def _compute_err_ext(self, sci_ext):
"""
Compute the error image for a science image
For a image in [e], the module computes the associated
error image assuming a simple noise model with photon shot noise
and readout noise.
@param sci_ext: the input image
@type sci_extsci_ext: string
"""
# unlearn some iraf tasks
iraf.unlearn('imexpr')
# get a random filename
tmpfile1 = get_random_filename('t', '.fits')
# compute the error array
expression = "sqrt(a + b*b)"
iraf.imexpr(expr=expression,
output=tmpfile1,
a=sci_ext,
b=self.rdnoise,
Stdout=1)
return tmpfile1
def _make_real_sciimage(self, in_image, bck_flux, exptime):
"""
Create the science extension
Starting from a simulated image in [e/s], the module adds
background and scales to [e]. The output image is returned.
@param in_image: the simulated image
@type in_image: string
@param bck_flux: background flux [e/s]
@type bck_flux: float
@param exptime: the exposure time
@type exptime: float
"""
# get a random filename
tmpfile1 = get_random_filename('t', '.fits')
# add background; scale by exptime
expression = "(a + b)*c"
iraf.imexpr(expr=expression,
output=tmpfile1,
a=in_image,
b=bck_flux,
c=exptime,
Stdout=1)
# return the image name
return tmpfile1
def rssflux(self, obj, sens, do_error=None):
do_error = do_error if do_error is not None else self.do_error
rt.rmexist([obj.flux2d])
if not rt.header(obj.bkg_var,'AIRMASS'): rt.rssairmass(obj.bkg_var)
iraf.longslit.calibrate(input=obj.bkg, output=obj.flux2d, extinct='yes',
flux='yes', fnu='no',sensitivity=sens,
extinction=self.extinction)
rt.putheader(obj.flux2d, 'STDNAME', sens)
if do_error:
rt.rmexist([obj.flux2d_var, obj.flux2d_err])
# Convert variance to error
iraf.imexpr("sqrt(a)", obj.bkg_err, a = obj.bkg_var)
iraf.longslit.calibrate(input=obj.bkg_err, output=obj.flux2d_err, extinct='yes',
flux='yes',observa='saao',fnu='no', sensitivity=sens,
extinction=self.extinction)
def skyest(inputimg, segimg, gsigma):
#if len(glob.glob("cutout.fits")):
# os.system("rm cutout.fits")
#iraf.imcopy("%s[%d:%d,%d:%d]"%(inputimg,xmin,xmax,ymin,ymax),"cutout.fits")
#iraf.imcopy(segimg+"[%d:%d,%d:%d]"%(xmin,xmax,ymin,ymax),"segcutout.fits")
if len(glob.glob('segcutout*.fits')):
os.system('rm segcutout*.fits')
iraf.imexpr("a > 0 ? 100 : 0", "segcutout2.fits", a=segimg)
# grow mask by Gaussian wing
iraf.gauss(input="segcutout2.fits", output="segcutout3.fits", sigma=gsigma)
h1 = pyfits.open(inputimg)
h2 = pyfits.open('segcutout3.fits')
him1 = h1[0].data # image data
him2 = h2[0].data
skyim = compress(him2.ravel() < 10., him1.ravel())
bkgnd = median(skyim) # take the median of unmasked sky
#os.system('rm cutout.fits')
os.system('rm segcutout*.fits')
return bkgnd
def prepare_extraction(self):
"""
Prepares the aXe extraction
The module does some preparatory stuff before the extraction
can start. This includes copying the simulated dispersed image
to AXE_IMAGE_PATH and subtracting the background on this copy.
"""
import shutil
from pyraf import iraf
# give brief feedback
print('Dummy extraction on the dispersed image:')
sys.stdout.flush()
# get a random filenames
tmpfile1 = get_random_filename('t', '.fits')
tmpfile2 = get_random_filename('t', '.fits')
# copy the grism image to AXE_IMAGE_PATH
shutil.copy(getOUTSIM(self.simul_grisim), getIMAGE(tmpfile1))
# subtract the background from
# the grism image
expression = "(a - b)"
iraf.imexpr(expr=expression,
output=tmpfile2,
a=getIMAGE(tmpfile1) + '[SCI]',
b=self.bck_flux,
Stdout=1)
# copy the background subracted image to the grism image, sci-extension
iraf.imcopy(input=tmpfile2,
output=getIMAGE(tmpfile1) + '[SCI,overwrite]',
Stdout=1)
# delete the background subtracted
# tmp image
os.unlink(tmpfile2)
# store the name of the background
# subtracted grism image
self.dispersed_image = tmpfile1
def skyest(inputimg, segimg, gsigma):
"""
Rough estimate of local sky background.
