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NAME

       fors_pmos_extract - Extraction of scientific spectra

SYNOPSIS

       esorex fors_pmos_extract [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   .

       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_SCI_X_PMOS           FITS image  X Stokes parameter (and L)
         REDUCED_ERROR_X_PMOS         FITS image  Error on X Stokes parameter
         REDUCED_NUL_X_PMOS           FITS image  Null parameter for X
         REDUCED_POL_ANGLE_PMOS       FITS image  Direction of linear polarization
         REDUCED_POL_ANGLE_ERROR_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
         GLOBAL_SKY_SPECTRUM_PMOS     FITS table  Global sky spectrum
         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>
              Resampling  step  (Angstrom/pixel)  (float;  default:  0.0).  The full name of this
              option for  the  EsoRex  configuration  file  is  fors.fors_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_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_pmos_extract.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_extract.chromatism [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_extract.check  [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 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_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_pmos_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