def prep_direct_grism_pair(direct_asn='goodss-34-F140W_asn.fits', grism_asn='goodss-34-G141_asn.fits', radec=None, raw_path='../RAW/', mask_grow=18, scattered_light=False, final_scale=None, skip_direct=False, ACS=False, jump=False, order=2, get_shift=True, align_threshold=20, column_average=True, sky_iter=3):
"""
Process both the direct and grism observations of a given visit
"""
import threedhst.prep_flt_astrodrizzle as prep
import drizzlepac
from stwcs import updatewcs
import time
t0 = time.time()
#direct_asn='goodss-34-F140W_asn.fits'; grism_asn='goodss-34-G141_asn.fits'; radec=None; raw_path='../RAW/'
#radec = os.getenv('THREEDHST') + '/ASTRODRIZZLE_FLT/Catalog/goodss_radec.dat'
################################
#### Direct image processing
################################
#### xx add astroquery 2MASS/SDSS workaround for radec=None
if not skip_direct:
#### Get fresh FLTS from ../RAW/
asn = threedhst.utils.ASNFile(direct_asn)
if ACS:
for exp in asn.exposures:
print 'cp %s/%s_flc.fits.gz .' %(raw_path, exp)
os.system('cp %s/%s_flc.fits.gz .' %(raw_path, exp))
os.system('gunzip %s_flc.fits.gz' %(exp))
else:
threedhst.process_grism.fresh_flt_files(direct_asn, from_path=raw_path)
if (not ACS):
#### Subtract WFC3/IR direct backgrounds
prep.subtract_flt_background(root=direct_asn.split('_asn')[0], scattered_light=scattered_light, order=order)
#### Flag IR CRs again within runTweakReg
#### Run TweakReg
if (radec is None) & (not ACS):
drizzlepac.astrodrizzle.AstroDrizzle(direct_asn, clean=True, final_scale=None, final_pixfrac=0.8, context=False, final_bits=576, preserve=False, driz_cr_snr='5.0 4.0', driz_cr_scale = '2.5 0.7') # ,
else:
if get_shift:
prep.runTweakReg(asn_file=direct_asn, master_catalog=radec, final_scale=None, ACS=ACS, threshold=align_threshold)
#### Subtract background of direct ACS images
if ACS:
for exp in asn.exposures:
flc = pyfits.open('%s_flc.fits' %(exp), mode='update')
for ext in [1,4]:
threedhst.showMessage('Subtract background from %s_flc.fits[%d] : %.4f' %(exp, ext, flc[ext].header['MDRIZSKY']))
flc[ext].data -= flc[ext].header['MDRIZSKY']
flc[ext].header['MDRIZSK0'] = flc[ext].header['MDRIZSKY']
flc[ext].header['MDRIZSKY'] = 0.
#
flc.flush()
else:
pass
#### Do this later, gives segfaults here???
#prep.subtract_flt_background(root=direct_asn.split('_asn')[0], scattered_light=scattered_light)
#### Flag CRs again on BG-subtracted image
#drizzlepac.astrodrizzle.AstroDrizzle(direct_asn, clean=True, final_scale=None, final_pixfrac=0.8, context=False, final_bits=576, preserve=False, driz_cr_snr='5.0 4.0', driz_cr_scale = '2.5 0.7') # ,
################################
#### Grism image processing
################################
if grism_asn:
asn = threedhst.utils.ASNFile(grism_asn)
if ACS:
for exp in asn.exposures:
print 'cp %s/%s_flc.fits.gz .' %(raw_path, exp)
os.system('cp %s/%s_flc.fits.gz .' %(raw_path, exp))
os.system('gunzip %s_flc.fits.gz' %(exp))
updatewcs.updatewcs('%s_flc.fits' %(exp))
prep.copy_adriz_headerlets(direct_asn=direct_asn, grism_asn=grism_asn, ACS=True)
