Frequently Asked Questions

    1. 1 - Numeric MLab module not found
    2. 2 - Plotutils compilation failed
    3. 3 - RADIAL VELOCITY, RV erroneous helio/barycentric correction
    4. 4 - RADIAL VELOCITY binary mask
    5. 5 - ThAr wavelength; and
    6. 6 - SKY SUBTRACTION till rel 1.12
    7. 7 -, Signs '+' '-' '*' in KW 'ESO OBS TARG NAME'
    8. 8 - Use of with data produced by Paranal pipeline
    9. 9 - Where to start if I know nothing about the data structure and reduction
    10. 10 - Gawk parse error, problem with scripts (Wed Mar 23 06:15:21 CLT 2005)
    11. 11 - Best accuracy in RV
    12. 12 - FLAT FIELDING in ARGUS
    13. 13 - PIPE, Word too long, csh
    14. 14 - Transfering Localisation and Simultaneous calibration from other science frame
    15. 15 - ARGUS, orientation on the sky, image reconstruction

    Numeric MLab module not found
     depending on existing system wide python Numeric installation,
     it happens that  the MLab module is not found.
     To get rid of this problem you have to install the girBLDRS own
     python Numeric module, that is the one, and precisely THIS ONE
     available at
     Download the preceding URL to the REQUIRED directory in the girBLDRS
     source tree, where you find the script, and run
     this script, then re-run the installation script

    [004 00NumericMLab.txt ]

    Plotutils compilation failed
    To compile plotutils, your system need to have the X11 and Xaw 
    packages installed, and also their development part: X11-dev
    and Xaw-dev.
    The real name of these packages 'rpm' or 'deb' is different
    depending on your installed Linux distribution, RedHat, Sebian,
    Suse, etc...

    [004 00PlotutilsCompile.txt ]

    RADIAL VELOCITY, RV erroneous helio/barycentric correction
      What  sign  should  be  Paranal  geographical longitude. It seems that +70 rather than -70
      given by image header is the correct value. ?
    ANSWER (AB):
     It  appears  that  the  (general) convention used for Geographical Longitude and assumed in
     computation  of the Geocentric Radial Velocity correction in assuming +sign for
     West  longitude  is  in  DESAGREEMENT  with ESO KW 'ESO TEL GEOLON' which gives for Paranal
    Impact on the GIRAFFE BLDRS:
      Unless you modifed KW 'ESO TEL GEOLON', all releases till 1.13 included are affected Worst
      case error reaches +-0.75 km/sec for object at the equator and vary with date and time.
      The  error  is  mostly systematic for observations taken with similar hour angles while it
      produces random scatter for observations taken at distant dates
    Correction in release 1.13
    Edit installed $GIR_ROOT/python/share/bin/
     go to line 1373 which should be:
      "if verbose: print 'MJD,EXPOSURE,LON,LAT,ELE ..."
     add (beware indentation):
      if LON is not None: 
        if abs(70.403+LON)<0.001: 
          if verbose>=0: print '# Setting longitude +sign for Paranal'
     check the syntax: -h

    [2004 50RadialVelocity.txt ]

    RADIAL VELOCITY binary mask
  Wed, 27 Oct 2004 12:10:07:
      Is  it  possible  to create a binary mask for radial velocities measurements to be used in
      pipe-line task?
    Answer (AB):
      That is something marginally supported; you may proceed as follows:
      cd $GIR_CALIB
      Get ASCII format of any H9A table:
        fitstotable girG2H9A.tfits | justify > girG2H9Atest.r
      Edit girG2H9Atest.r and remove lines with unsupported keys:
      # SIMPLE  =T / file does conform to FITS standard
      # ESO INS GRAT NAME='HR316' / Grating common name (hls).
      # ESO INS GRAT WLEN=525.8 / Grating central wavelength [nm] (hs).
      # OGL PRO REBIN LAMBDA STEP=0.0 / wlen step used for rebinning
      Use  your tools (good editor - better to make tabs visible) to adjust WLEN1 WLEN2 columns;
      other  columns  has no effect on but should be there. Be careful to keep 
      convert to tfits using:
      tabletofits -b girG2H9test.r > girG2H9test.tfits
      use with -T girG2H9test.tfits option

