def main(argv):
if len(sys.argv)!=2:
print("usage : %s lkl_file")
sys.exit(1)
if clik.try_lensing(argv[1]):
main_lensing(argv)
return
main_CMB(argv)
def main(argv):
if clik.try_lensing(argv[1]):
main_lensing(argv)
return
main_CMB(argv)
def initialize(self):
if "2015" in self.name:
for line in _deprecation_msg_2015.split("\n"):
self.log.warning(line)
code_path = common_path
data_path = get_data_path(self.__class__.get_module_name())
if self.path:
has_clik = False
else:
try:
import clik
has_clik = True
except ImportError:
has_clik = False
if not has_clik:
if not self.path:
if self.path_install:
self.path_clik = os.path.join(self.path_install, "code",
code_path)
else:
raise LoggedError(
self.log,
"No path given to the Planck likelihood. Set the "
"likelihood property 'path' or the common property "
"'%s'.", _path_install)
else:
self.path_clik = self.path
self.log.info("Importing clik from %s", self.path_clik)
# test and import clik
is_installed_clik(self.path_clik,
log_and_fail=True,
import_it=False)
import clik
# Loading the likelihood data
if not os.path.isabs(self.clik_file):
self.path_data = getattr(
self, "path_data",
os.path.join(self.path or self.path_install, "data",
data_path))
self.clik_file = os.path.join(self.path_data, self.clik_file)
# Differences in the wrapper for lensing and non-lensing likes
self.lensing = clik.try_lensing(self.clik_file)
try:
self.clik = (clik.clik_lensing(self.clik_file)
if self.lensing else clik.clik(self.clik_file))
except clik.lkl.CError:
# Is it that the file was not found?
if not os.path.exists(self.clik_file):
raise LoggedError(
self.log,
"The .clik file was not found where specified in the "
"'clik_file' field of the settings of this likelihood. Maybe the "
"'path' given is not correct? The full path where the .clik file was "
"searched for is '%s'", self.clik_file)
# Else: unknown clik error
self.log.error(
"An unexpected error occurred in clik (possibly related to "
"multiple simultaneous initialization, or simultaneous "
"initialization of incompatible likelihoods (e.g. polarised "
"vs non-polarised 'lite' likelihoods. See error info below:")
raise
# Check that the parameters are the right ones
self.expected_params = list(self.clik.extra_parameter_names)
differences = are_different_params_lists(self.input_params,
self.expected_params,
name_A="given",
name_B="expected")
if differences:
raise LoggedError(
self.log, "Configuration error in parameters: %r. "
"If this has happened without you fiddling with the defaults, "
"please open an issue in GitHub.", differences)
# Placeholder for vector passed to clik
self.l_maxs = self.clik.get_lmax()
length = (len(self.l_maxs)
if self.lensing else len(self.clik.get_has_cl()))
self.vector = np.zeros(
np.sum(self.l_maxs) + length + len(self.expected_params))
def initialize(self):
if "2015" in self.get_name():
for line in _deprecation_msg_2015.split("\n"):
self.log.warning(line)
code_path = common_path
data_path = get_data_path(self.__class__.get_qualified_class_name())
if self.path:
has_clik = False
else:
try:
import clik
has_clik = True
except ImportError:
clik = None
has_clik = False
if not has_clik:
if not self.path:
if self.packages_path:
self.path_clik = os.path.join(self.packages_path, "code", code_path)
else:
raise LoggedError(
self.log, "No path given to the Planck likelihood. Set the "
"likelihood property 'path' or the common property "
"'%s'.", _packages_path)
else:
self.path_clik = self.path
self.log.info("Importing clik from %s", self.path_clik)
# test and import clik
is_installed_clik(self.path_clik, log_and_fail=True, import_it=False)
import clik
# Loading the likelihood data
if not os.path.isabs(self.clik_file):
self.path_data = getattr(self, "path_data", os.path.join(
self.path or self.packages_path, "data", data_path))
self.clik_file = os.path.join(self.path_data, self.clik_file)
# Differences in the wrapper for lensing and non-lensing likes
self.lensing = clik.try_lensing(self.clik_file)
try:
self.clik = clik.clik_lensing(self.clik_file) if self.lensing \
else clik.clik(self.clik_file)
except clik.lkl.CError:
