def normcheckpath(path, checkdir=False):
"""Normalize a path and check that it exists.
Useful e.g. so that different path specifications that resolve to the same
location will resolve to the same string.
Parameters
----------
path : string
Path to check
checkdir : bool
Whether `path` is expected to be a directory
Returns
-------
normpath : string
Normalized path
"""
normpath = find_resource(path)
if checkdir:
kind = 'dir'
check = isdir
else:
kind = 'file'
check = isfile
if not check(normpath):
raise IOError('Path "%s" which resolves to "%s" is not a %s.' %
(path, normpath, kind))
return normpath
def read(self, filenames, encoding=None):
"""Override `read` method to interpret `filenames` as PISA resource
locations, then call overridden `read` method. Also, IOError fails
here, whereas it is ignored in RawConfigParser.
For further help on this method and its arguments, see
:method:`~backports.configparser.configparser.read`
"""
if isinstance(filenames, str):
filenames = [filenames]
resource_locations = []
for filename in filenames:
resource_location = find_resource(filename)
if not isfile(resource_location):
raise ValueError('"%s" is not a file or could not be located' %
filename)
resource_locations.append(resource_location)
filenames = resource_locations
# NOTE: From here on, most of the `read` method is copied, but
# ignoring IOError exceptions is removed here. Python copyrights apply.
if isinstance(filenames, str):
filenames = [filenames]
read_ok = []
for filename in filenames:
with open(filename, encoding=encoding) as fp:
self._read(fp, filename)
read_ok.append(filename)
return read_ok
def save(self, fpath, ver=None, **kwargs):
"""Save cross sections (and the energy specification) to a file at
`fpath`."""
if ver is None:
if self._ver is None:
raise ValueError(
'Either a ver must be specified in call to `save` or it '
'must have been set prior to the invocation of `save`.'
)
ver = self._ver
else:
assert ver == self._ver
try:
fpath = find_resource(fpath)
except IOError:
pass
fpath = os.path.expandvars(os.path.expanduser(fpath))
all_xs = {}
# Get any existing data from file
if os.path.exists(fpath):
all_xs = from_file(fpath)
# Validate existing data by instantiating objects from each
for v, d in all_xs.items():
CrossSections(ver=v, energy=d['energy'], xsec=d['xsec'])
if ver in all_xs:
logging.warning('Overwriting existing version "' + ver +
'" in file ' + fpath)
all_xs[ver] = {'xsec':self, 'energy':self.energy}
to_file(all_xs, fpath, **kwargs)
def __init__(
self,
events_file,
files_per_flavor,
output_names,
reco,
keys,
cuts,
track_E_cut=None,
**std_kwargs,
):
# instantiation args that should not change
self.events_file = find_resource(events_file)
# init base class
super().__init__(
expected_params=(),
**std_kwargs,
)
self.output_names = output_names
self.reco = reco
self.files_per_flavor = split(files_per_flavor)
self.track_E_cut = track_E_cut
self.keys = split(keys)
self.cuts = eval(cuts)
def setup_function(self):
# load MCeq tables
spline_tables_dict = pickle.load(
BZ2File(find_resource(self.params.table_file.value)))
self.data.data_specs = self.calc_specs
for container in self.data:
container['sys_flux'] = np.empty((container.size, 2), dtype=FTYPE)
if self.calc_mode == 'binned':
# speed up calculation by adding links
# as layers don't care about flavour
self.data.link_containers('nu', [
'nue_cc', 'numu_cc', 'nutau_cc', 'nue_nc', 'numu_nc',
'nutau_nc', 'nuebar_cc', 'numubar_cc', 'nutaubar_cc',
'nuebar_nc', 'numubar_nc', 'nutaubar_nc'
])
for container in self.data:
# evaluate the splines (flux and deltas) for each E/CZ point
# at the moment this is done on CPU, therefore we force 'host'
for key in spline_tables_dict.keys():
logging.info(
'Evaluating MCEq splines for %s for Barr parameter %s' %
(container.name, key))
container['barr_' + key] = np.empty((container.size, 8),
dtype=FTYPE)
self.eval_spline(container['true_energy'].get('host'),
container['true_coszen'].get('host'),
spline_tables_dict[key],
out=container['barr_' + key].get('host'))
container['barr_' + key].mark_changed('host')
self.data.unlink_containers()
def setup_function(self):
# object for oscillation parameters
self.osc_params = OscParams()
# setup the layers
#if self.params.earth_model.value is not None:
earth_model = find_resource(self.params.earth_model.value)
YeI = self.params.YeI.value.m_as('dimensionless')
YeO = self.params.YeO.value.m_as('dimensionless')
YeM = self.params.YeM.value.m_as('dimensionless')
prop_height = self.params.prop_height.value.m_as('km')
detector_depth = self.params.detector_depth.value.m_as('km')
self.layers = Layers(earth_model, detector_depth, prop_height)
self.layers.setElecFrac(YeI, YeO, YeM)
# set the correct data mode
self.data.data_specs = self.calc_specs
# --- calculate the layers ---
if self.calc_mode == 'binned':
# speed up calculation by adding links
# as layers don't care about flavour
self.data.link_containers('nu', [
'nue_cc', 'numu_cc', 'nutau_cc', 'nue_nc', 'numu_nc',
'nutau_nc', 'nuebar_cc', 'numubar_cc', 'nutaubar_cc',
'nuebar_nc', 'numubar_nc', 'nutaubar_nc'
])
for container in self.data:
self.layers.calcLayers(container['true_coszen'].get('host'))
container['densities'] = self.layers.density.reshape(
(container.size, self.layers.max_layers))
container['distances'] = self.layers.distance.reshape(
(container.size, self.layers.max_layers))
# don't forget to un-link everything again
self.data.unlink_containers()
# --- setup empty arrays ---
if self.calc_mode == 'binned':
self.data.link_containers('nu', [
