def calib(self):
dolamps=no
lampfilts=[]
lampfiles=[]
lamponfiles={}
lampofffiles={}
allfiles=glob.glob(self.inpat)
# Look for flatfield images
for image in allfiles:
# Criteria for flatfield images
lampval=get_head(image,self.lampkey)
if re.search(self.lampon,lampval,re.I) or \
re.search(self.lampoff,lampval,re.I):
dolamps=yes
filter=wirc_filter(image)
if filter not in lampfilts:
lampfilts.append(filter)
if re.search(self.lampon,lampval,re.I):
update_head(image,self.lampfkey,'On-'+filter,
"Lamp status + Filter setting")
lampfiles.append(image)
if lamponfiles.has_key(filter):
lamponfiles[filter].append(image)
else:
lamponfiles[filter]=[image]
elif re.search(self.lampoff,lampval,re.I):
update_head(image,self.lampfkey,'Off-'+filter,
"Lamp status + Filter setting")
lampfiles.append(image)
if lampofffiles.has_key(filter):
lampofffiles[filter].append(image)
else:
lampofffiles[filter]=[image]
lamplist=','.join(lampfiles)
# Use flatfield images to make our calibration files
if dolamps:
# Make lamp-on and lamp-off flats & bad-pixel mask
iraf.iqcals(lamplist,dobias=no,biasproc=no,
doflats=yes,flatproc=no,flatkey=self.flatkey,
flatre=self.flatre,filtkey=self.lampfkey,
flatpre=self.flatpre,flatscale="none",
statsec=self.statsec,normflat=no,
dobpm=yes,bpmmethod='flatratio',
bpmroot=self.bpmroot,
bpmffilt=self.bpmffilt,classkey="",
mosaic=no,clobber=self.clobber,
verbose=self.verbose)
# Subtract lamp-off flat from lamp-on flat, if necessary
for filter in lamponfiles.keys():
onflat=self.flatpre+'On-'+filter+'.fits'
offflat=self.flatpre+'Off-'+filter+'.fits'
outflat=self.flatpre+filter+'.fits'
check_exist(outflat,'w',self.clobber)
if filter in self.onofflist:
if not lampofffiles.has_key(filter):
print "Need lamp-off flats for filter '%s'" % filter
continue
iraf.imarith(onflat,'-',offflat,outflat,
verbose=self.verbose,noact=no)
else:
# For some filters "lampsoff" counts are negligible
iraf.imcopy(onflat,outflat,verbose=yes)
update_head(outflat,self.filtset,filter)
medflat=wirc_sky(outflat,"")
#update_head(outflat,"NORMFLAT",1,
update_head(outflat,"NORMFLAT",0,
"Has flatfield been normalized?")
update_head(outflat,"MEDFLAT",medflat,
"Median value of original flatfield")
def iqp60(inpat,endhow="never",endwhen="",focmode="all",
logfile="",clobber=globclob,verbose=globver):
""" intelligent processing of P60 data files """
# Defaults
twait=30
reduced={}
filtkey="FILTER"
biaskey="IMGTYPE"
biasre="BIAS"
biasroot="Bias"
biaspfx="b"
flatkey="IMGTYPE"
flatre="DOMEFLAT"
flatpre="Flat-"
flatpfx="f"
bpm0root="BPM0"
bpmroot="BPM"
binkey="CCDSUM"
detseckey="DETSEC"
binroikey="BINROI"
binroidef="A"
nfocus=10
focuskey="IMGTYPE"
focusre="^FOCUS"
fseqkey="FOCUSSEQ"
skipkey="IMGTYPE"
skipre="SAOFOCUS"
statsec=""
reqkeys=['IMGTYPE','OBJECT','FILTER','BINROI',
'CCDSUM','DETSEC','ROISEC']
sigma=3.0
minraw=0.0
maxraw=65535.0
satval=50000.0
masksfx="mask"
rawpix=0.3787
zptkey="ZEROPT"
zpukey="ZEROPTU"
# For now:
#catmags={'B':'BMAG','V':'BMAG','g':'BMAG',
