def mpdaf_process(self,
refpath='./esocombine/',
deepwhite='./esocombine/IMAGE_FOV_0001.fits',
extmask=None,
extmaskonly=False,
nproc=24):
"""
Produces final cubes optimised for fields that are relatively
empty in continuum sources using the GTO/MPDAF procedures
refpath -> where the reference cubes for wcs resempling are
otherwise the cube itself is used
deepwhite -> the best white image available to mask sources
skymask -> mask this region in the mpdaf reduction (selfcalibrate and zap) Format: ds9 region in image units
extmaskonly -> if true ose only the skymask supplied externally, if false merge sextractor and skymasks
nproc -> number of processors
"""
import os
import glob
import subprocess
import muse_redux_mpdaf as ex
#first, list how many OBs are there
listob = glob.glob('OB*')
listob.sort()
nobs = len(listob)
print('Process {} OBs'.format(nobs))
#now make space as needed for final products
if not os.path.exists('mpdafcombine'):
os.makedirs('mpdafcombine')
#rerun pipe enabling resampling on final ESO cube
ex.individual_resample(listob, refpath=refpath)
#now perform self-calibration on pixel table
ex.selfcalibrate(listob,
deepwhite,
refpath=refpath,
extmask=extmask,
extmaskonly=extmaskonly,
nproc=nproc)
#now perform sky subtraction on cubes with zap
ex.zapskysub(listob, extmask=extmask, extmaskonly=extmaskonly)
#finally, coadd data
ex.coaddcubes(listob)
print("All done!")
def line_process(self,
skymode='internal',
refpath='./esocombine/',
skymask=None,
lmin=4900,
lmax=9000,
deepwhite=None):
"""
Produces final cubes optimised for fields that are relatively
empty in continuum sources but that may have very extended
emission lines.
lmin -> the minimum wavelength to consider
lmax -> the maximum wavelength to consider
refpath -> where the reference cubes for wcs resempling are
skymask -> a skymask to be used for identify good regions for skysubtraction
(expected in image coordinates)
skymode -> internal: use good pixels (i.e. not containing sources or defined in skymask) to perform
skysubtraction plus run ZAP on it.
deepwhite -> if set to an image, this is used to mask sources during sky subtraction.
otherwise the cube itself is used
"""
import os
import glob
import subprocess
import muse_redux_line as ex
#first, list how many OBs are there
listob = glob.glob('OB*')
listob.sort()
nobs = len(listob)
print('Process {} OBs'.format(nobs))
#now make space as needed for final products
if not os.path.exists('linecombine'):
os.makedirs('linecombine')
#rerun pipe enabling resampling on final ESO cube
ex.individual_resample(listob, refpath=refpath)
#next construct the ifu mask for each exposure
ex.make_ifumasks(listob, refpath=refpath)
#compute illumination correction
ex.make_illcorr(listob)
#now do background subtraction
if ('internal' in skymode):
ex.internalskysub(listob, skymask, deepwhite=deepwhite)
else:
print("Sky subtraction mode {} not supported".format(skymode))
#change dir
currdir = os.getcwd()
os.chdir('linecombine')
print('Changing dir to linecombine...')
fl1 = open('cubes.lst', 'w')
fl2 = open('masks.lst', 'w')
#loop over OBs
for oob in range(nobs):
#count how many science exposures
nsci = len(
glob.glob("../{}/Proc/Basic/OBJECT_RED_0*.fits*".format(
listob[oob])))
#reconstruct names
for ll in range(nsci):
fl1.write(
'../{}/Proc/Line/DATACUBE_FINAL_LINEWCS_EXP{}_zapsky.fits\n'
.format(listob[oob], ll + 1))
fl2.write(
'../{}/Proc/Line/MASK_EXP{}_ILLCORR_edges.fits\n'.format(
listob[oob], ll + 1))
fl1.close()
fl2.close()
#make the temp combine
ex.combine_cubes("cubes.lst", "masks.lst")
os.chdir(currdir)
print("All done!")