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NAME

       fors_pmos_science - Extraction of scientific spectra

SYNOPSIS

       esorex fors_pmos_science [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe  is  used  to  reduce  scientific  spectra  using the extraction mask and the
       products created by the recipe fors_mpol_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 input dispersion coefficients 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).

       Either a scientific or a standard star exposure can be specified in input.

       The acronym SCI on products should be read STD in case of standard stars observations.

       Input files:

         DO category:               Type:       Explanation:            Required:
         SCIENCE_PMOS                  Raw         Scientific exposure      Y
         or STANDARD_PMOS              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_PMOS         Calib       Normalised flat field    .

         DISP_COEFF_PMOS               Calib       Inverse dispersion       Y
         CURV_COEFF_PMOS               Calib       Spectral curvature       Y
         SLIT_LOCATION_PMOS            Calib       Slits positions table    Y
         RETARDER_WAVEPLATE_CHROMATISM Calib       Chromatism correction    .

         STD_PMOS_TABLE                Calib       Linear pol. of std stars .

       Output files:

         DO category:               Data type:  Explanation:
         REDUCED_SCI_PMOS             FITS image  Extracted scientific spectra
         REDUCED_SKY_SCI_PMOS         FITS image  Extracted sky spectra
         REDUCED_ERROR_SCI_PMOS       FITS image  Errors on extracted spectra
         REDUCED_X_SCI_PMOS           FITS image  X Stokes parameter (and L)
         REDUCED_ERROR_X_SCI_PMOS     FITS image  Error on X Stokes parameter
         REDUCED_NUL_X_SCI_PMOS       FITS image  Null parameter for X
         REDUCED_ANGLE_SCI_PMOS       FITS image  Direction of linear polarization
         REDUCED_ERROR_ANGLE_SCI_PMOS FITS image  Error on polarization direction
         UNMAPPED_SCI_PMOS            FITS image  Sky subtracted scientific spectra
         MAPPED_SCI_PMOS              FITS image  Rectified scientific spectra
         MAPPED_ALL_SCI_PMOS          FITS image  Rectified science spectra with sky
         MAPPED_SKY_SCI_PMOS          FITS image  Rectified sky spectra
         UNMAPPED_SKY_SCI_PMOS        FITS image  Sky on CCD
         OBJECT_TABLE_SCI_PMOS        FITS table  Positions of detected objects
         OBJECT_TABLE_POL_SCI_PMOS    FITS table  Positions of real objects

         Only if the sky-alignment of the wavelength solution is requested:
         DISP_COEFF_SCI_PMOS          FITS table  Upgraded dispersion coefficients
         WAVELENGTH_MAP_SCI_PMOS      FITS image  Upgraded wavelength map

OPTIONS

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

       --rebin <long>
              Rebin  (pixel)  (long;  default:  1).  The  full name of this option for the EsoRex
              configuration file is fors.fors_pmos_science.rebin [default = 1].

       --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_pmos_science.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_pmos_science.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_pmos_science.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_pmos_science.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_pmos_science.flux [default = True].

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

       --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_pmos_science.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_pmos_science.skylocal
              [default = True].

       --cosmics <bool>
              Eliminate cosmic rays hits (only if local sky subtraction is also requested) (bool;
              default:  False). The full name of this option for the EsoRex configuration file is
              fors.fors_pmos_science.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_pmos_science.slit_margin [default = 3].

       --ext_radius <long>
              Maximum extraction radius for detected objects (pixel)  (long;  default:  12).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              fors.fors_pmos_science.ext_radius [default = 12].

       --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_pmos_science.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_pmos_science.ext_mode [default = 1].

       --match_tolerance <float>
              Tolerance for matching spectra from the same object at different angles  and  beams
              (pixel)  (float;  default:  5.0).  The  full  name  of  this  option for the EsoRex
              configuration file is fors.fors_pmos_science.match_tolerance [default = 5.0].

       --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_pmos_science.time_normalise [default = True].

       --chromatism <bool>
              Chromatism correction to polarization angles (bool; default: True). The  full  name
              of     this     option     for     the     EsoRex     configuration     file     is
              fors.fors_pmos_science.chromatism [default = True].

       --wollaston <bool>
              Wollaston mounting (FORS2 only): true = 0 degrees (ord. beam on top, extr. beam  on
              bottom),  false  =  180  degrees  (beams are reversed), for FORS1 is frozen to true
              (bool; default: True). The full name of this option for  the  EsoRex  configuration
              file is fors.fors_pmos_science.wollaston [default = True].

       --check <bool>
              Create  intermediate  products (bool; default: False). The full name of this option
              for the  EsoRex  configuration  file  is  fors.fors_pmos_science.check  [default  =
              False].

       --qc <bool>
              Compute  QC1 parameters (bool; default: True). The full name of this option for the
              EsoRex configuration file is fors.fors_pmos_science.qc [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(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_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_pmos_science 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