"""
if len(glob.glob('segcutout*.fits')):
os.system('rm segcutout*.fits')
iraf.imexpr("a > 0 ? 100 : 0", "segcutout2.fits", a=segimg)
# grow mask by Gaussian wing
iraf.gauss(input="segcutout2.fits", output="segcutout3.fits", sigma=gsigma)
h1 = pyfits.open(inputimg)
h2 = pyfits.open('segcutout3.fits')
him1 = h1[0].data # image data
him2 = h2[0].data
skyim = np.compress(him2.ravel() < 10., him1.ravel())
bkgnd = np.median(skyim) # take the median of unmasked sky
#os.system('rm cutout.fits')
os.system('rm segcutout*.fits')
return bkgnd
def reduce2d(self, obj, arc, do_error=None):
images = obj.name
do_error = do_error if do_error is not None else self.do_error
hduorig= fits.open(images)
os.remove(images)
hduimg = fits.PrimaryHDU(data=hduorig[0].data,header=hduorig[0].header)
hduimg.writeto(images)
hduvarimg = fits.PrimaryHDU(data=hduorig[1].data,header=hduorig[0].header)
rt.rmexist([obj.var])
hduvarimg.writeto(obj.var)
rt.prepare_image(images, do_error=do_error)
self.rssidentify(arc)
nxpix = obj.header['NAXIS1']
rt.loadparam(self.rssconfig, ['iraf.transform', 'iraf.fit1d'])
config= self.rssconfig
if self.do_error:
iraf.errorpars.errtype='uniform'
iraf.errorpars.resample='no'
iraf.samplepars.axis=1
iraf.samplepars.setParam('naverage', config['iraf.fit1d']['naverage'])
iraf.samplepars.setParam('low_reject', config['iraf.fit1d']['low_reject'])
iraf.samplepars.setParam('high_reject', config['iraf.fit1d']['high_reject'])
iraf.samplepars.setParam('niterate', config['iraf.fit1d']['niterate'])
iraf.samplepars.setParam('grow', config['iraf.fit1d']['grow'])
rt.rmexist([obj.wave, obj.bkg, obj.wave_var, obj.bkg_var])
# Wavelength calibration
iraf.transform(obj.noext, obj.wave, fitnames = arc.noext, logfiles = self.logfile)
iraf.fit1d(obj.wave, obj.sky, "fit", axis=2)
iraf.imarith(obj.wave, "-", obj.sky, obj.bkg)
# Calibrated error file
if do_error:
iraf.transform(obj.var, obj.wave_var, fitnames = arc.noext, logfiles = self.logfile)
iraf.gfit1d(obj.wave, 'tmptab.tab', function=config['iraf.fit1d']['function'],
order=config['iraf.fit1d']['order'], xmin=1, xmax=nxpix, interactive='no')
iraf.tabpar('tmptab.tab',"rms", 1, Stdout=self.logfile)
rmsval = float(iraf.tabpar.value)
tmpval=rmsval*rmsval
print('RMS of the fit (for VAR plane propagation) = %s ' %rmsval)
iraf.imexpr("a+b",obj.bkg_var, a=obj.wave_var, b=tmpval)
print("**** Done with image %s ****" % (images))
def mkIrafIm(self):
""" make the detection image. This method creates the detection
Image using the CHI^2 algorithm.
"""
self.logfile.write('Generating detection Image...')
cwd = os.getcwd()
os.chdir(self.obsFits) # cd to the observations Images dir
self.logfile.write('cd to observation Images dir ' + self.obsFits)
for i in range(len(self.statsList)):
image, background, noise = self.statsList[i]
expr = "((a - %s)/%s)**2" % (background, noise)
self.logfile.write(
'Generating background subtracted, squared image: ' +
'subtracted_' + image)
iraf.imexpr(expr, 'subtracted_' + image, a=image)
inputString = string.join(
map(lambda x: 'subtracted_' + x, self.sciImageList), ',')
iraf.unlearn(iraf.imsum)
iraf.imsum(input=inputString, output='dummy.fits', option='sum')
iraf.unlearn(iraf.imexpr)
self.logfile.write('Generating detectionImage.fits for observation...')
iraf.imexpr('sqrt(a)', self.detImName, a="dummy.fits")
self.logfile.write('Removing dummy image...')
iraf.imdelete('dummy.fits', verify='no')
self.logfile.write('Removing subtraction images...')
iraf.imdelete(inputString, verify='no')
# the header of the image produced by iraf is junk. fix it up
self._fixIrafHeader()
os.chdir(cwd) # return to orig dir.
return
def wirc_flatscale(infiles,inflat,outflat,clipfrac=0.03,
clobber=globclob):
# "infiles" is a list of filenames
inlist=','.join(infiles)
bpmfile=get_head(infiles[0],'BPM')
# Make a median combination of input files
imcmb1=iraf.mktemp("iqwircc")+".fits"
iraf.imcombine(inlist,imcmb1,combine="median",reject="none",
project=no,outtype="real",outlimits="",offsets="",
masktype="none",blank=0.0,scale="!SKYBKG",zero="none",
weight="none",statsec="",lthreshold="INDEF",
hthreshold="INDEF",nkeep=1)
[naxis1,naxis2]=get_head(imcmb1,['NAXIS1','NAXIS2'])
npixall=float(naxis1)*float(naxis2)
