def hopr_brodwin():
import unicorn
import wfc3_gyro.prepare
import threedhst.prep_flt_astrodrizzle as init
os.chdir('/3DHST/Spectra/Work/14114/TEST_HOPR_BRODWIN/REDUCE/')
unicorn.candels.make_asn_files()
RAW_PATH = '../RAW'
prep_brodwin_drifted()
os.system('rsync -av {}/ib2u72*_flt.fits.gz .'.format(RAW_PATH))
os.system('gunzip -f ib2u72*_flt.fits.gz')
init.prep_direct_grism_pair(direct_asn='BRODWIN-72-260-F160W_asn.fits', grism_asn=None, radec='../REF/radec.cat',
raw_path = '../RAW/', mask_grow=8, scattered_light=False, final_scale = 0.06,
skip_direct=False, ACS=False, align_threshold=6)
for master_root in ['BRODWIN-22-051-F160W','BRODWIN-72-260-F160W']:
asn = threedhst.utils.ASNFile('{}_asn.fits'.format(master_root))
for root in asn.exposures:
wfc3_gyro.prepare.split_IMA(root=root)
wfc3_gyro.prepare.make_pointing_asn(root=root, master_root=master_root)
wfc3_gyro.prepare.subtract_background_reads(root=root, master_root=master_root)
wfc3_gyro.prepare.fix_cosmic_rays(root=root, master_root=master_root)
wfc3_gyro.prepare.align_reads(root=root, refimage='../REF/BRODWIN-72-260-F160W_drz_sci.fits', final_scale=0.12,
master_catalog='../REF/BRODWIN-72-260-F160W_drz_sci.cat', refxcol = 13, refycol = 14)
for root in ['ib2u72','ib2u22']:
drizzle_flts(root=root)
def prep_cooper_repeat():
import threedhst
import threedhst.prep_flt_astrodrizzle as init
os.chdir('/3DHST/Spectra/Work/14114/TEST_HOPR_COOPER/PREP/')
unicorn.candels.make_asn_files()
init.prep_direct_grism_pair(direct_asn='EGS13034445-55-081-F140W_asn.fits', grism_asn=None, radec=None,
raw_path = '../RAW/', mask_grow=8, scattered_light=False, final_scale = 0.06,
skip_direct=False, ACS=False, align_threshold=6)
os.system('rsync -av EGS13034445-55-081-F140W_drz* ../REF/')
os.chdir('/3DHST/Spectra/Work/14114/TEST_HOPR_COOPER/REF/')
wfc3_gyro.prepare.run_sextractor(mosaic='EGS13034445-55-081-F140W_drz_sci.fits',
weight='EGS13034445-55-081-F140W_drz_wht.fits')
threedhst.sex.sexcatRegions('EGS13034445-55-081-F140W_drz_sci.cat','EGS13034445-55-081-F140W_drz_sci.reg', format=1)
### make an radec cat from sextractor cat
os.chdir('/3DHST/Spectra/Work/14114/TEST_HOPR_COOPER/PREP/')
init.prep_direct_grism_pair(direct_asn='EGS13034445-55-081-F140W_asn.fits', grism_asn=None, radec='../REF/radec.cat',
raw_path = '../RAW/', mask_grow=8, scattered_light=False, final_scale = 0.06,
skip_direct=False, ACS=False, align_threshold=6)
def align_all(visits=[], make_asn = False, program=14227):
"""
The catalog for ERSPRIME is South.
"""
print paths
print visits
shutil.copy('../RAW/files.info', 'files.info')
cleanup_outputs()
fetch_gz(visits)
if make_asn:
unicorn.candels.make_asn_files()
# Lower case the filenames
asn_files = glob.glob('*asn.fits')
for asn in asn_files:
os.rename(asn, '{}_asn.fits'.format(asn.split('_')[0].upper()))
#os.rename(asn, asn.upper())
direct_files = glob.glob('*105*_asn.fits')
print direct_files
for direct in direct_files:
# Check that not accidently looping over a program 13420 visit if
# processing a 14227 visit of same number.
if program == 14227 and 'GDN' not in direct:
grism = direct.replace('F105W', 'G102')
print " "
print direct, grism
#if 'GDN' in grism:
# visit = int(grism.split('-')[1])
#else:
# visit = int(grism[4:6])
visit = int(grism.split('-')[1])
print "Visit: {}".format(visit)
# Only reprocess the visits in the list, or reprocess
# everything if the list is empty.
if ((visits != []) and (visit in visits)) or (visits == []):
if 'GN' in direct.upper() or 'GDN' in direct.upper():
cat_file = 'goodsn_radec.cat'
print "Using radec cat for NORTH, {}".format(cat_file)
elif 'GS' in direct.upper() or 'ERSPRIME' in direct.upper():
cat_file = 'goodss_3dhst.v4.1.radec.cat'
print "Using radec cat for SOUTH, {}".format(cat_file)
init.prep_direct_grism_pair(direct_asn=direct, grism_asn=grism,
radec=os.path.join(paths['path_to_ref_files'], 'REF', cat_file),
raw_path = paths['path_to_RAW'], mask_grow=8,
scattered_light=False, final_scale = None,
skip_direct=False, ACS=False, align_threshold=6)
cleanup_gz()
def prep_clear(field, make_asn = True, check_background = False,
run_prep = True):
import threedhst.prep_flt_astrodrizzle as init
import unicorn.interlace_test as test
if make_asn:
unicorn.candels.make_asn_files()
if check_background:
#os.chdir('/Users/imomcheva/Work/CLEAR/RAW')
os.chdir(paths['path_to_RAW'])
asn_files = glob.glob('*asn.fits')
for asn in asn_files:
root = asn.split('_asn')[0]
png = glob.glob(root+'*orbit.*')
if (len(png) > 0):
continue
try:
mywfc3.bg.show_orbit_limbangle(asn = [root])
except:
fp = open(root+'_orbit.failed','w')
fp.write('---')
fp.close()
os.chdir(paths['path_to_PREPARE'])
if remove_satelites:
#os.chdir('/Users/imomcheva/Work/CLEAR/RAW/')
os.chdir(paths['path_to_RAW'])
unicorn.prepare.make_IMA_FLT(raw='icxt31r3q_raw.fits', pop_reads=[2])
os.chdir(paths['path_to_PREPARE'])
if run_prep:
os.chdir(paths['path_to_PREPARE'])
grism_files = glob.glob(field + '*G102_asn.fits')
direct_files = glob.glob(field + '*F105W_asn.fits')
for direct, grism in zip(direct_files, grism_files):
init.prep_direct_grism_pair(direct_asn=direct, grism_asn=grism,
radec=paths['path_to_ref_files']+'REF/goodss_3dhst.v4.1.radec.cat',
raw_path = paths['path_to_RAW'], mask_grow=8,
scattered_light=False, final_scale = None,
skip_direct=False, ACS=False, align_threshold=6)
def prep_brodwin_repeat():
import threedhst
import threedhst.prep_flt_astrodrizzle as init
os.chdir('/3DHST/Spectra/Work/14114/TEST_HOPR_BRODWIN/PREP/')
init.prep_direct_grism_pair(direct_asn='BRODWIN-72-260-F160W_asn.fits', grism_asn=None, radec=None,
raw_path = '../RAW/', mask_grow=8, scattered_light=False, final_scale = 0.06,
