def assemble_interpolated_fits(fit_directory, output_file):
"""After all of the fits on the cluster are done, assemble the results to one JSON.
The JSON produced by this function is what `load_interpolated_hypersurfaces`
expects.
"""
assert os.path.isdir(fit_directory), "fit directory does not exist"
metadata = from_json(os.path.join(fit_directory, "metadata.json"))
combined_data = collections.OrderedDict()
combined_data["interpolation_param_spec"] = metadata["interpolation_param_spec"]
hs_fits = []
grid_shape = tuple(metadata["grid_shape"])
for job_idx, grid_idx in enumerate(np.ndindex(grid_shape)):
gridpoint_json = os.path.join(fit_directory, f"gridpoint_{job_idx:06d}.json.bz2")
logging.info(f"Reading {gridpoint_json}")
gridpoint_data = from_json(gridpoint_json)
assert job_idx == gridpoint_data["job_idx"]
assert np.all(grid_idx == gridpoint_data["grid_idx"])
# TODO: Offer to run incomplete fits locally
assert gridpoint_data["fit_successful"], f"job no. {job_idx} not finished"
hs_fits.append(collections.OrderedDict(
param_values=gridpoint_data["param_values"],
hs_fit=gridpoint_data["hs_fit"]
))
combined_data["hs_fits"] = hs_fits
to_json(combined_data, output_file)
def assemble_interpolated_fits(fit_directory,
output_file,
drop_fit_maps=False):
"""After all of the fits on the cluster are done, assemble the results to one JSON.
The JSON produced by this function is what `load_interpolated_hypersurfaces`
expects.
"""
assert os.path.isdir(fit_directory), "fit directory does not exist"
metadata = from_json(os.path.join(fit_directory, "metadata.json"))
combined_data = collections.OrderedDict()
combined_data["interpolation_param_spec"] = metadata[
"interpolation_param_spec"]
# Loop over grid points
hs_fits = []
grid_shape = tuple(metadata["grid_shape"])
for job_idx, grid_idx in enumerate(np.ndindex(grid_shape)):
# Load grid point data
gridpoint_json = os.path.join(fit_directory,
f"gridpoint_{job_idx:06d}.json.bz2")
logging.info(f"Reading {gridpoint_json}")
gridpoint_data = from_json(gridpoint_json)
# Check the loaded data
assert job_idx == gridpoint_data["job_idx"]
assert np.all(grid_idx == gridpoint_data["grid_idx"])
# TODO: Offer to run incomplete fits locally
assert gridpoint_data[
"fit_successful"], f"job no. {job_idx} not finished"
# Drop fit maps if requested (can significantly reduce file size)
if drop_fit_maps:
for key, hs_state in gridpoint_data["hs_fit"].items():
hs_state["fit_maps_raw"] = None
hs_state["fit_maps_norm"] = None
# Add grid point data to output file
hs_fits.append(
collections.OrderedDict(
param_values=gridpoint_data["param_values"],
hs_fit=gridpoint_data["hs_fit"]))
# Write the output file
combined_data["hs_fits"] = hs_fits
to_file(combined_data, output_file)
def __init__(self,ebins,czbins,aeff_egy_par,aeff_coszen_par,**params):
'''
Parameters:
* aeff_egy_par - effective area vs. Energy 1D parameterizations for each flavor,
in a text file (.dat)
* aeff_coszen_par - json file containing 1D coszen parameterization for each flavor
'''
logging.info('Initializing AeffServicePar...')
self.ebins = ebins
self.czbins = czbins
## Load the info from .dat files into a dict...
## Parametric approach treats all NC events the same
aeff_coszen_par_str = from_json(find_resource(aeff_coszen_par))
aeff2d_nc = self.get_aeff_flavor('NC',aeff_egy_par,aeff_coszen_par_str)
aeff2d_nc_bar = self.get_aeff_flavor('NC_bar',aeff_egy_par,aeff_coszen_par_str)
self.aeff_dict = {}
logging.info("Creating effective area parametric dict...")
for flavor in ['nue','nue_bar','numu','numu_bar','nutau','nutau_bar']:
flavor_dict = {}
logging.debug("Working on %s effective areas"%flavor)
aeff2d = self.get_aeff_flavor(flavor,aeff_egy_par,aeff_coszen_par_str)
flavor_dict['cc'] = aeff2d
flavor_dict['nc'] = aeff2d_nc_bar if 'bar' in flavor else aeff2d_nc
self.aeff_dict[flavor] = flavor_dict
return
def __init__(self,ebins,czbins,settings_file=None):
'''
settings - expects the dictionary from a .json file with
entries of 'a_eff_files', & 'a_eff_coszen_dep'
'''
self.ebins = ebins
self.czbins = czbins
##Load the settings from the file
settings = from_json(find_resource(settings_file))
## Load the info from .dat files into a dict...
## Parametric approach treats all NC events the same
aeff2d_nc = self.get_aeff_flavor('NC',settings)
aeff2d_nc_bar = self.get_aeff_flavor('NC_bar',settings)
self.aeff_dict = {}
logging.info("Creating effective area parametric dict...")
for flavor in ['nue','nue_bar','numu','numu_bar','nutau','nutau_bar']:
flavor_dict = {}
logging.debug("Working on %s effective areas"%flavor)
aeff2d = self.get_aeff_flavor(flavor,settings)
flavor_dict['cc'] = aeff2d
flavor_dict['nc'] = aeff2d_nc_bar if 'bar' in flavor else aeff2d_nc
self.aeff_dict[flavor] = flavor_dict
return
def from_json(cls, resource):
"""Instantiate a new TransformSet object from a JSON file.
Parameters
----------
resource : str
A PISA resource specification (see pisa.utils.resources)
See Also
--------
to_json
pisa.utils.jsons.to_json
"""
state = jsons.from_json(resource)
transforms = []
for module, classname, transform_state in state['transforms']:
clsmembers = inspect.getmembers(sys.modules[__name__],
inspect.isclass)
# First try to get a class within this module/namespace
classes = [c[1] for c in clsmembers if c[0] == classname]
if len(classes) > 0:
class_ = classes[0]
# Otherwise try to import the module recorded in the JSON file
else:
module = importlib.import_module(module)
# and then get the class
class_ = getattr(module, classname)
transforms.append(class_(**transform_state))
state['transforms'] = transforms
# State is a dict, so instantiate with double-asterisk syntax
return cls(**state)
def get_pid_kernels(self, pid_kernelfile=None, **kwargs):
logging.info('Opening file: %s'%(pid_kernelfile))
try:
self.pid_kernels = from_json(find_resource(pid_kernelfile))
except IOError, e:
logging.error("Unable to open kernel file %s"%pid_kernelfile)
logging.error(e)
sys.exit(1)
def get_pid_kernels(self, pid_kernelfile=None, **kwargs):
logging.info('Opening file: %s' % (pid_kernelfile))
try:
self.pid_kernels = from_json(find_resource(pid_kernelfile))
except IOError, e:
logging.error("Unable to open kernel file %s" % pid_kernelfile)
logging.error(e)
sys.exit(1)
def _get_reco_kernels(self, kernelfile=None, **kwargs):
for reco_scale in ['e_reco_scale', 'cz_reco_scale']:
if reco_scale in kwargs:
if not kwargs[reco_scale]==1:
raise ValueError('%s = %.2f not valid for RecoServiceKernelFile!'
%(reco_scale, kwargs[reco_scale]))
if not kernelfile in [self.kernelfile, None]:
logging.info('Reconstruction from non-default kernel file %s!'%kernelfile)
return from_json(find_resource(kernelfile))
if not hasattr(self, 'kernels'):
logging.info('Using file %s for default reconstruction'%(kernelfile))
self.kernels = from_json(find_resource(kernelfile))
return self.kernels
def get_incomplete_job_idx(fit_directory):
"""Get job indices of fits that are not flagged as successful."""
assert os.path.isdir(fit_directory), "fit directory does not exist"
metadata = from_json(os.path.join(fit_directory, "metadata.json"))
grid_shape = tuple(metadata["grid_shape"])
failed_idx = []
for job_idx, grid_idx in enumerate(np.ndindex(grid_shape)):
try:
gridpoint_json = os.path.join(fit_directory,
f"gridpoint_{job_idx:06d}.json.bz2")
logging.info(f"Reading {gridpoint_json}")
gridpoint_data = from_json(gridpoint_json)
except:
break
if not gridpoint_data["fit_successful"]:
failed_idx.append(job_idx)
job_idx += 1
return failed_idx
def from_file(fname, fmt=None, **kwargs):
"""Dispatch correct file reader based on `fmt` (if specified) or guess
based on file name's extension.
Parameters
----------
fname : string
File path / name from which to load data.
fmt : None or string
If string, for interpretation of the file according to this format. If
None, file format is deduced by an extension found in `fname`.
**kwargs
All other arguments are passed to the function dispatched to read the
file.
Returns
-------
Object instantiated from the file (string, dictionary, ...). Each format
is interpreted differently.
