def psf(args):
""" Calculate the PSF of an image.
"""
# Read the seeing and sigma of the sky from the header
seeing, sigma = utils.get_from_header(args.input, args.FWHM_key, args.sigma)
# Do photometry on the image
#print "photometry: \n"
photfile_name = args.input + ".mag.1"
utils.if_exists_remove(photfile_name)
iraf.phot(args.input, output=photfile_name, coords=args.stars,
wcsin=args.coords, fwhm=seeing,
sigma=sigma, datamax=args.maxval, datamin=args.minval,
ccdread=args.ron_key, gain=args.gain_key, exposure=args.expt_key,
airmass=args.airm_key, annulus=36, dannulus=18,
apert=18, verbose="no", verify="no", interac="no")
# Select stars on the image
#print "pstselect: \n"
pstfile_name = args.input + ".pst.1"
utils.if_exists_remove(pstfile_name)
iraf.pstselect(args.input, photfile=photfile_name, pstfile=pstfile_name,
maxnpsf=20, fwhm=seeing, sigma=sigma,
datamax=args.maxval, ccdread=args.ron_key, gain=args.gain_key,
exposure=args.expt_key, function="auto", nclean=1,
psfrad=36, fitrad=18, maxnstar=20, verbose="no", interac="no",
verify="no")
# Build psf of the stars
#print "psf: \n"
psffile_table = args.input + ".psf.1.fits" # iraf keeps adding the .fits :(
psgfile_name = args.input + ".psg.1"
pstfile_name2 = args.input + ".pst.2"
utils.if_exists_remove(psffile_table,psgfile_name, pstfile_name2)
iraf.psf( args.input, photfile=photfile_name, pstfile=pstfile_name,
groupfile=psgfile_name, opstfile=pstfile_name2,
psfimage=psffile_table,fwhm=seeing, sigma=sigma, datamax=args.maxval,
datamin=args.minval, ccdread=args.ron_key, gain=args.gain_key,
exposure=args.expt_key, function="moffat25", nclean=1,
psfrad=36, fitrad=18, maxnstar=20, interactive="no",
varorder=args.varorder, verbose="no",verify="no")
# Use seepsf to build the image of the psf
psffile_name = args.input + ".psf.fits"
utils.if_exists_remove(psffile_name)
iraf.seepsf(psffile_table, psffile_name)
return psffile_name
def apply_psf(args, phot_file, pst_file):
with tempfile.NamedTemporaryFile(suffix=".psf.1.fits") as fd0:
psffile_table = fd0.name
with tempfile.NamedTemporaryFile(suffix=".psf") as fd1:
psf_name = fd1.name
with tempfile.NamedTemporaryFile(suffix=".psg.1") as fd2:
psg_name = fd2.name
with tempfile.NamedTemporaryFile(suffix=".pst.2") as fd3:
pst2_name = fd3.name
hdr = args.image.header # for short
seeing, sigma = utils.get_from_header(args.image.im_name, hdr.seeingk, hdr.sigmak)
iraf.psf(
args.image.im_name,
photfile=phot_file,
pstfile=pst_file,
groupfile=psg_name,
opstfile=pst2_name,
psfimage=psffile_table,
fwhm=seeing,
sigma=sigma,
ccdread=hdr.ccdronk,
gain=hdr.gaink,
exposure=hdr.exptimek,
function="auto",
nclean=1,
psfrad=6 * seeing,
fitrad=5 * seeing,
interactive="no",
varorder=-1,
verbose="no",
verify="no",
)
# Use seepsf to make an image of the PSF
iraf.seepsf(psffile_table, psf_name)
print "\n PSF file: ", psf_name
return psf_name
def psfphot(image,coords,pststars,refstar,centre=True,vary=False):
"""PSF photometry. Centering is through phot on refstar.
Assume coords is a .als file for now. Recentering is always done
for the reference star, never for the targets."""
iraf.dele('temp.mag*')
iraf.dele('temp.psf.fits')
iraf.dele('temp.als')
if centre:
xsh,ysh = recentre(image,refstar)
print "Fine Centring: ", xsh,ysh
else: xsh,ysh = 0,0
if vary:
setaperture(image,refstar)
shift_file_coords(coords,xsh,ysh,'tempcoords2',sort='als')
shift_file_coords(pststars,xsh,ysh,'temppst2',sort='pst')
iraf.phot(image,'tempcoords2','temp.mag2',inter="no",calgorithm='none',
mode='h',verify='no',update='no',verbose='no')
iraf.psf(image,'temp.mag2','temppst2','temp.psf','temp.mag.pst','temp.mag.psg',
inter='no',mode='h',verify='no',update='no',verbose='no')
iraf.allstar(image,'temp.mag2','temp.psf','temp.als','temp.mag.arj',"default",
mode='h',verify='no',update='no',verbose='no')
out = iraf.pdump('temp.als','id,mag,merr,msky','yes',Stdout=1)
return out
def psffit(img,
fwhm,
psfstars,
hdr,
interactive,
_datamin,
_datamax,
psffun='gauss',
fixaperture=False):
'''
giving an image, a psffile compute the psf using the file _psf.coo
'''
import lsc
_ron = lsc.util.readkey3(hdr, 'ron')
_gain = lsc.util.readkey3(hdr, 'gain')
if not _ron:
_ron = 1
print 'warning ron not defined'
if not _gain:
_gain = 1
print 'warning gain not defined'
iraf.digiphot(_doprint=0)
iraf.daophot(_doprint=0)
zmag = 0.
varord = 0 # -1 analitic 0 - numeric
if fixaperture:
print 'use fix aperture 5 8 10'
hdr = lsc.util.readhdr(img + '.fits')
_pixelscale = lsc.util.readkey3(hdr, 'PIXSCALE')
a1, a2, a3, a4, = float(5. / _pixelscale), float(
5. / _pixelscale), float(8. / _pixelscale), float(10. /
_pixelscale)
else:
a1, a2, a3, a4, = int(fwhm + 0.5), int(fwhm * 2 +
0.5), int(fwhm * 3 +
0.5), int(fwhm * 4 +
0.5)
iraf.fitskypars.annulus = a4
iraf.fitskypars.salgori = 'mean' #mode,mean,gaussian
iraf.photpars.apertures = '%d,%d,%d' % (a2, a3, a4)
iraf.datapars.datamin = _datamin
iraf.datapars.datamax = _datamax
iraf.datapars.readnoise = _ron
iraf.datapars.epadu = _gain
iraf.datapars.exposure = 'EXPTIME'
iraf.datapars.airmass = ''
iraf.datapars.filter = ''
iraf.centerpars.calgori = 'centroid'
iraf.centerpars.cbox = a2
iraf.daopars.recenter = 'yes'
iraf.photpars.zmag = zmag
psfout = img.replace('.zogypsf', '') + '.psf.fits'
iraf.delete('_psf.ma*,_psf.ps*,_psf.gr?,_psf.n*,_psf.sub.fit?,' + psfout,
verify=False)
iraf.phot(img + '[0]',
'_psf.coo',
'_psf.mag',
interac=False,
verify=False,
verbose=False)
# removes saturated stars from the list (IRAF just issues a warning)
with open('_psf.mag') as f:
text = f.read()
text = re.sub('(.*\n){6}.*BadPixels\* \n', '', text)
with open('_psf.mag', 'w') as f:
f.write(text)
iraf.daopars.psfrad = a4
iraf.daopars.functio = psffun
iraf.daopars.fitrad = a1
iraf.daopars.fitsky = 'yes'
iraf.daopars.sannulus = a4
iraf.daopars.recenter = 'yes'
iraf.daopars.varorder = varord
if interactive: # not possible to run pstselect or psf interactively on 64-bit linux (Error 851)
os.system('cp _psf.mag _psf.pst')
print '_' * 80
print '>>> Mark good stars with "a" or "d"-elete. Then "f"-it,' + \
' "w"-write and "q"-uit (cursor on ds9)'
print '-' * 80
else:
iraf.pstselect(img + '[0]',
'_psf.mag',
'_psf.pst',
psfstars,
interac=False,
verify=False)
iraf.psf(img + '[0]',
'_psf.mag',
'_psf.pst',
psfout,
'_psf.psto',
'_psf.psg',
interac=interactive,
verify=False,
verbose=False)
iraf.group(img + '[0]',
'_psf.mag',
psfout,
'_psf.grp',
verify=False,
verbose=False)
iraf.nstar(img + '[0]',
'_psf.grp',
psfout,
'_psf.nst',
'_psf.nrj',
verify=False,
verbose=False)
photmag = iraf.txdump("_psf.mag",
'xcenter,ycenter,id,mag,merr',
expr='yes',
Stdout=1)
pst = iraf.txdump("_psf.pst", 'xcenter,ycenter,id', expr='yes', Stdout=1)
fitmag = iraf.txdump("_psf.nst",
'xcenter,ycenter,id,mag,merr',
expr='yes',
Stdout=1)
return photmag, pst, fitmag
def psffit(img, fwhm, psfstars, hdr, interactive, _datamax=45000, psffun='gauss', fixaperture=False):
import agnkey
iraf.digiphot(_doprint=0)
iraf.daophot(_doprint=0)
zmag = 0.
varord = 0 # -1 analitic 0 - numeric
if fixaperture:
print 'use fix aperture 5 8 10'
hdr = agnkey.util.readhdr(img+'.fits')
_pixelscale = agnkey.util.readkey3(hdr, 'PIXSCALE')
a1, a2, a3, a4, = float(5. / _pixelscale), float(5. / _pixelscale), float(8. / _pixelscale), float(
10. / _pixelscale)
# a1, a2, a3, a4, = int(5), int(8), int(10), int(12)
else:
a1, a2, a3, a4, = int(fwhm + 0.5), int(fwhm * 2 + 0.5), int(fwhm * 3 + 0.5), int(fwhm * 4 + 0.5)
_center='no'
iraf.fitskypars.annulus = a4
iraf.fitskypars.dannulus = a4
iraf.noao.digiphot.daophot.daopars.sannulus = int(a4)
iraf.noao.digiphot.daophot.daopars.wsannul = int(a4)
iraf.fitskypars.salgori = 'mean' #mode,mean,gaussian
iraf.photpars.apertures = '%d,%d,%d' % (a2, a3, a4)
# iraf.photpars.apertures = '%d,%d,%d'%(a2,a3,a4)
iraf.datapars.datamin = -100
iraf.datapars.datamax = _datamax
iraf.datapars.readnoise = agnkey.util.readkey3(hdr, 'ron')
iraf.datapars.epadu = agnkey.util.readkey3(hdr, 'gain')
iraf.datapars.exposure = 'exptime' #agnkey.util.readkey3(hdr,'exptime')
iraf.datapars.airmass = 'airmass'
iraf.datapars.filter = 'filter2'
iraf.centerpars.calgori = 'gauss'
iraf.centerpars.cbox = 1
iraf.daopars.recenter = _center
iraf.photpars.zmag = zmag
iraf.delete('_psf.ma*,' + img + '.psf.fit?,_psf.ps*,_psf.gr?,_psf.n*,_psf.sub.fit?', verify=False)
iraf.phot(img+'[0]', '_psf.coo', '_psf.mag', interac=False, verify=False, verbose=False)
iraf.daopars.psfrad = a4
iraf.daopars.functio = psffun
iraf.daopars.fitrad = a1
iraf.daopars.fitsky = 'yes'
iraf.daopars.sannulus = int(a4)
iraf.daopars.wsannul = int(a4)
iraf.daopars.recenter = _center
iraf.daopars.varorder = varord
if interactive:
shutil.copyfile('_psf.mag', '_psf.pst')
print '_' * 80
print '>>> Mark good stars with "a" or "d"-elete. Then "f"-it,' + \
' "w"-write and "q"-uit (cursor on ds9)'
print '-' * 80
else:
iraf.pstselect(img+'.fits[0]', '_psf.mag', '_psf.pst', psfstars, interac=False, verify=False)
iraf.psf(img+'.fits[0]', '_psf.mag', '_psf.pst', img + '.psf', '_psf.psto', '_psf.psg', interac=interactive,
verify=False, verbose=False)
# if os.path.isfile(img + '.psf.fits'):
# print 'file there'
iraf.group(img+'.fits[0]', '_psf.mag', img + '.psf.fits', '_psf.grp', verify=False, verbose=False)
iraf.nstar(img+'.fits[0]', '_psf.grp', img + '.psf.fits', '_psf.nst', '_psf.nrj', verify=False, verbose=False)
photmag = iraf.txdump("_psf.mag", 'xcenter,ycenter,id,mag,merr', expr='yes', Stdout=1)
pst = iraf.txdump("_psf.pst", 'xcenter,ycenter,id', expr='yes', Stdout=1)
fitmag = iraf.txdump("_psf.nst", 'xcenter,ycenter,id,mag,merr', expr='yes', Stdout=1)
return photmag, pst, fitmag
def performPhotometry(task, logger):
#iraf.prcacheOff()
[iraf.unlearn(t) for t in ('phot','pstselect','psf','allstar')]
iraf.set(imtype="fits,noinherit") # set image output format
iraf.set(clobber="yes")
hdu=pyfits.open(task['images'])[0]
hdr = hdu.header
imdata = hdu.data
for key,value in task['fits'].iteritems():
task[key] = hdr.get(value,1)
#Sextractor to find stars; add an object for the force detect
logger.info('Running SExtractor on [%s]' % os.path.basename(task['images']))
sex = sextractor.SExtractor()
makeSexConfig(sex,task)
sex.run(task['images'])
catalog = sex.catalog()
#Set up image parameters
MIN_X = max(1,int(task['numpixx']*task['filtfactor']))
MIN_Y = max(1,int(task['numpixy']*task['filtfactor']))
MAX_X = int(task['numpixx']*(1-task['filtfactor']))
MAX_Y = int(task['numpixy']*(1-task['filtfactor']))
AREAXY = '[%s:%s,%s:%s]' % (MIN_X, MAX_X, MIN_Y, MAX_Y)
AREANO = '[%s:%s,%s:%s]' % (MIN_X, MAX_X-2*MIN_X, MIN_Y, MAX_Y-2*MIN_Y)
try:
task['pixscale'] = abs(hdr.get('CD1_1'))*3600.