# 'R':'RMAG','r':'RMAG','I':'IMAG',
# 'i':'IMAG','ip':'IMAG','z':'IMAG',
# 'zp':'IMAG','zl':'IMAG','zs':'IMAG'}
## In the future, once Sloan mags are written to the ubcone output:
catmags={'B':'BMAG','V':'VMAG','g':'GPMAG',
'R':'RMAG','r':'RPMAG','I':'IMAG',
'i':'IMAG','ip':'IPMAG','z':'ZPMAG',
'zp':'ZPMAG','zl':'ZPMAG','zs':'ZPMAG',
'upr':'UPMAG','gpr':'GPMAG','rpr':'RPMAG',
'ipr':'IPMAG','zpr':'ZPMAG'}
exptmkey="EXPTIME"
exptmstd=60.0
minzpts={}
minskys={}
fwhm0=1.5
gain=2.3
readn=7.5
crsfx="crm"
statfile="Status_Science.txt"
# Parse end-condition "time"
if endhow=="time":
re1=re.search("^(\d+):(\d+)",endwhen)
if re1:
tnow=time.gmtime()
# Force UT calculation w/ ignoring of DST issues
reftime=time.mktime([tnow[0],tnow[1],tnow[2],
int(re1.group(1)),int(re1.group(2)),0,
tnow[6],tnow[7],0]) - time.timezone
if reftime<time.time():
reftime+=86400
if verbose:
print "Running until %s" % \
time.strftime("%d %b %H:%M",time.gmtime(reftime))
else:
print "Failed to parse %s as UT time" % endwhen
print "Running until stopped..."
endhow="never"
# Parse focmode setting
fonly=0
if focmode=="nofocus":
skipre="FOCUS"
elif focmode=="focus":
fonly=1
skipre="SCIENCE"
# Parse logfile setting
if len(logfile)>0:
check_exist(logfile,'w',yes)
try:
log=open(logfile,'w')
sys.stdout=log
except:
print "Failed to open logfile %s for writing" % logfile
# Setup ccdproc options
ccdproc=iraf.ccdred.ccdproc
ccdproc.overscan=yes
ccdproc.trim=yes
ccdproc.zerocor=no
ccdproc.interactive=no
ccdproc.function="chebyshev"
ccdproc.order=3
ccdproc.sample="*"
ccdproc.naverage=3
ccdproc.niterate=2
ccdproc.low_reject=3.0
ccdproc.high_reject=3.0
ccdproc.grow=0.0
# Demosaic all the files
allfiles=glob.glob(inpat)
alllist=','.join(allfiles)
iraf.iqmosaic(alllist,outpfx="",biassec="!BIASSEC",
trimsec="!TRIMSEC",joinkeys="CCDSIZE,DETSEC,ROISEC",
splitkeys="AMPSEC,CCDSEC,TRIM,OVERSCAN,CCDPROC",
clobber=yes,verbose=verbose)
iraf.add_wcs(alllist,instrument="p60new",binkey=binkey)
# Set ccdproc params for bias-subtraction only
ccdproc.overscan=no
ccdproc.trim=no
ccdproc.zerocor=yes
# Determine if we need to make calibration files
dobias=no
doflats=no
for image in allfiles:
# Criteria for bias image
biasval,flatval=get_head(image,[biaskey,flatkey])
if re.search(biasre,biasval,re.I):
dobias=yes
reduced[image]=yes
elif re.search(flatre,flatval,re.I):
doflats=yes
reduced[image]=yes
# Calibrations
if (dobias or doflats) and not fonly:
iraf.iqcals(alllist,dobias=dobias,biasproc=no,
biaskey=biaskey,biasre=biasre,biasroot=biasroot,
doflats=doflats,flatproc=yes,flatkey=flatkey,
flatre=flatre,filtkey=filtkey,flatpre=flatpre,
flatscale="mode",statsec="",normflat=yes,
dobpm=no,bpmroot=bpmroot,classkey=binroikey,
classdef=binroidef,mosaic=no,
clobber=clobber,verbose=verbose)
# Delete binroi-specific BPMs and flatfields
oldbpms=glob.glob(bpmroot+'-'+'*.pl')
for oldbpm in oldbpms:
iraf.imdel(oldbpm,verify=no,go_ahead=yes)
oldflats=glob.glob(flatpre+'*-*.fits')
for oldflat in oldflats:
