Exemple #1
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def calc_resolution(hdu):
    """Calculate the resolution for a setup"""
    instrume=saltkey.get('INSTRUME', hdu[0]).strip()
    grating=saltkey.get('GRATING', hdu[0]).strip()
    grang=saltkey.get('GR-ANGLE', hdu[0])
    grasteps=saltkey.get('GRTILT', hdu[0])
    arang=saltkey.get('AR-ANGLE', hdu[0])
    arsteps=saltkey.get('CAMANG', hdu[0])
    rssfilter=saltkey.get('FILTER', hdu[0])
    specmode=saltkey.get('OBSMODE', hdu[0])
    masktype=saltkey.get('MASKTYP', hdu[0]).strip().upper()
    slitname=saltkey.get('MASKID', hdu[0])
    xbin, ybin = saltkey.ccdbin( hdu[0], '')
    slit=st.getslitsize(slitname)
    
    #create RSS Model
    rss=RSSModel.RSSModel(grating_name=grating.strip(), gratang=grang, \
                          camang=arang,slit=slit, xbin=xbin, ybin=ybin, \
                          )
    res=1e7*rss.calc_resolelement(rss.alpha(), -rss.beta())
    return res 
Exemple #2
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def calc_resolution(hdu):
    """Calculate the resolution for a setup"""
    instrume=saltkey.get('INSTRUME', hdu[0]).strip()
    grating=saltkey.get('GRATING', hdu[0]).strip()
    grang=saltkey.get('GR-ANGLE', hdu[0])
    grasteps=saltkey.get('GRTILT', hdu[0])
    arang=saltkey.get('AR-ANGLE', hdu[0])
    arsteps=saltkey.get('CAMANG', hdu[0])
    rssfilter=saltkey.get('FILTER', hdu[0])
    specmode=saltkey.get('OBSMODE', hdu[0])
    masktype=saltkey.get('MASKTYP', hdu[0]).strip().upper()
    slitname=saltkey.get('MASKID', hdu[0])
    xbin, ybin = saltkey.ccdbin( hdu[0], '')
    slit=st.getslitsize(slitname)
    
    #create RSS Model
    rss=RSSModel.RSSModel(grating_name=grating.strip(), gratang=grang, \
                          camang=arang,slit=slit, xbin=xbin, ybin=ybin, \
                          )
    res=1e7*rss.calc_resolelement(rss.alpha(), -rss.beta())
    return res 
Exemple #3
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def rssinfo(grating, grang, arang, slitname, xbin, ybin):
   """RSSINFO--Given informtion about the set up of the spectrograph,
      return information about the spectrograph
    
      grating--name of the grating used
      gratang--angle of the grating in degrees
      arang--articulation ange in degrees
      slitname--name of the slit being used
      xbin--binning in x-direction
      ybin--binning in y-direction

      returns central wavelength, blue wavelength, red wavelenth, resolution
              resolution element
   """

   #get the slitsize
   slit=getslitsize(slitname)

   #set up the rss model
   rss=RSSModel.RSSModel(grating_name=grating, gratang=grang, \
                         camang=arang,slit=slit, xbin=xbin, ybin=ybin)

   #calcuation the resolution element
   res=1e7*rss.calc_resolelement(rss.alpha(), -rss.beta())

   #calculate the central wavelength
   wcen=1e7*rss.calc_centralwavelength()

   #calculate the wavelength edges
   w2=1e7*rss.calc_bluewavelength()
   w1=1e7*rss.calc_redwavelength()
   print w1,w2

   #calculate the 
   R=rss.calc_resolution(wcen/1e7, rss.alpha(), rss.beta())
 
   return wcen, w1, w2, res, R, slit
Exemple #4
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def rssinfo(grating, grang, arang, slitname, xbin, ybin):
    """RSSINFO--Given informtion about the set up of the spectrograph,
      return information about the spectrograph
    
      grating--name of the grating used
      gratang--angle of the grating in degrees
      arang--articulation ange in degrees
      slitname--name of the slit being used
      xbin--binning in x-direction
      ybin--binning in y-direction

      returns central wavelength, blue wavelength, red wavelenth, resolution
              resolution element
   """

    #get the slitsize
    slit = getslitsize(slitname)

    #set up the rss model
    rss=RSSModel.RSSModel(grating_name=grating, gratang=grang, \
                          camang=arang,slit=slit, xbin=xbin, ybin=ybin)

    #calcuation the resolution element
    res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())

    #calculate the central wavelength
    wcen = 1e7 * rss.calc_centralwavelength()

    #calculate the wavelength edges
    w2 = 1e7 * rss.calc_bluewavelength()
    w1 = 1e7 * rss.calc_redwavelength()
    print w1, w2

    #calculate the
    R = rss.calc_resolution(wcen / 1e7, rss.alpha(), rss.beta())

    return wcen, w1, w2, res, R, slit
Exemple #5
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def rectify(hdu, soldict, caltype='line', function='poly', order=3, inttype='interp',
            w1=None, w2=None, dw=None, nw=None, blank=0, pixscale=0.0, time_interp=False,
            conserve=False, nearest=False, clobber=True, log=None, verbose=True):
    """Read in an image and a set of wavlength solutions.  Calculate the best
       wavelength solution for a given dataset and then apply that data set to the
       image

     return
    """

    # set the basic values
    set_w1 = (w1 is None)
    set_w2 = (w2 is None)
    set_dw = (dw is None)
    set_nw = (nw is None)

    # set up the time of the observation
    dateobs = saltkey.get('DATE-OBS', hdu[0])
    utctime = saltkey.get('TIME-OBS', hdu[0])
    exptime = saltkey.get('EXPTIME', hdu[0])
    instrume = saltkey.get('INSTRUME', hdu[0]).strip()
    grating = saltkey.get('GRATING', hdu[0]).strip()
    if caltype == 'line':
        grang = saltkey.get('GRTILT', hdu[0])
        arang = saltkey.get('CAMANG', hdu[0])
    else:
        grang = saltkey.get('GR-ANGLE', hdu[0])
        arang = saltkey.get('AR-ANGLE', hdu[0])
    filtername = saltkey.get('FILTER', hdu[0]).strip()
    slitname = saltkey.get('MASKID', hdu[0])
    slit = st.getslitsize(slitname)
    xbin, ybin = saltkey.ccdbin(hdu[0])

    timeobs = enterdatetime('%s %s' % (dateobs, utctime))