except TypeError:
task['pixscale'] = abs(hdr.get('CDELT1'))*3600.
task['seeing'] = np.median( sorted([i['FWHM_IMAGE'] for i in catalog])[:int(-len(catalog)*0.5)] ) #Take the median of the "bottom" 50% of objects
logger.info('--> %s SExtractor detected bright objects in the field' % (len(catalog),) )
logger.info('--> %0.2f median FWHM of bright objects in the field, in arcsec' % (task['seeing']*task['pixscale'],))
task['objects'] = [(i['ALPHA_J2000'],i['DELTA_J2000']) for i in catalog]
task['objects'].append(task['objwcs'])
task['objectlist'] = open(os.path.join(task['output_directory'],'objectlist'),'w')
task['objectlist'].write('\n'.join([' %s %s' % (i[0],i[1]) for i in task['objects']]))
task['objectlist'].close()
logger.info('Running iraf.imstat')
irafoutput = iraf.imstat(images=task['images']+AREANO,fields='midpt,min,max,stddev', format=0, Stdout=1)
task['nimgs'] = hdr.get('NIMGS',1)
task['gain'] *= task['nimgs']*2/3.
task['ron'] *= np.sqrt(task['nimgs'])/task['nimgs']*constants.INTERPSM[task['band']]
task['datamean'], task['datamin'], task['datamax'], task['datastdev'] = map(float, irafoutput[0].split())
irafoutput = iraf.imstat(images=task['images'],fields='stddev,midpt',nclip=25,format=0,cache='yes',Stdout=1)
task['skynoise'], task['datamean'] = map(float, irafoutput[0].split() )
task['skynoise'] *= constants.INTERPSM[task['band']]
task['airmass'] = hdr.get('AIRMASS',1)
task['zmag'] -= (float(task['airmass'])-1.0)*constants.extinction_coefficients[task['band']]
task['match_proximity'] = 2.5 * task['seeing']
logger.info('--> %5.2f counts: Sky noise, corrected for drizzle imcombine' % task['skynoise'])
logger.info('--> %5.2f Median count value, after background subtraction' % task['datamean'])
logger.info('--> %5.2f Airmass' % task['airmass'])
#prepare temp files that iraf will use
for filename in ('photfile','pstfile','psfimg','opstfile','groupfile','allstarfile','rejfile','subimage'):
task[filename] = open(os.path.join(task['output_directory'],filename),'w')
task[filename].close()
#iraf.phot to get APP magnitudes
logger.info('Running iraf.apphot.phot')
#apsizes = [i*task['faperture']*task['seeing'] for i in (0.4,0.5,0.6,0.8,1.0,1.2,1.5,2.0,2.5,3.0)]
#irafapsizes = ','.join(['%.2f' % i for i in apsizes])
irafapsizes = '%0.2f' % (task['faperture']*task['seeing'])
kwargs = dict(image=task['images'],coords=task['objectlist'].name,
output=task['photfile'].name,
interac='no',scale=1,
fwhmpsf=task['seeing'],
wcsin='world', wcsout='physical',
sigma=task['skynoise'],
datamin=task['datamin'],
datamax=task['datamax'],
readnoi=task['ron'],
epadu=task['gain'],
itime=task['exposure'],
xairmass=task['airmass'],
ifilter=task['band'],
otime=task['dateobs'],
aperture= irafapsizes,
zmag=task['zmag'],
annulus=task['fannulus']*task['seeing'],
dannulus=task['fdannulus']*task['seeing'],
calgorithm='gauss',
cbox = 1.5*task['seeing'],
maxshift=2.0*task['seeing'],
mode="h",Stdout=1,verify=0)
iraf.phot(**kwargs)
if task['band'] not in constants.infrared:
#iraf.pstselect to choose objects for PSF modelling
logger.info('Running iraf.daophot.pstselect')
kwargs = dict(image=task['images'],
photfile=task['photfile'].name,pstfile=task['pstfile'].name,
maxnpsf=task['pstnumber'],
wcsin='physical',
wcsout='physical',
interac="no",verify='no',scale=1,
fwhmpsf=task['seeing'],
datamin=0,
datamax=task['datamax'],
psfrad=3.0*task['seeing'],
fitrad=1.0*task['seeing'],
recente='yes',
nclean=task['nclean'],
mode="h",Stdout=1)
iraf.pstselect(**kwargs)
#iraf.psf to model PSF
logger.info('Running iraf.daophot.psf')
kwargs = dict( image=task['images'],
photfile=task['photfile'].name,
pstfile=task['pstfile'].name,
psfimage=task['psfimg'].name,
opstfile=task['opstfile'].name,
groupfile=task['groupfile'].name,
wcsin='physical',wcsout='physical',
interac="no",verify="no",scale=1,
fwhmpsf=task['seeing'],
sigma=task['skynoise'],
datamin=task['datamin'],
datamax=task['datamax'],
readnoi=task['ron'],
epadu=task['gain'],
itime=task['exposure'],
xairmass=task['airmass'],
ifilter=task['band'],
otime=task['dateobs'],
function=task['func'],
varorder=task['varorder'],
saturat='no',
psfrad=3.0*task['seeing'],
fitrad=1.*task['faperture']*task['seeing'],
nclean=task['nclean'],
mergerad=1.5*task['seeing'],
mode='h',Stdout=1)
iraf.psf(**kwargs)
logger.info('Running iraf.daophot.allstar')
#iraf.allstars to compute PSF photometry; recenter with recenter='yes', mergerad=<value> to avoid duplicate detection
kwargs = dict(image=task['images'],
photfile=task['photfile'].name,
wcsin='physical',
wcsout='physical',
psfimage=task['psfimg'].name,
allstarf=task['allstarfile'].name,
rejfile=task['rejfile'].name,
subimage=task['subimage'].name,
verbose=1,verify='no',scale=1,
fwhmpsf=task['seeing'],
sigma=task['skynoise'],
datamin=task['datamin'],
datamax=task['datamax'],
readnoi=task['ron'],
epadu=task['gain'],
itime=task['exposure'],
xairmass=task['airmass'],
ifilter=task['band'],
otime=task['dateobs'],
function=task['func'],
varorder=task['varorder'],
psfrad=3.*task['seeing'],
fitrad=1.*task['faperture']*task['seeing'],
recenter='yes',
mergerad=1.5*task['seeing'],
mode='h',Stdout=1)
iraf.allstar(**kwargs)
#Parse both photometry, convert to RA,DEC,MAG,MAGERR
logger.info('iraf tasks complete. Parsing results and calibrating')
photometry = {}
photometry['APP'] = iraf.txdump(textfiles=task['photfile'].name,
fields='XCENTER,YCENTER,MAG,MERR',expr='yes',
headers='no',Stdout=1)
if task['band'] not in constants.infrared:
photometry['PSF'] = iraf.txdump(textfiles=task['allstarfile'].name,
fields='XCENTER,YCENTER,MAG,MERR',expr='yes',
headers='no',Stdout=1)
for phototype in photometry:
kwargs = dict(input='STDIN',
output='STDOUT',
insystem='%s physical' % task['images'],
outsystem='%s world' % task['images'],
ilatuni='physical',
ilnguni='physical',
olnguni='degrees',
olatuni='degrees',
ilngfor='%10.7f',
ilatfor='%10.7f',
olngfor='%10.5f',
olatfor='%10.5f',
Stdin=photometry[phototype],Stdout=1)
photometry[phototype] = [i.split() for i in iraf.skyctran(**kwargs) if i and not i.startswith('#') and 'INDEF' not in i]
photometry[phototype] = [map(float,(i[4],i[5],i[2],i[3])) for i in photometry[phototype] ] #Now we have [(ra,dec,'mag','mageerr'),...]
results = calibrate((task['objwcs'][0],task['objwcs'][1]),task,photometry,logger)
# if 'PSF' not in results:
return results
pstfile = open(FitsFileName+'.pst.1', 'a+r')
pstfile.write("#N ID XCENTER YCENTER MAG MSKY \\\n")
pstfile.write("#U ## pixels pixels magnitudes counts \\\n")
pstfile.write("#F %-9d %-10.3f %-10.3f %-12.3f %-15.7g \n")
pstfile.write("#\n")
np.savetxt(pstfile,g.take([-1,0,1,2,3],axis=1),fmt=['%-9d','%-10.3f','%-10.3f','%-12.3f','%-15.7g'])
pstfile.close()
iraf.daopars.setParam('matchra',fwhm)
iraf.daopars.setParam('psfrad',4*fwhm+1)
iraf.daopars.setParam('fitrad',fwhm)
iraf.daopars.setParam('sannulu',2*fwhm)
iraf.daopars.setParam('wsannul',4*fwhm)
iraf.psf.setParam('image',FitsFileName)
iraf.psf(mode='h')
iraf.seepsf(psfimage=FitsFileName+'.psf.1.fits',image=base+'psfim'+ext+'.fits',magnitu='18.0')
iraf.allstar.setParam('image',FitsFileName)
iraf.allstar(mode='h',verbose='no')
if os.path.exists(base+'allstartmp') == True: os.remove(base+'allstartmp')
iraf.txdump(textfile=FitsFileName+'.als.1',fields='xcenter,ycenter,mag,merr,id',expr='mag\
!= INDEF && merr != INDEF', Stdout=base+'allstartmp')
outmags = np.loadtxt(base+'allstartmp')
if os.path.exists(base+'allstartmp') == True: os.remove(base+'allstartmp')
if int(ext) <= 4:
shifty = 0.0
shiftx = (float(ext) - 1.)*sx
else:
shifty = sy
def psfphot(image,
coofile,
ot,
wtimage="",
varorder=1,
clobber=globclob,
verbose=globver,
pixtol=3.0,
maxnpsf=25):
""" perform PSF-based photometry on a single target star (SN?) at RA, Dec and
also on a set of comparison stars, using daophot. simultaneously
perform aperture photometry on all the comparison stars (after
subtracting off contributions from neighbors) to enable absolute
photometry by comparison to aperture photometry of standard stars
observed in other fields """
# Defaults / constants
psfmult = 5.0 #standard factor (multiplied by fwhm to get psfradius)
psfmultsmall = 3.0 #similar to psfmult, adjusted for nstar and substar
# Necessary package
iraf.imutil()
iraf.digiphot()
iraf.daophot()
# Detect stars
iqobjs("%s.sub.fits" % image[:-5],
1.5,
12000.0,
wtimage=wtimage,
skyval="0.0")
root = image[:-5]
[gain, rnoise, fwhm] = get_head(image, ["GAIN", "READN", "SEEPIX"])
fwhm = float(fwhm)
rnoise = float(rnoise)
iraf.iterstat(image)
# Saturation level
if not check_head(image, "SATURATE"):
saturate = 60000.0
else:
saturate = get_head(image, "SATURATE")
# Update datapars and daopars
iraf.datapars.fwhmpsf = fwhm
iraf.datapars.sigma = iraf.iterstat.sigma
iraf.datapars.datamin = iraf.iterstat.median - 10 * iraf.iterstat.sigma
iraf.datapars.datamax = 0.50 * saturate
iraf.datapars.readnoise = rnoise
iraf.datapars.epadu = gain
iraf.daopars.psfrad = psfmult * fwhm
iraf.daopars.fitrad = fwhm
iraf.daopars.function = "gauss,moffat15,moffat25,lorentz,penny1"
iraf.daopars.varorder = varorder
# Reference stars file
stars = Starlist(coofile)
stars.wcs2pix(image)
outf = open("%s.coo.1" % image[:-5], "w")
for star in stars:
outf.write("%10.3f%10.3f\n" % (star.xval, star.yval))
outf.close()
#Aperture photometry
iraf.daophot.phot(root,
'default',
'default',
apertures=fwhm,
verify=no,
interac=no,
verbose=verbose)
iraf.datapars.datamax = 0.50 * saturate
iraf.pstselect(root,
'default',
'default',
maxnpsf,
interactive=no,
verify=no,
verbose=verbose)
iraf.psf(root,
'default',
'default',
'default',
'default',
'default',
interactive=no,
showplots=no,
verify=no,
verbose=verbose)
iraf.allstar(root,
'default',
'default',
'default',
'default',
'default',
verify=no,
verbose=verbose)
# Prep for subtracted image
iraf.iterstat("%s.sub.fits" % root)
iraf.datapars.sigma = iraf.iterstat.sigma
iraf.datapars.datamin = iraf.iterstat.median - 10 * iraf.iterstat.sigma
iraf.datapars.datamax = saturate
# Look for source at OT location
substars = Starlist("%s.sub.fits.stars" % image[:-5])
otstars = Starlist(ot)
otstars.wcs2pix("%s.sub.fits" % image[:-5])
smatch, omatch = substars.match(otstars, tol=pixtol, useflags=no)
# Generate coo file
otcoo = open("%s.sub.coo.1" % image[:-5], "w")
if len(smatch) == 0:
otcoo.write("%10.3f%10.3f\n" % (otstars[0].xval, otstars[0].yval))
else:
otcoo.write("%10.3f%10.3f\n" % (smatch[0].xval, smatch[0].yval))
otcoo.close()
iraf.daophot.phot("%s.sub.fits" % root,
"%s.sub.coo.1" % image[:-5],
'default',
'default',
apertures=fwhm,
calgorithm="none",
interac=no,
verify=no,
verbose=verbose)
if len(smatch) == 0:
print "No match in subtracted image: %s.sub.fits" % root
else:
iraf.allstar("%s.sub.fits" % root,
'default',
"%s.psf.1.fits" % root,
'default',
'default',
'default',
verify=no,
verbose=no)
return
def psfphot(inlist, ra, dec, reffilt, interact, fwhm, readnoise, gain,
threshold,refimage=None,starfile=None,maxnpsf=5,
clobber=globclob,verbose=globver,skykey='SKYBKG',
filtkey='FILTER',pixtol=3.0):
""" perform PSF-based photometry on a single target star (SN?) at RA, Dec and
also on a set of comparison stars, using daophot. simultaneously
perform aperture photometry on all the comparison stars (after
subtracting off contributions from neighbors) to enable absolute
photometry by comparison to aperture photometry of standard stars
observed in other fields """
# Defaults / constants
psfmult=5.0 #standard factor (multiplied by fwhm to get psfradius)
psfmultsmall=3.0 #similar to psfmult, adjusted for nstar and substar
# Necessary package
iraf.imutil()
# Parse inputs
infiles=iraffiles(inlist)
# Which file is reffilt? call it refimage
if refimage==None:
for image in infiles:
if check_head(image, filtkey):
try:
imgfilt = get_head(image, filtkey)
if imgfilt == reffilt:
refimage = image
break
except:
pass
if not refimage:
print "BAD USER! No image corresponds to the filter: %s" % reffilt
return
else:
refroot='s'+refimage.split('.')[0]
#first make sure to add back in background of sky
iraf.iqsubsky(inlist, sub=no, skykey=skykey)
#put reference image first on list
infiles.remove(refimage)
infiles.insert(0,refimage)
#setup for keywords
if gain == "!GAIN":
try: gainval = float(get_head(image, gain))
except:
print "Bad header keyword for gain."