skip_direct=False, ACS=False, align_threshold=6)
os.system('rsync -av BRODWIN-72-260-F160W_drz* ../REF/')
### make an radec cat from sextractor cat
os.chdir('/3DHST/Spectra/Work/14114/TEST_HOPR_BRODWIN/REF/')
wfc3_gyro.prepare.run_sextractor(mosaic='BRODWIN-72-260-F160W_drz_sci.fits',weight='BRODWIN-72-260-F160W_drz_wht.fits')
threedhst.sex.sexcatRegions('BRODWIN-72-260-F160W_drz_sci.cat','BRODWIN-72-260-F160W_drz_sci.reg', format=1)
os.chdir('/3DHST/Spectra/Work/14114/TEST_HOPR_BRODWIN/PREP/')
init.prep_direct_grism_pair(direct_asn='BRODWIN-72-260-F160W_asn.fits', grism_asn=None, radec='../REF/radec.cat',
raw_path = '../RAW/', mask_grow=8, scattered_light=False, final_scale = 0.06,
skip_direct=False, ACS=False, align_threshold=6)
def acs():
"""
Script to reduce ACS Cluster data
"""
import glob
import os
import drizzlepac
import numpy as np
import threedhst
import threedhst.prep_flt_astrodrizzle as init
from threedhst import catIO
import unicorn
import unicorn.interlace_acs
field = 'MACS*1149'
### First, in PREP_FLT, run "flt_info.sh"
### Make ACS associations
unicorn.candels.make_asn_files(uniquename=True, translate={'-ROT':''})
### Need to take out "_flc" extension from the ASN files
files=glob.glob('*asn.fits')
for asn_file in files:
asn = threedhst.utils.ASNFile(asn_file)
## print asn.exposures
for i in range(len(asn.exposures)):
asn.exposures[i] = asn.exposures[i].split('_flc')[0]
#
asn.write(asn_file)
#
#### Combine parallels
for par in [1,2]:
for filter in ['F775W','F850LP']:
files=glob.glob(field+'*-ACSPAR%d-[AB]*-%s*' %(par, filter))
print files
list = []
for file in files:
asn = threedhst.utils.ASNFile(file)
list.extend(asn.exposures)
os.remove(file)
asn.exposures = list
asn.product = 'MACS0416-ACSPAR%d-%s' %(par, filter)
asn.write('%s_asn.fits' %(asn.product))
files, radec = glob.glob('MACS0416-ACSPA*asn.fits'), 'subaru.radec'
files, radec = glob.glob('MACS0416-2403*asn.fits'), 'clash_radec.dat'
files, radec = glob.glob('*0717*F814W*asn.fits'), 'subaru_macs0717.radec'
files, radec = glob.glob(field+'*POS5-1?*814*asn.fits'), 'macs0717_subaru_radec.dat'
files, radec = glob.glob(field+'*PAR1*775*asn.fits'), 'macs0416_subaru_radec.dat'
files, radec = glob.glob(field+'*814*asn.fits'), 'macs1149_radec.dat'
refimage='hlsp_XXX'
files, radec = glob.glob('*asn.fits'), 'clash_radec.dat'
files, radec = glob.glob('*LENS*asn.fits'), 'clash_radec.dat'
from socket import gethostname as hostname
for asn_file in files:
#if os.path.exists(asn_file.replace('asn', 'drc_sci')):
#continue
#
init.prep_direct_grism_pair(direct_asn=asn_file, grism_asn=None, radec=radec, ACS=True, align_threshold=5)
if 'science' in hostname():
asn = threedhst.utils.ASNFile(asn_file)
for exp in asn.exposures:
os.remove('../RAW/%s_flc.fits.gz' %(exp))
##### Combine visits on the cluster to flag CRs
info = catIO.Table("files.info")
filters = np.unique(info['FILTER'])
for filter in filters:
#### Get all FLTs
flt_list = []
files=glob.glob('MACS*0416-2403-??-???-%s_asn.fits' %(filter))
#files=glob.glob('MACS*1149*%s_asn.fits' %(filter))
for asn_file in files:
asn = threedhst.utils.ASNFile(asn_file)
for exp in asn.exposures:
flt_list.append('%s_flc.fits' %(exp))
#
bits = 96 #+512
skyuser = '******'
#### Ignore MDRIZSKY
fp = open('ACS.skyfile','w')
fp.writelines(['%s 0.0\n' %(file) for file in flt_list])
fp.close()
#
#### Run AstroDrizzle to flag CRs on both orients
drizzlepac.astrodrizzle.AstroDrizzle(flt_list, output='MACS0717+3745-%s_total_comb' %(filter), clean=True, context=False, preserve=False, skysub=True, skyfile='ACS.skyfile', driz_separate=True, driz_sep_wcs=True, median=True, blot=True, driz_cr=True, driz_combine=True, final_wcs=True, final_refimage=None, final_scale=0.065, final_pixfrac=0.8, final_rot=0, final_kernel='square', resetbits=0, final_bits=bits, final_wht_type='IVM')
#
#drizzlepac.astrodrizzle.AstroDrizzle(flt_list, output='MACS0416-2403-30mas-%s' %(filter), clean=True, context=False, preserve=False, skysub=True, skyfile='ACS.skyfile', driz_separate=False, driz_sep_wcs=False, median=False, blot=False, driz_cr=False, driz_combine=True, final_wcs=True, final_refimage='hlsp_clash_hst_acs-30mas_macs0416_f475w_v1_drz.fits', final_pixfrac=0.8, final_kernel='square', resetbits=0, final_bits=bits, final_wht_type='IVM')
#
#drizzlepac.astrodrizzle.AstroDrizzle(flt_list, output='MACS1149-2223-Mosaic-%s' %(filter), clean=True, context=False, preserve=False, skysub=True, skyfile='ACS.skyfile', driz_separate=False, driz_sep_wcs=False, median=False, blot=False, driz_cr=False, driz_combine=True, final_wcs=True, final_scale=0.05, final_rot=0, final_pixfrac=0.8, final_kernel='square', resetbits=0, final_bits=bits, final_wht_type='IVM')
#### MACS0717 mosaic
for filter in filters:
flt_list = []
#files=glob.glob('MACS0416-2403-??-???-%s_asn.fits' %(filter))
files=glob.glob(field+'*%s_asn.fits' %(filter))
for asn_file in files:
asn = threedhst.utils.ASNFile(asn_file)
for exp in asn.exposures:
if os.path.exists('%s_flc.fits' %(exp)):
flt_list.append('%s_flc.fits' %(exp))
#
bits = 96 #+512
skyuser = '******'
#### Ignore MDRIZSKY
fp = open('ACS.skyfile','w')
fp.writelines(['%s 0.0\n' %(file) for file in flt_list])
fp.close()
#
#drizzlepac.astrodrizzle.AstroDrizzle(flt_list, output='MACS0717-Mosaic-%s' %(filter), clean=True, context=False, preserve=False, skysub=True, skyfile='ACS.skyfile', driz_separate=False, driz_sep_wcs=False, median=False, blot=False, driz_cr=False, driz_combine=True, final_wcs=True, final_rot=0, final_pixfrac=0.8, final_kernel='square', resetbits=0, final_bits=bits, final_wht_type='IVM', final_ra=1.093574923885E+02, final_dec=3.778490152063E+01, final_scale=0.1798, final_outnx=4185, final_outny=4670)
