예제 #1
0
def saltfpevelocity(infile, existfit, xc, yc, rmax, logfile, verbose):
    """XXX"""

    # getting paths for filenames

    pathin = os.path.dirname(infile)
    basein = os.path.basename(infile)
    pathlog = os.path.dirname(logfile)
    baselog = os.path.basename(logfile)

    print pathin, basein

    # start log now that all parameters are set up
    with logging(logfile, debug) as log:

        # Some basic checks, some tests are done in the FORTRAN code itself
        # is the input file specified?
        saltsafeio.filedefined('Input', infile)

        # if the input file is a file, does it exist?
        if basein[0] != '@':
            saltsafeio.fileexists(infile)

# if a list is input throw an error
        if basein[0] == '@':
            raise SaltIOError(basein + ' list input instead of a file')

# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename

        testfile = open(infile)
        print testfile
        for i in range(1, 5):
            line = testfile.readline()

        line = 'dummy'
        infiles = []
        while (len(line.strip()) != 0):
            line = testfile.readline()
            if (len(line.strip()) > 0):
                linearray = line.split()
                infiles.append(linearray[6])

# check input files exist
        saltsafeio.filesexist(infiles, '', 'r')

        # convert existfile to a one letter string
        if existfit == 'yes':
            existfit == 'y'
        else:
            existfit == 'n'

# If all looks OK, run the FORTRAN code

        print infile, 'input filename'
        print existfit, xc, yc, rmax

        evelocity_wrapper2.evelocity2(infile, existfit, xc, yc, rmax)
예제 #2
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def saltfpeprofile(plottype, infile, logfile, verbose):
    """Line profile fitting and display"""

    plottype = str(plottype)
    plottype = plottype.strip()
    if plottype == 'xwindow':
        plottype = '/xw'
    else:
        plottype = '/ps'

# getting paths for filenames

    pathin = os.path.dirname(infile)
    basein = os.path.basename(infile)
    pathlog = os.path.dirname(logfile)
    baselog = os.path.basename(logfile)

    print pathin, basein

    # start log now that all parameters are set up
    with logging(logfile, debug) as log:

        # Some basic checks, some tests are done in the FORTRAN code itself
        # is the input file specified?
        saltsafeio.filedefined('Input', infile)

        # if the input file is a file, does it exist?
        if basein[0] != '@':
            saltsafeio.fileexists(infile)

# if a list is input throw an error
        if basein[0] == '@':
            raise SaltIOError(basein + ' list input instead of a file')

# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename

        testfile = open(infile)
        print testfile
        for i in range(1, 5):
            line = testfile.readline()

        line = 'dummy'
        infiles = []
        while (len(line.strip()) != 0):
            line = testfile.readline()
            if (len(line.strip()) > 0):
                linearray = line.split()
                infiles.append(linearray[6])

# check input files exist
        saltsafeio.filesexist(infiles, '', 'r')

        # If all looks OK, run the FORTRAN code

        print 'input filename = ', infile

        eprofile_wrapper.eprofile(plottype, infile)
예제 #3
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def slotpreview(images,outfile,ampperccd=2,ignorexp=6,recenter_radius=5,
                tgt_col='b',cmp_col='g', tgt_lw=2,cmp_lw=2,cmap='gray',
                scale='zscale',contrast=0.1,clobber=True,logfile='salt.log',
                verbose=True):

    with logging(logfile,debug) as log:
        
        # 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
        imlist=saltsafeio.listparse('Raw image',images,'','','')

        # check input files exist
        saltsafeio.filesexist(imlist,'','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')

        # Get the number of ccds to calculate the number of frames to skip
        try:
            nccds=pyfits.getheader(imlist[0])['NCCDS']
        except:
            raise SaltIOError('Could not read NCCDS parameter from header of first fits file.')

        # Create GUI
        App = QtGui.QApplication(sys.argv)
        aw = ApplicationWindow(imlist=imlist,
                number=ignorexp*ampperccd*nccds+1,
                config=outfile, target_line_color=tgt_col,
                comparison_line_color=cmp_col, target_line_width=tgt_lw,
                comparison_line_width=cmp_lw, distance=recenter_radius,
                cmap=cmap, scale=scale, contrast=contrast)
        aw.show()

        # Start application event loop
        exit=App.exec_()

        # Check if GUI was executed succesfully
        if exit!=0:
            log.warning('Slotpreview GUI has unexpected exit status'+str(exit))
예제 #4
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def saltfpcalibrate(plottype, infile, outfile, calibratelogfile, logfile,
                    verbose):
    """Determines the wavelength calibration of the Fabry-Perot    
   interactively, using the ring measurements from the CALRING program."""

    plottype = str(plottype)
    plottype = plottype.strip()
    if plottype == 'xwindow':
        plottype = '/xw'
    else:
        plottype = '/ps'

# start log now that all parameter are set up
    with logging(logfile, debug) as log:

        # Some basic checks, many tests are done in the FORTRAN code itself
        # is the input file specified?
        saltsafeio.filedefined('Input', infile)

        # The input file in this case is a file, does it exist?
        if infile[0] != '@':
            saltsafeio.fileexists(infile)

# is the proposed output file specified?

        saltsafeio.filedefined('Output', outfile)

        # check whether the proposed output file exists

        path = os.path.dirname(infile)

        if len(path) > 0:
            dir = path + '/'
        else:
            dir = './'

        print dir, ' directory with data'
        outfile = outfile.strip()
        if os.path.isfile(outfile):
            print 'output file exists, appending'
#            saltsafeio.delete(outfile)

# check whether the calibrate logfile is defined

        saltsafeio.filedefined('Log', calibratelogfile)

        # Get current working directory as the Fortran code changes dir
        startdir = os.getcwd()

        # If all looks OK, run the FORTRAN code

        calibrate_wrapper.calibrate(plottype, infile, outfile,
                                    calibratelogfile)

        # go back to starting directory
        os.chdir(startdir)
예제 #5
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def saltfpcalibrate(plottype,infile,outfile,calibratelogfile,logfile,verbose):  

    """Determines the wavelength calibration of the Fabry-Perot    
   interactively, using the ring measurements from the CALRING program."""

    plottype = str(plottype)
    plottype = plottype.strip()
    if plottype == 'xwindow':
        plottype = '/xw'
    else:
        plottype = '/ps'
            
# start log now that all parameter are set up          
    with logging(logfile, debug) as log:

# Some basic checks, many tests are done in the FORTRAN code itself
# is the input file specified?
        saltsafeio.filedefined('Input',infile)