# Is it that the file was not found?
if not os.path.exists(self.clik_file):
raise LoggedError(
self.log, "The .clik file was not found where specified in the "
"'clik_file' field of the settings of this likelihood. "
"Maybe the 'path' given is not correct? The full path where"
" the .clik file was searched for is '%s'", self.clik_file)
# Else: unknown clik error
self.log.error("An unexpected error occurred in clik (possibly related to "
"multiple simultaneous initialization, or simultaneous "
"initialization of incompatible likelihoods (e.g. polarised "
"vs non-polarised 'lite' likelihoods. See error info below:")
raise
self.l_maxs = self.clik.get_lmax()
# calculate requirements here so class can also be separately instantiated
requested_cls = ["tt", "ee", "bb", "te", "tb", "eb"]
if self.lensing:
has_cl = [lmax != -1 for lmax in self.l_maxs]
requested_cls = ["pp"] + requested_cls
else:
has_cl = self.clik.get_has_cl()
self.requested_cls = [cl for cl, i in zip(requested_cls, has_cl) if int(i)]
self.l_maxs_cls = [lmax for lmax, i in zip(self.l_maxs, has_cl) if int(i)]
self.expected_params = list(self.clik.extra_parameter_names)
# Placeholder for vector passed to clik
length = (len(self.l_maxs) if self.lensing else len(self.clik.get_has_cl()))
self.vector = np.zeros(np.sum(self.l_maxs) + length + len(self.expected_params))
def main(argv):
if len(sys.argv) < 4:
print(
"usage : %s lkl_file_1 lkl_file_2 [lkl_file_3 ...] result_lkl_file"
)
sys.exit(1)
for fl in sys.argv[1:-1]:
if clik.try_lensing(fl):
print("clik_join doesn't work yet with lensing likelihood, sorry")
sys.exit(1)
lkls = [hpy.File(ll)["clik"] for ll in sys.argv[1:-1]]
reslkl = hpy.File(sys.argv[-1], "w", ty=lkls[0])
nlkl = 0
lmax = -nm.ones(6, dtype=nm.int)
resclik = reslkl.create_group("clik")
name = []
loc = []
defn = []
defloc = []
var = nm.zeros((0, 0))
for lklin in lkls:
if "prior" in lklin:
prid = lklin["prior"]
pname = [n.strip() for n in prid.attrs["name"].split('\0') if n]
for n in name:
if n in pname:
raise Exception("already got a prior on %s" % n)
ploc = prid["loc"][:]
pvar = prid["var"][:]
if len(pvar) == len(ploc):
pvar = nm.diag(pvar)
pvar.shape = (len(ploc), -1)
nvar = nm.zeros((len(loc) + len(ploc), len(loc) + len(ploc)))
nvar[:len(loc), :len(loc)] = var
nvar[len(loc):, len(loc):] = pvar
var = nvar
name = list(name) + list(pname)
loc = nm.concatenate((loc, ploc))
lmaxin = lklin.attrs["lmax"]
lmax = nm.max((lmax, lmaxin), 0)
nlklin = lklin.attrs["n_lkl_object"]
for i in range(nlklin):
grpin = "lkl_%d" % i
grpout = "lkl_%d" % nlkl
nlkl += 1
lklin.copy(lklin[grpin], resclik, grpout)
if "default" in lklin:
prid = lklin["default"]
pname = [n.strip() for n in prid.attrs["name"].split('\0') if n]
ploc = prid["loc"][:]
for i, n in enumerate(pname):
l = ploc[i]
add = True
for ii, nn in enumerate(defn):
if n == nn:
if l != defloc[ii]:
raise Exception(
"cannot fix the same parameter with different values"
)
add = False
break
if add:
defn += [n]
defloc += [l]
if len(name):
prid = resclik.create_group("prior")
prid.attrs["name"] = php.pack256(*name)
prid.create_dataset("loc", data=loc.flat[:])
prid.create_dataset("var", data=var.flat[:])
if len(defn):
prid = resclik.create_group("default")
prid.attrs["name"] = php.pack256(*defn)
prid.create_dataset("loc", data=nm.array(defloc).flat[:])
resclik.attrs["lmax"] = lmax.astype(nm.int)
resclik.attrs["n_lkl_object"] = nlkl
reslkl.close()