iraf.imdel(oldflat,verify=no,go_ahead=yes)
# Clip all flatfields and update BPM as we go
bpm0name=bpm0root+'.pl'
bpmname=bpmroot+'.pl'
if os.path.exists(bpmname):
check_exist(bpm0name,'w',clobber=yes)
iraf.imrename(bpmname,bpm0name,verbose=no)
allflats=glob.glob(flatpre+'*.fits')
for flatimg in allflats:
iraf.iqclip(flatimg,lthresh=0.75,hthresh=1.25,bookend=no,
replace=1.0,maskin=bpm0name,maskout=bpmname,
maskval=1,clobber=yes,verbose=no)
iraf.imdel(bpm0name,verify=no,go_ahead=yes)
iraf.imrename(bpmname,bpm0name,verbose=no)
update_head(flatimg,"CLIPFLAT",1,"Has flatfield been clipped?")
update_head(flatimg,"CLIPREPL",1.0,
"Replacement value for clipped pixels")
iraf.imrename(bpm0name,bpmname,verbose=no)
##################################################
# Lists of focusfiles
allfocus=[]
focusfiles=[]
# Should additional calibrations be taken later on...
biasfiles=[]
flatfiles=[]
# Big Loop
done=no
while not done:
# Parse inputs
allfiles=glob.glob(inpat)
newfiles=[]
for image in allfiles:
if not reduced.has_key(image):
# Exclude Bias & Flats
if re.search(biasroot,image,re.I) or \
re.search(flatpre,image,re.I):
reduced[image]=yes
continue
# Exclude calibration files (for now)
biasval,flatval=get_head(image,[biaskey,flatkey])
if re.search(biasre,biasval,re.I):
biasfiles.append(image)
reduced[image]=yes
elif re.search(flatre,flatval,re.I):
flatfiles.append(image)
reduced[image]=yes
# Exclude "skippable" files
skipval=get_head(image,skipkey)
if re.search(skipre,skipval,re.I):
reduced[image]=yes
# Queue file for processing
else:
reduced[image]=no
newfiles.append(image)
elif not reduced[image]:
# Attempted reduction before, but failed?
newfiles.append(image)
if newfiles:
# Brief pause to avoid file conflicts (?)
time.sleep(3.0)
# Demosaic
newlist=','.join(newfiles)
ccdproc.overscan=yes
ccdproc.trim=yes
ccdproc.zerocor=no
iraf.iqmosaic(newlist,outpfx="",biassec="!BIASSEC",
trimsec="!TRIMSEC",joinkeys="DETSEC",
splitkeys="AMPSEC,CCDSEC,TRIM,OVERSCAN",
clobber=yes,verbose=verbose)
iraf.add_wcs(newlist,instrument="p60new",binkey=binkey)
# Reset ccdproc params for bias-subtraction only
ccdproc.overscan=no
ccdproc.biassec=""
ccdproc.trim=no
ccdproc.trimsec=""
ccdproc.zerocor=yes
ccdproc.flatcor=no
##############################
# Process new images
for image in newfiles:
# Required keyword check
if not check_head(image,reqkeys):
print "Image %s is missing required keywords" % image
continue
# Attempt processing only once per image
reduced[image]=yes
if verbose:
print "Reducing new image %s" % image
# Track useful status information
scistat={}
# Prepare for processing
pix=rawpix
binroi=binroidef
biasname=biasroot+'.fits'
bpmname=bpmroot+'.pl'
filt=get_head(image,filtkey)
flatname=flatpre+filt+".fits"
# Calibration files for BINROI setting
if check_head(image,binroikey):
binroi=get_head(image,binroikey)
if binroi != binroidef:
# Get the right calibration files
fullbias=biasname
biasname=biasroot+'-'+binroi+'.fits'