else:
gainval = float(gain)
if readnoise == "!READNOISE":
try: readval = float(get_head(image, readnoise))
except:
print "Bad header keyword for readnoise."
else:
readval = float(readnoise)
# Process each file in turn
for image in infiles:
# Check that the image is there
check_exist(image,"r")
# Grab image root name
root=image.split('.')[0]
# Map image to reference image
if not (image==refimage):
[nx,ny]=get_head(image,['NAXIS1','NAXIS2'])
stars=Starlist(get_head(image,'STARFILE'))
refstars=Starlist(get_head(refimage,'STARFILE'))
refstars.pix2wcs(refimage)
refstars.wcs2pix(image)
match,refmatch=stars.match(refstars,useflags=yes,tol=10.0)
nstars=len(match)
if not (nstars>2):
print 'Could not find star matches between reference and %s' % image
infiles.remove(image)
continue
refmatch.pix2wcs(image)
refmatch.wcs2pix(refimage)
matchfile=open('%s.match' % root, 'w')
for i in range(len(match)):
matchfile.write('%10.3f%10.3f%10.3f%10.3f\n' %
(refmatch[i].xval,refmatch[i].yval,
match[i].xval,match[i].yval))
matchfile.close()
check_exist('%s.geodb' % root, 'w', clobber=clobber)
iraf.geomap('%s.match' % root,'%s.geodb' % root,1.0,nx,1.0,ny,
verbose=no,interactive=no)
check_exist('s%s.fits' % root, 'w', clobber=clobber)
iraf.geotran(image,'s%s' % root,'%s.geodb' % root,
'%s.match' % root,geometry="geometric",
boundary="constant",verbose=no)
else:
iraf.imcopy(image,'s%s' % root)
root='s%s' % root
#get sky level and calculate sigma
#if check_head(image, skykey):
# try:
# sky=float(get_head(image, skykey))
# except:
# print "No sky levels in header."
#sigma= (((sky * gainval) + readval**2)**.5) / gainval
iraf.iterstat(image)
# Saturation level
if not check_head(image, "SATURATE"):
saturate = 60000.0
else:
saturate = get_head(image, "SATURATE")
# Update datapars and daopars
iraf.datapars.fwhmpsf=fwhm
iraf.datapars.sigma=iraf.iterstat.sigma
iraf.datapars.datamin=iraf.iterstat.median-10*iraf.iterstat.sigma
iraf.datapars.datamax=0.90*saturate
iraf.datapars.readnoise=readval
iraf.datapars.epadu=gainval
iraf.datapars.filter=filtkey
iraf.daopars.psfrad=psfmult*fwhm
iraf.daopars.fitrad=fwhm
iraf.daopars.function="gauss,moffat15,moffat25,lorentz,penny1"
#find stars in image unless a starlist is given
if image==refimage and starfile==None:
iraf.daophot.daofind(root,'refimage.coo.1',threshold=threshold,verify=no,
verbose=verbose)
elif image==refimage:
shutil.copy(starfile,'refimage.coo.1')
#initial photometry
iraf.daophot.phot(root,'refimage.coo.1','default',aperture=fwhm,verify=no,
verbose=verbose)
#select stars for psf the first time
refstarsfile = "refimage.pst.1"
if image == refimage:
iraf.pstselect(root,'default',refstarsfile,maxnpsf,
interactive=yes,verify=no,verbose=verbose)
#fit the psf
iraf.psf(root,'default',refstarsfile,'default','default','default',
interactive=interact,verify=no,verbose=verbose)
#identify neighboring/interfering stars to selected stars
groupingfile = root+".psg.1"
iraf.nstar(root,groupingfile,'default','default','default',
psfrad= psfmultsmall * fwhm,verify=no,verbose=verbose)
#subtract out neighboring stars from image
iraf.substar(root,'default',refstarsfile,'default','default',
psfrad=psfmultsmall*fwhm,verify=no,verbose=verbose)
#repeat psf to get better psf model
#IRAF's interactive version usually crashes
subtractedimage = root+".sub.1"
iraf.psf(subtractedimage,root+".nst.1",refstarsfile,'%s.psf.2' % root,
'%s.pst.2' % root,'%s.psg.2' % root,interactive=interact,
verify=no,verbose=verbose)
#Need to make sure SN was detected by daofind
stars=Starlist('%s.mag.1' % root)
SN=Star(name='SN',radeg=ra,dcdeg=dec,fwhm=2.0,fwhmw=2.0)
SNlis=Starlist(stars=[SN])
SNlis.wcs2pix(image)
if (len(stars.match(SNlis)[0])==0):
#No match - need to add to daofind file
print "No match!"
coofile=open('refimage.coo.1', 'a+')
coofile.write('%10.3f%10.3f%9.3f%8.3f%13.3f%12.3f%8i\n' % (SNlis[0].xval, SNlis[0].yval,99.999,0.500,0.000,0.000,999))
coofile.close()
#repeat aperture photometry to get good comparisons to standard fields
iraf.daophot.phot(root,'refimage.coo.1','default',aperture=psfmult*fwhm,
verify=no,verbose=verbose)
# allstar run
iraf.allstar(root,'default','default','default','default','default',
verify=no,verbose=verbose)
def build(f):
### is this an MEF file
current_ext = 0
NEXTEND = 0
EXTEND = f[0].header["EXTEND"]
if EXTEND == "T":
NEXTEND = f[0].header["NEXTEND"]
current_ext = 1
### create the name of the output MEF psf file
if not f[0].header.has_key("FILENAME"):
os.unlink(opt.filename)
sys.exit("The fits file " + opt.filename + " has no EXPNUM keyword\n")
sexp = f[0].header["FILENAME"]
mef_psf = sexp + "p_psf_iraf.fits"
### create an MEF file that will contian the PSF(s)
import pyfits
fitsobj = pyfits.HDUList()
prihdu = pyfits.PrimaryHDU()
import re
prihdu.header.update("FILENAME", sexp, comment="CFHT Exposure Numebr")
prihdu.header.update("NEXTEND", NEXTEND, comment="number of extensions")
version = re.match(r"\$Rev.*: (\d*.\d*) \$", __Version__).group(1)
prihdu.header.update("MKPSF_V", float(version), comment="Version number of mkpsf")
fitsobj.append(prihdu)
if os.access(mef_psf, os.F_OK):
os.unlink(mef_psf)
fitsobj.writeto(mef_psf)
fitsobj.close()
outfits = pyfits.open(mef_psf, "append")
prihdr = outfits[0].header
import jjkmode
### Get my python routines
from pyraf import iraf
from pyraf.irafpar import IrafParList
### keep all the parameters locally cached.
iraf.set(uparm="./")
### Load the required IRAF packages
iraf.digiphot()
iraf.apphot()
iraf.daophot()
### temp file name hash.
tfile = {}
while current_ext <= NEXTEND:
### this is a psf SCRIPT so the showplots and interactive are off by force
print "Working on image section " + str(current_ext)
iraf.findpars.sharplo = 0
iraf.findpars.sharphi = 0.7
iraf.findpars.roundlo = -0.7
iraf.findpars.roundhi = 0.7
iraf.datapars.datamax = 20000
iraf.datapars.airmass = "AIRMASS"
iraf.datapars.filter = "FILTER"
iraf.datapars.obstime = "TIME-OBS"
iraf.datapars.exposure = "EXPTIME"
iraf.datapars.gain = "GAIN"
iraf.datapars.ccdread = "RDNOISE"
iraf.datapars.fwhmpsf = opt.fwhm
iraf.daopars.nclean = 2
iraf.daopars.psfrad = 5.0 * opt.fwhm
iraf.daopars.fitrad = 0.85 * opt.fwhm
iraf.daopars.function = "gauss"
iraf.centerpars.calgorithm = "centroid"
zero_mag = 26.19
iraf.photpars.zmag = zero_mag
iraf.photpars.apertures = int(0.85 * opt.fwhm)
iraf.fitskypars.annulus = 2 + int(opt.fwhm * 4.00)
iraf.fitskypars.dannulus = int(opt.fwhm * 2.0)
iraf.daophot.verbose = no
iraf.daophot.verify = no
iraf.daophot.update = no
iraf.psf.interactive = no
iraf.pstselect.interactive = no
iraf.datapars.saveParList()
iraf.fitskypars.saveParList()
iraf.centerpars.saveParList()
iraf.findpars.saveParList()
iraf.photpars.saveParList()
tfiles = [
"coo_bright",
"coo_ok",
"coo_faint",
"mag_all",
"mag_bright",
"mag_ok",
"mag_good",
"mag_best",
"pst_in",
"pst_out",
"pst_out2",
"prf",
"psg_org",
"psg",
"psf_1.fits",
"psf_2.fits",
"psf_final.fits",
"psf_3.fits",
"psf_4.fits",
"mag_pst",
"coo_pst",
"nst",
"nrj",
"seepsf.fits",
"sub.fits",
"fwhm",
"apcor",
]
for file in tfiles:
extname = "chip" + str(f[current_ext].header.get("IMAGEID", str(current_ext))).zfill(2)
tfile[file] = sexp + "_" + extname + "." + file
if os.access(tfile[file], os.F_OK):
os.unlink(tfile[file])
if EXTEND == "T":
this_image = opt.filename + "[" + extname + "]"
else:
this_image = opt.filename
gain = f[current_ext].header.get("GAIN", 1.0)
#### set sky/sigma parameters specific to this frame.
(skyvalue, sigma) = jjkmode.stats(f[current_ext].data)
import math
sigma = math.sqrt(skyvalue / gain)
datamin = float(skyvalue) - 8.0 * float(sigma)
print "Determined sky level to be " + str(skyvalue) + " +/-" + str(sigma)
iraf.datapars.datamin = datamin
iraf.datapars.sigma = float(sigma)
iraf.datapars.saveParList()
iraf.fitskypars.skyvalue = skyvalue
iraf.fitskypars.saveParList()
### find the bright stars in the image.
print "sextracting for stars in " + this_image
###iraf.daophot.daofind(image=this_image,
### output=tfile['coo_bright'],threshold=4.0)
os.system(
"sex -c /home/cadc/kavelaar/12kproc/config/default.sex -SATUR_LEVEL 25000 -CATALOG_NAME "
+ tfile["coo_bright"]
+ " "
+ this_image
)
### print "finding stellar locus in sround/ground space"
print "clipping using star_class > 0.85 "
fcoo = open(tfile["coo_bright"], "r")
lines = fcoo.readlines()
fcoo.close()
import numarray, math
fout = open(tfile["coo_ok"], "w")
for line in lines:
if re.match(r"^#", line) or re.search(r"INDEF", line):
continue
values = line.split()
star_class = float(values[2])
if star_class > 0.75:
fout.write(line)
fout.close()
print "Measuring photometry for psf candidate stars in " + tfile["coo_ok"]
iraf.daophot.phot(image=this_image, coords=tfile["coo_ok"], output=tfile["mag_bright"])
### do this selection in 2 steps because of the way IRAF handles INDEFs
print "Selecting stars that have good centroids and magnitudes "
iraf.pselect(
tfile["mag_bright"], tfile["mag_ok"], "(CIER==0)&&(PIER==0)&&(SIER==0)&&(MSKY>0)&&(MSKY<2e5)&&(MSKY!=INDEF)"
)
print "Selecting stars that have normal sky levels"
condition = "(abs(MSKY -" + str(skyvalue) + ") < 5.0*" + str(sigma) + ")"
iraf.pselect(tfile["mag_ok"], tfile["mag_good"], condition)
a = iraf.txdump(tfile["mag_good"], "SSKEW", iraf.yes, Stdout=1)
aa = []
for v in a:
aa.append(float(v))
a = numarray.array(aa)
mean = a.mean()
aa = a * a
stddev = math.sqrt(aa.sum() / len(aa) - mean ** 2)
limit = mean + 2 * stddev
os.unlink(tfile["mag_good"])
condition = condition + " && SSKEW < " + str(limit)
iraf.pselect(tfile["mag_ok"], tfile["mag_good"], condition)
print "Choosing the psf stars"
iraf.pstselect(image=this_image, photfile=tfile["mag_good"], pstfile=tfile["pst_in"], maxnpsf=25)
## construct an initial PSF image
print "computing psf with neighbor stars based on complete star list"
iraf.psf.mode = "a"
iraf.psf(
image=this_image,
photfile=tfile["mag_bright"],
pstfile=tfile["pst_in"],
psfimage=tfile["psf_1.fits"],
opstfile=tfile["pst_out"],
groupfile=tfile["psg_org"],
varorder=0,
)
try:
print "subtracting the psf neighbors and placing the results in " + tfile["sub.fits"]
iraf.daophot.nstar(
image=this_image,
groupfile=tfile["psg_org"],
psfimage=tfile["psf_1.fits"],
nstarfile=tfile["nst"],
rejfile=tfile["nrj"],
)
iraf.daophot.substar(
image=this_image,
photfile=tfile["nst"],
exfile=tfile["pst_in"],
psfimage=tfile["psf_1.fits"],
subimage=tfile["sub.fits"],
)
a = iraf.daophot.txdump(tfile["nst"], "chi", "yes", Stdout=1)
aa = []
for v in a:
aa.append(float(v))
a = numarray.array(aa)
mean = a.mean()
aa = a * a
stddev = math.sqrt(aa.sum() / len(aa) - mean ** 2)
limit = mean + 2.5 * stddev
print "Selecting those psf stars with CHI^2 <" + str(limit) + " after fitting with trial psf"
iraf.pselect(tfile["nst"], tfile["mag_best"], "CHI < " + str(limit))
os.unlink(tfile["pst_out"])
