def process_roi(self, index):
""" special for batch: manage the log file, make sure an exception closes it
"""
print 'Setting up ROI #%04d ...' % index,
sys.stdout.flush()
self.setup_roi(index)
if self.outdir is not None:
logpath = os.path.join(self.outdir, 'log')
if not os.path.exists(logpath): os.mkdir(logpath)
outtee = tools.OutputTee(os.path.join(logpath, self.name+'.txt'))
else: outtee=None
print 'Processing...'
sys.stdout.flush()
try:
self.process()
finally:
if outtee is not None: outtee.close()
def main(args=None):
if os.path.exists('kill'):
raise Exception('Kill this job')
if args is not None:
stage = args.stage[0]
nocreate = False # Was True, but only important to run the creation for large data sets
else:
# if called directly, may create
stage = os.environ.get('stage', 'create')
nocreate = False
stage = stage.split('_')[0]
if stage != 'create' and stage != 'monthly':
print 'Not creating a model: assume data validated'
return
pointlike_dir = os.environ.get('POINTLIKE_DIR', '.')
skymodel = os.environ.get('SKYMODEL_SUBDIR', '.')
stream = os.environ.get('PIPELINE_STREAM', '-1')
absskymodel = os.path.join(pointlike_dir,
skymodel) if args is not None else '.'
if args is not None:
tee = tools.OutputTee(os.path.join(absskymodel, 'summary_log.txt'))
current = str(datetime.datetime.today())[:16]
print '\n%s stage %s stream %s model %s ' % (current, stage, stream,
absskymodel)
if 'CUSTOM_IRF_DIR' not in os.environ and os.path.exists(
os.path.expandvars('$FERMI/custom_irfs')):
os.environ['CUSTOM_IRF_DIR'] = os.path.expandvars('$FERMI/custom_irfs')
rc = dataset.validate(absskymodel, nocreate=nocreate, quiet=False)
print 'Data is validated' if rc else 'NOT validated'
if args is not None:
tee.close()
if not rc: raise Exception('Failed to validate data')
def main(args):
"""
"""
def fixpath(s):
if os.path.exists(s): return s
r= s.replace('/a/wain025/g.glast.u55','/afs/slac/g/glast/groups')
assert os.path.exists(r), 'paths do not exist: %s or %s' % (s,r)
return r
pointlike_dir=fixpath(args.pointlike_dir) # = os.environ.get('POINTLIKE_DIR', '.')
skymodel =fixpath(args.skymodel) # = os.environ.get('SKYMODEL_SUBDIR', sys.argv[1] )
stream_id = args.stream
stagelist = args.stage
if hasattr(stagelist, '__iter__'): stagelist=stagelist[0] #handle local or from uwpipeline.py
#piperaise Exception('killing this sequence!')
absskymodel = os.path.join(pointlike_dir, skymodel)
def make_zip(fname, ext='pickle', select=None):
"""fname : string
name of a folder containing files to be zipped
"""
if os.path.exists(fname+'zip') and \
os.path.getmtime(fname) < os.path.getmtime(fname+'.zip'):
print 'Not updating %s' % fname+'.zip'
return
if select is not None:
ff = glob.glob(os.path.join(absskymodel, select))
else:
ff = glob.glob(os.path.join(absskymodel, fname, '*.'+ext))
if len(ff)==0:
print 'no files found to zip in folder %s' %fname
return
if len(ff)!=1728 and fname=='pickle' and not stagelist.startswith('addseeds'):
raise Exception('Stage {}: Found {} pickle files, expected 1728'.format(stagelist, len(ff)))
print 'found %d *.%s in folder %s ...' % ( len(ff),ext, fname,) ,
with zipfile.ZipFile(os.path.join(absskymodel, fname+'.zip'), 'w') as z:
for filename in ff:
z.write( filename, os.path.join(fname,os.path.split(filename)[-1]))
print ' zipped into file %s.zip' %fname
def create_stream(newstage, job_list='joblist.txt'):
print 'Starting stage %s' % newstage
ps = stream.PipelineStream()
ps(newstage, job_list=job_list, test=False)
next = args.next
print 'next: {}'.format(next)
if not args.test:
tee = tools.OutputTee(os.path.join(absskymodel, 'summary_log.txt'))
