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NAME

       vmmosobsjitter - Reduce and combine a set of jittered MOS observations.

SYNOPSIS

       esorex vmmosobsjitter [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe is used to apply basic reduction steps to a sequence of exposures made in MOS
       mode, to combine them in a single image, to locate objects, and to optimally extract their
       spectra.  Each  input  image  is  processed  in  the  same way as by recipe vmmosobsstare,
       therefore what mainly characterises the vmmosobsjitter recipe is the task of combining the
       input frames.

       Input files:

         DO category:             Type:       Explanation:          Required:
         MOS_SCIENCE              Raw         Science exposure          Y
         MASTER_BIAS              Calib       Master bias               Y
         MASTER_DARK              Calib       Master dark               .

         MOS_MASTER_SCREEN_FLAT   Calib       Normalised flat field     .

         EXTRACT_TABLE            Calib       Extraction table          .

         GRISM_TABLE              Calib       Grism table               Y
         MOS_FRINGES_SKY          Calib       Sky+fringes map (´Raw´)   .

         MOS_FRINGES              Calib       Fringe map (´Resampled´)  .

         EXTINCT_TABLE            Calib       Atmospheric extinction    .

         MOS_SPECPHOT_TABLE       Calib       Response curve            .

         CCD_TABLE                Calib       Bad pixel table           .

       Output files:

         DO category:             Data type:  Explanation:
         MOS_SCIENCE_REDUCED      FITS image  Extracted objects spectra
         MOS_SCIENCE_FLUX_REDUCED FITS image  Flux calibrated objects spectra
         MOS_SCIENCE_EXTRACTED    FITS image  Sky subtracted slit spectra
         MOS_SCIENCE_SKY          FITS image  Sky slit spectra
         MOS_SKY_REDUCED          FITS image  Extracted sky spectra
         MOS_FRINGES_SKY          FITS image  Sky+fringes map (method ´Raw´)
         MOS_FRINGES              FITS image  Fringe map (method ´Resampled´)
         OBJECT_TABLE             FITS table  Objects spectra identification
         WINDOW_TABLE             FITS table  Objects positions in slit

       A flat field correction is applied only if a normalised master flat field (produced by the
       recipe vmspflat) is specified.

       The extraction table is the product of the local spectral distortions modelling  performed
       by  the  recipe  vmspcaldisp.  If  an  extraction  table is not specified, then the global
       distortion models read from the science frame header are used.

       The grism table contains necessary information to control the way spectra  are  extracted,
       starting from the reference wavelength (header entry PRO WLEN CEN), on a specific range of
       pixels above and below its position on the CCD (header entries PRO SPECT LLEN LO  and  PRO
       SPECT  LLEN HI). Other parameters, used in the extraction of the science slit spectra, are
       the start and the end wavelength of the  image  of  the  extracted  slit  spectra  (header
       entries  PRO  WLEN  START  and  PRO  WLEN  END),  and  the  step of the sampling along the
       dispersion direction (header entry PRO WLEN INC). Finally,  the  wavelengths  of  the  sky
       lines  used  in  the  alignment  of the spectral distortion models, necessary to keep into
       account the possible coordinates shifts  introduced  by  a  variation  of  the  instrument
       flexures  between  the  science  and  the  calibration exposures, are listed in the header
       keywords PRO SKY WLENi, with i ranging from 1 to the number specified in the  keyword  PRO
       SKY NO.

       A CCD table must be specified in input only if a bad pixel cleaning is requested.

       The  slit  spectra  are  remapped  with  the instrument distortions removed and at a fixed
       wavelength step. A sky value is estimated for each wavelength and then subtracted from the
       data.   The  result  is  stored  in  the  MOS_SCIENCE_EXTRACTED  image,  while  the  image
       MOS_SCIENCE_SKY contains the subtracted sky model. The 1D extracted spectra are stored  in
       the MOS_SCIENCE_REDUCED image, while the corresponding sky spectra extracted with the same
       method are stored in the MOS_SKY_REDUCED image.

       The positions of the extracted slit spectra and of the  detected  objects  that  they  may
       contain are listed in the window table.

       If  a  spectro-photometric  table  (produced  by  the  recipe  vmmosstandard) is specified
       together with an atmospheric extinction table, and a flux calibration is requested, then a
       MOS_SCIENCE_FLUX_REDUCED   image   is  also  created.  This  image  is  identical  to  the
       MOS_SCIENCE_REDUCED, but the spectra it contains are flux  calibrated,  and  expressed  in
       units of erg/cm/cm/s/Angstrom.

       Sky  fringes may be subtracted from the data using two different methods. The ´Raw´ method
       will subtract the median sky+fringes pattern from each input image, and then fit away  the
       residuals  possibly introduced by sky variations between exposures. The ´Resampled´ method
       will fit the sky first, and then subtract the median image of the residuals (stored in the
       product MOS_FRINGES).

       For more details, please refer to the VIMOS Pipeline User´s Guide.

OPTIONS

       --BiasMethod <str>
              Bias  removal  method.  (str; default: ´Zmaster´). The full name of this option for
              the EsoRex configuration file is vimos.Parameters.bias.removing.method  [default  =
              Zmaster].

       --StackMethod <str>
              Frames  combination  method (str; default: ´Average´). The full name of this option
              for the EsoRex configuration file is  vimos.Parameters.stacking.method  [default  =
              Average].

       --KSigmaLow <float>
              Low  threshold for K-sigma clipping method. (float; default: 5.0). The full name of
              this      option      for      the      EsoRex      configuration      file      is
              vimos.Parameters.stacking.ksigma.low [default = 5.0].