    # check to see if there is more than one solution
    if caltype == 'line':
        if len(soldict) == 1:
            sol = soldict.keys()[0]
            slitid = None
            if not matchobservations(
                    soldict[sol], instrume, grating, grang, arang, filtername, slitid):
                msg = 'Observations do not match setup for transformation but using the solution anyway'
                if log:
                    log.warning(msg)

    for i in range(1, len(hdu)):
        if hdu[i].name == 'SCI':
            if log:
                log.message('Correcting extension %i' % i)
            istart = int(0.5 * len(hdu[i].data))
            # open up the data
            # set up the xarr and initial wavlength solution
            xarr = np.arange(len(hdu[i].data[istart]), dtype='int64')

            # get the slitid
            try:
                slitid = saltkey.get('SLITNAME', hdu[i])
            except:
                slitid = None
            # set up a wavelength solution
            try:
                w_arr = findsol(xarr, soldict, istart, caltype, nearest, timeobs, exptime, instrume, grating, grang, arang, filtername,
                                slit, xbin, ybin, slitid, function, order)
            except SALTSpecError as e:
                if slitid:
                    msg = 'SLITID %s: %s' % (slitid, e)
                    if log:
                        log.warning(msg)
                    continue
                else:
                    raise SALTSpecError(e)

            if w_arr is None:
                w_arr = findsol(xarr, soldict, istart, 'rss', nearest, timeobs, exptime, instrume, grating, grang, arang, filtername,
                                slit, xbin, ybin, slitid, function, order)

            # set up the output x-axis

            if set_w1:
                w1 = w_arr.min()
            if set_w2:
                w2 = w_arr.max()
            if set_nw:
                nw = len(xarr)
            if set_dw:
                dw = float(w2 - w1) / nw
            nw_arr = createoutputxaxis(w1, w2, nw)

            # setup the VARIANCE and BPM frames
            if saltkey.found('VAREXT', hdu[i]):
                varext = saltkey.get('VAREXT', hdu[i])
            else:
                varext = None

            # setup the BPM frames
            if saltkey.found('BPMEXT', hdu[i]):
                bpmext = saltkey.get('BPMEXT', hdu[i])
            else:
                bpmext = None

            # for each line in the data, determine the wavelength solution
            # for a given line in the image
            for j in range(len(hdu[i].data)):
                # find the wavelength solution for the data
                w_arr = findsol(xarr, soldict, j, caltype, nearest, timeobs, exptime, instrume, grating, grang, arang, filtername,
                                slit, xbin, ybin, slitid, function, order)

                # apply that wavelength solution to the data
                if w_arr is not None:
                    try:
                        hdu[i].data[
                            j,
                            :] = st.interpolate(
                            nw_arr,
                            w_arr,
                            hdu[i].data[
                                j,
                                :],
                            inttype,
                            left=blank,
                            right=blank)
                    except Exception as e:
                        hdu[i].data[j, :] = hdu[i].data[j, :] * 0.0 + blank
                        msg = 'In row %i, solution cannot be found due to %s' % (
                            i, e)

                    # correct the variance frame
                    if varext:
                        try:
                            hdu[varext].data[
                                j,
                                :] = st.interpolate(
                                nw_arr,
                                w_arr,
                                hdu[varext].data[
                                    j,
                                    :],
                                inttype,
                                left=blank,
                                right=blank)
                        except Exception as e:
                            msg = 'In row %i, solution cannot be found due to %s' % (
                                i, e)

                    # correct the BPM frame
                    if bpmext:
                        try:
                            hdu[bpmext].data[
                                j,
                                :] = st.interpolate(
                                nw_arr,
                                w_arr,
                                hdu[bpmext].data[
                                    j,
                                    :],
                                inttype,
                                left=blank,
                                right=blank)
                        except Exception as e:
                            msg = 'In row %i, solution cannot be found due to %s' % (
                                i, e)
                else:
                    hdu[i].data[j, :] = hdu[i].data[j, :] * 0.0 + blank

            if conserve:
                hdu[i].data = hdu[i].data / dw
                if varext:
                    hdu[varext].data = hdu[varext].data / dw

            # Add WCS information
            saltkey.new('CTYPE1', 'LAMBDA', 'Coordinate Type', hdu[i])
            saltkey.new('CTYPE2', 'PIXEL', 'Coordinate Type', hdu[i])
            saltkey.new(
                'CD1_1',
                dw,
                'WCS: Wavelength Dispersion in angstrom/pixel',
                hdu[i])
            saltkey.new('CD2_1', 0.0, 'WCS: ', hdu[i])
            saltkey.new('CD1_2', 0.0, 'WCS: ', hdu[i])
            saltkey.new('CD2_2', ybin * pixscale, 'WCS: ', hdu[i])
            saltkey.new('CRPIX1', 0.0, 'WCS: X Reference pixel', hdu[i])
            saltkey.new('CRPIX2', 0.0, 'WCS: Y Reference pixel', hdu[i])
            saltkey.new('CRVAL1', w1, 'WCS: X Reference pixel', hdu[i])
            saltkey.new('CRVAL2', 0.0, 'WCS: Y Reference pixel', hdu[i])
            saltkey.new('CDELT1', 1.0, 'WCS: X pixel size', hdu[i])
            saltkey.new('CDELT2', 1.0, 'WCS: Y pixel size', hdu[i])
            saltkey.new('DC-FLAG', 0, 'Dispesion Corrected image', hdu[i])

    return hdu
Exemple #6
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def rectify(hdu, soldict, caltype='line', function='poly', order=3, inttype='interp', 
            w1=None, w2=None, dw=None, nw=None,
            blank=0, pixscale=0.0, time_interp=False, clobber=True, log=None, verbose=True):
   """Read in an image and a set of wavlength solutions.  Calculate the best
      wavelength solution for a given dataset and then apply that data set to the 
      image 

    return
   """
 
