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NAME

       fors_science - Extraction of scientific spectra

SYNOPSIS

       esorex fors_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_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).

       In  the table below the MXU acronym can be read alternatively as MOS and LSS, depending on
       the instrument mode of the input data. The acronym SCI on products should be read  STD  in
       case of standard stars observations A CURV_COEFF table is not (yet) expected for LSS data.

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

       Only  in  case  of  a standard star exposure input, the atmospheric extinction table and a
       table with the physical fluxes of the observed standard star must be specified  in  input,
       and  a  spectro-photometric table is created in output. This table can then be input again
       to this recipe, always  with  an  atmospheric  extinction  table,  and  if  a  photometric
       calibration  is  requested then flux calibrated spectra (in units of erg/cm/cm/s/Angstrom)
       are also written in output.

       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    .

         DISP_COEFF_MXU             Calib       Inverse dispersion       Y
         CURV_COEFF_MXU             Calib       Spectral curvature       Y
         SLIT_LOCATION_MXU          Calib       Slits positions table    Y
         FLAT_SED_MXU      Calib       Slits dispersion profile .

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

         MASTER_NORM_FLAT_LONG_MXU  Calib       Normalised flat field    .

         DISP_COEFF_LONG_MXU        Calib       Inverse dispersion       Y
         SLIT_LOCATION_LONG_MXU     Calib       Slits positions table    Y
         GLOBAL_DISTORTION_TABLE    Calib       Global distortion        .

         In case STANDARD_MXU is specified in input,

         EXTINCT_TABLE              Calib       Atmospheric extinction   Y
         STD_FLUX_TABLE             Calib       Standard star flux       Y
         TELLURIC_CONTAMINATION     Calib       Telluric regions list    .

         The following input files are mandatory if photometric calibrated  spectra are desired:

         EXTINCT_TABLE              Calib       Atmospheric extinction   Y
         SPECPHOT_TABLE             Calib       Response curves          Y

         If requested for standard star data, the SPECPHOT_TABLE can be dropped:
         in this case the correction is applied using the SPECPHOT_TABLE produced
         in the same run.

       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
         OBJECT_TABLE_SCI_MXU       FITS table  Positions of detected objects

         Only if the global sky subtraction is requested:
         GLOBAL_SKY_SPECTRUM_MXU    FITS table  Global sky spectrum

         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

         Only if a STANDARD_MXU is specified in input:
         SPECPHOT_TABLE             FITS table  Efficiency and response curves

         Only if a photometric calibration was requested:
         REDUCED_FLUX_SCI_MXU       FITS image  Flux calibrated scientific spectra
         REDUCED_FLUX_ERROR_SCI_MXU FITS image  Errors on flux calibrated spectra
         MAPPED_FLUX_SCI_MXU        FITS image  Flux calibrated slit spectra

OPTIONS

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

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

       --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_science.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_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_science.skylocal  [default  =
              True].

       --cosmics <bool>
              Eliminate  cosmic  rays  hits,  only  if  either  global or local (not for LSS) sky
              subtraction is also requested. (bool; default: False). The full name of this option
              for the EsoRex configuration file is fors.fors_science.cosmics [default = False].

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

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

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

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

       --resp_fit_nknots <int>
              Number  of knots in spline fitting of the instrument response. (-1: No fitting. -2:
              Read from grism table) (int; default: -2). The full name of  this  option  for  the
              EsoRex configuration file is fors.fors_science.resp_fit_nknots [default = -2].

       --resp_fit_degree <int>
              Degree  of  polynomial  in fitting of the instrument response. (-1: No fitting. -2:
              Read from grism table) (int; default: -2). The full name of  this  option  for  the
              EsoRex configuration file is fors.fors_science.resp_fit_degree [default = -2].

       --resp_ignore_mode <str>
              Types  of lines/regions to ignore in response. Valid ones are ´stellar_absorption´,
              ´telluric´ and ´command_line´ (from  parameter  resp_ignore_lines)  (str;  default:
              ´stellar_absorption,telluric,command_line´).  The  full name of this option for the
              EsoRex  configuration  file  is   fors.fors_science.resp_ignore_mode   [default   =
              stellar_absorption,telluric,command_line].

       --resp_ignore_points <str>
              Extra  lines/regions to ignore in response. Use a comma separated list of values. A
              range can be specified like 4500.0-4600.0 (str; default: ´´). The full name of this
              option  for  the  EsoRex configuration file is fors.fors_science.resp_ignore_points
              [default = ].

       --resp_use_flat_sed <str>
              Use the flat SED  to  normalise  the  observed  spectra.  Value  are  true,  false,
              grism_table.  (str;  default:  ´grism_table´). The full name of this option for the
              EsoRex  configuration  file  is  fors.fors_science.resp_use_flat_sed   [default   =
              grism_table].

       --nonlinear_level <float>
              Level  above  which  the detector is not linear (float; default: 60000.0). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              fors.fors_science.nonlinear_level [default = 60000.0].

       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
       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  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_pmos_science(7),     fors_remove_bias(7),    fors_resample(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)

VERSION

       fors_science 5.3.32

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)  2002-2011
       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