def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
limitfile = args.limitfile
first = args.seed
last = first + args.nsims
flist = [limitfile.replace("_SEED.fits", "_%06i.fits" % seed)\
for seed in range(first, last)]
spec_config = load_yaml(args.specconfig)
specs = spec_config['specs']
sum_specs = specs.copy()
outfile = args.outfile
summaryfile = args.summaryfile
hdus = sum_specs + ['INDICES']
out_tables, out_names = vstack_tables(flist, hdus)
if is_not_null(outfile):
fits_utils.write_tables_to_fits(outfile,
out_tables,
namelist=out_names)
if is_not_null(summaryfile):
summary_tables = []
for ot in out_tables[0:-1]:
summary_table = summarize_limits_results(ot)
summary_tables.append(summary_table)
summary_tables.append(Table(out_tables[-1][0]))
fits_utils.write_tables_to_fits(summaryfile,
summary_tables,
namelist=out_names)
def write_fits(self, filepath, clobber=False):
""" Write this object to a FITS file
Paramters
---------
filepath : str
Path to output file
clobber : bool
Flag to allow overwriting existing files
"""
tables = [self._e_table]
tablenames = ["EBOUNDS"]
ref_cards = [{}]
for key, val in self._s_tables.items():
tables.append(val)
tablenames.append(key)
ref_cards.append(self._ref_val_dict[key])
fits_utils.write_tables_to_fits(filepath,
tables,
clobber=clobber,
namelist=tablenames,
cardslist=ref_cards)
def write_stacked(basedir, roster_name, stacked_dict, jprior_key, clobber):
""" Write the stacked DMCastroData object to a FITS file
"""
outdir = os.path.join(basedir, "stacked")
try:
os.makedirs(outdir)
except OSError:
pass
outpath = os.path.join(
outdir, "results_%s_%s.fits" % (roster_name, jprior_key))
print("Writing stacked results %s" % outpath)
channels = stacked_dict.keys()
t_list = []
n_list = []
mass_table = None
for chan in channels:
stacked = stacked_dict[chan]
if mass_table is None:
mass_table = stacked.build_mass_table()
t_list.append(stacked.build_scandata_table())
n_list.append(chan)
t_list.append(mass_table)
n_list.append("MASSES")
fits_utils.write_tables_to_fits(outpath,
t_list,
clobber=clobber,
namelist=n_list)
def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
channels = [
'ee', 'mumu', 'tautau', 'bb', 'tt', 'gg', 'ww', 'zz', 'cc', 'uu',
'dd', 'ss'
]
norm_type = 'eflux'
spec_table = DMSpecTable.create_from_fits(args.spec)
profile = load_yaml(args.profile_yaml)
j_value = profile.get('j_integ')
j_sigma = profile.get('j_sigma', None)
if args.jprior is None or args.jprior == 'None' or j_sigma is None or j_sigma == 0.0:
j_factor = j_value
j_prior_key = 'none'
else:
j_factor = dict(functype=args.jprior,
j_value=j_value,
mu=j_value,
sigma=j_sigma)
j_prior_key = args.jprior
sed = CastroData.create_from_sedfile(args.sed_file, norm_type)
c_list, t_list, n_list = DMCastroConvertor.convert_sed_to_dm(
spec_table, sed, channels, norm_type, j_factor)
fits_utils.write_tables_to_fits(args.outfile,
t_list,
clobber=args.clobber,
namelist=n_list)
def write_fits(self, filepath, clobber=False):
""" Write this object to a FITS file
"""
fits_utils.write_tables_to_fits(filepath,
[self._e_table, self._s_table],
clobber=clobber,
namelist=["EBOUNDS", "SPECDATA"],
cardslist=[{}, self._ref_vals])
def write_fits_files(stacked_dict, resultsfile, limitfile, clobber=False):
""" Write the stacked DMCastroData object and limits a FITS files
Parameters
----------
stacked_dict : dict
Dictionary of `DMCastroData` objects, keyed by channel
resultsfile : str
Path to the output file to write the `DMCastroData` objects to
limitfile : str
Path to write the upper limits to
clobber : bool
Overwrite existing files