    [2004 51RVcreatePrivatMask.txt ]

    ThAr wavelength; and
      What   is  the  source  of  reference  wavelength  used  to  build  the  binary  masks  for
      cross-correlation ?
    ANSWER (PN):
      Palmer  B.A.  &  Engleman R. Jr., 1983, Atlas of the Thorium spectrum, Los Alamos National

    [004 52ThArWavelengthSource.txt ]

    SKY SUBTRACTION till rel 1.12
  22 Nov 2004 10:39:36
        when trying to subtract the sky (both with the pipe command skyss
        with the python command I obtain the message of error:
          Not enough valid bins in sky spectra: [  3  15  17  19  25 ...]
                                                [0 0 0 0 0 0 0 0 .....
    Answer (AB):
      The  reason  is  the presence of one ore more inconsistent sky spectra (very different from
      others). It will be properly solved in 1.13. In mean time several ways to get around.
      1. Give list of good sky spectra using '-S' option; proceed as follows:
        - run  giSky  in  verbose  mode;  '-v'  option
        - and look for line: 'Rejected sky spectra: [bad1,bad2,..]'
          this line appears after 'Model-rawdata for Integrated Sky; nspec ...'
        - run giSky with option -S sp1,sp2,sp3,.... dropping spectra numbers bad1,bad2,... 
      2. Increase  the  sigma-clipping limit to prevent the rejection of a complete spectrum as
        - run ' ---skInt -,-,-5 ...'      -5 stands for nsigma = 5 (default is 3)
      While method 2. is simple, for obvious reasons the 1. is better

    [2004 53SkySubtractionNot_enough_valid_bins.txt ], Signs '+' '-' '*' in KW 'ESO OBS TARG NAME'
       produces  error  '**ERROR**  Input  file of the expression do not exists'
        while  the referenced file, NGC-3623ArgusL4Seq01bSub1??.fits, DOES exits. The problems
        seems to be related to the symbol '-' present in the filename which has been generated
        by the previous step within the pipe.
    ANSWER (AB):
      The  pipe  uses the KW 'ESO OBS TARG NAME' to generate default for the first part of the
      intermediate  filenames  governed  by the pipe parameter 'OBJ'. If one of characters '+'
      '-'  '*'  is  present  within  the  KW  it  is  interpreted by as arithmetic
      operation leading to pipe failure since the file is not found.
      You  should  therefore specify pipe parameter 'OBJ'. In your case you may add to the pipe
      command 'OBJ=ngc3623' so as to have for exemple:
        pipe extract RAW=../raw/GIRAF.2003-01-28T05:49:49.211.fits OBJ=ngc3623

    [004 54TargetNameWithForbidenCharacters.txt ]

    Use of with data produced by Paranal pipeline
      QUESTION:, and others
      I  have  been  trying  to  use  girBLDRS,  in  particular  the  function, on
      pipeline-reduced  data  in order to calculate radial velocities but kept obtaining error
      messages starting by:
      ***WARNING: absent or empty ozPoz table, we asume all spectra listed in Fibre table ...
    ANSWER (AB):
      The  Paranal  pipeline does not produce the data in the format compatible with the BLDRS
      python  release  till 1.12. The main difference concerns the changes in KW names and the
      absence  of  the  binary  tables  in  reduced  data.  Though  the  BLDRS release 1.13 in
      preparation  will support at least at some basic level the output from Paranal pipeline,
      unfortunatelly we must accept that Python and Paranal version diverge since even the low
      level  c-code  evolved independently during the past 18 months. We strongly recommend to
      users  desiring  to  use  correlation,  sky subtraction or image reconstruction to fully
      reprocess the data using the Python version.