'nue_cc', 'numu_cc', 'nutau_cc', 'nue_nc', 'numu_nc',
'nutau_nc'
])
self.data.link_containers('nubar', [
'nuebar_cc', 'numubar_cc', 'nutaubar_cc', 'nuebar_nc',
'numubar_nc', 'nutaubar_nc'
])
for container in self.data:
container['probability'] = np.empty((container.size, 3, 3),
dtype=FTYPE)
self.data.unlink_containers()
# setup more empty arrays
for container in self.data:
container['prob_e'] = np.empty((container.size), dtype=FTYPE)
container['prob_mu'] = np.empty((container.size), dtype=FTYPE)
def setup_function(self):
# setup Earth model
if self.params.earth_model.value is not None:
earth_model = find_resource(self.params.earth_model.value)
YeI = self.params.YeI.value.m_as('dimensionless')
YeO = self.params.YeO.value.m_as('dimensionless')
YeM = self.params.YeM.value.m_as('dimensionless')
else:
earth_model = None
# setup the layers
prop_height = self.params.prop_height.value.m_as('km')
detector_depth = self.params.detector_depth.value.m_as('km')
self.layers = Layers(earth_model, detector_depth, prop_height)
if earth_model is not None:
self.layers.setElecFrac(YeI, YeO, YeM)
# set the correct data mode
self.data.representation = self.calc_mode
# --- calculate the layers ---
if self.data.is_map:
# speed up calculation by adding links
# as layers don't care about flavour
self.data.link_containers('nu', ['nue_cc', 'numu_cc', 'nutau_cc',
'nue_nc', 'numu_nc', 'nutau_nc',
'nuebar_cc', 'numubar_cc', 'nutaubar_cc',
'nuebar_nc', 'numubar_nc', 'nutaubar_nc'])
for container in self.data:
if self.params.earth_model.value is not None:
self.layers.calcLayers(container['true_coszen'])
container['densities'] = self.layers.density.reshape((container.size, self.layers.max_layers))
container['distances'] = self.layers.distance.reshape((container.size, self.layers.max_layers))
else:
self.layers.calcPathLength(container['true_coszen'])
container['distances'] = self.layers.distance
# don't forget to un-link everything again
self.data.unlink_containers()
# --- setup empty arrays ---
if self.data.is_map:
self.data.link_containers('nu', ['nue_cc', 'numu_cc', 'nutau_cc',
'nue_nc', 'numu_nc', 'nutau_nc'])
self.data.link_containers('nubar', ['nuebar_cc', 'numubar_cc', 'nutaubar_cc',
'nuebar_nc', 'numubar_nc', 'nutaubar_nc'])
for container in self.data:
container['probability'] = np.empty((container.size, 3, 3), dtype=FTYPE)
self.data.unlink_containers()
# setup more empty arrays
for container in self.data:
container['prob_e'] = np.empty((container.size), dtype=FTYPE)
container['prob_mu'] = np.empty((container.size), dtype=FTYPE)
def __load(self, fname):
fpath = resources.find_resource(fname)
with h5py.File(fpath, 'r') as open_file:
meta = dict(open_file.attrs)
for k, v in meta.items():
if hasattr(v, 'tolist'):
meta[k] = v.tolist()
data = hdf.from_hdf(open_file)
self.validate(data)
return data, meta
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 __init__(self, fp, fpname, fpath=None):
self._iter_stack = []
"""Stack for storing dicts with 'fp', 'fpname', 'fpath', 'lineno', and
'line' for keeping track of the hierarchy of master config & included
configs"""
# It's ok to not find the fpname / fpname to not be a file for the
# *master* config, since this could e.g. be a io.StringIO file-like
# object (`read_string`) which comes from no actual file/resource on
# disk.
if not fpname and hasattr(fp, 'name'):
fpname = fp.name
if fpath is None:
try:
resource = find_resource(fpname)
except IOError:
pass
else:
if isfile(resource):
fpath = abspath(expanduser(expandvars(fpname)))
if fpath is None:
try:
resource = find_resource(fpname)
except IOError:
pass
else:
if isfile(resource):
fpath = resource
if fpath is None:
self.fpaths_processed = []
else:
self.fpaths_processed = [fpath]
self.fps_processed = [fp]
record = dict(fp=fp, fpname=fpname, fpath=fpath, lineno=0, line='')
self._iter_stack.append(record)
self.file_hierarchy = OrderedDict([(fpname, OrderedDict())])
def __init__(self, airs_spline, **std_kwargs):
_airs_spline_loc = find_resource(airs_spline)
self.airs_spline = photospline.SplineTable(_airs_spline_loc)
expected_params = [
"airs_scale",
]
super().__init__(
expected_params=expected_params,
**std_kwargs,
)
def normcheckpath(path, checkdir=False):
normpath = find_resource(path)
if checkdir:
kind = 'dir'
check = os.path.isdir
else:
kind = 'file'
check = os.path.isfile
if not check(normpath):
raise IOError('Path "%s" which resolves to "%s" is not a %s.'
% (path, normpath, kind))
return normpath
def __init__(
self,
in_files,
lic_files,
output_names,
n_files: int,
diff_nu_cc_xs="dsdxdy_nu_CC_iso.fits",
diff_nubar_cc_xs="dsdxdy_nubar_CC_iso.fits",
diff_nu_nc_xs="dsdxdy_nu_NC_iso.fits",
diff_nubar_nc_xs="dsdxdy_nubar_NC_iso.fits",
**std_kwargs
):
if isinstance(lic_files, str):
self._lic_files_paths = [
find_resource(lic_files),
]
elif isinstance(lic_files, (list, tuple)):
self._lic_files_paths = [find_resource(lic_file) for lic_file in lic_files]
else:
raise TypeError("Unknown lic_file datatype {}".format(type(lic_files)))
if isinstance(in_files, str):
self.in_files = [
find_resource(in_files),
]
elif isinstance(in_files, (tuple, list)):
self.in_files = [find_resource(in_file) for in_file in in_files]
else:
raise TypeError("Unknown in_files datatype {}".format(type(in_files)))
# load the lic files!
self.lic_files = [
LW.MakeGeneratorsFromLICFile(name) for name in self._lic_files_paths
]
self.xs_obj = LW.CrossSectionFromSpline(
find_resource(diff_nu_cc_xs),
find_resource(diff_nubar_cc_xs),
find_resource(diff_nu_nc_xs),
find_resource(diff_nubar_nc_xs),
)