# The input file in this case is a file, does it exist?
        if infile[0] != '@':
            saltsafeio.fileexists(infile)

# is the proposed output file specified?

        saltsafeio.filedefined('Output',outfile)

# check whether the proposed output file exists

        path = os.path.dirname(infile)

        if len(path) > 0:
            dir = path + '/'
        else:
            dir = './'

        print dir, ' directory with data'
        outfile = outfile.strip()
        if os.path.isfile(outfile):
            print 'output file exists, appending'
#            saltsafeio.delete(outfile)

# check whether the calibrate logfile is defined

        saltsafeio.filedefined('Log',calibratelogfile)

        # Get current working directory as the Fortran code changes dir
        startdir = os.getcwd()
    
# If all looks OK, run the FORTRAN code
            
        calibrate_wrapper.calibrate(plottype,infile, outfile, calibratelogfile)

        # go back to starting directory
        os.chdir(startdir)   
예제 #6
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def slotpreview(images,
                outfile,
                ampperccd=2,
                ignorexp=6,
                recenter_radius=5,
                tgt_col='b',
                cmp_col='g',
                tgt_lw=2,
                cmp_lw=2,
                cmap='gray',
                scale='zscale',
                contrast=0.1,
                clobber=True,
                logfile='salt.log',
                verbose=True):

    with logging(logfile, debug) as log:

        # 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
        imlist = saltsafeio.listparse('Raw image', images, '', '', '')

        # check input files exist
        saltsafeio.filesexist(imlist, '', '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')

        # Get the number of ccds to calculate the number of frames to skip
        try:
            nccds = pyfits.getheader(imlist[0])['NCCDS']
        except:
            raise SaltIOError(
                'Could not read NCCDS parameter from header of first fits file.'
            )

        # Create GUI
        App = QtGui.QApplication(sys.argv)
        aw = ApplicationWindow(imlist=imlist,
                               number=ignorexp * ampperccd * nccds + 1,
                               config=outfile,
                               target_line_color=tgt_col,
                               comparison_line_color=cmp_col,
                               target_line_width=tgt_lw,
                               comparison_line_width=cmp_lw,
                               distance=recenter_radius,
                               cmap=cmap,
                               scale=scale,
                               contrast=contrast)
        aw.show()

        # Start application event loop
        exit = App.exec_()

        # Check if GUI was executed succesfully
        if exit != 0:
            log.warning('Slotpreview GUI has unexpected exit status' +
                        str(exit))
예제 #7
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def saltheadtime(images,timetype,writetoheader,clobber,logfile,verbose,debug):
    # Start log.
    with logging(logfile,debug) as log:

        # 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')
        
        # Loop over the input files.
        for file in infiles:
            print '---------------------------------------------------------\n\
            '
            print 'Reading file ', file
            openfile= saltsafeio.openfits(file)
            
            #Get information from header, display it, and close file.
            headers=openfile[0].header
            dateTimeString=[]
            ra=headers['RA']
            dec=headers['DEC']
            objEpoch=headers['EPOCH']
            obsEquinox=headers['EQUINOX'] 
                  
            if headers['DETMODE']=='SLOT':
               numExtensions=headers['NEXTEND']
               print 'Detector mode is slot. Number of extensions in this file is '+str(numExtensions)+'.'
               for num in range(numExtensions+1):
                    extheader=openfile[num].header
                    dateTimeString.append(extheader['DATE-OBS']+extheader['TIME-OBS'])       
            else:
                dateTimeString.append(headers['DATE-OBS']+headers['TIME-OBS'])                
            
            openfile.close()

            #Convert times. All equations are in library, salttime.py.
            newTime=[]
            if timetype=="JD(UTC)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoJDUTC(dateTimeString[num]))
                    keyword='JDUT-OBS'
                    comment='Julian Date ref. to UTC.'
                    print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
                    print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
                    '
            elif timetype=="JD(TT)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoJD(dateTimeString[num]))
                    keyword='JD-OBS'
                    comment='Julian Date ref. to TT (Terrestrial timescale)'
                    print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
                    print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
                    '
            elif timetype=="MJD(TT)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoMJD(dateTimeString[num]))
                    keyword='MJD-OBS'
                    comment='Modified JD ref. to TT (Terrestrial timescale)'
                    print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
                    print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
                    '
            elif timetype=="HJD(TT)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoHJD(dateTimeString[num],ra,dec))
                    keyword='HJD-OBS'
                    comment='Heliocentric JD ref. to TT (Terrestrial timescale)'
                    print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
                    print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
                    '
            elif timetype=="BJD(TDB)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoBJD(dateTimeString[num],ra,dec))
                    keyword='BJD-OBS'
                    comment='Barycentric JD ref. to TDB (Barycentric Dynamical Time)'
                    print 'The date and time from header extension '+ str(num) +' are:', dateTimeString[num], "UTC"
                    print 'Converted time ('+ timetype +') ='+str(newTime[num])+'\n\
                    '
           
            
            #Open file to write new time to header, if desired.
            if writetoheader:
                try:
                    filetowrite=fits.open(file,mode='update')
                except Exception, e:
                    print e
                
                for num in range(len(dateTimeString)):
                    hdr=filetowrite[num].header
                    if hdr.has_key(keyword)==1:
                        if clobber:
                            hdr.update(keyword,newTime[num],comment)
                            print 'Keyword ' +keyword +' has been updated in header extension '+str(num)+' to the following value: '+ str(newTime[num])
                        else:
                            print 'Keyword '+keyword+' has not been updated.'
                    else:   
                        hdr.update(keyword,newTime[num],comment,after='TIME-OBS')
                        print 'Keyword ' + keyword +' has been added to header extension '+str(num)+' as the following value: '+ str(newTime[num])
                
                    filetowrite.flush()
                filetowrite.close()
예제 #8
0
def saltfpringfilter(axc,ayc,arad,rxc,ryc,filterfreq,filterwidth,itmax,conv, fitwidth,image,logfile,useconfig,configfile,verbose):  

    """ Determines the center coordinates of a ring, bins the ring radially and computes its power spectrum, and allows the user to select a smoothing filter for the ring.  """

# default parameter values are set up in the pyraf .par file. The values used are then changed if a FORTRAN config file exists and the user elects to override the pyraf .par file.