"""
channels = list(stacked_dict.keys())
t_list = []
n_list = []
lim_list = []
lim_table_list = []
mass_table = None
alphas = [0.68, 0.95]
for chan in channels:
is_decay = chan.find('_decay') >= 0
stacked = stacked_dict[chan]
mles = stacked.mles()
limit_dict = dict(mles=mles)
for alpha in alphas:
if is_decay:
limits = stacked.getLimits(1. - alpha)
limit_dict['ll_%.02f' % alpha] = limits
else:
limits = stacked.getLimits(alpha)
limit_dict['ul_%.02f' % alpha] = limits
tab_limits = stacked.build_limits_table(limit_dict)
if mass_table is None:
mass_table = stacked.build_mass_table()
t_list.append(stacked.build_scandata_table())
n_list.append(chan)
lim_list.append(limit_dict)
lim_table_list.append(tab_limits)
t_list.append(mass_table)
lim_table_list.append(mass_table)
n_list.append("MASSES")
fits_utils.write_tables_to_fits(resultsfile,
t_list,
clobber=clobber,
namelist=n_list)
fits_utils.write_tables_to_fits(limitfile,
lim_table_list,
clobber=clobber,
namelist=n_list)
def write_table_file(self, table_file=None):
"""Write the table to self._table_file"""
if self._table is None:
raise RuntimeError("No table to write")
if table_file is not None:
self._table_file = table_file
if self._table_file is None:
raise RuntimeError("No output file specified for table")
write_tables_to_fits(self._table_file, [self._table], clobber=True,
namelist=['FILE_ARCHIVE'])
def write_table_file(self, table_file=None):
"""Write the table to self._table_file"""
if self._table is None:
raise RuntimeError("No table to write")
if table_file is not None:
self._table_file = table_file
if self._table_file is None:
raise RuntimeError("No output file specified for table")
write_tables_to_fits(self._table_file, [self._table],
clobber=True,
namelist=['FILE_ARCHIVE'])
def write_table_file(self, job_table_file=None, file_table_file=None):
"""Write the table to self._table_file"""
if self._table is None:
raise RuntimeError("No table to write")
if self._table_ids is None:
raise RuntimeError("No ID table to write")
if job_table_file is not None:
self._table_file = table_file
if self._table_file is None:
raise RuntimeError("No output file specified for table")
write_tables_to_fits(self._table_file, [self._table, self._table_ids], clobber=True,
namelist=['JOB_ARCHIVE', 'FILE_IDS'])
self._file_archive.write_table_file(file_table_file)
def write_table_file(self, job_table_file=None, file_table_file=None):
"""Write the table to self._table_file"""
if self._table is None:
raise RuntimeError("No table to write")
if self._table_ids is None:
raise RuntimeError("No ID table to write")
if job_table_file is not None:
self._table_file = job_table_file
if self._table_file is None:
raise RuntimeError("No output file specified for table")
write_tables_to_fits(self._table_file, [self._table, self._table_ids],
clobber=True,
namelist=['JOB_ARCHIVE', 'FILE_IDS'])
self._file_archive.write_table_file(file_table_file)
def write_fits(self, filepath, clobber=False):
""" Write this object to a FITS file
Paramters
---------
filepath : str
Path to output file
clobber : bool
Flag to allow overwriting existing files
"""
fits_utils.write_tables_to_fits(filepath, [self._e_table, self._s_table],
clobber=clobber,
namelist=["EBOUNDS", "SPECDATA"],
cardslist=[{}, self._ref_vals])
def write_fits_files(stacked_dict, resultsfile, limitfile, clobber=False):
""" Write the stacked StackCastroData object and limits a FITS files
Parameters
----------
stacked_dict : dict
Dictionary of `StackCastroData` objects, keyed by spec
resultsfile : str
Path to the output file to write the `StackCastroData` objects to
