def lacosmic(name, irafhome, la_iter):
import time
iraf.task(lacos_spec=irafhome + "lacos_spec.cl")
outname = "la" + name
pl = "mask" + name
iraf.lacos_spec(
input=name,
output=outname,
outmask=pl,
gain=1.0,
readn=2.89,
xorder=9,
yorder=0,
sigclip=4.5,
sigfrac=0.5,
objlim=1.0,
niter=la_iter,
verbose="yes",
mode="al",
)
old = time.time()
pidds9 = subprocess.Popen(["ds9", pl, outname, "-zscale"]).pid
os.system("mv %s history/" % (name))
return pidds9
def cosmic_rays (List_image):
full_path = List_image
path = os.path.dirname(full_path)
List_image = full_path.replace(path + '/','')
os.chdir(path)
iraf.chdir(path)
image_list = open(List_image,'r')
image_out = open('c'+List_image,'w')
for line in image_list:
line = line.split('\n')
print 'Cosmic rays removal: ' + line[0]
hdulist = fits.open(line[0])
#print hdulist[0].header['HIERARCH ESO DET OUT1 RON']
iraf.lacos_spec.input = line[0]
iraf.lacos_spec.output = 'c' + line[0]
if os.path.isfile('c' + line[0]):
os.system('rm c'+line[0])
if os.path.isfile('mask_'+line[0]):
os.system('rm mask_'+line[0])
iraf.lacos_spec.outmask= 'mask_'+line[0]
iraf.lacos_spec.readn= hdulist[0].header['HIERARCH ESO DET OUT1 RON']
iraf.lacos_spec.gain = hdulist[0].header['HIERARCH ESO DET OUT1 GAIN']
iraf.lacos_spec.verbose = 'no'
iraf.lacos_spec(mode='h')
os.system('rm mask_'+line[0])
image_out.write('c'+line[0]+'\n')
hdulist.close()
image_list.close()
image_out.close()
def lacosmic(name,irafhome):
import time
iraf.task(lacos_spec=irafhome+'lacos_spec.cl')
outname = 'la'+name
pl = 'mask'+name
iraf.lacos_spec(input=name,output=outname,outmask=pl,gain=1.,readn=2.89,
xorder=9,yorder=0,sigclip=4.5,sigfrac=0.5,objlim=1.,niter=7,verbose='yes',mode='al')
old = time.time()
os.system('ds9 %s -zscale %s -zscale -blink &' % (pl,name))
os.system('ds9 %s -zscale &' % outname)
return
def call_lacos(args, science, Nslits=0, longslit=False):
outfile = '{0}_lacos.fits'.format(science)
#if os.path.isfile(outfile):
#os.remove(outfile)
if utils.skip(args, 'lacos', outfile):
return outfile[:-5]
print()
print('-' * 30)
print()
print('Removing cosmic rays with LACos ...')