## os.unlink(tfile['psg'])
## rebuild the PSF file with the psf stars that fit well..
## using the neighbor subtracted image
print "Rebuilding the PSF"
iraf.daophot.psf(
image=tfile["sub.fits"],
photfile=tfile["mag_best"],
pstfile=tfile["pst_in"],
psfimage=tfile["psf_2.fits"],
opstfile=tfile["pst_out"],
groupfile=tfile["psg"],
varorder=0,
)
print "re-subtracting with rebuilt psf"
os.unlink(tfile["nst"])
os.unlink(tfile["nrj"])
iraf.daophot.nstar(
image=this_image,
groupfile=tfile["psg"],
psfimage=tfile["psf_2.fits"],
nstarfile=tfile["nst"],
rejfile=tfile["nrj"],
)
os.unlink(tfile["sub.fits"])
iraf.daophot.substar(
image=this_image,
photfile=tfile["nst"],
exfile=tfile["pst_in"],
psfimage=tfile["psf_2.fits"],
subimage=tfile["sub.fits"],
)
os.unlink(tfile["psg"])
os.unlink(tfile["pst_out"])
iraf.daophot.psf(
image=tfile["sub.fits"],
photfile=tfile["mag_best"],
pstfile=tfile["pst_in"],
psfimage=tfile["psf_3.fits"],
opstfile=tfile["pst_out"],
groupfile=tfile["psg"],
varorder=0,
)
os.unlink(tfile["nrj"])
os.unlink(tfile["nst"])
iraf.daophot.nstar(
image=this_image,
groupfile=tfile["psg"],
psfimage=tfile["psf_3.fits"],
nstarfile=tfile["nst"],
rejfile=tfile["nrj"],
)
a = iraf.daophot.txdump(tfile["nst"], "chi", "yes", Stdout=1)
aa = []
for v in a:
aa.append(float(v))
a = numarray.array(aa)
mean = a.mean()
aa = a * a
stddev = math.sqrt(aa.sum() / len(aa) - mean ** 2)
limit = mean + 2 * stddev
limit = 2.0
# print "Selecting those psf stars with CHI^2 < "+str(limit)+" after fit with GOOD psf"
os.unlink(tfile["mag_best"])
iraf.pselect(tfile["nst"], tfile["mag_best"], "CHI < " + str(limit))
print "Building final PSF.... "
os.unlink(tfile["sub.fits"])
iraf.daophot.substar(
image=this_image,
photfile=tfile["nst"],
exfile=tfile["pst_in"],
psfimage=tfile["psf_3.fits"],
subimage=tfile["sub.fits"],
)
os.unlink(tfile["psg"])
os.unlink(tfile["pst_out"])
iraf.daophot.psf(
image=tfile["sub.fits"],
photfile=tfile["mag_best"],
pstfile=tfile["pst_in"],
psfimage=tfile["psf_final.fits"],
opstfile=tfile["pst_out"],
groupfile=tfile["psg"],
varorder=0,
)
print "building an analytic psf for the FWHM calculations"
os.unlink(tfile["pst_out"])
os.unlink(tfile["psg"])
iraf.daophot.psf(
image=tfile["sub.fits"],
photfile=tfile["mag_best"],
pstfile=tfile["pst_in"],
psfimage=tfile["psf_4.fits"],
opstfile=tfile["pst_out"],
groupfile=tfile["psg"],
varorder=-1,
)
except:
print sys.exc_info()[1]
print "ERROR: Reverting to first pass psf"
tfile["psf_final.fits"] = tfile["psf_1.fits"]
iraf.daophot.psf(
image=this_image,
photfile=tfile["mag_best"],
pstfile=tfile["pst_in"],
psfimage=tfile["psf_4.fits"],
opstfile=tfile["pst_out2"],
groupfile=tfile["psg"],
varorder=-1,
)
psf_ap = iraf.photpars.apertures
ap1 = int(psf_ap)
ap2 = int(4.0 * opt.fwhm)
apcor = "INDEF"
aperr = "INDEF"
if 0:
# try
### now that we have the psf use the output list of psf stars
### to compute the aperature correction
lines = iraf.txdump(tfile["pst_out"], "xcen,ycen,mag,id", iraf.yes, Stdout=tfile["coo_pst"])
## set the lower ap value for the COG (normally set to 2)
if ap1 < 3:
smallap = 1
else:
smallap = 2 - ap1 + 1
ap1 = 2
ap2 = int(math.floor(4.0 * opt.fwhm))
naperts = ap2 - ap1 + 1
iraf.photpars.apertures = str(ap1) + ":" + str(ap2) + ":1"
iraf.photpars.saveParList()
iraf.daophot.phot(image=this_image, coords=tfile["coo_pst"], output=tfile["mag_pst"])
iraf.photcal()
iraf.photcal.mkapfile(
tfile["mag_pst"],
naperts=naperts,
apercors=tfile["apcor"],
smallap=smallap,
verify="no",
gcommands="",
interactive=0,
)
fin = open(tfile["apcor"], "r")
lines = fin.readlines()
values = lines[2].split()
apcor = values[1]
aperr = values[2]
# except:
## compute the FWHM of the PSF image using the analytic PSF (VarOrd=-1)
psf_file = pyfits.open(tfile["psf_4.fits"])
fwhm = psf_file[0].header.get("PAR1", 99.0) + psf_file[0].header.get("PAR2", 99.0)
psf_file.close()
# ## Open the psf.fits
infits = pyfits.open(tfile["psf_final.fits"])
hdu = infits[0]
inhdu = hdu.header
inhdu.update("XTENSION", "IMAGE", before="SIMPLE")
inhdu.update("PCOUNT", 0, after="NAXIS2")
inhdu.update("GCOUNT", 1, after="PCOUNT")
del hdu.header["SIMPLE"]
del hdu.header["EXTEND"]
inhdu.update("EXTNAME", extname, comment="image extension identifier")
# inhdu.update("SLOW",slow,comment="SROUND low cutoff")
# inhdu.update("SIGH",sigh,comment="SROUND high cutoff")
inhdu.update("PFWHM", fwhm, comment="FWHM of stars based on PSF fitting")
inhdu.update("ZMAG", zero_mag, comment="ZMAG of PSF ")
inhdu.update("BCKG", skyvalue, comment="Mean sky level in counts")
inhdu.update("BCKG_STD", sigma, comment="standard deviation of sky in counts")
inhdu.update("AP1", psf_ap, comment="Apperture used for PSF flux")
inhdu.update("AP2", ap2, comment="Full Flux aperture")
inhdu.update("APCOR", apcor, comment="Apperture correction (ap1->ap2)")
inhdu.update("APERR", apcor, comment="Uncertainty in APCOR")
# ### append this psf to the output images....
print "Sticking this PSF onto the output file"
f[current_ext].header.update("PFWHM", fwhm, comment="FWHM of stars based on PSF fitting")
f[current_ext].header.update("BCKG", skyvalue, comment="Mean sky level in counts")
f[current_ext].header.update("BCKG_STD", sigma, comment="Standard deviation of sky in counts")
f.flush()
outfits.append(hdu)
outfits.flush()
infits.close()
### remove the temp file we used for this computation.
for tf in tfile.keys():
if os.access(tfile[tf], os.F_OK):
os.unlink(tfile[tf])
current_ext = current_ext + 1
outfits.close()
return mef_psf
def psffit(img, fwhm, psfstars, hdr, interactive, _datamax, psffun='gauss', fixaperture=False):
'''
giving an image, a psffile compute the psf using the file _psf.coo
'''
import lsc
_ron = lsc.util.readkey3(hdr, 'ron')
_gain = lsc.util.readkey3(hdr, 'gain')
if not _ron:
_ron = 1
print 'warning ron not defined'
if not _gain:
_gain = 1
print 'warning ron not defined'
iraf.digiphot(_doprint=0)
iraf.daophot(_doprint=0)
zmag = 0.
varord = 0 # -1 analitic 0 - numeric
if fixaperture:
print 'use fix aperture 5 8 10'
hdr = lsc.util.readhdr(img+'.fits')
_pixelscale = lsc.util.readkey3(hdr, 'PIXSCALE')
a1, a2, a3, a4, = float(5. / _pixelscale), float(5. / _pixelscale), float(8. / _pixelscale), float(
10. / _pixelscale)
else:
a1, a2, a3, a4, = int(fwhm + 0.5), int(fwhm * 2 + 0.5), int(fwhm * 3 + 0.5), int(fwhm * 4 + 0.5)
iraf.fitskypars.annulus = a4
iraf.fitskypars.salgori = 'mean' #mode,mean,gaussian
iraf.photpars.apertures = '%d,%d,%d' % (a2, a3, a4)
iraf.datapars.datamin = -100
iraf.datapars.datamax = _datamax
iraf.datapars.readnoise = _ron
iraf.datapars.epadu = _gain
iraf.datapars.exposure = 'EXPTIME'
iraf.datapars.airmass = ''
iraf.datapars.filter = ''
iraf.centerpars.calgori = 'centroid'
iraf.centerpars.cbox = a2
iraf.daopars.recenter = 'yes'
iraf.photpars.zmag = zmag
iraf.delete('_psf.ma*,' + img + '.psf.fit?,_psf.ps*,_psf.gr?,_psf.n*,_psf.sub.fit?', verify=False)
iraf.phot(img+'[0]', '_psf.coo', '_psf.mag', interac=False, verify=False, verbose=False)
# removes saturated stars from the list (IRAF just issues a warning)
with open('_psf.mag') as f:
text = f.read()
text = re.sub('(.*\n){6}.*BadPixels\* \n', '', text)
with open('_psf.mag', 'w') as f:
f.write(text)
iraf.daopars.psfrad = a4
iraf.daopars.functio = psffun
iraf.daopars.fitrad = a1
iraf.daopars.fitsky = 'yes'
iraf.daopars.sannulus = a4
iraf.daopars.recenter = 'yes'
iraf.daopars.varorder = varord
if interactive: # not possible to run pstselect or psf interactively on 64-bit linux (Error 851)
shutil.copyfile('_psf.mag', '_psf.pst')
print '_' * 80
print '>>> Mark good stars with "a" or "d"-elete. Then "f"-it,' + \
' "w"-write and "q"-uit (cursor on ds9)'
print '-' * 80
else:
iraf.pstselect(img+'[0]', '_psf.mag', '_psf.pst', psfstars, interac=False, verify=False)
iraf.psf(img + '[0]', '_psf.mag', '_psf.pst', img + '.psf', '_psf.psto', '_psf.psg', interac=interactive,
verify=False, verbose=False)
iraf.group(img + '[0]', '_psf.mag', img + '.psf', '_psf.grp', verify=False, verbose=False)
iraf.nstar(img + '[0]', '_psf.grp', img + '.psf', '_psf.nst', '_psf.nrj', verify=False, verbose=False)
photmag = iraf.txdump("_psf.mag", 'xcenter,ycenter,id,mag,merr', expr='yes', Stdout=1)
pst = iraf.txdump("_psf.pst", 'xcenter,ycenter,id', expr='yes', Stdout=1)
fitmag = iraf.txdump("_psf.nst", 'xcenter,ycenter,id,mag,merr', expr='yes', Stdout=1)
return photmag, pst, fitmag
def psffit(img, fwhm, psfstars, hdr, interactive, _datamax=45000, psffun='gauss', fixaperture=False):
'''
giving an image, a psffile compute the psf using the file _psf.coo
'''
import lsc
_ron = lsc.util.readkey3(hdr, 'ron')
_gain = lsc.util.readkey3(hdr, 'gain')
if not _ron:
_ron = 1
print 'warning ron not defined'
if not _gain:
_gain = 1
print 'warning ron not defined'
iraf.digiphot(_doprint=0)
iraf.daophot(_doprint=0)
zmag = 0.