### Here, specify the output image size, pixel scale, etc.
#drizzlepac.astrodrizzle.AstroDrizzle(flt_list, output='MACS0717-Mosaic-%s' %(filter), clean=True,
# context=False, preserve=False, skysub=True, skyfile='ACS.skyfile', driz_separate=False,
# driz_sep_wcs=False, median=False, blot=False, driz_cr=False, driz_combine=True, final_wcs=True,
# final_rot=0, final_pixfrac=0.8, final_kernel='square', resetbits=0, final_bits=bits, final_wht_type='IVM',
# final_ra=1.093574923885E+02, final_dec=3.778490152063E+01, final_scale=0.1, final_outnx=7524, final_outny=8397)
### Here, force the output to match the FF mosaic
#drizzlepac.astrodrizzle.AstroDrizzle(flt_list, output='MACS1149-Mosaic-%s' %(filter), clean=True,
# context=False, preserve=False, skysub=True, skyfile='ACS.skyfile', driz_separate=False,
# driz_sep_wcs=False, median=False, blot=False, driz_cr=False, driz_combine=True, final_wcs=True,
# final_rot=0, final_pixfrac=0.8, final_kernel='square', resetbits=0, final_bits=bits, final_wht_type='IVM',
# final_refimage=refimage)
drizzlepac.astrodrizzle.AstroDrizzle(flt_list, output='MACS1149-Mosaic-v2-%s' %(filter), clean=True,
context=True, preserve=False, skysub=True, skyfile='ACS.skyfile', driz_separate=False,
driz_sep_wcs=False, median=False, blot=False, driz_cr=False, driz_combine=True, final_wcs=True,
final_rot=0, final_pixfrac=0.8, final_kernel='square', resetbits=0, final_bits=bits, final_wht_type='IVM',
final_ra=177.405988, final_dec=22.343847, final_outnx=11658, final_outny=16355)
def prep():
import glob
import os
import threedhst
import threedhst.prep_flt_astrodrizzle as init
from threedhst import catIO
import unicorn
import research.hawkiff
### Make ACS associations
unicorn.candels.make_asn_files(uniquename=True, translate={'-ROT': ''})
threedhst.options['FLT_PERSISTENCE_PATH'] = '../Persistence/'
#### IR
files = glob.glob('*-F1*asn.fits')
radec = None
for asn_file in files:
init.prep_direct_grism_pair(direct_asn=asn_file,
grism_asn=None,
radec=radec,
ACS=False,
align_threshold=5,
raw_path='../RAW/',
order=0)
###
for asn_file in files:
drizzlepac.astrodrizzle.AstroDrizzle(
asn_file,
static=False,
skysub=False,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
final_wht_type='IVM',
clean=True,
final_wcs=True,
final_refimage='IRAS23436+5257-87-304-F814W_drc_sci.fits',
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=576,
preserve=False)
### Match WCS of NB observations
init.copy_adriz_headerlets(glob.glob('*-F1*[MW]*asn.fits')[0],
glob.glob('*-F1*[N]*asn.fits')[0],
order=[1, 0])
### Flag negative pixels
for asn_file in files:
asn = threedhst.utils.ASNFile(asn_file)
for exp in asn.exposures:
im = pyfits.open('%s_flt.fits' % (exp), mode='update')
neg = im['SCI'].data < -3 * im['ERR'].data
print '%s #negative = %d' % (exp, neg.sum())
im['DQ'].data[neg] |= 4096
im.flush()
#
drizzlepac.astrodrizzle.AstroDrizzle(asn_file,
skysub=True,
static=True,
driz_separate=True,
driz_sep_wcs=True,
median=True,
blot=True,
driz_cr=True,
driz_combine=True,
clean=True,
final_wcs=True,
final_scale=0.1,
final_rot=0,
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=64,
preserve=False)
sci = pyfits.open(asn_file.replace('_asn', '_drz_sci'), mode='update')
wht = pyfits.open(asn_file.replace('_asn', '_drz_wht'))
sci[0].data[wht[0].data == 0] = 0
sci.flush()
#### ACS / UVIS
files = glob.glob('*-F6*asn.fits')
files = glob.glob('*-F[48]*asn.fits')
files.sort()
for asn_file in files[::-1]:
asn = threedhst.utils.ASNFile(asn_file)
for i in range(len(asn.exposures)):
asn.exposures[i] = asn.exposures[i].split('_flc')[0]
print asn_file, asn.exposures
asn.write(asn_file)
if ('814' in asn_file) | ('625' in asn_file):
radec = None
else:
root = glob.glob('*-F[86]*W*sci.fits')[0].split('_sci')[0]
if not os.path.exists('%s_sci.cat' % (root)):
os.system(
'cp /user/brammer/software/share/gauss_5.0_9x9.conv .')