    # Is the input FORTRAN config file specified? 
    # If it is blank, then it will be ignored.        
    if useconfig:
        configfile = configfile.strip()
        if len(configfile) > 0:
            #check exists
            saltsafeio.fileexists(configfile) 

# read updated parameters from the file 
            array=getpfp(configfile,"axc")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                axc=float(array[0])

            array=getpfp(configfile,"ayc")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                ayc=float(array[0])                

            array=getpfp(configfile,"arad")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                arad=float(array[0])
   
            array=getpfp(configfile,"rxc")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                rxc=float(array[0])

            array=getpfp(configfile,"ryc")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                ryc=float(array[0])

            array=getpfp(configfile,"calring_filter_width")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                filterwidth=int(array[0])

            array=getpfp(configfile,"calring_filter_freq")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                filterfreq=int(array[0])

            array=getpfp(configfile,"calring_itmax")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                itmax=int(array[0])

            array=getpfp(configfile,"calring_conv")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                conv=float(array[0])

            array=getpfp(configfile,"calring_fitwidth")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                fitwidth=float(array[0])


# getting paths for filenames

    pathin = os.path.dirname(image)
    basein = os.path.basename(image)
    pathlog = os.path.dirname(logfile)
    baselog =  os.path.basename(logfile)

# forcing logfiles to be created in the same directory as the input data
# (we change to this directory once starting the fortran code)

    if len(pathin) > 0:
        logfile = baselog
    
# start log now that all parameter are set up          
    with logging(logfile, debug) as log:

# Some basic checks, many tests are done in the FORTRAN code itself
# is the input file specified?
        saltsafeio.filedefined('Input',image)

# if the input file is a file, does it exist?
        if basein[0] != '@':
            saltsafeio.fileexists(image)
            infile = image

# if the input file is a list, throw an error
        if basein[0] == '@':
            raise SaltIOError(basein + ' list input instead of a file' )

# optionally update the FORTRAN config file with new values  - not implemented currently

# If all looks OK, run the FORTRAN code
        if len(pathin) > 0:
            dir = pathin
        else:
            dir = './'
        infile = basein
        print(dir, infile, 'input directory and input file')

        # Get current working directory as the Fortran code changes dir
        startdir = os.getcwd()
            
        ringfilter_wrapper.ringfilter(dir,axc, ayc,arad, rxc,ryc,filterfreq,filterwidth,itmax,conv,fitwidth,infile)

    # go back to starting directory
    os.chdir(startdir) 
예제 #9
0
def saltfpringfilter(axc, ayc, arad, rxc, ryc, filterfreq, filterwidth, itmax,
                     conv, fitwidth, image, logfile, useconfig, configfile,
                     verbose):
    """ Determines the center coordinates of a ring, bins the ring radially and computes its power spectrum, and allows the user to select a smoothing filter for the ring.  """

    # default parameter values are set up in the pyraf .par file. The values used are then changed if a FORTRAN config file exists and the user elects to override the pyraf .par file.

    # Is the input FORTRAN config file specified?
    # If it is blank, then it will be ignored.
    if useconfig:
        configfile = configfile.strip()
        if len(configfile) > 0:
            #check exists
            saltsafeio.fileexists(configfile)

            # read updated parameters from the file
            array = getpfp(configfile, "axc")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                axc = float(array[0])

            array = getpfp(configfile, "ayc")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                ayc = float(array[0])

            array = getpfp(configfile, "arad")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                arad = float(array[0])

            array = getpfp(configfile, "rxc")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                rxc = float(array[0])

            array = getpfp(configfile, "ryc")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                ryc = float(array[0])

            array = getpfp(configfile, "calring_filter_width")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                filterwidth = int(array[0])

            array = getpfp(configfile, "calring_filter_freq")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                filterfreq = int(array[0])

            array = getpfp(configfile, "calring_itmax")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                itmax = int(array[0])

            array = getpfp(configfile, "calring_conv")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                conv = float(array[0])

            array = getpfp(configfile, "calring_fitwidth")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                fitwidth = float(array[0])

# getting paths for filenames

    pathin = os.path.dirname(image)
    basein = os.path.basename(image)
    pathlog = os.path.dirname(logfile)
    baselog = os.path.basename(logfile)

    # forcing logfiles to be created in the same directory as the input data
    # (we change to this directory once starting the fortran code)

    if len(pathin) > 0:
        logfile = baselog

# start log now that all parameter are set up
    with logging(logfile, debug) as log:

        # Some basic checks, many tests are done in the FORTRAN code itself
        # is the input file specified?
        saltsafeio.filedefined('Input', image)

        # if the input file is a file, does it exist?
        if basein[0] != '@':
            saltsafeio.fileexists(image)
            infile = image

# if the input file is a list, throw an error
        if basein[0] == '@':
            raise SaltIOError(basein + ' list input instead of a file')

# optionally update the FORTRAN config file with new values  - not implemented currently

# If all looks OK, run the FORTRAN code
        if len(pathin) > 0:
            dir = pathin
        else:
            dir = './'
        infile = basein
        print dir, infile, 'input directory and input file'

        # Get current working directory as the Fortran code changes dir
        startdir = os.getcwd()

        ringfilter_wrapper.ringfilter(dir, axc, ayc, arad, rxc, ryc,
                                      filterfreq, filterwidth, itmax, conv,
                                      fitwidth, infile)

    # go back to starting directory
    os.chdir(startdir)
예제 #10
0
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)
예제 #11
0
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))
예제 #12
0
def saltfpeprofile(plottype,infile,logfile, verbose):  

    """Line profile fitting and display"""

    plottype = str(plottype)
    plottype = plottype.strip()
    if plottype == 'xwindow':
        plottype = '/xw'
    else:
        plottype = '/ps'
        
# getting paths for filenames

    pathin = os.path.dirname(infile)
    basein = os.path.basename(infile)
    pathlog = os.path.dirname(logfile)
    baselog = os.path.basename(logfile)

    print pathin, basein
    
# start log now that all parameters are set up          
    with logging(logfile, debug) as log:

# Some basic checks, some tests are done in the FORTRAN code itself
# is the input file specified?
        saltsafeio.filedefined('Input',infile)

# if the input file is a file, does it exist? 
        if basein[0] != '@':
            saltsafeio.fileexists(infile)


# if a list is input throw an error
        if basein[0] == '@':
            raise SaltIOError(basein + ' list input instead of a file' )

# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename

        testfile= open(infile)
        print testfile
        for i in range(1, 5):
            line = testfile.readline()

        line = 'dummy'
        infiles=[]
        while (len(line.strip()) != 0):
            line = testfile.readline()
            if (len(line.strip()) > 0):
                linearray = line.split()
                infiles.append(linearray[6])

