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NAME

       kmos_extract_spec - Extract a spectrum from a cube

SYNOPSIS

       esorex kmos_extract_spec [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe  extracts a spectrum from a datacube. The datacube is with or without noise).
       The output will be a similarly formatted FITS file.

         Input files:

          DO                    KMOS
          category              Type   Explanation                Required #Frames
          --------              -----  -----------                -------- -------
          <none or any>         F3I    The datacubes                 Y        1
          <none or any>         F2I    The mask                      N       0,1

         Output files:

          DO                    KMOS
          category              Type   Explanation
          --------              -----  -----------
          EXTRACT_SPEC          F1I    Extracted spectrum
          EXTRACT_SPEC_MASK     F2I    (optional, if --save_mask=true and
                                   --mask_method=´optimal´: The calculated mask)

OPTIONS

       --mask_method <str>
              Method used : mask, integrated or optimal (str; default:  ´integrated´).  The  full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              kmos.kmos_extract_spec.mask_method [default = integrated].

       --centre <str>
              The centre of the circular mask (pixel) (str; default: ´7.5,7.5´). The full name of
              this  option  for  the  EsoRex  configuration file is kmos.kmos_extract_spec.centre
              [default = 7.5,7.5].

       --radius <float>
              The radius of the circular mask (pixel) (float; default: 3.0).  The  full  name  of
              this  option  for  the  EsoRex  configuration file is kmos.kmos_extract_spec.radius
              [default = 3.0].

       --save_mask <bool>
              Flag to save the mask (bool; default: False). The full name of this option for  the
              EsoRex configuration file is kmos.kmos_extract_spec.save_mask [default = False].

       --cmethod <str>
              Apply "average", "median", "sum", "min_max." or "ksigma". (str; default: ´ksigma´).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              kmos.kmos_extract_spec.cmethod [default = ksigma].

       --cpos_rej <float>
              The   positive  rejection  threshold  for  kappa-sigma-clipping  (sigma).   (float;
              default: 3.0). The full name of this option for the EsoRex  configuration  file  is
              kmos.kmos_extract_spec.cpos_rej [default = 3.0].

       --cneg_rej <float>
              The   negative  rejection  threshold  for  kappa-sigma-clipping  (sigma).   (float;
              default: 3.0). The full name of this option for the EsoRex  configuration  file  is
              kmos.kmos_extract_spec.cneg_rej [default = 3.0].

       --citer <long>
              The  number  of  iterations  for kappa-sigma-clipping. (long; default: 3). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              kmos.kmos_extract_spec.citer [default = 3].

       --cmax <long>
              The  number of maximum pixel values to clip with min/max-clipping.  (long; default:
              1).  The  full  name  of  this  option  for  the  EsoRex  configuration   file   is
              kmos.kmos_extract_spec.cmax [default = 1].

       --cmin <long>
              The  number of minimum pixel values to clip with min/max-clipping.  (long; default:
              1).  The  full  name  of  this  option  for  the  EsoRex  configuration   file   is
              kmos.kmos_extract_spec.cmin [default = 1].

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

              ftp://ftp.eso.org/pub/dfs/pipelines/kmos/kmos-pipeline-manual-2.9.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   kmos   pipeline   are   kmo_arithmetic(7),   kmo_copy(7),
       kmo_fit_profile(7), kmo_fits_strip(7), kmo_make_image(7), kmo_noise_map(7), kmo_rotate(7),
       kmo_shift(7), kmo_sky_mask(7), kmo_stats(7), kmos_combine(7), kmos_dark(7),  kmos_flat(7),
       kmos_gen_reflines(7),   kmos_gen_telluric(7),  kmos_illumination(7),  kmos_reconstruct(7),
       kmos_sci_red(7), kmos_sky_tweak(7), kmos_std_star(7), kmos_test(7), kmos_wave_cal(7)

VERSION

       kmos_extract_spec 1.4.3

AUTHOR

       Alex Agudo Berbel, Y. Jung <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  part  of  the  CRIRES Instrument Pipeline Copyright (C) 2002,2003 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., 59 Temple Place, Suite 330, Boston,
       MA  02111-1307  USA