Python saltsafeio.openfits函数代码示例

def specselfid(images, outimages, outpref, refimage=None, ystart='middlerow',
               rstep=3, clobber=False, logfile='salt.log', verbose=True):

    with logging(logfile, debug) as log:

        # set up the variables
        infiles = []
        outfiles = []

        # Check the input images
        infiles = saltio.argunpack('Input', images)

        # create list of output files
        outfiles = saltio.listparse(
            'Outimages',
            outimages,
            outpref,
            infiles,
            '')

        # set up defaults
        if saltio.checkfornone(refimage) is not None:
            rhdu = saltio.openfits(refimage)
        else:
            refimage = None

        # read in rectify each image
        for img, oimg, in zip(infiles, outfiles):
            hdu = saltio.openfits(img)
            log.message(
                'Performing self-identification and rectification on %s' %
                img)
            for i in range(1, len(hdu)):
                if hdu[i].name == 'SCI':
                    if refimage is None:
                        sdata = hdu[i].data
                    else:
                        sdata = rhdu[i].data
                    hdu[i].data = selfid(
                        hdu[i].data,
                        sdata,
                        ystart=ystart,
                        rstep=rstep)
                    if saltkey.found('VAREXT', hdu[i]):
                        varext = saltkey.get('VAREXT', hdu[i])
                        hdu[varext].data = selfid(
                            hdu[varext].data,
                            sdata,
                            ystart=ystart,
                            rstep=rstep)
                    if saltkey.found('BPMEXT', hdu[i]):
                        bpmext = saltkey.get('BPMEXT', hdu[i])
                        hdu[bpmext].data = selfid(
                            hdu[bpmext].data,
                            sdata,
                            ystart=ystart,
                            rstep=rstep)

            # write out the oimg
            saltio.writefits(hdu, oimg, clobber=clobber)

def saltprepare(images,outimages,outpref,createvar=False, badpixelimage=None, clobber=True,logfile='salt.log',verbose=True):

   with logging(logfile,debug) as log:

       # Check the input images 
       infiles = saltio.argunpack ('Input',images)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')

       #verify that the input and output lists are the same length
       saltio.comparelists(infiles,outfiles,'Input','output')

       # open the badpixel image
       if saltio.checkfornone(badpixelimage) is None:
          badpixelstruct=None
       else:
           try:
               badpixelstruct = saltio.openfits(badpixelimage)
           except saltio.SaltIOError,e:
               msg='badpixel image must be specificied\n %s' % e
               raise SaltError(msg)

       # open each raw image file
       for img, oimg, in zip(infiles, outfiles):

           #open the fits file
           struct=saltio.openfits(img)

           #if createvar, throw a warning if it is using slotmode
           if saltkey.fastmode(saltkey.get('DETMODE', struct[0])) and createvar:
               msg='Creating variance frames for slotmode data in %s' % img
               log.warning(msg)
  
           # identify instrument
           instrume,keyprep,keygain,keybias,keyxtalk,keyslot = saltkey.instrumid(struct)

           # has file been prepared already?
           try:
               key = struct[0].header[keyprep]
               message = 'ERROR -- SALTPREPARE: File ' + infile
               message += ' has already been prepared'
               raise SaltError(message)
           except:
               pass


           # prepare file
           struct=prepare(struct,createvar=createvar, badpixelstruct=badpixelstruct)

           # housekeeping keywords
           fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
           saltkey.housekeeping(struct[0],keyprep, 'File prepared for IRAF', hist)

           # write FITS file
           saltio.writefits(struct,oimg, clobber=clobber)
           saltio.closefits(struct)

           message = 'SALTPREPARE -- %s => %s' % (img, oimg)
           log.message(message, with_header=False)

def saltarith(operand1, op, operand2, result, outpref, divzero=0, clobber=False,     \
             logfile='salt.log',verbose=True):


   with logging(logfile,debug) as log:

       # Check the input images 
       infiles = saltio.argunpack ('Input',operand1)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', result, outpref, infiles,'')

       #verify that the input and output lists are the same length
       saltio.comparelists(infiles,outfiles,'Input','output')

