def create_expmap(cmp):
cmap = 'none'
appname = 'gtexpcube2'
outfile = cfg['gtlike']['bexpmap'] % ('_' + cmp['name'])
if os.path.isfile(outfile) and not overwrite:
logger.info('skipping {}'.format(outfile))
return
kw = dict(
infile=cfg['data']['ltcube'],
cmap=cmap,
ebinalg='LOG',
emin=cmp['selection']['emin'],
emax=cmp['selection']['emax'],
enumbins=cmp['binning']['enumbins'],
outfile=outfile,
proj='CAR',
nxpix=360,
nypix=180,
binsz=1,
xref=0.0,
yref=0.0,
evtype=cmp['selection']['evtype'],
thmax=cfg['selection']['thmax'], #THB
irfs=cfg['gtlike']['irfs'],
coordsys=cfg['binning']['coordsys'],
chatter=cfg['logging']['chatter'])
gtanalysis.run_gtapp(appname, logger, kw, loglevel=logging.INFO)
if not os.path.isfile(kw['outfile']):
logger.error('Failed to create output file')
logger.error('{} keywords:'.format(appname))
for k, v in kw.items():
logger.error(' {:10s}: {}'.format(k, v))
else:
logger.info('created {}'.format(outfile))
def _compute_lc_exp(self,
srcmdl='none',
target="",
specin=-2.1,
overwrite=False,
**kwargs):
"""
Run gtexposure to compute the exposure for a light curve
"""
loglevel = kwargs.get('loglevel', self.loglevel)
for i, c in enumerate(self.components):
kw = dict(infile=c.files['lcmap'],
scfile=c.data_files['scfile'],
irfs = c.config['gtlike']['irfs'],
srcmdl = path.join(self.workdir,'{1:s}_{0:02n}.xml'.format(i,srcmdl)) \
if not target == "" else "none",
target = target,
specin = specin,
emin = c.config['selection']['emin'],
emax = c.config['selection']['emax'],
enumbins = self.enumbins
)
print kw['target'], kw['srcmdl']
run_gtapp('gtexposure', self.logger, kw, loglevel=loglevel)
return
def _compute_diffrsp(self, srcmdl, overwrite=False, **kwargs):
"""
Run gtsrcprob on an ft1 file
"""
loglevel = kwargs.get('loglevel', self.loglevel)
for i, c in enumerate(self.components):
kw = dict(evfile=c.files['ft1'],
scfile=c.data_files['scfile'],
irfs=c.config['gtlike']['irfs'],
evtype=c.config['selection']['evtype'],
srcmdl=path.join(self.workdir,
'{1:s}_{0:02n}.xml'.format(i, srcmdl)))
logging.info("Using srcmdl {0:s}".format(kw['srcmdl']))
run_gtapp('gtdiffrsp', self.logger, kw, loglevel=loglevel)
return
def _bin_data_lc(self, overwrite=False, dtime=0., **kwargs):
"""
Run gtbin for a light curve counts map
"""
if dtime > 0.:
self.config['lightcurve']['binsz'] = dtime
logging.info("Binning for LC: {0}".format(
self.config['lightcurve']['binsz']))
loglevel = kwargs.get('loglevel', self.loglevel)
for i, c in enumerate(self.components):
self.components[i]._files['lcmap'] = path.join(
self.workdir, 'lcmap{0[file_suffix]:s}.fits'.format(c.config))
kw = dict(algorithm='lc',
evfile=c.files['ft1'],
outfile=c.files['lcmap'],
scfile=c.data_files['scfile'],
emin=c.config['selection']['emin'],
emax=c.config['selection']['emax'],
tstart=c.config['selection']['tmin'],
tstop=c.config['selection']['tmax'],
chatter=self.config['logging']['chatter'])
if isinstance(self.config['lightcurve']['binsz'], str):
kw['tbinalg'] = 'FILE'
kw['tbinfile'] = self.config['lightcurve']['binsz'],
else:
kw['tbinalg'] = 'LIN'
kw['dtime'] = self.config['lightcurve']['binsz']
if not os.path.isfile(c.files['lcmap']) or overwrite:
run_gtapp('gtbin', self.logger, kw, loglevel=loglevel)
else:
self.logger.debug('Skipping gtbin.')
