def __init_spline(self, knots, coeffs, deg, units=None):
knots = interpret_quantity(knots, expect_sequence=True)
self._state_attrs.extend(['knots', 'coeffs', 'deg'])
self.kind = 'spline'
if isunitless(knots):
knots = ureg.Quantity(knots, units)
elif units is not None:
units = ureg.Unit(units)
assert knots.dimensionality == units.dimensionality
knots = knots.to(units)
self.units = str(knots.units)
self.knots = knots
self.coeffs = coeffs
self.deg = deg
def llh(x):
x = self.__strip(self.__convert(x))
return splev(x, tck=(self.__strip(self.knots), coeffs, deg), ext=2)
self.llh = llh
self.max_at = fminbound(
func=self.__attach_units_to_args(self.chi2),
x1=np.min(self.__strip(self.knots)),
x2=np.max(self.__strip(self.knots)),
)
if self.units is not None:
self.max_at = self.max_at * ureg(self.units)
self.max_at_str = self.__stringify(self.max_at)
self.valid_range = (np.min(self.knots) * ureg(self.units),
np.max(self.knots) * ureg(self.units))
self._str = lambda s: 'spline prior: deg=%d, valid in [%s, %s]%s; max at %s%s' \
%(self.deg, self.__stringify(np.min(self.knots)),
self.__stringify(np.max(self.knots)), self.units_str,
self.max_at_str, self.units_str)
def parse_fit_config(fit_cfg):
"""Perform sanity checks on and parse fit configuration file.
Parameters
----------
fit_cfg : str
path to a fit configuration file
Returns
-------
fit_cfg : PISAConfigParser
parsed fit configuration
sys_list : list of str
parsed names of systematic parameters
units_list : list of str
units corresponding to each discrete systematic
combine_regex : list of str
each string is a regular expression for combining pipeline outputs; see
:func:`pisa.core.map.MapSet.combine_regex` for details.
"""
fit_cfg = from_file(fit_cfg)
no_ws_section_map = {s.strip(): s for s in fit_cfg.sections()}
if GENERAL_SECTION_NAME not in no_ws_section_map.values():
raise KeyError('Fit config is missing the "%s" section!' %
GENERAL_SECTION_NAME)
general_section = fit_cfg[GENERAL_SECTION_NAME]
if SYS_LIST_OPTION not in general_section:
raise KeyError(
"Fit config has to specify systematic parameters as"
' "%s" option in "%s" section (comma-separated list of names).' %
(SYS_LIST_OPTION, GENERAL_SECTION_NAME))
sys_list = [s.strip() for s in general_section[SYS_LIST_OPTION].split(",")]
if UNITS_OPTION in general_section:
units_list = []
units_specs = (general_section[UNITS_OPTION].replace(
UNITS_SPECIFIER, "").split(","))
for units_spec in units_specs:
# Make sure units are interpret-able by Pint
try:
ureg.Unit(units_spec)
except:
logging.error(
'Unit "%s" specified by "%s" option in "general" section is not'
"interpret-able by Pint",
units_spec,
UNITS_OPTION,
)
raise
units_list.append(units_spec)
else:
units_list = ["dimensionless" for s in sys_list]
logging.warn(
"No %s option found in %s section; assuming systematic parameters are"
" dimensionless",
UNITS_OPTION,
GENERAL_SECTION_NAME,
)
if len(units_list) != len(sys_list):
raise ValueError(
'{} units specified by "{}" option but {} systematics specified by "{}"'
"option; must be same number of each.".format(
len(units_list), UNITS_OPTION, len(sys_list), SYS_LIST_OPTION))
logging.info(
"Found systematic parameters %s",
["{} ({})".format(s, u) for s, u in zip(sys_list, units_list)],
)
combine_regex = general_section.get(COMBINE_REGEX_OPTION, None)
if combine_regex:
try:
combine_regex = literal_eval(combine_regex)
except (SyntaxError, ValueError):
logging.warn(
'Deprecated syntax for "combine_re" (make into a Python-evaluatable'
"sequence of strings instead) :: combine_regex = %s",
combine_regex,
)
combine_regex = [r.strip() for r in combine_regex.split(",")]
if APPLY_ALL_SECTION_NAME in no_ws_section_map:
apply_all_section = fit_cfg[no_ws_section_map[APPLY_ALL_SECTION_NAME]]
for no_ws_sname, sname in no_ws_section_map.items():
if not (no_ws_sname.startswith(NOMINAL_SET_PFX)
or no_ws_sname.startswith(SYS_SET_PFX)):
continue
sys_set_section = fit_cfg[sname]
for option, val in apply_all_section.items():
sys_set_section[option] = val
return fit_cfg, sys_list, units_list, combine_regex
def __init__(
self,
fit_results_file,
data=None,
params=None,
input_names=None,
output_names=None,
debug_mode=None,
error_method=None,
input_specs=None,
calc_specs=None,
output_specs=None,
links=None,
):
# -- Read fit_results_file and extract necessary info -- #
fit_results = from_file(fit_results_file)
# handle backwards compatibility for old style fit results files
if "hyperplanes" in fit_results:
using_old_fit_file = False
elif "sys_list" in fit_results:
using_old_fit_file = True
else:
raise ValueError("Unrecognised format for input fit file")