fullbpm =bpmroot+'.pl'
bpmname =bpmroot+'-'+binroi+'.pl'
fullflat=flatname
flatname=flatpre+filt+'-'+binroi+".fits"
# Details of this binning/roi combo
[binval,detsec]=get_head(image,[binkey,detseckey])
binning=p60parsebin(binval)
roi=p60parseroi(detsec)
# Pixel scale (no anisotropic binning, sorry)
pix=binning[0]*rawpix
# Check for existance of bias; make it if we have to
if not os.path.exists(biasname):
print ("Failed to find bias for %s=%s; "+ \
"constructing one from full-frame bias") % \
(binroikey,binroi)
p60roiflat(fullbias,biasname,binning,roi)
# Produce the flatfield if necessary
if not os.path.exists(flatname):
p60roiflat(fullflat,flatname,binning,roi)
# Produce the bad-pixel mask if necessary
if not os.path.exists(bpmname):
# Get BPM into FITS format
bpm1=iraf.mktemp("iqbpm")+".fits"
iraf.imcopy(fullbpm,bpm1,verbose=no)
# Adjust BPM for binning/ROI
bpm2=iraf.mktemp("iqbpm")+".fits"
p60roibpm(bpm1,bpm2,binning,roi)
# Convert BPM to PL format
iraf.imcopy(bpm2,bpmname,verbose=no)
# Delete temporary files
iraf.imdel(bpm1,verify=no,go_ahead=yes)
iraf.imdel(bpm2,verify=no,go_ahead=yes)
# Bias subtraction
check_exist(biasname,"r")
ccdproc.zero=biasname
image1=biaspfx+image
check_exist(image1,'w',clobber)
iraf.ccdproc(image,output=image1,Stdout=1)
# Flatfielding
check_exist(flatname,"r")
iraf.iqflatten(image1,flatname,outpfx=flatpfx,
normflat=no,clipflat=no,
statsec=statsec,subsky=yes,
vignflat=no,clobber=yes,verbose=no)
imagef=flatpfx+image1
# Clip (bookend) flattened & sky-subtracted image
skybkg=float(get_head(image1,'SKYBKG'))
iraf.iqclip(image1,lthresh=minraw-skybkg,hthresh=maxraw-skybkg,
bookend=yes,maskin="",maskout="",clobber=yes,
verbose=no)
# Rename the file, if everything is well-behaved
reim=re.search('^%s%s(.+[^r])r?\.fits' % (flatpfx,biaspfx),
imagef,re.I)
if reim:
image2=reim.group(1)+'p.fits'
check_exist(image2,"w",yes)
iraf.imrename(imagef,image2,verbose=verbose)
else:
image2=imagef
# Set bad pixels to zero
update_head(image2,'BPM',bpmname,"Bad Pixel Mask")
iraf.iqmask(image2,mask='!BPM',method='constant',value='0.0',
clobber=yes,verbose=no)
# Defringing happens later, in bunches
# Cosmic Ray Rejection
tmpimg=iraf.mktemp("iqcr")+".fits"
check_exist("%s_%s.fits" % (image2[:15],crsfx),"w",clobber)
iraf.lacos_im(image2,tmpimg,"%s_%s.fits" % (image2[:15],crsfx),
gain=gain,readn=readn,skyval=skybkg,sigclip=4.5,
sigfrac=0.5,objlim=1.0,niter=1)
iraf.imdel(image2,verify=no,go_ahead=yes)
iraf.imcopy(tmpimg,image2,verbose=no)
iraf.imdel(tmpimg,verify=no,go_ahead=yes)
# Object-detection
if scistat.has_key("SEEING_%s" % file):
try:
fwhm=float(scistat["SEEING_%s" % file])
except:
fwhm=fwhm0
else:
fwhm=fwhm0
iraf.iqobjs(image2,sigma,satval,skyval="!SKYBKG",masksfx=masksfx,
wtimage="",fwhm=fwhm,pix=rawpix,aperture=2*fwhm/rawpix,
gain=gain,minlim=no,clobber=yes,verbose=no)
# Track some status information
nstars=get_head(image2,'NSTARS')
scistat['NSTARS']=nstars
if minskys.has_key(filt):
minsky=minskys[filt]