       #let's keep track of whether operand2 is an image or not
       is_image = False

       #load in operand2, or, if it's not an image, assume it's a number
       try: operand2struct = float(operand2)
       except ValueError:
          operand2struct = saltio.openfits(operand2)
          is_image = True

       #open the input image files
       for infile, outfile in zip(infiles,outfiles):
           struct = saltio.openfits(infile)

           #do some math!
           outstruct = arith(struct, op, operand2struct, is_image, divzero)
           try:
               pass 
           except Exception as e:
               msg='Unable to do math %s because %s' % (infile, e)
               raise SaltError(msg)

           #update header stuff
           fname, hist = history(level=1, wrap=False)
           saltkey.housekeeping(struct[0],'SARITH', 'Some arithmatic was performed',hist)

           #write it. close it.
           saltio.writefits(outstruct,outfile,clobber=clobber)
           saltio.closefits(struct)

           #output the information
           log.message('imarith: %s %s %s %s' % (infile, op, operand2, outfile), with_header=False, with_stdout=verbose)

       #close the operand2 image
       if is_image: saltio.closefits(operand2struct)

def identify(img, oimg, slines, sfluxes, guesstype, guessfile, function, order,  
             rstep, interact, clobber, verbose):
   """For a given image, find the solution for each row in the file.  Use the appropriate first guess and 
      guess type along with the appropriate function and order for the fit.

      Write out the new image with the solution in the headers and/or as a table in the multi-extension
      fits file

       returns the status
   """
   status=0
   ImageSolution={}

   #Open up the image
   hdu=saltsafeio.openfits(img)   

   #Read in important keywords

   #determine the central row and read it in
   try:
       data=hdu[1].data
       midline=int(0.5*len(data))
       xarr=np.arange(len(data[midline]))
       specarr=st.flatspectrum(xarr, data[midline, :], mode='poly', order=2)
   except Exception, e:
       message = 'Unable to read in data array in %s because %s' % (img, e)
       raise SALTSpecError(message)

def saltillum(images, outimages, outpref, mbox=11, clobber=False, logfile="salt.log", verbose=True):

    with logging(logfile, debug) as log:

        # Check the input images
        infiles = saltio.argunpack("Input", images)

        # create list of output files
        outfiles = saltio.listparse("Outfile", outimages, outpref, infiles, "")

        # verify that the input and output lists are the same length
        saltio.comparelists(infiles, outfiles, "Input", "output")

        # open each raw image file
        for infile, outfile in zip(infiles, outfiles):
            struct = saltio.openfits(infile)

            struct = illum_cor(struct, mbox)

            # add any header keywords like history
            fname, hist = history(level=1, wrap=False)
            saltkey.housekeeping(struct[0], "SILLUM", "File Illumination corrected", hist)

            # write it out and close it
            saltio.writefits(struct, outfile, clobber=clobber)
            saltio.closefits(struct)

            # output the information
            log.message("Illumination corrected image %s " % (infile), with_header=False, with_stdout=verbose)

def hrsstack(images, outimages, outpref, clobber=True, logfile='salt.log',verbose=True):
    """Convert MEF HRS data into a single image.  If variance frames and BPMs, then 
       convert them to the same format as well.   Returns an MEF image but that is
       combined into a single frame

    """
 
    with logging(logfile,debug) as log:

       # Check the input images 
       infiles = saltio.argunpack ('Input',images)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')

       #verify that the input and output lists are the same length
       saltio.comparelists(infiles,outfiles,'Input','output')

       #open the file and write out as a fits files in the output directory
       for img,oimg in zip(infiles, outfiles):
          hdu=saltio.openfits(img)
          hdu=stack(hdu)
          log.message('Stacking HRS %s to %s' % (img, oimg), with_header=False)
          saltio.writefits(hdu, oimg, clobber=clobber)
    
 
    return 

def saltsurface(images,outimages,outpref, mask=True,  order=3, minlevel=0,
             clobber=False, logfile='salt.log',verbose=True):


   with logging(logfile,debug) as log:

       # Check the input images 
       infiles = saltio.argunpack ('Input',images)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')