# get list of systematic parameter names fitted; need to conserve order here!
if using_old_fit_file:
fit_param_names = fit_results["sys_list"]
else:
fit_param_names = fit_results["param_names"]
if "param_units" in fit_results:
fit_param_units = fit_results["param_units"]
else:
fit_param_units = ["dimensionless" for _ in fit_param_names]
fit_param_units = [ureg.Unit(u) for u in fit_param_units]
# Perfer to have the actual binning, so we can compare bin edges to
# "reasonable" precision to make sure the hyperplane fits are applicable to the
# current binning.
#
# If there is no binning in the hyperplane fit results file, look for a hash
# value; barring that, just ensure that the dimensionality & number of bins
# match.
binning_spec = fit_results.get("binning", None)
if binning_spec is not None:
fit_binning = MultiDimBinning(**binning_spec)
else:
fit_binning = None
if fit_binning is not None:
fit_binning_hash = fit_binning.hash
else:
fit_binning_hash = fit_results.get("binning_hash", None)
if fit_binning_hash is None:
logging.warn("Cannot determine the hash of the binning employed"
" for the hyperplane fits. Correct application of"
" fits is not guaranteed!")
# -- Expected input / output names -- #
input_names = ()
output_names = ()
# -- Which keys are added or altered for the outputs during `apply` -- #
input_calc_keys = ()
output_calc_keys = ("hyperplane_scalefactors", )
if error_method == "sumw2":
output_apply_keys = ("weights", "errors")
input_apply_keys = output_apply_keys
else:
output_apply_keys = ("weights", )
input_apply_keys = output_apply_keys
# -- Initialize base class -- #
super(pi_hyperplanes, self).__init__(
data=data,
params=params,
expected_params=fit_param_names,
input_names=input_names,
output_names=output_names,
debug_mode=debug_mode,
error_method=error_method,
input_specs=input_specs,
calc_specs=calc_specs,
output_specs=output_specs,
input_calc_keys=input_calc_keys,
output_calc_keys=output_calc_keys,
input_apply_keys=input_apply_keys,
output_apply_keys=output_apply_keys,
)
# -- Only allowed/implemented modes -- #
assert self.input_mode is not None
assert self.calc_mode == "binned"
assert self.output_mode is not None
self.links = ast.literal_eval(links)
# -- Add attrs to `self` specific to `pi_hyperplanes` -- #
self.fit_results_file = fit_results_file
"""str : path to hyperplane fit results file"""
self.using_old_fit_file = using_old_fit_file
"""bool : whether the hyperplane fit file is in the "old" format"""
self.fit_results = fit_results
"""OrderedDict : parsed hyperplane fit file"""
self.fit_param_names = fit_param_names
"""list : param names used in hyperplane fit, in order they appear in file"""
self.fit_param_units = fit_param_units
"""list : param untis used in hyperplane fit, in order they appear in file"""
self.fit_binning = fit_binning
"""MultiDimBinning : binning used for hyperplane fits; one hyperplane per bin"""
self.fit_binning_hash = fit_binning_hash
"""str : hash of the binning used for hyperplane fits"""
def __init__(
self,
fit_results_file,
data=None,
params=None,
input_names=None,
output_names=None,
debug_mode=None,
error_method=None,
input_specs=None,
calc_specs=None,
output_specs=None,
links=None,
):
# -- Read fit_results_file and extract necessary info -- #
if fit_results_file.endswith('.csv'):
# in this case those are datarelease files
form = 'datarelease'
import pandas as pd
fit_results = {}
fit_results['nue_cc+nuebar_cc'] = pd.read_csv(
fit_results_file.replace('*', 'nue_cc'))
fit_results['numu_cc+numubar_cc'] = pd.read_csv(