research.hawkiff.make_catalog(root=root,
sci_ext='sci',
threshold=3,
use_rms=False,
subtract_background=True)
cat = catIO.Table('%s_sci.cat' % (root))
cat['X_WORLD',
'Y_WORLD'].write('ref_opt.radec',
format='ascii.commented_header')
radec = 'ref_opt.radec'
radec = None
init.prep_direct_grism_pair(direct_asn=asn_file,
grism_asn=None,
radec=radec,
ACS=True,
align_threshold=5,
raw_path='../RAW/')
#
for asn_file in files:
radec = None
init.prep_direct_grism_pair(direct_asn=asn_file,
grism_asn=None,
radec=radec,
ACS=True,
align_threshold=5,
raw_path='../RAW/')
files = glob.glob('*sci.fits')
ims = {}
for file in files:
im = pyfits.open(file)
filter = file.split('-')[-1][:5]
pix = np.sqrt(im[0].header['CD1_1']**2 +
im[0].header['CD1_2']**2) * 3600
scl = im[0].header['PHOTFLAM'] / 1.e-19 * (0.1 / pix)**2
im[0].data *= scl
ims[filter] = im
### Try Multidrizzle CR with combined image
import drizzlepac
asn_files = glob.glob('*-F[4-8]*asn.fits')
exposures = []
for file in asn_files:
asn = threedhst.utils.ASNFile(file)
exposures.extend(asn.exposures)
target = '-'.join(file.split('-')[:-1])
asn.exposures = exposures
asn.product = target
asn_file = '%s_asn.fits' % (asn.product)
asn.write(asn_file, clobber=True)
### modify: make copy of FLCs, make new mosaic and then copy FLCs back
##xxx
drizzlepac.astrodrizzle.AstroDrizzle(asn_file,
skysub=False,
clean=True,
final_wcs=True,
final_scale=0.05,
final_pixfrac=0.8,
context=False,
resetbits=4096,
final_bits=576,
preserve=False)
#
bits = 576
drizzlepac.astrodrizzle.AstroDrizzle(asn_file,
static=False,
skysub=False,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
final_wht_type='IVM',
clean=True,
final_wcs=True,
final_rot=0,
final_scale=0.1,
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=bits,
preserve=False)
#### rerun final mosaics
refimage = '%s_drz_sci.fits' % (target)
for file in asn_files:
drizzlepac.astrodrizzle.AstroDrizzle(file,
static=False,
skysub=False,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
final_wht_type='IVM',
clean=True,
final_wcs=True,
final_refimage=refimage,
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=bits,
preserve=False)
for file in asn_files:
print file
sci = pyfits.open(glob.glob(file.replace('_asn', '_dr?_sci'))[0],
mode='update')
wht = pyfits.open(sci.filename().replace('_sci', '_wht'))
sci[0].data[wht[0].data == 0] = 0
sci.flush()
#### Try own driz CR
import stwcs
from drizzlepac import astrodrizzle, quickDeriv
import scipy.ndimage as nd
ref_file = 'ESO550-IG02-13-083-F435W_drc_sci.fits'
ref_file = 'ESO550-IG02-13-083-F814W_drc_sci.fits'
ref_file = 'ESO550-IG02-13-083_drc_sci.fits'
ref_ext = 0
ref = pyfits.open(ref_file)
ref_wcs = stwcs.wcsutil.HSTWCS(ref, ext=ref_ext)
asn_file = 'ESO550-IG02-13-083-F814W_asn.fits'
asn = threedhst.utils.ASNFile(asn_file)
for exp in asn.exposures:
flt = pyfits.open('%s_flc.fits' % (exp)) #, mode='update')
for ext in [1, 2]:
flt_wcs = stwcs.wcsutil.HSTWCS(flt, ext=('sci', ext))
blotted_ref = astrodrizzle.ablot.do_blot(ref[ref_ext].data,
ref_wcs,
flt_wcs,
1,
coeffs=True,
interp='nearest',
sinscl=1.0,
stepsize=10,
wcsmap=None)
#
blotDeriv = quickDeriv.qderiv(blotted_ref)
scl = flt['sci', ext].header['PHOTFLAM'] / ref[0].header[
'PHOTFLAM'] / flt[0].header['EXPTIME']
noise = flt['err', ext].data
driz_scale = 1.2
driz_snr = 3.5
driz_scale = 1.0
driz_snr = 6
driz_f = 2
# |data_image - blotted_image| > scale x deriv + SNR x noise
abs = np.abs(flt['sci', ext].data * scl - blotted_ref * driz_f)
xderiv = driz_scale * blotDeriv
xsnr = driz_snr * scl * noise
mask = abs > (xderiv + xsnr)
new_dq = mask & ((flt['dq', ext].data & 4096) == 0)
### Try "cosmics" LA Cosmic
im = pyfits.open('ESO550-IG02-13-083-F814W_drc_sci.fits')
slx, sly = slice(1500, 2600), slice(1800, 2800)
ext = 0
subim = im[ext].data[sly, slx]
h = im[ext].header
subim *= im[0].header['EXPTIME']
#### FLT
im = pyfits.open('j9cv13pcq_flc.fits')
ext = 0
slx, sly = slice(1500, 2600), slice(0, 400)
subim = im[4].data[sly, slx]
h = im[0].header
import cosmics
c = cosmics.cosmicsimage(subim,
pssl=20.0,
gain=1,
readnoise=h['READNSEA'],
sigclip=4.0,
sigfrac=0.3,
objlim=3.8,
satlevel=84700.0,
verbose=True)
c.run(maxiter=4)
crflux = subim * c.mask
plt.hist(np.log10(crflux[c.mask]), range=[1, 6], bins=100, alpha=0.5)
####
import research.pab.pab
files = glob.glob('*-F*asn.fits')
#files=glob.glob('IC*-F814*asn.fits')
for file in files:
asn = threedhst.utils.ASNFile(file)
for exp in asn.exposures:
flc = pyfits.open('%s_flc.fits' % (exp))
research.pab.pab.run_lacosmic('%s_flc.fits' % (exp),
split=2048,
sigclip=5,
pssl=flc[1].header['MDRIZSK0'])
#
drizzlepac.updatehdr.update_from_shiftfile(
file.replace('asn.fits', 'shifts.txt'))
drizzlepac.astrodrizzle.AstroDrizzle(file,
skysub=True,
clean=True,
final_wcs=True,
final_scale=0.05,
final_pixfrac=0.8,
context=False,
resetbits=0,
final_bits=576,
preserve=False)
drizzlepac.astrodrizzle.AstroDrizzle(file,
output='sub_' +
file.split('_asn')[0],
skysub=True,
static=True,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
clean=True,
final_wcs=True,
final_scale=0.08,
final_ra=60.635233,
final_dec=60.344597,
final_outnx=800,
final_outny=800,
final_rot=0,
final_pixfrac=0.8,
context=False,
resetbits=0,
final_bits=576,
preserve=False)
### Final mosaics
f110w = glob.glob('*110W*asn.fits')[0]
drizzlepac.astrodrizzle.AstroDrizzle(f110w,
output='sub_' +
f110w.split('_asn')[0],
skysub=True,
static=True,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
clean=True,
final_wcs=True,
final_scale=0.1,
final_rot=0,
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=576 - 512,
preserve=False)
files = glob.glob('*-F*asn.fits')
for file in files:
if 'F110W' in file:
continue
#
drizzlepac.astrodrizzle.AstroDrizzle(
file,
output='sub_' + file.split('_asn')[0],
skysub=True,
static=True,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
clean=True,
final_wcs=True,
final_refimage='sub_' + f110w.replace('_asn', '_drz_sci'),
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=576 - 512 * ('-F1' in file),
preserve=False)
for sci_im in glob.glob('sub*sci.fits'):
print sci_im
sci = pyfits.open(sci_im, mode='update')
wht = pyfits.open(sci_im.replace('_sci', '_wht'))
sci[0].data[wht[0].data == 0] = 0
sci.flush()
#### Test alignment
import align
ra_list, de_list = np.loadtxt('f814w.radec', unpack=True)
for geom in ['shift', 'shift', 'rxyscale', 'shift', 'shift']:
align.get_align_to_subaru(
sci='sub_ESO550-IG025-41-115-F673N_drc_sci.fits',
wht='sub_ESO550-IG025-41-115-F673N_drc_wht.fits',
verbose=False,
fitgeometry=geom,
align_data=(ra_list, de_list, ra_list * 0),
THRESH=1.2)
#drizzlepac.tweakback.tweakback('ESO550-IG025-41-115-F673N_drc_sci.fits', force=True, verbose=True) #, origwcs='DRZWCS')
ra_list, de_list = np.loadtxt('f110w.radec', unpack=True)
for geom in ['shift', 'shift', 'rxyscale', 'shift', 'shift']:
align.get_align_to_subaru(
sci='sub_ESO550-IG025-41-115-F132N_drz_sci.fits',
wht='sub_ESO550-IG025-41-115-F132N_drz_wht.fits',
verbose=False,
fitgeometry=geom,
align_data=(ra_list, de_list, ra_list * 0),
THRESH=1.2)
def run_wfc3(run_prep=True,
run_interlace=True,
run_redshifts=True,
align_threshold=6):
"""
Run end-to-end WFC3 test
"""
import os
import glob
import time
import astropy.io.fits as pyfits
from astropy.table import Table as table
import threedhst
import threedhst.prep_flt_astrodrizzle as init
import unicorn
import unicorn.interlace_test as test
#### Preparation steps
#run_prep = True
root = 'goodss-34'
if run_prep:
#### Make ASN files
unicorn.candels.make_asn_files(uniquename=False)
#### Run main preparation wrapper to align to reference and
#### subtract backgrounds
init.prep_direct_grism_pair(direct_asn=root + '-F140W_asn.fits',
grism_asn=root + '-G141_asn.fits',
radec='../Catalog/goodss_radec.dat',
raw_path='../RAW/',
mask_grow=8,
scattered_light=False,
final_scale=None,
skip_direct=False,
ACS=False,
align_threshold=align_threshold)
#### test
# if True:
# import threedhst.prep_flt_astrodrizzle as init
# init.subtract_flt_background(root=root+'-F140W', scattered_light=False)
#### Interlaced images + reference
#run_interlace = True
if run_interlace:
#### Interlace images themselves
NGROWX = 180
NGROWY = 30
grow, auto_off = 2, False
#grow, auto_off = 1, True
unicorn.reduce.interlace_combine(root=root + '-F140W',
view=False,
use_error=True,
make_undistorted=False,
pad=60,
NGROWX=NGROWX,
NGROWY=NGROWY,
ddx=0,
ddy=0,
growx=grow,
growy=grow,
auto_offsets=auto_off,
ref_exp=0)
unicorn.reduce.interlace_combine(root=root + '-G141',
view=False,
use_error=True,
make_undistorted=False,
pad=60,
NGROWX=NGROWX,
NGROWY=NGROWY,
ddx=0,
ddy=0,
growx=grow,
growy=grow,
auto_offsets=auto_off,
ref_exp=0)
#### Interlaced reference
adriz_blot = unicorn.reduce.adriz_blot_from_reference
adriz_blot(pointing=root + '-F140W',
pad=60,
NGROWX=NGROWX,
NGROWY=NGROWY,
growx=grow,
growy=grow,
auto_offsets=auto_off,
ref_exp=0,
ref_image='../Catalog/goodss_3dhst.v4.0.IR_cutout_sci.fits',
ref_ext=0,
ref_filter='F140W',
seg_image='../Catalog/goodss_3dhst.v4.0.IR_cutout_seg.fits',
cat_file='../Catalog/goodss_3dhst.v4.0.IR_cutout.cat')
#### Make a model to 25 AB
model = unicorn.reduce.process_GrismModel(
root=root,
grow_factor=grow,
growx=grow,
growy=grow,
MAG_LIMIT=25,
REFINE_MAG_LIMIT=21,
make_zeroth_model=False,
use_segm=False,
model_slope=0,
model_list=None,
direct='F140W',
grism='G141',
BEAMS=['A', 'B', 'C', 'D', 'E'],
align_reference=True)
#### Remove residual backgroudn with model mask
model.refine_mask_background(threshold=0.002,
grow_mask=14,
update=True,
resid_threshold=4,
clip_left=640,
save_figure=True,
interlace=True)
#run_redshifts = True
if run_redshifts:
model = unicorn.reduce.process_GrismModel(
root=root,
grow_factor=2,
growx=2,
growy=2,
MAG_LIMIT=25,
REFINE_MAG_LIMIT=21,
make_zeroth_model=False,
use_segm=False,
model_slope=0,
model_list=None,
direct='F140W',
grism='G141',
BEAMS=['A', 'B', 'C', 'D', 'E'])
#### Some objects with z_spec, em lines; v4.0 IDs
ids = [
25778, 25909, 26087, 26550, 28052, 28870, 29122, 30309, 30520,
30662
]
for id in ids:
if os.path.exists('%s_%05d.2D.fits' % (model.baseroot, id)):
continue
#
model.twod_spectrum(id=id,
grow=1,
miny=-36,
maxy=None,
CONTAMINATING_MAGLIMIT=23,
refine=False,
verbose=False,
force_refine_nearby=False,
USE_REFERENCE_THUMB=True,
USE_FLUX_RADIUS_SCALE=3,
BIG_THUMB=False,
extract_1d=True)
#
### Original fit
gris = unicorn.interlace_fit.GrismSpectrumFit(
root='%s_%05d' % (model.baseroot, id),
FIGURE_FORMAT='png',
verbose=True,
lowz_thresh=0.4,
fix_direct_thumbnail=True,
RELEASE=False,
OUTPUT_PATH='./',
BASE_PATH='./',
skip_photometric=False,
p_flat=0.0001,
use_mag_prior=True,
dr_match=1.0)
gris.fit_in_steps(dzfirst=0.003,
zrfirst=(0.3, 3.3),
dzsecond=0.0002,
save=True,
make_plot=True,
skip_second=False,
oned=False)
### New fit
gris = test.SimultaneousFit(root='%s_%05d' % (model.baseroot, id),
FIGURE_FORMAT='png',
lowz_thresh=0.4)
gris.new_fit_constrained(zrfirst=[0.6, 3.3],
dzfirst=0.005,
dzsecond=0.0005,
make_plot=True,
ignore_photometry=False,
ignore_spectrum=False,
refit_norm=False,
get_tilt=True,
faint_limit=24)
def run_acs(run_prep=True, run_interlace=True, run_redshifts=True):
import glob
import threedhst
import threedhst.prep_flt_astrodrizzle as init
import unicorn
import unicorn.interlace_acs
### Make ACS associations
files = glob.glob('../RAW/j*asn.fits')
for file in files:
pointing = threedhst.prep_flt_files.make_targname_asn(
file, newfile=True, field='goodss-34', ext='flc')
if run_prep:
### Alignment and background subtraction
init.prep_direct_grism_pair(direct_asn='goodss-34-03-F814W_asn.fits',
grism_asn='goodss-34-03-G800L_asn.fits',
radec='../Catalog/goodss_radec.dat',
ACS=True)
if run_interlace:
#### Interlace images
interlace_acs = unicorn.interlace_acs.interlace_combine_acs
for chip in [1, 2]:
interlace_acs(root='goodss-34-03-F814W',
view=False,
chip=chip,
filter='F814W',
outroot='goodss-34-03',
center=True,
pad=100,
growx=1,
growy=1)
interlace_acs(root='goodss-34-03-G800L',
view=False,
chip=chip,
filter='G800L',
outroot='goodss-34-03',
center=True,
pad=100,
growx=1,
growy=1)
#### Interlaced reference, self as reference image
adriz_blot = unicorn.reduce.adriz_blot_from_reference
adriz_blot(pointing='goodss-34-03-F814W',
ACS=True,
pad=100,
NGROWX=0,
NGROWY=0,
growx=1,
growy=1,
auto_offsets=False,
ref_exp=0,
ref_image='goodss-34-03-F814W_drc_sci.fits',
ref_ext=0,
ref_filter='F814W',
seg_image='Catalog/goodss_3dhst.v4.0.IR_cutout_seg.fits',
cat_file='Catalog/goodss_3dhst.v4.0.IR_cutout.cat')
### test blot from UDF reference [works]
#adriz_blot(pointing='goodss-34-03-F814W', ACS=True, pad=100, NGROW=0, growx=1, growy=1, auto_offsets=False, ref_exp=0, ref_image='hlsp_xdf_hst_acswfc-60mas_hudf_f814w_v1_sci.fits', ref_ext=0, ref_filter='F140W', seg_image='Catalog/goodss_3dhst.v4.0.IR_cutout_seg.fits', cat_file='Catalog/goodss_3dhst.v4.0.IR_cutout.cat')
if run_redshifts:
import unicorn.interlace_test
ids = {1: [27549, 30367, 30861], 2: []}
for chip in ids.keys():
model = unicorn.reduce.process_GrismModel(
root='goodss-34-03-chip%d' % (chip),
grow_factor=1,
growx=1,
growy=1,
MAG_LIMIT=21,
REFINE_MAG_LIMIT=21,
make_zeroth_model=False,
use_segm=False,
model_slope=0,
model_list=None,
direct='F814W',
grism='G800L',
BEAMS=['A', 'B', 'C', 'D', 'E', 'F', 'G'])
#
# model = unicorn.reduce.GrismModel('goodss-34-03-chip%d' %(chip), grow_factor=1, growx=1, growy=1, MAG_LIMIT=28, use_segm=False, grism='G800L', direct='F814W')
# MLIM = [21,21]
# model.compute_full_model(refine=False, MAG_LIMIT=MLIM[0], save_pickle=False, model_slope=0, BEAMS=['A','B','C','D','E','F','G'])
# ### For the brighter galaxies, refine the model with the observed spectrum
# model.compute_full_model(refine=True, MAG_LIMIT=MLIM[1], save_pickle=True, model_slope=0, BEAMS=['A','B','C','D','E','F','G'])
#
for id in ids[chip]:
model.twod_spectrum(id=id,
grow=1,
miny=-40,
maxy=None,
CONTAMINATING_MAGLIMIT=23,
refine=False,
verbose=False,
force_refine_nearby=False,
USE_REFERENCE_THUMB=True,
USE_FLUX_RADIUS_SCALE=3,
BIG_THUMB=False,
extract_1d=True)
model.show_2d(savePNG=True, verbose=False)
#
gris = unicorn.interlace_fit.GrismSpectrumFit(
root='%s_%05d' % (model.baseroot, id),
FIGURE_FORMAT='png',
verbose=True,
lowz_thresh=0.05,
fix_direct_thumbnail=True,
RELEASE=False,
OUTPUT_PATH='./',
BASE_PATH='./',
skip_photometric=False,
p_flat=0.0001,
use_mag_prior=True,
dr_match=1.0)
#
gris = unicorn.interlace_test.SimultaneousFit(
root='%s_%05d' % (model.baseroot, id),
FIGURE_FORMAT='png',
verbose=True,
lowz_thresh=0.05,
fix_direct_thumbnail=True,
RELEASE=False,
OUTPUT_PATH='./',
BASE_PATH='./',
skip_photometric=False,
p_flat=0.0001,
use_mag_prior=True,
dr_match=1.0)
gris.new_fit_constrained(zrfirst=[0.05, 0.8],
dzfirst=0.005,
dzsecond=0.0005,
make_plot=True,
ignore_photometry=False,
ignore_spectrum=False,
refit_norm=False,
get_tilt=True,
faint_limit=24)
def figs_gn1(make_asn = True, check_background = True, run_prep = True, run_interlace=True, make_model=True):
import mywfc3.bg
import threedhst.prep_flt_astrodrizzle as init
from unicorn.reduce import adriz_blot_from_reference as adriz_blot
import unicorn.interlace_test as test
if make_asn:
unicorn.candels.make_asn_files()
if check_background:
os.chdir('/Users/imomcheva/Work/FIGS/RAW')
asn_files = glob.glob('*asn.fits')
for asn in asn_files:
root = asn.split('_asn')[0]
png = glob.glob(root+'*orbit.*')
if (len(png) > 0):
continue
try:
mywfc3.bg.show_orbit_limbangle(asn = [root])
except:
fp = open(root+'_orbit.failed','w')
fp.write('---')
fp.close()
os.chdir('/Users/imomcheva/Work/FIGS/PREPARE/')
if run_prep:
os.chdir('/Users/imomcheva/Work/FIGS/PREPARE/')
grism_files = glob.glob('FIGS-GN1*G102_asn.fits')
direct_files = glob.glob('FIGS-GN1*F105W_asn.fits')
for direct, grism in zip(direct_files, grism_files):
init.prep_direct_grism_pair(direct_asn=direct, grism_asn=grism, radec='../REF/goodsn_3dhst.v4.1.radec.cat',
raw_path = '../RAW/', mask_grow=8, scattered_light=False, final_scale = None,
skip_direct=False, ACS=False, align_threshold=6)
if run_interlace:
NGROWX = 200
NGROWY = 30
pad = 60
CATALOG = '/3DHST/Photometry/Release/v4.0/GOODS-N/Detection/goodsn_3dhst.v4.0.F125W_conv.cat'
REF_IMAGE = '../REF/goodsn_3dhst.v4.0.F125W_orig_sci.fits'
REF_EXT = 0
SEG_IMAGE = '/3DHST/Photometry/Release/v4.0/GOODS-N/Detection/goodsn_3dhst.v4.0.F160W_seg.fits'
REF_FILTER = 'F125W'
grism = glob.glob('FIGS-GN1*G102_asn.fits')
special_point = ['FIGS-GN1-3E-217-G102', 'FIGS-GN1-3E-217-G102', 'FIGS-GN1-3E-217-G102',\
'FIGS-GN1-3E-217-G102', 'FIGS-GN1-3E-217-G102', 'FIGS-GN1-3E-217-G102', 'FIGS-GN1-3E-217-G102',\
'FIGS-GN1-3E-217-G102', 'FIGS-GN1-3E-217-G102', 'FIGS-GN1-3E-217-G102', 'FIGS-GN1-3E-217-G102',\
'FIGS-GN1-3E-217-G102']
"""
for i in range(len(grism)):
pointing=grism[i].split('_asn')[0]
if pointing in special_point:
ref_exp = 3
else:
ref_exp = 0
adriz_blot(pointing=pointing, pad=pad, NGROWX=NGROWX, NGROWY=NGROWY, growx=1,
growy=1, auto_offsets=True, ref_exp=ref_exp, ref_image=REF_IMAGE, ref_ext=REF_EXT,