# Calculate sky background & divide, subtract 1
skybkg=wirc_sky(imcmb1,bpmfile)
imcmb2=iraf.mktemp("iqwircc")+".fits"
iraf.imarith(imcmb1,'/',skybkg,imcmb2,verbose=no,noact=no)
iraf.imdel(imcmb1,verify=no,go_ahead=yes)
iraf.imarith(imcmb2,'-',1.0,imcmb1,verbose=no,noact=no)
# Surface fit to median image
imsurf1=iraf.mktemp("iqwircs")+".fits"
iraf.imsurfit(imcmb1,imsurf1,xorder=6,yorder=6,type_output="fit",
function="chebyshev",cross_terms=yes,
xmedian=21,ymedian=21,median_percent=50.0,
lower=0.0,upper=0.0,ngrow=0,niter=0,
regions="all",rows="*",columns="*",border=50,
sections="",circle="",div_min="INDEF")
# Corresponding bad pixel mask
imbpm1=iraf.mktemp("iqwircb")+".pl"
iraf.imexpr("abs(x)>%.3f ? 0 : 1" % clipfrac,imbpm1,x=imsurf1)
# Subtract 1.0 from flatfield
imflat1=iraf.mktemp("iqwircf")+".fits"
iraf.imarith(inflat,'-',1.0,imflat1,verbose=no,noact=no)
# Surface fit to the flatfield
imsurf2=iraf.mktemp("iqwircs")+".fits"
iraf.imsurfit(imflat1,imsurf2,xorder=6,yorder=6,type_output="fit",
function="chebyshev",cross_terms=yes,
xmedian=21,ymedian=21,median_percent=50.0,
lower=0.0,upper=0.0,ngrow=0,niter=0,
regions="all",rows="*",columns="*",border=50,
sections="",circle="",div_min="INDEF")
# Corresponding bad pixel mask
imbpm2=iraf.mktemp("iqwircb")+".pl"
iraf.imexpr("abs(x)>%.3f ? 0 : 1" % clipfrac,imbpm2,x=imsurf2)
# Combine bad pixel masks for median + flat
imbpm3=iraf.mktemp("iqwircb")+".pl"
iraf.imexpr("(x>0 || y>0) ? 1 : 0",imbpm3,x=imbpm1,y=imbpm2)
# Calculate the ratio image
imratio=iraf.mktemp("iqwircr")+".fits"
iraf.imexpr("z>0 ? 0 : x/y",imratio,x=imsurf1,y=imsurf2,z=imbpm3)
# Mimstat on the ratio image
mimstat=iraf.mimstatistics(imratio,imasks=imbpm3,omasks="",
fields='image,npix,mean,stddev,min,max,mode',
lower='INDEF',upper='INDEF',nclip=4,
lsigma=5.0,usigma=5.0,binwidth=0.1,
format=no,Stdout=1,Stderr=1)
mimels=mimstat[0].split()
npix=float(mimels[1])
xmult=float(mimels[2])
# Check that a reasonable number of pixels have made the grade
check_exist(outflat,'w',clobber=clobber)
if npix<0.05*npixall:
print "Less than 5% of pixels passed the cut... preserving flatfield"
iraf.imcopy(inflat,outflat,verbose=no)
xmult=1.0
else:
# Create the final flatfield image
iraf.imexpr("x*%.3f + 1" % xmult,outflat,x=imflat1)
# Update header keywords
update_head(outflat,'RESCALE',1,"Flatfield has been rescaled")
update_head(outflat,'ORIGFLAT',inflat,
"Input flatfield name (before rescaling)")
update_head(outflat,'XMULT',xmult,
"Multiplied ORIGFLAT by this factor to rescale")
# Clean up
iraf.imdel(imcmb1,verify=no,go_ahead=yes)
iraf.imdel(imcmb2,verify=no,go_ahead=yes)
iraf.imdel(imsurf1,verify=no,go_ahead=yes)
iraf.imdel(imsurf2,verify=no,go_ahead=yes)
iraf.imdel(imbpm1,verify=no,go_ahead=yes)
iraf.imdel(imbpm2,verify=no,go_ahead=yes)
iraf.imdel(imbpm3,verify=no,go_ahead=yes)
iraf.imdel(imflat1,verify=no,go_ahead=yes)
iraf.imdel(imratio,verify=no,go_ahead=yes)
for row in chm_data:
col = 0
for elem in row:
if elem == 1:
orig_data[lin, col] = int(999999)
col = col + 1
lin = lin + 1
hd_orig[0].data = orig_data
hd_orig.writeto(fich_ch)
hd_orig.close()
#cria mascara.pl
# bad: 0 -> 1
# god: 999999 -> 0
iraf.imexpr(expr='(a == 0) ? 1 : 0', output=fich_mask, a=fich_ch)
#======================================================
## number of sigma-clip iterations
iraf.samplepar.nclip = 12
## Parametros da geometria EM IMG
iraf.geompar.x0 = x0
iraf.geompar.y0 = y0
iraf.geompar.ellip0 = 0.1
iraf.geompar.sma0 = 15
## ----- nao ajustamos em menos de 1 pixels ##
iraf.geompar.minsma = 1
def ratir_doall(name, ra, dec, refdate, cat="SDSS-R9", varorder=1):
"""Full pipeline for image subtractions with RATIR data."""
filts = ["r", "i", "Z", "Y", "J", "H"]
pixscale_dict = {
'r': 0.317,
'i': 0.317,
'Z': 0.292,
'Y': 0.292,
'J': 0.292,
'H': 0.292
}
exptime_dict = {
'r': 80.0,
'i': 80.0,
'Z': 67.11,
'Y': 67.11,
'J': 67.11,
'H': 67.11
}
gain_dict = {
'r': 1.23,
'i': 1.23,
'Z': 2.20,
'Y': 2.20,
'J': 2.40,
'H': 2.40
}
readn_dict = {
'r': 13.6,
'i': 13.6,
'Z': 14.70,
'Y': 14.70,
'J': 11.25,
'H': 11.25
}
sat_dict = {
'r': 50000.0,
'i': 50000.0,
'Z': 24000.0,
'Y': 24000.0,
'J': 24000.0,
'H': 24000.0
}
dirs = glob.glob("20??????")