# the target containers!
self.output_names = output_names
# with this, we just need to multiply the weight by the actual flux. Then it'll work!
self._one_weighter = LW.Weighter(
LW.ConstantFlux(1.0 / n_files), self.xs_obj, self.lic_files
)
def _compute_nominal_outputs(self):
'''
load events, perform sanity check and put them into histograms,
if alt_bg file is specified, also put these events into separate histograms,
that are normalized to the nominal ones (we are only interested in the shape difference)
'''
# get params
icc_bg_file = self.params.icc_bg_file.value
if 'shape' in self.error_method:
alt_icc_bg_file = self.params.alt_icc_bg_file.value
else:
alt_icc_bg_file = None
sim_ver = self.params.sim_ver.value
use_def1 = self.params.use_def1.value
bdt_cut = self.params.bdt_cut.m_as('dimensionless')
self.bin_names = self.output_binning.names
self.bin_edges = []
for name in self.bin_names:
if 'energy' in name:
bin_edges = self.output_binning[name].bin_edges.to('GeV').magnitude
else:
bin_edges = self.output_binning[name].bin_edges.magnitude
self.bin_edges.append(bin_edges)
# the rest of this function is PISA v2 legacy code...
logging.info('Initializing BackgroundServiceICC...')
logging.info('Opening file: %s'%(icc_bg_file))
try:
bg_file = h5py.File(find_resource(icc_bg_file),'r')
if alt_icc_bg_file is not None:
alt_bg_file = h5py.File(find_resource(alt_icc_bg_file),'r')
except IOError,e:
logging.error("Unable to open icc_bg_file %s"%icc_bg_file)
logging.error(e)
sys.exit(1)
def setup_function(self):
import ROOT
# setup the layers
earth_model = find_resource(self.earth_model)
self.layers = Layers(earth_model, self.detector_depth,
self.prop_height)
# This is a bit hacky, but setting the electron density to 1.
# gives us the total density of matter, which is what we want.
self.layers.setElecFrac(1., 1., 1.)
# setup cross-sections
self.xsroot = ROOT.TFile(self.xsec_file)
# set the correct data mode
self.data.data_specs = self.calc_specs
# --- calculate the layers ---
if self.calc_mode == 'binned':
# layers don't care about flavor
self.data.link_containers('nu', [
'nue_cc', 'numu_cc', 'nutau_cc', 'nue_nc', 'numu_nc',
'nutau_nc', 'nuebar_cc', 'numubar_cc', 'nutaubar_cc',
'nuebar_nc', 'numubar_nc', 'nutaubar_nc'
])
for container in self.data:
self.layers.calcLayers(container['true_coszen'].get(WHERE))
container['densities'] = self.layers.density.reshape(
(container.size, self.layers.max_layers))
container['distances'] = self.layers.distance.reshape(
(container.size, self.layers.max_layers))
container['rho_int'] = np.empty((container.size), dtype=FTYPE)
# don't forget to un-link everything again
self.data.unlink_containers()
# --- setup cross section and survival probability ---
if self.calc_mode == 'binned':
# The cross-sections do not depend on nc/cc, so we can at least link those containers
self.data.link_containers('nue', ['nue_cc', 'nue_nc'])
self.data.link_containers('nuebar', ['nuebar_cc', 'nuebar_nc'])
self.data.link_containers('numu', ['numu_cc', 'numu_nc'])
self.data.link_containers('numubar', ['numubar_cc', 'numubar_nc'])
self.data.link_containers('nutau', ['nutau_cc', 'nutau_nc'])
self.data.link_containers('nutaubar',
['nutaubar_cc', 'nutaubar_nc'])
for container in self.data:
container['xsection'] = np.empty((container.size), dtype=FTYPE)
container['survival_prob'] = np.empty((container.size),
dtype=FTYPE)
self.data.unlink_containers()
def __init__(
self,
events_file,
**std_kwargs,
):
# instantiation args that should not change
self.events_file = find_resource(events_file)
expected_params = ('atm_muon_scale', )
# init base class
super().__init__(
expected_params=expected_params,
**std_kwargs,
)
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 setup_function(self):
sys.path.append(self.globes_wrapper)
import GLoBES
### you need to start GLoBES from the folder containing a dummy experiment
# therefore we go to the folder, load GLoBES and then go back
curdir = os.getcwd()
os.chdir(self.globes_wrapper)
self.globes_calc = GLoBES.GLoBESCalculator("calc")
os.chdir(curdir)
self.globes_calc.InitSteriles(2)
# object for oscillation parameters
self.osc_params = OscParams()
earth_model = find_resource(self.earth_model)
prop_height = self.prop_height.m_as('km')
detector_depth = self.detector_depth.m_as('km')
self.layers = Layers(earth_model, detector_depth, prop_height)
# The electron fractions are taken into account internally by GLoBES/SNU.
# See the SNU patch for details. It uses the density to decide
# whether it is in the core or in the mantle. Therefore, we just multiply by
# one to give GLoBES the raw densities.
self.layers.setElecFrac(1., 1., 1.)
# set the correct data mode
self.data.data_specs = self.calc_specs
# --- calculate the layers ---
if self.calc_mode == 'binned':
# speed up calculation by adding links
# as layers don't care about flavour
self.data.link_containers('nu', ['nue_cc', 'numu_cc', 'nutau_cc',
'nue_nc', 'numu_nc', 'nutau_nc',
'nuebar_cc', 'numubar_cc', 'nutaubar_cc',
'nuebar_nc', 'numubar_nc', 'nutaubar_nc'])
for container in self.data:
self.layers.calcLayers(container['true_coszen'].get('host'))
container['densities'] = self.layers.density.reshape((container.size, self.layers.max_layers))
container['distances'] = self.layers.distance.reshape((container.size, self.layers.max_layers))
# don't forget to un-link everything again
self.data.unlink_containers()
# setup probability containers
for container in self.data:
container['prob_e'] = np.empty((container.size), dtype=FTYPE)
container['prob_mu'] = np.empty((container.size), dtype=FTYPE)
container['prob_nonsterile'] = np.empty((container.size), dtype=FTYPE)
def __init__(
self,
events_file,
output_names,
**std_kwargs,
):
# instantiation args that should not change
self.events_file = find_resource(events_file)
# init base class
super().__init__(
expected_params=(),
**std_kwargs,
)
self.output_names = output_names
def read(self, filenames, encoding=None):
"""Override `read` method to interpret `filenames` as PISA resource
locations, then call overridden `read` method. Also, IOError fails
here, whereas it is ignored in RawConfigParser.
