def slotback(images,
outfits,
extension,
imgtype='image',
subbacktype='median',
sigback=3,
mbin=7,
sorder=3,
niter=5,
ampperccd=2,
ignorexp=6,
clobber=False,
logfile='salt.log',
verbose=True):
with logging(logfile, debug) as log:
# set up the variables
order = sorder
plotfreq = 0.01
ftime = plotfreq
# is the input file specified?
infiles = saltio.argunpack('Input', images)
# is the output file specified?
saltio.filedefined('Output', outfits)
#open the first file and check its charactistics
struct = saltio.openfits(infiles[0])
# how many extensions?
nextend = saltkey.get('NEXTEND', struct[0])
if nextend < extension:
msg = 'Insufficient number of extensions in %s' % (infile)
raise SaltIOError(msg)
# how many amplifiers?
amplifiers = saltkey.get('NCCDS', struct[0])
amplifiers = int(ampperccd * float(amplifiers))
if ampperccd > 0:
nframes = nextend / amplifiers
nstep = amplifiers
else:
nframes = nextend
nstep = 1
ntotal = nframes * len(infiles)
# image size
naxis1 = saltkey.get('NAXIS1', struct[extension])
naxis2 = saltkey.get('NAXIS2', struct[extension])
# CCD binning
ccdsum = saltkey.get('CCDSUM', struct[0])
binx = int(ccdsum.split(' ')[0])
biny = int(ccdsum.split(' ')[1])
# If a total file is to written out, create it and update it
hdu = 1
# delete the file if clobber is on and the file exists
if os.path.isfile(outfits):
if clobber:
saltio.delete(outfits)
else:
raise SaltIOError(
'Output fits file ' + writenewfits +
'already exists. Use Clobber=yes to overwrite file')
# create the output file
try:
hdu = pyfits.PrimaryHDU()
hdu.header = struct[0].header
hdu.header['NCCDS'] = 1
hdu.header['NSCIEXT'] = ntotal - ignorexp
hdu.header['NEXTEND'] = ntotal - ignorexp
hduList = pyfits.HDUList(hdu)
hduList.verify()
hduList.writeto(outfits)
except:
raise SaltIOError('Could not create new fits file named ' +
writenewfits)
# read it back in for updating
hduList = saltio.openfits(outfits, mode='update')
# set up the completeness tracker
if verbose:
j = 0
x2 = float(j) / float(ntotal)
ctext = 'Percentage Complete: %3.2f' % x2
sys.stdout.write(ctext)
sys.stdout.flush()
for infile in infiles:
struct = saltio.openfits(infile)
# Skip through the frames and process each frame individually
for i in range(nframes):
if not (infile == infiles[0] and i < ignorexp):
hdu = extension + i * nstep
try:
header = struct[hdu].header
array = struct[hdu].data
array = array * 1.0
except Exception, e:
msg = 'Unable to open extension %i in image %s because %s' % (
hdu, infile, e)
raise SaltIOError(msg)
# start the analysis of each frame
# gain and readout noise
try:
gain = float(header['GAIN'])
except:
gain = 1
log.warning('Gain not specified in image header')
try:
rdnoise = float(header['RDNOISE'])
except:
rdnoise = 0
log.warning('RDNOISE not specified in image header')
# background subtraction
if not subbacktype == 'none':
try:
narray = subbackground(array, sigback, mbin, order,
niter, subbacktype)
except:
log.warning('Image ' + infile + ' extention ' +
str(i) + ' is blank, skipping')
continue
# create output array
try:
if imgtype == 'background':
oarray = narray - array
else:
oarray = narray
except:
oarray = array
# print progress
if verbose:
x2 = float(j) / float(ntotal)
if x2 > ftime:
ctext = '\b\b\b\b\b %3.2f' % x2
sys.stdout.write(ctext)
sys.stdout.flush()
ftime += plotfreq
# update the header values with the image name and extension number
try:
hdue = pyfits.ImageHDU(oarray)
hdue.header = header
hdue.header.update('ONAME', infile,
'Original image name')
hdue.header.update('OEXT', hdu,
'Original extension number')
except Exception, e:
msg='SALTPHOT--WARNING: Could not update image in newfits file for %s ext %i because %s' \
% (infile, hdu, e)
raise SaltIOError(msg)
hduList.append(hdue)
j += 1
# close FITS file
saltio.closefits(struct)
def slotback(images,outfits,extension,imgtype='image',subbacktype='median',
sigback=3,mbin=7,sorder=3,niter=5,ampperccd=2,ignorexp=6,
clobber=False,logfile='salt.log',verbose=True):
with logging(logfile,debug) as log:
# set up the variables
order=sorder
plotfreq=0.01
ftime=plotfreq
# is the input file specified?
infiles = saltio.argunpack ('Input',images)
# is the output file specified?
saltio.filedefined('Output',outfits)
#open the first file and check its charactistics
struct=saltio.openfits(infiles[0])
# how many extensions?
nextend=saltkey.get('NEXTEND',struct[0])
if nextend < extension:
msg='Insufficient number of extensions in %s' % (infile)
raise SaltIOError(msg)
# how many amplifiers?
amplifiers=saltkey.get('NCCDS',struct[0])
amplifiers = int(ampperccd*float(amplifiers))
if ampperccd>0:
nframes = nextend/amplifiers
nstep=amplifiers
else:
nframes = nextend
nstep=1
ntotal=nframes*len(infiles)
# image size
naxis1=saltkey.get('NAXIS1',struct[extension])
naxis2=saltkey.get('NAXIS2',struct[extension])
# CCD binning
ccdsum=saltkey.get('CCDSUM',struct[0])
binx=int(ccdsum.split(' ')[0])
biny=int(ccdsum.split(' ')[1])
# If a total file is to written out, create it and update it
hdu = 1
# delete the file if clobber is on and the file exists
if os.path.isfile(outfits):
if clobber:
saltio.delete(outfits)
else:
raise SaltIOError('Output fits file '+writenewfits+'already exists. Use Clobber=yes to overwrite file')
# create the output file
try:
hdu = pyfits.PrimaryHDU()
hdu.header=struct[0].header
hdu.header['NCCDS']=1
hdu.header['NSCIEXT']=ntotal-ignorexp
hdu.header['NEXTEND']=ntotal-ignorexp
hduList = pyfits.HDUList(hdu)
hduList.verify()
hduList.writeto(outfits)
except:
raise SaltIOError('Could not create new fits file named '+writenewfits)
# read it back in for updating
hduList = saltio.openfits(outfits,mode='update')
# set up the completeness tracker
if verbose:
j=0
x2=float(j)/float(ntotal)
ctext='Percentage Complete: %3.2f' % x2
sys.stdout.write(ctext)
sys.stdout.flush()
for infile in infiles:
struct=saltio.openfits(infile)
# Skip through the frames and process each frame individually
for i in range(nframes):
if not (infile==infiles[0] and i < ignorexp):
hdu=extension+i*nstep
try:
header=struct[hdu].header
array=struct[hdu].data
array=array*1.0
except Exception as e:
msg='Unable to open extension %i in image %s because %s' % (hdu, infile, e)
raise SaltIOError(msg)
# start the analysis of each frame
# gain and readout noise
try:
gain=float(header['GAIN'])
except:
gain=1
log.warning('Gain not specified in image header')
try:
rdnoise=float(header['RDNOISE'])
except:
rdnoise=0
log.warning('RDNOISE not specified in image header')
# background subtraction
if not subbacktype=='none':
try:
narray=subbackground(array, sigback, mbin, order, niter, subbacktype)
except:
log.warning('Image '+infile+' extention '+str(i)+' is blank, skipping')
continue
# create output array
try:
if imgtype=='background':
oarray=narray-array
else:
oarray=narray
except:
oarray=array
# print progress
if verbose:
x2=float(j)/float(ntotal)
if x2 > ftime:
ctext='\b\b\b\b\b %3.2f' % x2
sys.stdout.write(ctext)