# check input files exist
        saltsafeio.filesexist(infiles,'','r')


# If all looks OK, run the FORTRAN code
    
        print 'input filename = ', infile

        eprofile_wrapper.eprofile(plottype,infile)
예제 #13
0
def saltheadtime(images, timetype, writetoheader, clobber, logfile, verbose,
                 debug):
    # Start log.
    with logging(logfile, debug) as log:

        # 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')

        # Loop over the input files.
        for file in infiles:
            print '---------------------------------------------------------\n\
            '

            print 'Reading file ', file
            openfile = saltsafeio.openfits(file)

            #Get information from header, display it, and close file.
            headers = openfile[0].header
            dateTimeString = []
            ra = headers['RA']
            dec = headers['DEC']
            objEpoch = headers['EPOCH']
            obsEquinox = headers['EQUINOX']

            if headers['DETMODE'] == 'SLOT':
                numExtensions = headers['NEXTEND']
                print 'Detector mode is slot. Number of extensions in this file is ' + str(
                    numExtensions) + '.'
                for num in range(numExtensions + 1):
                    extheader = openfile[num].header
                    dateTimeString.append(extheader['DATE-OBS'] +
                                          extheader['TIME-OBS'])
            else:
                dateTimeString.append(headers['DATE-OBS'] +
                                      headers['TIME-OBS'])

            openfile.close()

            #Convert times. All equations are in library, salttime.py.
            newTime = []
            if timetype == "JD(UTC)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoJDUTC(dateTimeString[num]))
                    keyword = 'JDUT-OBS'
                    comment = 'Julian Date ref. to UTC.'
                    print 'The date and time from header extension ' + str(
                        num) + ' are:', dateTimeString[num], "UTC"
                    print 'Converted time (' + timetype + ') =' + str(
                        newTime[num]) + '\n\
                    '

            elif timetype == "JD(TT)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoJD(dateTimeString[num]))
                    keyword = 'JD-OBS'
                    comment = 'Julian Date ref. to TT (Terrestrial timescale)'
                    print 'The date and time from header extension ' + str(
                        num) + ' are:', dateTimeString[num], "UTC"
                    print 'Converted time (' + timetype + ') =' + str(
                        newTime[num]) + '\n\
                    '

            elif timetype == "MJD(TT)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoMJD(dateTimeString[num]))
                    keyword = 'MJD-OBS'
                    comment = 'Modified JD ref. to TT (Terrestrial timescale)'
                    print 'The date and time from header extension ' + str(
                        num) + ' are:', dateTimeString[num], "UTC"
                    print 'Converted time (' + timetype + ') =' + str(
                        newTime[num]) + '\n\
                    '

            elif timetype == "HJD(TT)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoHJD(dateTimeString[num], ra,
                                                  dec))
                    keyword = 'HJD-OBS'
                    comment = 'Heliocentric JD ref. to TT (Terrestrial timescale)'
                    print 'The date and time from header extension ' + str(
                        num) + ' are:', dateTimeString[num], "UTC"
                    print 'Converted time (' + timetype + ') =' + str(
                        newTime[num]) + '\n\
                    '

            elif timetype == "BJD(TDB)":
                for num in range(len(dateTimeString)):
                    newTime.append(convertUTtoBJD(dateTimeString[num], ra,
                                                  dec))
                    keyword = 'BJD-OBS'
                    comment = 'Barycentric JD ref. to TDB (Barycentric Dynamical Time)'
                    print 'The date and time from header extension ' + str(
                        num) + ' are:', dateTimeString[num], "UTC"
                    print 'Converted time (' + timetype + ') =' + str(
                        newTime[num]) + '\n\
                    '

            #Open file to write new time to header, if desired.
            if writetoheader:
                try:
                    filetowrite = fits.open(file, mode='update')
                except Exception, e:
                    print e

                for num in range(len(dateTimeString)):
                    hdr = filetowrite[num].header
                    if hdr.has_key(keyword) == 1:
                        if clobber:
                            hdr.update(keyword, newTime[num], comment)
                            print 'Keyword ' + keyword + ' has been updated in header extension ' + str(
                                num) + ' to the following value: ' + str(
                                    newTime[num])
                        else:
                            print 'Keyword ' + keyword + ' has not been updated.'
                    else:
                        hdr.update(keyword,
                                   newTime[num],
                                   comment,
                                   after='TIME-OBS')
                        print 'Keyword ' + keyword + ' has been added to header extension ' + str(
                            num) + ' as the following value: ' + str(
                                newTime[num])

                    filetowrite.flush()
                filetowrite.close()
예제 #14
0
def slotutcfix(images, update, outfile, ampperccd, ignorexp, droplimit, inter,
               plotdata, logfile, verbose, debug):

    with logging(logfile, debug) as log:
        # set up the variables
        utc_list = []

        # 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 and place them in order
        infiles = saltsafeio.listparse('Raw image', images, '', '', '')
        infiles.sort()

        # check input files exist
        saltsafeio.filesexist(infiles, '', 'r')

        # check to see if the output file exists and if so, clobber it
        if os.path.isfile(outfile):
            try:
                os.remove(outfile)
            except:
                raise SaltIOError('File ' + outfile + ' can not be removed')

        # open the outfile
        if outfile:
            try:
                fout = open(outfile, 'w')
            except:
                raise SaltIOError('File ' + outfile + ' can not be opened')

        # get time of first exposure and basic information about the observations
        infile = infiles[0]
        struct = saltsafeio.openfits(infile)

        # check to make sure slotmode data
        detmode = saltsafekey.get('DETMODE', struct[0], infile)
        if detmode != 'Slot Mode':
            raise SaltIOError('Data are not Slot Mode Observations')

        # Check to see if SLOTUTCFIX has already been run
        # and print a warning if they have
        if saltsafekey.found('SLOTUTC', struct[0]):
            message = 'Data have already been processed by SLOTUTCFIX'
            log.warning(message)

        # check to make sure that it is the right version of the software
        scamver = saltsafekey.get('DETSWV', struct[0], infile)
        try:
            scamver = float(scamver.split('-')[-1])
            if 4.42 <= scamver <= 5.00:
                pass
            else:
                raise SaltError(
                    'cannot currently correct this version of the SCAM software.'
                )

        except:
            raise SaltError('Not able to read software version')