For further help on this method and its arguments, see
:method:`~backports.configparser.configparser.read`
"""
if isinstance(filenames, basestring):
filenames = [filenames]
resource_locations = []
for filename in filenames:
resource_location = find_resource(filename)
if not isfile(resource_location):
raise ValueError('"%s" is not a file or could not be located' %
filename)
resource_locations.append(resource_location)
filenames = resource_locations
# NOTE: From here on, most of the `read` method is copied, but
# ignoring IOError exceptions is removed here. Python copyrights apply.
if PY2 and isinstance(filenames, bytes):
# we allow for a little unholy magic for Python 2 so that
# people not using unicode_literals can still use the library
# conveniently
warnings.warn(
"You passed a bytestring as `filenames`. This will not work"
" on Python 3. Use `cp.read_file()` or switch to using Unicode"
" strings across the board.",
DeprecationWarning,
stacklevel=2,
)
filenames = [filenames]
elif isinstance(filenames, str):
filenames = [filenames]
read_ok = []
for filename in filenames:
with c_open(filename, encoding=encoding) as fp:
self._read(fp, filename)
read_ok.append(filename)
return read_ok
def __init__(self, run_settings, detector=None):
super().__init__()
if isinstance(run_settings, str):
rsd = fileio.from_file(resources.find_resource(run_settings))
elif isinstance(run_settings, dict):
rsd = run_settings
else:
raise TypeError('Unhandled run_settings type passed in arg: ' +
type(run_settings))
if detector:
detector = str(detector).strip()
self.detector = detector
# Determine how deeply nested runs are in the dict to allow for
# user to specify a dict that has multiple detectors in it OR
# a dict with just a single detector in it
if 'flavints' in rsd.values()[0]:
runs_d = rsd
elif 'flavints' in rsd.values()[0].values()[0]:
if self.detector is None:
if len(rsd) == 1:
runs_d = rsd.values()[0]
else:
raise ValueError('Must specify which detector; detectors '
'found: ' + str(rsd.keys()))
else:
runs_d = rsd[self.detector.strip()]
else:
raise Exception('dict must either be 3 levels: '
'{DET:{RUN:{...}}}; or 2 levels: {RUN:{...}}')
# Force run numbers to be strings (JSON files cannot have an int as
# a key, so it is a string upon import, and it's safest to keep it as
# a string considering how non-standardized naming is in IceCube) and
# convert actual run settings dict to MCSimRunSettings instances
runs_d = {str(k): MCSimRunSettings(v) for k, v in runs_d.items()}
# Save the runs_d to this object instance, which behaves like a dict
self.update(runs_d)
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 load_events(self, events):
"""Load events from path given by `events`. Stored as `self.events`.
Parameters
----------
events : string or Events object
If string, load events from that location. If Events object,
deepcopy to obtain `self.events`
"""
if isinstance(events, Param):
events = events.value
elif isinstance(events, basestring):
events = find_resource(events)
this_hash = hash_obj(events, full_hash=self.full_hash)
if self._events_hash is not None and this_hash == self._events_hash:
return
logging.debug("Extracting events from Events obj or file: %s", events)
events_obj = Events(events)
events_hash = this_hash
self.events = events_obj
self._events_hash = events_hash
def _compute_nominal_outputs(self):
'''
load events, perform sanity check and put them into histograms,
if alt_bg file is specified, also put these events into separate histograms,
that are normalized to the nominal ones (we are only interested in the shape difference)
'''
# get params
icc_bg_file = self.params.icc_bg_file.value
if 'shape' in self.error_method:
alt_icc_bg_file = self.params.alt_icc_bg_file.value
else:
alt_icc_bg_file = None
sim_ver = self.params.sim_ver.value
use_def1 = self.params.use_def1.value
bdt_cut = self.params.bdt_cut.m_as('dimensionless')
self.bin_names = self.output_binning.names
self.bin_edges = []
for name in self.bin_names:
if 'energy' in name:
bin_edges = self.output_binning[name].bin_edges.to(
'GeV').magnitude
else:
bin_edges = self.output_binning[name].bin_edges.magnitude
self.bin_edges.append(bin_edges)
# the rest of this function is PISA v2 legacy code...
logging.info('Initializing BackgroundServiceICC...')
logging.info('Opening file: %s', icc_bg_file)
try:
bg_file = h5py.File(find_resource(icc_bg_file), 'r')
if alt_icc_bg_file is not None:
alt_bg_file = h5py.File(find_resource(alt_icc_bg_file), 'r')
except IOError as e:
logging.error("Unable to open icc_bg_file %s", icc_bg_file)
logging.error(e)
sys.exit(1)
# sanity check
santa_doms = bg_file['IC86_Dunkman_L6_SANTA_DirectDOMs']['value']
l3 = bg_file['IC86_Dunkman_L3']['value']
l4 = bg_file['IC86_Dunkman_L4']['result']
l5 = bg_file['IC86_Dunkman_L5']['bdt_score']
l6 = bg_file['IC86_Dunkman_L6']
if use_def1:
l4_pass = np.all(l4 == 1)
else:
if sim_ver in ['5digit', 'dima']:
l4_invVICH = bg_file['IC86_Dunkman_L4']['result_invertedVICH']
l4_pass = np.all(np.logical_or(l4 == 1, l4_invVICH == 1))
else:
logging.info(
'For the old simulation, def.2 background not done yet,'
' so still use def1 for it.')
l4_pass = np.all(l4 == 1)
assert (np.all(santa_doms >= 3) and np.all(l3 == 1) and l4_pass
and np.all(l5 >= 0.1))
corridor_doms_over_threshold = l6['corridor_doms_over_threshold']
inverted_corridor_cut = corridor_doms_over_threshold > 1
assert (np.all(inverted_corridor_cut)
and np.all(l6['santa_direct_doms'] >= 3)
and np.all(l6['mn_start_contained'] == 1.)
and np.all(l6['mn_stop_contained'] == 1.))