sys.stdout.flush()
ftime += plotfreq
# update the header values with the image name and extension number
try:
hdue = pyfits.ImageHDU(oarray)
hdue.header=header
hdue.header.update('ONAME',infile,'Original image name')
hdue.header.update('OEXT',hdu,'Original extension number')
except Exception as e:
msg='SALTPHOT--WARNING: Could not update image in newfits file for %s ext %i because %s' \
% (infile, hdu, e)
raise SaltIOError(msg)
hduList.append(hdue)
j +=1
# close FITS file
saltio.closefits(struct)
# close the output fits file:
try:
# write out the file
hduList.flush()
hduList.close()
except Exception as e:
raise SaltIOError('Failed to write %s because %s' % (outfits, e))
def slotphot(images,outfile,srcfile,newfits=None,phottype='square',
subbacktype='median',sigback=3,mbin=7,sorder=3,niter=5,sigdet=5,
contpix=10,ampperccd=2,ignorexp=6,driftlimit=10.,finddrift=True,
outtype='ascii',reltime=True,clobber=True,logfile='salt.log',
verbose=True):
"""Perform photometry on listed SALT slotmode *images*."""
with logging(logfile,debug) as log:
# set up the variables
entries = []
vig_lo = {}
vig_hi = {}
amp = {}
x = {}
y = {}
x_o = {}
y_o = {}
r = {}
br1 = {}
br2 = {}
hour = 0
min = 0
sec = 0.
time0 = 0.
nframes = 0
bin=mbin
order=sorder
# is the input file specified?
saltsafeio.filedefined('Input',images)
# if the input file is a list, does it exist?
if images[0] == '@':
saltsafeio.listexists('Input',images)
# parse list of input files
infiles=saltsafeio.listparse('Raw image',images,'','','')
# check input files exist
saltsafeio.filesexist(infiles,'','r')
# is the output file specified?
saltsafeio.filedefined('Output',outfile)
# check output file does not exist, optionally remove it if it does exist
if os.path.exists(outfile) and clobber:
os.remove(outfile)
elif os.path.exists(outfile) and not clobber:
raise SaltIOError('File '+outfile+' already exists, use clobber=y')
# open output ascii file
if outtype=='ascii':
try:
lc = open(outfile,'a')
except:
raise SaltIOError('Cannot open ouput file '+outfile)
# is the extraction region defintion file specified?
saltsafeio.filedefined('Extraction region defintion',srcfile)
# check extraction region defintion file exists
srcfile = srcfile.strip()
saltsafeio.fileexists(srcfile)
# read extraction region defintion file
amp, x, y, x_o, y_o, r, br1, br2=slottool.readsrcfile(srcfile)
# set the writenewfits parameter
if not newfits or newfits=='none':
writenewfits=False
else:
writenewfits=newfits
# get time of first exposure and basic information about the observations
infile=infiles[0]
struct=saltsafeio.openfits(infile)
# identify instrument
instrume,keyprep,keygain,keybias,keyxtalk,keyslot=saltsafekey.instrumid(struct,infile)
# how many extensions?
nextend=saltsafekey.get('NEXTEND',struct[0],infile)
if nextend < amp['comparison']:
msg='Insufficient number of extensions in %s' % (infile)
raise SaltIOError(msg)