fit_results_file.replace('*', 'numu_cc'))
fit_results['nutau_cc+nutaubar_cc'] = pd.read_csv(
fit_results_file.replace('*', 'nutau_cc'))
fit_results['nu_nc+nubar_nc'] = pd.read_csv(
fit_results_file.replace('*', 'all_nc'))
fit_param_names = [
a for a in fit_results['nu_nc+nubar_nc'].columns
if a not in ['pid', 'reco_energy', 'reco_coszen', 'offset']
]
fit_binning = calc_specs
else:
fit_results = from_file(fit_results_file)
# handle backwards compatibility for old style fit results files
if "hyperplanes" in fit_results:
form = 'linear'
elif "sys_list" in fit_results:
form = 'legacy'
else:
raise ValueError("Unrecognised format for input fit file")
# get list of systematic parameter names fitted; need to conserve order here!
if form == 'legacy':
fit_param_names = fit_results["sys_list"]
else:
fit_param_names = fit_results["param_names"]
# Perfer to have the actual binning, so we can compare bin edges to
# "reasonable" precision to make sure the hyperplane fits are applicable to the
# current binning.
#
# If there is no binning in the hyperplane fit results file, look for a hash
# value; barring that, just ensure that the dimensionality & number of bins
# match.
binning_spec = fit_results.get("binning", None)
if binning_spec is not None:
fit_binning = MultiDimBinning(**binning_spec)
else:
fit_binning = None
if "param_units" in fit_results:
fit_param_units = fit_results["param_units"]
else:
fit_param_units = ["dimensionless" for _ in fit_param_names]
fit_param_units = [ureg.Unit(u) for u in fit_param_units]
if fit_binning is not None:
fit_binning_hash = fit_binning.hash
else:
fit_binning_hash = fit_results.get("binning_hash", None)
if fit_binning_hash is None:
logging.warning("Cannot determine the hash of the binning employed"
" for the hyperplane fits. Correct application of"
" fits is not guaranteed!")
# -- Expected input / output names -- #
input_names = ()
output_names = ()
# -- Which keys are added or altered for the outputs during `apply` -- #
input_calc_keys = ()
output_calc_keys = ("hyperplane_scalefactors", )
if error_method == "sumw2":
output_apply_keys = ("weights", "errors")
input_apply_keys = output_apply_keys
else:
output_apply_keys = ("weights", )
input_apply_keys = output_apply_keys
# -- Initialize base class -- #
super().__init__(
data=data,
params=params,
expected_params=fit_param_names,
input_names=input_names,
output_names=output_names,
debug_mode=debug_mode,
error_method=error_method,
input_specs=input_specs,
calc_specs=calc_specs,
output_specs=output_specs,
input_calc_keys=input_calc_keys,
output_calc_keys=output_calc_keys,
input_apply_keys=input_apply_keys,
output_apply_keys=output_apply_keys,
)
# -- Only allowed/implemented modes -- #
assert self.input_mode is not None
assert self.calc_mode == "binned"
assert self.output_mode is not None
self.links = ast.literal_eval(links)
# -- Add attrs to `self` specific to `pi_hyperplanes` -- #
self.fit_results_file = fit_results_file
"""str : path to hyperplane fit results file"""
self.fit_results = fit_results
"""OrderedDict : parsed hyperplane fit file"""
self.fit_param_names = fit_param_names
"""list : param names used in hyperplane fit, in order they appear in file"""
self.fit_param_units = fit_param_units
"""list : param untis used in hyperplane fit, in order they appear in file"""
self.fit_binning = fit_binning
"""MultiDimBinning : binning used for hyperplane fits; one hyperplane per bin"""
self.fit_binning_hash = fit_binning_hash
"""str : hash of the binning used for hyperplane fits"""
self.form = form
"""str : format of input file"""