varord = 0 # -1 analitic 0 - numeric
if fixaperture:
print 'use fix aperture 5 8 10'
hdr = lsc.util.readhdr(img+'.fits')
_pixelscale = lsc.util.readkey3(hdr, 'PIXSCALE')
a1, a2, a3, a4, = float(5. / _pixelscale), float(5. / _pixelscale), float(8. / _pixelscale), float(
10. / _pixelscale)
else:
a1, a2, a3, a4, = int(fwhm + 0.5), int(fwhm * 2 + 0.5), int(fwhm * 3 + 0.5), int(fwhm * 4 + 0.5)
iraf.fitskypars.annulus = a4
iraf.fitskypars.salgori = 'mean' #mode,mean,gaussian
iraf.photpars.apertures = '%d,%d,%d' % (a2, a3, a4)
iraf.datapars.datamin = -100
iraf.datapars.datamax = _datamax
iraf.datapars.readnoise = _ron
iraf.datapars.epadu = _gain
iraf.datapars.exposure = 'EXPTIME'
iraf.datapars.airmass = ''
iraf.datapars.filter = ''
iraf.centerpars.calgori = 'centroid'
iraf.centerpars.cbox = a2
iraf.daopars.recenter = 'yes'
iraf.photpars.zmag = zmag
iraf.delete('_psf.ma*,' + img + '.psf.fit?,_psf.ps*,_psf.gr?,_psf.n*,_psf.sub.fit?', verify=False)
iraf.phot(img+'[0]', '_psf.coo', '_psf.mag', interac=False, verify=False, verbose=False)
iraf.daopars.psfrad = a4
iraf.daopars.functio = psffun
iraf.daopars.fitrad = a1
iraf.daopars.fitsky = 'yes'
iraf.daopars.sannulus = a4
iraf.daopars.recenter = 'yes'
iraf.daopars.varorder = varord
if interactive:
shutil.copyfile('_psf.mag', '_psf.pst')
print '_' * 80
print '>>> Mark good stars with "a" or "d"-elete. Then "f"-it,' + \
' "w"-write and "q"-uit (cursor on ds9)'
print '-' * 80
else:
iraf.pstselect(img+'[0]', '_psf.mag', '_psf.pst', psfstars, interac=False, verify=False)
iraf.psf(img + '[0]', '_psf.mag', '_psf.pst', img + '.psf', '_psf.psto', '_psf.psg', interac=interactive,
verify=False, verbose=False)
iraf.group(img + '[0]', '_psf.mag', img + '.psf', '_psf.grp', verify=False, verbose=False)
iraf.nstar(img + '[0]', '_psf.grp', img + '.psf', '_psf.nst', '_psf.nrj', verify=False, verbose=False)
photmag = iraf.txdump("_psf.mag", 'xcenter,ycenter,id,mag,merr', expr='yes', Stdout=1)
pst = iraf.txdump("_psf.pst", 'xcenter,ycenter,id', expr='yes', Stdout=1)
fitmag = iraf.txdump("_psf.nst", 'xcenter,ycenter,id,mag,merr', expr='yes', Stdout=1)
return photmag, pst, fitmag
def psfphot(image,
clobber=globclob,
verbose=globver,
pixtol=3.0,
maxnpsf=5,
interact=yes):
""" perform PSF-based photometry on a single target star (SN?) at RA, Dec and
also on a set of comparison stars, using daophot. simultaneously
perform aperture photometry on all the comparison stars (after
subtracting off contributions from neighbors) to enable absolute
photometry by comparison to aperture photometry of standard stars
observed in other fields """
# Defaults / constants
psfmult = 5.0 #standard factor (multiplied by fwhm to get psfradius)
psfmultsmall = 3.0 #similar to psfmult, adjusted for nstar and substar
# Necessary package
iraf.imutil()
# Detect stars
iqpkg.iqobjs(image, 3.0, 50000.0, wtimage="", skyval="!MEDSKY")
root = image[:-5]
[gain, rnoise, fwhm] = get_head(image, ["GAIN", "READNOI", "SEEPIX"])
fwhm = float(fwhm)
rnoise = float(rnoise)
iraf.iterstat(image)
# Saturation level
if not check_head(image, "SATURATE"):
saturate = 60000.0
else:
saturate = get_head(image, "SATURATE")
# Update datapars and daopars
iraf.datapars.fwhmpsf = fwhm
iraf.datapars.sigma = iraf.iterstat.sigma
iraf.datapars.datamin = iraf.iterstat.median - 10 * iraf.iterstat.sigma
iraf.datapars.datamax = 70000.0
iraf.datapars.readnoise = rnoise
iraf.datapars.epadu = gain
iraf.daopars.psfrad = psfmult * fwhm
iraf.daopars.fitrad = fwhm
iraf.daopars.function = "gauss,moffat15,moffat25,lorentz,penny1"
# coo file
stars = Starlist("%s.stars" % image)
outf = open("%s.coo.1" % image[:-5], "w")
for star in stars:
outf.write("%10.3f%10.3f\n" % (star.xval, star.yval))
outf.close()
#initial photometry
iraf.daophot.phot(root,
'default',
'default',
aperture=fwhm,
verify=no,
verbose=verbose)
iraf.datapars.datamax = 30000.0
iraf.pstselect(root,
'default',
'default',
maxnpsf,
interactive=yes,
verify=no,
verbose=verbose)
iraf.psf(root,
'default',
'default',
'default',
'default',
'default',
interactive=interact,
verify=no,
verbose=verbose)
iraf.allstar(root,
'default',
'default',
'default',
'default',
'default',
verify=no,
verbose=verbose)
iraf.iterstat("%s.sub.fits" % root)
iraf.datapars.sigma = iraf.iterstat.sigma
iraf.datapars.datamin = iraf.iterstat.median - 10 * iraf.iterstat.sigma
iraf.datapars.datamax = 70000.0
iraf.daophot.phot("%s.sub.fits" % root,
"SN.coo",
'default',
'default',
aperture=fwhm,
verify=no,
verbose=verbose)
iraf.datapars.datamax = 30000.0
iraf.daopars.fitrad = fwhm * 2.0
iraf.allstar("%s.sub.fits" % root,
'default',
"%s.psf.1.fits" % root,
'default',
'default',
'default',
verify=no,
verbose=no)
def psfphot(inlist,
ra,
dec,
reffilt,
interact,
fwhm,
readnoise,
gain,
threshold,
refimage=None,
starfile=None,
maxnpsf=5,
clobber=globclob,
verbose=globver,
skykey='SKYBKG',
filtkey='FILTER',
pixtol=3.0):
""" perform PSF-based photometry on a single target star (SN?) at RA, Dec and
also on a set of comparison stars, using daophot. simultaneously
perform aperture photometry on all the comparison stars (after
subtracting off contributions from neighbors) to enable absolute
photometry by comparison to aperture photometry of standard stars
observed in other fields """
# Defaults / constants
psfmult = 5.0 #standard factor (multiplied by fwhm to get psfradius)
psfmultsmall = 3.0 #similar to psfmult, adjusted for nstar and substar
# Necessary package
iraf.imutil()
# Parse inputs
infiles = iraffiles(inlist)
# Which file is reffilt? call it refimage
if refimage == None:
for image in infiles:
if check_head(image, filtkey):
try:
imgfilt = get_head(image, filtkey)
if imgfilt == reffilt:
refimage = image
break
except:
pass
if not refimage:
print "BAD USER! No image corresponds to the filter: %s" % reffilt
return
else:
refroot = 's' + refimage.split('.')[0]
#first make sure to add back in background of sky
iraf.iqsubsky(inlist, sub=no, skykey=skykey)
#put reference image first on list
infiles.remove(refimage)
infiles.insert(0, refimage)
#setup for keywords
if gain == "!GAIN":
try:
gainval = float(get_head(image, gain))
except:
print "Bad header keyword for gain."
else:
gainval = float(gain)
if readnoise == "!READNOISE":
try:
readval = float(get_head(image, readnoise))
except:
print "Bad header keyword for readnoise."
else:
readval = float(readnoise)
# Process each file in turn
for image in infiles:
# Check that the image is there
check_exist(image, "r")
# Grab image root name
root = image.split('.')[0]
# Map image to reference image
if not (image == refimage):
[nx, ny] = get_head(image, ['NAXIS1', 'NAXIS2'])
stars = Starlist(get_head(image, 'STARFILE'))
refstars = Starlist(get_head(refimage, 'STARFILE'))
refstars.pix2wcs(refimage)
refstars.wcs2pix(image)
match, refmatch = stars.match(refstars, useflags=yes, tol=10.0)
nstars = len(match)
if not (nstars > 2):
print 'Could not find star matches between reference and %s' % image
infiles.remove(image)
continue
refmatch.pix2wcs(image)
refmatch.wcs2pix(refimage)
matchfile = open('%s.match' % root, 'w')
for i in range(len(match)):
matchfile.write('%10.3f%10.3f%10.3f%10.3f\n' %
(refmatch[i].xval, refmatch[i].yval,
match[i].xval, match[i].yval))
matchfile.close()
check_exist('%s.geodb' % root, 'w', clobber=clobber)
iraf.geomap('%s.match' % root,
'%s.geodb' % root,
1.0,
nx,
1.0,
ny,
verbose=no,
interactive=no)
check_exist('s%s.fits' % root, 'w', clobber=clobber)
iraf.geotran(image,
's%s' % root,
'%s.geodb' % root,
'%s.match' % root,
geometry="geometric",
boundary="constant",
verbose=no)
else:
iraf.imcopy(image, 's%s' % root)
root = 's%s' % root
#get sky level and calculate sigma
#if check_head(image, skykey):
# try:
# sky=float(get_head(image, skykey))
# except:
# print "No sky levels in header."
#sigma= (((sky * gainval) + readval**2)**.5) / gainval
iraf.iterstat(image)
# Saturation level
if not check_head(image, "SATURATE"):
saturate = 60000.0
else:
saturate = get_head(image, "SATURATE")
# Update datapars and daopars
iraf.datapars.fwhmpsf = fwhm
iraf.datapars.sigma = iraf.iterstat.sigma
iraf.datapars.datamin = iraf.iterstat.median - 10 * iraf.iterstat.sigma
iraf.datapars.datamax = 0.90 * saturate
iraf.datapars.readnoise = readval
iraf.datapars.epadu = gainval
iraf.datapars.filter = filtkey
iraf.daopars.psfrad = psfmult * fwhm
iraf.daopars.fitrad = fwhm
iraf.daopars.function = "gauss,moffat15,moffat25,lorentz,penny1"
#find stars in image unless a starlist is given
if image == refimage and starfile == None:
iraf.daophot.daofind(root,
'refimage.coo.1',
threshold=threshold,
verify=no,
verbose=verbose)
elif image == refimage:
shutil.copy(starfile, 'refimage.coo.1')
#initial photometry
iraf.daophot.phot(root,
'refimage.coo.1',
'default',
aperture=fwhm,
verify=no,
verbose=verbose)
#select stars for psf the first time
refstarsfile = "refimage.pst.1"
if image == refimage:
iraf.pstselect(root,
'default',
refstarsfile,
maxnpsf,
interactive=yes,
verify=no,
verbose=verbose)
#fit the psf
iraf.psf(root,
'default',
refstarsfile,
'default',
'default',
'default',
interactive=interact,
verify=no,
verbose=verbose)
#identify neighboring/interfering stars to selected stars
groupingfile = root + ".psg.1"
iraf.nstar(root,
groupingfile,
'default',
'default',
'default',
psfrad=psfmultsmall * fwhm,
verify=no,
verbose=verbose)
#subtract out neighboring stars from image
iraf.substar(root,
'default',
refstarsfile,
'default',
'default',
psfrad=psfmultsmall * fwhm,
verify=no,
verbose=verbose)
#repeat psf to get better psf model
#IRAF's interactive version usually crashes
subtractedimage = root + ".sub.1"
iraf.psf(subtractedimage,
root + ".nst.1",
refstarsfile,
'%s.psf.2' % root,
'%s.pst.2' % root,
'%s.psg.2' % root,
interactive=interact,
verify=no,
verbose=verbose)
#Need to make sure SN was detected by daofind
stars = Starlist('%s.mag.1' % root)
SN = Star(name='SN', radeg=ra, dcdeg=dec, fwhm=2.0, fwhmw=2.0)
SNlis = Starlist(stars=[SN])
SNlis.wcs2pix(image)
if (len(stars.match(SNlis)[0]) == 0):
#No match - need to add to daofind file
print "No match!"
coofile = open('refimage.coo.1', 'a+')
coofile.write('%10.3f%10.3f%9.3f%8.3f%13.3f%12.3f%8i\n' %
(SNlis[0].xval, SNlis[0].yval, 99.999, 0.500, 0.000,
0.000, 999))
coofile.close()
#repeat aperture photometry to get good comparisons to standard fields
iraf.daophot.phot(root,
'refimage.coo.1',
'default',
aperture=psfmult * fwhm,
verify=no,
verbose=verbose)
# allstar run
iraf.allstar(root,
'default',
'default',
'default',
'default',
'default',
verify=no,
verbose=verbose)
def build(f):
### is this an MEF file
current_ext = 0
NEXTEND = 0
EXTEND = f[0].header['EXTEND']
if (EXTEND == "T"):
NEXTEND = f[0].header['NEXTEND']
current_ext = 1
### create the name of the output MEF psf file
if not f[0].header.has_key('FILENAME'):
os.unlink(opt.filename)
sys.exit('The fits file ' + opt.filename + ' has no EXPNUM keyword\n')
sexp = f[0].header['FILENAME']
mef_psf = sexp + "p_psf_iraf.fits"
### create an MEF file that will contian the PSF(s)
import pyfits
fitsobj = pyfits.HDUList()
prihdu = pyfits.PrimaryHDU()
import re
prihdu.header.update('FILENAME', sexp, comment='CFHT Exposure Numebr')
prihdu.header.update('NEXTEND', NEXTEND, comment='number of extensions')
version = re.match(r'\$Rev.*: (\d*.\d*) \$', __Version__).group(1)
prihdu.header.update('MKPSF_V',
float(version),
comment="Version number of mkpsf")
fitsobj.append(prihdu)
if os.access(mef_psf, os.F_OK):
os.unlink(mef_psf)
fitsobj.writeto(mef_psf)
fitsobj.close()
outfits = pyfits.open(mef_psf, "append")
prihdr = outfits[0].header
import jjkmode
### Get my python routines
from pyraf import iraf
from pyraf.irafpar import IrafParList
### keep all the parameters locally cached.
iraf.set(uparm="./")
### Load the required IRAF packages
iraf.digiphot()
iraf.apphot()
iraf.daophot()
### temp file name hash.
tfile = {}
while (current_ext <= NEXTEND):
### this is a psf SCRIPT so the showplots and interactive are off by force
print "Working on image section " + str(current_ext)
iraf.findpars.sharplo = 0
iraf.findpars.sharphi = 0.7
iraf.findpars.roundlo = -0.7
iraf.findpars.roundhi = 0.7
iraf.datapars.datamax = 20000
iraf.datapars.airmass = 'AIRMASS'
iraf.datapars.filter = 'FILTER'
iraf.datapars.obstime = 'TIME-OBS'
iraf.datapars.exposure = 'EXPTIME'
iraf.datapars.gain = 'GAIN'
iraf.datapars.ccdread = 'RDNOISE'
iraf.datapars.fwhmpsf = opt.fwhm
iraf.daopars.nclean = 2
iraf.daopars.psfrad = 5.0 * opt.fwhm
iraf.daopars.fitrad = 0.85 * opt.fwhm
iraf.daopars.function = "gauss"
iraf.centerpars.calgorithm = 'centroid'
zero_mag = 26.19
iraf.photpars.zmag = zero_mag
iraf.photpars.apertures = int(0.85 * opt.fwhm)
iraf.fitskypars.annulus = 2 + int(opt.fwhm * 4.00)
iraf.fitskypars.dannulus = int(opt.fwhm * 2.0)
iraf.daophot.verbose = no
iraf.daophot.verify = no
iraf.daophot.update = no
iraf.psf.interactive = no
iraf.pstselect.interactive = no
iraf.datapars.saveParList()
iraf.fitskypars.saveParList()
iraf.centerpars.saveParList()
iraf.findpars.saveParList()
iraf.photpars.saveParList()
tfiles = [
'coo_bright', 'coo_ok', 'coo_faint', 'mag_all', 'mag_bright',
'mag_ok', 'mag_good', 'mag_best', 'pst_in', 'pst_out', 'pst_out2',
'prf', 'psg_org', 'psg', 'psf_1.fits', 'psf_2.fits',
'psf_final.fits', 'psf_3.fits', 'psf_4.fits', 'mag_pst', 'coo_pst',
'nst', 'nrj', 'seepsf.fits', 'sub.fits', 'fwhm', 'apcor'
]
for file in tfiles:
extname = "chip" + str(f[current_ext].header.get(
'IMAGEID', str(current_ext))).zfill(2)
tfile[file] = sexp + "_" + extname + "." + file
if (os.access(tfile[file], os.F_OK)):
os.unlink(tfile[file])
if (EXTEND == "T"):
this_image = opt.filename + "[" + extname + "]"
else:
this_image = opt.filename
gain = f[current_ext].header.get('GAIN', 1.0)