    [2005 55useBldrsWithDataFromParanalPipeline.txt ]

    Where to start if I know nothing about the data structure and reduction
      QUESTION: Thu, 10 Mar 2005 17:05:15
        I  recently  installed  the latest girBLDR software in order to reduce some data taken
        with  Giraffe  in ARGUS mode. I have taken a look to the Reference Manual as well. The
        problem  is  that  it  is my first time reducing this kind of data and I'm quite a bit
    ANSWER (AB):
      I would recommend followings:
        Run the complete test 'time ptest' after the girbldrs_girbldrs-pipe pipe installations
        (see  file  INSTALL_EXAMPLE  in  the  distribution  which  gives  full  example of the
        installation including test data download).
        Declare test calibration as current calibration directory 
          setenv GIR_CALIB ../calib
        Get list of 'ptest' by typing: 'ptest -2'
        Execute  test  1-by-1  and try to understand what is it doing. Use your usual tools to
        look  on  produced  fits  files  (rtd,  ...)  then graphic tool specific to
        Would  be useful to read in parallel sub-sections 4.1 (pipe INTRODUCTION) - 4.4 (DATA
        REDUCTION COOK_BOOK) [4.5] of the Reference Manual
        Install the calibrations you need for your data from:

        In case of problem have a look on FAQ at:

    [2005 56whereToStart.txt ]

    Gawk parse error, problem with scripts (Wed Mar 23 06:15:21 CLT 2005)
      QUESTION: I have the following problem with fhead
         I cannot get any suitable answer anymore.
         dfits ../raw/*fits | fhead
           gawk: compute.gawk.23212:7: $2=sprintf("%5i",$2); 
           DATE=substr(DATE,1,length(DATE)-7); if (length(FILT)>0) {s1=substr(FILT,1,1); 
           s2=substr(FILT,3); FILT=sprintf("%s%2.2i",s1,s2)}$3substr$31length$3
           7iflength$90s1substr$911s2substr$93$9sprintf"%s%2.2i"s1s2;print $0
           gawk: compute.gawk.23212:7: 
                                                 ^ parse errorI cannot get any suitable answer anymore.
    ANSWER (AB):
      Must be a conflict between your local SW and girbldrs-pipe. Check followings:
         dfits ../raw/*fits   
           # must be a list of KWs something like
           ====> ../raw/GIRAF.2004-04-14T07:53:47.450.fits (main) <====
           SIMPLE   =T / Standard FITS format (NOST-100.0)
           BITPIX   =16 / # of bits storing pix values
         # check /rdb scripts used within commands by piping most of scripts toogether
         echo "1" | number nu 5 | addcol nn | compute 'nn=10*nu' | column nu | rename nu NU \
         | sorttable -nr NU | addccol addedstring str | tabletolist | listtotable | rmcol str \
         | row 'NU<3' |headoff
         # the output should be '1'
         In  case  of  problem  run  the  /rdb  test partially till you localise the offending
         command  and  consult  your local guru. I would suspect that your path and/or gawk is
         the source of problem.

    [2005 57gawk_parse_error_problem_with_scripts.txt ]