        # requested exposure time
        req_texp = saltsafekey.get('EXPTIME', struct[0], infile)

        # how many extensions?
        nextend = saltsafekey.get('NEXTEND', struct[0], infile)

        # how many amplifiers
        amplifiers = saltsafekey.get('NCCDS', struct[0], infile)
        amplifiers = int(ampperccd * float(amplifiers))
        if ampperccd > 0:
            nframes = nextend / amplifiers
            nstep = amplifiers
        else:
            nframes = nextend
            nstep = 1

        # how many total frame and unique times
        ntotal = nextend * len(infiles)
        nunique = len(infiles) * nframes - ignorexp + 1

        # Create arrays necessary for analysis
        id_arr = np.arange(nunique)
        utc_arr = np.zeros(nunique, dtype=float)

        # Read in each file and make a list of the UTC values
        if verbose:
            log.message('Reading in files to create list of UTC values.')

        j = 0
        for n, infile in enumerate(infiles):
            # Show progress
            if verbose:
                percent = 100. * float(n) / float(len(infiles))
                ctext = 'Percentage Complete: %.2f\r' % percent
                sys.stdout.write(ctext)
                sys.stdout.flush()

            struct = saltsafeio.openfits(infile)
            if not len(struct) - 1 == nextend:
                raise SaltIOError(
                    infile,
                    ' has a different number of extensions from the first file'
                )

            # Skip through the frames and read in the utc
            istart = 1
            if infile == infiles[0]:
                istart = ignorexp * amplifiers + 1
            for i in range(istart, len(struct), amplifiers):
                try:
                    utc_list.append(
                        saltsafekey.get('UTC-OBS', struct[i], infile))
                    utc_arr[j] = slottool.getobstime(struct[i], infile)
                    j += 1
                except Exception, e:
                    raise SaltIOError(
                        'Unable to create array of UTC times.  Please check the number of extensions in the files'
                    )

            # close FITS file
            saltsafeio.closefits(struct)

        # set up the other important arrays
        try:
            diff_arr = utc_arr.copy()
            diff_arr[1:] = diff_arr[1:] - utc_arr[:-1]
            diff_arr[0] = -1
            dsec_arr = utc_arr - utc_arr.astype(int)
        except:
            raise SaltIOError('Unable to create timing arrays')

        # calculate the real exposure time
        if verbose:
            log.message('Calculating real exposure time.')

        real_expt, med_expt, t_start, t_arr, ysum_arr = calculate_realexptime(
            id_arr, utc_arr, dsec_arr, diff_arr, req_texp, utc_list)

        # plot the results
        if plotdata:
            if verbose:
                log.message('Plotting data.')
            plt.ion()
            plt.plot(t_arr,
                     ysum_arr,
                     linewidth=0.5,
                     linestyle='-',
                     marker='',
                     color='b')
            plt.xlabel('Time (s)')
            plt.ylabel('Fit')

        # Calculate the corrrect values
        if verbose:
            log.message('Calculating correct values')

        i_start = abs(utc_arr - t_start).argmin()
        t_diff = utc_arr * 0.0 + real_expt
        nd = utc_arr * 0.0
        ndrop = 0
        for i in range(len(utc_arr)):
            if utc_arr[i] >= t_start:
                t_new = t_start + real_expt * (i - i_start + ndrop)
                t_diff[i] = utc_arr[i] - t_new
                while (t_diff[i] > real_expt and nd[i] < droplimit):
                    nd[i] += 1
                    t_new = t_start + real_expt * (i - i_start + ndrop + nd[i])
                    t_diff[i] = utc_arr[i] - t_new
                if (nd[i] < droplimit):
                    ndrop += nd[i]
            else:
                t_new = t_start + real_expt * (i - i_start)
                t_diff[i] = utc_arr[i] - t_new
                while (t_diff[i] > real_expt and nd[i] < droplimit):
                    nd[i] += 1
                    t_new = t_start + real_expt * (i - i_start - nd[i])
                    t_diff[i] = utc_arr[i] - t_new

        # calculate the corrected timestamp by counting 6 record files forward and
        # 8 recored + unrecorded files back--or just 8*t_exp forward.
        # if the object is near the end of the run, then just replace it with
        # the correct value assuming no dropped exposures.

        # first make the array of new times
        new_arr = utc_arr - t_diff

        # Next loop through them to find the corrected time
        corr_arr = utc_arr * 0.0

        for i in range(len(new_arr)):
            if i + 6 < len(new_arr) - 1:
                corr_arr[i] = new_arr[i + 6] - 8 * real_expt
            else:
                corr_arr[i] = new_arr[i] - 2 * real_expt

        t_diff = utc_arr - corr_arr

        # write out the first results
        msg = "Dwell Time=%5.3f Requested Exposure Time=%5.3f Nobs = %i Dropped = %i" % (
            real_expt, req_texp, nunique, ndrop)
        if verbose:
            log.message(msg)

        if outfile:
            fout.write('#' + msg + '\n')
            fout.write('#%23s %2s %12s %12s %10s %8s %4s \n' %
                       ('File', 'N', 'UTC_old', 'UTC_new', 'UTC_new(s)',
                        'Diff', 'drop'))

        # Give the user a chance to update the value
        if inter:
            message = 'Update headers with a dwell time of %5.3f s [y/n]? ' % real_expt
            update = saltsafeio.yn_ask(message)
            if not update:
                message = 'Set Dwell Time manually [y/n]? '
                update = saltsafeio.yn_ask(message)
                if update:
                    message = 'New Dwell Time: '
                    real_expt = saltsafeio.ask(message)
                    try:
                        real_expt = float(real_expt)
                    except Exception, e:
                        msg = 'Could not set user dwell time because %s' % e
                        raise SaltError(msg)
예제 #15
0
def saltfpcalprofile(axc,ayc,arad,rxc,ryc,filter, filterfreq,filterwidth,plottype,itmax,conv, fitwidth,rlo,rhi,rfixed,cenfixed,images,outfile,comment,cala, calb, calc, cald, calf,calprofilelogfile,logfile,useconfig,configfile,verbose):  

    """Fits a Voigt profile to a ring in one or more Fabry-Perot calibration ring images"""

# default parameter values are set up in the pyraf .par file. The values used are then changed if a FORTRAN config file exists and the user elects to override the pyraf .par file.