dirs.remove(refdate)
# Create directory structure
for filt in filts:
os.mkdir(filt)
# Rename "new" files
for dir in dirs:
if os.path.exists("%s/stack_C0_r.fits" % dir) and os.path.exists(
"%s/stack_C0_r.rms.fits" % dir):
shutil.copy("%s/stack_C0_r.fits" % dir, "r/%s_r.fits" % dir)
shutil.copy("%s/stack_C0_r.rms.fits" % dir,
"r/%s_r.rms.fits" % dir)
if os.path.exists("%s/stack_C1_i.fits" % dir) and os.path.exists(
"%s/stack_C1_i.rms.fits" % dir):
shutil.copy("%s/stack_C1_i.fits" % dir, "i/%s_i.fits" % dir)
shutil.copy("%s/stack_C1_i.rms.fits" % dir,
"i/%s_i.rms.fits" % dir)
if os.path.exists("%s/stackA_C2_ZY.fits" % dir) and os.path.exists(
"%s/stackA_C2_ZY.rms.fits" % dir):
shutil.copy("%s/stackA_C2_ZY.fits" % dir, "Z/%s_Z.fits" % dir)
shutil.copy("%s/stackA_C2_ZY.rms.fits" % dir,
"Z/%s_Z.rms.fits" % dir)
if os.path.exists("%s/stackB_C2_ZY.fits" % dir) and os.path.exists(
"%s/stackB_C2_ZY.rms.fits" % dir):
shutil.copy("%s/stackB_C2_ZY.fits" % dir, "Y/%s_Y.fits" % dir)
shutil.copy("%s/stackB_C2_ZY.rms.fits" % dir,
"Y/%s_Y.rms.fits" % dir)
if os.path.exists("%s/stackA_C3_JH.fits" % dir) and os.path.exists(
"%s/stackA_C3_JH.rms.fits" % dir):
shutil.copy("%s/stackA_C3_JH.fits" % dir, "J/%s_J.fits" % dir)
shutil.copy("%s/stackA_C3_JH.rms.fits" % dir,
"J/%s_J.rms.fits" % dir)
if os.path.exists("%s/stackB_C3_JH.fits" % dir) and os.path.exists(
"%s/stackB_C3_JH.rms.fits" % dir):
shutil.copy("%s/stackB_C3_JH.fits" % dir, "H/%s_H.fits" % dir)
shutil.copy("%s/stackB_C3_JH.rms.fits" % dir,
"H/%s_H.rms.fits" % dir)
# Rename reference files
shutil.copy("%s/stack_C0_r.fits" % refdate, "r/ref_r.fits")
shutil.copy("%s/stack_C0_r.rms.fits" % refdate, "r/ref_r.rms.fits")
shutil.copy("%s/stack_C1_i.fits" % refdate, "i/ref_i.fits")
shutil.copy("%s/stack_C1_i.rms.fits" % refdate, "i/ref_i.rms.fits")
shutil.copy("%s/stackA_C2_ZY.fits" % refdate, "Z/ref_Z.fits")
shutil.copy("%s/stackA_C2_ZY.rms.fits" % refdate, "Z/ref_Z.rms.fits")
shutil.copy("%s/stackB_C2_ZY.fits" % refdate, "Y/ref_Y.fits")
shutil.copy("%s/stackB_C2_ZY.rms.fits" % refdate, "Y/ref_Y.rms.fits")
shutil.copy("%s/stackA_C3_JH.fits" % refdate, "J/ref_J.fits")
shutil.copy("%s/stackA_C3_JH.rms.fits" % refdate, "J/ref_J.rms.fits")
shutil.copy("%s/stackB_C3_JH.fits" % refdate, "H/ref_H.fits")
shutil.copy("%s/stackB_C3_JH.rms.fits" % refdate, "H/ref_H.rms.fits")
# Create ds9 region file for OT location
coofile = open("Coords.reg", "w")
coofile.write('fk5;circle(%10.5f,%10.5f,1.0") # text={%s}' %
(ra, dec, name))
coofile.close()
# Get SDSS reference stars
os.system("getsdss.pl -r 7.0 -f sdss.reg -p %10.5f %10.5f sdss.txt" %
(ra, dec))
# Get 2MASS stars
os.system(
"getastrom.pl -d 2mass -r 7.0 -f temp.reg %10.5f %10.5f 2mass.txt" %
(ra, dec))
tmass = Starlist("temp.reg")
for star in tmass:
star.mags["YMAG"] = star.mags["JMAG"] + 0.5 * (
star.mags["JMAG"] - star.mags["HMAG"]) + 0.08
tmass.write("2mass.reg")
os.remove("temp.reg")
# If no SDSS coverage, copy 2mass.reg to sdss.reg (kludge until PS1)
if os.stat("sdss.txt")[6] == 0:
shutil.copy("ps1.reg", "sdss.reg")
# Loop over filters
for filt in filts:
iraf.chdir(filt)
# Update ref header
update_head("ref_%s.fits" % filt, ["PIXSCALE", "SATURATE"],
[pixscale_dict[filt], sat_dict[filt]])
# Generate mask for reference
iraf.imexpr("a == 0 ? 1 : 0", "ref_%s.mask.fits" % filt,
"ref_%s.fits" % filt)
# Generate variance for reference
iraf.imcopy("ref_%s.rms.fits" % filt, "ref_%s.var.fits" % filt)
iraf.imreplace("ref_%s.var.fits" % filt,
1.0e31,
lower=INDEF,
upper=0.0)
# Detect objects in reference
iqobjs("ref_%s.fits" % filt,
3.0,
sat_dict[filt],
wtimage="ref_%s.var.fits" % filt,