if os.path.exists(str(stream_id)):
print 'Abort since detected file with stream name'
raise Exception('Abort since detected file with stream name')
if stream_id!=-1:
streamInfo(stream_id, absskymodel)
os.chdir(absskymodel) # useful for diagnostics below
current = str(datetime.datetime.today())[:16]
print '\n%s stage %s stream %s model %s ' % (current, stagelist, stream_id, absskymodel)
if os.path.exists('failed_rois.txt'):
failed = sorted(map(int, open('failed_rois.txt').read().split()))
print 'failed rois %s' % failed
raise Exception('failed rois %s' % failed)
t = stagelist.split(':',1)
if len(t)==2:
stage, nextstage = t
else: stage,nextstage = t[0], None
ss = stage.split('_')
stage = ss[0]
stage_args = ss[1:] if len(ss)>1 else ['none']
next_stage = stagedict.stagenames[stage].get('next', None)
# always update the pickle for the ROIs, if changed
make_zip('pickle')
if stage=='update' or stage=='betafix':
logto = open(os.path.join(absskymodel,'converge.txt'), 'a')
qq=pipe.check_converge(absskymodel, tol=12, log=logto)
r = pipe.roirec(absskymodel)
q = pipe.check_converge(absskymodel, tol=12 , add_neighbors=False)
open('update_roi_list.txt', 'w').write('\n'.join(map(str, sorted(qq))))
if stage_args[0]!='only' and stage_args[0]!='associations':
if len(q)>1:
if len(qq)> 200:
create_stream('update')
else:
create_stream('update', job_list='$SKYMODEL_SUBDIR/update_roi_list.txt')
else:
model_name = os.getcwd().split('/')[-1]
create_stream('finish' if model_name.find('month')<0 else 'finish_month')
elif stage=='sedinfo':
make_zip('sedinfo')
make_zip('sedfig','png')
elif stage=='create' or stage=='create_reloc':
# always do one more stream after initial
if nextstage is None:
create_stream('update_full') # always start an update
elif stage=='diffuse':
make_zip('galfit_plots', 'png')
make_zip('galfits_all')
elif stage=='isodiffuse':
make_zip('isofit_plots', 'png')
make_zip('isofits')
elif stage=='limb':
make_zip('limb')
#elif stage=='finish' or stage=='counts':
elif stage=='tables':
names = 'ts kde'.split() if stage_args==['none'] else stage_args
if 'ts' in names:
if not os.path.exists('hptables_ts_kde_512.fits'):
healpix_map.assemble_tables(names)
modelname = os.getcwd().split('/')[-1]
check_ts.pipe_make_seeds( modelname, 'seeds_ts.txt')
if next_stage is not None:
create_stream(next_stage)
elif 'hard' in names:
healpix_map.assemble_tables('hard')
modelname = os.getcwd().split('/')[-1]
check_ts.pipe_make_seeds( modelname, 'seeds_hard.txt')
if next_stage is not None:
create_stream(next_stage)
elif 'mspsens' in names:
healpix_map.assemble_tables(names, nside=256) # assume nside
elif 'all' in names:
print 'Finished tables_all'
else:
print 'Unexpected table name: {}'.format(names)
elif stage=='ptables':
names = ['tsp']
healpix_map.assemble_tables(names)
elif stage=='pulsar':
healpix_map.assemble_tables(['pts'])
elif stage=='seedcheck':
key = stage_args[0]
print 'Processing seedcheck with key %s' % key
make_zip('seedcheck' , select=None if key=='none' else 'seedcheck_%s/*' %key)
if key=='pgw': # processing a month
seedcheck.SeedCheck().all_plots();
create_stream('update_seeds')
elif stage=='sourcefinding':
raise Exception('place holder -- will call code for inclusive template ts maps')
else: # catch fluxcorr, any others like
# also perhaps start another stage
if os.path.exists(stage):
make_zip(stage)
if next_stage is not None:
job_list = stagedict.stagenames[next_stage].get('job_list', 'job_list')
create_stream(next_stage, job_list)
else:
print 'stage %s not recognized for summary'%stage
if not args.test:
if nextstage:
create_stream(nextstage)
tee.close()