return
def main():
usage = "usage: %(prog)s [options] "
description = "Run gtselect and gtmktime on one or more FT1 files. "
"Note that gtmktime will be skipped if no FT2 file is provided."
parser = argparse.ArgumentParser(usage=usage, description=description)
add_lsf_args(parser)
parser.add_argument('--zmax', default=100., type=float, help='')
parser.add_argument('--dcostheta', default=0.025, type=float, help='')
parser.add_argument('--binsz', default=1.0, type=float, help='')
parser.add_argument('--outdir',
default=None,
type=str,
help='Path to output directory used when merge=False.')
parser.add_argument('--outfile',
default=None,
type=str,
help='Path to output file used when merge=True.')
parser.add_argument('--scfile',
default=None,
type=str,
help='',
required=True)
parser.add_argument('--dry_run', default=False, action='store_true')
parser.add_argument('--overwrite', default=False, action='store_true')
parser.add_argument('--merge',
default=False,
action='store_true',
help='Merge input FT1 files into a single file.')
parser.add_argument('files',
nargs='+',
default=None,
help='List of directories in which the analysis will '
'be run.')
args = parser.parse_args()
args.outdir = os.path.abspath(args.outdir)
args.scfile = os.path.abspath(args.scfile)
mkdir(args.outdir)
input_files = [[os.path.abspath(x)] for x in args.files]
output_files = [
os.path.join(args.outdir, os.path.basename(x)) for x in args.files
]
if args.batch:
opts = copy.deepcopy(args.__dict__)
opts.pop('files')
opts.pop('batch')
submit_jobs('python ' + os.path.abspath(__file__.rstrip('cd')),
input_files, output_files, {k: v
for k, v in opts.items()})
sys.exit(0)
logger = Logger.get(os.path.basename(__file__), None, logging.INFO)
logger.info('Starting.')
cwd = os.getcwd()
user = os.environ['USER']
tmpdir = tempfile.mkdtemp(prefix=user + '.', dir='/scratch')
os.chdir(tmpdir)
logger.info('tmpdir %s', tmpdir)
logger.info('outdir %s', args.outdir)
logger.info('outfile %s', args.outfile)
for infiles, outfile in zip(input_files, output_files):
logger.info('infiles %s', pprint.pformat(infiles))
logger.info('outfile %s', outfile)
kw = dict(evfile='list.txt',
scfile=args.scfile,
outfile='ltcube.fits',
binsz=args.binsz,
dcostheta=args.dcostheta,
zmax=args.zmax)
create_filelist(infiles, 'list.txt')
staged_outfile = kw['outfile']
run_gtapp('gtltcube', logger, kw)
logger.info('cp %s %s', staged_outfile, outfile)
shutil.copy(staged_outfile, outfile)
os.chdir(cwd)
logger.info('Deleting %s', tmpdir)
shutil.rmtree(tmpdir)
logger.info('Done.')
def main():
usage = "usage: %(prog)s [options] "
description = "Run gtselect and gtmktime on one or more FT1 files. "
"Note that gtmktime will be skipped if no FT2 file is provided."
parser = argparse.ArgumentParser(usage=usage, description=description)
add_lsf_args(parser)
parser.add_argument('--zmax', default=100., type=float, help='')
parser.add_argument('--dcostheta', default=0.025, type=float, help='')
parser.add_argument('--binsz', default=1.0, type=float, help='')
parser.add_argument('--outdir', default=None, type=str,
help='Path to output directory used when merge=False.')
parser.add_argument('--outfile', default=None, type=str,
help='Path to output file used when merge=True.')