# how many amplifiers?
amplifiers=saltsafekey.get('NCCDS',struct[0],infile)
amplifiers = int(ampperccd*float(amplifiers))
if ampperccd>0:
nframes = int(nextend/amplifiers)
nstep=amplifiers
else:
nframes = nextend
nstep=1
ntotal=nframes*len(infiles)
# image size
naxis1=saltsafekey.get('NAXIS1',struct[amp['comparison']],infile)
naxis2=saltsafekey.get('NAXIS2',struct[amp['comparison']],infile)
# CCD binning
ccdsum=saltsafekey.get('CCDSUM',struct[0],infile)
binx=int(ccdsum.split(' ')[0])
biny=int(ccdsum.split(' ')[1])
# Identify the time of the observations
ext = 1
try:
time0=slottool.getobstime(struct[ext], infile+'['+str(ext)+']')
dateobs=saltsafekey.get('DATE-OBS',struct[ext],infile)
dateobs=dateobs.replace('-','/')
except:
raise SaltIOError('No time or obsdate in first image')
# If a total file is to be written out, create it and update it
if writenewfits:
if os.path.isfile(writenewfits):
if clobber:
saltsafeio.delete(writenewfits)
else:
raise SaltIOError('Newfits file exists, use clobber')
try:
hdu=pyfits.PrimaryHDU()
hdu.header=struct[0].header
hdu.header['NCCDS']=1
hdu.header['NSCIEXT']=ntotal-ignorexp
hdu.header['NEXTEND']=ntotal-ignorexp
hduList=pyfits.HDUList(hdu)
hduList.verify()
hduList.writeto(writenewfits)
except:
raise SaltIOError('Could not create newfits file, '+writenewfits)
# Close image file
saltsafeio.closefits(struct)
# Read newfits file back in for updating
if writenewfits:
try:
hduList=pyfits.open(writenewfits,mode='update')
except:
raise SaltIOError('Cannot open newfits file '+writenewfits+' for updating.')
# set up the arrays
j=0
time=np.zeros(ntotal ,dtype='float')-1.0
dx=np.zeros(ntotal ,dtype='float')
dy=np.zeros(ntotal ,dtype='float')
tflux=np.zeros(ntotal ,dtype='float')
terr =np.zeros(ntotal ,dtype='float')
cflux=np.zeros(ntotal ,dtype='float')
cerr =np.zeros(ntotal ,dtype='float')
ratio=np.zeros(ntotal ,dtype='float')
rerr =np.zeros(ntotal ,dtype='float')
tgt_x=np.zeros(ntotal ,dtype='float')
tgt_y=np.zeros(ntotal ,dtype='float')
cmp_x=np.zeros(ntotal ,dtype='float')
cmp_y=np.zeros(ntotal ,dtype='float')
p_one=100./ntotal # One percent
p_old=-1 # Previous completed percentage
p_new=0 # New completed percentage
p_n=1 # Counter number
for infile in infiles:
# Log
if verbose:
log.message('Starting photometry on file '+infile, with_stdout=False)
struct=pyfits.open(infile)
# Skip through the frames and process each frame individually
for i in range(nframes):
# Show progress
if verbose:
p_new=int(p_n*p_one)
p_n+=1
if p_new!=p_old:
ctext='Percentage Complete: %d\r' % p_new
sys.stdout.write(ctext)
sys.stdout.flush()
p_old=p_new
if not (infile==infiles[0] and i < ignorexp):
ext=amp['comparison']+i*nstep
try:
header=struct[ext].header
array=struct[ext].data
array=array*1.0
except:
msg='Unable to open extension %i in image %s' % (ext, infile)
raise SaltIOError(msg)
# starti the analysis of each frame
# get the time
time[j]=slottool.getobstime(struct[ext],infile+'['+str(ext)+']')
# gain and readout noise
try:
gain=float(header['GAIN'])
except:
gain=1
raise SaltIOError('Gain not specified in image header')
try:
rdnoise=float(header['RDNOISE'])
except:
rdnoise=0
raise SaltIOError('RDNOISE not specified in image header')
# background subtraction
if not subbacktype=='none':
try:
array=subbackground(array, sigback, bin, order, niter, subbacktype)
except SaltError:
log.warning('Image '+infile+' extention '+str(ext)+' is blank, skipping')
continue
# x-y fit to the comparison star and update the x,y values
if finddrift:
carray, fx,fy=slottool.finddrift(array, x['comparison'], y['comparison'], r['comparison'], naxis1, naxis2, sigdet, contpix, sigback, driftlimit, niter)
if fx > -1 and fy > -1:
if fx < naxis1 and fy < naxis2:
dx[j]=x['comparison']-fx
dy[j]=y['comparison']-fy
x['comparison']=fx
y['comparison']=fy
x['target']=x['target']-dx[j]
y['target']=y['target']-dy[j]
else:
dx[j]=0
dy[j]=0
x['comparison']=x_o['comparison']
y['comparison']=y_o['comparison']
x['target']=x_o['target']
y['target']=y_o['target']
else:
msg='No comparison object found in image file ' + infile+' on extension %i skipping.' % ext
log.warning(msg)
pass
# do photometry
try:
tflux[j],terr[j],cflux[j],cerr[j],ratio[j],rerr[j]=slottool.dophot(phottype, array, x, y, r, br1, br2, gain, rdnoise, naxis1, naxis2)
except SaltError, e:
msg='Could not do photometry on extension %i in image %s because %s skipping.' % (ext, infile, e)
log.warning(msg)
tgt_x[j]=x['target']
tgt_y[j]=y['target']
cmp_x[j]=x['comparison']
cmp_y[j]=y['comparison']
# record results
# TODO! This should be removed in favor of the write all to disk in the end
if outtype=='ascii':
slottool.writedataout(lc, j+1, time[j], x, y, tflux[j], terr[j], cflux[j],cerr[j],ratio[j],rerr[j],time0, reltime)
# write newfits file
if writenewfits:
# add original name and extension number to header
try:
hdue=pyfits.ImageHDU(array)
hdue.header=header
hdue.header.update('ONAME',infile,'Original image name')
hdue.header.update('OEXT',ext,'Original extension number')
hduList.append(hdue)
except:
log.warning('Could not update image in newfits '+infile+' '+str(ext))
# increment counter
j+=1
# close FITS file
saltsafeio.closefits(struct)
# close newfits file
if writenewfits:
try:
hduList.flush()
hduList.close()
except:
raise SaltIOError('Cannot close newfits file.')
# write to output
if outtype=='ascii':
# close output ascii file
try:
lc.close()
except:
raise SaltIOError('Cannot close ouput file ' + outfile)
elif outtype=='fits':
print 'writing fits'
try:
c1=pyfits.Column(name='index',format='D',array=np.arange(ntotal))
if reltime:
c2=pyfits.Column(name='time',format='D',array=time-time0)
else:
c2=pyfits.Column(name='time',format='D',array=time)
c3=pyfits.Column(name='tgt_x',format='D',array=tgt_x)
c4=pyfits.Column(name='tgt_y',format='D',array=tgt_y)
c5=pyfits.Column(name='tgt_flux',format='D',array=tflux)
c6=pyfits.Column(name='tgt_err',format='D',array=terr)
c7=pyfits.Column(name='cmp_x',format='D',array=cmp_x)
c8=pyfits.Column(name='cmp_y',format='D',array=cmp_y)
c9=pyfits.Column(name='cmp_flux',format='D',array=cflux)
c10=pyfits.Column(name='cmp_err',format='D',array=cerr)
c11=pyfits.Column(name='flux_ratio',format='D',array=ratio)
c12=pyfits.Column(name='flux_ratio_err',format='D',array=rerr)
tbhdu=pyfits.new_table([c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12])
# Add header information
tbhdu.header.update('RELTIME',str(reltime),'Time relative to first datapoint or absolute.')
tbhdu.writeto(outfile)
print 'fits written to ',outfile
except:
raise SaltIOError('Could not write to fits table.')