   #set the 
   set_w1=(w1 is  None)
   set_w2=(w2 is  None)
   set_dw=(dw is  None)
   set_nw=(nw is  None)

   #set up the time of the observation
   dateobs=saltkey.get('DATE-OBS', hdu[0])
   utctime=saltkey.get('TIME-OBS', hdu[0])
   exptime=saltkey.get('EXPTIME', hdu[0])
   instrume=saltkey.get('INSTRUME', hdu[0]).strip()
   grating=saltkey.get('GRATING', hdu[0]).strip()
   if caltype=='line':
      grang=saltkey.get('GRTILT', hdu[0])
      arang=saltkey.get('CAMANG', hdu[0])
   else:
      grang=saltkey.get('GR-ANGLE', hdu[0])
      arang=saltkey.get('AR-ANGLE', hdu[0])
   filtername=saltkey.get('FILTER', hdu[0]).strip()
   slitname=saltkey.get('MASKID', hdu[0])
   slit=st.getslitsize(slitname)
   xbin, ybin = saltkey.ccdbin( hdu[0])

   timeobs=enterdatetime('%s %s' % (dateobs, utctime))

   #check to see if there is more than one solution
   if caltype=='line':
    if len(soldict)==1:
      sol=soldict.keys()[0]
      slitid=None
      if not matchobservations(soldict[sol], instrume, grating, grang, arang, filtername, slitid):
         msg='Observations do not match setup for transformation but using the solution anyway'
         if log: log.warning(msg)

   for i in range(1,len(hdu)):
     if hdu[i].name=='SCI':
       if log: log.message('Correcting extension %i' % i)
       istart=int(0.5*len(hdu[i].data))
       #open up the data
       #set up the xarr and initial wavlength solution
       xarr=np.arange(len(hdu[i].data[istart]), dtype='int64')

       #get the slitid
       try:
          slitid=saltkey.get('SLITNAME', hdu[i])
       except:
          slitid=None
       #set up a wavelength solution
       try:
           w_arr=findsol(xarr, soldict, istart, caltype, timeobs, exptime, instrume, grating, grang, arang, filtername, 
              slit, xbin, ybin, slitid, function, order )
       except SALTSpecError, e:
           if slitid: 
              msg='SLITID %s: %s' % (slitid, e)
              if log: log.warning(msg)
              continue
           else:
              raise SALTSpecError(e)
 
       if w_arr is None: 
          w_arr=findsol(xarr, soldict, istart, 'rss', timeobs, exptime, instrume, grating, grang, arang, filtername, 
              slit, xbin, ybin, slitid, function, order )
  
       #set up the output x-axis

       if set_w1: w1=w_arr.min()
       if set_w2: w2=w_arr.max()
       if set_nw: nw=len(xarr)
       if set_dw: dw=float(w2-w1)/nw
       nw_arr=createoutputxaxis(w1, w2, nw)

       #setup the VARIANCE and BPM frames       
       if saltkey.found('VAREXT', hdu[i]):
           varext=saltkey.get('VAREXT', hdu[i])
       else:
           varext=None

       #setup the BPM frames       
       if saltkey.found('BPMEXT', hdu[i]):
           bpmext=saltkey.get('BPMEXT', hdu[i])
       else:
           bpmext=None

       #for each line in the data, determine the wavelength solution
       #for a given line in the image
       for j in range(len(hdu[i].data)):
           #find the wavelength solution for the data
           w_arr=findsol(xarr, soldict, j, caltype, timeobs, exptime, instrume, grating, grang, arang, filtername, 
              slit, xbin, ybin, slitid, function, order )

           #apply that wavelength solution to the data
           if w_arr is not None:
               try:
                  hdu[i].data[j,:]=st.interpolate(nw_arr, w_arr, hdu[i].data[j,:], inttype, left=blank, right=blank)
               except Exception, e:
                  hdu[i].data[j,:]=hdu[i].data[j,:]*0.0+blank
                  msg='In row %i, solution cannot be found due to %s' % (i, e)  

               #correct the variance frame
               if varext:
                   try:
                       hdu[varext].data[j,:]=st.interpolate(nw_arr, w_arr, hdu[varext].data[j,:], inttype, left=blank, right=blank)
                   except Exception, e:
                       msg='In row %i, solution cannot be found due to %s' % (i, e)  

               #correct the BPM frame
               if bpmext:
                   try:
                       hdu[bpmext].data[j,:]=st.interpolate(nw_arr, w_arr, hdu[bpmext].data[j,:], inttype, left=blank, right=blank)
                   except Exception, e:
                       msg='In row %i, solution cannot be found due to %s' % (i, e)  
Exemple #7
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def specidentify(images, linelist, outfile, guesstype='rss', guessfile='',
                 automethod='Matchlines', function='poly', order=3, rstep=100,
                 rstart='middlerow', mdiff=5, thresh=3, niter=5, smooth=0,
                 subback=0, inter=True, startext=0,  clobber=False, 
                 textcolor='black', 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.argunpack('Output', outfile)

        # open the line lists
        slines, sfluxes = st.readlinelist(linelist)

        # Identify the lines in each file
        for img, ofile in zip(infiles, outfiles):

            # open the image
            hdu = saltio.openfits(img)

            # get the basic information about the spectrograph
            dateobs = saltkey.get('DATE-OBS', hdu[0])
            try:
                utctime = saltkey.get('UTC-OBS', hdu[0])
            except SaltError:
                utctime = saltkey.get('TIME-OBS', hdu[0])

            instrume = saltkey.get('INSTRUME', hdu[0]).strip()
            grating = saltkey.get('GRATING', hdu[0]).strip()
            grang = saltkey.get('GR-ANGLE', hdu[0])
            grasteps = saltkey.get('GRTILT', hdu[0])
            arang = saltkey.get('AR-ANGLE', hdu[0])
            arsteps = saltkey.get('CAMANG', hdu[0])
            rssfilter = saltkey.get('FILTER', hdu[0])
            specmode = saltkey.get('OBSMODE', hdu[0])
            masktype = saltkey.get('MASKTYP', hdu[0]).strip().upper()
            slitname = saltkey.get('MASKID', hdu[0])
            xbin, ybin = saltkey.ccdbin(hdu[0], img)

            for i in range(startext, len(hdu)):
                if hdu[i].name == 'SCI':
                    log.message('Proccessing extension %i in  %s' % (i, img))
                    # things that will change for each slit

                    if masktype == 'LONGSLIT':
                        slit = st.getslitsize(slitname)
                        xpos = -0.2666
                        ypos = 0.0117
                        objid = None
                    elif masktype == 'MOS':
                        slit = 1.5
                        #slit=saltkey.get('SLIT', hdu[i])