    Best accuracy in RV
      QUESTION: Claudio Melo  Tue Apr 12 13:44:47 MEST 2005
    ANSWER (AB):
       Here  is  the  description  what  I  will  do  (with some comments). The data reduction
       strategy  and  final  accuracy will depend on many factor such as time coverage, setup,
       fibre  assignment  and  scientific  goal.I  will just make few hints on what should be
       looked  at.  An  example  of reduction in Medusa1H12 setup is given. It is assumed that
       master  calibrations  exists  in $GIR_CALIB.
      The standard calibration if available in:
      provides the elements of the standard solution:
        $GIR_CALIB/girSlitGeoMedusa1H12.tfits   # slit geometry
        ThArMedusa1H12dbSub.extsp.xores.tfits   # optical+Cheby W-solution
      For science exposure with simultaneous wavelength calibration, this solution is adjusted
      using  the  during  the  standard  extraction  and  therefore  YOU NEED THE
      CALIBRATION  only as accuracy check. The accuracy with your actual data could be checked
      using the standard extraction:
        pipe extract OBJ=ThAr EMETHOD=SUMM NAM=Seq01 RAW=../raw/WcalFile#1
        pipe extract OBJ=ThAr EMETHOD=SUMM NAM=Seq02 RAW=../raw/WcalFile#2  -N  0:-0  --txts  -g  5  -T  \
        ThArMedusa1H12Seq01dbSub.extsp.rebinlin.fits \
        ThArMedusa1H12Seq02dbSub.extsp.rebinlin.fits \
        The output ends by:
        # Average fluxes - CALSIM: 17465, CAL: 2246 
        # Medusa1H12: average RV -37 +- 111[m/sec] using 131 RV determination out of 132 valid
        RV peaks, \
    		preliminary list of invalid spectra: 24C
        In  the  above  case  (2 calibration 1 year apart) the noise added by calibration (i.e
        fibre-to-fibre) is 111/(2**0.5)=78[m/sec] while exposure-to-exposure accuracy obtained
        by comparison of several files is ~100m/sec
      For science exposure use standard extraction:
        pipe extract RAW=../raw/file_name
      The simultaneous calibration is detected and processed automatically 
      #1.  Make  new  empty  directory  for reduced data. If you have several images in the same
      setup you would better make 1 directory/image since intermediate calibration data will be
      located  there  and  the  naming  scheme  of intermediate data does not support multiple
      instances of the same setup.
      #2. Run locMast with 'MAST=no' option which will not modify data in $GIR_CALIB
         pipe locMast RAW=../raw/GIRAF.2004-05-15T15:09:52.586.fits MAST=no
      #3.  Run  wcalMast  with 'MAST=no' option
         pipe wcalMast RAW=../raw/GIRAF.2004-05-15T15:13:54.653.fits MAST=no
         It produces the W-solution using the slit geometry from the $GIR_CALIB. At this stage
         you can check the accuracy:
           dfits -x0 ThArMedusa1H12dbSub.extsp.rebinlin.fits | egrep QC
             OGL PRO QC LOC COURBMAX =	7.86811007897 / max ydiff within any spect
             OGL PRO QC PSF COURBMAX =	8.08508513408 / max ydiff of 2 adjacent pi
             OGL PRO QC WSRMS OPT =	'1.04' / Wcal: RMS[pixel] optical model
             OGL PRO QC WSRMS CHEB =	'0.16' / Wcal: RMS[pixel] after chebycheff
             OGL PRO QC WSLINE PERCENT =	99 / Wcal: Percentage of accepted lines
             OGL PRO QC SLIT RV AVERAGE =	3 / CC: Average RV[m/s] of residuals
             OGL PRO QC SLIT RV RMS =	63 / CC: RMS[m/s] of residuals
             OGL PRO QC SLIT RV NSP =	132 / CC: nombre of fibres used
             OGL PRO QC SLIT RV SPOUT =	'42L,27M' / CC: list of rejected fibres
           Mainly  OGL  PRO  QC  WSRMS CHEB gives the accuracy of single line in pixels. In the
           above     case     it     would     mean     approximately     that     we     have
           DRV=BAND*0.16*300000/(4000.*WLEN)=0.5[km/sec/line]  accuracy.  You  can  expect  on
           final data using this calibration the random error due to the calibration of 
         You  can  either  run wcalMast once per run using one or several calibration files or