skyval="0.0")
# Tweak WCS in reference image
p60scamp("ref_%s.fits" % filt,
distortdeg=1,
match=yes,
rms=True,
mask=True,
cat=cat)
os.remove("ref_%s.cat" % filt)
# Get reference stars for PSF matching
sdss = Starlist("../sdss.reg")
ref = Starlist("ref_%s.fits.stars" % filt)
sdss.wcs2pix("ref_%s.fits" % filt)
a, b = sdss.match(ref, maxnum=1000)
a.write("psf_%s.reg" % filt)
# Loop over "new images"
ims = glob.glob("????????_%s.fits" % filt)
for im in ims:
# Update headers
nstack = int(get_head(im, "EXPTIME") / exptime_dict[filt])
update_head(im, ["GAIN", "READN", "SATURATE"], [
nstack * gain_dict[filt], readn_dict[filt] / np.sqrt(nstack),
sat_dict[filt]
])
# Create variance files
iraf.imcopy("%s.rms.fits" % im[:-5], "%s.var.fits" % im[:-5])
iraf.imreplace("%s.var.fits" % im[:-5],
1.0e31,
lower=INDEF,
upper=0.0)
# Create bad pixel mask
iraf.imexpr("a == 0 ? 1 : 0", "%s.mask.fits" % im[:-5], im)
# Update WCS for new images
p60scamp(im, distortdeg=1, match=yes, rms=True, mask=True, cat=cat)
os.remove("%s.cat" % im[:-5])
# Detect objects and measure seeing
iqobjs(im,
5.0,
sat_dict[filt],
wtimage="%s.var.fits" % im[:-5],
skyval="0.0")
# Match sources for PSF determination
newstars = Starlist("%s.stars" % im)
newstars.pix2wcs(im)
newstars.wcs2pix("ref_%s.fits" % filt)
c, d = newstars.match(a, maxnum=1000)
d.write("psf_%s.%s.reg" % (filt, im[:-5]))
# If there was a problem with alignment, will be no PSF stars
if not os.stat("psf_%s.%s.reg" % (filt, im[:-5]))[6] == 0:
if varorder == 0:
#if (filt=="J") or (filt=="H"):
p60sdsssub(im,
"ref_%s.fits" % filt,
"../Coords.reg",
stamps="psf_%s.%s.reg" % (filt, im[:-5]),
nsx=2,
nsy=2,
ko=0,
distortdeg=1)
else:
p60sdsssub(im,
"ref_%s.fits" % filt,
"../Coords.reg",
stamps="psf_%s.%s.reg" % (filt, im[:-5]),
nsx=5,
nsy=5,
ko=1,
distortdeg=1)
# PSF photometry
for im in ims:
if os.path.exists("%s.sub.fits" % im[:-5]):
psfphot(im,
"psf_%s.reg" % filt,
"../Coords.reg",
wtimage="ref_%s.var.fits" % filt,
varorder=varorder)
# Photometry
if (filt == "J") or (filt == "H") or (filt == "Y"):
ratircal("%s.%s.dat" % (name, filt), ims, "../2mass.reg", filt)
else:
ratircal("%s.%s.dat" % (name, filt), ims, "../sdss.reg", filt)
iraf.chdir("../")
return
def p60swarp(image,
outfile,
ractr=None,
dcctr=None,
pixscale=None,
size=None,
backsub=no,
refimage=None,
rms=True,
mask=True):
'''Run SWarp on P60 images'''
swarpcmd = 'swarp %s ' % image
if ractr != None or dcctr != None:
swarpcmd += '-CENTER_TYPE MANUAL -CENTER "%s, %s" ' % (ractr, dcctr)
if pixscale != None:
swarpcmd += '-PIXELSCALE_TYPE MANUAL -PIXEL_SCALE %f ' % pixscale
if size != None:
swarpcmd += '-IMAGE_SIZE "%i, %i" ' % (size[0], size[1])
if backsub == no:
swarpcmd += '-SUBTRACT_BACK N '
swarpcmd += '-COPY_KEYWORDS OBJECT,SKYSUB,SKYBKG,SEEPIX '
if refimage != None:
[
nax1, nax2, crval1, crval2, crpix1, crpix2, cd1_1, cd1_2, cd2_1,
cd2_2
] = get_head(refimage, [
"NAXIS1", "NAXIS2", "CRVAL1", "CRVAL2", "CRPIX1", "CRPIX2",
"CD1_1", "CD1_2", "CD2_1", "CD2_2"
])
hout = open("coadd.head", "w")
hout.write("CRVAL1 = %.8g\n" % crval1)
hout.write("CRVAL2 = %.8g\n" % crval2)
hout.write("CRPIX1 = %.8g\n" % crpix1)
hout.write("CRPIX2 = %.8g\n" % crpix2)
hout.write("CD1_1 = %.8g\n" % cd1_1)
hout.write("CD1_2 = %.8g\n" % cd1_2)
hout.write("CD2_1 = %.8g\n" % cd2_1)
hout.write("CD2_2 = %.8g\n" % cd2_2)
hout.write("END")
hout.close()
swarpcmd += '-IMAGE_SIZE "%i, %i" ' % (nax1, nax2)
scmd = os.popen(swarpcmd, 'r', -1)
scmd.readlines()
shutil.move('coadd.fits', outfile)
if rms == True:
swarpcmd = 'swarp %s.rms.fits ' % image[:-5]
if ractr != None or dcctr != None:
swarpcmd += '-CENTER_TYPE MANUAL -CENTER "%s, %s" ' % (ractr,