scistat["SKYBKG_%s" % filt]=skybkg/minsky
# Is it a focus frame?
focusval=get_head(image2,focuskey)
# Focus frame actions
if re.search(focusre,focusval,re.I):
focusfiles.append(image2)
# Find its place in the sequence
focusseq=get_head(image2,fseqkey)
ref=re.search("(\d+)of(\d+)",focusseq,re.I)
if ref:
ifocus=int(ref.group(1))
nfocus=int(ref.group(2))
# Non-focus frame actions
else:
# Make a new keyword for mosaic objects
objkey='OBJECT'
if check_head(image2,'MSCSIZE'):
mscsize=get_head(image2,'MSCSIZE')
mscdims=mscsize.split(',')
if int(mscdims[0])>1 or int(mscdims[1])>1:
object=get_head(image2,'OBJECT')
mscposn=get_head(image2,'MSCPOSN')
objmsc=object+'-'+mscposn
update_head(image2,'OBJMSC',objmsc,
'Object Name/Mosaic Position')
objkey='OBJMSC'
# Refine WCS (also calculates seeing in arcsec)
iraf.iqwcs(image2,objkey=objkey,rakey='RA',
deckey='DEC',pixtol=0.05,starfile='!STARFILE',
nstar=40,catalog='web',ubhost="localhost",
diffuse=yes,clobber=yes,verbose=verbose,
nstarmax=40)
# Retry if unsuccessful
if not check_head(image2,'IQWCS'):
iraf.iqwcs(image2,objkey=objkey,rakey='RA',
deckey='DEC',pixtol=0.05,starfile="!STARFILE",
nstar=40,catalog='web',ubhost="localhost",
diffuse=yes,clobber=yes,verbose=verbose,
nstarmax=1000)
# Calculate further quantities if WCS was successful
extinct='INDEF'
if check_head(image2,'IQWCS'):
scistat['WCSGOOD'] = 1
scistat["SEEING_%s" % filt]=get_head(image2,'SEEING')
[rapt,dcpt,lenx,leny]=get_head(image2,
['RA','DEC','NAXIS1','NAXIS2'])
[[ractr,dcctr]]=impix2wcs(image2,0.5*(1+float(lenx)),
0.5*(1+float(leny)))
coopt=astrocoords(rapt,dcpt)
cooctr=astrocoords(ractr,dcctr)
[offra,offdc]=radecdiff(coopt.radeg(),coopt.dcdeg(),
cooctr.radeg(),cooctr.dcdeg())
update_head(image2,'PTOFFSET',"%.2f %.2f" % \
(offra,offdc),
"Offset from nominal pointing (arcsec)")
scistat['PTOFFSET']="%.2f,%.2f" % (offra,offdc)
# Get zero-point against SDSS/NOMAD/USNO-B
if catmags.has_key(filt):
if check_head(image2,'OBJMSC'):
object=get_head(image2,'OBJMSC')
else:
object=get_head(image2,'OBJECT')
zpcat=""
# See if attempt already made for SDSS
if not (os.path.exists("%s.sdss" % object)):
getsdss(image2, "%s.sdss" % object)
# If successful, set to SDSS
sdssfile=open("%s.sdss" % object)
if (len(sdssfile.readlines())>2):
catalog="%s.sdss" % object
zpcat="SDSS"
# If SDSS unsuccessful, update USNO-B
if not zpcat:
update_usnob("%s.cat" % object,
outfile="%s.reg" % object)
catalog="%s.reg" % object
zpcat="USNO-B"
# Update image header
update_head(image2,"ZPCAT",zpcat)
# Run the zeropoint calculation
iraf.iqzeropt(image2,catmags[filt],
starfile="!STARFILE",catalog=catalog,
pixtol=3.0,useflags=yes,maxnum=50,
method="mean",rejout=1,fencelim=0.50,
sigma=1.5,maxfrac=0.25,
zptkey=zptkey,zpukey=zpukey,