#load events
if sim_ver == '4digit':
variable = 'IC86_Dunkman_L6_MultiNest8D_PDG_Neutrino'
elif sim_ver in ['5digit', 'dima']:
variable = 'IC86_Dunkman_L6_PegLeg_MultiNest8D_NumuCC'
else:
raise ValueError('Only allow sim_ver 4digit, 5 digit or dima!')
reco_energy_all = np.array(bg_file[variable]['energy'])
reco_coszen_all = np.array(np.cos(bg_file[variable]['zenith']))
pid_all = np.array(bg_file['IC86_Dunkman_L6']['delta_LLH'])
if alt_icc_bg_file is not None:
alt_reco_energy_all = np.array(alt_bg_file[variable]['energy'])
alt_reco_coszen_all = np.array(
np.cos(alt_bg_file[variable]['zenith']))
alt_pid_all = np.array(alt_bg_file['IC86_Dunkman_L6']['delta_LLH'])
alt_l5 = alt_bg_file['IC86_Dunkman_L5']['bdt_score']
# Cut: Only keep bdt score >= 0.2 (from MSU latest result, make data/MC
# agree much better)
cut_events = {}
cut = l5 >= bdt_cut
cut_events['reco_energy'] = reco_energy_all[cut]
cut_events['reco_coszen'] = reco_coszen_all[cut]
cut_events['pid'] = pid_all[cut]
if alt_icc_bg_file is not None:
# Cut: Only keep bdt score >= 0.2 (from MSU latest result, make
# data/MC agree much better)
alt_cut_events = {}
alt_cut = alt_l5 >= bdt_cut
alt_cut_events['reco_energy'] = alt_reco_energy_all[alt_cut]
alt_cut_events['reco_coszen'] = alt_reco_coszen_all[alt_cut]
alt_cut_events['pid'] = alt_pid_all[alt_cut]
logging.info("Creating a ICC background hists...")
# make histo
if self.params.kde_hist.value:
self.icc_bg_hist = self.kde_histogramdd(
np.array([cut_events[bin_name]
for bin_name in self.bin_names]).T,
binning=self.output_binning,
coszen_name='reco_coszen',
use_cuda=True,
bw_method='silverman',
alpha=0.3,
oversample=10,
coszen_reflection=0.5,
adaptive=True)
else:
self.icc_bg_hist, _ = np.histogramdd(sample=np.array(
[cut_events[bin_name] for bin_name in self.bin_names]).T,
bins=self.bin_edges)
conversion = self.params.atm_muon_scale.value.m_as(
'dimensionless') / ureg('common_year').to('seconds').m
logging.info('nominal ICC rate at %.6E Hz',
self.icc_bg_hist.sum() * conversion)
if alt_icc_bg_file is not None:
if self.params.kde_hist.value:
self.alt_icc_bg_hist = self.kde_histogramdd(
np.array([
alt_cut_events[bin_name] for bin_name in self.bin_names
]).T,
binning=self.output_binning,
coszen_name='reco_coszen',
use_cuda=True,
bw_method='silverman',
alpha=0.3,
oversample=10,
coszen_reflection=0.5,
adaptive=True)
else:
self.alt_icc_bg_hist, _ = np.histogramdd(sample=np.array([
alt_cut_events[bin_name] for bin_name in self.bin_names
]).T,
bins=self.bin_edges)
# only interested in shape difference, not rate
scale = self.icc_bg_hist.sum() / self.alt_icc_bg_hist.sum()
self.alt_icc_bg_hist *= scale
def switch_to_file(self, fp=None, fpname=None):
"""Switch iterator to a new resource location to continue processing.
Parameters
----------
fp : None or file-like object
If `fp` is specified, this takes precedence over `fpname`.
fpname : None or string
Path of the file or resource to read from. This resource will be
located and opened if `fp` is None.
encoding
Argument is passed to the builtin ``open`` function for opening
the file.
"""
fpath = None
if fp is None:
assert fpname
resource = find_resource(fpname)
if isfile(resource):
fpath = abspath(expanduser(expandvars(resource)))
if fpath in self.fpaths_processed:
self._cleanup()
raise ValueError(
'Circular reference; already processed "%s" at path'
' "%s"' % (fpname, fpath))
else:
self._cleanup()
raise ValueError('`fpname` "%s" is not a file')
fp_ = c_open(fpath, encoding=None)
else:
fp_ = fp
if fpname is None:
if hasattr(fp_, 'name'):
fpname = fp_.name
else:
fpname = ''
try:
resource = find_resource(fpname)
except IOError:
pass
else:
if isfile(resource):
fpath = resource
if fp in self.fps_processed:
self._cleanup()
raise ValueError(
'Circular reference; already processed file pointer "%s"'
' at path "%s"' % (fp_, fpname))
if fpath is not None:
if fpath in self.fpaths_processed:
self._cleanup()
raise ValueError(
'Circular reference; already processed "%s" at path'
' "%s"' % (fpname, fpath))
self.fpaths_processed.append(fpath)
self.fps_processed.append(fp)
if fpath is not None:
self.fpaths_processed.append(fpath)
logging.trace('Switching to "%s" at path "%s"' % (fpname, fpath))
record = dict(fp=fp_, fpname=fpname, fpath=fpath, lineno=0, line='')
self._iter_stack.append(record)
def make_toy_events(outdir, num_events, energy_range, spectral_index,
coszen_range, num_sets, first_set, aeff_energy_param,
aeff_coszen_param, reco_param, pid_param, pid_dist):
"""Make toy events and store to a file.