       --KSigmaHigh <float>
              High threshold for K-sigma clipping method. (float; default: 5.0). The full name of
              this      option      for      the      EsoRex      configuration      file      is
              vimos.Parameters.stacking.ksigma.high [default = 5.0].

       --MinRejection <long>
              Number of lowest rejected values for rejection method. (long; default: 1). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              vimos.Parameters.stacking.minmax.minimum [default = 1].

       --MaxRejection <long>
              Number  of  highest  rejected  values for rejection method. (long; default: 1). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              vimos.Parameters.stacking.minmax.maximum [default = 1].

       --SkyMethod <str>
              Sky  level  determination  method.  (str; default: ´Median´). The full name of this
              option for the EsoRex configuration file is vimos.Parameters.sky.method [default  =
              Median].

       --PolyOrder <long>
              Degree of polynomial used when the SkyMethod is set to Fit. (long; default: 2). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              vimos.Parameters.sky.order [default = 2].

       --SkyKSigmaLow <float>
              Low threshold for K-sigma rejection in sky fitting. (float; default: 1.0). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              vimos.Parameters.sky.ksigma.low [default = 1.0].

       --SkyKSigmaHigh <float>
              High  threshold  for  K-sigma  rejection in sky fitting. (float; default: 1.0). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              vimos.Parameters.sky.ksigma.high [default = 1.0].

       --Fuzz <long>
              Extra  pixels  from  expected  position  of  spectrum  edge  in extraction.  (long;
              default: 5). The full name of this option for  the  EsoRex  configuration  file  is
              vimos.Parameters.extraction.fuzz [default = 5].

       --SlitMargin <long>
              Number  of  excluded  pixels  at  slit  ends  in  object  search  or  in  sky level
              determination. (long; default: 2). The full name of  this  option  for  the  EsoRex
              configuration file is vimos.Parameters.detection.exclude [default = 2].

       --LineWidth <long>
              Size  of spectrum to extract around any skyline. (long; default: 16). The full name
              of this option for the EsoRex configuration file is  vimos.Parameters.sky.linewidth
              [default = 16].

       --DetectionLevel <float>
              Object  detection  level in units of sigma. (float; default: 2.0). The full name of
              this option for the EsoRex configuration file  is  vimos.Parameters.detection.sigma
              [default = 2.0].

       --WatershedLevels <long>
              Number  of levels in the watershed method in object detection. (long; default: 32).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              vimos.Parameters.detection.levels [default = 32].

       --WatershedFraction <float>
              Flux  fraction  to  use in watershed. (float; default: 0.01). The full name of this
              option for the EsoRex  configuration  file  is  vimos.Parameters.detection.fraction
              [default = 0.01].

       --MinObjectSize <long>
              Minimal  size  for an object candidate to be considered an object.  (long; default:
              2).  The  full  name  of  this  option  for  the  EsoRex  configuration   file   is
              vimos.Parameters.detection.minsize [default = 2].

       --MaxObjectSize <long>
              Maximal  size  for  an  object  candidate for not trying deblend into sub- objects.
              (long; default: 7). The full name of this option for the EsoRex configuration  file
              is vimos.Parameters.detection.maxsize [default = 7].

       --CleanBadPixel <bool>
              Bad pixel correction on MOS science exposure. (bool; default: False). The full name
              of this option for the EsoRex configuration file is vimos.Parameters.badpixel.clean
              [default = False].

       --CalibrateFlux <bool>
              Extracted  spectra  are  flux  calibrated. (bool; default: False). The full name of
              this option for the EsoRex configuration file is  vimos.Parameters.flux.calibration
              [default = False].

       --FringingCorr <bool>
              Apply  fringing  corrections.  (bool; default: False). The full name of this option
              for the EsoRex configuration file is vimos.Parameters.fringing [default = False].

       --FringingMethod <str>
              Sky fringes removal method. (str; default: ´Raw´). The full name of this option for
              the EsoRex configuration file is vimos.Parameters.fringing.removing.method [default
              = Raw].

       --FringingOffset <float>
              Minimum required offset between exposures for applying the sky fringing correction.
              (float;  default:  3.0).  The full name of this option for the EsoRex configuration
              file is vimos.Parameters.fringing.offset [default = 3.0].

       --HorneExtraction <bool>
              Use 1D Horne extraction (bool; default: False). The full name of  this  option  for
              the  EsoRex  configuration  file  is vimos.Parameters.extraction.optimal [default =
              False].

       --ModelSlit <bool>
              Model wavelength solution within each slit. (bool; default: True). The full name of
              this  option  for  the  EsoRex  configuration  file  is vimos.Parameters.slit.model
              [default = True].

       --ModelSlitOrder <long>
              Order of polynomial for wavelength solution  modeling  within  each  slit.   (long;
              default:  0).  The  full  name  of this option for the EsoRex configuration file is
              vimos.Parameters.slit.order [default = 0].

       --UseSkylines <bool>
              Use sky lines to refine the wavelength calibration (bool; default: True). The  full
              name of this option for the EsoRex configuration file is vimos.Parameters.sky.align
              [default = True].

       --SaveIntermediate <bool>
              Save intermediate reduction steps (bool; default: False). The  full  name  of  this
              option  for  the  EsoRex  configuration  file is vimos.Parameters.save.intermediate
              [default = False].

       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
       http://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
       http://packages.python.org/python-cpl/index.html for further information.

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

VERSION

       vmmosobsjitter 2.9.9

AUTHOR

       ESO VIMOS Pipeline Team and VIMOS Consortium <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)  2002-2011
       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