ref_filter=REF_FILTER, seg_image=SEG_IMAGE, cat_file=CATALOG, grism='G102')
unicorn.reduce.interlace_combine(pointing.replace('G102','F105W'), view=False, use_error=True,
make_undistorted=False, pad=pad, NGROWX=NGROWX, NGROWY=NGROWY, ddx=0, ddy=0,
growx=1, growy=1, auto_offsets=True, ref_exp=0)
unicorn.reduce.interlace_combine(pointing, view=False, use_error=True,
make_undistorted=False, pad=pad, NGROWX=NGROWX, NGROWY=NGROWY, ddx=0, ddy=0,
growx=1, growy=1, auto_offsets=True, ref_exp=0)
"""
if make_model:
grism = glob.glob('FIGS-GN1*G102_asn.fits')
for i in range(len(grism)):
root = grism[i].split('-G102')[0]
m0 = unicorn.reduce.GrismModel(root=root,grow_factor=1, growx=1, growy=1,
direct='F105W', grism='G102', MAG_LIMIT=27)
model_list = m0.get_eazy_templates(dr_min=0.5, MAG_LIMIT=25)
model = unicorn.reduce.process_GrismModel(root=root, grow_factor=1, growx=1, growy=1,
MAG_LIMIT=27, REFINE_MAG_LIMIT=21, make_zeroth_model=False, use_segm=False,
model_slope=0, direct='F105W', grism='G102', BEAMS=['A', 'B', 'C', 'D', 'E'],
align_reference=True)
if not os.path.exists(os.path.basename(model.root) + '-G141_maskbg.dat'):
model.refine_mask_background(threshold=0.002, grow_mask=14, update=True, resid_threshold=4,
clip_left=640, save_figure=True, interlace=True)
if extract:
id = 32031
grism = glob.glob('FIGS-GN1*G102_asn.fits')
for i in range(len(grism)):
root = grism[i].split('-G102')[0]
model = unicorn.reduce.process_GrismModel(root=root, grow_factor=1, growx=1, growy=1,
MAG_LIMIT=27, REFINE_MAG_LIMIT=21, make_zeroth_model=False, use_segm=False,
model_slope=0, direct='F105W', grism='G102', BEAMS=['A', 'B', 'C', 'D', 'E'])
model.twod_spectrum(id=id, grow=1, miny=-36, maxy=None, CONTAMINATING_MAGLIMIT=27,
refine=True, verbose=False, force_refine_nearby=True, USE_REFERENCE_THUMB=True,
USE_FLUX_RADIUS_SCALE=3, BIG_THUMB=False, extract_1d=True)
model.show_2d(savePNG=True)
def prep():
import glob
import os
import threedhst
import threedhst.prep_flt_astrodrizzle as init
from threedhst import catIO
import unicorn
import research.hawkiff
### Make ACS associations
unicorn.candels.make_asn_files(uniquename=True, translate={'-ROT': ''})
threedhst.options['FLT_PERSISTENCE_PATH'] = '../Persistence/'
#### IR
files = glob.glob('*-F1*asn.fits')
radec = None
for asn_file in files:
init.prep_direct_grism_pair(
direct_asn=asn_file,
grism_asn=None,
radec=radec,
ACS=False,
align_threshold=5,
raw_path='../RAW/',
order=0)
###
for asn_file in files:
drizzlepac.astrodrizzle.AstroDrizzle(
asn_file,
static=False,
skysub=False,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
final_wht_type='IVM',
clean=True,
final_wcs=True,
final_refimage='IRAS23436+5257-87-304-F814W_drc_sci.fits',
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=576,
preserve=False)
### Match WCS of NB observations
init.copy_adriz_headerlets(
glob.glob('*-F1*[MW]*asn.fits')[0],
glob.glob('*-F1*[N]*asn.fits')[0],
order=[1, 0])
### Flag negative pixels
for asn_file in files:
asn = threedhst.utils.ASNFile(asn_file)
for exp in asn.exposures:
im = pyfits.open('%s_flt.fits' % (exp), mode='update')
neg = im['SCI'].data < -3 * im['ERR'].data
print '%s #negative = %d' % (exp, neg.sum())
im['DQ'].data[neg] |= 4096
im.flush()
#
drizzlepac.astrodrizzle.AstroDrizzle(
asn_file,
skysub=True,
static=True,
driz_separate=True,
driz_sep_wcs=True,
median=True,
blot=True,
driz_cr=True,
driz_combine=True,
clean=True,
final_wcs=True,
final_scale=0.1,
final_rot=0,
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=64,
preserve=False)
sci = pyfits.open(asn_file.replace('_asn', '_drz_sci'), mode='update')
wht = pyfits.open(asn_file.replace('_asn', '_drz_wht'))
sci[0].data[wht[0].data == 0] = 0
sci.flush()
#### ACS / UVIS
files = glob.glob('*-F6*asn.fits')
files = glob.glob('*-F[48]*asn.fits')
files.sort()
for asn_file in files[::-1]:
asn = threedhst.utils.ASNFile(asn_file)
for i in range(len(asn.exposures)):
asn.exposures[i] = asn.exposures[i].split('_flc')[0]
print asn_file, asn.exposures
asn.write(asn_file)
if ('814' in asn_file) | ('625' in asn_file):
radec = None
else:
root = glob.glob('*-F[86]*W*sci.fits')[0].split('_sci')[0]
if not os.path.exists('%s_sci.cat' % (root)):
os.system(
'cp /user/brammer/software/share/gauss_5.0_9x9.conv .')
research.hawkiff.make_catalog(
root=root,
sci_ext='sci',
threshold=3,
use_rms=False,
subtract_background=True)
cat = catIO.Table('%s_sci.cat' % (root))
cat['X_WORLD', 'Y_WORLD'].write(
'ref_opt.radec', format='ascii.commented_header')
radec = 'ref_opt.radec'
radec = None
init.prep_direct_grism_pair(
direct_asn=asn_file,
grism_asn=None,
radec=radec,
ACS=True,
align_threshold=5,
raw_path='../RAW/')
#
for asn_file in files:
radec = None
init.prep_direct_grism_pair(
direct_asn=asn_file,
grism_asn=None,
radec=radec,
ACS=True,
align_threshold=5,
raw_path='../RAW/')
files = glob.glob('*sci.fits')
ims = {}
for file in files:
im = pyfits.open(file)
filter = file.split('-')[-1][:5]
pix = np.sqrt(im[0].header['CD1_1']**2 +
im[0].header['CD1_2']**2) * 3600
scl = im[0].header['PHOTFLAM'] / 1.e-19 * (0.1 / pix)**2
im[0].data *= scl
ims[filter] = im
### Try Multidrizzle CR with combined image
import drizzlepac
asn_files = glob.glob('*-F[4-8]*asn.fits')
exposures = []
for file in asn_files:
asn = threedhst.utils.ASNFile(file)
exposures.extend(asn.exposures)
target = '-'.join(file.split('-')[:-1])
asn.exposures = exposures
asn.product = target
asn_file = '%s_asn.fits' % (asn.product)
asn.write(asn_file, clobber=True)
### modify: make copy of FLCs, make new mosaic and then copy FLCs back
##xxx
drizzlepac.astrodrizzle.AstroDrizzle(
asn_file,
skysub=False,
clean=True,
final_wcs=True,
final_scale=0.05,
final_pixfrac=0.8,
context=False,
resetbits=4096,
final_bits=576,
preserve=False)
#
bits = 576
drizzlepac.astrodrizzle.AstroDrizzle(
asn_file,
static=False,
skysub=False,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
final_wht_type='IVM',
clean=True,
final_wcs=True,
final_rot=0,
final_scale=0.1,
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=bits,
preserve=False)
#### rerun final mosaics
refimage = '%s_drz_sci.fits' % (target)
for file in asn_files:
drizzlepac.astrodrizzle.AstroDrizzle(
file,
static=False,
skysub=False,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
final_wht_type='IVM',
clean=True,
final_wcs=True,
final_refimage=refimage,
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=bits,
preserve=False)
for file in asn_files:
print file
sci = pyfits.open(
glob.glob(file.replace('_asn', '_dr?_sci'))[0], mode='update')
wht = pyfits.open(sci.filename().replace('_sci', '_wht'))
sci[0].data[wht[0].data == 0] = 0
sci.flush()
#### Try own driz CR
import stwcs
from drizzlepac import astrodrizzle, quickDeriv
import scipy.ndimage as nd
ref_file = 'ESO550-IG02-13-083-F435W_drc_sci.fits'
ref_file = 'ESO550-IG02-13-083-F814W_drc_sci.fits'
ref_file = 'ESO550-IG02-13-083_drc_sci.fits'
ref_ext = 0
ref = pyfits.open(ref_file)
ref_wcs = stwcs.wcsutil.HSTWCS(ref, ext=ref_ext)
asn_file = 'ESO550-IG02-13-083-F814W_asn.fits'
asn = threedhst.utils.ASNFile(asn_file)
for exp in asn.exposures:
flt = pyfits.open('%s_flc.fits' % (exp)) #, mode='update')
for ext in [1, 2]:
flt_wcs = stwcs.wcsutil.HSTWCS(flt, ext=('sci', ext))
blotted_ref = astrodrizzle.ablot.do_blot(
ref[ref_ext].data,
ref_wcs,
flt_wcs,
1,
coeffs=True,
interp='nearest',
sinscl=1.0,
stepsize=10,
wcsmap=None)
#
blotDeriv = quickDeriv.qderiv(blotted_ref)
scl = flt['sci', ext].header['PHOTFLAM'] / ref[0].header[
'PHOTFLAM'] / flt[0].header['EXPTIME']
noise = flt['err', ext].data
driz_scale = 1.2
driz_snr = 3.5
driz_scale = 1.0
driz_snr = 6
driz_f = 2
# |data_image - blotted_image| > scale x deriv + SNR x noise
abs = np.abs(flt['sci', ext].data * scl - blotted_ref * driz_f)
xderiv = driz_scale * blotDeriv
xsnr = driz_snr * scl * noise
mask = abs > (xderiv + xsnr)
new_dq = mask & ((flt['dq', ext].data & 4096) == 0)
### Try "cosmics" LA Cosmic
im = pyfits.open('ESO550-IG02-13-083-F814W_drc_sci.fits')
slx, sly = slice(1500, 2600), slice(1800, 2800)
ext = 0
subim = im[ext].data[sly, slx]
h = im[ext].header
subim *= im[0].header['EXPTIME']
#### FLT
im = pyfits.open('j9cv13pcq_flc.fits')
ext = 0
slx, sly = slice(1500, 2600), slice(0, 400)
subim = im[4].data[sly, slx]
h = im[0].header
import cosmics
c = cosmics.cosmicsimage(
subim,
pssl=20.0,
gain=1,
readnoise=h['READNSEA'],
sigclip=4.0,
sigfrac=0.3,
objlim=3.8,
satlevel=84700.0,
verbose=True)
c.run(maxiter=4)
crflux = subim * c.mask
plt.hist(np.log10(crflux[c.mask]), range=[1, 6], bins=100, alpha=0.5)
####
import research.pab.pab
files = glob.glob('*-F*asn.fits')
#files=glob.glob('IC*-F814*asn.fits')
for file in files:
asn = threedhst.utils.ASNFile(file)
for exp in asn.exposures:
flc = pyfits.open('%s_flc.fits' % (exp))
research.pab.pab.run_lacosmic(
'%s_flc.fits' % (exp),
split=2048,
sigclip=5,
pssl=flc[1].header['MDRIZSK0'])
#
drizzlepac.updatehdr.update_from_shiftfile(
file.replace('asn.fits', 'shifts.txt'))
drizzlepac.astrodrizzle.AstroDrizzle(
file,
skysub=True,
clean=True,
final_wcs=True,
final_scale=0.05,
final_pixfrac=0.8,
context=False,
resetbits=0,
final_bits=576,
preserve=False)
drizzlepac.astrodrizzle.AstroDrizzle(
file,
output='sub_' + file.split('_asn')[0],
skysub=True,
static=True,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
clean=True,
final_wcs=True,
final_scale=0.08,
final_ra=60.635233,
final_dec=60.344597,
final_outnx=800,
final_outny=800,
final_rot=0,
final_pixfrac=0.8,
context=False,
resetbits=0,
final_bits=576,
preserve=False)
### Final mosaics
f110w = glob.glob('*110W*asn.fits')[0]
drizzlepac.astrodrizzle.AstroDrizzle(
f110w,
output='sub_' + f110w.split('_asn')[0],
skysub=True,
static=True,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
clean=True,
final_wcs=True,
final_scale=0.1,
final_rot=0,
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=576 - 512,
preserve=False)
files = glob.glob('*-F*asn.fits')
for file in files:
if 'F110W' in file:
continue
#
drizzlepac.astrodrizzle.AstroDrizzle(
file,
output='sub_' + file.split('_asn')[0],
skysub=True,
static=True,
driz_separate=False,
driz_sep_wcs=False,
median=False,
blot=False,
driz_cr=False,
driz_combine=True,
clean=True,
final_wcs=True,
final_refimage='sub_' + f110w.replace('_asn', '_drz_sci'),
final_pixfrac=1,
context=False,
resetbits=0,
final_bits=576 - 512 * ('-F1' in file),
preserve=False)
for sci_im in glob.glob('sub*sci.fits'):
print sci_im
sci = pyfits.open(sci_im, mode='update')
wht = pyfits.open(sci_im.replace('_sci', '_wht'))
sci[0].data[wht[0].data == 0] = 0
sci.flush()
#### Test alignment
import align
ra_list, de_list = np.loadtxt('f814w.radec', unpack=True)
for geom in ['shift', 'shift', 'rxyscale', 'shift', 'shift']:
align.get_align_to_subaru(
sci='sub_ESO550-IG025-41-115-F673N_drc_sci.fits',
wht='sub_ESO550-IG025-41-115-F673N_drc_wht.fits',
verbose=False,
fitgeometry=geom,
align_data=(ra_list, de_list, ra_list * 0),
THRESH=1.2)
#drizzlepac.tweakback.tweakback('ESO550-IG025-41-115-F673N_drc_sci.fits', force=True, verbose=True) #, origwcs='DRZWCS')
ra_list, de_list = np.loadtxt('f110w.radec', unpack=True)
for geom in ['shift', 'shift', 'rxyscale', 'shift', 'shift']:
align.get_align_to_subaru(
sci='sub_ESO550-IG025-41-115-F132N_drz_sci.fits',
wht='sub_ESO550-IG025-41-115-F132N_drz_wht.fits',
verbose=False,
fitgeometry=geom,
align_data=(ra_list, de_list, ra_list * 0),
THRESH=1.2)
