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.')