                        # set up the x and y positions
                        miny = hdu[i].header['MINY']
                        maxy = hdu[i].header['MAXY']
                        ras = hdu[i].header['SLIT_RA']
                        des = hdu[i].header['SLIT_DEC']
                        objid = hdu[i].header['SLITNAME']

                        # TODO: Check the perfomance of masks at different PA
                        rac = hdu[0].header['MASK_RA']
                        dec = hdu[0].header['MASK_DEC']
                        pac = hdu[0].header['PA']

                        # these are hard wired at the moment
                        xpixscale = 0.1267 * xbin
                        ypixscale = 0.1267 * ybin
                        cx = int(3162 / xbin)
                        cy = int(2050 / ybin)

                        x, y = mt.convert_fromsky(ras, des, rac, dec, xpixscale=xpixscale, ypixscale=ypixscale,
                                                  position_angle=-pac, ccd_cx=cx, ccd_cy=cy)
                        xpos = 0.015 * 2 * (cx - x[0])
                        ypos = 0.0117
                    else:
                        msg = '%s is not a currently supported masktype' % masktype
                        raise SALTSpecError(msg)

                    if instrume not in ['PFIS', 'RSS']:
                        msg = '%s is not a currently supported instrument' % instrume
                        raise SALTSpecError(msg)

                    # create RSS Model
                    rss = RSSModel.RSSModel(grating_name=grating.strip(), gratang=grang,
                                            camang=arang, slit=slit, xbin=xbin, ybin=ybin,
                                            xpos=xpos, ypos=ypos)
                    res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())
                    dres = res / 10.0
                    wcen = 1e7 * rss.calc_centralwavelength()
                    R = rss.calc_resolution(
                        wcen / 1e7, rss.alpha(), -rss.beta())
                    logmsg = '\nGrating\tGR-ANGLE\tAR-ANGLE\tSlit\tWCEN\tR\n'
                    logmsg += '%s\t%8.3f\t%8.3f\t%4.2f\t%6.2f\t%4f\n' % (
                        grating, grang, arang, slit, wcen, R)
                    if log:
                        log.message(logmsg, with_header=False)

                    # set up the data for the source
                    try:
                        data = hdu[i].data
                    except Exception as e:
                        message = 'Unable to read in data array in %s because %s' % (
                            img, e)
                        raise SALTSpecError(message)

                    # set up the center row
                    if rstart == 'middlerow':
                        ystart = int(0.5 * len(data))
                    else:
                        ystart = int(rstart)

                    rss.gamma = 0.0
                    if masktype == 'MOS':
                        rss.gamma = 180.0 / math.pi * math.atan((y * rss.detector.pix_size * rss.detector.ybin
                                                                 - 0.5 * rss.detector.find_height()) / rss.camera.focallength)

                    # set up the xarr array based on the image
                    xarr = np.arange(len(data[ystart]), dtype='int64')

                    # get the guess for the wavelength solution
                    if guesstype == 'rss':
                        # set up the rss model
                        ws = st.useRSSModel(
                            xarr, rss, function=function, order=order, gamma=rss.gamma)
                    elif guesstype == 'file':
                        soldict = {}
                        soldict = readsolascii(guessfile, soldict)
                        timeobs = enterdatetime('%s %s' % (dateobs, utctime))
                        exptime = saltkey.get('EXPTIME', hdu[0])
                        filtername = saltkey.get('FILTER', hdu[0]).strip()
                        try:
                            slitid = saltkey.get('SLITNAME', hdu[i])
                        except:
                            slitid = None

                        function, order, coef = findlinesol(
                            soldict, ystart, True, timeobs, exptime, instrume, grating, grang, arang, filtername, slitid, xarr=xarr)
                        ws = WavelengthSolution.WavelengthSolution(
                            xarr, xarr, function=function, order=order)
                        ws.set_coef(coef)
                    else:
                        raise SALTSpecError(
                            'This guesstype is not currently supported')

                    # identify the spectral lines
                    ImageSolution = identify(data, slines, sfluxes, xarr, ystart, ws=ws, function=function,
                                             order=order, rstep=rstep,  mdiff=mdiff, thresh=thresh, niter=niter,
                                             method=automethod, res=res, dres=dres, smooth=smooth, inter=inter, filename=img,
                                             subback=0, textcolor=textcolor, log=log, verbose=verbose)

                    if outfile and len(ImageSolution):
                        writeIS(ImageSolution, outfile, dateobs=dateobs, utctime=utctime, instrume=instrume,
                                grating=grating, grang=grang, grasteps=grasteps, arsteps=arsteps,
                                arang=arang, rfilter=rssfilter, slit=slit, xbin=xbin,
                                ybin=ybin, objid=objid,
                                filename=img, log=log, verbose=verbose)
Exemple #8
0
def wavemap(
    hdu,
    soldict,
    caltype="line",
    function="poly",
    order=3,
    blank=0,
    nearest=False,
    array_only=False,
    clobber=True,
    log=None,
    verbose=True,
):
    """Read in an image and a set of wavlength solutions.  Calculate the best
       wavelength solution for a given dataset and then apply that data set to the
       image

     return
    """

    # set up the time of the observation
    dateobs = saltkey.get("DATE-OBS", hdu[0])
    utctime = saltkey.get("TIME-OBS", hdu[0])
    exptime = saltkey.get("EXPTIME", hdu[0])
    instrume = saltkey.get("INSTRUME", hdu[0]).strip()
    grating = saltkey.get("GRATING", hdu[0]).strip()
    if caltype == "line":
        grang = saltkey.get("GRTILT", hdu[0])
        arang = saltkey.get("CAMANG", hdu[0])
    else:
        grang = saltkey.get("GR-ANGLE", hdu[0])
        arang = saltkey.get("AR-ANGLE", hdu[0])
    filtername = saltkey.get("FILTER", hdu[0]).strip()
    slitname = saltkey.get("MASKID", hdu[0])
    slit = st.getslitsize(slitname)
    xbin, ybin = saltkey.ccdbin(hdu[0])

    timeobs = sr.enterdatetime("%s %s" % (dateobs, utctime))

