cosmo
self.attrs['cosmo'] = dict(self.cosmo)
def __init__(self, simname, halo_finder, redshift, comm=None):
from halotools.sim_manager import CachedHaloCatalog, DownloadManager
from halotools.sim_manager.supported_sims import supported_sim_dict
# do seme setup
self.comm = comm
meta_cols = ['Lbox', 'redshift', 'particle_mass']
# try to automatically load from the Halotools cache
exception = None
if self.comm.rank == 0:
kws = {
'simname': simname,
'halo_finder': halo_finder,
'redshift': redshift
}
try:
cached_halos = CachedHaloCatalog(dz_tol=0.1, **kws)
fname = cached_halos.fname # the filename to load
meta = {k: getattr(cached_halos, k) for k in meta_cols}
except Exception as e:
# try to download on the root rank
try:
# download
dl = DownloadManager()
dl.download_processed_halo_table(dz_tol=0.1, **kws)
# access the cached halo catalog and get fname attribute
# NOTE: this does not read the data
cached_halos = CachedHaloCatalog(dz_tol=0.1, **kws)
fname = cached_halos.fname
meta = {k: getattr(cached_halos, k) for k in meta_cols}
except Exception as e:
exception = e
else:
fname = None
meta = None
# re-raise a download error on all ranks if it occurred
exception = self.comm.bcast(exception, root=0)
if exception is not None:
raise exception
# broadcast the file we are loading
fname = self.comm.bcast(fname, root=0)
meta = self.comm.bcast(meta, root=0)
# initialize an HDF catalog and add Position/Velocity
cat = HDFCatalog(fname, comm=comm)
cat['Position'] = transform.StackColumns(cat['halo_x'], cat['halo_y'],
cat['halo_z'])
cat['Velocity'] = transform.StackColumns(cat['halo_vx'],
cat['halo_vy'],
cat['halo_vz'])
# get the cosmology from Halotools
cosmo = supported_sim_dict[simname](
).cosmology # this is astropy cosmology
cosmo = Cosmology.from_astropy(cosmo)
# initialize the HaloCatalog
HaloCatalog.__init__(self,
cat,
cosmo,
meta['redshift'],
mdef='vir',
mass='halo_mvir')
# add some meta-data
# NOTE: all Halotools catalogs have to these attributes
self.attrs['BoxSize'] = meta['Lbox']
self.attrs['redshift'] = meta['redshift']
self.attrs['particle_mass'] = meta['particle_mass']
# save the cosmology
self.cosmo = cosmo
self.attrs['cosmo'] = dict(self.cosmo)