Parameters
----------
outdir : string
num_events : int
energy_range : 2-tuple of floats
spectral_index : float
coszen_range : 2-tuple of floats
num_sets : int
first_set : int
aeff_energy_param : string
aeff_coszen_param : string
reco_param : string
pid_param : string
pid_dist : string
Returns
-------
events : :class:`pisa.core.events.Events`
"""
energy_range = sorted(energy_range)
coszen_range = sorted(coszen_range)
# Validation of args
assert energy_range[0] > 0 and energy_range[1] < 1e9
assert coszen_range[0] >= -1 and coszen_range[1] <= 1
assert np.diff(energy_range)[0] > 0, str(energy_range)
assert np.diff(coszen_range)[0] > 0, str(coszen_range)
assert spectral_index >= 0, str(spectral_index)
assert first_set >= 0, str(first_set)
assert num_sets >= 1, str(first_set)
# Make sure resources specified actually exist
for arg in [aeff_energy_param, aeff_coszen_param, reco_param, pid_param]:
find_resource(arg)
mkdir(outdir, warn=False)
set_indices = list(range(first_set, first_set + num_sets))
# The following loop is for validation only
for num, index in product(num_events, set_indices):
mcgen_random_state(num_events=num, set_index=index)
for num, set_index in product(num_events, set_indices):
mcevts_fname = FNAME_TEMPLATE.format(
file_type='events',
detector='vlvnt',
e_min=format_num(energy_range[0]),
e_max=format_num(energy_range[1]),
spectral_index=format_num(spectral_index,
sigfigs=2,
trailing_zeros=True),
cz_min=format_num(coszen_range[0]),
cz_max=format_num(coszen_range[1]),
num_events=format_num(num, sigfigs=3, sci_thresh=(1, -1)),
set_index=format_num(set_index, sci_thresh=(10, -10)),
extension='hdf5')
mcevts_fpath = os.path.join(outdir, mcevts_fname)
if os.path.isfile(mcevts_fpath):
logging.warn('File already exists, skipping: "%s"', mcevts_fpath)
continue
logging.info('Working on set "%s"', mcevts_fname)
# TODO: pass filepaths / resource locations via command line args
# Create a single random state object to pass from function to function
random_state = mcgen_random_state(num_events=num, set_index=set_index)
mc_events = generate_mc_events(
num_events=num,
energy_range=energy_range,
coszen_range=coszen_range,
spec_ind=spectral_index,
aeff_energy_param_source=aeff_energy_param,
aeff_coszen_param_source=aeff_coszen_param,
random_state=random_state)
populate_reco_observables(mc_events=mc_events,
param_source=reco_param,
random_state=random_state)
populate_pid(mc_events=mc_events,
param_source=pid_param,
random_state=random_state,
dist=pid_dist)
to_file(mc_events, mcevts_fpath)
return mc_events
def _compute_nominal_outputs(self):
"""load the evnts from file, perform sanity checks and histogram them
(into final MapSet)
"""
# get params
data_file_name = self.params.data_file.value
sim_version = self.params.sim_ver.value
bdt_cut = self.params.bdt_cut.value.m_as('dimensionless')
self.bin_names = self.output_binning.names
# TODO: convert units using e.g. `comp_units` in stages/reco/hist.py
self.bin_edges = []
for name in self.bin_names:
if 'energy' in name:
bin_edges = self.output_binning[name].bin_edges.to('GeV').magnitude
else:
bin_edges = self.output_binning[name].bin_edges.magnitude
self.bin_edges.append(bin_edges)
# the rest of this function is PISA v2 legacy code...
# right now only use burn sample with sim_version = '4digit'
#print "sim_version == ", sim_version
if sim_version == "4digit":
Reco_Neutrino_Name = 'IC86_Dunkman_L6_MultiNest8D_PDG_Neutrino'
Reco_Track_Name = 'IC86_Dunkman_L6_MultiNest8D_PDG_Track'
elif sim_version == "5digit" or sim_version=="dima":
Reco_Neutrino_Name = 'IC86_Dunkman_L6_PegLeg_MultiNest8D_NumuCC'
Reco_Track_Name = 'IC86_Dunkman_L6_PegLeg_MultiNest8D_Track'
else:
raise ValueError(
'only allow 4digit, 5digit(H2 model for hole ice) or'
' dima (dima p1 and p2 for hole ice)!'
)
data_file = h5py.File(find_resource(data_file_name), 'r')
L6_result = np.array(data_file['IC86_Dunkman_L6']['result'])
dLLH = np.array(data_file['IC86_Dunkman_L6']['delta_LLH'])
reco_energy_all = np.array(data_file[Reco_Neutrino_Name]['energy'])
reco_coszen_all = np.array(np.cos(
data_file[Reco_Neutrino_Name]['zenith']
))
reco_trck_len_all = np.array(data_file[Reco_Track_Name]['length'])
#print "before L6 cut, no. of burn sample = ", len(reco_coszen_all)
# sanity check
santa_doms = data_file['IC86_Dunkman_L6_SANTA_DirectDOMs']['value']
l3 = data_file['IC86_Dunkman_L3']['value']
l4 = data_file['IC86_Dunkman_L4']['result']
l5 = data_file['IC86_Dunkman_L5']['bdt_score']
assert(np.all(santa_doms>=3) and np.all(l3 == 1) and np.all(l5 >= 0.1))
# l4==1 was not applied when i3 files were written to hdf5 files, so do
# it here
dLLH = dLLH[l4==1]
reco_energy_all = reco_energy_all[l4==1]
reco_coszen_all = reco_coszen_all[l4==1]
l5 = l5[l4==1]
L6_result = L6_result[l4==1]
data_file.close()
dLLH_L6 = dLLH[L6_result==1]
l5 = l5[L6_result==1]
reco_energy_L6 = reco_energy_all[L6_result==1]
reco_coszen_L6 = reco_coszen_all[L6_result==1]
#print "after L6 cut, no. of burn sample = ", len(reco_coszen_L6)
