def findWorldPosition(self, write=False):
# Convert the GRB pixel position to WCS
# Make the input file for the IRAF task
if self._pixelx == "" or self._pixely == "":
print "You did not set an pixel x or pixel y"
return 1
coordfilenamein = "%s" % (self._parentimage.replace(".fits", "_skyctran_pixel_in.coo"))
coordfilenameout = "%s" % (self._parentimage.replace(".fits", "_skyctran_pixel_out.coo"))
try:
self.cleanOutputFiles(coordfilenameout)
except:
print "Error cleaning files"
print sys.exc_info()[0]
try:
coordout = open(coordfilenamein, "w")
coordout.write("%10.7f %10.7f" % (self._pixelx, self._pixely))
coordout.close()
except:
print "File opening failed:"
print sys.exc_info()[0]
# This subroutine lies in imcoords on IRAF
iraf.image()
iraf.imcoords()
# Set the parameters of skyctran
#
# input
# output
# insystem: input coordinate system
# outsystem: output coordinate system
# lngcolu: RA column no.
# latcolu: DEC column no.
# ilnguni: RA input coord type
# ilnlatuni: DEC input coord type
# olnguni: RA output coord type
# olatuni: DEC output coord type
# ilngfor: RA input float format
# ilatfor: DEC input float format
# olngfor: RA output float format
# olatfor: DEC output float format
iraf.skyctran.setParam('input', coordfilenamein)
iraf.skyctran.setParam('output', coordfilenameout)
iraf.skyctran.setParam('insystem', '%s logical' % self._parentimage)
iraf.skyctran.setParam('outsystem', '%s world' % self._parentimage)
iraf.skyctran.setParam('lngcolu', '1')
iraf.skyctran.setParam('latcolu', '2')
iraf.skyctran.setParam('ilnguni', 'logical')
iraf.skyctran.setParam('ilatuni', 'logical')
iraf.skyctran.setParam('olnguni', 'degrees')
iraf.skyctran.setParam('olatuni', 'degrees')
iraf.skyctran.setParam('ilngfor', '%10.7f')
iraf.skyctran.setParam('ilatfor', '%10.7f')
iraf.skyctran.setParam('olngfor', '%10.3f')
iraf.skyctran.setParam('olatfor', '%10.3f')
iraf.skyctran.setParam('verbose', 'yes')
# savepars
skyctran = "skyctranpars.par"
#iraf.skyctran.saveParList(skyctran)
# run skyctran
tmp = iraf.skyctran(mode='h', Stdout=1)
# Set properties of this object from the output
try:
coordfile = open(coordfilenameout, "r")
# parse the input file
coords = coordfile.readlines()
coordfile.close()
for coord in coords:
if coord[0] != "#" and coord[0] != "\n":
coordinates = [i for i in coord.replace("\n","").split(" ") if i != ""]
# Set the object parameters
self._ra = float(coordinates[2])
self._dec = float(coordinates[3])
except:
print "File opening failed"
print sys.exc_info()[0]
# region file for object of interest
if write:
try:
regionout = open("%s" % (self._parentimage.replace(".fits", "_skyctran_object.reg")), "w")
if self._MEDFWHM == "":
circ = 4.0
else:
circ = self._MEDFWHM*1.5
regionout.write("image; circle(%f,%f,%f) # color = red\n" % (self._pixelx, self._pixely, circ))
regionout.close()
except:
print "Unexpected error:"
print sys.exc_info()[0]
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