dcctr)
if pixscale != None:
swarpcmd += '-PIXELSCALE_TYPE MANUAL -PIXEL_SCALE %f ' % pixscale
if size != None:
swarpcmd += '-IMAGE_SIZE "%i, %i" ' % (size[0], size[1])
if backsub == no:
swarpcmd += '-SUBTRACT_BACK N '
swarpcmd += '-COPY_KEYWORDS OBJECT,SKYSUB,SKYBKG,SEEPIX '
if refimage != None:
[
nax1, nax2, crval1, crval2, crpix1, crpix2, cd1_1, cd1_2,
cd2_1, cd2_2
] = get_head(refimage, [
"NAXIS1", "NAXIS2", "CRVAL1", "CRVAL2", "CRPIX1", "CRPIX2",
"CD1_1", "CD1_2", "CD2_1", "CD2_2"
])
hout = open("coadd.head", "w")
hout.write("CRVAL1 = %.8g\n" % crval1)
hout.write("CRVAL2 = %.8g\n" % crval2)
hout.write("CRPIX1 = %.8g\n" % crpix1)
hout.write("CRPIX2 = %.8g\n" % crpix2)
hout.write("CD1_1 = %.8g\n" % cd1_1)
hout.write("CD1_2 = %.8g\n" % cd1_2)
hout.write("CD2_1 = %.8g\n" % cd2_1)
hout.write("CD2_2 = %.8g\n" % cd2_2)
hout.write("END")
hout.close()
swarpcmd += '-IMAGE_SIZE "%i, %i" ' % (nax1, nax2)
scmd = os.popen(swarpcmd, 'r', -1)
scmd.readlines()
shutil.move('coadd.fits', '%s.rms.fits' % outfile[:-5])
if mask == True:
swarpcmd = 'swarp %s.mask.fits ' % image[:-5]
if ractr != None or dcctr != None:
swarpcmd += '-CENTER_TYPE MANUAL -CENTER "%s, %s" ' % (ractr,
dcctr)
if pixscale != None:
swarpcmd += '-PIXELSCALE_TYPE MANUAL -PIXEL_SCALE %f ' % pixscale
if size != None:
swarpcmd += '-IMAGE_SIZE "%i, %i" ' % (size[0], size[1])
if backsub == no:
swarpcmd += '-SUBTRACT_BACK N '
swarpcmd += '-COPY_KEYWORDS OBJECT,SKYSUB,SKYBKG,SEEPIX '
if refimage != None:
[
nax1, nax2, crval1, crval2, crpix1, crpix2, cd1_1, cd1_2,
cd2_1, cd2_2
] = get_head(refimage, [
"NAXIS1", "NAXIS2", "CRVAL1", "CRVAL2", "CRPIX1", "CRPIX2",
"CD1_1", "CD1_2", "CD2_1", "CD2_2"
])
hout = open("coadd.head", "w")
hout.write("CRVAL1 = %.8g\n" % crval1)
hout.write("CRVAL2 = %.8g\n" % crval2)
hout.write("CRPIX1 = %.8g\n" % crpix1)
hout.write("CRPIX2 = %.8g\n" % crpix2)
hout.write("CD1_1 = %.8g\n" % cd1_1)
hout.write("CD1_2 = %.8g\n" % cd1_2)
hout.write("CD2_1 = %.8g\n" % cd2_1)
hout.write("CD2_2 = %.8g\n" % cd2_2)
hout.write("END")
hout.close()
swarpcmd += '-IMAGE_SIZE "%i, %i" ' % (nax1, nax2)
scmd = os.popen(swarpcmd, 'r', -1)
scmd.readlines()
iraf.imexpr("a > 0 ? 1 : 0", "%s.mask.fits" % outfile[:-5],
"coadd.fits")
os.remove("coadd.fits")
return
def fitone(self, objectid, psffile=None, magzpt=None, exptime=1.0):
"""
A driver function that fits one object, given its ID.
Most of the work is done here.
Provide a PSF file and magnitude zero point for each object!
"""
if psffile == None: psffile = self.psffile
if magzpt == None: magzpt = self.magzpt
idcrit = (self.id_array == objectid)
ra = self.ra_array[idcrit][0]
dec = self.dec_array[idcrit][0]
mag = self.mag_array[idcrit][0]
Re = self.Re_array[idcrit][0]
axratio = self.axratio_array[idcrit][0]
theta = self.theta_array[idcrit][0]
isoarea = self.isoarea_array[idcrit][0]
# Now figure out image coordinates
x = self.x_array[idcrit][0]
y = self.y_array[idcrit][0]
print "x, y =", x, y
OUT1 = open(self.crashes, "ab")
OUT2 = open(self.fitted, "ab")
# now create arrays that will be included in this GALFIT run
id_fit = [objectid]
mag_fit = [mag]
Re_fit = [Re]
x_fit = [x]
y_fit = [y]
theta_fit = [theta]
axratio_fit = [axratio]
# step 1: determine temporary image size
# Experimental image size
majx = abs(N.sqrt(isoarea) * 4. *
N.sin(theta / 180. * N.pi)) # convert degree into radian
majy = abs(N.sqrt(isoarea) * 4. * N.cos(theta / 180. * N.pi))
minx = axratio * N.sqrt(isoarea) * 4. * abs(
N.sin((theta + N.pi / 2.) / 180. * N.pi))
miny = axratio * N.sqrt(isoarea) * 4. * abs(
N.sin((theta + N.pi / 2.) / 180. * N.pi))
#Re_max = 20.
Re_max = 60
if Re > Re_max:
Re_max = Re
xsize = majx
# determine the offset of this cutout relative to the entire mosaic
if minx >= majx:
xsize = minx
if xsize <= 30.:
xsize = 30.
ysize = majy
if miny >= majy:
ysize = miny
if ysize <= 30.:
ysize = 30.
xmin = int(x - xsize)
if xmin <= 0:
xmin = 1
xmax = int(x + xsize)
ymin = int(y - ysize)
if ymin <= 0:
ymin = 1
ymax = int(y + ysize)
# construct postage stamp name
outname = self.root + '/obj%d_out.fits' % objectid
# step 2: determine which objects to be included
for jj in range(self.nobj_all): # iterate through other objects
if self.id_array[jj] != objectid:
dx = x - self.x_array[jj]
dy = y - self.y_array[jj]
dist = N.sqrt(dx**2 + dy**2)
# Fit all objects that fall within a certain
# radius of the central object:
radck = N.sqrt(self.isoarea_array[jj])
angle = N.arctan2(dy, dx)
phi = N.pi / 2. - (self.theta_array[jj] / 180. * N.pi +
N.pi / 2. - angle)
thetap = N.arctan2(self.axratio_array[jj] * N.tan(phi), 1.)
isorad = radck * N.sqrt((self.axratio_array[jj] *
N.cos(thetap))**2 + N.sin(thetap)**2)
# If object is within the fitted image region...
if (((self.x_array[jj] >= xmin) and
(self.x_array[jj] <= xmax) and
(self.y_array[jj] >= ymin) and
(self.y_array[jj] <= ymax) and
# but is greater than 2 Re away, and is not more than 3 mag fainter, or
((dist > 2 * Re and self.mag_array[jj] - 3. <= mag) or
# is less than 2 Re away and not more than 5 mag fainter, or
(dist < 2. * Re and self.mag_array[jj] - 5. <= mag))) or
# is outside image, but is about 3 Re away and 1 mag brighter
((self.x_array[jj] >= (xmin - isorad) and
(self.x_array[jj] <= (xmax + isorad) and
(self.y_array[jj] >=
(ymin - isorad)) and (self.y_array[jj] <=
(ymax + isorad)) and
(self.mag_array[jj] + 1.) <= mag)))):
id_fit += [self.id_array[jj]]
x_fit += [self.x_array[jj]]
y_fit += [self.y_array[jj]]
mag_fit += [self.mag_array[jj]]
Re_fit += [self.Re_array[jj]]
axratio_fit += [self.axratio_array[jj]]
theta_fit += [self.theta_array[jj]]
if self.Re_array[jj] > Re_max:
Re_max = self.Re_array[jj]
# step 3: determine fitting size & copy images
# Determine image fitting size and convolution box info
# into the galfit template file
Refrac = 0.7
#Refrac = 2.0
if xmin >= min(x_fit) - Refrac * Re_max:
xmin = min(x_fit) - Refrac * Re_max
if xmin < 1:
xmin = 1
if ymin >= min(y_fit) - Refrac * Re_max:
ymin = min(y_fit) - Refrac * Re_max
if ymin < 1:
ymin = 1
if xmax <= max(x_fit) + Refrac * Re_max:
xmax = max(x_fit) + Refrac * Re_max
if ymax <= max(y_fit) + Refrac * Re_max:
ymax = max(y_fit) + Refrac * Re_max
#cbox = 60
imgxsize = xmax - xmin + 1
imgysize = ymax - ymin + 1
if os.path.exists(outname):
os.remove(outname)
# copy drizzled images
if os.path.exists(self.root + '/obj%d_drz.fits' % objectid):
os.system('rm %s/obj%d_drz.fits' % (self.root, objectid))
drzimg = self.sci_image + '[%d:%d,%d:%d]' % (xmin, xmax, ymin, ymax)
iraf.imcopy(drzimg, self.root + '/obj%d_drz.fits' % objectid)
h = pyfits.open(self.root + '/obj%d_drz.fits' % objectid, 'update')
h[0].header.update('xmin', xmin)
h[0].header.update('xmax', xmax)
h[0].header.update('ymin', ymin)
h[0].header.update('ymax', ymax)
h[0].header.update('exptime', exptime)
h.flush()
h.close()
# copy sigma image
if os.path.exists(self.root + '/obj%d_rms.fits' % objectid):
os.system('rm %s/obj%d_rms.fits' % (self.root, objectid))
iraf.imcopy(
self.rms_image + '[%d:%d,%d:%d]' % (xmin, xmax, ymin, ymax),
self.root + '/obj%d_rms.fits' % objectid)
# copy segmentation images
if os.path.exists(self.root + '/obj%d_seg.fits' % objectid):
os.system('rm %s/obj%d_seg.fits' % (self.root, objectid))
iraf.imcopy(
self.seg_image + '[%d:%d,%d:%d]' % (xmin, xmax, ymin, ymax),
self.root + '/obj%d_seg.fits' % objectid)
# make mask image -- zero-out the included components in the mask image
if os.path.exists("mask2.fits"):
iraf.imdelete("mask2.fits")
if os.path.exists("mask3.fits"):
iraf.imdelete("mask3.fits")
maskexpr = ""
maskname = self.root + "/obj%d_seg.fits" % objectid
print "id_fit", id_fit
for j in range(len(id_fit)):
inid = id_fit[j]
maskexpr = maskexpr + "(a==%d)" % inid
if j != len(id_fit) - 1:
maskexpr = maskexpr + "||"
print maskexpr
# Now make the masks
# In GALFIT, good pixels have mask value 0, while bad pixels have mask values > 0
iraf.imexpr(maskexpr + " ? 0 : a", "mask2.fits", a=maskname)