parser.add_argument('--scfile', default=None, type=str, help='',
required=True)
parser.add_argument('--dry_run', default=False, action='store_true')
parser.add_argument('--overwrite', default=False, action='store_true')
parser.add_argument('--merge', default=False, action='store_true',
help='Merge input FT1 files into a single file.')
parser.add_argument('files', nargs='+', default=None,
help='List of directories in which the analysis will '
'be run.')
args = parser.parse_args()
args.outdir = os.path.abspath(args.outdir)
args.scfile = os.path.abspath(args.scfile)
mkdir(args.outdir)
input_files = [[os.path.abspath(x)] for x in args.files]
output_files = [os.path.join(args.outdir, os.path.basename(x))
for x in args.files]
if args.batch:
opts = copy.deepcopy(args.__dict__)
opts.pop('files')
opts.pop('batch')
submit_jobs('python ' + os.path.abspath(__file__.rstrip('cd')),
input_files, output_files, {k: v for k, v in opts.items()})
sys.exit(0)
logger = Logger.get(os.path.basename(__file__), None, logging.INFO)
logger.info('Starting.')
cwd = os.getcwd()
user = os.environ['USER']
tmpdir = tempfile.mkdtemp(prefix=user + '.', dir='/scratch')
os.chdir(tmpdir)
logger.info('tmpdir %s', tmpdir)
logger.info('outdir %s', args.outdir)
logger.info('outfile %s', args.outfile)
for infiles, outfile in zip(input_files, output_files):
logger.info('infiles %s', pprint.pformat(infiles))
logger.info('outfile %s', outfile)
kw = dict(evfile='list.txt',
scfile=args.scfile,
outfile='ltcube.fits',
binsz=args.binsz,
dcostheta=args.dcostheta,
zmax=args.zmax)
create_filelist(infiles, 'list.txt')
staged_outfile = kw['outfile']
run_gtapp('gtltcube', logger, kw)
logger.info('cp %s %s', staged_outfile, outfile)
shutil.copy(staged_outfile, outfile)
os.chdir(cwd)
logger.info('Deleting %s', tmpdir)
shutil.rmtree(tmpdir)
logger.info('Done.')
def main():
gtselect_keys = ['tmin','tmax','emin','emax','zmax','evtype','evclass',
'phasemin','phasemax','convtype','rad','ra','dec']
gtmktime_keys = ['roicut','filter']
usage = "usage: %(prog)s [options] "
description = "Run gtselect and gtmktime on one or more FT1 files. "
"Note that gtmktime will be skipped if no FT2 file is provided."
parser = argparse.ArgumentParser(usage=usage, description=description)
add_lsf_args(parser)
for k in gtselect_keys:
if k in ['evtype','evclass','convtype']:
parser.add_argument('--%s'%k, default=None, type=int, help='')
else:
parser.add_argument('--%s'%k, default=None, type=float, help='')
for k in gtmktime_keys:
parser.add_argument('--%s'%k, default=None, type=str, help='')
parser.add_argument('--rock_angle', default=None, type=float, help='')
parser.add_argument('--outdir', default=None, type=str,
help='Path to output directory used when merge=False.')
parser.add_argument('--outfile', default=None, type=str,
help='Path to output file used when merge=True.')
parser.add_argument('--scfile', default=None, type=str, help='')
parser.add_argument('--dry_run', default=False, action='store_true')
parser.add_argument('--overwrite', default=False, action='store_true')
parser.add_argument('--merge', default=False, action='store_true',
help='Merge input FT1 files into a single file.')
parser.add_argument('files', nargs='+', default=None,
help='List of directories in which the analysis will '
'be run.')
args = parser.parse_args()
if args.merge:
if not args.outfile:
raise Exception('No output file defined.')