         take  for  each  observation the closest calibration. The later becomes compulsory if
         you  do  not have simultaneous W-calibration, but I am not sure that for a run of few
         days WITH simultaneous W-calibration it will bring any improvement.
      #4. Adjust slit Geometry (only once per setup)
         pipe wcalSlit RAW=../raw/GIRAF.2004-05-15T15:13:54.653.fits
           This  produces  the new slit geometry and new rebinned ThAr file. The graphic shows
           the  residual  RV of spectra rebinned using the standard girSlitGeoMedusa1H12.tfits
           taken  from  $GIR_CALIB. If you repeat the pipe wcalSlit you will see the residuals
           decrease  to almost arbitrary low level which does not reflect the actual accuracy.
           In most cases 2 iterations are enough to reach few m/sec.
           This  step  (#4)  produces  new $GIR_CALIB/girSlitGeoMedusa1H12.tfits which will be
           used  for all subsequent W-calibrations of the same setup within the observing run.
           This  is also the only operation which modify the archive in $GIR_CALIB. In case of
           doubt  you  can  check  with results of other calibrations (you will have to rename
           'girSlitGeoMedusa1H12.tfits'  by  hand),  but  very  likely  the  use  of  the same
           girSlitGeoMedusa1H12.tfits for all data will lead to the best accuracy.
           You completed the global W-calibration. The result used for subsequent rebinning of
           science data is in 2 files:
             $GIR_CALIB/girSlitGeoMedusa1H12.tfits   # slit geometry
             ThArMedusa1H12dbSub.extsp.xores.tfits   # optical+Cheby W-solution
         You can check the accuracy of rebinned data by the same method as above:
          pipe extract OBJ=ThAr EMETHOD=SUMM NAM=Seq01 RAW=../raw/WcalFile#1
          pipe extract OBJ=ThAr EMETHOD=SUMM NAM=Seq02 RAW=../raw/WcalFile#2
  -N  0:-0  --txts  -g  5  -T  \
          ThArMedusa1H12Seq01dbSub.extsp.rebinlin.fits \
          ThArMedusa1H12Seq02dbSub.extsp.rebinlin.fits \
         Typical systematic error (exposure-to-exposure) RMS is 60 m/sec and 
         fibre-to-fibre RMS 50m/sec.
      #5. Extract and rebin science data
         pipe extract RAW=../raw/GIRAF.2004-05-15T08:17:51.045.fits
        If  you  want  a  set  of  RVs to compare objet-to-object RV the use of binary mask is
        best solution; for example:
 -N 1:30:1 -O ngc --txts -V -200,200,1 -T girK0 -R 1 \
        If  you want optimize the accuracy of RV curves for individual objects you may use the CC
        against the selected spectrum of each object (within the same setup):
 -N 1:-0 -O ngc --txts -T Selected_exposureframe. \
        Do not omit '.' after Selected_exposureframe which indicates that same spectra should
        be taken. If you do not have same fibre assignment for all exposure you must give the
        list  of  correspondence after the dot (see -h). You can check the quality
        of this correlation by correlating frame against itself as:
 -N 1:-0 -O ngc --txts -T . --Vcorr n \
        The column rv should have |average value| and RMS ~ few 10m/sec on good spectrum.
          The  RV  obtained  are  values relative to the difference between average position of
          ThAr  lines  of  the  setup and average of science object spectra lines within mask.
          Moreover  there  is  an  additional unknown shift between 5 simultaneous spectra and
          science  spectra  due  to the (usually very) different illumination of simultaneous
          calibration  fibres  and other fibres on the W-calibration ThAr exposures. These are
          which  could be several 100 m/sec apart. If you want to merge 2 or several setup RVs
          you  must use an extra piece of information to adjust the difference (standard star,
          time overlap ...). This is also the best way to evaluate the final accuracy you got.
    Created Thu Apr 14 09:27:42 MEST 2005