    # Is the input FORTRAN config file specified? 
    # If it is blank, then it will be ignored.        
    if useconfig:
        configfile = configfile.strip()
        if len(configfile) > 0:
            #check exists
            saltsafeio.fileexists(configfile) 

# read updated parameters from the file 
            array=getpfp(configfile,"axc")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                axc=float(array[0])

            array=getpfp(configfile,"ayc")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                ayc=float(array[0])                

            array=getpfp(configfile,"arad")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                arad=float(array[0])
   
            array=getpfp(configfile,"rxc")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                rxc=float(array[0])

            array=getpfp(configfile,"ryc")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                ryc=float(array[0])

            array=getpfp(configfile,"calring_filter")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                filter=str(array[0])


            array=getpfp(configfile,"calring_filter_width")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                filterwidth=int(array[0])

            array=getpfp(configfile,"calring_filter_freq")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                filterfreq=int(array[0])

            array=getpfp(configfile,"calring_itmax")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                itmax=int(array[0])

            array=getpfp(configfile,"calring_conv")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                conv=float(array[0])

            array=getpfp(configfile,"calring_fitwidth")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                fitwidth=float(array[0])

            array=getpfp(configfile,"calring_rlo")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                rlo=float(array[0])

            array=getpfp(configfile,"calring_rhi")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                rhi=float(array[0])

            array=getpfp(configfile,"calring_fixed")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                cenfixed=str(array[0])
      
            
            array=getpfp(configfile,"calibration_a")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                cala=float(array[0])


            array=getpfp(configfile,"calibration_b")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                calb=float(array[0])

            array=getpfp(configfile,"calibration_c")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                calc=float(array[0])

            array=getpfp(configfile,"calibration_d")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                cald=float(array[0])

            array=getpfp(configfile,"calibration_f")
            s=len(array)
            flag = array[s-1]
            if flag == 1: 
                calf=float(array[0])


    cenfixed=str(cenfixed)
    if cenfixed[0] == 'y' or cenfixed[0] == 'Y':
        cenfixed = 1
    else:
        cenfixed = 0
    cenfixed = bool(cenfixed)
        
    filter = str(filter)
    if filter[0] == 'y' or filter[0] == 'Y':
        filter = 1
    else:
        filter = 0
    filter = bool(filter)

    plottype = str(plottype)
    plottype = plottype.strip()
    if plottype == 'xwindow':
        plottype = '/xw'
    else:
        plottype = '/ps'
        
# getting paths for filenames

    pathin = os.path.dirname(images)
    basein = os.path.basename(images)
    pathout = os.path.dirname(outfile)
    baseout = os.path.basename(outfile)
    pathlog = os.path.dirname(logfile)
    baselog =  os.path.basename(logfile)
    pathcalprofilelog = os.path.dirname(calprofilelogfile)
    basecalprofilelog =  os.path.basename(calprofilelogfile)

# forcing logfiles to be created in the same directory as the input data
# (we change to this directory once starting the fortran code)

    if len(pathin) > 0:
        logfile = baselog
        calprofilelogfile = basecalprofilelog
    
# start log now that all parameter are set up          
    with logging(logfile, debug) as log:

# Some basic checks, many tests are done in the FORTRAN code itself
# is the input file specified?
        saltsafeio.filedefined('Input',images)

# if the input file is a file, does it exist?
        if basein[0] != '@':
            saltsafeio.fileexists(images)
            infile = images

# if the input file is a list, does it exist?
        if basein[0] == '@':
            infile2 = basein.lstrip('@')
            if (len(pathin) > 0):
                infile = pathin + '/' + infile2
            else:
                infile = infile2
            saltsafeio.listexists('Input',infile)

# parse list of input files
            infiles=fpsafeio.fplistparse('Raw image',images,'','','')
# check input files exist
            saltsafeio.filesexist(infiles,'','r')

# is the proposed output file specified?

        saltsafeio.filedefined('Output',outfile)

# check whether the proposed output file exists

        path = os.path.dirname(images)

        if len(path) > 0:
            dir = path + '/'
        else:
            dir = './'

#        print dir, ' directory with data'
        outfile = outfile.strip()
        if os.path.isfile(outfile):
            print 'output file exists, appending'
#            saltsafeio.delete(outfile)


# optionally update the FORTRAN config file with new values  - not implemented currently

# If all looks OK, run the FORTRAN code

        infile = basein
        if len(pathout) > 0 :
            if (pathin == pathout):
                outfile = baseout
        # absolute path then leave alone
            elif pathout[0] == '/':
                outfile = outfile
            else:
   # as will move to directory of input data, need to strip this off if its in the path
                a = pathout.lstrip(pathin)
                b = a.lstrip('/')
                outfile = b + '/' + baseout
            
        
    
        print dir, infile, outfile, 'input directory, input and output files'
        if basein[0] == '@':
            print infiles,'infiles'

        # Get current working directory as the Fortran code changes dir
        startdir = os.getcwd()
            
        calprofile_wrapper.calprofile(dir,calprofilelogfile,outfile,comment, axc, ayc,arad, rxc,ryc,filter,filterfreq,filterwidth,plottype,itmax,conv,fitwidth,rlo,rhi,rfixed, cenfixed,infile, cala, calb, calc, cald, calf)

        # go back to starting directory
        os.chdir(startdir)   
예제 #16
0
def saltfpnightring(axc, ayc, arad, rxc, ryc, filter, filterfreq, filterwidth,
                    plot, plottype, itmax, conv, fitwidth, images, outfile,
                    comment, cala, calb, calc, cald, calf, nightringlogfile,
                    logfile, useconfig, configfile, verbose):
    """Measures the centre coordinates and radius of one or more
  night-time calibration rings  """

    # default parameter values are set up in the pyraf .par file. The values used are then changed if a FORTRAN config file exists and the user elects to override the pyraf .par file.

    # Is the input FORTRAN config file specified?
    # If it is blank, then it will be ignored.
    if useconfig:
        configfile = configfile.strip()
        if len(configfile) > 0:
            #check exists
            saltsafeio.fileexists(configfile)