limitfile : str
Path to write the upper limits to
clobber : bool
Overwrite existing files
"""
specs = stacked_dict.keys()
t_list = []
n_list = []
lim_list = []
lim_table_list = []
alphas = [0.68, 0.95]
for spec in specs:
stacked = stacked_dict[spec]
mles = stacked.mles()
limit_dict = dict(mles=mles)
for alpha in alphas:
limits = stacked.getLimits(alpha)
limit_dict['ul_%.02f' % alpha] = limits
tab_limits = stacked.build_limits_table(limit_dict)
t_list.append(stacked.build_scandata_table())
n_list.append(spec)
lim_list.append(limit_dict)
lim_table_list.append(tab_limits)
fits_utils.write_tables_to_fits(resultsfile,
t_list,
clobber=clobber,
namelist=n_list)
fits_utils.write_tables_to_fits(limitfile,
lim_table_list,
clobber=clobber,
namelist=n_list)
def run_analysis(self, argv):
"""Run this analysis"""
args = self._parser.parse_args(argv)
limitfile = args.limitfile
first = args.seed
last = first + args.nsims
flist = [limitfile.replace("_SEED.fits", "_%06i.fits" % seed)\
for seed in range(first, last)]
spec_config = load_yaml(args.specconfig)
channels = spec_config['channels']
sum_chans = CollectLimits.select_channels(channels, limitfile)
outfile = args.outfile
summaryfile = args.summaryfile
hdus = sum_chans + ['MASSES']
out_tables, out_names = vstack_tables(flist, hdus)
if is_not_null(outfile):
fits_utils.write_tables_to_fits(outfile,
out_tables,
namelist=out_names)
if is_not_null(summaryfile):
summary_tables = []
for ot, chan in zip(out_tables[0:-1], sum_chans):
decay = chan.find('_decay') >= 0
summary_table = summarize_limits_results(ot, decay)
summary_tables.append(summary_table)
summary_tables.append(Table(out_tables[-1][0]))
fits_utils.write_tables_to_fits(summaryfile,
summary_tables,
namelist=out_names)
def main():
""" Hook for command line access """
# Argument defintion
usage = "usage: %(prog)s [input]"
description = "Collect all the new source"
parser = argparse.ArgumentParser(usage=usage, description=description)
parser.add_argument('--input',
'-i',
default='roi_set.yaml',
help='ROI set definition file.')
parser.add_argument('--output',
'-o',
type=argparse.FileType('w'),
help='Output file.')
parser.add_argument('--clobber',
action='store_true',
help='Overwrite output file.')
parser.add_argument('--targets', '-t', type=str, help='Target file.')
parser.add_argument('--filestr',
'-f',
default="tscube.fits",
help="Name of file within each ROI sub-directory")
# Argument parsing
args = parser.parse_args()
# Read the target file
targ_type = os.path.splitext(args.targets)[1]
print targ_type
if targ_type in ['.fit', '.fits']:
targets = DMTargetFactory.read_table(args.targets)
roster = None
else:
targets, roster = DMTargetFactory.make_table([args.targets])
# Get the sky_crds
sky_crds = DMTargetFactory.get_sky_crds(targets)
# Make the roi_set object
roi_set, basedir = dmp_roi.DMROISet.create_from_yaml(args.input)
# extract the data
out_table = roi_set.extract_table_data(sky_crds,
args.filestr,
basedir=basedir,
tables=["SCANDATA", "FITDATA"])
# add_names_column(out_table,targets['name'])
col_names = [
'name', 'ra', 'dec', 'distance', 'proftype', 'glat', 'glon', 'j_integ',
'd_integ'
]
add_columns(out_table, targets, col_names)
ebounds_table = roi_set.extract_single_table(args.filestr,
basedir=basedir,
table="EBOUNDS")
# Write the output
fits_utils.write_tables_to_fits(args.output, [out_table, ebounds_table],
clobber=args.clobber,
namelist=["SCANDATA", "EBOUNDS"])
def convert_sed(spec_table, channels, sed_file, outfile, limitfile,
**kwargs):
"""Convert a single SED to DM space.
