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NAME

       vmmoscalib - Determination of the extraction mask

SYNOPSIS

       esorex vmmoscalib [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe  is used to identify reference lines on MOS arc lamp exposures, and trace the
       spectral edges on the corresponding flat field exposures.  This  information  is  used  to
       determine  the  spectral  extraction  mask to be applied in the scientific data reduction,
       performed with the recipe vimos_science. The input arc lamp and flat field  exposures  are
       assumed  to  be  obtained quasi-simultaneously, so that they would be described by exactly
       the same instrument distortions.

       A line catalog must be specified, containing the wavelengths of  the  reference  arc  lamp
       lines  used  for  the  wavelength  calibration.  A grism table (typically depending on the
       instrument mode, and in particular on the grism used) may also be  specified:  this  table
       contains a default recipe parameter setting to control the way spectra are extracted for a
       specific instrument mode, as it is used for automatic run of the pipeline on  Paranal  and
       in  Garching.  If  this  table  is  specified, it will modify the default recipe parameter
       setting, with the exception of those parameters which have been explicitly modifyed on the
       command line.

       If  a grism table is not specified, the input recipe parameters values will always be read
       from the command line, or from an esorex configuration file  if  present,  or  from  their
       generic  default  values (that are rarely meaningful). Finally a master bias frame must be
       input to this recipe.

       In   the   table    below    the    MOS_CURV_COEFF,    MOS_CURV_TRACES,    MOS_SPATIAL_MAP
       MOS_ARC_SPECTRUM_EXTRACTED,  MOS_SPECTRA_DETECTION,  MOS_SLIT_MAP,  and MOS_SLIT_LOCATION,
       are never created in case of long-slit-like data.

       The products MOS_SPECTRA_DETECTION, MOS_SLIT_MAP, and MOS_DISP_RESIDUALS, are just created
       if  the  --check  parameter  is  set  to true. The product GLOBAL_DISTORTION_TABLE is just
       created if more than 12 separate spectra are found in the CCD.

       Input files:

         DO category:               Type:       Explanation:         Required:
         MOS_SCREEN_FLAT            Raw         Flat field exposures    Y
         MOS_ARC_SPECTRUM           Raw         Arc lamp exposure       Y
         MASTER_BIAS                Calib       Bias frame              Y
         LINE_CATALOG               Calib       Line catalog            Y
         CONFIG_TABLE               Calib       Grism table             .

       Output files:

         DO category:               Data type:  Explanation:
         MOS_COMBINED_SCREEN_FLAT   FITS image  Combined (sum) flat field
         MOS_MASTER_SCREEN_FLAT     FITS image  Normalised flat field
         MOS_ARC_SPECTRUM_EXTRACTED FITS image  Wavelength calibrated arc spectrum
         MOS_DISP_COEFF             FITS table  Inverse dispersion coefficients
         MOS_DISP_RESIDUALS         FITS image  Residuals in wavelength calibration
         MOS_DISP_RESIDUALS_TABLE   FITS table  Residuals in wavelength calibration
         MOS_DELTA_IMAGE            FITS image  Offset vs linear wavelength calib
         MOS_WAVELENGTH_MAP         FITS image  Wavelength for each pixel on CCD
         MOS_SPECTRA_DETECTION      FITS image  Check for preliminary detection
         MOS_SLIT_MAP               FITS image  Map of central wavelength on CCD
         MOS_CURV_TRACES            FITS table  Spectral curvature traces
         MOS_CURV_COEFF             FITS table  Spectral curvature coefficients
         MOS_SPATIAL_MAP            FITS image  Spatial position along slit on CCD
         MOS_SPECTRAL_RESOLUTION    FITS table  Resolution at reference arc lines
         MOS_SLIT_LOCATION          FITS table  Slits on product frames and CCD
         GLOBAL_DISTORTION_TABLE    FITS table  Global distortions table

OPTIONS

       --dispersion <float>
              Expected spectral dispersion (Angstrom/pixel) (float; default: 0.0). The full  name
              of  this  option  for  the EsoRex configuration file is vimos.vmmoscalib.dispersion
              [default = 0.0].

       --peakdetection <float>
              Initial peak detection threshold (ADU) (float; default: 0.0). The full name of this
              option for the EsoRex configuration file is vimos.vmmoscalib.peakdetection [default
              = 0.0].

       --wdegree <int>
              Degree of wavelength calibration polynomial (int; default: 0).  The  full  name  of
              this  option for the EsoRex configuration file is vimos.vmmoscalib.wdegree [default
              = 0].

       --wradius <int>
              Search radius if iterating pattern-matching with first-guess method  (pixel)  (int;
              default:  4).  The  full  name  of this option for the EsoRex configuration file is
              vimos.vmmoscalib.wradius [default = 4].

       --wreject <float>
              Rejection threshold in dispersion relation fit (pixel) (float; default:  1.0).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              vimos.vmmoscalib.wreject [default = 1.0].

       --wmodelss <int>
              Interpolation mode of wavelength solution (0 = no interpolation, 1 = fill gaps, 2 =
              global  model)  (int;  default:  2).  The  full  name of this option for the EsoRex
              configuration file is vimos.vmmoscalib.wmodelss [default = 2].

       --wmodemos <int>
              Interpolation mode of wavelength solution (0 = no interpolation, 1 =  local  (slit)
              solution, 2 = global model) (int; default: 1). The full name of this option for the
              EsoRex configuration file is vimos.vmmoscalib.wmodemos [default = 1].