    # check to see if there is more than one solution
    if caltype == "line":
        if len(soldict) == 1:
            sol = soldict.keys()[0]
            slitid = None
            if not sr.matchobservations(soldict[sol], instrume, grating, grang, arang, filtername, slitid):
                msg = "Observations do not match setup for transformation but using the solution anyway"
                if log:
                    log.warning(msg)

    for i in range(1, len(hdu)):
        if hdu[i].name == "SCI":
            if log:
                log.message("Correcting extension %i" % i)
            istart = int(0.5 * len(hdu[i].data))

            # open up the data
            # set up the xarr and initial wavlength solution
            xarr = np.arange(len(hdu[i].data[istart]), dtype="int64")

            # get the slitid
            try:
                slitid = saltkey.get("SLITNAME", hdu[i])
            except:
                slitid = None

            # check to see if wavext is already there and if so, then check update
            # that for the transformation from xshift to wavelength
            if saltkey.found("WAVEXT", hdu[i]):
                w_ext = saltkey.get("WAVEXT", hdu[i]) - 1
                wavemap = hdu[w_ext].data
                function, order, coef = sr.findlinesol(
                    soldict,
                    istart,
                    nearest,
                    timeobs,
                    exptime,
                    instrume,
                    grating,
                    grang,
                    arang,
                    filtername,
                    slitid,
                    xarr,
                )
                ws = WavelengthSolution.WavelengthSolution(xarr, xarr, function=function, order=order)
                ws.set_coef(coef)
                for j in range(len(hdu[i].data)):
                    wavemap[j, :] = ws.value(wavemap[j, :])
                if array_only:
                    return wavemap
                hdu[w_ext].data = wavemap
                continue

            # set up a wavelength solution -- still in here for testing MOS data
            try:
                w_arr = sr.findsol(
                    xarr,
                    soldict,
                    istart,
                    caltype,
                    nearest,
                    timeobs,
                    exptime,
                    instrume,
                    grating,
                    grang,
                    arang,
                    filtername,
                    slit,
                    xbin,
                    ybin,
                    slitid,
                    function,
                    order,
                )
            except SALTSpecError as e:
                if slitid:
                    msg = "SLITID %s: %s" % (slitid, e)
                    if log:
                        log.warning(msg)
                    continue
                else:
                    raise SALTSpecError(e)

            if w_arr is None:
                w_arr = sr.findsol(
                    xarr,
                    soldict,
                    istart,
                    "rss",
                    nearest,
                    timeobs,
                    exptime,
                    instrume,
                    grating,
                    grang,
                    arang,
                    filtername,
                    slit,
                    xbin,
                    ybin,
                    slitid,
                    function,
                    order,
                )

            # for each line in the data, determine the wavelength solution
            # for a given line in the image
            wavemap = np.zeros_like(hdu[i].data)
            for j in range(len(hdu[i].data)):
                # find the wavelength solution for the data
                w_arr = sr.findsol(
                    xarr,
                    soldict,
                    j,
                    caltype,
                    nearest,
                    timeobs,
                    exptime,
                    instrume,
                    grating,
                    grang,
                    arang,
                    filtername,
                    slit,
                    xbin,
                    ybin,
                    slitid,
                    function,
                    order,
                )
                if w_arr is not None:
                    wavemap[j, :] = w_arr
            if array_only:
                return wavemap

            # write out the oimg
            hduwav = fits.ImageHDU(data=wavemap, header=hdu[i].header, name="WAV")
            hdu.append(hduwav)
            saltkey.new("WAVEXT", len(hdu) - 1, "Extension for Wavelength Map", hdu[i])

    return hdu
def specarcstraighten(images, outfile, function='poly', order=3, rstep=1,
                      rstart='middlerow', nrows=1, 
                      y1=None, y2=None, sigma=5, sections=3, niter=5,
                      startext=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.argunpack('Output', outfile)

        # Identify the lines in each file
        for img, ofile in zip(infiles, outfiles):

            # open the image
            hdu = saltio.openfits(img)

            # get the basic information about the spectrograph
            dateobs = saltkey.get('DATE-OBS', hdu[0])
            try:
                utctime = saltkey.get('UTC-OBS', hdu[0])
            except SaltError:
                utctime = saltkey.get('TIME-OBS', hdu[0])

            instrume = saltkey.get('INSTRUME', hdu[0]).strip()
            grating = saltkey.get('GRATING', hdu[0]).strip()
            grang = saltkey.get('GR-ANGLE', hdu[0])
            grasteps = saltkey.get('GRTILT', hdu[0])
            arang = saltkey.get('AR-ANGLE', hdu[0])
            arsteps = saltkey.get('CAMANG', hdu[0])
            rssfilter = saltkey.get('FILTER', hdu[0])
            specmode = saltkey.get('OBSMODE', hdu[0])
            masktype = saltkey.get('MASKTYP', hdu[0]).strip().upper()
            slitname = saltkey.get('MASKID', hdu[0])
            xbin, ybin = saltkey.ccdbin(hdu[0], img)

            for i in range(startext, len(hdu)):
                if hdu[i].name == 'SCI':
                    log.message('Proccessing extension %i in  %s' % (i, img))
                    # things that will change for each slit

                    if masktype == 'LONGSLIT':
                        slit = st.getslitsize(slitname)
                        objid = None
                    #elif masktype == 'MOS':
                        #slit = 1.5
                        # slit=saltkey.get('SLIT', hdu[i])

                        # set up the x and y positions
                        #miny = hdu[i].header['MINY']
                        #maxy = hdu[i].header['MAXY']
                        #ras = hdu[i].header['SLIT_RA']
                        #des = hdu[i].header['SLIT_DEC']
                        #objid = hdu[i].header['SLITNAME']

