def create_job_array(jobname, commands, logfiles=None, sleep='1m'):
subdir=mkdir("sub")
outdir=mkdir("log")
subbase=os.path.join(subdir,basename(jobname))
outbase=os.path.join(outdir,basename(jobname))
create_scripts(commands,subbase,sleep)
if logfiles is not None:
link_logfiles(logfiles,outbase)
submit="sh "+subbase+".${LSB_JOBINDEX}";
output=outbase+".%I"
njobs = len(commands)
params = dict(name=jobname,
cmnd=submit,
log=output,
njobs=njobs)
job = """-oo %(log)s -J %(name)s[1-%(njobs)i] %(cmnd)s"""%(params)
return job
(norm, flux, lnl, p1lnl, flnl) = pd[0]
p2lnl = LnLFn(pd[1][0],pd[1][3])(norm)
m1lnl = np.zeros(np.shape(p2lnl))
### FIXME! TRY WITH THIS ONE FIRST! -- still broken!
#m1lnl = LnLFn(pd[2][0],pd[2][3])(norm)
profile_data[spparam[i]] = dict(norm=norm,flux=flux,lnl=lnl,p1lnl=p1lnl,
flnl=flnl,p2lnl=p2lnl,m1lnl=m1lnl)
# Write logLike to text file
if not opts.text_output: continue
#outfile=join(workdir,splitext(basename(infile))[0]+"_logLike.dat")
outfile=join(workdir,outfile)
mkdir(dirname(outfile))
print "Writing %s"%outfile
data = np.vstack( (norm, flux, lnl, p1lnl, flnl, p2lnl, m1lnl) ).T
out = open(outfile,'w')
out.write('%-15s %-15s %-15s %-15s %-15s %-15s %-15s\n'%('# normPar','flux[ph/cm2/s]','logLike',
'p1logLike','flogLike','p2logLike','m1logLike'))
np.savetxt(out,data,fmt='%-15.6g %-15.6g %-15.6g %-15.6g %-15.6g %-15.6g %-15.6g')
out.close()
lnlfile = join(workdir,'%s_%s.yaml'%(target,suffix))
print "Writing %s"%lnlfile
tools.yaml_dump(dict(lnldata = profile_data,param=spparam,
jvalue=jvalue,jsigma=jsigma,
jnominal=jnominal,rjvalues=rjvalues),lnlfile)
"""
def gtltcuber(queue='long',**kwargs):
""" Submit a set of ltcubes to the batch and collect them at the end
evfile : List of LAT ft1 fits files
scfile : LAT spacecraft file
outfile : Output summed ltcube
tmin : Minimum time
tmax : Maximum time"""
workdir = mkdtemp(dir='./')
tmp = mkdir('/tmp/%s/'%os.environ['USER'])
os.environ['PFILES']=tmp+';'+os.environ['PFILES'].split(';')[-1]
tmin = kwargs.get('tmin',0)
tmax = kwargs.get('tmax',0)
zmax = kwargs.get('zmax',0)
dcostheta = kwargs.get('dcostheta',180)
binsz = kwargs.get('binsz',1)
chatter = kwargs.get('chatter',2)
sleep = kwargs.get('sleep','5m')
if kwargs['evfile'].startswith('@'):
evfiles = np.loadtxt(kwargs['evfile'].strip('@'),dtype='str')
else:
evfiles = [ kwargs['evfile'] ]
#### Calculated the ltcubes ####
jobname = 'gtltcube.%s'%os.path.basename(workdir)
lst, cmnds,logs = [],[],[]
i = 0
for evfile in evfiles:
#### gtltcube doesn't treat tmin/tmax sensibly ####
header = pyfits.open(evfile)[0].header
tstart = int(float(header['TSTART']))
tstop = int(float(header['TSTOP']))
if tstart >= tmax or tstop <= tmin:
print "Skipping %s"%evfile
continue
tbegin = tmin if tmin > tstart else tstart
tend = tmax if tmax < tstop else tstop
i += 1
ltfile = join(workdir,'ltcube_%03i.fits'%i)
select = join(workdir,'select_%03i.fits'%i)
params = dict( evfile=evfile,
select=select,
ltfile=ltfile,
scfile=kwargs['scfile'],
tmin=tbegin, tmax=tend,
zmax=zmax
)
print params
select = """gtselect \
infile=%(evfile)s \
outfile=%(select)s \
tmin=%(tmin)s tmax=%(tmax)s zmax=%(zmax)s \
ra=0 dec=0 rad=180 emin=1 emax=1e6 \
chatter=4 clobber=yes;
"""%params
#### tmin and tmax ignored by ltcube ####
ltcube = """gtltcube\
evfile="%(select)s" \
outfile="%(ltfile)s" \
scfile="%(scfile)s" \
dcostheta=0.025 binsz=1 \
zmax=%(zmax)d tmin=%(tmin)d tmax=%(tmax)d \
chatter=4 clobber=yes;
"""%params
cmnd = select + '\n\n' + ltcube
cmnds.append(cmnd)
lst.append(ltfile)
bsub(jobname,cmnds,logfile=None,q=queue,sleep=sleep)
ltcube_lst = join(workdir,'ltcubes.lst')
np.savetxt(ltcube_lst,lst,fmt="%s")
#### Combine ltcubes ####
depend = "done(%s)"%jobname
jobname='merge.%s'%os.path.basename(workdir)
script = join(workdir,'merge.py')
params = dict( script = script,
workdir=workdir)
#cmnd ="""python %(script)s; rm -rf %(workdir)s"""%params
cmnd ="""python %(script)s"""%params
open(script,'w').write("""\
from dsphs.utils.apps import gtltsumr;
import os
gtltsumr("@%s","%s")
""" % (ltcube_lst,kwargs['outfile']) )
bsub(jobname,[cmnd],q=queue,w=depend)