Parameters
----------
spec_table : `DMSpecTable`
Object with all the DM spectra
channels : list
List of the channels to convert
sed_file : str
Path to the SED file
outfile : str
Path to write the output `DMCastroData` object to
limitfile : str
Path to write the output limits to.
Keyword arguments
-----------------
norm_type : str
Normalization type to use
j_factor : dict
Dictionary with information about the J-factor
d_factor : dict
Dictionary with information about the J-factor
clobber : bool
Flag to overwrite existing files.
"""
norm_type = kwargs.get('norm_type', 'eflux')
j_factor = kwargs.get('j_factor', None)
d_factor = kwargs.get('d_factor', None)
clobber = kwargs.get('clobber', False)
use_chans = ConvertCastro.select_channels(channels, sed_file)
exttype = os.path.splitext(sed_file)[-1]
if exttype in ['.fits', '.npy']:
sed = CastroData.create_from_sedfile(sed_file, norm_type)
elif exttype in ['.yaml']:
sed = CastroData.create_from_yamlfile(sed_file)
else:
raise ValueError("Can not read file type %s for SED" % exttype)
c_list, t_list, n_list = ConvertCastro.convert_sed_to_dm(
spec_table,
sed,
use_chans,
norm_type=norm_type,
j_val=j_factor,
d_val=d_factor)
if is_not_null(outfile):
fits_utils.write_tables_to_fits(outfile,
t_list,
clobber=clobber,
namelist=n_list)
if is_not_null(limitfile):
mass_table = t_list[-1]
_, t_list_lim, n_list_lim = ConvertCastro.extract_dm_limits(
c_list, use_chans, [0.68, 0.95], mass_table)
fits_utils.write_tables_to_fits(limitfile,
t_list_lim,
clobber=clobber,
namelist=n_list_lim)
def convert_sed(spec_table, specs, sed_file, outfile, limitfile, **kwargs):
"""Convert a single SED to stacking space.
Parameters
----------
spec_table : `StackSpecTable`
Object with all the stacking spectra
specs : list
List of the specs to convert
sed_file : str
Path to the SED file
outfile : str
Path to write the output `StackCastroData` object to
limitfile : str
Path to write the output limits to.
Keyword arguments
-----------------
norm_type : str
Normalization type to use
astro_val : dict
Dictionary with information about the astrophysical norm
clobber : bool
Flag to overwrite existing files.
"""
norm_type = kwargs.get('norm_type', 'eflux')
astro_val = kwargs.get('astro_val', None)
clobber = kwargs.get('clobber', False)
use_specs = specs
exttype = os.path.splitext(sed_file)[-1]
if exttype in ['.fits', '.npy']:
sed = CastroData.create_from_sedfile(sed_file, norm_type)
elif exttype in ['.yaml']:
sed = CastroData.create_from_yamlfile(sed_file)
else:
raise ValueError("Can not read file type %s for SED" % exttype)
c_list, t_list, n_list = ConvertCastro.convert_sed_to_stack_var(
spec_table, sed, norm_type=norm_type, astro_val=astro_val)
if is_not_null(outfile):
fits_utils.write_tables_to_fits(outfile,
t_list,
clobber=clobber,
namelist=n_list)
if is_not_null(limitfile):
stacked_lists = ConvertCastro.extract_stack_limits(
c_list, use_specs, [0.68, 0.95])
fits_utils.write_tables_to_fits(limitfile,
stacked_lists[1],
clobber=clobber,
namelist=stacked_lists[2])