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NAME

       kmos_illumination - Create a frame to correct spatial non-uniformity of flatfield

SYNOPSIS

       esorex kmos_illumination [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe  creates  the  spatial  non-uniformity calibration frame needed for all three
       detectors. It must be called after the kmo_wave_cal-recipe, which generates  the  spectral
       calibration  frame needed in this recipe. As input at least a sky, a master dark, a master
       flat and the spatial and spectral cali- bration frames are required.

       The created product, the illumination correction, can be used as  input  for  kmo_std_star
       and kmo_sci_red.

   BASIC PARAMETERS
       --imethod The interpolation method used for reconstruction.

       --range The spectral ranges to combine when collapsing the reconstructed cubes. e.g.

       "x1_start,x1_end;x2_start,x2_end" (microns)

   ADVANCED PARAMETERS
       --flux Specify if flux conservation should be applied.

       --add-all   By   default   the   first   FLAT_SKY   frame   is   omitted,   since  in  the
       KMOS_spec_cal_skyflat template this  is  an  acquisition  frame  to  estimate  the  needed
       exposure  time  for  the  subsequent  FLAT_SKY  frames.  If  anyway  all  frames should be
       considered, set this parameter to TRUE.

       --neighborhoodRange Defines the range to search for neighbors during reconstruction

       --b_samples The number of samples in spectral direction for the reconstructed cube.

       Ideally this number should be greater than 2048, the detector size.

       --b_start  --b_end  Used  to  define  manually  the  start  and  end  wavelength  for  the
       reconstructed cube. By default the internally defined values are used.

       --cmethod Following methods of frame combination are available:
          * ´ksigma´ (Default)
          An iterative sigma clipping. For each position all pixels in the spectrum
          are examined. If they deviate significantly, they will be rejected
          according to the conditions:
              val > mean + stdev * cpos_rej
          and
              val < mean - stdev * cneg_rej
          where --cpos_rej, --cneg_rej and --citer are the corresponding
          configuration parameters. In the first iteration median and percentile
          level are used.

          * ´median´
          At each pixel position the median is calculated.

          * ´average´
          At each pixel position the average is calculated.

          * ´sum´
          At each pixel position the sum is calculated.

          * ´min_max´
          The specified nb of minimum and maximum pixel values will be rejected.

          --cmax and --cmin apply to this method.

       --cpos_rej --cneg_rej --citer see --cmethod=´ksigma´

       --cmax --cmin see --cmethod=´min_max´

       --pix_scale  Change  the  pixel  scale  [arcsec].  Default  of  0.2" results into cubes of
       14x14pix, a scale of 0.1" results into cubes of 28x28pix, etc.

       --suppress_extension If set to TRUE, the arbitrary filename extensions are  supressed.  If
       multiple products with the same category are produced, they will be numbered consecutively
       starting from 0.

         Input files:

          DO CATG           Type   Explanation                    Required #Frames
          --------          -----  -----------                    -------- -------
          FLAT_SKY           F2D   Sky exposures                     Y      1-n
                                   (at least 3 frames recommended)
          MASTER_DARK        F2D   Master dark                       Y       1
          MASTER_FLAT        F2D   Master flat                       Y       1
          XCAL               F2D   x calibration frame               Y       1
          YCAL               F2D   y calibration frame               Y       1
          LCAL               F2D   Wavelength calib. frame           Y       1
          WAVE_BAND          F2L   Table with start-/end-wavelengths Y       1
          FLAT_EDGE          F2L   Table with fitted slitlet edges   N      0,1

         Output files:

          DO CATG           Type   Explanation
          --------          -----  -----------
          ILLUM_CORR        F2I    Illumination calibration frame
          If FLAT_EDGE is provided:
          SKYFLAT_EDGE      F2L    Frame containing parameters of fitted
                                   slitlets of all IFUs of all detectors

OPTIONS

       --imethod <str>
              Method to use for interpolation: ["NN" (nearest neighbour), "lwNN" (linear weighted
              nearest  neighbor),  "swNN"  (square  weighted  nearest  neighbor),  "MS" (Modified
              Shepard´s method), "CS" (Cubic spline)] (str; default: ´CS´). The full name of this
              option for the EsoRex configuration file is kmos.kmos_illumination.imethod [default
              = CS].

       --neighborhoodRange <float>
              Range (pixels) to search for neighbors (float; default: 1.001). The  full  name  of
              this      option      for      the      EsoRex      configuration      file      is
              kmos.kmos_illumination.neighborhoodRange [default = 1.001].

       --range <str>
              The spectral ranges to  combine  when  collapsing  the  reconstructed  cubes.  e.g.
              "x1_start,x1_end;x2_start,x2_end"  (microns)  (str;  default: ´´). The full name of
              this option for  the  EsoRex  configuration  file  is  kmos.kmos_illumination.range
              [default = ].

       --flux <bool>
              TRUE:  Apply  flux  conservation. FALSE: otherwise (bool; default: False). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              kmos.kmos_illumination.flux [default = False].

       --add-all <bool>
              FALSE:  omit  1st FLAT_SKY frame (acquisition), TRUE: don´t perform any checks, add
              them all (bool; default: False). The full  name  of  this  option  for  the  EsoRex
              configuration file is kmos.kmos_illumination.add-all [default = False].

       --pix_scale <float>
              Change  the pixel scale [arcsec]. Default of 0.2" results into cubes of 14x14pix, a
              scale of 0.1" results into cubes of 28x28pix, etc. (float; default: 0.2). The  full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              kmos.kmos_illumination.pix_scale [default = 0.2].

       --suppress_extension <bool>
              Suppress filename extension. (TRUE (apply) or FALSE (don´t apply)  (bool;  default:
              False).  The  full  name  of  this  option  for  the  EsoRex  configuration file is
              kmos.kmos_illumination.suppress_extension [default = False].

       --b_samples <long>
              The number of samples in wavelength for  the  reconstructed  cube  (long;  default:
              2048).  The  full  name  of  this  option  for  the  EsoRex  configuration  file is
              kmos.kmos_illumination.b_samples [default = 2048].

       --b_start <float>
              The lowest  wavelength  [um]  to  use  when  reconstructing.  Derived  by  default,
              depending  on the band (float; default: -1.0). The full name of this option for the
              EsoRex configuration file is kmos.kmos_illumination.b_start [default = -1.0].

       --b_end <float>
              The highest wavelength  [um]  to  use  when  reconstructing.  Derived  by  default,
              depending  on the band (float; default: -1.0). The full name of this option for the
              EsoRex configuration file is kmos.kmos_illumination.b_end [default = -1.0].

       --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_illumination.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_illumination.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_illumination.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_illumination.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_illumination.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_illumination.cmin [default = 1].

       --det <long>
              Only reduce the specified detector (long; default: 0). The full name of this option
              for the EsoRex configuration file is kmos.kmos_illumination.detector [default = 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 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_check(7),   kmo_fits_strip(7),   kmo_illumination_flat(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_extract_spec(7),   kmos_flat(7),
       kmos_gen_reflines(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_illumination 1.3.17

AUTHOR

       Alex Agudo Berbel, Yves 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