#### set sky/sigma parameters specific to this frame.
(skyvalue, sigma) = jjkmode.stats(f[current_ext].data)
import math
sigma = math.sqrt(skyvalue / gain)
datamin = float(skyvalue) - 8.0 * float(sigma)
print "Determined sky level to be " + str(skyvalue) + " +/-" + str(
sigma)
iraf.datapars.datamin = datamin
iraf.datapars.sigma = float(sigma)
iraf.datapars.saveParList()
iraf.fitskypars.skyvalue = skyvalue
iraf.fitskypars.saveParList()
### find the bright stars in the image.
print "sextracting for stars in " + this_image
###iraf.daophot.daofind(image=this_image,
### output=tfile['coo_bright'],threshold=4.0)
os.system(
"sex -c /home/cadc/kavelaar/12kproc/config/default.sex -SATUR_LEVEL 25000 -CATALOG_NAME "
+ tfile['coo_bright'] + " " + this_image)
### print "finding stellar locus in sround/ground space"
print "clipping using star_class > 0.85 "
fcoo = open(tfile['coo_bright'], 'r')
lines = fcoo.readlines()
fcoo.close()
import numarray, math
fout = open(tfile['coo_ok'], 'w')
for line in lines:
if re.match(r'^#', line) or re.search(r'INDEF', line):
continue
values = line.split()
star_class = float(values[2])
if star_class > 0.75:
fout.write(line)
fout.close()
print "Measuring photometry for psf candidate stars in " + tfile[
'coo_ok']
iraf.daophot.phot(image=this_image,
coords=tfile['coo_ok'],
output=tfile['mag_bright'])
### do this selection in 2 steps because of the way IRAF handles INDEFs
print "Selecting stars that have good centroids and magnitudes "
iraf.pselect(
tfile['mag_bright'], tfile['mag_ok'],
"(CIER==0)&&(PIER==0)&&(SIER==0)&&(MSKY>0)&&(MSKY<2e5)&&(MSKY!=INDEF)"
)
print "Selecting stars that have normal sky levels"
condition = "(abs(MSKY -" + str(skyvalue) + ") < 5.0*" + str(
sigma) + ")"
iraf.pselect(tfile['mag_ok'], tfile['mag_good'], condition)
a = iraf.txdump(tfile['mag_good'], "SSKEW", iraf.yes, Stdout=1)
aa = []
for v in a:
aa.append(float(v))
a = numarray.array(aa)
mean = a.mean()
aa = a * a
stddev = math.sqrt(aa.sum() / len(aa) - mean**2)
limit = mean + 2 * stddev
os.unlink(tfile['mag_good'])
condition = condition + " && SSKEW < " + str(limit)
iraf.pselect(tfile['mag_ok'], tfile['mag_good'], condition)
print "Choosing the psf stars"
iraf.pstselect(image=this_image,
photfile=tfile['mag_good'],
pstfile=tfile['pst_in'],
maxnpsf=25)
## construct an initial PSF image
print "computing psf with neighbor stars based on complete star list"
iraf.psf.mode = 'a'
iraf.psf(image=this_image,
photfile=tfile['mag_bright'],
pstfile=tfile['pst_in'],
psfimage=tfile['psf_1.fits'],
opstfile=tfile['pst_out'],
groupfile=tfile['psg_org'],
varorder=0)
try:
print "subtracting the psf neighbors and placing the results in " + tfile[
'sub.fits']
iraf.daophot.nstar(image=this_image,
groupfile=tfile['psg_org'],
psfimage=tfile['psf_1.fits'],
nstarfile=tfile['nst'],
rejfile=tfile['nrj'])
iraf.daophot.substar(image=this_image,
photfile=tfile['nst'],
exfile=tfile['pst_in'],
psfimage=tfile['psf_1.fits'],
subimage=tfile['sub.fits'])
a = iraf.daophot.txdump(tfile['nst'], 'chi', 'yes', Stdout=1)
aa = []
for v in a:
aa.append(float(v))
a = numarray.array(aa)
mean = a.mean()
aa = a * a
stddev = math.sqrt(aa.sum() / len(aa) - mean**2)
limit = mean + 2.5 * stddev
print "Selecting those psf stars with CHI^2 <" + str(
limit) + " after fitting with trial psf"
iraf.pselect(tfile['nst'], tfile['mag_best'],
"CHI < " + str(limit))
os.unlink(tfile['pst_out'])
## os.unlink(tfile['psg'])
## rebuild the PSF file with the psf stars that fit well..
## using the neighbor subtracted image
print "Rebuilding the PSF"
iraf.daophot.psf(image=tfile['sub.fits'],
photfile=tfile['mag_best'],
pstfile=tfile['pst_in'],
psfimage=tfile['psf_2.fits'],
opstfile=tfile['pst_out'],
groupfile=tfile['psg'],
varorder=0)
print "re-subtracting with rebuilt psf"
os.unlink(tfile['nst'])
os.unlink(tfile['nrj'])
iraf.daophot.nstar(image=this_image,
groupfile=tfile['psg'],
psfimage=tfile['psf_2.fits'],
nstarfile=tfile['nst'],
rejfile=tfile['nrj'])
os.unlink(tfile['sub.fits'])
iraf.daophot.substar(image=this_image,
photfile=tfile['nst'],
exfile=tfile['pst_in'],
psfimage=tfile['psf_2.fits'],
subimage=tfile['sub.fits'])
os.unlink(tfile['psg'])
os.unlink(tfile['pst_out'])
iraf.daophot.psf(image=tfile['sub.fits'],
photfile=tfile['mag_best'],
pstfile=tfile['pst_in'],
psfimage=tfile['psf_3.fits'],
opstfile=tfile['pst_out'],
groupfile=tfile['psg'],
varorder=0)
os.unlink(tfile['nrj'])
os.unlink(tfile['nst'])
iraf.daophot.nstar(image=this_image,
groupfile=tfile['psg'],
psfimage=tfile['psf_3.fits'],
nstarfile=tfile['nst'],
rejfile=tfile['nrj'])
a = iraf.daophot.txdump(tfile['nst'], 'chi', 'yes', Stdout=1)
aa = []
for v in a:
aa.append(float(v))
a = numarray.array(aa)
mean = a.mean()
aa = a * a
stddev = math.sqrt(aa.sum() / len(aa) - mean**2)
limit = mean + 2 * stddev
limit = 2.0
#print "Selecting those psf stars with CHI^2 < "+str(limit)+" after fit with GOOD psf"
os.unlink(tfile['mag_best'])
iraf.pselect(tfile['nst'], tfile['mag_best'],
"CHI < " + str(limit))
print "Building final PSF.... "
os.unlink(tfile['sub.fits'])
iraf.daophot.substar(image=this_image,
photfile=tfile['nst'],
exfile=tfile['pst_in'],
psfimage=tfile['psf_3.fits'],
subimage=tfile['sub.fits'])
os.unlink(tfile['psg'])
os.unlink(tfile['pst_out'])
iraf.daophot.psf(image=tfile['sub.fits'],
photfile=tfile['mag_best'],
pstfile=tfile['pst_in'],
psfimage=tfile['psf_final.fits'],
opstfile=tfile['pst_out'],
groupfile=tfile['psg'],
varorder=0)
print "building an analytic psf for the FWHM calculations"
os.unlink(tfile['pst_out'])
os.unlink(tfile['psg'])
iraf.daophot.psf(image=tfile['sub.fits'],
photfile=tfile['mag_best'],
pstfile=tfile['pst_in'],
psfimage=tfile['psf_4.fits'],
opstfile=tfile['pst_out'],
groupfile=tfile['psg'],
varorder=-1)
except:
print sys.exc_info()[1]
print "ERROR: Reverting to first pass psf"
tfile['psf_final.fits'] = tfile['psf_1.fits']
iraf.daophot.psf(image=this_image,
photfile=tfile['mag_best'],
pstfile=tfile['pst_in'],
psfimage=tfile['psf_4.fits'],
opstfile=tfile['pst_out2'],
groupfile=tfile['psg'],
varorder=-1)
psf_ap = iraf.photpars.apertures
ap1 = int(psf_ap)
ap2 = int(4.0 * opt.fwhm)
apcor = "INDEF"
aperr = "INDEF"
if (0):
#try
### now that we have the psf use the output list of psf stars
### to compute the aperature correction
lines = iraf.txdump(tfile['pst_out'],
'xcen,ycen,mag,id',
iraf.yes,
Stdout=tfile['coo_pst'])
## set the lower ap value for the COG (normally set to 2)
if (ap1 < 3):
smallap = 1
else:
smallap = 2 - ap1 + 1
ap1 = 2
ap2 = int(math.floor(4.0 * opt.fwhm))
naperts = ap2 - ap1 + 1
iraf.photpars.apertures = str(ap1) + ":" + str(ap2) + ":1"
iraf.photpars.saveParList()
iraf.daophot.phot(image=this_image,
coords=tfile['coo_pst'],
output=tfile['mag_pst'])
iraf.photcal()
iraf.photcal.mkapfile(tfile['mag_pst'],
naperts=naperts,
apercors=tfile['apcor'],
smallap=smallap,
verify='no',
gcommands='',
interactive=0)
fin = open(tfile['apcor'], 'r')
lines = fin.readlines()
values = lines[2].split()
apcor = values[1]
aperr = values[2]
#except:
## compute the FWHM of the PSF image using the analytic PSF (VarOrd=-1)
psf_file = pyfits.open(tfile['psf_4.fits'])
fwhm = (psf_file[0].header.get('PAR1', 99.0) +
psf_file[0].header.get('PAR2', 99.0))
psf_file.close()
# ## Open the psf.fits
infits = pyfits.open(tfile['psf_final.fits'])
hdu = infits[0]
inhdu = hdu.header
inhdu.update('XTENSION', 'IMAGE', before='SIMPLE')
inhdu.update('PCOUNT', 0, after='NAXIS2')
inhdu.update('GCOUNT', 1, after='PCOUNT')
del hdu.header['SIMPLE']
del hdu.header['EXTEND']
inhdu.update("EXTNAME", extname, comment="image extension identifier")
#inhdu.update("SLOW",slow,comment="SROUND low cutoff")
#inhdu.update("SIGH",sigh,comment="SROUND high cutoff")
inhdu.update("PFWHM",
fwhm,
comment="FWHM of stars based on PSF fitting")
inhdu.update("ZMAG", zero_mag, comment="ZMAG of PSF ")
inhdu.update("BCKG", skyvalue, comment="Mean sky level in counts")
inhdu.update("BCKG_STD",
sigma,
comment="standard deviation of sky in counts")
inhdu.update("AP1", psf_ap, comment="Apperture used for PSF flux")
inhdu.update("AP2", ap2, comment="Full Flux aperture")
inhdu.update("APCOR", apcor, comment="Apperture correction (ap1->ap2)")
inhdu.update("APERR", apcor, comment="Uncertainty in APCOR")
# ### append this psf to the output images....
print "Sticking this PSF onto the output file"
f[current_ext].header.update(
"PFWHM", fwhm, comment="FWHM of stars based on PSF fitting")
f[current_ext].header.update("BCKG",
skyvalue,
comment="Mean sky level in counts")
f[current_ext].header.update(
"BCKG_STD", sigma, comment="Standard deviation of sky in counts")
f.flush()
outfits.append(hdu)
outfits.flush()
infits.close()
### remove the temp file we used for this computation.
for tf in tfile.keys():
if os.access(tfile[tf], os.F_OK):
os.unlink(tfile[tf])
current_ext = current_ext + 1
outfits.close()
return mef_psf
def doaphot_psf_photometry(path, imageFile, extent, extension):
data, image, hdulist, size, mid_point = load_image_data(
imageFile, extent, extension=extension)
# garbage collect data and image
data = None
image = None
# import IRAF packages
iraf.digiphot(_doprint=0)
iraf.daophot(_doprint=0)
# dao_params.txt must be created manually using daoedit in iraf/pyraf for 5 stars
dao_params = extract_dao_params(
imageFile.strip(".fits") + "_dao_params.txt")
sky = dao_params[0]
sky_sigma = dao_params[1]
fwhm = dao_params[2]
datamin = dao_params[3]
aperature_radius = dao_params[4]
annulus_inner_radius = dao_params[5]
annulus_outer_radius = dao_params[6]
# get datapars
datapars = extract_header_info(hdulist)
datamax = datapars[0]
ccdread = datapars[1]
gain = datapars[2]
readnoise = datapars[3]
epadu = datapars[4]
exposure = datapars[5]
airmass = datapars[6]
filter = datapars[7]
obstime = datapars[8]
itime = datapars[9]
xairmass = datapars[10]
ifilter = datapars[11]
otime = datapars[12]
# set datapars
iraf.datapars.unlearn()
iraf.datapars.setParam('fwhmpsf', fwhm)
iraf.datapars.setParam('sigma', sky_sigma)
iraf.datapars.setParam('datamin', datamin)
iraf.datapars.setParam('datamax', datamax)
iraf.datapars.setParam('ccdread', ccdread)
iraf.datapars.setParam('gain', gain)
iraf.datapars.setParam('readnoise', readnoise)
iraf.datapars.setParam('epadu', epadu)
iraf.datapars.setParam('exposure', exposure)
iraf.datapars.setParam('airmass', airmass)
iraf.datapars.setParam('filter', filter)
iraf.datapars.setParam('obstime', obstime)
iraf.datapars.setParam('itime', itime)
iraf.datapars.setParam('xairmass', xairmass)
iraf.datapars.setParam('ifilter', ifilter)
iraf.datapars.setParam('otime', otime)
# set photpars
iraf.photpars.unlearn()
iraf.photpars.setParam('apertures', aperature_radius)
zp_estimate = iraf.photpars.getParam('zmag')
# set centerpars
iraf.centerpars.unlearn()
iraf.centerpars.setParam('calgorithm', 'centroid')
iraf.centerpars.setParam('cbox', 5.)