       #verify that the input and output lists are the same length
       saltio.comparelists(infiles,outfiles,'Input','output')

       # open each raw image file
       for infile, outfile in zip(infiles,outfiles):
           struct = saltio.openfits(infile)

           
           struct = surface_fit(struct, order=order, mask=mask, minlevel=minlevel)

           #add any header keywords like history 
           fname, hist=history(level=1, wrap=False)
           saltkey.housekeeping(struct[0],'SURFIT', 'File fit by a surface', hist)

           #write it out and close it
           saltio.writefits(struct,outfile,clobber=clobber)
           saltio.closefits(struct)

           #output the information
           log.message('Surface fitted image %s ' % (infile), with_header=False, with_stdout=verbose)

def specsky(images,outimages,outpref, method='normal', section=None, 
            function='polynomial', order=2, 
            clobber=True,logfile='salt.log',verbose=True):

   with logging(logfile,debug) as log:

       # Check the input images 
       infiles = saltio.argunpack ('Input',images)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')

       if method not in ['normal', 'fit']: 
           msg='%s mode is not supported yet' % method
           raise SALTSpecError(msg)

       if section is None:
           section=saltio.getSection(section)
           msg='This mode is not supported yet'
           raise SALTSpecError(msg)
       else:
           section=saltio.getSection(section)

       # Identify the lines in each file
       for img, ofile in zip(infiles, outfiles):
          log.message('Subtracting sky spectrum in image %s into %s' % (img, ofile))
          #open the images
          hdu=saltio.openfits(img)

          #sky subtract the array
          hdu=skysubtract(hdu, method=method, section=section, funct=function, order=order) 

          #write out the image
          if clobber and os.path.isfile(ofile): saltio.delete(ofile)
          hdu.writeto(ofile)

def hrsprepare(images, outimages, outpref, clobber=True, logfile='salt.log',verbose=True):
    """Convert .fit files to .fits files and place HRS data into 
       standard SALT FITS format

    """
 
    with logging(logfile,debug) as log:

       # Check the input images 
       infiles = saltio.argunpack ('Input',images)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')

       #verify that the input and output lists are the same length
       saltio.comparelists(infiles,outfiles,'Input','output')

       #open the file and write out as a fits files in the output directory
       for img,oimg in zip(infiles, outfiles):
          hdu=saltio.openfits(img)
          hdu=prepare(hdu)
          log.message('Preparing HRS %s to %s' % (img, oimg), with_header=False)
          saltio.writefits(hdu, oimg, clobber=clobber)
    
 
    return 

def saltfpskyring(
    images,
    outimages,
    outpref,
    axc,
    ayc,
    arad,
    rxc,
    ryc,
    pmin,
    pmax,
    swindow=5,
    clobber=False,
    logfile="salt.log",
    verbose=True,
):
    """Sky subtracts Fabry-Perot images"""

    # start log now that all parameter are set up

    with logging(logfile, debug) as log:

        # Check the input images
        infiles = saltio.argunpack("Input", images)

        # create list of output files
        outfiles = saltio.listparse("Outfile", outimages, outpref, infiles, "")

        # verify that the input and output lists are the same length
        saltio.comparelists(infiles, outfiles, "Input", "output")

        for img, oimg in zip(infiles, outfiles):

            # open up the file
            hdu = saltio.openfits(img)

            # determine the azimuthally averaged profile
            rpro, radial_profile = median_radial_profile(
                hdu[0].data, xc=axc, yc=ayc, rmax=arad, nbins=100, pmin=pmin, pmax=pmax
            )

            if swindow > 1:
                radial_profile = np.convolve(radial_profile, np.ones(swindow), mode="same") / swindow

            # calculate the indices from the image
            y, x = np.indices(hdu[0].data.shape)
            radius = np.hypot(x - axc, y - ayc)

            # subtract off the sky data
            mdata = hdu[0].data - np.interp(radius, rpro, radial_profile)
            hdu[0].data = mdata

