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NAME

       kmos_flat - Create master flatfield frame and badpixel map

SYNOPSIS

       esorex kmos_flat [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe  creates  the  master  flat  field  and calibration frames needed for spatial
       calibration for all three detectors. It must be called after  the  kmo_dark-recipe,  which
       generates  a  bad  pixel  mask (badpixel_dark.fits). The bad pixel mask will be updated in
       this recipe.

       As input at least 3 dark  frames,  3  frames  with  the  flat  lamp  on  are  recommended.
       Additionally a badpixel mask from kmo_dark is required.

       The badpixel mask contains 0 for bad pixels and 1 for good ones.

       The structure of the resulting xcal and ycal frames is quite complex since the arrangement
       of the IFUs isn´t just  linear  on  the  detector.  Basically  the  integer  part  of  the
       calibration  data  shows  the  offset of each pixels centre in mas (Milli arcsec) from the
       field centre. The viewing of an IFU is 2800 mas (14pix*0.2arcsec/pix). So  the  values  in
       these  two frames will vary between +/-1500 (One would expect 1400, but since the slitlets
       aren´t expected to be exactly vertical, the values can even go up to around 1500).

       Additionally in the  calibration  data  in  y-direction  the  decimal  part  of  the  data
       designates the IFU to which the slitlet corresponds to (for each detector from 1 to 8).

       Because  of  the irregular arrangement of the IFUs not all x-direction calibration data is
       found in xcal and similarly not all y-direction calibration data is located in  ycal.  For
       certain IFUs they are switched
        and/or  flipped  in  x-  or y-direction: For IFUs 1,2,3,4,13,14,15,16:  x- and y- data is
       switched  For  IFUs  17,18,19,20:           y-data  is  flipped  For   IFUs   21,22,23,24:
       x-data is flipped For IFUs 5,6,7,8,9,10,11,12:   x- and y- data is switched and
                                      x- and y- data is flipped

       Furthermore  frames can be provided for several rotator angles. In this case the resulting
       calibration frames for each detector are repeatedly saved as extension for every angle.

       Advanced features: ------------------ To  create  the  badpixel  mask  the  edges  of  all
       slitlets  are  fitted  to  a  polynomial.  Since  it can happen that some of these fits (3
       detectors 8 IFUs * 14slitlets * 2 edges  (left and right  edge  of  slitlet)=  672  edges)
       fail, the fit parameters are themselves fitted again to detect any outliers.

       By  default,  the  parameters of all left and all right edges are grouped individually and
       then fitted using chebyshev polynomials. The advantage of a chebyshev polynomial is,  that
       it  consists  in  fact  of  a  series  of  orthogonal  polynomials.  This implies that the
       parameters of the polynomials are independent. This fact predestines the use of  chebyshev
       polynomials for our case. So each individual parameter can be examined independently.

       The  reason  why  the  left  and  right  edges  are fitted individually is that there is a
       systematic pattern specific to these groups. The reason for this pattern is probably to be
       found in the optical path the light is traversing.

   BASIC PARAMETERS
       --badpix_thresh  The  threshold  level to mark pixels as bad on the dark subtracted frames
       [%] --surrounding_pixels The amount of bad pixels to surround a specific pixel, to let  it
       be marked bad as well.

       --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 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 number of min and max pixel values will be rejected.

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

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

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

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

         Input files:
          DO CATG           Type   Explanation                    Required #Frames
          -------           -----  -----------                    -------- -------
          FLAT_ON           RAW    Flatlamp-on exposures             Y       1-n
                                   (at least 3 frames recommended)
          FLAT_OFF          RAW    Flatlamp-off exposures            Y       1-n
                                   (at least 3 frames recommended)
          BADPIXEL_DARK     B2D    Bad pixel mask                    Y        1

         Output files:
          DO CATG           Type   Explanation
          -------           -----  -----------
          MASTER_FLAT       F2D    Normalised flat field
                                   (6 extensions: alternating data & noise
          BADPIXEL_FLAT     B2D    Updated bad pixel mask (3 Extensions)
          XCAL              F2D    Calibration frame 1 (3 Extensions)
          YCAL              F2D    Calibration frame 2 (3 Extensions)
          FLAT_EDGE         F2L    Frame containing parameters of fitted
                                   slitlets of all IFUs of all detectors

OPTIONS

       --badpix_thresh <long>
              The  threshold  level to mark bad pixels [%]. (long; default: 35). The full name of
              this option for  the  EsoRex  configuration  file  is  kmos.kmos_flat.badpix_thresh
              [default = 35].

       --surrounding_pixels <long>
              The nb of bad surrounding pix to mark a pixel bad (long; default: 5). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              kmos.kmos_flat.surrounding_pixels [default = 5].

       --suppress_extension <bool>
              Suppress arbitrary filename extension (bool; default: False). The full name of this
              option for  the  EsoRex  configuration  file  is  kmos.kmos_flat.suppress_extension
              [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_flat.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_flat.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_flat.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_flat.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_flat.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_flat.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_flat.detector [default = 0].

       --angle <float>
              Only reduce the specified angle (float; default: 370.0).  The  full  name  of  this
              option for the EsoRex configuration file is kmos.kmos_flat.angle [default = 370.0].

       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_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_extract_spec(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_flat 1.4.3

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