to = time()
head = pyfits.getheader(science + '.fits')
gain = head['GAIN']
rdnoise = head['RDNOISE']
#utils.delete(outfile)
if os.path.isfile(outfile):
iraf.imdelete(outfile)
os.system('cp -p ' + science + '.fits ' + outfile)
utils.removedir('slits')
utils.makedir('slits')
iraf.imcopy.unlearn()
if longslit:
slit = '{0}[sci,1]'.format(science)
outslit = os.path.join('slits' '{0}_long'.format(science))
outmask = os.path.join('slits' '{0}_longmask'.format(science))
iraf.lacos_spec(slit, outslit, outmask, gain=gain, readn=rdnoise)
iraf.imcopy(outslit, '{0}[SCI,1,overwrite]'.format(outfile[:-5]),
verbose='no')
else:
for i in xrange(1, Nslits+1):
slit = '{0}[sci,{1}]'.format(science, i)
print('slit =', slit)
outslit = os.path.join('slits', '{0}_{1}'.format(science, i))
outmask = os.path.join('slits', '{0}_mask{1}'.format(science, i))
if os.path.isfile(outslit):
iraf.imdelete(outslit)
if os.path.isfile(outmask):
iraf.imdelete(outmask)
iraf.lacos_spec(slit, outslit, outmask, gain=gain, readn=rdnoise)
iraf.imcopy(
outslit, '{0}[SCI,{1},overwrite]'.format(outfile[:-5], i),
verbose='yes')
utils.delete('lacos*')
utils.removedir('slits')
print(outfile[:-5])
print('Done in {0:.2f}'.format((time()-to)/60))
print()
print('-' * 30)
print()
return outfile[:-5]
def single_cosmic (image):
hdulist = fits.open(image)
iraf.lacos_spec.input = image
iraf.lacos_spec.output = 'c' + image
if os.path.isfile('c' + image):
os.system('rm c'+image)
if os.path.isfile('mask_'+image):
os.system('rm mask_'+image)
iraf.lacos_spec.outmask= 'mask_'+image
iraf.lacos_spec.readn= hdulist[0].header['HIERARCH ESO DET OUT1 RON']
iraf.lacos_spec.gain = hdulist[0].header['HIERARCH ESO DET OUT1 GAIN']
iraf.lacos_spec.verbose = 'no'
iraf.lacos_spec(mode='h')
os.system('rm mask_'+ image)
hdulist.close()
return 'c' + image
def lacosmic(name, irafhome, la_iter):
import time
iraf.task(lacos_spec=irafhome + 'lacos_spec.cl')
outname = 'la' + name
pl = 'mask' + name
iraf.lacos_spec(input=name,
output=outname,
outmask=pl,
gain=1.,
readn=2.89,
xorder=9,
yorder=0,
sigclip=4.5,
sigfrac=0.5,
objlim=1.,
niter=la_iter,
verbose='yes',
mode='al')
old = time.time()
pidds9 = subprocess.Popen(['ds9', pl, outname, '-zscale']).pid
os.system('mv %s history/' % (name))
return pidds9
ptfsn2 = 'ptfsn2.fits'
ptfstar1 = 'ptfstar1.fits'
ptfstar2 = 'ptfstar2.fits'
#Cosmic Cleaned Version
ptfsn1cr = 'ptfsn1.cr'
ptfsn2cr = 'ptfsn2.cr'
#Cosmic Rejection
iraf.lacos_spec(input=ptfsn1,
output=ptfsn1cr,
outmask='ptfsn1.crmask',
gain=1.0,
readn=3.85,
xorder=9,
yorder=3,
sigclip=4.5,
sigfrac=0.5,
objlim=1.0,
niter=3,
verbose=yes,
mode='al')
iraf.lacos_spec(input=ptfsn2,
output=ptfsn2cr,
outmask='ptfsn2.crmask',
gain=1.0,
readn=3.85,
xorder=9,
yorder=3,
sigclip=4.5,
print "Exiting!! CANT process files while output files already exist, delete these then re-run"
## starting to process files
if outfile == 'false':
print "Files to process: ", i
##EPAR settings for LACOS.SPEC
iraf.lacos_spec.gain = 1.2
iraf.lacos_spec.readn = 4.2
iraf.lacos_spec.xorder = 3.0
iraf.lacos_spec.yorder = 3.0
iraf.lacos_spec.sigclip = 3.9
iraf.lacos_spec.sigfrac = 2.0
iraf.lacos_spec.objlim = 1.0
iraf.lacos_spec.niter = 4
iraf.lacos_spec.verbose = "n"
#processing LACOS on each file
start = time.time()
n=0
while n < i:
print "workin on file", inlist[n], "(", n+1, ")"
iraf.lacos_spec(inlist[n], outlist[n], 'temp.pl')
n +=1
os.remove('temp.pl')
time.sleep(5) #Needed as LACOS was slow at deleting LACOS files when it finishes
end = time.time()
print "Run Time: ", end - start
print 'Program finished'