input_files = [[os.path.abspath(x) for x in args.files]]
output_files = [os.path.abspath(args.outfile)]
else:
args.outdir = os.path.abspath(args.outdir)
mkdir(args.outdir)
input_files = [[os.path.abspath(x)] for x in args.files]
output_files = [os.path.join(args.outdir,os.path.basename(x)) for x in args.files]
if args.batch:
opts = vars(args).copy()
del opts['files']
del opts['batch']
submit_jobs('fermipy-select',
input_files, opts, output_files, overwrite=args.overwrite,
dry_run=args.dry_run)
sys.exit(0)
logger = Logger.get(os.path.basename(__file__),None,logging.INFO)
logger.info('Starting.')
if args.scfile is not None:
args.scfile = os.path.abspath(args.scfile)
cwd = os.getcwd()
user = os.environ['USER']
tmpdir = tempfile.mkdtemp(prefix=user + '.', dir='/scratch')
os.chdir(tmpdir)
logger.info('tmpdir %s',tmpdir)
logger.info('outdir %s',args.outdir)
logger.info('outfile %s',args.outfile)
for infiles, outfile in zip(input_files,output_files):
logger.info('infiles %s',pprint.pformat(infiles))
logger.info('outfile %s',outfile)
kw = { k : args.__dict__[k] for k in gtselect_keys }
if kw['emax'] is None:
kw['emax'] = 1E6
create_filelist(infiles,'list.txt')
kw['infile'] = 'list.txt'
kw['outfile'] = 'out.fits'
staged_outfile = kw['outfile']
run_gtapp('gtselect',logger,kw)
kw = { k : args.__dict__[k] for k in gtmktime_keys }
if kw['roicut'] is None:
kw['roicut'] = 'no'
if kw['filter'] is None:
kw['filter'] = 'DATA_QUAL==1 && LAT_CONFIG==1'
if args.rock_angle is not None:
kw['filter'] += ' && ABS(ROCK_ANGLE)<%(rock)s '%dict(rock=args.rock_angle)
kw['evfile'] = 'out.fits'
kw['outfile'] = 'out_filtered.fits'
if args.scfile is not None:
kw['scfile'] = args.scfile
staged_outfile = kw['outfile']
run_gtapp('gtmktime',logger,kw)
logger.info('cp %s %s',staged_outfile,outfile)
shutil.copy(staged_outfile,outfile)
os.chdir(cwd)
logger.info('Deleting %s',tmpdir)
shutil.rmtree(tmpdir)
logger.info('Done.')
def main():
gtselect_keys = [
'tmin', 'tmax', 'emin', 'emax', 'zmax', 'evtype', 'evclass',
'phasemin', 'phasemax', 'convtype', 'rad', 'ra', 'dec'
]
gtmktime_keys = ['roicut', 'filter']
usage = "usage: %(prog)s [options] "
description = "Run gtselect and gtmktime on one or more FT1 files. "
"Note that gtmktime will be skipped if no FT2 file is provided."
parser = argparse.ArgumentParser(usage=usage, description=description)
add_lsf_args(parser)
for k in gtselect_keys:
if k in ['evtype', 'evclass', 'convtype']:
parser.add_argument('--%s' % k, default=None, type=int, help='')
else:
parser.add_argument('--%s' % k, default=None, type=float, help='')
for k in gtmktime_keys:
parser.add_argument('--%s' % k, default=None, type=str, help='')
parser.add_argument('--rock_angle', default=None, type=float, help='')
parser.add_argument('--outdir',
default=None,
type=str,
help='Path to output directory used when merge=False.')
parser.add_argument('--output',
default=None,
type=str,
help='Path to output file used when merge=True.')
parser.add_argument('--scfile', default=None, type=str, help='')
parser.add_argument('--dry_run', default=False, action='store_true')
parser.add_argument('--overwrite', default=False, action='store_true')
parser.add_argument(
'--merge',
default=False,
action='store_true',
help='Merge input FT1 files into N files where N is determined '
'by files_per_split.')