# Cut: Only keep bdt score >= 0.2 (from MSU latest result, make data/MC
# agree much better); if use no such further cut, use bdt_cut = 0.1
logging.info(
"Cut2, removing events with bdt_score < %s i.e. only keep bdt > %s"
%(bdt_cut, bdt_cut)
)
cut_events = {}
cut = l5>=bdt_cut
cut_events['reco_energy'] = reco_energy_L6[cut]
cut_events['reco_coszen'] = reco_coszen_L6[cut]
cut_events['pid'] = dLLH_L6[cut]
hist, _ = np.histogramdd(sample = np.array(
[cut_events[bin_name] for bin_name in self.bin_names]
).T, bins=self.bin_edges)
maps = [Map(name=self.output_names[0], hist=hist,
binning=self.output_binning)]
self.template = MapSet(maps, name='data')
def test_CrossSections(outdir=None):
"""Unit tests for CrossSections class"""
from shutil import rmtree
from tempfile import mkdtemp
remove_dir = False
if outdir is None:
remove_dir = True
outdir = mkdtemp()
try:
# "Standard" location of cross sections file in PISA; retrieve 2.6.4 for
# testing purposes
pisa_xs_file = 'cross_sections/cross_sections.json'
xs = CrossSections(ver='genie_2.6.4', xsec=pisa_xs_file)
# Location of the root file to use (not included in PISA at the moment)
test_dir = expand(os.path.join('/tmp', 'pisa_tests', 'cross_sections'))
#root_xs_file = os.path.join(test_dir, 'genie_2.6.4_simplified.root')
root_xs_file = find_resource(os.path.join(
#'tests', 'data', 'xsec', 'genie_2.6.4_simplified.root'
'cross_sections', 'genie_xsec_H2O.root'
))
# Make sure that the XS newly-imported from ROOT match those stored in
# PISA
if os.path.isfile(root_xs_file):
xs_from_root = CrossSections.new_from_root(root_xs_file,
ver='genie_2.6.4')
logging.info('Found and loaded ROOT source cross sections file %s',
root_xs_file)
#assert xs_from_root.allclose(xs, rtol=1e-7)
# Check XS ratio for numu_cc to numu_cc + numu_nc (user must inspect)
kg0 = NuFlavIntGroup('numu_cc')
kg1 = NuFlavIntGroup('numu_nc')
logging.info(
r'\int_1^80 xs(numu_cc) E^{-1} dE = %e',
xs.get_xs_ratio_integral(kg0, None, e_range=[1, 80], gamma=1)
)
logging.info(
'(int E^{-gamma} * (sigma_numu_cc)/int(sigma_(numu_cc+numu_nc)) dE)'
' / (int E^{-gamma} dE) = %e',
xs.get_xs_ratio_integral(kg0, kg0+kg1, e_range=[1, 80], gamma=1,
average=True)
)
# Check that XS ratio for numu_cc+numu_nc to the same is 1.0
int_val = xs.get_xs_ratio_integral(kg0+kg1, kg0+kg1, e_range=[1, 80],
gamma=1, average=True)
if not recursiveEquality(int_val, 1):
raise ValueError('Integral of nc + cc should be 1.0; get %e'
' instead.' % int_val)
# Check via plot that the
# Plot all cross sections stored in PISA xs file
try:
alldata = from_file(pisa_xs_file)
xs_versions = alldata.keys()
for ver in xs_versions:
xs = CrossSections(ver=ver, xsec=pisa_xs_file)
xs.plot(save=os.path.join(
outdir, 'pisa_' + ver + '_nuxCCNC_H2O_cross_sections.pdf'
))
except ImportError as exc:
logging.debug('Could not plot; possible that matplotlib not'
'installed. ImportError: %s', exc)
finally:
if remove_dir:
rmtree(outdir)
def main():
"""Do the conversion."""
args = parse_args()
in_fpath = os.path.expanduser(os.path.expandvars(args.config[0]))
out_fpath = in_fpath + '.new'
with open(in_fpath, 'r') as infile:
orig_contents = infile.readlines()
osc_stage_header_line = None
section_names_with_colons = {}
new_contents = []
for lineno, orig_line in enumerate(orig_contents, start=1):
# Remove trailing whitespace, including newline character(s)
new_line = orig_line.rstrip()
# Empty (or whitespace-only) line is trivial
if new_line == '':
new_contents.append(new_line)
continue
# Replace text substitution ("config file variables") syntax
new_line = OLD_SUB_RE.sub(repl=replace_substitution, string=new_line)
# Replace stage headers. E.g.
# `` [ stage :stage_name ]``
# is replaced by
# `` [stage.stage_name]``
# I.e. retain any whitespace before (and after... though this is
# already removed) the brackets but swap colon for period and remove
# whitespace within the brackets.
new_line = OLD_STAGE_SECTION_RE.sub(
repl=lambda m: '[stage.%s]' % m.groups(), string=new_line)
# Replace stage:key variables. E.g. what should now look like
# `` ${ stage : key } ``
# should look like
# `` ${stage.key} ``
new_line = OLD_STAGE_VARIABLE_RE.sub(
repl=lambda m: '${stage.%s}' % m.groups(), string=new_line)
stripped = new_line.strip()
# Replace order string
if stripped.startswith('order'):
new_line = OLD_ORDER_RE.sub(repl=replace_order, string=new_line)
# Record line on which the [stage.osc] section occurs (if any)
elif stripped == '[stage.osc]':
osc_stage_header_line = lineno - 1
# Convert ``#include x`` to ``#include x as y``, where appropriate
new_line = PISAConfigParser.INCLUDE_RE.sub(repl=append_include_as,
string=new_line)
# Convert JSON filenames to .json.bz2 that are now bzipped
if '.json' in new_line:
for json_re in JSON_NO_BZ2_RE_LIST:
new_line = json_re.sub(repl='.json.bz2', string=new_line)
# Replace changed names
for orig_name, new_name in NAMES_CHANGED_MAP.items():
new_line = new_line.replace(orig_name, new_name)