            # read updated parameters from the file
            array = getpfp(configfile, "axc")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                axc = float(array[0])

            array = getpfp(configfile, "ayc")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                ayc = float(array[0])

            array = getpfp(configfile, "arad")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                arad = float(array[0])

            array = getpfp(configfile, "rxc")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                rxc = float(array[0])

            array = getpfp(configfile, "ryc")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                ryc = float(array[0])

            array = getpfp(configfile, "calring_filter")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                filter = str(array[0])

            array = getpfp(configfile, "calring_filter_width")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                filterwidth = int(array[0])

            array = getpfp(configfile, "calring_filter_freq")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                filterfreq = int(array[0])

            array = getpfp(configfile, "calring_itmax")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                itmax = int(array[0])

            array = getpfp(configfile, "calring_conv")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                conv = float(array[0])

            array = getpfp(configfile, "calring_fitwidth")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                fitwidth = float(array[0])

            array = getpfp(configfile, "calibration_a")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                cala = float(array[0])

            array = getpfp(configfile, "calibration_b")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                calb = float(array[0])

            array = getpfp(configfile, "calibration_c")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                calc = float(array[0])

            array = getpfp(configfile, "calibration_d")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                cald = float(array[0])

            array = getpfp(configfile, "calibration_f")
            s = len(array)
            flag = array[s - 1]
            if flag == 1:
                calf = float(array[0])

    filter = str(filter)
    if filter[0] == 'y' or filter[0] == 'Y':
        filter = 1
    else:
        filter = 0
    filter = bool(filter)

    plot = str(plot)
    if plot[0] == 'y' or plot[0] == 'Y':
        plot = 1
    else:
        plot = 0
    plot = bool(plot)

    plottype = str(plottype)
    plottype = plottype.strip()
    if plottype == 'xwindow':
        plottype = '/xw'
    else:
        plottype = '/ps'

# additional verbose command as required in the fortran code too. Set this to whatever is input in the epar file.

    verb = str(verbose)
    if verb[0] == 'y' or verb[0] == 'Y':
        verb = 1
    else:
        verb = 0
    verb = bool(verb)

    # getting paths for filenames

    pathin = os.path.dirname(images)
    basein = os.path.basename(images)
    pathout = os.path.dirname(outfile)
    baseout = os.path.basename(outfile)
    pathlog = os.path.dirname(logfile)
    baselog = os.path.basename(logfile)
    pathnightringlog = os.path.dirname(nightringlogfile)
    basenightringlog = os.path.basename(nightringlogfile)

    # forcing logfiles to be created in the same directory as the input data
    # (we change to this directory once starting the fortran code)

    if len(pathin) > 0:
        logfile = baselog
        nightringlogfile = basenightringlog

# start log now that all parameter are set up
    with logging(logfile, debug) as log:

        # Some basic checks, many tests are done in the FORTRAN code itself
        # is the input file specified?
        saltsafeio.filedefined('Input', images)

        # if the input file is a file, does it exist?
        if basein[0] != '@':
            saltsafeio.fileexists(images)
            infile = images

# if the input file is a list, does it exist?
        if basein[0] == '@':
            infile2 = basein.lstrip('@')
            if (len(pathin) > 0):
                infile = pathin + '/' + infile2
            else:
                infile = infile2
            saltsafeio.listexists('Input', infile)

            # parse list of input files
            infiles = fpsafeio.fplistparse('Raw image', images, '', '', '')
            # check input files exist
            saltsafeio.filesexist(infiles, '', 'r')

# is the proposed output file specified?

        saltsafeio.filedefined('Output', outfile)

        # check whether the proposed output file exists

        path = os.path.dirname(images)

        if len(path) > 0:
            dir = path + '/'
        else:
            dir = './'

#        print dir, ' directory with data'
        outfile = outfile.strip()
        if os.path.isfile(outfile):
            print 'output file exists, appending'
#            saltsafeio.delete(outfile)

# optionally update the FORTRAN config file with new values  - not implemented currently

# If all looks OK, run the FORTRAN code

        infile = basein
        if len(pathout) > 0:
            if (pathin == pathout):
                outfile = baseout
        # absolute path then leave alone
            elif pathout[0] == '/':
                outfile = outfile
            else:
                # as will move to directory of input data, need to strip this off if its in the path
                a = pathout.lstrip(pathin)
                b = a.lstrip('/')
                outfile = b + '/' + baseout

        print dir, infile, outfile, 'input directory, input and output files'
        if basein[0] == '@':
            print infiles, 'infiles'

        # Get current working directory as the Fortran code changes dir
        startdir = os.getcwd()

        nightring_wrapper.nightring(dir, nightringlogfile, outfile, comment,
                                    axc, ayc, arad, rxc, ryc, filter,
                                    filterfreq, filterwidth, plot, plottype,
                                    itmax, conv, fitwidth, infile, cala, calb,
                                    calc, cald, calf, verb)

        # go back to starting directory
        os.chdir(startdir)
예제 #17
0
def saltfpevelocity(infile,existfit,xc,yc,rmax,logfile, verbose):  

    """XXX"""
        
# getting paths for filenames

    pathin = os.path.dirname(infile)
    basein = os.path.basename(infile)
    pathlog = os.path.dirname(logfile)
    baselog = os.path.basename(logfile)

    print(pathin, basein)
    
# start log now that all parameters are set up          
    with logging(logfile, debug) as log:

# Some basic checks, some tests are done in the FORTRAN code itself
# is the input file specified?
        saltsafeio.filedefined('Input',infile)

# if the input file is a file, does it exist? 
        if basein[0] != '@':
            saltsafeio.fileexists(infile)


# if a list is input throw an error
        if basein[0] == '@':
            raise SaltIOError(basein + ' list input instead of a file' )

# The file contains a list of images, check they exist
# format is 4x dummy lines, then a line/lines containing: x,y,wave0,sn,norm,dnorm,filename

        testfile= open(infile)
        print(testfile)
        for i in range(1, 5):
            line = testfile.readline()

        line = 'dummy'
        infiles=[]
        while (len(line.strip()) != 0):
            line = testfile.readline()
            if (len(line.strip()) > 0):
                linearray = line.split()
                infiles.append(linearray[6])

# check input files exist
        saltsafeio.filesexist(infiles,'','r')

# convert existfile to a one letter string
        if existfit == 'yes':
            existfit == 'y'
        else:
            existfit =='n'


# If all looks OK, run the FORTRAN code
    
        print(infile,  'input filename')
        print(existfit, xc, yc, rmax)

        evelocity_wrapper2.evelocity2(infile,existfit,xc,yc,rmax)
예제 #18
0
def slotutcfix(images,update,outfile,ampperccd,ignorexp,droplimit,inter,plotdata,logfile,verbose,debug):
    
    with logging(logfile,debug) as log:
        # set up the variables
        utc_list = []


        # 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 and place them in order
        infiles=saltsafeio.listparse('Raw image',images,'','','')
        infiles.sort()

        # check input files exist
        saltsafeio.filesexist(infiles,'','r')

        # check to see if the output file exists and if so, clobber it
        if os.path.isfile(outfile):
            try:
                os.remove(outfile)
            except:
                raise SaltIOError('File ' + outfile + ' can not be removed')

        # open the outfile
        if outfile:
            try:
                fout=open(outfile,'w')
            except:
                raise SaltIOError('File ' + outfile + ' can not be opened')