# set fitskypars
iraf.fitskypars.unlearn()
iraf.fitskypars.setParam('annulus', annulus_inner_radius)
iraf.fitskypars.setParam('dannulus', annulus_outer_radius)
# run phot
run_phot(imageFile, imageFile + ".quality.coo")
# set daopars
iraf.daopars.unlearn()
iraf.daopars.setParam('function', 'auto')
iraf.daopars.setParam('psfrad', 2 * int(fwhm) + 1)
iraf.daopars.setParam('fitrad', fwhm)
# select a psf/prf star
# taking whatever the default selection is, can't see a way to pass coords of desired
# stars, if could would use those in dao_params.txt
# An alternative is to reorder the objects so those in dao_params.txt are at top of
# sources table, assuming those are the defaults selected here.
iraf.pstselect.unlearn()
iraf.pstselect.setParam('maxnpsf', 5)
iraf.pstselect(image=imageFile,
photfile=imageFile + ".mags.1",
pstfile=imageFile + ".pst.1",
interactive='no')
# fit the psf
iraf.psf.unlearn()
iraf.psf(image=imageFile, \
photfile=imageFile+".mags.1",\
pstfile=imageFile+".pst.1",\
psfimage=imageFile+".psf.1.fits",\
opstfile=imageFile+".pst.2",\
groupfile=imageFile+".psg.1",\
interactive='no')
# check the psf
# perhaps pass it through ML and visualise
# save visualisation for later manual checks
iraf.seepsf.unlearn()
iraf.seepsf(psfimage=imageFile + ".psf.1.fits",
image=imageFile + ".psf.1s.fits")
hdulist_psf = fits.open(imageFile + ".psf.1s.fits")
#print "[*] plotting PSF for visual check."
#plt.imshow(hdulist_psf[0].data, interpolation="nearest",cmap="hot")
#plt.axis("off")
#plt.show()
# perform photometry
run_allstar(imageFile, imageFile + ".psf.1.fits")
return zp_estimate, imageFile + ".psf.1.fits"
def doaphot_psf_photometry(path, imageFile, extent, extension):
data, image, hdulist, size, mid_point = load_image_data(imageFile, extent, extension=extension)
# garbage collect data and image
data = None
image = None
# import IRAF packages
iraf.digiphot(_doprint=0)
iraf.daophot(_doprint=0)
# dao_params.txt must be created manually using daoedit in iraf/pyraf for 5 stars
dao_params = extract_dao_params(imageFile.strip(".fits")+"_dao_params.txt")
sky = dao_params[0]
sky_sigma = dao_params[1]
fwhm = dao_params[2]
datamin = dao_params[3]
aperature_radius = dao_params[4]
annulus_inner_radius = dao_params[5]
annulus_outer_radius = dao_params[6]
# get datapars
datapars = extract_header_info(hdulist)
datamax = datapars[0]
ccdread = datapars[1]
gain = datapars[2]
readnoise = datapars[3]
epadu = datapars[4]
exposure = datapars[5]
airmass = datapars[6]
filter = datapars[7]
obstime = datapars[8]
itime = datapars[9]
xairmass = datapars[10]
ifilter = datapars[11]
otime = datapars[12]
# set datapars
iraf.datapars.unlearn()
iraf.datapars.setParam('fwhmpsf',fwhm)
iraf.datapars.setParam('sigma',sky_sigma)
iraf.datapars.setParam('datamin',datamin)
iraf.datapars.setParam('datamax',datamax)
iraf.datapars.setParam('ccdread',ccdread)
iraf.datapars.setParam('gain',gain)
iraf.datapars.setParam('readnoise',readnoise)
iraf.datapars.setParam('epadu',epadu)
iraf.datapars.setParam('exposure',exposure)
iraf.datapars.setParam('airmass',airmass)
iraf.datapars.setParam('filter',filter)
iraf.datapars.setParam('obstime',obstime)
iraf.datapars.setParam('itime',itime)
iraf.datapars.setParam('xairmass',xairmass)
iraf.datapars.setParam('ifilter',ifilter)
iraf.datapars.setParam('otime',otime)
# set photpars
iraf.photpars.unlearn()
iraf.photpars.setParam('apertures',aperature_radius)
zp_estimate = iraf.photpars.getParam('zmag')
# set centerpars
iraf.centerpars.unlearn()
iraf.centerpars.setParam('calgorithm','centroid')
iraf.centerpars.setParam('cbox',5.)
# set fitskypars
iraf.fitskypars.unlearn()
iraf.fitskypars.setParam('annulus',annulus_inner_radius)
iraf.fitskypars.setParam('dannulus',annulus_outer_radius)
# run phot
run_phot(imageFile, imageFile+".quality.coo")
# set daopars
iraf.daopars.unlearn()
iraf.daopars.setParam('function','auto')
iraf.daopars.setParam('psfrad', 2*int(fwhm)+1)
iraf.daopars.setParam('fitrad', fwhm)
# select a psf/prf star
# taking whatever the default selection is, can't see a way to pass coords of desired
# stars, if could would use those in dao_params.txt
# An alternative is to reorder the objects so those in dao_params.txt are at top of
# sources table, assuming those are the defaults selected here.
iraf.pstselect.unlearn()
iraf.pstselect.setParam('maxnpsf',5)
iraf.pstselect(image=imageFile,photfile=imageFile+".mags.1",pstfile=imageFile+".pst.1",interactive='no')
# fit the psf
iraf.psf.unlearn()
iraf.psf(image=imageFile, \
photfile=imageFile+".mags.1",\
pstfile=imageFile+".pst.1",\
psfimage=imageFile+".psf.1.fits",\
opstfile=imageFile+".pst.2",\
groupfile=imageFile+".psg.1",\
interactive='no')
# check the psf
# perhaps pass it through ML and visualise
# save visualisation for later manual checks
iraf.seepsf.unlearn()
iraf.seepsf(psfimage=imageFile+".psf.1.fits", image=imageFile+".psf.1s.fits")
hdulist_psf = fits.open(imageFile+".psf.1s.fits")
#print "[*] plotting PSF for visual check."
#plt.imshow(hdulist_psf[0].data, interpolation="nearest",cmap="hot")
#plt.axis("off")
#plt.show()
# perform photometry
run_allstar(imageFile,imageFile+".psf.1.fits")
return zp_estimate, imageFile+".psf.1.fits"
continue
pst1.add_row(
(mag1['ID'][ind[0]], mag1['XINIT'][ind[0]], mag1['YINIT'][ind[0]],
mag1['MAG'][ind[0]], mag1['MSKY'][ind[0]]))
pst1.write(fn[:-5] + '.pst.0',
format='ascii.commented_header',
delimiter='\t',
comment='#N ID XCENTER YCENTER \
MAG MSKY\n#U ## pixels pixels magnitudes counts\n#F %-9d %-10.3f %-10.3f %-12.3f %-15.7g\n#'
)
original = sys.stdout
try:
sys.stdout = open(fn[:-5] + '.psf1.out', 'w')
iraf.psf(fn[:-5],photfile=fn[:-5]+'.mag.1',pstfile=fn[:-5]+'.pst.0',psfimage=fn[:-5]+'.psf.1',opstfile=fn[:-5]+'.pst.1', \
groupfile=fn[:-5]+'.psg.1',verify='no',interactive='no',plotfile=fn[:-5]+'.psf1.plots')
iraf.allstar(fn[:-5],photfile=fn[:-5]+'.psg.1',psfimage=fn[:-5]+'.psf.1',allstarfile=fn[:-5]+'.als.1',rejfile=fn[:-5]+ \
'.arj.1',subimage=fn[:-5]+'.sub.1',verify='no',verbos='no')
iraf.substar(fn[:-5],photfile=fn[:-5]+'.als.1',exfile=fn[:-5]+'.pst.1',psfimage=fn[:-5]+'.psf.1',subimage=fn[:-5]+ \
'.sub.11',verify='no',verbose='no')
sys.stdout = open(fn[:-5] + '.psf2.out', 'w')
iraf.psf(fn[:-5]+'.sub.11',photfile=fn[:-5]+'.mag.1',pstfile=fn[:-5]+'.pst.1',psfimage=fn[:-5]+'.psf.2', \
opstfile=fn[:-5]+'.pst.2', groupfile=fn[:-5]+'.psg.2',verify='no',interactive='no')
iraf.allstar(fn[:-5],photfile=fn[:-5]+'.psg.2',psfimage=fn[:-5]+'.psf.2',allstarfile=fn[:-5]+'.als.2',rejfile=fn[:-5]+ \
'.arj.2',subimage=fn[:-5]+'.sub.2',verify='no',verbos='no')
iraf.substar(fn[:-5],photfile=fn[:-5]+'.als.2',exfile=fn[:-5]+'.pst.2',psfimage=fn[:-5]+'.psf.2',subimage=fn[:-5]+ \
'.sub.22',verify='no',verbose='no')
sys.stdout = open(fn[:-5] + '.psf3.out', 'w')
iraf.psf(fn[:-5]+'.sub.22',photfile=fn[:-5]+'.mag.1',pstfile=fn[:-5]+'.pst.2',psfimage=fn[:-5]+'.psf.3',opstfile \
star_id = prts[0]
xpos = prts[1]
ypos = prts[2]
#print star_id, xpos, ypos
pstregfl.write('point(' + str(xpos) + ',' + str(ypos) +
') # point=cross text={' + star_id + '}\n')
pstregfl.close()
os.system("/usr/local/bin//ds9 " + flnm + '.sub.0.fits' +
" -regions " + flnm + ".pst.1.reg" + " &")
tfs = time.time()
iraf.psf(image=flnm + '.sub.0.fits',
photfile=flnm + '.sub.0.mag',
pstfile=flnm + '.pst.1',
psfimage=flnm + '.psf.fits',
opstfile=flnm + '.pst.2',
groupfile=flnm + '.grf.psg',
interactive="no",
showplots="no",
verify="no")
tfe = time.time()
times[runnm + '_psf'] = tfe - tfs
iraf.seepsf(psfimage=flnm + '.psf.fits',
image=flnm + '.image_of_psf.fits')
if i == 0:
shutil.copy(runnm + '.mag',
runnm + '.tot.mag') # formatting reasons only
else:
print "========================================="
print "...merging phot lists"
def compute_psf_image(params,g,psf_deg=1,psf_rad=8,
star_file='phot.mags',psf_image='psf.fits',edge_dist=5):
iraf.digiphot()
iraf.daophot()
fp = params.loc_output+os.path.sep
f_im = g.image*g.mask
f = fp+'temp.ref.fits'
write_image(f_im,f)
g.fw = np.max([1.5,g.fw])
g.fw = np.min([0.5*params.psf_max_radius,g.fw])
logfile = fp+'psf.log'
fd = fits.getdata(f)
xmax = fd.shape[0] - edge_dist
ymax = fd.shape[1] - edge_dist
for d in ['temp.stars','temp.phot','temp.phot1','temp.phot2','temp.pst',
'temp.opst','temp.opst2',
'temp.psf.fits','temp.psf1.fits','temp.psf2.fits','temp.psg',
'temp.psg2','temp.psg3','temp.psg5','temp.rej','temp.rej2',
'temp.sub.fits','temp.sub1.fits',
'temp.sub2.fits','temp.opst1','temp.opst3','temp.rej3',
'temp.nst','temp.stars1','ref.mags',psf_image,'temp.als',
'temp.als2']:
if os.path.exists(fp+d):
os.remove(fp+d)
# locate stars
iraf.daofind(image=f,output=fp+'temp.stars',interactive='no',verify='no',
threshold=3,sigma=params.star_detect_sigma,fwhmpsf=g.fw,
datamin=1,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,
noise='poisson')
if params.star_file:
als_recenter = 'no'
all_template_stars = np.genfromtxt(params.star_file)
all_new_stars = np.genfromtxt(fp+'temp.stars')
if all_new_stars.shape[0] > params.star_file_number_match:
new_stars = all_new_stars[all_new_stars[:,2].argsort()][:params.star_file_number_match]
else:
new_stars = all_new_stars
if all_template_stars.shape[0] > params.star_file_number_match:
template_stars = all_template_stars[all_template_stars[:,3].argsort()][:params.star_file_number_match]
else:
template_stars = all_template_stars
tx, ty = compute_xy_shift(new_stars,template_stars[:,1:3],0.5,
degree=params.star_file_transform_degree)
if params.star_file_has_magnitudes:
star_positions = all_template_stars[:,1:4]
xx = (star_positions[:,0]-np.mean(new_stars[:,0]))/np.mean(new_stars[:,0])
yy = (star_positions[:,1]-np.mean(new_stars[:,1]))/np.mean(new_stars[:,1])
for m in range(params.star_file_transform_degree+1):
for n in range(params.star_file_transform_degree+1-m):
star_positions[:,0] += tx[m,n]* xx**m * yy**n
star_positions[:,1] += ty[m,n]* xx**m * yy**n
np.savetxt(fp+'temp.stars.1',star_positions,fmt='%10.3f %10.3f %10.3f')
else:
star_positions = all_template_stars[:,1:3]
xx = (star_positions[:,0]-np.mean(new_stars[:,0]))/np.mean(new_stars[:,0])