# Search for any colons used in section names. This is illegal, as a
# section name can be used as a variable where the syntax is
# ``${section_name:key}``
# so any colons in section_name will make the parser choke.
for match in SECTION_NAME_WITH_COLON_RE.finditer(new_line):
section_name_with_colons = match.groups()[0]
if NEW_VARIABLE_RE.match(section_name_with_colons):
if section_name_with_colons.count(':') > 1:
raise ValueError(
'Multiple colons in new-style variable, line %d:\n'
'>> Original line:\n%s\n>> New line:\n%s\n' %
(lineno, orig_line, new_line))
else:
continue
section_name_without_colons = section_name_with_colons.replace(
':', OTHER_SECTION_NAME_SEPARATOR)
section_names_with_colons[section_name_with_colons] = (
section_name_without_colons)
new_contents.append(new_line)
#for item in section_names_with_colons.items():
# print '%s --> %s' % item
# Go back through and replace colon-sparated section names with
# ``OTHER_SECTION_NAME_SEPARATOR``-separated section names
all_names_to_replace = section_names_with_colons.keys()
def replace_var(match):
"""Closure to replace variable names"""
whole_string, var_name = match.groups()
if var_name in all_names_to_replace:
return '${%s}' % section_names_with_colons[var_name]
return whole_string
def replace_section_name(match):
"""Closure to replace section names"""
whole_string, section_name = match.groups()
if section_name in all_names_to_replace:
return whole_string.replace(
section_name, section_names_with_colons[section_name])
return whole_string
for lineno, new_line in enumerate(new_contents, start=1):
if not new_line:
continue
new_line = NEW_VARIABLE_RE.sub(repl=replace_var, string=new_line)
new_line = NEW_SECTION_RE.sub(repl=replace_section_name,
string=new_line)
#new_line = NEW_SECTION_RE.sub(repl=replace_colon_names,
# string=new_line)
#for with_colons, without_colons in section_names_with_colons:
# new_line = new_line.replace(with_colons, without_colons)
# Check for multiple colons in a variable (which is illegal)
if MULTI_COLON_VAR_RE.findall(new_line):
raise ValueError(
'Multiple colons in variable, line %d:\n>> Original'
' line:\n%s\n>> New line:\n%s\n' %
(lineno, orig_contents[lineno - 1], new_line))
new_contents[lineno - 1] = new_line
# Parse the new config file with the PISAConfigParser to see if NSI
# parameters are defined in the `stage.osc` section (if the latter is
# present). If needed, insert appropriate #include in the section
pcp = PISAConfigParser()
missing_section_header = False
try:
pcp.read_string(('\n'.join(new_contents) + '\n').decode('utf-8'))
except MissingSectionHeaderError:
missing_section_header = True
pcp.read_string(('\n'.join(['[dummy section header]'] + new_contents) +
'\n').decode('utf-8'))
if 'stage.osc' in pcp:
keys_containing_eps = [
k for k in pcp['stage.osc'].keys() if '.eps_'.encode('utf-8') in k
]
nsi_params_present = []
nsi_params_missing = []
for nsi_param, nsi_param_re in NSI_PARAM_RE_MAP.items():
found = None
for key_idx, key in enumerate(keys_containing_eps):
if nsi_param_re.match(key):
found = key_idx
nsi_params_present.append(nsi_param)
if found is None:
nsi_params_missing.append(nsi_param)
else:
# No need to search this key again
keys_containing_eps.pop(found)
if set(nsi_params_present) == set(NSI_PARAM_RE_MAP.keys()):
all_nsi_params_defined = True
elif set(nsi_params_missing) == set(NSI_PARAM_RE_MAP.keys()):
all_nsi_params_defined = False
else:
raise ValueError(
'Found a subset of NSI params defined; missing %s' %
str(nsi_params_missing))
# NOTE: since for now the contents of nsi_null.cfg are commented out
# (until merging NSI branch), the above check will say NSI params are
# missing if the #include statement was made. So check to see if
# settings/osc/nsi_null.cfg _has_ been included (we can't tell what
# section it is in, but we'll have to just accept that).
#
# We will probably want to remove this stanza as soon as NSI brnach is
# merged, since this is imprecise and can introduce other weird corner
# cases.
rsrc_loc = find_resource('settings/osc/nsi_null.cfg')
for file_iter in pcp.file_iterators:
if rsrc_loc in file_iter.fpaths_processed:
all_nsi_params_defined = True
if not all_nsi_params_defined and osc_stage_header_line is None:
raise ValueError(
"Found a stage.osc section without NSI params defined (using"
" PISAConfigParser) but could not find the line of the"
" `[stage.osc]` header. This could occur if `[stage.osc]` came"
" from an `#include`'d file. You can manually define the NSI"
" parameters in this file or in the included file e.g. as"
" found in `settings/osc/nsi_null.cfg` or simply add the"
" statement ``#include settings/osc/nsi_null.cfg`` to either"
" file (so long as that statement it falls within the"
" stage.osc section).")
# Add ``#include settings/osc/nsi_null.cfg`` at top of stage.osc
# section if a stage.osc section is present and no NSI params were
# specified in that section
if not all_nsi_params_defined:
# Add an #include to set all NSI parameters to 0
new_contents.insert(osc_stage_header_line + 1,
'#include settings/osc/nsi_null.cfg')
# Add an extra blank line after the #include line
new_contents.insert(osc_stage_header_line + 2, '')
if not new_contents:
raise ValueError('Empty file after conversion; quitting.')
# Note that newlines are added but no join is performed for comparison
# against `orig_contents`
new_contents = [line + '\n' for line in new_contents]
# Now for validation, try to parse the new config file with the
# PISAConfigParser
pcp = PISAConfigParser()
if missing_section_header:
pcp.read_string((''.join(['[dummy section header]\n'] + new_contents) +
'\n').decode('utf-8'))
else:
pcp.read_string((''.join(new_contents)).decode('utf-8'))
if new_contents == orig_contents:
sys.stdout.write('Nothing modified in the original file (ok!).\n')
return
if args.validate_only:
raise ValueError(
'Original config file "%s" would be modfied (and so may be'
' invalid). Re-run this script without the --validate-only flag to'
' produce an appropriately-converted config file.' %
args.config[0])
sys.stdout.write('Writing modified config file to "%s"\n' % out_fpath)
with open(out_fpath, 'w') as outfile:
outfile.writelines(new_contents)
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'])