        # get time of first exposure and basic information about the observations
        infile=infiles[0]
        struct=saltsafeio.openfits(infile)

        # check to make sure slotmode data
        detmode=saltsafekey.get('DETMODE',struct[0], infile)
        if detmode != 'Slot Mode':
            raise SaltIOError('Data are not Slot Mode Observations')

        # Check to see if SLOTUTCFIX has already been run
        # and print a warning if they have
        if saltsafekey.found('SLOTUTC', struct[0]):
            message='Data have already been processed by SLOTUTCFIX'
            log.warning(message)

        # check to make sure that it is the right version of the software
        scamver=saltsafekey.get('DETSWV', struct[0], infile)
        try:
            scamver=float(scamver.split('-')[-1])
            if 4.42 <= scamver <= 5.00:
                pass
            else:
                raise SaltError('cannot currently correct this version of the SCAM software.')

        except:
            raise SaltError('Not able to read software version')

        # requested exposure time
        req_texp=saltsafekey.get('EXPTIME',struct[0],infile)

        # how many extensions?
        nextend=saltsafekey.get('NEXTEND',struct[0],infile)

        # how many amplifiers
        amplifiers=saltsafekey.get('NCCDS',struct[0],infile)
        amplifiers = int(ampperccd*float(amplifiers))
        if ampperccd>0:
            nframes = nextend/amplifiers
            nstep=amplifiers
        else:
            nframes = nextend
            nstep=1

        # how many total frame and unique times
        ntotal=nextend*len(infiles)
        nunique=len(infiles)*nframes-ignorexp+1

        # Create arrays necessary for analysis
        id_arr=np.arange(nunique)
        utc_arr=np.zeros(nunique,dtype=float)

        # Read in each file and make a list of the UTC values
        if verbose:
            log.message('Reading in files to create list of UTC values.')

        j=0
        for n,infile in enumerate(infiles):
            # Show progress
            if verbose:
                percent=100.*float(n)/float(len(infiles))
                ctext='Percentage Complete: %.2f\r' % percent
                sys.stdout.write(ctext)
                sys.stdout.flush()

            struct=saltsafeio.openfits(infile)
            if not len(struct)-1==nextend:
                raise SaltIOError(infile,' has a different number of extensions from the first file')

            # Skip through the frames and read in the utc
            istart=1
            if infile==infiles[0]:
                istart=ignorexp*amplifiers+1
            for i in range(istart,len(struct), amplifiers):
                try:
                    utc_list.append(saltsafekey.get('UTC-OBS', struct[i], infile))
                    utc_arr[j]=slottool.getobstime(struct[i], infile)
                    j += 1
                except Exception, e:
                    raise SaltIOError('Unable to create array of UTC times.  Please check the number of extensions in the files')

            # close FITS file
            saltsafeio.closefits(struct)

        # set up the other important arrays
        try:
            diff_arr=utc_arr.copy()
            diff_arr[1:]=diff_arr[1:]-utc_arr[:-1]
            diff_arr[0]=-1
            dsec_arr=utc_arr-utc_arr.astype(int)
        except:
            raise SaltIOError('Unable to create timing arrays')

        # calculate the real exposure time
        if verbose:
            log.message('Calculating real exposure time.')

        real_expt, med_expt, t_start, t_arr, ysum_arr=calculate_realexptime(id_arr, utc_arr, dsec_arr, diff_arr, req_texp, utc_list)

        # plot the results
        if plotdata:
            if verbose:
                log.message('Plotting data.')
            plt.ion()
            plt.plot(t_arr,ysum_arr,linewidth=0.5,linestyle='-',marker='',color='b')
            plt.xlabel('Time (s)')
            plt.ylabel('Fit')

        # Calculate the corrrect values
        if verbose:
            log.message('Calculating correct values')

        i_start = abs(utc_arr-t_start).argmin()
        t_diff=utc_arr*0.0+real_expt
        nd=utc_arr*0.0
        ndrop=0
        for i in range(len(utc_arr)):
            if utc_arr[i] >= t_start:
                t_new=t_start+real_expt*(i-i_start+ndrop)
                t_diff[i]=utc_arr[i]-t_new
                while (t_diff[i]>real_expt and nd[i] < droplimit):
                    nd[i]+= 1
                    t_new=t_start+real_expt*(i-i_start+ndrop+nd[i])
                    t_diff[i]=utc_arr[i]-t_new
                if (nd[i]<droplimit):
                    ndrop += nd[i]
            else:
                t_new=t_start+real_expt*(i-i_start)
                t_diff[i]=utc_arr[i]-t_new
                while (t_diff[i]>real_expt and nd[i] < droplimit):
                    nd[i]+= 1
                    t_new=t_start+real_expt*(i-i_start-nd[i])
                    t_diff[i]=utc_arr[i]-t_new

        # calculate the corrected timestamp by counting 6 record files forward and
        # 8 recored + unrecorded files back--or just 8*t_exp forward.
        # if the object is near the end of the run, then just replace it with
        # the correct value assuming no dropped exposures.

        # first make the array of new times
        new_arr=utc_arr-t_diff

        # Next loop through them to find the corrected time
        corr_arr=utc_arr*0.0

        for i in range(len(new_arr)):
            if i+6 < len(new_arr)-1:
                corr_arr[i]=new_arr[i+6]-8*real_expt
            else:
                corr_arr[i]=new_arr[i]-2*real_expt

        t_diff=utc_arr-corr_arr

        # write out the first results
        msg="Dwell Time=%5.3f Requested Exposure Time=%5.3f Nobs = %i Dropped = %i" % (real_expt, req_texp,  nunique, ndrop)
        if verbose:
            log.message(msg)

        if outfile:
            fout.write('#'+msg+'\n')
            fout.write('#%23s %2s %12s %12s %10s %8s %4s \n' % ('File', 'N', 'UTC_old', 'UTC_new', 'UTC_new(s)', 'Diff', 'drop' ))

        # Give the user a chance to update the value
        if inter:
            message='Update headers with a dwell time of %5.3f s [y/n]? ' % real_expt
            update=saltsafeio.yn_ask(message)
            if not update:
                message='Set Dwell Time manually [y/n]? '
                update=saltsafeio.yn_ask(message)
                if update:
                    message='New Dwell Time: '
                    real_expt=saltsafeio.ask(message)
                    try:
                        real_expt=float(real_expt)
                    except Exception, e:
                        msg='Could not set user dwell time because %s' % e
                        raise SaltError(msg)
예제 #19
0
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.')