            # write FITS file
            saltio.writefits(hdu, oimg, clobber=clobber)
            saltio.closefits(hdu)

            message = "SALTFPSKYRING -- Subtracted sky from  %s" % (img)
            log.message(message, with_header=False)

def saltcrclean(images,outimages,outpref,crtype='fast',thresh=5,mbox=3,         \
                bthresh=3, flux_ratio=0.2, bbox=11, gain=1, rdnoise=5, fthresh=5,\
                bfactor=2, gbox=3, maxiter=5, multithread=False, update=True,
                clobber=True,  logfile='salt.log', verbose=True):


   with logging(logfile,debug) as log:


       # Check the input images 
       infiles = saltio.argunpack ('Input',images)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')

       #verify that the input and output lists are the same length
       saltio.comparelists(infiles,outfiles,'Input','output')

       #check to see if multithreading is available
       if mp:
          pass
       else:
          multithread=False
          log.warning('multiprocessing module is not available.  Setting multiththread=False')


       # Begin processes each file
       for infile,outfile in zip(infiles,outfiles):

           #open the infile
           struct=saltio.openfits(infile)

           #clean the cosmic rays
           if multithread and len(struct)>1:
               struct=multicrclean(struct, crtype, thresh, mbox, bbox, bthresh, flux_ratio, \
                          gain, rdnoise, bfactor, fthresh, gbox, maxiter, log, verbose=verbose)
           else:
               struct=crclean(struct, crtype, thresh, mbox, bbox, bthresh, flux_ratio, \
                          gain, rdnoise, bfactor, fthresh, gbox, maxiter, update, log, verbose=verbose)
          
           #log the call
           #log.message('Cleaned %i cosmic rays from %s using %s method' % (totcr, infile, crtype), with_header=False)
           log.message('', with_header=False, with_stdout=verbose)

           #add house keeping keywords
           saltkey.put('SAL-TLM',time.asctime(time.localtime()), struct[0])
   
           #add the history keyword
           fname, hist=history(level=1, wrap=False)
           saltkey.history(struct[0],hist)

           #write out the file
           saltio.writefits(struct, outfile, clobber=clobber)

           #close the image
           saltio.closefits(struct)

def saltxtalk(images,outimages,outpref,xtalkfile=None, usedb=False,
              clobber=True, logfile='salt.log',verbose=True):

   #start logging
   with logging(logfile,debug) as log:

       # Check the input images 
       infiles = saltio.argunpack ('Input',images)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')

       # are input and output lists the same length?
       saltio.comparelists(infiles,outfiles,'Input','output')

       # does crosstalk coefficient data exist
       if usedb:
           xtalkfile = xtalkfile.strip()
           xdict = saltio.readxtalkcoeff(xtalkfile)
       else:
           xdict=None

       for img, oimg in zip(infiles, outfiles):

           #open the fits file
           struct=saltio.openfits(img)

           #find the best xcoeff for the image if using the db
           if usedb:
              obsdate=saltkey.get('DATE-OBS', struct[0])
              obsdate=int('%s%s%s' % (obsdate[0:4],obsdate[5:7], obsdate[8:]))
              xkey=np.array(xdict.keys())
              date=xkey[abs(xkey-obsdate).argmin()]
              xcoeff=xdict[date]
           else:
              xcoeff=[]

           # identify instrument
           instrume,keyprep,keygain,keybias,keyxtalk,keyslot = saltkey.instrumid(struct)

           # has file been prepared already?
           if saltkey.found(keyxtalk, struct[0]):
               message='%s has already been xtalk corrected' % img
               raise SaltError(message)


           #apply the cross-talk correction
           struct = xtalk(struct, xcoeff, log=log, verbose=verbose)

           # housekeeping keywords
           fname, hist=history(level=1, wrap=False, exclude=['images', 'outimages', 'outpref'])
           saltkey.housekeeping(struct[0], 'SXTALK', 'Images have been xtalk corrected', hist)

           # write FITS file
           saltio.writefits(struct,oimg, clobber=clobber)
           saltio.closefits(struct)

def specwavemap(
    images,
    outimages,
    outpref,
    solfile=None,
    caltype="line",
    function="polynomial",
    order=3,
    blank=0,
    nearest=False,
    clobber=True,
    logfile="salt.log",
    verbose=True,
):

    with logging(logfile, debug) as log:

        # set up the variables
        infiles = []
        outfiles = []

        # Check the input images
        infiles = saltsafeio.argunpack("Input", images)

        # create list of output files
        outfiles = saltsafeio.listparse("Outimages", outimages, outpref, infiles, "")

        # read in the wavelength solutions and enter them into
        # there own format
        if caltype == "line":
            soldict = sr.entersolution(solfile)
        else:
            soldict = None

        # read in rectify each image
        for img, oimg in zip(infiles, outfiles):
            if caltype == "line":
                msg = "Creating wave map image %s from image %s using files %s" % (oimg, img, solfile)
            else:
                msg = "Creating wave map image %s from image %s using RSS Model" % (oimg, img)
            log.message(msg)
            hdu = saltsafeio.openfits(img)
            hdu = wavemap(
                hdu,
                soldict,
                caltype=caltype,
                function=function,
                order=order,
                blank=blank,
                nearest=nearest,
                clobber=clobber,
                log=log,
                verbose=verbose,
            )
            saltsafeio.writefits(hdu, oimg, clobber=clobber)

def specprepare(images,outimages,outpref,badpixelimage='', \
                clobber=True,logfile='salt.log',verbose=True):

   with logging(logfile,debug) as log:


       # Check the input images 
       infiles = saltio.argunpack ('Input',images)

       # create list of output files 
       outfiles=saltio.listparse('Outfile', outimages, outpref,infiles,'')

       #verify that the input and output lists are the same length
       saltio.comparelists(infiles,outfiles,'Input','output')

       # open the badpixel image
       if saltio.checkfornone(badpixelimage) is None:
          badpixelstruct=None
       else:
           try:
               badpixelstruct = saltio.openfits(badpixelimage)
           except saltio.SaltIOError,e:
               msg='badpixel image must be specificied\n %s' % e
               raise SALTSpecError(msg)

       # open each raw image file

       for img, oimg, in zip(infiles, outfiles):

          #open the fits file
	  struct=saltio.openfits(img)

          # prepare file
	  struct=prepare(struct,badpixelstruct)

          # write FITS file
          saltio.writefits(struct,oimg, clobber=clobber)
          saltio.closefits(struct)

	  message = 'SPECPREPARE -- %s => %s' % (img, oimg)
          log.message(message)

def obslog(infiles, log=None):
   """For a set of input files, create a dictionary contain all the header 
      information from the files.  Will print things to a saltlog if log is
      not None
    
      returns Dictionary
   """
   #create the header dictionary
   headerDict={}
   for k in headerList: headerDict[k]=[]
   for k in scamheaderList: headerDict[k]=[]
   for k in rssheaderList: headerDict[k]=[]

   # interate over and open image files
   infiles.sort()
   for infile in infiles:

       #open the file
       struct = saltio.openfits(infile)

       # instrument
       scam = False
       rss = False
       instrume = saltkey.get('INSTRUME', struct[0])
       if (instrume=='RSS'): rss = True
       if (instrume=='SALTICAM'): scam=True

       #add in the image name
       headerDict['FILENAME'].append(os.path.basename(infile))

       # ingest primary keywords from files in the image list
       for k,f in zip(headerList[1:], formatList[1:]):
           default=finddefault(f)
           headerDict[k].append(getkey(struct[0], k, default=default, log=log, warn=True))

       # ingest scam specific primary keywords from files in the image list
       for k,f in zip(scamheaderList[1:], scamformatList[1:]):
           default=finddefault(f)
           headerDict[k].append(getkey(struct[0], k, default=default, log=log, warn=scam))

       # ingest rss specific primary keywords from files in the image list
       for k,f in zip(rssheaderList[1:], rssformatList[1:]):
           default=finddefault(f)
           headerDict[k].append(getkey(struct[0], k, default=default, log=log, warn=rss))

       # close image files
       saltio.closefits(struct)

       if log: log.message('SALTOBSLOG -- read %s' % infile, with_header=False)

   return headerDict