                        # Check the perfomance of masks at different PA
                        #rac = hdu[0].header['MASK_RA']
                        #dec = hdu[0].header['MASK_DEC']
                        #pac = hdu[0].header['PA']

                    else:
                        msg = '%s is not a currently supported masktype' % masktype
                        raise SALTSpecError(msg)

                    if instrume not in ['PFIS', 'RSS']:
                        msg = '%s is not a currently supported instrument' % instrume
                        raise SALTSpecError(msg)

                    # set up the data for the source
                    try:
                        data = hdu[i].data
                    except Exception as e:
                        message = 'Unable to read in data array in %s because %s' % (
                            img, e)
                        raise SALTSpecError(message)

                    # set up the center row
                    if rstart == 'middlerow':
                        ystart = int(0.5 * len(data))
                    else:
                        ystart = rstart


                    # set up the xarr array based on the image
                    xarr = np.arange(len(data[ystart]), dtype='int64')

                    # calculate the transformation
                    ImageSolution = arcstraight(data, xarr, ystart, function=function, order=order, 
                                                rstep=rstep, y1=y1, y2=y2, sigma=sigma, sections=sections,
                                                niter=niter, log=log, verbose=verbose)

                    if outfile and len(ImageSolution):
                        writeIS(ImageSolution, outfile, dateobs=dateobs, utctime=utctime, instrume=instrume,
                                grating=grating, grang=grang, grasteps=grasteps, arsteps=arsteps,
                                arang=arang, rfilter=rssfilter, slit=slit, xbin=xbin,
                                ybin=ybin, objid=objid,
                                filename=img, log=log, verbose=verbose)
Exemple #10
0
def auto_arc_lens(arc_image, dbfile='wav.db', ndstep=20, logfile='salt.log'):
    """Automatically process an arc image for the SALT Lens project

    """
    hdu = fits.open(arc_image)
    hdr = hdu[0].header
    if hdr['LAMPID'] == 'Xe' and hdr['GRATING'] == 'PG0900' and hdr['GRTILT'] == 15.875:
        print('Automatically processing arc image')
        data = hdu[1].data
        ystart = int(0.5 * len(data))
        xarr = np.arange(len(data[ystart]), dtype='int64')
        farr = data[ystart]

        lampfile = os.path.dirname(__file__)+'/data/Xe.lens'
        guessfile = os.path.dirname(__file__)+'/data/lens.db'

        slines, sfluxes = st.readlinelist(lampfile)
        spectrum = Spectrum.Spectrum(
            slines, sfluxes, dw=0.1, stype='line', sigma=6)
        swarr = spectrum.wavelength
        sfarr = spectrum.flux * farr.max() / spectrum.flux.max()

        soldict = readsolascii(guessfile, {})
        soldict = (soldict[soldict.keys()[0]])
        ws = WavelengthSolution.WavelengthSolution(
             xarr, xarr, function=soldict[7], order=soldict[8])
        ws.func.func.domain = soldict[11]
        ws.set_coef(soldict[10][2])
 
        # start the pre processing
        dcoef = ws.coef * 0.0
        dcoef[0] = 0.05 * ndstep
        dcoef[1] = 0.01 * ws.coef[1]
        ws = st.findxcor(xarr, farr, swarr, sfarr, ws,
                         dcoef=dcoef, ndstep=ndstep, best=False, inttype='interp')
        xp, wp = st.crosslinematch(xarr, farr, slines, sfluxes, ws,
                                   res=6, mdiff=20, wdiff=10,
                                   sections=3, sigma=5, niter=5)
        ws = st.findfit(np.array(xp), np.array(wp), ws=ws, thresh=ws.thresh)
        print(ws)
        with logging(logfile, True) as log:
            iws = ai.AutoIdentify(xarr, data, slines, sfluxes, ws, farr=farr,
                      method='Matchlines', rstep=100, istart=ystart, nrows=1,
                      res=6, dres=0.25, mdiff=20, sigma=5,
                      smooth=3, niter=5, dc=5, ndstep=ndstep, 
                      oneline=False, log=log, verbose=True)

            # get the basic information about the spectrograph
            dateobs = saltkey.get('DATE-OBS', hdu[0])
            try:
                utctime = saltkey.get('UTC-OBS', hdu[0])
            except SaltError:
                utctime = saltkey.get('TIME-OBS', hdu[0])

            instrume = saltkey.get('INSTRUME', hdu[0]).strip()
            grating = saltkey.get('GRATING', hdu[0]).strip()
            grang = saltkey.get('GR-ANGLE', hdu[0])
            grasteps = saltkey.get('GRTILT', hdu[0])
            arang = saltkey.get('AR-ANGLE', hdu[0])
            arsteps = saltkey.get('CAMANG', hdu[0])
            rssfilter = saltkey.get('FILTER', hdu[0])
            specmode = saltkey.get('OBSMODE', hdu[0])
            masktype = saltkey.get('MASKTYP', hdu[0]).strip().upper()
            slitname = saltkey.get('MASKID', hdu[0])
            slit = st.getslitsize(slitname)
            xbin, ybin = saltkey.ccdbin(hdu[0], arc_image)
            writeIS(iws, dbfile, dateobs=dateobs, utctime=utctime, instrume=instrume,
                    grating=grating, grang=grang, grasteps=grasteps, arsteps=arsteps,
                    arang=arang, rfilter=rssfilter, slit=slit, xbin=xbin,
                    ybin=ybin, objid=None, filename=arc_image, log=log, verbose=True)
        print(iws)

        #self.findfit()

 
    else:
        lamp = hdr['LAMPID']
        lampfile=iraf.osfn("pysalt$data/linelists/%s.salt" % lamp)
        lampfile = 'Xe.lens'
        specidentify(arc_image, lampfile, dbfile, guesstype='rss', 
                  guessfile=None, automethod='Matchlines',  function='legendre',  order=3,
                  rstep=100, rstart='middlerow', mdiff=20, thresh=5, niter=5, smooth=3,
                  inter=True, clobber=True,  preprocess=True, logfile=logfile, verbose=True)
        print("Running specidenity in interactive mode")
Exemple #11
0
def wavemap(hdu,
            soldict,
            caltype='line',
            function='poly',
            order=3,
            blank=0,
            nearest=False,
            array_only=False,
            clobber=True,
            log=None,
            verbose=True):
    """Read in an image and a set of wavlength solutions.  Calculate the best
       wavelength solution for a given dataset and then apply that data set to the
       image

     return
    """