prep.subtract_acs_grism_background(asn_file=grism_asn, final_scale=None)
else:
#### Remove the sky and flag CRs
## with mask from rough zodi-only subtraction
prep.subtract_grism_background(asn_file=grism_asn, PATH_TO_RAW='../RAW/', final_scale=None, visit_sky=True, column_average=False, mask_grow=mask_grow, first_run=True)
## Redo making mask from better combined image
prep.subtract_grism_background(asn_file=grism_asn, PATH_TO_RAW='../RAW/', final_scale=final_scale, visit_sky=True, column_average=column_average, mask_grow=mask_grow, first_run=False, sky_iter=sky_iter)
#### Copy headers from direct images
if radec is not None:
prep.copy_adriz_headerlets(direct_asn=direct_asn, grism_asn=grism_asn, ACS=False)
#### Run CR rejection with final shifts
drizzlepac.astrodrizzle.AstroDrizzle(grism_asn, clean=True, skysub=False, final_wcs=True, final_scale=final_scale, final_pixfrac=0.8, context=False, final_bits=576, driz_sep_bits=576, preserve=False, driz_cr_snr='8.0 5.0', driz_cr_scale='2.5 0.7') # driz_cr_snr='5.0 4.0', driz_cr_scale = '2.5 0.7')
if not grism_asn:
t1 = time.time()
threedhst.showMessage('direct: %s\n\nDone (%d s).' %(direct_asn, int(t1-t0)))
else:
t1 = time.time()
threedhst.showMessage('direct: %s\ngrism: %s\n\nDone (%d s).' %(direct_asn, grism_asn, int(t1-t0)))
def prep_direct_grism_pair(direct_asn='goodss-34-F140W_asn.fits', grism_asn='goodss-34-G141_asn.fits', radec=None, raw_path='../RAW/', mask_grow=18, scattered_light=False, final_scale=None, skip_direct=False, ACS=False, jump=False, order=2, get_shift=True, align_threshold=20, column_average=True, sky_iter=3, run_acs_lacosmic=False):
"""
Process both the direct and grism observations of a given visit
"""
import threedhst.prep_flt_astrodrizzle as prep
import drizzlepac
from stwcs import updatewcs
import time
t0 = time.time()
#direct_asn='goodss-34-F140W_asn.fits'; grism_asn='goodss-34-G141_asn.fits'; radec=None; raw_path='../RAW/'
#radec = os.getenv('THREEDHST') + '/ASTRODRIZZLE_FLT/Catalog/goodss_radec.dat'
################################
#### Direct image processing
################################
#### xx add astroquery 2MASS/SDSS workaround for radec=None
if not skip_direct:
#### Get fresh FLTS from ../RAW/
asn = threedhst.utils.ASNFile(direct_asn)
if ACS:
for exp in asn.exposures:
print 'cp %s/%s_flc.fits.gz .' %(raw_path, exp)
os.system('cp %s/%s_flc.fits.gz .' %(raw_path, exp))
os.system('gunzip -f %s_flc.fits.gz' %(exp))
if run_acs_lacosmic:
try:
import lacosmicx
status = True
except:
print 'import lacosmicx failed!'
status = False
if status:
im = pyfits.open('%s_flc.fits' %(exp), mode='update')
for ext in [1,2]:
indata = im['SCI',ext].data
#inmask = im['DQ',ext].data > 0
if im['SCI',ext].header['BUNIT'] == 'ELECTRONS':
gain = 1
else:
gain = 1./im[0].header['EXPTIME']
if 'MDRIZSK0' in im['SCI',ext].header:
pssl = im['SCI',ext].header['MDRIZSK0']
else:
pssl = 0.
if 'FLASHLVL' in im[0].header:
pssl += im[0].header['FLASHLVL']
sig_scale = 1.8
else:
sig_scale = 1.