    [2005 58HowtogetbestRV.txt ]

      QUESTION: Which FF is better, Nasmyth screen or Calibration unit (Wed Nov 16 10:39:06 CLST 2005)
    ANSWER (AB):
       It  appears  that the calibration unit does not provide the uniform illumination of the
       ARGUS field. Data taken in October 2005 illustrates the situation.
    	 On  the  right,  reconstructed  image  of  FF taken  with  Calibration  Unit  shows  the
    	 gradient  in  illumination  on horizontal axis, while the left image reconstructed from
    	 Nasmyth  screen  illuminated  exposure  has only the fibre-fibre random variation. Note
    	 that uppermost row and rightmost column of Nasmyth image seems to suffer also some systematic effect.
      Use  Nasmyth  screen  data  or  remove  smooth  gradient from Calibration Unit data (for
      example using the average row to divide all rows).
      Ask ESO to improve the Calibration Unit 
    Created Wed Nov 16 11:14:52 CLST 2005

    [2005 59ArgusFFVignettingProblem.txt ]

    PIPE, Word too long, csh
      QUESTION: hector.flores@obspm.Fr
        In my new machine I've installed Knoppix (debian like)
        Linux  2.6.12 #2 SMP Tue Aug 9 23:20:52 CEST 2005 i686 GNU/Linux
        when running the pipe for installation test
          pipe -t locMast
          I got:
           Word too long.
          [1]: No match.    
        After  looking  for "Word too long" error on the network, I found a possible source of
        the problem on the csh and/or tcsh shell command,
      ANSWER (AB):
        You are right, this a problem of c-shell
        Standard  recent installations reserve 10240 characters for the word which is 10-times
        more  then necessary for GIRAFFE SW. You can check how much your installation supports
           echo `echo "qq" | gawk '{imax=1024; for (i=1;i<=imax;i++) {o=o "Q"}; print o}'`
        Modify  "imax=.." till you have/have_not the message "Word too long". If you are below
        1024 you should install a better version of c-shell.
    Fri Feb 10 12:54:40 CLST 2006

    [2006 60Wordtoolong.txt ]

    Transfering Localisation and Simultaneous calibration from other science frame
      QUESTION: (Mon, 10 Apr 2006)
        I  have,  within the night, only one science exposure with simultaneous calibration. I
        would  like  to  use the localisation and wavelength solution adjusted on the exposure
        with simultaneous calibration for other exposures within the night. Any possibility to
        do it ?
      ANSWER (AB):
        Yes, you should proceed as follows:
          1. Extract the exposure with simultaneous calibration:
            pipe extract RAW=your_science_frame_with_simcal_exposure_Name
            EX: pipe extract RAW=../raw/GIRAF.2005-04-30T05:16:30.215.fits
            in data product you will find (ls *.clocy.fits *.wlenRes.tfits):
              a. adjusted localisation named something like:  ObjectSetup...dbSub.clocy.fits
                                                         EX:  HE1503_fieldArgusL7dbSub.clocy.fits
              b. fibre-to-fibre correction table           :  ObjectSetup...dbSub.wlenRes.tfits
                                                         EX:  HE1503_fieldArgusL7dbSub.wlenRes.tfits
          2. Make the a) master localisation
             mv ObjectSetup...dbSub.clocy.fits SetupMast.clocy.fits
             EX: mv HE1503_fieldArgusL7dbSub.clocy.fits ArgusL7Mast.clocy.fits
          3. Run "extract" pipe on all science data in the setup WITHOUT simultaneous calibration:
            pipe extract RAW=your_science_frameName
            EX: pipe extract RAW=../raw/GIRAF.2005-04-30T05:17:39.741.fits
          4.  One more rebin/science_file  manualy  using the correction 1.b: 
              type: "extract -t your_science_frameName"
              pick the last line and add after " " the    option:
                --wres  ObjectSetup...dbSub.wlenRes.tfits
                EX: --wres  HE1503_fieldArgusL7dbSub.wlenRes.tfits
              the command in the example will be:
     --wres HE1503_fieldArgusL7dbSub.wlenRes.tfits -w --bnstep - --bnrange=setup \
              --sgtable $GIR_CALIB/girSlitGeoArgusL7.tfits --bnlin --bnmethod linear \
              HE1503_fieldArgusL7dbSub.oxtsp.fits - HE1503_fieldArgusL7dbSub.clocy.fits -
    Tue Apr 11 03:19:05 CLT 2006

    [2006 61LocalisationTransfer.txt ]

    ARGUS, orientation on the sky, image reconstruction
        How is the ARGUS reconstructed image oriented on the sky ?
      ANSWER (AB):
        The  ARGUS  position angle from North to East is given by the KW ARGPOSAN in the header
        of the OzPoz table
         to see the angle use: dfits -x0 fits_file | egrep ARGPOSAN 
        The  reconstructed image has the major axis along the ARGPOSAN angle and is right-left
        inverted along the minor axis. To get the 1-st pixel in the S-W corner you should flip
        the image around the minor axis and (clockwise) rotate of ARGPOSAN angle.
        EXAMPLE:  for  ARGPOS=330  I would rotate image 30 degrees counter-clockwise then flip
        around the major axis.
    Wed Aug  2 06:21:47 CLT 2006

    [006 62Argusorientation.txt ]

Comments / Modifications: