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NAME

       fors_extract - Extraction of scientific spectra

SYNOPSIS

       esorex fors_extract [OPTIONS] FILE.sof

DESCRIPTION

       This recipe is used to reduce scientific spectra using the global distortion table created
       by the recipe fors_calib. The spectra are bias subtracted, flat fielded (if  a  normalised
       flat  field is specified) and remapped eliminating the optical distortions. The wavelength
       calibration can be optionally upgraded using a number  of  sky  lines:  if  no  sky  lines
       catalog of wavelengths is specified, an internal one is used instead.

       If  the  alignment to the sky lines is performed, the applied dispersion coefficient table
       is upgraded and saved to disk, and a new CCD wavelengths map is created.

       This recipe accepts both FORS1 and FORS2 frames. 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).

       In the table below the MXU acronym can be read alternatively as MOS and LSS, depending  on
       the instrument mode of the input data. Either a scientific or a standard star exposure can
       be specified in input (not both).

       Input files:

         DO category:               Type:       Explanation:         Required:
         SCIENCE_MXU                Raw         Scientific exposure     Y
         or STANDARD_MXU            Raw         Standard star exposure  Y
         MASTER_BIAS                Calib       Master bias             Y
         GRISM_TABLE                Calib       Grism table             .

         MASTER_SKYLINECAT          Calib       Sky lines catalog       .

         MASTER_NORM_FLAT_MXU       Calib       Normalised flat field   .

         MASTER_DISTORTION_TABLE    Calib       Global distortion model .

         or, in case of LSS-like MOS/MXU data,

         MASTER_NORM_FLAT_LONG_MXU  Calib       Normalised flat field   .

       Output files:

         DO category:               Data type:  Explanation:
         REDUCED_SCI_MXU            FITS image  Extracted scientific spectra
         REDUCED_SKY_SCI_MXU        FITS image  Extracted sky spectra
         REDUCED_ERROR_SCI_MXU      FITS image  Errors on extracted spectra
         UNMAPPED_SCI_MXU           FITS image  Sky subtracted scientific spectra
         MAPPED_SCI_MXU             FITS image  Rectified scientific spectra
         MAPPED_ALL_SCI_MXU         FITS image  Rectified science spectra with sky
         MAPPED_SKY_SCI_MXU         FITS image  Rectified sky spectra
         UNMAPPED_SKY_SCI_MXU           FITS image  Sky on CCD
         GLOBAL_SKY_SPECTRUM_MXU    FITS table  Global sky spectrum
         OBJECT_TABLE_SCI_MXU       FITS table  Positions of detected objects

         Only if the sky-alignment of the wavelength solution is requested:
         SKY_SHIFTS_LONG_SCI_MXU    FITS table  Sky lines offsets (LSS-like data)
         or SKY_SHIFTS_SLIT_SCI_MXU FITS table  Sky lines offsets (MOS-like data)
         DISP_COEFF_SCI_MXU         FITS table  Upgraded dispersion coefficients
         WAVELENGTH_MAP_SCI_MXU     FITS image  Upgraded wavelength map

OPTIONS

       --dispersion <float>
              Resampling step (Angstrom/pixel) (float; default:  0.0).  The  full  name  of  this
              option for the EsoRex configuration file is fors.fors_extract.dispersion [default =
              0.0].

       --skyalign <long>
              Polynomial order for sky lines alignment, or -1 to avoid alignment (long;  default:
              0).   The   full  name  of  this  option  for  the  EsoRex  configuration  file  is
              fors.fors_extract.skyalign [default = 0].

       --wcolumn <str>
              Name of sky line catalog table column with wavelengths (str; default: ┬┤WLEN┬┤).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              fors.fors_extract.wcolumn [default = WLEN].

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

       --flux <bool>
              Apply flux conservation (bool; default: True). The full name of this option for the
              EsoRex configuration file is fors.fors_extract.flux [default = True].

       --flatfield <bool>
              Apply  flat  field  (bool;  default:  False).  The full name of this option for the
              EsoRex configuration file is fors.fors_extract.flatfield [default = False].

       --skyglobal <bool>
              Subtract global sky spectrum from CCD (bool; default: False). The full name of this
              option  for the EsoRex configuration file is fors.fors_extract.skyglobal [default =
              False].

       --skymedian <bool>
              Sky subtraction from extracted slit spectra (bool; default: False). The  full  name
              of  this  option  for  the EsoRex configuration file is fors.fors_extract.skymedian
              [default = False].

       --skylocal <bool>
              Sky subtraction from CCD slit spectra (bool; default: True). The full name of  this
              option  for  the EsoRex configuration file is fors.fors_extract.skylocal [default =
              True].

       --cosmics <bool>
              Eliminate cosmic rays hits (only if  global  sky  subtraction  is  also  requested)
              (bool;  default:  False). The full name of this option for the EsoRex configuration
              file is fors.fors_extract.cosmics [default = False].

       --slit_margin <long>
              Number of pixels to exclude at each slit in object detection and extraction  (long;
              default:  3).  The  full  name  of this option for the EsoRex configuration file is
              fors.fors_extract.slit_margin [default = 3].

       --ext_radius <long>
              Maximum extraction radius for detected objects (pixel) (long; default: 6). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              fors.fors_extract.ext_radius [default = 6].

       --cont_radius <long>
              Minimum distance at which two objects of equal luminosity do not  contaminate  each
              other  (pixel)  (long;  default:  0).  The  full name of this option for the EsoRex
              configuration file is fors.fors_extract.cont_radius [default = 0].

       --ext_mode <long>
              Object extraction method: 0  =  aperture,  1  =  Horne  optimal  extraction  (long;
              default:  1).  The  full  name  of this option for the EsoRex configuration file is
              fors.fors_extract.ext_mode [default = 1].

       --time_normalise <bool>
              Normalise output spectra by the exposure time (bool; default: True). The full  name
              of     this     option     for     the     EsoRex     configuration     file     is
              fors.fors_extract.time_normalise [default = True].

       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 fors pipeline can be downloaded as a  PDF  file  using  the
       following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/fors/fors-pipeline-manual-4.9.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  fors  pipeline are fors_align_sky(7), fors_align_sky_lss(7),
       fors_bias(7),   fors_calib(7),   fors_config(7),   fors_dark(7),   fors_detect_objects(7),
       fors_detect_spectra(7), fors_extract_objects(7), fors_extract_slits(7), fors_flatfield(7),
       fors_img_science(7),            fors_img_screen_flat(7),             fors_img_sky_flat(7),
       fors_normalise_flat(7),   fors_photometry(7),   fors_pmos_calib(7),  fors_pmos_extract(7),
       fors_pmos_science(7),     fors_remove_bias(7),     fors_resample(7),      fors_science(7),
       fors_spec_mflat(7),   fors_subtract_sky(7),   fors_subtract_sky_lss(7),   fors_sumflux(7),
       fors_trace_flat(7),   fors_wave_calib(7),    fors_wave_calib_lss(7),    fors_zeropoint(7),
       montecarlo(7), test_hough(7)

VERSION

       fors_extract 5.1.4

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  FORS  Instrument  Pipeline  Copyright  (C)  2002-2010
       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