parser.add_argument('--files_per_split',
default=100,
type=int,
help='Set the number of files to combine in each '
'split of the input file list.')
parser.add_argument('--file_idx_min',
default=None,
type=int,
help='Set the number of files to assign to '
'each batch job.')
parser.add_argument('--file_idx_max',
default=None,
type=int,
help='Set the number of files to assign to '
'each batch job.')
parser.add_argument('files',
nargs='+',
default=None,
help='List of files.')
args = parser.parse_args()
batch = vars(args).pop('batch')
files = vars(args).pop('files')
args.outdir = os.path.abspath(args.outdir)
files = [os.path.abspath(f) for f in files]
ft1_files = get_files(files, ['.fit', '.fits'])
for i, f in enumerate(ft1_files):
if re.search('^root\:\/\/', f) is None:
ft1_files[i] = os.path.abspath(f)
input_files = []
output_files = []
files_idx_min = []
files_idx_max = []
opts = []
if args.file_idx_min is not None and args.file_idx_max is not None:
files_idx_min = [args.file_idx_min]
files_idx_max = [args.file_idx_max]
input_files = [files]
output_files = [args.output]
elif args.merge:
if not args.output:
raise Exception('No output file defined.')
nfiles = len(ft1_files)
njob = int(np.ceil(nfiles / float(args.files_per_split)))
for ijob, i in enumerate(range(0, nfiles, args.files_per_split)):
if args.outdir is not None:
mkdir(args.outdir)
outdir = os.path.abspath(args.outdir)
else:
outdir = os.path.dirname(os.path.dirname(args.output))
outfile = os.path.splitext(os.path.basename(args.output))[0]
outfile += '_%03i.fits' % (ijob)
outfile = os.path.join(outdir, outfile)
input_files += [files]
output_files += [outfile]
files_idx_min += [i]
files_idx_max += [i + args.files_per_split]
opts += [vars(args).copy()]
opts[-1]['output'] = outfile
opts[-1]['file_idx_min'] = i
opts[-1]['file_idx_max'] = i + args.files_per_split
else:
input_files = ft1_files
files_idx_min = [i for i in range(len(ft1_files))]
files_idx_max = [i + 1 for i in range(len(ft1_files))]
output_files = [
os.path.join(args.outdir, os.path.basename(x)) for x in ft1_files
]
opts = [vars(args).copy() for x in ft1_files]
if batch:
submit_jobs('fermipy-select',
input_files,
opts,
output_files,
overwrite=args.overwrite,
dry_run=args.dry_run)
sys.exit(0)
logger = Logger.configure(os.path.basename(__file__), None, logging.INFO)
logger.info('Starting.')
if args.scfile is not None:
args.scfile = os.path.abspath(args.scfile)
cwd = os.getcwd()
user = os.environ['USER']
tmpdir = tempfile.mkdtemp(prefix=user + '.', dir='/scratch')
os.chdir(tmpdir)
logger.info('tmpdir %s', tmpdir)
logger.info('outdir %s', args.outdir)
logger.info('output %s', args.output)
for infiles, outfile, idx_min, idx_max in zip(input_files, output_files,
files_idx_min,
files_idx_max):
logger.info('infiles %s', pprint.pformat(infiles))
logger.info('outfile %s', outfile)
infiles = get_files(infiles, ['.fit', '.fits'])
if idx_min is not None:
infiles = infiles[idx_min:idx_max]
for i, f in enumerate(infiles):
if re.search('^root\:\/\/', f) is None:
continue
os.system('xrdcp %s %s' % (f, f.split('/')[-1]))
infiles[i] = os.path.join(tmpdir, f.split('/')[-1])
kw = {k: args.__dict__[k] for k in gtselect_keys}
if kw['emax'] is None:
kw['emax'] = 1E6
create_filelist(infiles, 'list.txt')
kw['infile'] = 'list.txt'
kw['outfile'] = 'out.fits'
staged_outfile = kw['outfile']
run_gtapp('gtselect', logger, kw)
kw = {k: args.__dict__[k] for k in gtmktime_keys}
if kw['roicut'] is None:
kw['roicut'] = 'no'
if kw['filter'] is None:
kw['filter'] = 'DATA_QUAL==1 && LAT_CONFIG==1'
if args.rock_angle is not None:
kw['filter'] += ' && ABS(ROCK_ANGLE)<%(rock)s ' % dict(
rock=args.rock_angle)
kw['evfile'] = 'out.fits'
kw['outfile'] = 'out_filtered.fits'
if args.scfile is not None:
kw['scfile'] = args.scfile
staged_outfile = kw['outfile']
run_gtapp('gtmktime', logger, kw)
logger.info('cp %s %s', staged_outfile, outfile)
shutil.copy(staged_outfile, outfile)
os.chdir(cwd)
logger.info('Deleting %s', tmpdir)
shutil.rmtree(tmpdir)
logger.info('Done.')