yy = (star_positions[:,1]-np.mean(new_stars[:,1]))/np.mean(new_stars[:,1])
for m in range(params.star_file_transform_degree+1):
for n in range(params.star_file_transform_degree+1-m):
star_positions[:,0] += tx[m,n]* xx**m * yy**n
star_positions[:,1] += ty[m,n]* xx**m * yy**n
np.savetxt(fp+'temp.stars.1',star_positions,fmt='%10.3f %10.3f')
all_template_stars[:,1] = star_positions[:,0]
all_template_stars[:,2] = star_positions[:,1]
else:
als_recenter = 'yes'
star_positions = np.genfromtxt(fp+'temp.stars')
np.savetxt(fp+'temp.stars.1',star_positions[:,:2],fmt='%10.3f %10.3f')
iraf.phot(image=f,output=fp+'temp.phot',coords=fp+'temp.stars.1',interactive='no',
verify='no',
sigma=params.star_detect_sigma,fwhmpsf=g.fw,apertures=g.fw,
datamin=1,
datamax=2*params.pixel_max,epadu=params.gain,annulus=3*g.fw,
dannulus=3.0,
readnoise=params.readnoise,noise='poisson')
print 'fw = ',g.fw
#fw = np.max([4.0,fw])
#print 'fw = ',fw
# select PSF stars
iraf.pstselect(image=f,photfile=fp+'temp.phot',pstfile=fp+'temp.pst',maxnpsf=40,
interactive='no',verify='no',datamin=1,fitrad=2.0,
datamax=params.pixel_max,epadu=params.gain,psfrad=np.max([3.0,g.fw]),
readnoise=params.readnoise,noise='poisson')
if params.star_file and params.star_file_has_magnitudes:
# We don't need to do the photometry - only make the PSF
# Initial PSF estimate to generate PSF groups
#psfrad=3*np.max([g.fw,1.8])
iraf.psf(image=f,photfile=fp+'temp.phot',pstfile=fp+'temp.pst',psfimage=fp+'temp.psf',
function=params.psf_profile_type,opstfile=fp+'temp.opst',
groupfile=fp+'temp.psg',
interactive='no',
verify='no',varorder=0 ,psfrad=2*np.max([g.fw,1.8]),
datamin=-10000,datamax=0.95*params.pixel_max,
scale=1.0)
# construct a file of the psf neighbour stars
slist = []
psf_stars = np.loadtxt(fp+'temp.opst',usecols=(0,1,2))
for star in range(psf_stars.shape[0]):
xp = psf_stars[star,1]
yp = psf_stars[star,2]
xmin = np.max([np.int(xp-10*g.fw),0])
xmax = np.min([np.int(xp+10*g.fw),f_im.shape[0]])
ymin = np.max([np.int(yp-10*g.fw),0])
ymax = np.min([np.int(yp+10*g.fw),f_im.shape[1]])
p = star_positions[np.logical_and(np.logical_and(star_positions[:,0]>xmin,
star_positions[:,0]<xmax),
np.logical_and(star_positions[:,1]>ymin,
star_positions[:,1]<ymax))]
slist.append(p)
group_stars = np.concatenate(slist)
np.savetxt(fp+'temp.nst',group_stars,fmt='%10.3f %10.3f %10.3f')
# subtract PSF star neighbours
iraf.substar(image=f,photfile=fp+'temp.nst',psfimage=fp+'temp.psf',
exfile=fp+'temp.opst',fitrad=2.0,
subimage=fp+'temp.sub1',verify='no',datamin=1,
datamax=params.pixel_max,epadu=params.gain,
readnoise=params.readnoise,noise='poisson')
# final PSF
iraf.psf(image=fp+'temp.sub1',photfile=fp+'temp.phot',pstfile=fp+'temp.opst',
psfimage=psf_image,psfrad=2*g.fw,
function=params.psf_profile_type,opstfile=fp+'temp.opst2',
groupfile=fp+'temp.psg2',
interactive='no',
verify='no',varorder=0,
datamin=1,datamax=0.95*params.pixel_max,
scale=1.0)
np.savetxt(fp+'ref.mags',all_template_stars,fmt='%7d %10.3f %10.3f %10.3f')
stars = all_template_stars
else:
# initial PSF estimate
iraf.psf(image=f,photfile=fp+'temp.phot',pstfile=fp+'temp.pst',psfimage=fp+'temp.psf',
function=params.psf_profile_type,opstfile=fp+'temp.opst',
groupfile=fp+'temp.psg1',
interactive='no',
verify='no',varorder=0 ,psfrad=2*g.fw,
datamin=1,datamax=0.95*params.pixel_max,
scale=1.0)
# separation distance of near neighbours
separation = np.max([rewrite_psg(fp+'temp.psg1',fp+'temp.psg2'),3])
print 'separation = ',separation
# subtract all stars using truncated PSF
iraf.allstar(image=f,photfile=fp+'temp.phot',psfimage=fp+'temp.psf',
allstarfile=fp+'temp.als',rejfile='',
subimage=fp+'temp.sub',verify='no',psfrad=2*g.fw,fitrad=2.0,
recenter='yes',groupsky='yes',fitsky='yes',sannulus=7,wsannulus=10,
datamin=1,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,
noise='poisson')
if params.star_file:
os.system('cp '+fp+'temp.phot '+fp+'temp.phot2')
else:
# locate new stars
iraf.daofind(image=fp+'temp.sub',output=fp+'temp.stars1',interactive='no',verify='no',
threshold=3,sigma=params.star_detect_sigma,fwhmpsf=2*g.fw,
datamin=1,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,
noise='poisson')
# magnitudes for new stars
iraf.phot(image=fp+'temp.sub',output=fp+'temp.phot1',coords=fp+'temp.stars1',
interactive='no',
verify='no',sigma=params.star_detect_sigma,
fwhmpsf=g.fw,datamin=1,
datamax=params.pixel_max,epadu=params.gain,
readnoise=params.readnoise,noise='poisson')
# join star lists together
iraf.pconcat(infiles=fp+'temp.phot,'+fp+'temp.phot1',outfile=fp+'temp.phot2')
# new PSF estimate to generate PSF groups
iraf.psf(image=f,photfile=fp+'temp.phot2',pstfile=fp+'temp.pst',psfimage=fp+'temp.psf2',
function=params.psf_profile_type,opstfile=fp+'temp.opst2',
groupfile=fp+'temp.psg3',
interactive='no',
verify='no',varorder=0 ,psfrad=2*g.fw,
datamin=-10000,datamax=0.95*params.pixel_max,
scale=1.0)
# magnitudes for PSF group stars
iraf.nstar(image=f,groupfile=fp+'temp.psg3',psfimage=fp+'temp.psf2',
nstarfile=fp+'temp.nst',
rejfile='',verify='no',psfrad=2*g.fw,fitrad=2.0,
recenter='no',
groupsky='yes',fitsky='yes',sannulus=7,wsannulus=10,
datamin=1,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,noise='poisson')
# subtract PSF star neighbours
iraf.substar(image=f,photfile=fp+'temp.nst',psfimage=fp+'temp.psf2',
exfile=fp+'temp.opst2',fitrad=2.0,
subimage=fp+'temp.sub1',verify='no',datamin=1,
datamax=params.pixel_max,epadu=params.gain,
readnoise=params.readnoise,noise='poisson')
# final PSF
iraf.psf(image=fp+'temp.sub1',photfile=fp+'temp.phot2',
pstfile=fp+'temp.opst2',
psfimage=psf_image,psfrad=2*g.fw,
function=params.psf_profile_type,opstfile=fp+'temp.opst3',
groupfile=fp+'temp.psg5',
interactive='no',
verify='no',varorder=0,
datamin=1,datamax=0.95*params.pixel_max,
scale=1.0)
# final photometry
iraf.allstar(image=g.fullname,photfile=fp+'temp.phot2',psfimage=psf_image,
allstarfile=fp+'temp.als2',rejfile='',
subimage=fp+'temp.sub2',verify='no',psfrad=2*g.fw,
recenter=als_recenter,groupsky='yes',fitsky='yes',sannulus=7,
wsannulus=10,fitrad=2.0,
datamin=params.pixel_min,datamax=params.pixel_max,
epadu=params.gain,readnoise=params.readnoise,
noise='poisson')
psfmag = 10.0
for line in open(fp+'temp.als2','r'):
sline = line.split()
if sline[1] == 'PSFMAG':
psfmag = float(sline[3])
break
if params.star_file:
iraf.psort(infiles=fp+'temp.als2',field='ID')
os.system('cp '+fp+'temp.als2 '+fp+'temp.als3')
else:
selection = 'XCE >= '+str(edge_dist)+' && XCE <= '+str(xmax)+' && YCE >= '+str(edge_dist)+' && YCE <= '+str(ymax)+' && MAG != INDEF'
iraf.pselect(infiles=fp+'temp.als2',outfiles=fp+'temp.als3',expr=selection)
iraf.psort(infiles=fp+'temp.als3',field='MAG')
iraf.prenumber(infile=fp+'temp.als3')
s = iraf.pdump(infiles=fp+'temp.als3',Stdout=1,
fields='ID,XCENTER,YCENTER,MAG,MERR,MSKY,SHARPNESS,CHI',expr='yes')
sf = [k.replace('INDEF','22.00') for k in s]
stars = np.zeros([len(sf),5])
for i, line in enumerate(sf):
stars[i,:] = np.array(map(float,sf[i].split()[1:6]))
s = iraf.pdump(infiles=fp+'temp.als3',Stdout=1,
fields='ID,XCENTER,YCENTER,MAG,MERR,SHARPNESS,CHI,MSKY',expr='yes')
sf = [k.replace('INDEF','22.00') for k in s]
with open(fp+'ref.mags','w') as fid:
for s in sf:
fid.write(s+'\n')
return stars
def psffit(img, fwhm, psfstars, hdr, interactive, _datamax=45000, psffun='gauss', fixaperture=False):
import agnkey
iraf.digiphot(_doprint=0)
iraf.daophot(_doprint=0)
zmag = 0.
varord = 0 # -1 analitic 0 - numeric
if fixaperture:
print 'use fix aperture 5 8 10'
hdr = agnkey.util.readhdr(img+'.fits')
_pixelscale = agnkey.util.readkey3(hdr, 'PIXSCALE')
a1, a2, a3, a4, = float(5. / _pixelscale), float(5. / _pixelscale), float(8. / _pixelscale), float(
10. / _pixelscale)
# a1, a2, a3, a4, = int(5), int(8), int(10), int(12)
else:
a1, a2, a3, a4, = int(fwhm + 0.5), int(fwhm * 2 + 0.5), int(fwhm * 3 + 0.5), int(fwhm * 4 + 0.5)
_center='no'
iraf.fitskypars.annulus = a4
iraf.fitskypars.dannulus = a4
iraf.noao.digiphot.daophot.daopars.sannulus = int(a4)
iraf.noao.digiphot.daophot.daopars.wsannul = int(a4)
iraf.fitskypars.salgori = 'mean' #mode,mean,gaussian
iraf.photpars.apertures = '%d,%d,%d' % (a2, a3, a4)
# iraf.photpars.apertures = '%d,%d,%d'%(a2,a3,a4)
iraf.datapars.datamin = -100
iraf.datapars.datamax = _datamax
iraf.datapars.readnoise = agnkey.util.readkey3(hdr, 'ron')
iraf.datapars.epadu = agnkey.util.readkey3(hdr, 'gain')
iraf.datapars.exposure = 'exptime' #agnkey.util.readkey3(hdr,'exptime')
iraf.datapars.airmass = 'airmass'
iraf.datapars.filter = 'filter2'
iraf.centerpars.calgori = 'gauss'
iraf.centerpars.cbox = 1
iraf.daopars.recenter = _center
iraf.photpars.zmag = zmag
iraf.delete('_psf.ma*,' + img + '.psf.fit?,_psf.ps*,_psf.gr?,_psf.n*,_psf.sub.fit?', verify=False)
iraf.phot(img+'[0]', '_psf.coo', '_psf.mag', interac=False, verify=False, verbose=False)
iraf.daopars.psfrad = a4
iraf.daopars.functio = psffun
iraf.daopars.fitrad = a1
iraf.daopars.fitsky = 'yes'
iraf.daopars.sannulus = int(a4)
iraf.daopars.wsannul = int(a4)
iraf.daopars.recenter = _center
iraf.daopars.varorder = varord
if interactive:
shutil.copyfile('_psf.mag', '_psf.pst')
print '_' * 80
print '>>> Mark good stars with "a" or "d"-elete. Then "f"-it,' + \
' "w"-write and "q"-uit (cursor on ds9)'
print '-' * 80
else:
iraf.pstselect(img+'.fits[0]', '_psf.mag', '_psf.pst', psfstars, interac=False, verify=False)
iraf.psf(img+'.fits[0]', '_psf.mag', '_psf.pst', img + '.psf', '_psf.psto', '_psf.psg', interac=interactive,
verify=False, verbose=False)
# if os.path.isfile(img + '.psf.fits'):
# print 'file there'
iraf.group(img+'.fits[0]', '_psf.mag', img + '.psf.fits', '_psf.grp', verify=False, verbose=False)
iraf.nstar(img+'.fits[0]', '_psf.grp', img + '.psf.fits', '_psf.nst', '_psf.nrj', verify=False, verbose=False)
photmag = iraf.txdump("_psf.mag", 'xcenter,ycenter,id,mag,merr', expr='yes', Stdout=1)
pst = iraf.txdump("_psf.pst", 'xcenter,ycenter,id', expr='yes', Stdout=1)
fitmag = iraf.txdump("_psf.nst", 'xcenter,ycenter,id,mag,merr', expr='yes', Stdout=1)
return photmag, pst, fitmag