out = lacosmicx.lacosmicx(indata, inmask=None,
sigclip=3.5*sig_scale, sigfrac=0.2,
objlim=7.0, gain=gain,
readnoise=im[0].header['READNSEA'],
satlevel=np.inf, pssl=pssl, niter=5,
sepmed=True, cleantype='meanmask',
fsmode='median', psfmodel='gauss',
psffwhm=2.5,psfsize=7, psfk=None,
psfbeta=4.765, verbose=True)
crmask, cleanarr = out
im['DQ',ext].data |= 16*crmask
### Low pixels
if im[0].header['INSTRUME'] == 'WFC3':
bad = im['SCI',ext].data < -4*im['ERR',ext].data
im['DQ',ext].data |= 16*bad
im.flush()
else:
threedhst.process_grism.fresh_flt_files(direct_asn, from_path=raw_path)
if (not ACS):
#### Subtract WFC3/IR direct backgrounds
prep.subtract_flt_background(root=direct_asn.split('_asn')[0], scattered_light=scattered_light, order=order)
#### Flag IR CRs again within runTweakReg
#### Run TweakReg
if (radec is None) & (not ACS):
print len(asn.exposures)
if len(asn.exposures) > 1:
drizzlepac.astrodrizzle.AstroDrizzle(direct_asn, clean=True, final_scale=None, final_pixfrac=0.8, context=False, final_bits=576, preserve=False, driz_cr_snr='5.0 4.0', driz_cr_scale = '2.5 0.7')
else:
drizzlepac.astrodrizzle.AstroDrizzle(direct_asn, clean=True, final_scale=None, final_pixfrac=1, context=False, final_bits=576, preserve=False, driz_separate=False, driz_sep_wcs=False, median=False, blot=False, driz_cr=False, driz_cr_corr=False, driz_combine=True)
else:
if get_shift:
prep.runTweakReg(asn_file=direct_asn, master_catalog=radec, final_scale=None, ACS=ACS, threshold=align_threshold)
#### Subtract background of direct ACS images
if ACS:
for exp in asn.exposures:
flc = pyfits.open('%s_flc.fits' %(exp), mode='update')
if 'SUB' in flc[0].header['APERTURE']:
extensions = [1]
else:
extensions = [1,4]
for ext in extensions:
threedhst.showMessage('Subtract background from %s_flc.fits[%d] : %.4f' %(exp, ext, flc[ext].header['MDRIZSKY']))
flc[ext].data -= flc[ext].header['MDRIZSKY']
flc[ext].header['MDRIZSK0'] = flc[ext].header['MDRIZSKY']
flc[ext].header['MDRIZSKY'] = 0.
#
flc.flush()
else:
pass
#### Do this later, gives segfaults here???
#prep.subtract_flt_background(root=direct_asn.split('_asn')[0], scattered_light=scattered_light)
#### Flag CRs again on BG-subtracted image
#drizzlepac.astrodrizzle.AstroDrizzle(direct_asn, clean=True, final_scale=None, final_pixfrac=0.8, context=False, final_bits=576, preserve=False, driz_cr_snr='5.0 4.0', driz_cr_scale = '2.5 0.7') # ,
################################
#### Grism image processing
################################
if grism_asn:
asn = threedhst.utils.ASNFile(grism_asn)
if ACS:
for exp in asn.exposures:
print 'cp %s/%s_flc.fits.gz .' %(raw_path, exp)
os.system('cp %s/%s_flc.fits.gz .' %(raw_path, exp))
os.system('gunzip -f %s_flc.fits.gz' %(exp))
updatewcs.updatewcs('%s_flc.fits' %(exp))
prep.copy_adriz_headerlets(direct_asn=direct_asn, grism_asn=grism_asn, ACS=True)
prep.subtract_acs_grism_background(asn_file=grism_asn, final_scale=None)
else:
#### Remove the sky and flag CRs
## with mask from rough zodi-only subtraction
prep.subtract_grism_background(asn_file=grism_asn, PATH_TO_RAW='../RAW/', final_scale=None, visit_sky=True, column_average=False, mask_grow=mask_grow, first_run=True)
## Redo making mask from better combined image
prep.subtract_grism_background(asn_file=grism_asn, PATH_TO_RAW='../RAW/', final_scale=final_scale, visit_sky=True, column_average=column_average, mask_grow=mask_grow, first_run=False, sky_iter=sky_iter)
#### Copy headers from direct images
if radec is not None:
prep.copy_adriz_headerlets(direct_asn=direct_asn, grism_asn=grism_asn, ACS=False)
#### Run CR rejection with final shifts
drizzlepac.astrodrizzle.AstroDrizzle(grism_asn, clean=True, skysub=False, final_wcs=True, final_scale=final_scale, final_pixfrac=0.8, context=False, final_bits=576, driz_sep_bits=576, preserve=False, driz_cr_snr='8.0 5.0', driz_cr_scale='2.5 0.7') # driz_cr_snr='5.0 4.0', driz_cr_scale = '2.5 0.7')
if not grism_asn:
t1 = time.time()
threedhst.showMessage('direct: %s\n\nDone (%d s).' %(direct_asn, int(t1-t0)))
else:
t1 = time.time()
threedhst.showMessage('direct: %s\ngrism: %s\n\nDone (%d s).' %(direct_asn, grism_asn, int(t1-t0)))