       --ignore_lines <str>
              Catalog lines nearest to wavelengths in this list will be  ignored  for  wavelength
              calibration  (str;  default:  ´´).  The  full  name  of  this option for the EsoRex
              configuration file is vimos.vmmoscalib.ignore_lines [default = ].

       --used_linesets <str>
              Linesets to use. Valid are ´standard´ and´extended´ (see  column  LINE_SET  in  the
              line  catalogue)  (str;  default: ´standard´). The full name of this option for the
              EsoRex configuration file is vimos.vmmoscalib.used_linesets [default = standard].

       --cdegree <int>
              Degree of spectral curvature polynomial (int; default: 0). The full  name  of  this
              option for the EsoRex configuration file is vimos.vmmoscalib.cdegree [default = 0].

       --cmode <int>
              Interpolation  mode  of  curvature  solution  applicable  to  MOS-like data (0 = no
              interpolation, 1 = fill gaps, 2 = global model) (int; default: 1). The full name of
              this  option for the EsoRex configuration file is vimos.vmmoscalib.cmode [default =
              1].

       --startwavelength <float>
              Start wavelength in spectral extraction (float; default: 0.0).  The  full  name  of
              this  option  for the EsoRex configuration file is vimos.vmmoscalib.startwavelength
              [default = 0.0].

       --endwavelength <float>
              End wavelength in spectral extraction (float; default: 0.0). The full name of  this
              option for the EsoRex configuration file is vimos.vmmoscalib.endwavelength [default
              = 0.0].

       --reference <float>
              Reference wavelength for slit map (float; default: 0.0).  The  full  name  of  this
              option  for  the EsoRex configuration file is vimos.vmmoscalib.reference [default =
              0.0].

       --slit_ident <bool>
              Attempt slit identification.For multiplexing data  slit  identification  is  always
              performed.  Switching  it  off  will  cause  systematic errors in the absolute flux
              calibration if the FLAT_SED correction is used (see pipeline  manual  for  details)
              (bool;  default:  True).  The full name of this option for the EsoRex configuration
              file is vimos.vmmoscalib.slit_ident [default = True].

       --s_degree <int>
              Polynomial degree for the flat field fitting along spatial direction (int; default:
              -1).   The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              vimos.vmmoscalib.s_degree [default = -1].

       --sradius <int>
              Smooth box radius for flat field along spatial direction (used  if  s_degree  <  0)
              (int;  default: -1). The full name of this option for the EsoRex configuration file
              is vimos.vmmoscalib.sradius [default = -1].

       --d_nknots <int>
              Number of knots in flat field fitting  splines  along  dispersion  direction  (int;
              default:  -1).  The  full  name of this option for the EsoRex configuration file is
              vimos.vmmoscalib.d_nknots [default = -1].

       --dradius <int>
              Smooth box radius for flat field along dispersion direction (if d_knots < 0)  (int;
              default:  10).  The  full  name of this option for the EsoRex configuration file is
              vimos.vmmoscalib.dradius [default = 10].

       --fit_threshold <float>
              Threshold percentage for flat spline fitting with respect to  the  maximum  (float;
              default:  0.01).  The full name of this option for the EsoRex configuration file is
              vimos.vmmoscalib.fit_threshold [default = 0.01].

       --line_ident_tol <float>
              Tolerance for the ratio of detected lines vs reference lines. This is  used  during
              for  arc  line identification. (float; default: 0.05). The full name of this option
              for the EsoRex configuration file  is  vimos.vmmoscalib.line_ident_tol  [default  =
              0.05].

       Note  that  it  is possible to create a configuration file containing these options, along
       with suitable default values. Please refer to the details provided by the 'esorex  --help'
       command.

SEE ALSO

       The  full  documentation  for the vimos pipeline can be downloaded as a PDF file using the
       following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/vimos/vimos-pipeline-manual-6.9.pdf

       An  overview  over  the  existing  ESO  pipelines  can  be   found   on   the   web   page
       https://www.eso.org/sci/software/pipelines/.

       Basic documentation about the EsoRex program can be found at the esorex (1) man page.

       It  is  possible  to  call  the  pipelines  from python using the python-cpl package.  See
       https://packages.python.org/python-cpl/index.html for further information.

       The other recipes of the vimos pipeline are vmbias(7), vmdark(7), vmdet(7), vmifucalib(7),
       vmifucombine(7),  vmifucombinecube(7),  vmifuscience(7), vmifustandard(7), vmimcalphot(7),
       vmimflatscreen(7), vmimflatsky(7), vmimobsjitter(7),  vmimobsstare(7),  vmimpreimaging(7),
       vmimstandard(7),  vmmoscombine(7),  vmmosobsjitter(7),  vmmosobsstare(7), vmmosscience(7),
       vmmosstandard(7), vmspcaldisp(7), vmspflat(7), vmspphot(7)

VERSION

       vmmoscalib 3.2.3

AUTHOR

       Carlo Izzo <usd-help@eso.org>

BUG REPORTS

       Please report any problems to usd-help@eso.org. Alternatively, you may send  a  report  to
       the ESO User Support Department <usd-help@eso.org>.

LICENSE

       This  file  is  currently  part  of  the VIMOS Instrument Pipeline Copyright (C) 2002-2006
       European Southern Observatory

       This program is free software; you can redistribute it and/or modify it under the terms of
       the  GNU  General  Public  License  as  published  by the Free Software Foundation; either
       version 2 of the License, or (at your option) any later version.

       This program is distributed in the hope that it will be useful, but WITHOUT ANY  WARRANTY;
       without  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
       See the GNU General Public License for more details.

       You should have received a copy of the GNU General Public License along with this program;
       if  not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
       MA  02110-1301  USA