Raises
------
ValueError
If extension is not recognized
"""
if fmt is None:
rootname, ext = os.path.splitext(fname)
ext = ext.replace('.', '').lower()
else:
rootname = fname
ext = fmt.lower()
if ext in ZIP_EXTS or ext in XOR_EXTS:
rootname, inner_ext = os.path.splitext(rootname)
inner_ext = inner_ext.replace('.', '').lower()
ext = inner_ext
fname = resources.find_resource(fname)
if ext in jsons.JSON_EXTS:
return jsons.from_json(fname, **kwargs)
if ext in hdf.HDF5_EXTS:
return hdf.from_hdf(fname, **kwargs)
if ext in PKL_EXTS:
return from_pickle(fname, **kwargs)
if ext in CFG_EXTS:
return from_cfg(fname, **kwargs)
if ext in TXT_EXTS:
return from_txt(fname, **kwargs)
errmsg = 'File "%s": unrecognized extension "%s"' % (fname, ext)
log.logging.error(errmsg)
raise ValueError(errmsg)
def get_pid_kernels(self, pid_paramfile=None,
PID_offset=0., PID_scale=1., **kwargs):
# load parametrization file
logging.info('Opening PID parametrization file %s'%pid_paramfile)
try:
param_str = from_json(find_resource(pid_paramfile))
except IOError, e:
logging.error("Unable to open PID parametrization file %s"
%pid_paramfile)
logging.error(e)
sys.exit(1)
def get_pid_kernels(self,
pid_paramfile=None,
PID_offset=0.,
PID_scale=1.,
**kwargs):
# load parametrization file
logging.info('Opening PID parametrization file %s' % pid_paramfile)
try:
param_str = from_json(find_resource(pid_paramfile))
except IOError, e:
logging.error("Unable to open PID parametrization file %s" %
pid_paramfile)
logging.error(e)
sys.exit(1)
def setup_function(self):
scale_file = find_resource(self.scale_file)
logging.info("Loading scaling factors from : %s", scale_file)
scaling_dict = from_json(scale_file)
scale_binning = MultiDimBinning(
**scaling_dict[self.variable]["binning"])
scale_factors = np.array(scaling_dict[self.variable]["scales"],
dtype=FTYPE)
logging.info(f"Binning for ad-hoc systematic: \n {str(scale_binning)}")
logging.info(
f"scaling factors of ad-hoc systematic:\n {str(scale_factors)}")
self.data.representation = scale_binning
for container in self.data:
container["adhoc_scale_factors"] = scale_factors
def from_file(fname, fmt=None):
"""Dispatch correct file reader based on fmt (if specified) or guess
based on file name's extension"""
if fmt is None:
base, ext = os.path.splitext(fname)
ext = ext.replace('.', '').lower()
else:
ext = fmt.lower()
if ext in JSON_EXTS:
return jsons.from_json(fname)
elif ext in HDF5_EXTS:
return hdf.from_hdf(fname)
elif ext in PKL_EXTS:
return cPickle.load(file(fname,'rb'))
else:
errmsg = 'Unrecognized file type/extension: ' + ext
logging.error(errmsg)
raise TypeError(errmsg)
def from_file(fname, fmt=None):
"""Dispatch correct file reader based on fmt (if specified) or guess
based on file name's extension"""
if fmt is None:
base, ext = os.path.splitext(fname)
ext = ext.replace('.', '').lower()
else:
ext = fmt.lower()
if ext in JSON_EXTS:
return jsons.from_json(fname)
elif ext in HDF5_EXTS:
return hdf.from_hdf(fname)
elif ext in PKL_EXTS:
return cPickle.load(file(fname, 'rb'))
else:
errmsg = 'Unrecognized file type/extension: ' + ext
logging.error(errmsg)
raise TypeError(errmsg)
def from_json(cls, resource):
"""Instantiate a new Map object from a JSON file.
The format of the JSON is generated by the `Map.to_json` method, which
converts a Map object to basic types and then numpy arrays are
converted in a call to `pisa.utils.jsons.to_json`.
Parameters
----------
resource : str
A PISA resource specification (see pisa.utils.resources)
See Also
--------
to_json
pisa.utils.jsons.to_json
"""
state = jsons.from_json(resource)
# State is a dict for Map, so instantiate with double-asterisk syntax
return cls(**state)
def __init__(self,
detector,
geom,
proc_ver,
pid_spec_ver=1,
pid_specs=None):
geom = str(geom)
proc_ver = str(proc_ver)
pid_spec_ver = str(pid_spec_ver)
if pid_specs is None:
pid_specs = 'pid/pid_specifications.json'
if isinstance(pid_specs, str):
pid_specs = from_json(resources.find_resource(pid_specs))
elif isinstance(pid_specs, collections.Mapping):
pass
else:
raise TypeError('Unhandled `pid_specs` type: "%s"' %
type(data_proc_params))
self.detector = detector
self.proc_ver = proc_ver
self.pid_spec_ver = str(pid_spec_ver)
d = pid_specs
all_k = []
for wanted_key in [detector, geom, proc_ver, pid_spec_ver]:
wanted_key = wanted_key.replace("'", "").lower()
for orig_dict_key, subdict in d.items():
dict_key = orig_dict_key.replace("'", "").lower()
if (dict_key == wanted_key):
d = subdict
all_k.append(orig_dict_key)
if len(all_k) != 4:
raise ValueError('Could not find %s' %
str([detector, geom, proc_ver, pid_spec_ver]))
self.pid_spec = pid_specs[all_k[0]][all_k[1]][all_k[2]][all_k[3]]
# Enforce rules on PID spec:
self.validatePIDSpec(self.pid_spec)
def __init__(self, ebins, czbins, reco_param_file=None, **kwargs):
"""
Parameters needed to instantiate a reconstruction service with
parametrizations:
* ebins: Energy bin edges
* czbins: cos(zenith) bin edges
* reco_param_file: JSON containing the parametrizations
"""
# Load parametrization
logging.info('Opening reconstruction parametrization file %s'
%reco_param_file)
# Needed for self.read_param_string()
self.ebins = ebins
self.czbins = czbins
# Get parametrization
param_str = from_json(find_resource(reco_param_file))
self.parametrization = self.read_param_string(param_str)
# No **kwargs, so stored kernels will always have reco scales 1.0
RecoServiceBase.__init__(self, ebins, czbins,**kwargs)
def __init__(self, ebins, czbins, reco_param_file=None, **kwargs):
"""
Parameters needed to instantiate a reconstruction service with
parametrizations:
* ebins: Energy bin edges
* czbins: cos(zenith) bin edges
* reco_param_file: JSON containing the parametrizations
"""
# Load parametrization
logging.info('Opening reconstruction parametrization file %s' %
reco_param_file)
# Needed for self.read_param_string()
self.ebins = ebins
self.czbins = czbins
# Get parametrization
param_str = from_json(find_resource(reco_param_file))
self.parametrization = self.read_param_string(param_str)
# No **kwargs, so stored kernels will always have reco scales 1.0
RecoServiceBase.__init__(self, ebins, czbins, **kwargs)
def __init__(self, ebins, czbins, aeff_egy_par, aeff_coszen_par, **params):
'''
Parameters:
* aeff_egy_par - effective area vs. Energy 1D parameterizations for each flavor,
in a text file (.dat)
* aeff_coszen_par - json file containing 1D coszen parameterization for each flavor
'''
logging.info('Initializing AeffServicePar...')
self.ebins = ebins
self.czbins = czbins
## Load the info from .dat files into a dict...
## Parametric approach treats all NC events the same
aeff_coszen_par_str = from_json(find_resource(aeff_coszen_par))
aeff2d_nc = self.get_aeff_flavor('NC', aeff_egy_par,
aeff_coszen_par_str)
aeff2d_nc_bar = self.get_aeff_flavor('NC_bar', aeff_egy_par,
aeff_coszen_par_str)
self.aeff_dict = {}
logging.info("Creating effective area parametric dict...")
for flavor in [
'nue', 'nue_bar', 'numu', 'numu_bar', 'nutau', 'nutau_bar'
]:
flavor_dict = {}
logging.debug("Working on %s effective areas" % flavor)
aeff2d = self.get_aeff_flavor(flavor, aeff_egy_par,
aeff_coszen_par_str)
flavor_dict['cc'] = aeff2d
flavor_dict['nc'] = aeff2d_nc_bar if 'bar' in flavor else aeff2d_nc
self.aeff_dict[flavor] = flavor_dict
return
help="Save all stages.")
parser.add_argument('-o',
'--outfile',
dest='outfile',
metavar='FILE',
type=str,
action='store',
default="template.json",
help='file to store the output')
args = parser.parse_args()
set_verbosity(args.verbose)
with Timer() as t:
#Load all the settings
model_settings = from_json(args.template_settings)
#Select a hierarchy
logging.info('Selected %s hierarchy' %
('normal' if args.normal else 'inverted'))
params = select_hierarchy(model_settings['params'],
normal_hierarchy=args.normal)
#Intialize template maker
template_maker = TemplateMaker(get_values(params),
**model_settings['binning'])
tprofile.info(" ==> elapsed time to initialize templates: %s sec" %
t.secs)
#Now get the actual template
with Timer(verbose=False) as t:
def __init__(self, detector, proc_ver, data_proc_params=None):
super().__init__()
if data_proc_params is None:
data_proc_params = 'events/data_proc_params.json'
if isinstance(data_proc_params, str):
ps = jsons.from_json(resources.find_resource(data_proc_params))
elif isinstance(data_proc_params, dict):
ps = data_proc_params
else:
raise TypeError('Unhandled data_proc_params type passed in arg: ' +
type(data_proc_params))
self.detector = detector
self.proc_ver = str(proc_ver)
self.det_key = [k for k in ps.keys()
if k.lower() == self.detector.lower()][0]
for key in ps[self.det_key].keys():
lk = key.lower()
lpv = self.proc_ver.lower()
if lk == lpv or ('v'+lk == lpv) or (lk == 'v'+lpv):
self.procver_key = key
# This works for PINGU
elif ('msu_'+lk == lpv) or (lk == 'msu_'+lpv):
self.procver_key = key
elif ('nbi_'+lk == lpv) or (lk == 'nbi_'+lpv):
self.procver_key = key
# Generalising for DeepCore and different selections
ps = ps[self.det_key][self.procver_key]
self.update(ps)
self.trans_nu_code = False
if 'nu_code_to_pdg_map' in self:
self.trans_nu_code = True
try:
self.nu_code_to_pdg_map = {
int(code): pdg
for code, pdg in self['nu_code_to_pdg_map'].items()
}
except:
self.nu_code_to_pdg_map = self['nu_code_to_pdg_map']
# NOTE: the keys are strings so the particular string formatting is
# important for indexing into the dict!
# Add generic cuts
self['cuts'].update({
# Cut for particles only (no anti-particles)
str(NuFlav(12).bar_code).lower():
{'fields': ['nu_code'], 'pass_if': 'nu_code > 0'},
# Cut for anti-particles only (no particles)
str(NuFlav(-12).bar_code).lower():
{'fields': ['nu_code'], 'pass_if': 'nu_code < 0'},
# Cut for charged-current interactions only
str(IntType('cc')).lower():
{'fields': ['interaction_type'],
'pass_if': 'interaction_type == 1'},
# Cut for neutral-current interactions only
str(IntType('nc')).lower():
{'fields': ['interaction_type'],
'pass_if': 'interaction_type == 2'},
# True-upgoing cut usinng the zenith field
'true_upgoing_zen':
{'fields': ['true_zenith'], 'pass_if': 'true_zenith > pi/2'},
# True-upgoing cut usinng the cosine-zenith field
'true_upgoing_coszen':
{'fields': ['true_coszen'], 'pass_if': 'true_coszen < 0'},
})
# Enforce rules on cuts:
self.validate_cut_spec(self['cuts'])
assert len(llhfiles) <= len(logfiles), "Data and log directories don't match?"
# Output to save to hdf5 file:
output_data = {"minimizer_settings": {}, "template_settings": {}, "true_NMH": {}, "true_IMH": {}}
logging.warn("Processing {0:d} files".format(len(llhfiles)))
mod = len(llhfiles) // 20
start = time.time()
for i, filename in enumerate(llhfiles):
if (mod > 0) and (i % mod == 0):
logging.info(" >> {0:d} files done...".format(i))
try:
data = from_json(filename)
except Exception as inst:
# print(inst)
print("Skipping file: ", filename)
continue
if not output_data["minimizer_settings"]:
output_data["minimizer_settings"] = data["minimizer_settings"]
if not output_data["template_settings"]:
output_data["template_settings"] = data["template_settings"]
for key in ["true_NMH", "true_IMH"]:
appendTrials(output_data[key], data[key])
if args.log_dir is not None:
three_chi2s_theta23 = {}
three_chi2s_theta23['data_NMH'] = {}
three_chi2s_theta23['data_IMH'] = {}
ten_significances = {}
ten_significances['data_NMH'] = []
ten_significances['data_IMH'] = []
ten_chi2s_theta23 = {}
ten_chi2s_theta23['data_NMH'] = {}
ten_chi2s_theta23['data_IMH'] = {}
for infile in sorted(os.listdir(three_true_h_fid_dir)):
if os.path.isfile(three_true_h_fid_dir+infile):
indict = from_json(three_true_h_fid_dir+infile)
theta23_nh = indict['template_settings']['params']['theta23_nh']['value']
theta23_ih = indict['template_settings']['params']['theta23_ih']['value']
assert(theta23_nh == theta23_ih)
theta23vals.append(theta23_nh)
sin2theta23vals.append(math.pow(math.sin(theta23_nh),2))
three_chi2s_theta23['data_NMH'][theta23_nh] = {'true_h_fiducial': [], 'false_h_best': []}
three_chi2s_theta23['data_IMH'][theta23_nh] = {'true_h_fiducial': [], 'false_h_best': []}
ten_chi2s_theta23['data_NMH'][theta23_nh] = {'true_h_fiducial': [], 'false_h_best': []}
ten_chi2s_theta23['data_IMH'][theta23_nh] = {'true_h_fiducial': [], 'false_h_best': []}
theta23vals = sorted(theta23vals)
sin2theta23vals = sorted(sin2theta23vals)
for theta23 in theta23vals:
'--outfile',
type=str,
default='llh_data.json',
metavar='JSONFILE',
help="Output filename.")
parser.add_argument('-v',
'--verbose',
action='count',
default=None,
help='set verbosity level')
args = parser.parse_args()
set_verbosity(args.verbose)
#Read in the settings
template_settings = from_json(args.template_settings)
minimizer_settings = from_json(args.minimizer_settings)
pseudo_data_settings = from_json(
args.pseudo_data_settings
) if args.pseudo_data_settings is not None else template_settings
#Workaround for old scipy versions
import scipy
if scipy.__version__ < '0.12.0':
logging.warn('Detected scipy version %s < 0.12.0' % scipy.__version__)
if 'maxiter' in minimizer_settings:
logging.warn('Optimizer settings for \"maxiter\" will be ignored')
minimizer_settings.pop('maxiter')
# make sure that both pseudo data and template are using the same
# channel. Raise Exception and quit otherwise
action='store_false',
help="select the inverted hierarchy")
parser.add_argument('-v', '--verbose', action='count', default=None,
help='set verbosity level.')
parser.add_argument('-s', '--save_all', action='store_true', default=False,
help="Save all stages.")
parser.add_argument('-o', '--outfile', dest='outfile', metavar='FILE',
type=str, action='store',default="template.json",
help='file to store the output')
args = parser.parse_args()
set_verbosity(args.verbose)
with Timer() as t:
#Load all the settings
model_settings = from_json(args.template_settings)
#Select a hierarchy
logging.info('Selected %s hierarchy'%
('normal' if args.normal else 'inverted'))
params = select_hierarchy(model_settings['params'],
normal_hierarchy=args.normal)
#Intialize template maker
template_maker = TemplateMaker(get_values(params),
**model_settings['binning'])
profile.info(" ==> elapsed time to initialize templates: %s sec"%t.secs)
#Now get the actual template
with Timer(verbose=False) as t:
template_maps = template_maker.get_template(get_values(params),
def trace(self, message, *args, **kws):
self.log(logging.TRACE, message, *args, **kws)
logging.Logger.trace = trace
logging.RootLogger.trace = trace
logging.trace = logging.root.trace
#Don't move these up, as "trace" might be used in them
from pisa.utils.jsons import from_json
from pisa.resources.resources import find_resource
#Get the logging configuration
#Will search in local dir, $PISA and finally package resources
logconfig = from_json(find_resource('logging.json'))
#Setup the logging system with this config
logging.config.dictConfig(logconfig)
#Make the loggers public
#In case they haven't been defined, this will just inherit from the root logger
physics = logging.getLogger('physics')
profile = logging.getLogger('profile')
def set_verbosity(verbosity):
'''Overwrite the verbosity level for the root logger
Verbosity should be an integer with the levels just below.
'''
#Ignore if no verbosity is given
first_chi2s_livetime = {}
first_chi2s_livetime["data_NMH"] = {}
first_chi2s_livetime["data_IMH"] = {}
second_significances = {}
second_significances["data_NMH"] = []
second_significances["data_IMH"] = []
second_chi2s_livetime = {}
second_chi2s_livetime["data_NMH"] = {}
second_chi2s_livetime["data_IMH"] = {}
for infile in sorted(os.listdir(first_true_h_fid_dir)):
if os.path.isfile(first_true_h_fid_dir + infile):
indict = from_json(first_true_h_fid_dir + infile)
livetime = indict["template_settings"]["params"]["livetime"]["value"]
livetimevals.append(livetime)
first_chi2s_livetime["data_NMH"][livetime] = {"true_h_fiducial": [], "false_h_best": []}
first_chi2s_livetime["data_IMH"][livetime] = {"true_h_fiducial": [], "false_h_best": []}
second_chi2s_livetime["data_NMH"][livetime] = {"true_h_fiducial": [], "false_h_best": []}
second_chi2s_livetime["data_IMH"][livetime] = {"true_h_fiducial": [], "false_h_best": []}
livetimevals = sorted(livetimevals)
for livetime in livetimevals:
# Get chisquare values for first octant true_h_fiducial distributions
for trueinfile in sorted(os.listdir(first_true_h_fid_dir)):
if os.path.isfile(first_true_h_fid_dir + trueinfile):
indict = from_json(first_true_h_fid_dir + trueinfile)
def trace(self, message, *args, **kws):
self.log(logging.TRACE, message, *args, **kws)
logging.Logger.trace = trace
logging.RootLogger.trace = trace
logging.trace = logging.root.trace
# Don't move these up, as "trace" might be used in them
from pisa.utils.jsons import from_json
from pisa.resources.resources import find_resource
# Get the logging configuration
# Will search in local dir, $PISA and finally package resources
logconfig = from_json(find_resource("logging.json"))
# Setup the logging system with this config
logging.config.dictConfig(logconfig)
# Make the loggers public
# In case they haven't been defined, this will just inherit from the root logger
physics = logging.getLogger("physics")
profile = logging.getLogger("profile")
def set_verbosity(verbosity):
"""Overwrite the verbosity level for the root logger
Verbosity should be an integer with the levels just below.
"""
# Ignore if no verbosity is given
def load_interpolated_hypersurfaces(input_file):
'''
Load a set of interpolated hypersurfaces from a file.
Analogously to "load_hypersurfaces", this function returns a
collection with a HypersurfaceInterpolator object for each Map.
Parameters
----------
input_file : str
A JSON input file as produced by fit_hypersurfaces if interpolation params
were given. It has the form::
{
interpolation_param_spec = {
'param1': {"values": [val1_1, val1_2, ...], "scales_log": True/False}
'param2': {"values": [val2_1, val2_2, ...], "scales_log": True/False}
...
'paramN': {"values": [valN_1, valN_2, ...], "scales_log": True/False}
},
'hs_fits': [
<list of dicts where keys are map names such as 'nue_cc' and values
are hypersurface states>
]
}
Returns
-------
collections.OrderedDict
dictionary with a :obj:`HypersurfaceInterpolator` for each map
'''
assert isinstance(input_file, str)
if input_file.endswith("json") or input_file.endswith("json.bz2"):
logging.info(f"Loading interpolated hypersurfaces from file: {input_file}")
input_data = from_json(input_file)
assert set(['interpolation_param_spec', 'hs_fits']).issubset(
set(input_data.keys())), 'missing keys'
map_names = None
# input_data['hs_fits'] is a list of dicts, each dict contains "param_values"
# and "hs_fit"
logging.info("Reading file complete, generating hypersurfaces...")
for hs_fit_dict in input_data['hs_fits']:
# this is still not the actual Hypersurface, but a dict with the (linked)
# maps and the HS fit for the map...
hs_state_maps = hs_fit_dict["hs_fit"]
if map_names is None:
map_names = list(hs_state_maps.keys())
else:
assert set(map_names) == set(hs_state_maps.keys()), "inconsistent maps"
# When data is recovered from JSON, the object states are not automatically
# converted to the corresponding objects, so we need to do it manually here.
for map_name in map_names:
hs_state_maps[map_name] = Hypersurface.from_state(hs_state_maps[map_name])
logging.info(f"Read hypersurface maps: {map_names}")
# Now we have a list of dicts where the map names are on the lower level.
# We need to convert this into a dict of HypersurfaceInterpolator objects.
output = collections.OrderedDict()
for m in map_names:
hs_fits = [{"param_values": fd["param_values"], "hs_fit": fd['hs_fit'][m]} for fd in input_data['hs_fits']]
output[m] = HypersurfaceInterpolator(input_data['interpolation_param_spec'], hs_fits)
else:
raise Exception("unknown file format")
return output
def run_interpolated_fit(fit_directory, job_idx, skip_successful=False):
"""Run the hypersurface fit for a grid point.
If `skip_successful` is true, do not run if the `fit_successful` flag is already
True.
"""
assert os.path.isdir(fit_directory), "fit directory does not exist"
gridpoint_json = os.path.join(fit_directory, f"gridpoint_{job_idx:06d}.json.bz2")
gridpoint_data = from_json(gridpoint_json)
if skip_successful and gridpoint_data["fit_successful"]:
logging.info(f"Fit at job index {job_idx} already successful, skipping...")
return
metadata = from_json(os.path.join(fit_directory, "metadata.json"))
interpolation_param_spec = metadata["interpolation_param_spec"]
# this is a pipeline configuration in the form of an OrderedDict
nominal_dataset = metadata["nominal_dataset"]
# Why can we still not load PISA objects from JSON that are inside a dict?! Grrr...
nominal_dataset["pipeline_cfg"] = pipeline_cfg_from_states(
nominal_dataset["pipeline_cfg"]
)
# this is a list of pipeline configurations
sys_datasets = metadata["sys_datasets"]
for sys_dataset in sys_datasets:
sys_dataset["pipeline_cfg"] = pipeline_cfg_from_states(
sys_dataset["pipeline_cfg"]
)
# this is a dict of param_name : value pairs
param_values = gridpoint_data["param_values"]
# we do a redundant check to make sure the parameter values at this grid point are
# correct
interpolation_param_names = metadata["interpolation_param_names"]
grid_shape = tuple(metadata["grid_shape"])
# the grid point index of this job
grid_idx = list(np.ndindex(grid_shape))[job_idx]
for i, n in enumerate(interpolation_param_names):
ms = "Inconsistent parameter values at grid point!"
assert interpolation_param_spec[n]["values"][grid_idx[i]] == param_values[n], ms
# now we need to adjust the values of the parameter in all pipelines for this point
logging.info(f"updating pipelines with parameter values: {param_values}")
for dataset in [nominal_dataset] + sys_datasets:
for stage_cfg in dataset["pipeline_cfg"].values():
if "params" not in stage_cfg.keys(): continue
for param in interpolation_param_names:
if param in stage_cfg["params"].names:
stage_cfg["params"][param].value = param_values[param]
# these are the parameters of the hypersurface, NOT the ones we interpolate them
# over!
hypersurface_params = []
for param_state in metadata["hypersurface_params"]:
hypersurface_params.append(HypersurfaceParam.from_state(param_state))
# We create Pipeline objects, get their outputs and then forget about the Pipeline
# object on purpose! The memory requirement to hold all systematic sets at the same
# time is just too large, especially on the cluster. The way we do it below we
# only need enough memory for one dataset at a time.
nominal_dataset["mapset"] = Pipeline(nominal_dataset["pipeline_cfg"]).get_outputs()
for sys_dataset in sys_datasets:
sys_dataset["mapset"] = Pipeline(sys_dataset["pipeline_cfg"]).get_outputs()
# Merge maps according to the combine regex, if one was provided
combine_regex = metadata["combine_regex"]
if combine_regex is not None:
nominal_dataset["mapset"] = nominal_dataset["mapset"].combine_re(combine_regex)
for sys_dataset in sys_datasets:
sys_dataset["mapset"] = sys_dataset["mapset"].combine_re(combine_regex)
hypersurface_fit_kw = metadata["hypersurface_fit_kw"]
hypersurfaces = collections.OrderedDict()
log = metadata["log"] # flag determining whether hs fit is run in log-space or not
for map_name in nominal_dataset["mapset"].names:
nominal_map = nominal_dataset["mapset"][map_name]
nominal_param_values = nominal_dataset["sys_params"]
sys_maps = [sys_dataset["mapset"][map_name] for sys_dataset in sys_datasets]
sys_param_values = [sys_dataset["sys_params"] for sys_dataset in sys_datasets]
hypersurface = Hypersurface(
# Yes, this MUST be a deepcopy! Otherwise weird memory overwrites happen
# and all the numbers get jumbled across the hypersurfaces of different maps
params=copy.deepcopy(hypersurface_params),
initial_intercept=0. if log else 1., # Initial value for intercept
log=log
)
hypersurface.fit(
nominal_map=nominal_map,
nominal_param_values=nominal_param_values,
sys_maps=sys_maps,
sys_param_values=sys_param_values,
norm=True,
# Is the space or loading time really a problem?
# keep_maps=False, # it would take a lot more space otherwise
**hypersurface_fit_kw
)
logging.debug("\nFitted hypersurface report:\n%s" % hypersurface)
hypersurfaces[map_name] = hypersurface
gridpoint_data["hs_fit"] = hypersurfaces
gridpoint_data["fit_successful"] = True
to_json(gridpoint_data, gridpoint_json)
help='''Settings related to the optimizer used in the LLR analysis.''')
parser.add_argument('-n','--ntrials',type=int, default = 1,
help="Number of trials to run")
parser.add_argument('-s','--save-steps',action='store_true',default=False,
dest='save_steps',
help="Save all steps the optimizer takes.")
parser.add_argument('-o','--outfile',type=str,default='llh_data.json',metavar='JSONFILE',
help="Output filename.")
parser.add_argument('-v', '--verbose', action='count', default=None,
help='set verbosity level')
args = parser.parse_args()
set_verbosity(args.verbose)
#Read in the settings
template_settings = from_json(args.template_settings)
minimizer_settings = from_json(args.minimizer_settings)
#Workaround for old scipy versions
import scipy
if scipy.__version__ < '0.12.0':
logging.warn('Detected scipy version %s < 0.12.0'%scipy.__version__)
if 'maxiter' in minimizer_settings:
logging.warn('Optimizer settings for \"maxiter\" will be ignored')
minimizer_settings.pop('maxiter')
#Get the parameters
params = template_settings['params']
#store results from all the trials
trials = []
help="Plot the fits of DOM efficiency and hole ice for each bin.")
parser.add_argument('--detector',type=str,default='',
help="Name of detector to put in plot titles")
parser.add_argument('--selection',type=str,default='',
help="Name of selection to put in plot titles")
parser.add_argument('-o','--outdir',type=str,
metavar='DIR', required = True, help='''Output directory''')
args = parser.parse_args()
#Read in the settings
detector = args.detector
selection = args.selection
outdir = args.outdir
utils.mkdir(outdir)
utils.mkdir(outdir+'/plots/')
template_settings = from_json(args.template_settings)
czbin_edges = template_settings['binning']['czbins']
ebin_edges = template_settings['binning']['ebins']
channel = template_settings['params']['channel']['value']
x_steps = 0.0001
if args.sim == '4digit':
MC_name = '1XXX'
elif args.sim == '5digit':
MC_name = '1XXXX'
elif args.sim == 'dima':
MC_name = 'Dima'
else:
MC_name = 'Other'
params = get_values(select_hierarchy(template_settings['params'],normal_hierarchy=True))
def fromFile(cls, filename):
"""
Load a Fisher matrix from a json file
"""
return cls(**from_json(filename))
chi2s_theta23['data_IMH'] = {}
chi2s_livetime = {}
chi2s_livetime['data_NMH'] = {}
chi2s_livetime['data_IMH'] = {}
chi2s = {}
chi2s['data_NMH'] = {}
chi2s['data_NMH']['true_h_fiducial'] = []
chi2s['data_NMH']['false_h_best'] = []
chi2s['data_IMH'] = {}
chi2s['data_IMH']['true_h_fiducial'] = []
chi2s['data_IMH']['false_h_best'] = []
for infile in sorted(os.listdir(true_h_fid_dir)):
if os.path.isfile(true_h_fid_dir+infile):
indict = from_json(true_h_fid_dir+infile)
if theta23analysis == True:
theta23_nh = indict['template_settings']['params']['theta23_nh']['value']
theta23_ih = indict['template_settings']['params']['theta23_ih']['value']
assert(theta23_nh == theta23_ih)
theta23vals.append(theta23_nh)
sin2theta23vals.append(math.pow(math.sin(theta23_nh),2))
chi2s_theta23['data_NMH'][theta23_nh] = {'true_h_fiducial': [], 'false_h_best': []}
chi2s_theta23['data_IMH'][theta23_nh] = {'true_h_fiducial': [], 'false_h_best': []}
if livetimeanalysis == True:
livetime = indict['template_settings']['params']['livetime']['value']
livetimevals.append(livetime)
chi2s_livetime['data_NMH'][livetime] = {'true_h_fiducial': [], 'false_h_best': []}
chi2s_livetime['data_IMH'][livetime] = {'true_h_fiducial': [], 'false_h_best': []}
'--outfile',
type=str,
default='alt_hypo_study.json',
metavar='JSONFILE',
help="Output filename.")
parser.add_argument('-v',
'--verbose',
action='count',
default=None,
help='set verbosity level')
args = parser.parse_args()
set_verbosity(args.verbose)
#Read in the settings
template_settings = from_json(args.template_settings)
minimizer_settings = from_json(args.minimizer_settings)
grid_settings = from_json(args.grid_settings)
if args.gpu_id is not None:
template_settings['params']['gpu_id'] = {}
template_settings['params']['gpu_id']['value'] = args.gpu_id
template_settings['params']['gpu_id']['fixed'] = True
with Timer() as t:
template_maker = TemplateMaker(get_values(template_settings['params']),
**template_settings['binning'])
profile.info("==> elapsed time to initialize templates: %s sec" % t.secs)
#Get the parameters
params = template_settings['params']
import numpy as np
import matplotlib.pyplot as plt
plt.rcParams['text.usetex'] = True
import scipy.interpolate
from pisa.utils.jsons import from_json
indict = from_json('/Users/steven/IceCube/PISA/pisa/pisa/resources/aeff/relative-crosssections/genie-weigthed-crosssections.json')
axislabels = {}
axislabels['nue'] = r'$\nu_e$ CC'
axislabels['nue_bar'] = r'$\bar{\nu}_e$ CC'
axislabels['numu'] = r'$\nu_{\mu}$ CC'
axislabels['numu_bar'] = r'$\bar{\nu}_{\mu}$ CC'
axislabels['nutau'] = r'$\nu_{\tau}$ CC'
axislabels['nutau_bar'] = r'$\bar{\nu}_{\tau}$ CC'
axislabels['nuall'] = r'$\nu$ NC'
axislabels['nuallbar'] = r'$\bar{\nu}$ NC'
GENIElabels = {}
GENIElabels['MaRES'] = r'$M_A^{RES}$'
GENIElabels['MaCCQE'] = r'$M_A^{CCQE}$'
GENIElabels['AhtBY'] = r'$A_{HT}$'
GENIElabels['BhtBY'] = r'$B_{BT}$'
GENIElabels['CV1uBY'] = r'$C_{\nu1u}$'
GENIElabels['CV2uBY'] = r'$C_{\nu2u}$'
GENIEcolours = {}
GENIEcolours['MaRES'] = 'b'
GENIEcolours['MaCCQE'] = 'r'
default=False, dest='save_templates',
help="Do not save the templates for the different test points.")
parser.add_argument('-o','--outdir',type=str,default=os.getcwd(),metavar='DIR',
help="Output directory")
parser.add_argument('-v', '--verbose', action='count', default=None,
help='set verbosity level')
args = parser.parse_args()
# Set verbosity level
set_verbosity(args.verbose)
# Read the template settings
template_settings = from_json(args.template_settings)
# This file only contains the number of test points for each parameter (and perhaps eventually a non-linearity criterion)
grid_settings = from_json(args.grid_settings)
# Get the Fisher matrices for the desired hierarchy and fiducial settings
fisher_matrices = get_fisher_matrices(template_settings,grid_settings,args.inverted_truth,args.normal_truth,
args.dump_all_stages,args.save_templates,args.outdir)
# Fisher matrices are saved in any case
for data_tag in fisher_matrices:
fisher_basename = 'fisher_data_%s'%data_tag
for chan in fisher_matrices[data_tag]:
if chan == 'comb':
outfile = os.path.join(args.outdir,fisher_basename+'.json')
parser.add_argument('-IH','--IH_osc_dir', type=str, required=True, help="Directory containing oscillation probabilties for different oversampling values for inverted ordring.")
parser.add_argument('-r','--reference',type=str,
help="Reference value for oversampling (i.e. highest value used)")
args = parser.parse_args()
NH_path = args.NH_osc_dir
IH_path = args.IH_osc_dir
reference = args.reference
NH_vals = {}
IH_vals = {}
os_vals = []
for f in sorted(os.listdir(NH_path)):
if os.path.isfile(NH_path+f):
osc_file = from_json(NH_path+f)
for os_key in osc_file.keys():
NH_vals[os_key] = osc_file[os_key]
if int(os_key) not in os_vals:
os_vals.append(int(os_key))
for f in sorted(os.listdir(IH_path)):
if os.path.isfile(IH_path+f):
osc_file = from_json(IH_path+f)
for os_key in osc_file.keys():
IH_vals[os_key] = osc_file[os_key]
os_vals = sorted(os_vals)
times = []
oversamples = []
titles["numubar"] = r"$\bar{\nu}_{\mu}$"
titles["nue_cc"] = r"$\nu_e$ CC"
titles["numu_cc"] = r"$\nu_{\mu}$ CC"
titles["nutau_cc"] = r"$\nu_{\tau}$ CC"
titles["nuall_nc"] = r"$\nu$ NC"
titles["nuebar_cc"] = r"$\bar{\nu}_e$ CC"
titles["numubar_cc"] = r"$\bar{\nu}_{\mu}$ CC"
titles["nutaubar_cc"] = r"$\bar{\nu}_{\tau}$ CC"
titles["nuallbar_nc"] = r"$\bar{\nu}$ NC"
titles["trck"] = r"Track-Like"
titles["cscd"] = r"Cascade-Like"
try:
cake_array1 = from_json(args.cake_file1)["maps"]
except:
cake_array1 = from_json(args.cake_file1)
try:
cake_array2 = from_json(args.cake_file2)["maps"]
except:
cake_array2 = from_json(args.cake_file2)
for cake_dict1, cake_dict2 in zip(cake_array1, cake_array2):
assert cake_dict1["name"] == cake_dict2["name"]
cake_map1 = {}
cake_map1["map"] = cake_dict1["hist"].T
dest="outfile",
metavar="FILE",
type=str,
action="store",
default="event_rate.json",
help="""file to store the output""",
)
parser.add_argument("-v", "--verbose", action="count", default=None, help="""set verbosity level""")
args = parser.parse_args()
# Set verbosity level
set_verbosity(args.verbose)
# Check binning
ebins, czbins = check_binning(args.osc_flux_maps)
logging.info("Defining aeff_service...")
if args.mc_mode:
logging.info(" Using effective area from EVENT DATA...")
aeff_service = AeffServiceMC(ebins, czbins, aeff_weight_file=args.weighted_aeff_file)
else:
logging.info(" Using effective area from PARAMETRIZATION...")
aeff_settings = from_json(find_resource(args.settings_file))
aeff_service = AeffServicePar(ebins, czbins, **aeff_settings)
event_rate_maps = get_event_rates(args.osc_flux_maps, aeff_service, args.livetime, args.aeff_scale)
logging.info("Saving output to: %s" % args.outfile)
to_json(event_rate_maps, args.outfile)
from pisa.utils.jsons import from_json, to_json
from copy import deepcopy as copy
parser = ArgumentParser(formatter_class=ArgumentDefaultsHelpFormatter)
parser.add_argument(
'papa_file',
type=str,
metavar='JSON',
help='papa settings file, containing the resolution parameterizations.')
parser.add_argument('outfile',
type=str,
metavar='JSON',
help='output file to store resolutions in PISA-format.')
args = parser.parse_args()
papa_settings = from_json(args.papa_file)
parameterizations = papa_settings['fiducial']['reco_parametrization']['value']
pisa_flavs = ['nue', 'numu', 'nutau']
mID = ['', '_bar']
intType = ['cc', 'nc']
recoType = ['coszen', 'energy']
papa_NC = parameterizations['NC']
egy_res = papa_NC['e']
papa_NC.pop('e')
papa_NC['energy'] = egy_res
pisa_reco_settings = {}
for flav in pisa_flavs:
papa_res = parameterizations[flav]
#Only show errors while parsing
set_verbosity(0)
parser = ArgumentParser(description='Takes a reco event rate file '
'as input and produces a set of reconstructed templates '
'of tracks and cascades.',
formatter_class=RawTextHelpFormatter)
parser.add_argument('reco_event_maps',metavar='RECOEVENTS',type=from_json,
help='''JSON reco event rate file with following parameters:
{"nue_cc": {'czbins':[...], 'ebins':[...], 'map':[...]},
"numu_cc": {...},
"nutau_cc": {...},
"nuall_nc": {...} }''')
parser.add_argument('--settings',metavar='SETTINGS',type=from_json,
default=from_json(find_resource('pid/V15_pid.json')),
help='''json file containing parameterizations of the particle ID for each event type.''')
parser.add_argument('-o', '--outfile', dest='outfile', metavar='FILE', type=str,
action='store',default="pid.json",
help='''file to store the output''')
parser.add_argument('-v', '--verbose', action='count', default=0,
help='''set verbosity level''')
args = parser.parse_args()
#Set verbosity level
set_verbosity(args.verbose)
#Check binning
ebins, czbins = check_binning(args.reco_event_maps)
type=str,
default=os.getcwd(),
metavar='DIR',
help="Output directory")
parser.add_argument('-v',
'--verbose',
action='count',
default=None,
help='set verbosity level')
args = parser.parse_args()
# Set verbosity level
set_verbosity(args.verbose)
# Read the template settings
template_settings = from_json(args.template_settings)
# This file only contains the number of test points for each parameter (and
# perhaps eventually a non-linearity criterion)
grid_settings = from_json(args.grid_settings)
# Get the Fisher matrices for the desired hierarchy and fiducial settings
fisher_matrices = get_fisher_matrices(template_settings=template_settings,
grid_settings=grid_settings,
IMH=args.inverted_truth,
NMH=args.normal_truth,
dump_all_stages=args.dump_all_stages,
save_templates=args.save_templates,
outdir=args.outdir)
# Fisher matrices are saved in any case
logging.warn("processing " + str(len(args.infiles)) + " files...")
logging.warn("Saving to file: %s" % args.outfile)
mod_num = len(args.infiles) / 20
start_time = datetime.now()
minimizer_settings = {}
template_settings = {}
pseudo_data_settings = {}
trials = {}
for i, filename in enumerate(args.infiles):
if mod_num > 0:
if i % mod_num == 0: print " >> %d files done..." % i
try:
data = from_json(filename)
except:
print "Skipping file: ", filename
continue
if not minimizer_settings:
minimizer_settings = data['minimizer_settings']
if not template_settings:
template_settings = data['template_settings']
if not pseudo_data_settings:
try:
pseudo_data_settings = data['pseudo_data_settings']
except:
pass
titles['nue_bar'] = r'$\bar{\nu}_e$'
titles['nuebar'] = r'$\bar{\nu}_e$'
titles['numu'] = r'$\nu_{\mu}$'
titles['numu_bar'] = r'$\bar{\nu}_{\mu}$'
titles['numubar'] = r'$\bar{\nu}_{\mu}$'
titles['nue_cc'] = r'$\nu_e$ CC'
titles['numu_cc'] = r'$\nu_{\mu}$ CC'
titles['nutau_cc'] = r'$\nu_{\tau}$ CC'
titles['nuall_nc'] = r'$\nu$ NC'
titles['trck'] = r'Track-Like'
titles['cscd'] = r'Cascade-Like'
try:
cake_array = from_json(args.cake_file)['maps']
except:
cake_array = from_json(args.cake_file)
pisa_dict = from_json(args.pisa_file)
for cake_dict in cake_array:
if cake_dict['name'] == 'numubar':
pisa_map = pisa_dict['numu_bar']
elif cake_dict['name'] == 'nuebar':
pisa_map = pisa_dict['nue_bar']
else:
pisa_map = pisa_dict[cake_dict['name']]
cake_map = {}
cake_map['map'] = cake_dict['hist'].T
free_chi2s_livetime = {}
free_chi2s_livetime['data_NMH'] = {}
free_chi2s_livetime['data_IMH'] = {}
prior_significances = {}
prior_significances['data_NMH'] = []
prior_significances['data_IMH'] = []
prior_chi2s_livetime = {}
prior_chi2s_livetime['data_NMH'] = {}
prior_chi2s_livetime['data_IMH'] = {}
for infile in sorted(os.listdir(free_true_h_fid_dir)):
if os.path.isfile(free_true_h_fid_dir+infile):
indict = from_json(free_true_h_fid_dir+infile)
livetime = indict['template_settings']['params']['livetime']['value']
livetimevals.append(livetime)
free_chi2s_livetime['data_NMH'][livetime] = {'true_h_fiducial': [], 'false_h_best': []}
free_chi2s_livetime['data_IMH'][livetime] = {'true_h_fiducial': [], 'false_h_best': []}
prior_chi2s_livetime['data_NMH'][livetime] = {'true_h_fiducial': [], 'false_h_best': []}
prior_chi2s_livetime['data_IMH'][livetime] = {'true_h_fiducial': [], 'false_h_best': []}
livetimevals = sorted(livetimevals)
for livetime in livetimevals:
# Get chisquare values for free octant true_h_fiducial distributions
for trueinfile in sorted(os.listdir(free_true_h_fid_dir)):
if os.path.isfile(free_true_h_fid_dir+trueinfile):
indict = from_json(free_true_h_fid_dir+trueinfile)
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
from pisa.utils.jsons import from_json, to_json
import numpy as np
parser = ArgumentParser(description='''Determines the false_h_best fiducial distribution, under the Gaussian assumption.''',
formatter_class=ArgumentDefaultsHelpFormatter)
parser.add_argument('-p','--pisa_file', type=str, required=True,
help="File containing PISA V2 event by event data")
args = parser.parse_args()
pisa_dict = from_json(args.pisa_file)['pid']['reduced']
to_json(pisa_dict,'better.json')
def plot_clsim_table_summary(
summaries, formats=None, outdir=None, no_legend=False
):
"""Plot the table summary produced by `summarize_clsim_table`.
Plots are made of marginalized 1D distributions, where mean, median, and/or
max are used to marginalize out the remaining dimensions (where those are
present in the summaries)..
Parameters
----------
summaries : string, summary, or iterable thereof
If string(s) are provided, each is glob-expanded. See
:method:`glob.glob` for valid syntax.
formats : None, string, or iterable of strings in {'pdf', 'png'}
If no formats are provided, the plot will not be saved.
outdir : None or string
If `formats` is specified and `outdir` is None, the plots are
saved to the present working directory.
no_legend : bool, optional
Do not display legend on plots (default is to display a legend)
Returns
-------
all_figs : list of three :class:`matplotlib.figure.Figure`
all_axes : list of three lists of :class:`matplotlib.axes.Axes`
summaries : list of :class:`collections.OrderedDict`
List of all summaries loaded
"""
orig_summaries = deepcopy(summaries)
if isinstance(summaries, (basestring, Mapping)):
summaries = [summaries]
tmp_summaries = []
for summary in summaries:
if isinstance(summary, Mapping):
tmp_summaries.append(summary)
elif isinstance(summary, basestring):
tmp_summaries.extend(glob(expand(summary)))
summaries = tmp_summaries
for summary_n, summary in enumerate(summaries):
if isinstance(summary, basestring):
summary = from_json(summary)
summaries[summary_n] = summary
if formats is None:
formats = []
elif isinstance(formats, basestring):
formats = [formats]
if outdir is not None:
outdir = expand(outdir)
mkdir(outdir)
n_summaries = len(summaries)
if n_summaries == 0:
raise ValueError(
'No summaries found based on argument `summaries`={}'
.format(orig_summaries)
)
for n, fmt in enumerate(formats):
fmt = fmt.strip().lower()
assert fmt in ('pdf', 'png'), fmt
formats[n] = fmt
all_items = OrderedDict()
for summary in summaries:
for key, value in summary.items():
if key == 'dimensions':
continue
if not all_items.has_key(key):
all_items[key] = []
all_items[key].append(value)
same_items = OrderedDict()
different_items = OrderedDict()
for key, values in all_items.items():
all_same = True
ref_value = values[0]
for value in values[1:]:
if np.any(value != ref_value):
all_same = False
if all_same:
same_items[key] = values[0]
else:
different_items[key] = values
if n_summaries > 1:
if same_items:
print('Same for all:\n{}'.format(same_items.keys()))
if different_items:
print('Different for some or all:\n{}'
.format(different_items.keys()))
same_label = formatter(same_items)
summary_has_detail = False
if set(['string', 'depth_idx', 'seed']).issubset(all_items.keys()):
summary_has_detail = True
strings = sorted(set(all_items['string']))
depths = sorted(set(all_items['depth_idx']))
seeds = sorted(set(all_items['seed']))
plot_kinds = ('mean', 'median', 'max')
plot_kinds_with_data = set()
dim_names = summaries[0]['dimensions'].keys()
n_dims = len(dim_names)
fig_x = 10 # inches
fig_header_y = 0.35 # inches
fig_one_axis_y = 5 # inches
fig_all_axes_y = n_dims * fig_one_axis_y
fig_y = fig_header_y + fig_all_axes_y # inches
all_figs = []
all_axes = []
for plot_kind in plot_kinds:
fig, f_axes = plt.subplots(
nrows=n_dims, ncols=1, squeeze=False, figsize=(fig_x, fig_y)
)
all_figs.append(fig)
f_axes = list(f_axes.flat)
for ax in f_axes:
ax.set_prop_cycle('color', COLOR_CYCLE_ORTHOG)
all_axes.append(f_axes)
n_lines = 0
xlims = [[np.inf, -np.inf]] * n_dims
summaries_order = []
if summary_has_detail:
for string, depth_idx, seed in product(strings, depths, seeds):
for summary_n, summary in enumerate(summaries):
if (summary['string'] != string
or summary['depth_idx'] != depth_idx
or summary['seed'] != seed):
continue
summaries_order.append((summary_n, summary))
else:
for summary_n, summary in enumerate(summaries):
summaries_order.append((summary_n, summary))
labels_assigned = set()
for summary_n, summary in summaries_order:
different_label = formatter({k: v[summary_n] for k, v in different_items.items()})
if different_label:
label = different_label
if label in labels_assigned:
label = None
else:
labels_assigned.add(label)
else:
label = None
for dim_num, dim_name in enumerate(dim_names):
dim_info = summary['dimensions'][dim_name]
dim_axes = [f_axes[dim_num] for f_axes in all_axes]
bin_edges = summary[dim_name + '_bin_edges']
if dim_name == 'deltaphidir':
bin_edges /= np.pi
xlims[dim_num] = [
min(xlims[dim_num][0], np.min(bin_edges)),
max(xlims[dim_num][1], np.max(bin_edges))
]
for ax, plot_kind in zip(dim_axes, plot_kinds):
if plot_kind not in dim_info:
continue
plot_kinds_with_data.add(plot_kind)
vals = dim_info[plot_kind]
ax.step(bin_edges, [vals[0]] + list(vals),
linewidth=1, clip_on=True,
label=label)
n_lines += 1
dim_labels = dict(
r=r'$r$',
costheta=r'$\cos\theta$',
t=r'$t$',
costhetadir=r'$\cos\theta_{\rm dir}$',
deltaphidir=r'$\Delta\phi_{\rm dir}$'
)
units = dict(r='m', t='ns', deltaphidir=r'rad/$\pi$')
logx_dims = []
logy_dims = ['r', 'time', 'deltaphidir']
flabel = ''
same_flabel = formatter(same_items, fname=True)
different_flabel = formatter(different_items, key_only=True, fname=True)
if same_flabel:
flabel += '__same__' + same_flabel
if different_flabel:
flabel += '__differ__' + different_flabel
for kind_idx, (plot_kind, fig) in enumerate(zip(plot_kinds, all_figs)):
if plot_kind not in plot_kinds_with_data:
continue
for dim_num, (dim_name, ax) in enumerate(zip(dim_names, all_axes[kind_idx])):
#if dim_num == 0 and different_items:
if different_items and not no_legend:
ax.legend(loc='best', frameon=False,
prop=dict(size=7, family='monospace'))
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.yaxis.set_ticks_position('none')
ax.xaxis.set_ticks_position('none')
ax.xaxis.tick_bottom()
ax.yaxis.tick_left()
ax.set_xlim(xlims[dim_num])
xlabel = dim_labels[dim_name]
if dim_name in units:
xlabel += ' ({})'.format(units[dim_name])
ax.set_xlabel(xlabel)
if dim_name in logx_dims:
ax.set_xscale('log')
if dim_name in logy_dims:
ax.set_yscale('log')
fig.tight_layout(rect=(0, 0, 1, fig_all_axes_y/fig_y))
suptitle = (
'Marginalized distributions (taking {} over all other axes)'
.format(plot_kind)
)
if same_label:
suptitle += '\n' + same_label
fig.suptitle(suptitle, y=(fig_all_axes_y + fig_header_y*0.8) / fig_y,
fontsize=9)
for fmt in formats:
outfpath = ('clsim_table_summaries{}__{}.{}'
.format(flabel, plot_kind, fmt))
if outdir:
outfpath = join(outdir, outfpath)
fig.savefig(outfpath, dpi=300)
print('Saved image to "{}"'.format(outfpath))
return all_figs, all_axes, summaries
def run_interpolated_fit(fit_directory, job_idx, skip_successful=False):
"""Run the hypersurface fit for a grid point.
If `skip_successful` is true, do not run if the `fit_successful` flag is already
True.
"""
#TODO a lot of this is copied from fit_hypersurfaces in hypersurface.py, would be safer to make more OAOO
#TODO Copy the param value storage stuff from fit_hypersurfaces across in the meantime
assert os.path.isdir(fit_directory), "fit directory does not exist"
gridpoint_json = os.path.join(fit_directory,
f"gridpoint_{job_idx:06d}.json.bz2")
gridpoint_data = from_json(gridpoint_json)
if skip_successful and gridpoint_data["fit_successful"]:
logging.info(
f"Fit at job index {job_idx} already successful, skipping...")
return
metadata = from_json(os.path.join(fit_directory, "metadata.json"))
interpolation_param_spec = metadata["interpolation_param_spec"]
# this is a pipeline configuration in the form of an OrderedDict
nominal_dataset = metadata["nominal_dataset"]
# Why can we still not load PISA objects from JSON that are inside a dict?! Grrr...
nominal_dataset["pipeline_cfg"] = pipeline_cfg_from_states(
nominal_dataset["pipeline_cfg"])
# this is a list of pipeline configurations
sys_datasets = metadata["sys_datasets"]
for sys_dataset in sys_datasets:
sys_dataset["pipeline_cfg"] = pipeline_cfg_from_states(
sys_dataset["pipeline_cfg"])
# this is a dict of param_name : value pairs
param_values = gridpoint_data["param_values"]
# we do a redundant check to make sure the parameter values at this grid point are
# correct
interpolation_param_names = metadata["interpolation_param_names"]
grid_shape = tuple(metadata["grid_shape"])
# the grid point index of this job
grid_idx = list(np.ndindex(grid_shape))[job_idx]
for i, n in enumerate(interpolation_param_names):
ms = "Inconsistent parameter values at grid point!"
assert interpolation_param_spec[n]["values"][
grid_idx[i]] == param_values[n], ms
# now we need to adjust the values of the parameter in all pipelines for this point
logging.info(f"updating pipelines with parameter values: {param_values}")
for dataset in [nominal_dataset] + sys_datasets:
for stage_cfg in dataset["pipeline_cfg"].values():
if "params" not in stage_cfg.keys(): continue
for param in interpolation_param_names:
if param in stage_cfg["params"].names:
stage_cfg["params"][param].value = param_values[param]
# these are the parameters of the hypersurface, NOT the ones we interpolate them
# over!
hypersurface_params = []
for param_state in metadata["hypersurface_params"]:
hypersurface_params.append(HypersurfaceParam.from_state(param_state))
def find_hist_stage(pipeline):
"""Locate the index of the hist stage in a pipeline."""
hist_idx_found = False
for i, s in enumerate(pipeline.stages):
if s.__class__.__name__ == "hist":
hist_idx = i
hist_idx_found = True
break
if not hist_idx_found:
raise RuntimeError(
"Could not find histogram stage in pipeline, aborting.")
return hist_idx
# We create Pipeline objects, get their outputs and then forget about the Pipeline
# object on purpose! The memory requirement to hold all systematic sets at the same
# time is just too large, especially on the cluster. The way we do it below we
# only need enough memory for one dataset at a time.
for dataset in [nominal_dataset] + sys_datasets:
pipeline = Pipeline(dataset["pipeline_cfg"])
dataset["mapset"] = pipeline.get_outputs()
# get the un-weighted event counts as well so that we can exclude bins
# with too little statistics
# First, find out which stage is the hist stage
hist_idx = find_hist_stage(pipeline)
pipeline.stages[hist_idx].unweighted = True
dataset["mapset_unweighted"] = pipeline.get_outputs()
del pipeline
# Merge maps according to the combine regex, if one was provided
combine_regex = metadata["combine_regex"]
if combine_regex is not None:
for dataset in [nominal_dataset] + sys_datasets:
dataset["mapset"] = dataset["mapset"].combine_re(combine_regex)
dataset["mapset_unweighted"] = dataset[
"mapset_unweighted"].combine_re(combine_regex)
minimum_mc = metadata["minimum_mc"]
# Remove bins (i.e. set their count to zero) that have too few MC events
for dataset in sys_datasets + [nominal_dataset]:
for map_name in dataset["mapset"].names:
insuff_mc = dataset["mapset_unweighted"][
map_name].nominal_values < minimum_mc
# Setting the hist to zero sets both nominal value and std_dev to zero
dataset["mapset"][map_name].hist[insuff_mc] = 0.
hypersurface_fit_kw = metadata["hypersurface_fit_kw"]
hypersurfaces = collections.OrderedDict()
log = metadata[
"log"] # flag determining whether hs fit is run in log-space or not
for map_name in nominal_dataset["mapset"].names:
nominal_map = nominal_dataset["mapset"][map_name]
nominal_param_values = nominal_dataset["sys_params"]
sys_maps = [
sys_dataset["mapset"][map_name] for sys_dataset in sys_datasets
]
sys_param_values = [
sys_dataset["sys_params"] for sys_dataset in sys_datasets
]
hypersurface = Hypersurface(
# Yes, this MUST be a deepcopy! Otherwise weird memory overwrites happen
# and all the numbers get jumbled across the hypersurfaces of different maps
params=copy.deepcopy(hypersurface_params),
initial_intercept=0. if log else 1., # Initial value for intercept
log=log)
hypersurface.fit(
nominal_map=nominal_map,
nominal_param_values=nominal_param_values,
sys_maps=sys_maps,
sys_param_values=sys_param_values,
norm=True,
# Is the space or loading time really a problem?
# keep_maps=False, # it would take a lot more space otherwise
**hypersurface_fit_kw)
logging.debug("\nFitted hypersurface report:\n%s" % hypersurface)
hypersurfaces[map_name] = hypersurface
gridpoint_data["hs_fit"] = hypersurfaces
gridpoint_data["fit_successful"] = True
to_json(gridpoint_data, gridpoint_json)
# author: Timothy C. Arlen # [email protected] # from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter from pisa.utils.jsons import from_json,to_json from copy import deepcopy as copy parser = ArgumentParser(formatter_class=ArgumentDefaultsHelpFormatter) parser.add_argument('papa_file',type=str,metavar='JSON', help='papa settings file, containing the resolution parameterizations.') parser.add_argument('outfile',type=str,metavar='JSON', help='output file to store resolutions in PISA-format.') args = parser.parse_args() papa_settings = from_json(args.papa_file) parameterizations = papa_settings['fiducial']['reco_parametrization']['value'] pisa_flavs = ['nue','numu','nutau'] mID = ['','_bar'] intType = ['cc','nc'] recoType = ['coszen','energy'] papa_NC = parameterizations['NC'] egy_res = papa_NC['e'] papa_NC.pop('e') papa_NC['energy'] = egy_res pisa_reco_settings = {} for flav in pisa_flavs: papa_res = parameterizations[flav]
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
from pisa.utils.jsons import from_json, to_json
import numpy as np
parser = ArgumentParser(description='''Determines the false_h_best fiducial distribution, under the Gaussian assumption.''',
formatter_class=ArgumentDefaultsHelpFormatter)
parser.add_argument('-c','--cake_file', type=str, required=True,
help="File containing CAKE (PISA V3) data")
args = parser.parse_args()
cake_array = from_json(args.cake_file)['maps']
output_array = []
total_trck_dict = {}
total_cscd_dict = {}
for cake_dict in cake_array:
if 'trck' in cake_dict['name']:
if len(total_trck_dict.keys()) == 0:
total_trck_dict = cake_dict
total_trck_dict['name'] = 'trck'
else:
total_trck_dict['hist'] += cake_dict['hist']
elif 'cscd' in cake_dict['name']:
if len(total_cscd_dict.keys()) == 0:
total_cscd_dict = cake_dict
total_cscd_dict['name'] = 'cscd'
else:
parser.add_argument('-v',
'--verbose',
action='count',
default=None,
help='''set verbosity level''')
args = parser.parse_args()
#Set verbosity level
set_verbosity(args.verbose)
#Check binning
ebins, czbins = check_binning(args.osc_flux_maps)
logging.info("Defining aeff_service...")
