def slotview(newfits,indata , fileout, srcfile, fps=10.0, phottype='square', sigdet=5, contpix=10, \ driftlimit=10, clobber=True,logfile='slotview.log',verbose=True): #set up the variables status = 0 entries = [] vig_lo = {} vig_hi = {} hour = 0 min = 0 sec = 0. time0 = 0. nframes = 0 sleep = 0 with logging(logfile, debug) as log: #enter in the input data saltio.fileexists(newfits) #set the sleep parameter if fps > 0: sleep = 1.0 / (fps) # read in the data file id, time, ratio, rerr, tx, ty, tflux, terr, cx, cy, cflux, cerr = st.readlcfile( indata) # read extraction region defintion file amp, x, y, x_o, y_o, r, br1, br2 = st.readsrcfile(srcfile) #determine the size of the data arrays struct = saltio.openfits(newfits) naxis1 = saltkey.get('NAXIS1', struct[1]) naxis2 = saltkey.get('NAXIS2', struct[1]) # Plot all of the data and the first image # Create GUI App = QtGui.QApplication([]) aw=SlotViewWindow(struct, id, tflux, cflux, ratio, time, phottype, sleep, \ tx, ty, cx, cy, r, br1, br2, naxis1, naxis2, sigdet, contpix, driftlimit) aw.show() # Start application event loop app_exit = App.exec_() # Check if GUI was executed succesfully if app_exit != 0: raise SALTError('InterIdentify GUI has unexpected exit status ' + str(exit)) ratio, tflux, cflux, gframe, newphot = aw.ratio, aw.tflux, aw.cflux, aw.goodframes, aw.newphot #close the input file saltio.closefits(struct) # Update the indata file if necessary lc = saltio.openascii(fileout, 'w') for i in range(len(ratio)): x['target'] = tx[i] x['comparison'] = cx[i] y['target'] = ty[i] y['comparison'] = cy[i] reltime = False if gframe[i]: st.writedataout(lc, id[i], time[i], x, y, tflux[i], terr[i], \ cflux[i], cerr[i], ratio[i], rerr[i], time[0], reltime) saltio.closeascii(lc)
def slotview(newfits,indata , fileout, srcfile, fps=10.0, phottype='square', sigdet=5, contpix=10, \ driftlimit=10, clobber=True,logfile='slotview.log',verbose=True): #set up the variables status = 0 entries = [] vig_lo = {} vig_hi = {} hour = 0 min = 0 sec = 0. time0 = 0. nframes = 0 sleep=0 with logging(logfile,debug) as log: #enter in the input data saltio.fileexists(newfits) #set the sleep parameter if fps>0: sleep=1.0/(fps) # read in the data file id, time, ratio, rerr, tx, ty, tflux, terr, cx, cy, cflux, cerr=st.readlcfile(indata) # read extraction region defintion file amp, x, y, x_o, y_o, r, br1, br2=st.readsrcfile(srcfile) #determine the size of the data arrays struct = saltio.openfits(newfits) naxis1 = saltkey.get('NAXIS1',struct[1]) naxis2 = saltkey.get('NAXIS2',struct[1]) # Plot all of the data and the first image # Create GUI App = QtGui.QApplication([]) aw=SlotViewWindow(struct, id, tflux, cflux, ratio, time, phottype, sleep, \ tx, ty, cx, cy, r, br1, br2, naxis1, naxis2, sigdet, contpix, driftlimit) aw.show() # Start application event loop app_exit=App.exec_() # Check if GUI was executed succesfully if app_exit!=0: raise SALTError('InterIdentify GUI has unexpected exit status '+str(exit)) ratio, tflux, cflux, gframe, newphot=aw.ratio, aw.tflux, aw.cflux, aw.goodframes, aw.newphot #close the input file saltio.closefits(struct) # Update the indata file if necessary lc=saltio.openascii(fileout,'w') for i in range(len(ratio)): x['target']=tx[i] x['comparison']=cx[i] y['target']=ty[i] y['comparison']=cy[i] reltime=False if gframe[i]: st.writedataout(lc, id[i], time[i], x, y, tflux[i], terr[i], \ cflux[i], cerr[i], ratio[i], rerr[i], time[0], reltime) saltio.closeascii(lc)
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.')