# After this step, the only non-zero pixels will be those belonging to the objects that are NOT
# included in the list id_fit.
# Now flatten the mask image and convolve with a Gaussian, in order to grow the masked region a little bit
# to account for wings of objects.
iraf.imexpr("a>0 ? 100. : 0.", "mask3.fits", a="mask2.fits")
iraf.gauss(input="mask3.fits", output="mask3.fits", sigma=5)
if os.path.exists(self.root + '/mask_obj%d.fits' % objectid):
os.remove(self.root + '/mask_obj%d.fits' % objectid)
iraf.imexpr("a<=10. ? 0. : a",
self.root + "/mask_obj%d.fits" % objectid,
a="mask3.fits")
os.remove("mask2.fits")
os.remove("mask3.fits")
# step 4: write GALFIT input file
parfile = "obj%d" % objectid
f = open(parfile, 'w')
# Write image parameters
print >> f, "==============================================================================="
print >> f, "# IMAGE PARAMETERS"
print >> f, "A) %s/obj%d_drz.fits # Input Data image (FITS file) " % (
self.root, objectid)
print >> f, "B) %s/obj%d_out.fits # Output data image block " % (
self.root, objectid)
print >> f, 'C) %s/obj%d_rms.fits # Noise image name (made from data if blank or "none") ' % (
self.root, objectid)
print >> f, "D) %s # Input PSF image for convolution (FITS file) " % psffile
print >> f, "E) 1 # PSF oversampling factor relative to data "
print >> f, "F) %s/mask_obj%d.fits # Bad pixel mask (FITS image or ASCII coord list)" % (
self.root, objectid)
print >> f, "G) %s # Parameter constraint file " % self.constraint_file
print >> f, "H) %d %d %d %d # Image region to fit " % (1, imgxsize, 1,
imgysize)
print >> f, "I) %d %d # Size of the convolution box (x y)" % (
self.cbox, self.cbox)
print >> f, "J) %f # Magnitude photometric zeropoint " % magzpt
print >> f, "K) %s %s # Plate scale (dx dy). " % (self.xscale,
self.yscale)
print >> f, "O) regular # Display type (regular, curses, both) "
print >> f, "P) 0 # Create ouput only? (1=yes; 0=optimize) "
print >> f, "S) 0 # Modify/create objects interactively? "
print >> f, ""
print >> f, "# INITIAL FITTING PARAMETERS "
print >> f, ""
print >> f, "# For object type, allowed functions are: sersic, nuker, "
print >> f, "# expdisk, devauc, moffat, gaussian. "
print >> f, ""
print >> f, "# Objtype: Fit? Parameters "
print >> f, ""
# Write individual component
for j in range(len(id_fit)):
self.component(f, j + 1, x_fit[j] - xmin + 1, y_fit[j] - ymin + 1,
mag_fit[j], Re_fit[j], axratio_fit[j], theta_fit[j])
# Make sky component
#bkgnd = skyest('images/obj%d_drz.fits'%objectid,'images/obj%d_seg.fits'%objectid,5.)
bkgnd = 0.
self.sky(f, len(id_fit) + 1, bkgnd)
f.close()
# step 5: run GALFIT
t1 = time.time()
galfitrun = subprocess.Popen(["galfit", parfile], stdout=sys.stdout)
# runs GALFIT
# ======================================================= #
# Try to time GALFIT and kill it after spending more than
# 10 min on one object
# ======================================================= #
timelimit = 10. * 60. # time limit: 10 minutes
timeint = 10. # check every 10 seconds
maxcheck = int(timelimit / timeint)
kill = 1
for j in range(maxcheck):
time.sleep(timeint) # sleep for check time interval
if galfitrun.poll() == None: # if it's still running:
pass # haven't reached time limit; let it run
else:
kill = 0 # finished before time limit; don't need to kill
break # jump out of process checking
if kill: # if reached time limit and still running:
os.kill(galfitrun.pid, signal.SIGKILL) # kill GALFIT
print "Killed GALFIT; GALFIT froze"
retcode = galfitrun.returncode
t2 = time.time()
try:
print >> OUT1, "returned code is %d" % retcode
except:
print >> OUT1, "returned code is ", retcode
dt = t2 - t1
if retcode != 7: # not sure about the behavior when GALFIT crashes...!!!
print >> OUT1, "%d %s" % (objectid, parfile)
else:
print >> OUT2, "%s-wmask-out.fits %.1f seconds" % (outname, dt)
OUT1.close()
OUT2.close()
print "Finishes GALFIT fitting"
def mkweightmap(bpm,outweight='weight.fits'):
iraf.unlearn('imexpr')
iraf.imexpr('a = 0 ? 1 : 0',outweight,a=bpm)