def main():
gtselect_keys = ['tmin','tmax','emin','emax','zmax','evtype','evclass',
'phasemin','phasemax','convtype','rad','ra','dec']
gtmktime_keys = ['roicut','filter']
usage = "usage: %(prog)s [options] "
description = "Run gtselect and gtmktime on one or more FT1 files. "
"Note that gtmktime will be skipped if no FT2 file is provided."
parser = argparse.ArgumentParser(usage=usage, description=description)
add_lsf_args(parser)
for k in gtselect_keys:
if k in ['evtype','evclass','convtype']:
parser.add_argument('--%s'%k, default=None, type=int, help='')
else:
parser.add_argument('--%s'%k, default=None, type=float, help='')
for k in gtmktime_keys:
parser.add_argument('--%s'%k, default=None, type=str, help='')
parser.add_argument('--rock_angle', default=None, type=float, help='')
parser.add_argument('--outdir', default=None, type=str,
help='Path to output directory used when merge=False.')
parser.add_argument('--outfile', default=None, type=str,
help='Path to output file used when merge=True.')
parser.add_argument('--scfile', default=None, type=str, help='')
parser.add_argument('--dry_run', default=False, action='store_true')
parser.add_argument('--overwrite', default=False, action='store_true')
parser.add_argument('--merge', default=False, action='store_true',
help='Merge input FT1 files into a single file.')
parser.add_argument('files', nargs='+', default=None,
help='List of directories in which the analysis will '
'be run.')
args = parser.parse_args()
if args.merge:
if not args.outfile:
raise Exception('No output file defined.')
input_files = [[os.path.abspath(x) for x in args.files]]
output_files = [os.path.abspath(args.outfile)]
else:
args.outdir = os.path.abspath(args.outdir)
mkdir(args.outdir)
input_files = [[os.path.abspath(x)] for x in args.files]
output_files = [os.path.join(args.outdir,os.path.basename(x)) for x in args.files]
if args.batch:
batch_opts = {'W' : args.time, 'R' : args.resources,
'oo' : 'batch.log' }
args.batch=False
for infile, outfile in zip(input_files,output_files):
if os.path.isfile(outfile) and not args.overwrite:
print('Output file exists, skipping.',outfile)
continue
batch_opts['oo'] = os.path.splitext(outfile)[0] + '_select.log'
dispatch_jobs('python ' + os.path.abspath(__file__.rstrip('cd')),
infile, args, batch_opts, dry_run=args.dry_run)
sys.exit(0)
logger = Logger.get(os.path.basename(__file__),None,logging.INFO)
logger.info('Starting.')
if args.scfile is not None:
args.scfile = os.path.abspath(args.scfile)
cwd = os.getcwd()
user = os.environ['USER']
tmpdir = tempfile.mkdtemp(prefix=user + '.', dir='/scratch')
os.chdir(tmpdir)
logger.info('tmpdir %s',tmpdir)
logger.info('outdir %s',args.outdir)
logger.info('outfile %s',args.outfile)
for infiles, outfile in zip(input_files,output_files):
logger.info('infiles %s',pprint.pformat(infiles))
logger.info('outfile %s',outfile)
kw = { k : args.__dict__[k] for k in gtselect_keys }
if kw['emax'] is None:
kw['emax'] = 1E6
create_filelist(infiles,'list.txt')
kw['infile'] = 'list.txt'
kw['outfile'] = 'out.fits'
staged_outfile = kw['outfile']
run_gtapp('gtselect',logger,kw)
kw = { k : args.__dict__[k] for k in gtmktime_keys }
if kw['roicut'] is None:
kw['roicut'] = 'no'
if kw['filter'] is None:
kw['filter'] = 'DATA_QUAL==1 && LAT_CONFIG==1'
if args.rock_angle is not None:
kw['filter'] += ' && ABS(ROCK_ANGLE)<%(rock)s '%dict(rock=args.rock_angle)
kw['evfile'] = 'out.fits'
kw['outfile'] = 'out_filtered.fits'
if args.scfile is not None:
kw['scfile'] = args.scfile
staged_outfile = kw['outfile']
run_gtapp('gtmktime',logger,kw)
logger.info('cp %s %s',staged_outfile,outfile)
shutil.copy(staged_outfile,outfile)
os.chdir(cwd)
logger.info('Deleting %s',tmpdir)
shutil.rmtree(tmpdir)
logger.info('Done.')
def main():
gtselect_keys = ['tmin', 'tmax', 'emin', 'emax', 'zmax', 'evtype', 'evclass',
'phasemin', 'phasemax', 'convtype', 'rad', 'ra', 'dec']
gtmktime_keys = ['roicut', 'filter']
usage = "usage: %(prog)s [options] "
description = "Run gtselect and gtmktime on one or more FT1 files. "
"Note that gtmktime will be skipped if no FT2 file is provided."
parser = argparse.ArgumentParser(usage=usage, description=description)
add_lsf_args(parser)
for k in gtselect_keys:
if k in ['evtype', 'evclass', 'convtype']:
parser.add_argument('--%s' % k, default=None, type=int, help='')
else:
parser.add_argument('--%s' % k, default=None, type=float, help='')
for k in gtmktime_keys:
parser.add_argument('--%s' % k, default=None, type=str, help='')
parser.add_argument('--rock_angle', default=None, type=float, help='')
parser.add_argument('--outdir', default=None, type=str,
help='Path to output directory used when merge=False.')
parser.add_argument('--output', default=None, type=str,
help='Path to output file used when merge=True.')
parser.add_argument('--scfile', default=None, type=str, help='')
parser.add_argument('--dry_run', default=False, action='store_true')
parser.add_argument('--overwrite', default=False, action='store_true')
parser.add_argument('--merge', default=False, action='store_true',
help='Merge input FT1 files into N files where N is determined '
'by files_per_split.')
parser.add_argument('--files_per_split', default=100,
type=int, help='Set the number of files to combine in each '
'split of the input file list.')
parser.add_argument('--file_idx_min', default=None,
type=int, help='Set the number of files to assign to '
'each batch job.')
parser.add_argument('--file_idx_max', default=None,
type=int, help='Set the number of files to assign to '
'each batch job.')
parser.add_argument('files', nargs='+', default=None,
help='List of files.')
args = parser.parse_args()
batch = vars(args).pop('batch')
files = vars(args).pop('files')
args.outdir = os.path.abspath(args.outdir)
files = [os.path.abspath(f) for f in files]
ft1_files = get_files(files, ['.fit', '.fits'])
for i, f in enumerate(ft1_files):
if re.search('^root\:\/\/', f) is None:
ft1_files[i] = os.path.abspath(f)
input_files = []
output_files = []
files_idx_min = []
files_idx_max = []
opts = []
if args.file_idx_min is not None and args.file_idx_max is not None:
files_idx_min = [args.file_idx_min]
files_idx_max = [args.file_idx_max]
input_files = [files]
output_files = [args.output]
elif args.merge:
if not args.output:
raise Exception('No output file defined.')