    # set up the time of the observation
    dateobs = saltkey.get('DATE-OBS', hdu[0])
    utctime = saltkey.get('TIME-OBS', hdu[0])
    exptime = saltkey.get('EXPTIME', hdu[0])
    instrume = saltkey.get('INSTRUME', hdu[0]).strip()
    grating = saltkey.get('GRATING', hdu[0]).strip()
    if caltype == 'line':
        grang = saltkey.get('GRTILT', hdu[0])
        arang = saltkey.get('CAMANG', hdu[0])
    else:
        grang = saltkey.get('GR-ANGLE', hdu[0])
        arang = saltkey.get('AR-ANGLE', hdu[0])
    filtername = saltkey.get('FILTER', hdu[0]).strip()
    slitname = saltkey.get('MASKID', hdu[0])
    slit = st.getslitsize(slitname)
    xbin, ybin = saltkey.ccdbin(hdu[0])

    timeobs = sr.enterdatetime('%s %s' % (dateobs, utctime))

    # check to see if there is more than one solution
    if caltype == 'line':
        if len(soldict) == 1:
            sol = soldict.keys()[0]
            slitid = None
            if not sr.matchobservations(soldict[sol], instrume, grating, grang,
                                        arang, filtername, slitid):
                msg = 'Observations do not match setup for transformation but using the solution anyway'
                if log:
                    log.warning(msg)

    for i in range(1, len(hdu)):
        if hdu[i].name == 'SCI':
            if log:
                log.message('Correcting extension %i' % i)
            istart = int(0.5 * len(hdu[i].data))

            # open up the data
            # set up the xarr and initial wavlength solution
            xarr = np.arange(len(hdu[i].data[istart]), dtype='int64')

            # get the slitid
            try:
                slitid = saltkey.get('SLITNAME', hdu[i])
            except:
                slitid = None

            #check to see if wavext is already there and if so, then check update
            #that for the transformation from xshift to wavelength
            if saltkey.found('WAVEXT', hdu[i]):
                w_ext = saltkey.get('WAVEXT', hdu[i]) - 1
                wavemap = hdu[w_ext].data
                function, order, coef = sr.findlinesol(
                    soldict, istart, nearest, timeobs, exptime, instrume,
                    grating, grang, arang, filtername, slitid, xarr)
                ws = WavelengthSolution.WavelengthSolution(xarr,
                                                           xarr,
                                                           function=function,
                                                           order=order)
                ws.set_coef(coef)
                for j in range(len(hdu[i].data)):
                    wavemap[j, :] = ws.value(wavemap[j, :])
                if array_only: return wavemap
                hdu[w_ext].data = wavemap
                continue

            # set up a wavelength solution -- still in here for testing MOS data
            try:
                w_arr = sr.findsol(xarr, soldict, istart, caltype, nearest,
                                   timeobs, exptime, instrume, grating, grang,
                                   arang, filtername, slit, xbin, ybin, slitid,
                                   function, order)
            except SALTSpecError as e:
                if slitid:
                    msg = 'SLITID %s: %s' % (slitid, e)
                    if log:
                        log.warning(msg)
                    continue
                else:
                    raise SALTSpecError(e)

            if w_arr is None:
                w_arr = sr.findsol(xarr, soldict, istart, 'rss', nearest,
                                   timeobs, exptime, instrume, grating, grang,
                                   arang, filtername, slit, xbin, ybin, slitid,
                                   function, order)

            # for each line in the data, determine the wavelength solution
            # for a given line in the image
            wavemap = np.zeros_like(hdu[i].data)
            for j in range(len(hdu[i].data)):
                # find the wavelength solution for the data
                w_arr = sr.findsol(xarr, soldict, j, caltype, nearest, timeobs,
                                   exptime, instrume, grating, grang, arang,
                                   filtername, slit, xbin, ybin, slitid,
                                   function, order)
                if w_arr is not None: wavemap[j, :] = w_arr
            if array_only: return wavemap

            # write out the oimg
            hduwav = fits.ImageHDU(data=wavemap,
                                   header=hdu[i].header,
                                   name='WAV')
            hdu.append(hduwav)
            saltkey.new('WAVEXT',
                        len(hdu) - 1, 'Extension for Wavelength Map', hdu[i])

    return hdu
Exemple #12
0
def specidentify(images,
                 linelist,
                 outfile,
                 guesstype='rss',
                 guessfile='',
                 automethod='Matchlines',
                 function='poly',
                 order=3,
                 rstep=100,
                 rstart='middlerow',
                 mdiff=5,
                 thresh=3,
                 niter=5,
                 smooth=0,
                 subback=0,
                 inter=True,
                 startext=0,
                 clobber=False,
                 textcolor='black',
                 preprocess=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.argunpack('Output', outfile)

        # open the line lists
        slines, sfluxes = st.readlinelist(linelist)

        # Identify the lines in each file
        for img, ofile in zip(infiles, outfiles):

            # open the image
            hdu = saltio.openfits(img)

            # get the basic information about the spectrograph
            dateobs = saltkey.get('DATE-OBS', hdu[0])
            try:
                utctime = saltkey.get('UTC-OBS', hdu[0])
            except SaltError:
                utctime = saltkey.get('TIME-OBS', hdu[0])

            instrume = saltkey.get('INSTRUME', hdu[0]).strip()
            grating = saltkey.get('GRATING', hdu[0]).strip()
            grang = saltkey.get('GR-ANGLE', hdu[0])
            grasteps = saltkey.get('GRTILT', hdu[0])
            arang = saltkey.get('AR-ANGLE', hdu[0])
            arsteps = saltkey.get('CAMANG', hdu[0])
            rssfilter = saltkey.get('FILTER', hdu[0])
            specmode = saltkey.get('OBSMODE', hdu[0])
            masktype = saltkey.get('MASKTYP', hdu[0]).strip().upper()
            slitname = saltkey.get('MASKID', hdu[0])
            xbin, ybin = saltkey.ccdbin(hdu[0], img)

            for i in range(startext, len(hdu)):
                if hdu[i].name == 'SCI':
                    log.message('Proccessing extension %i in  %s' % (i, img))
                    # things that will change for each slit

                    if masktype == 'LONGSLIT':
                        slit = st.getslitsize(slitname)
                        xpos = -0.2666
                        ypos = 0.0117
                        objid = None
                    elif masktype == 'MOS':
                        slit = 1.
                        #slit=saltkey.get('SLIT', hdu[i])