clobber=yes,verbose=verbose)
# Use that to get an extinction estimate
zeropt,zeroptu,exptime=get_head(image2,[zptkey,
zpukey,exptmkey])
zeropt=float(zeropt)
zeroptu=float(zeroptu)
exptime=float(exptime)
scistat["ZEROPT_%s" % filt] = \
zeropt - 2.5*math.log10(exptime/exptmstd)
if minzpts.has_key(filt):
extinct = zeropt - \
2.5*math.log10(exptime/exptmstd) - \
minzpts[filt]
scistat["EXTINCT_%s" % filt]=extinct
# Fix the SEEING keyword if WCS fit was not successful
else:
scistat['WCSGOOD'] = 0
try:
seepix=float(get_head(image2,'SEEPIX'))
seeing= "%.3f" % (pix*seepix)
except:
seeing='INDEF'
update_head(image2,'SEEING',seeing,
"Estimated seeing in arcsec or INDEF")
# Write Archive Keywords
update_head(image2,'PROCESSD',1,
"Image has been processed by iqp60")
update_head(image2,'PROCVER',version,
"Version number of iqp60 used")
update_head(image2,'EXTINCT',extinct,
"Estimated mags extinction or INDEF")
update_head(image2,'PROCPROB','None',
"Problems encountered in iqp60 processing")
# Update status file
p60status(statfile,image2,scistat)
# Clean up
check_exist(image1,"w",yes)
##############################
# If a set of focus images have been processed, find best focus
if len(focusfiles)>=nfocus:
print "%d focus images have been processed" % len(focusfiles)
# Pick a starfile
focusfiles.sort()
medfile=focusfiles[len(focusfiles)/2]
starfile=get_head(medfile,'STARFILE')
# Update seeing values in all images based on good
# stars in the starfile.
ffiles=','.join(focusfiles)
iraf.iqseeing(ffiles,stars=starfile,
seekey="SEEING",method="acorr",useflags=yes,
skipstars=0,usestars=10,boxsize=64,
strictbox=no,imgsec="[940:1980,64:1980]",
update=yes,clobber=yes,verbose=no)
# Grab focus positions and seeing values
focx=[]
focy=[]
for image in focusfiles:
[fpos,seep]=list2float(get_head(image,['FOCUSPOS','SEEING']))
fpos=float(fpos)
seep=float(seep)
focx.append(fpos)
pix=rawpix
if check_head(image,binkey):
binval=get_head(image,binkey)
binels=binval.split()
binning=[int(binels[0]),int(binels[1])]
# Let's hope we don't ever do asymmetric binning
pix=binning[0]*rawpix
focy.append(pix*seep)
update_head(image,'SEEING',pix*seep,
"Estimated seeing in arcsec")
# Choose best-seeing as minimum of these
bestsee=min(focy)
bestfoc=focx[focy.index(bestsee)]
# This was too much verbosity for Brad
if verbose and 0:
print "Focus settings: "+liststr(focx,"%.2f")
print "Seeing values: "+liststr(focy,"%.1f")
print
print "Best focus: %.2f" % bestfoc
# Expunge the focusfiles list
allfocus.append(focusfiles)
focusfiles=[]
##############################
# Test end conditions
if endhow=="never":
done=no
elif endhow=="once":
done=yes
elif endhow=="time":
if time.time()>reftime:
done=yes
# Wait a little while
if not done:
time.sleep(twait)