if args.mc_mode:
logging.info(" Using effective area from EVENT DATA...")
aeff_service = AeffServiceMC(ebins,
czbins,
aeff_weight_file=args.weighted_aeff_file)
else:
logging.info(" Using effective area from PARAMETRIZATION...")
aeff_settings = from_json(find_resource(args.settings_file))
aeff_service = AeffServicePar(ebins, czbins, **aeff_settings)
event_rate_maps = get_event_rates(args.osc_flux_maps, aeff_service,
args.livetime, args.aeff_scale)
logging.info("Saving output to: %s" % args.outfile)
to_json(event_rate_maps, args.outfile)
parser.add_argument('-pd','--pseudo_data_settings',type=str,
metavar='JSONFILE',default=None,
help='''Settings for pseudo data templates, if desired to be different from template_settings.''')
parser.add_argument('-s','--save-steps',action='store_true',default=False,
dest='save_steps',
help="Save all steps the optimizer takes.")
parser.add_argument('-o','--outfile',type=str,default='llh_data.json',metavar='JSONFILE',
help="Output filename.")
parser.add_argument('-v', '--verbose', action='count', default=None,
help='set verbosity level')
args = parser.parse_args()
set_verbosity(args.verbose)
# Read in the settings
template_settings = from_json(args.template_settings)
minimizer_settings = from_json(args.minimizer_settings)
pseudo_data_settings = from_json(args.pseudo_data_settings) if args.pseudo_data_settings is not None else template_settings
# Parse the metric to be used
metric_name = 'chisquare' if args.use_chisquare else 'llh'
# Workaround for old scipy versions
import scipy
if scipy.__version__ < '0.12.0':
logging.warn('Detected scipy version %s < 0.12.0'%scipy.__version__)
if 'maxiter' in minimizer_settings:
logging.warn('Optimizer settings for \"maxiter\" will be ignored')
minimizer_settings.pop('maxiter')
def summarize_clsim_table(table_fpath,
table=None,
save_summary=True,
outdir=None):
"""
Parameters
----------
table_fpath : string
Path to table (or just the table's filename if `outdir` is specified)
table : mapping, optional
If the table has already been loaded, it can be passed here to avoid
re-loading the table.
save_summary : bool
Whether to save the table summary to disk.
outdir : string, optional
If `save_summary` is True, write the summary to this directory. If
`outdir` is not specified and `save_summary` is True, the summary will
be written to the same directory that contains `table_fpath`.
Returns
-------
table
See `load_clsim_table` for details of the data structure
summary : OrderedDict
"""
t_start = time()
if save_summary:
from pisa.utils.jsons import from_json, to_json
table_fpath = expand(table_fpath)
srcdir, clsim_fname = dirname(table_fpath), basename(table_fpath)
invalid_fname = False
try:
fname_info = interpret_clsim_table_fname(clsim_fname)
except ValueError:
invalid_fname = True
fname_info = {}
if outdir is None:
outdir = srcdir
outdir = expand(outdir)
mkdir(outdir)
if invalid_fname:
metapath = None
else:
metaname = (CLSIM_TABLE_METANAME_PROTO[-1].format(
hash_val=fname_info['hash_val']))
metapath = join(outdir, metaname)
if metapath and isfile(metapath):
meta = from_json(metapath)
else:
meta = dict()
if table is None:
table = load_clsim_table(table_fpath)
summary = OrderedDict()
for key in table.keys():
if key == 'table':
continue
summary[key] = table[key]
if fname_info:
for key in ('hash_val', 'string', 'depth_idx', 'seed'):
summary[key] = fname_info[key]
# TODO: Add hole ice info when added to tray_kw_to_hash
if meta:
summary['n_events'] = meta['tray_kw_to_hash']['NEvents']
summary['ice_model'] = meta['tray_kw_to_hash']['IceModel']
summary['tilt'] = not meta['tray_kw_to_hash']['DisableTilt']
for key, val in meta.items():
if key.endswith('_binning_kw'):
summary[key] = val
elif 'fname_version' in fname_info and fname_info['fname_version'] == 1:
summary['n_events'] = fname_info['n_events']
summary['ice_model'] = 'spice_mie'
summary['tilt'] = False
summary['r_binning_kw'] = dict(min=0.0, max=400.0, n_bins=200, power=2)
summary['costheta_binning_kw'] = dict(min=-1, max=1, n_bins=40)
summary['t_binning_kw'] = dict(min=0.0, max=3000.0, n_bins=300)
summary['costhetadir_binning_kw'] = dict(min=-1, max=1, n_bins=20)
summary['deltaphidir_binning_kw'] = dict(min=0.0, max=np.pi, n_bins=20)
# Save marginal distributions and info to file
norm = (
1 / table['n_photons'] /
(SPEED_OF_LIGHT_M_PER_NS / table['phase_refractive_index'] *
np.mean(np.diff(table['t_bin_edges'])))
#* table['angular_acceptance_fract']
* (len(table['costheta_bin_edges']) - 1))
summary['norm'] = norm
dim_names = ('r', 'costheta', 't', 'costhetadir', 'deltaphidir')
n_dims = len(table['table_shape'])
assert n_dims == len(dim_names)
# Apply norm to underflow and overflow so magnitudes can be compared
# relative to plotted marginal distributions
for flow, idx in product(('underflow', 'overflow'), iter(range(n_dims))):
summary[flow][idx] = summary[flow][idx] * norm
wstderr('Finding marginal distributions...\n')
wstderr(' masking off zeros in table...')
t0 = time()
nonzero_table = np.ma.masked_equal(table['table'], 0)
wstderr(' ({} ms)\n'.format(np.round((time() - t0) * 1e3, 3)))
t0_marg = time()
summary['dimensions'] = OrderedDict()
for keep_axis, ax_name in zip(tuple(range(n_dims)), dim_names):
remove_axes = list(range(n_dims))
remove_axes.pop(keep_axis)
remove_axes = tuple(remove_axes)
axis = OrderedDict()
wstderr(' mean across non-{} axes...'.format(ax_name))
t0 = time()
axis['mean'] = norm * np.asarray(
np.mean(table['table'], axis=remove_axes))
wstderr(' ({} s)\n'.format(np.round(time() - t0, 3)))
wstderr(' median across non-{} axes...'.format(ax_name))
t0 = time()
axis['median'] = norm * np.asarray(
np.ma.median(nonzero_table, axis=remove_axes))
wstderr(' ({} s)\n'.format(np.round(time() - t0, 3)))
wstderr(' max across non-{} axes...'.format(ax_name))
t0 = time()
axis['max'] = norm * np.asarray(
np.max(table['table'], axis=remove_axes))
wstderr(' ({} s)\n'.format(np.round(time() - t0, 3)))
summary['dimensions'][ax_name] = axis
wstderr(' Total time to find marginal distributions: {} s\n'.format(
np.round(time() - t0_marg, 3)))
if save_summary:
ext = None
base_fname = clsim_fname
while ext not in ('', '.fits'):
base_fname, ext = splitext(base_fname)
ext = ext.lower()
outfpath = join(outdir, base_fname + '_summary.json.bz2')
to_json(summary, outfpath)
print('saved summary to "{}"'.format(outfpath))
wstderr('Time to summarize table: {} s\n'.format(
np.round(time() - t_start, 3)))
return table, summary
help="settings file to use for making templates.")
hselect = parser.add_mutually_exclusive_group(required=False)
hselect.add_argument('--normal', dest='normal', default=True,
action='store_true', help="select the normal hierarchy")
hselect.add_argument('--inverted', dest='normal', default = False,
action='store_false', help="select the inverted hierarchy")
parser.add_argument('-v','--verbose',action='count',default=None,
help='set verbosity level.')
args = parser.parse_args()
set_verbosity(args.verbose)
profile.info("start initializing")
#Load all the settings
model_settings = from_json(args.settings)
#Select a hierarchy
logging.info('Selected %s hierarchy'%
('normal' if args.normal else 'inverted'))
params = select_hierarchy(model_settings['params'],normal_hierarchy=args.normal)
#Intialize template maker
template_maker = TemplateMaker(get_values(params),**model_settings['binning'])
profile.info("stop initializing")
#Now get the actual template
profile.info("start template calculation")
template_maker.get_template(get_values(params))
profile.info("stop template calculation")