                        # set up the x and y positions
                        miny = hdu[i].header['MINY']
                        maxy = hdu[i].header['MAXY']
                        ras = hdu[i].header['SLIT_RA']
                        des = hdu[i].header['SLIT_DEC']
                        objid = hdu[i].header['SLITNAME']

                        # TODO: Check the perfomance of masks at different PA
                        rac = hdu[0].header['MASK_RA']
                        dec = hdu[0].header['MASK_DEC']
                        pac = hdu[0].header['PA']

                        # these are hard wired at the moment
                        xpixscale = 0.1267 * xbin
                        ypixscale = 0.1267 * ybin
                        cx = int(3162 / xbin)
                        cy = int(2050 / ybin)

                        x, y = mt.convert_fromsky(ras,
                                                  des,
                                                  rac,
                                                  dec,
                                                  xpixscale=xpixscale,
                                                  ypixscale=ypixscale,
                                                  position_angle=-pac,
                                                  ccd_cx=cx,
                                                  ccd_cy=cy)
                        xpos = 0.015 * 2 * (cx - x[0])
                        ypos = 0.0117
                    else:
                        msg = '%s is not a currently supported masktype' % masktype
                        raise SALTSpecError(msg)

                    if instrume not in ['PFIS', 'RSS']:
                        msg = '%s is not a currently supported instrument' % instrume
                        raise SALTSpecError(msg)

                    # create RSS Model
                    rss = RSSModel.RSSModel(grating_name=grating.strip(),
                                            gratang=grang,
                                            camang=arang,
                                            slit=slit,
                                            xbin=xbin,
                                            ybin=ybin,
                                            xpos=xpos,
                                            ypos=ypos)
                    res = 1e7 * rss.calc_resolelement(rss.alpha(), -rss.beta())
                    dres = res / 10.0
                    wcen = 1e7 * rss.calc_centralwavelength()
                    R = rss.calc_resolution(wcen / 1e7, rss.alpha(),
                                            -rss.beta())
                    logmsg = '\nGrating\tGR-ANGLE\tAR-ANGLE\tSlit\tWCEN\tR\n'
                    logmsg += '%s\t%8.3f\t%8.3f\t%4.2f\t%6.2f\t%4f\n' % (
                        grating, grang, arang, slit, wcen, R)
                    if log:
                        log.message(logmsg, with_header=False)

                    # set up the data for the source
                    try:
                        data = hdu[i].data
                    except Exception, e:
                        message = 'Unable to read in data array in %s because %s' % (
                            img, e)
                        raise SALTSpecError(message)

                    # set up the center row
                    if rstart == 'middlerow':
                        ystart = int(0.5 * len(data))
                    else:
                        ystart = int(rstart)

                    rss.gamma = 0.0
                    if masktype == 'MOS':
                        rss.gamma = 180.0 / math.pi * math.atan(
                            (y * rss.detector.pix_size * rss.detector.ybin -
                             0.5 * rss.detector.find_height()) /
                            rss.camera.focallength)

                    # set up the xarr array based on the image
                    xarr = np.arange(len(data[ystart]), dtype='int64')

                    # get the guess for the wavelength solution
                    if guesstype == 'rss':
                        # set up the rss model
                        ws = st.useRSSModel(xarr,
                                            rss,
                                            function=function,
                                            order=order,
                                            gamma=rss.gamma)
                        if function in ['legendre', 'chebyshev']:
                            ws.func.func.domain = [xarr.min(), xarr.max()]
                    elif guesstype == 'file':
                        soldict = {}
                        soldict = readsolascii(guessfile, soldict)
                        timeobs = enterdatetime('%s %s' % (dateobs, utctime))
                        exptime = saltkey.get('EXPTIME', hdu[0])
                        filtername = saltkey.get('FILTER', hdu[0]).strip()
                        try:
                            slitid = saltkey.get('SLITNAME', hdu[i])
                        except:
                            slitid = None

                        function, order, coef, domain = findlinesol(soldict,
                                                                    ystart,
                                                                    True,
                                                                    timeobs,
                                                                    exptime,
                                                                    instrume,
                                                                    grating,
                                                                    grang,
                                                                    arang,
                                                                    filtername,
                                                                    slitid,
                                                                    xarr=xarr)
                        ws = WavelengthSolution.WavelengthSolution(
                            xarr, xarr, function=function, order=order)
                        ws.func.func.domain = domain
                        ws.set_coef(coef)
                    else:
                        raise SALTSpecError(
                            'This guesstype is not currently supported')

                    # identify the spectral lines
                    ImageSolution = identify(data,
                                             slines,
                                             sfluxes,
                                             xarr,
                                             ystart,
                                             ws=ws,
                                             function=function,
                                             order=order,
                                             rstep=rstep,
                                             mdiff=mdiff,
                                             thresh=thresh,
                                             niter=niter,
                                             method=automethod,
                                             res=res,
                                             dres=dres,
                                             smooth=smooth,
                                             inter=inter,
                                             filename=img,
                                             subback=0,
                                             textcolor=textcolor,
                                             preprocess=preprocess,
                                             log=log,
                                             verbose=verbose)

                    if outfile and len(ImageSolution):
                        writeIS(ImageSolution,
                                outfile,
                                dateobs=dateobs,
                                utctime=utctime,
                                instrume=instrume,
                                grating=grating,
                                grang=grang,
                                grasteps=grasteps,
                                arsteps=arsteps,
                                arang=arang,
                                rfilter=rssfilter,
                                slit=slit,
                                xbin=xbin,
                                ybin=ybin,
                                objid=objid,
                                filename=img,
                                log=log,
                                verbose=verbose)