nfiles = len(ft1_files)
njob = int(np.ceil(nfiles / float(args.files_per_split)))
for ijob, i in enumerate(range(0, nfiles, args.files_per_split)):
if args.outdir is not None:
mkdir(args.outdir)
outdir = os.path.abspath(args.outdir)
else:
outdir = os.path.dirname(os.path.dirname(args.output))
outfile = os.path.splitext(os.path.basename(args.output))[0]
outfile += '_%03i.fits' % (ijob)
outfile = os.path.join(outdir, outfile)
input_files += [files]
output_files += [outfile]
files_idx_min += [i]
files_idx_max += [i + args.files_per_split]
opts += [vars(args).copy()]
opts[-1]['output'] = outfile
opts[-1]['file_idx_min'] = i
opts[-1]['file_idx_max'] = i + args.files_per_split
else:
input_files = ft1_files
files_idx_min = [i for i in range(len(ft1_files))]
files_idx_max = [i + 1 for i in range(len(ft1_files))]
output_files = [os.path.join(
args.outdir, os.path.basename(x)) for x in ft1_files]
opts = [vars(args).copy() for x in ft1_files]
if batch:
submit_jobs('fermipy-select',
input_files, opts, output_files, overwrite=args.overwrite,
dry_run=args.dry_run)
sys.exit(0)
logger = Logger.configure(os.path.basename(__file__), None, logging.INFO)
logger.info('Starting.')
if args.scfile is not None:
args.scfile = os.path.abspath(args.scfile)
cwd = os.getcwd()
user = os.environ['USER']
tmpdir = tempfile.mkdtemp(prefix=user + '.', dir='/scratch')
os.chdir(tmpdir)
logger.info('tmpdir %s', tmpdir)
logger.info('outdir %s', args.outdir)
logger.info('output %s', args.output)
for infiles, outfile, idx_min, idx_max in zip(input_files, output_files,
files_idx_min, files_idx_max):
logger.info('infiles %s', pprint.pformat(infiles))
logger.info('outfile %s', outfile)
infiles = get_files(infiles, ['.fit', '.fits'])
if idx_min is not None:
infiles = infiles[idx_min:idx_max]
for i, f in enumerate(infiles):
if re.search('^root\:\/\/', f) is None:
continue
os.system('xrdcp %s %s' % (f, f.split('/')[-1]))
infiles[i] = os.path.join(tmpdir, f.split('/')[-1])
kw = {k: args.__dict__[k] for k in gtselect_keys}
if kw['emax'] is None:
kw['emax'] = 1E6
create_filelist(infiles, 'list.txt')
kw['infile'] = 'list.txt'
kw['outfile'] = 'out.fits'
staged_outfile = kw['outfile']
run_gtapp('gtselect', logger, kw)
kw = {k: args.__dict__[k] for k in gtmktime_keys}
if kw['roicut'] is None:
kw['roicut'] = 'no'
if kw['filter'] is None:
kw['filter'] = 'DATA_QUAL==1 && LAT_CONFIG==1'
if args.rock_angle is not None:
kw['filter'] += ' && ABS(ROCK_ANGLE)<%(rock)s ' % dict(
rock=args.rock_angle)
kw['evfile'] = 'out.fits'
kw['outfile'] = 'out_filtered.fits'
if args.scfile is not None:
kw['scfile'] = args.scfile
staged_outfile = kw['outfile']
run_gtapp('gtmktime', logger, kw)
logger.info('cp %s %s', staged_outfile, outfile)
shutil.copy(staged_outfile, outfile)
os.chdir(cwd)
logger.info('Deleting %s', tmpdir)
shutil.rmtree(tmpdir)
logger.info('Done.')