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NAME

       xsh_mdark - Create the master dark frame

SYNOPSIS

       esorex xsh_mdark [OPTIONS] FILE.sof

DESCRIPTION

       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)

OPTIONS

       --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.

SEE ALSO

       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)

VERSION

       xsh_mdark 3.5.3

AUTHOR

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

BUG REPORTS

       Please  report  any  problems to amodigli@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  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