xsh_mdark - Create the master dark frame

       P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani <amodigli@eso.org>

       Please report any problems to amodigli@eso.org. Alternatively, you may send a  report  to  the  ESO  User
       Support Department <usd-help@eso.org>.

       This recipe creates a master dark frame Input Frames :
         - A set of n RAW frames (Format=RAW, n >=3, Tag = DARK_arm)
         - [UVB,VIS] A master bias frame (Format=PRE, Tag = MASTER_BIAS_arm)
         - [OPTIONAL] A map of non linear bad pixels (Format=QUP, Tag = BP_MAP_NL_arm)
         - [OPTIONAL] A map of reference bad pixels (Format = QUP,RAW, Tag = BP_MAP_RP_arm) Products :
         - A master dark frame (Format=PRE, PRO.CATG = MASTER_DARK_arm)
           A dark frame, (Format=PRE, PRO.CATG = DARK_arm)

       This file is part of the X-shooter Instrument Pipeline Copyright (C) 2006 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

xsh_mdark                                             3.5.3                                         XSH_MDARK(7)

       xsh_mdark - Create the master dark frame

--keep-temp<str>
              If  ´no´,  temporary files are deleted. (str; default: ´no´). The full name of this option for the
              EsoRex configuration file is xsh.xsh_mdark.keep-temp [default = no].

       --debug-level<str>
              Additional xshooter debug level. One of ´none´, ´low´, ´medium´, ´high´  (str;  default:  ´none´).
              The  full  name  of  this  option  for  the EsoRex configuration file is xsh.xsh_mdark.debug-level
              [default = none].

       --time-stamp<bool>
              Add timestamp to product file name. (bool; default: False). The full name of this option  for  the
              EsoRex configuration file is xsh.xsh_mdark.time-stamp [default = False].

       --decode-bp<int>
              Integer  representation  of  the  bits to be considered bad when decoding the bad pixel mask pixel
              values.   Most frequent codes relevant for the user:   0: good pixel,   8:  pick-up  noise,    16:
              cosmic-ray  removed,    32:  cosmic-ray unremoved,   128: calibration file defect, 256: hot pixel,
              512:  dark  pixel,    4096:  A/D  converted  saturation,  32768:  non  linear  pixel,     1048576:
              extrapolated   flux   in  NIR,  4194304:  Interpolated  flux  during  extraction.  (int;  default:
              2144337919).  The  full  name  of   this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_mdark.decode-bp [default = 2144337919].

       --pre-overscan-corr<int>
              pre-overscan  correction.  0: no correction 1: mean overscan correction 2: mean prescan correction
              3: (mean pre+mean overscan)/2 correction (int; default: 1). The full name of this option  for  the
              EsoRex configuration file is xsh.xsh_mdark.pre-overscan-corr [default = 1].

       --stack-method<str>
              Method  used to build master frame. (str; default: ´median´). The full name of this option for the
              EsoRex configuration file is xsh.xsh_mdark.stack-method [default = median].

       --klow<float>
              Kappa used to clip low level values, when method is set to ´mean´ (float; default: 5.0). The  full
              name of this option for the EsoRex configuration file is xsh.xsh_mdark.klow [default = 5.0].

       --khigh<float>
              Kappa used to clip high level values, when method is set to ´mean´ (float; default: 5.0). The full
              name of this option for the EsoRex configuration file is xsh.xsh_mdark.khigh [default = 5.0].

       --bp-output<bool>
              Flag indicating whether the noise bad pixel map is to be computed (bool; default: False). The full
              name  of  this  option  for  the  EsoRex  configuration file is xsh.xsh_mdark.bp-output [default =
              False].

       --crh-clip-kappa<float>
              Kappa value in sigma clipping during CRH rejection using multiple frames (float;  default:  -1.0).
              The  full  name  of  this option for the EsoRex configuration file is xsh.xsh_mdark.crh-clip-kappa
              [default = -1.0].

       --crh-clip-niter<int>
              Number of iterations in sigma clipping during CRH rejection using multiple frames  (int;  default:
              3). The full name of this option for the EsoRex configuration file is xsh.xsh_mdark.crh-clip-niter
              [default = 3].

       --crh-clip-frac<float>
              Minimal  ratio  of  points  accepted / total in sigma clipping during CRH rejection using multiple
              frames (float; default: 0.7). The full name of this option for the EsoRex  configuration  file  is
              xsh.xsh_mdark.crh-clip-frac [default = 0.7].

       --noise-clip-kappa<float>
              Multiple  of  sigma  in sigma clipping (float; default: 9.0). The full name of this option for the
              EsoRex configuration file is xsh.xsh_mdark.noise-clip-kappa [default = 9.0].

       --noise-clip-niter<int>
              Number of iterations in sigma clipping (int; default: 5). The full name of  this  option  for  the
              EsoRex configuration file is xsh.xsh_mdark.noise-clip-niter [default = 5].

       --noise-clip-frac<float>
              Minimal fractions of bad pixel allowed (float; default: 0.7). The full name of this option for the
              EsoRex configuration file is xsh.xsh_mdark.noise-clip-frac [default = 0.7].

       --noise-clip-diff<float>
              Minimum  relative  change in sigma for sigma clipping (float; default: 0.0). The full name of this
              option for the EsoRex configuration file is xsh.xsh_mdark.noise-clip-diff [default = 0.0].

       --noise-lower-rejection<float>
              Lower rejection percentile to flag bad pixels via noise (float; default: 10.0). The full  name  of
              this  option  for  the EsoRex configuration file is xsh.xsh_mdark.noise-lower-rejection [default =
              10.0].

       --noise-higher-rejection<float>
              Upper rejection percentile to flag bad pixels via noise (float; default: 10.0). The full  name  of
              this  option  for the EsoRex configuration file is xsh.xsh_mdark.noise-higher-rejection [default =
              10.0].

       --ref1_llx<int>
              Lower left X of reference region (int; default: -1). The full name of this option for  the  EsoRex
              configuration file is xsh.xsh_mdark.ref1_llx [default = -1].

       --ref1_lly<int>
              Lower  left  Y of reference region (int; default: -1). The full name of this option for the EsoRex
              configuration file is xsh.xsh_mdark.ref1_lly [default = -1].

       --ref1_urx<int>
              Upper right X of reference region (int; default: -1). The full name of this option for the  EsoRex
              configuration file is xsh.xsh_mdark.ref1_urx [default = -1].

       --ref1_ury<int>
              Upper  right Y of reference region (int; default: -1). The full name of this option for the EsoRex
              configuration file is xsh.xsh_mdark.ref1_ury [default = -1].

       --ron_llx<int>
              Lower left X of reference region to measure RON (int; default: -1). The full name of  this  option
              for the EsoRex configuration file is xsh.xsh_mdark.ron_llx [default = -1].

       --ron_lly<int>
              Lower  left  Y of reference region to measure RON (int; default: -1). The full name of this option
              for the EsoRex configuration file is xsh.xsh_mdark.ron_lly [default = -1].

       --ron_urx<int>
              Upper right X of reference region to measure RON (int; default: -1). The full name of this  option
              for the EsoRex configuration file is xsh.xsh_mdark.ron_urx [default = -1].

       --ron_ury<int>
              Upper  right Y of reference region to measure RON (int; default: -1). The full name of this option
              for the EsoRex configuration file is xsh.xsh_mdark.ron_ury [default = -1].

       --ron_hsize<int>
              Sampling area size (int; default: 4). The full name of this option for  the  EsoRex  configuration
              file is xsh.xsh_mdark.ron_hsize [default = 4].

       --ron_nsamples<int>
              Number  of  random  samples  (int;  default:  100).  The  full  name of this option for the EsoRex
              configuration file is xsh.xsh_mdark.ron_nsamples [default = 100].

       --fpn_llx<int>
              Lower left reference area X coordinate for Fixed Pattern Noise computation (int; default: -1). The
              full name of this option for the EsoRex configuration file  is  xsh.xsh_mdark.fpn_llx  [default  =
              -1].

       --fpn_lly<int>
              Lower left reference area Y coordinate for Fixed Pattern Noise computation (int; default: -1). The
              full  name  of  this  option for the EsoRex configuration file is xsh.xsh_mdark.fpn_lly [default =
              -1].

       --fpn_urx<int>
              Upper right reference area X coordinate for Fixed Pattern Noise computation  (int;  default:  -1).
              The full name of this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_urx [default =
              -1].

       --fpn_ury<int>
              Upper  right  reference  area Y coordinate for Fixed Pattern Noise computation (int; default: -1).
              The full name of this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_ury [default =
              -1].

       --fpn_hsize<int>
              Sample size for Fixed Pattern Noise computation (int; default: 4). The full name  of  this  option
              for the EsoRex configuration file is xsh.xsh_mdark.fpn_hsize [default = 4].

       --fpn_nsamples<int>
              Number  of  sampling points for Fixed Pattern Noise computation (int; default: 100). The full name
              of this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_nsamples [default = 100].

       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.

       The full documentation for the xshoo pipeline can be downloaded as a PDF file using the following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo-pipeline-manual-12.1.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  xshoo  pipeline  are  xsh_2dmap(7),  xsh_cfg_recover(7),  xsh_flexcomp(7),
       xsh_geom_ifu(7),   xsh_lingain(7),   xsh_mbias(7),   xsh_mflat(7),    xsh_orderpos(7),    xsh_predict(7),
       xsh_respon_slit_nod(7),  xsh_respon_slit_offset(7),  xsh_respon_slit_stare(7),  xsh_scired_ifu_offset(7),
       xsh_scired_ifu_offset_drl(7),            xsh_scired_ifu_stare(7),            xsh_scired_ifu_stare_drl(7),
       xsh_scired_slit_nod(7),    xsh_scired_slit_offset(7),    xsh_scired_slit_stare(7),   xsh_util_physmod(7),
       xsh_wavecal(7)

       esorex xsh_mdark [OPTIONS] FILE.sof

       xsh_mdark 3.5.3