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NAME

       muse_dark  - Combine several separate dark images into one master dark file and locate hot
       pixels.

SYNOPSIS

       esorex muse_dark [OPTIONS] FILE.sof

DESCRIPTION

       This recipe combines several separate dark images into one master dark  file.  The  master
       dark  contains  the  combined  pixel values of the raw dark exposures, with respect to the
       image combination method used and normalization time specified. Processing trims  the  raw
       data  and  records  the  overscan  statistics,  subtracts  the bias (taking account of the
       overscan, if --overscan is not "none") from each raw input image, converts them  from  adu
       to  count,  scales  them  according  to their exposure time, and combines them using input
       parameters. Hot pixels are then identified using image statistics and marked in  the  data
       quality extension. The combined image is normalized to 1 hour exposure time. QC statistics
       are computed on the output master dark.

OPTIONS

       --nifu <int>
              IFU to handle. If set to 0, all IFUs are processed serially. If set to -1, all IFUs
              are  processed in parallel. (int; default: 0). The full name of this option for the
              EsoRex configuration file is muse.muse_dark.nifu [default = 0].

       --overscan <str>
              If this is "none", stop when detecting discrepant overscan levels (see  ovscsigma),
              for  "offset" it assumes that the mean overscan level represents the real offset in
              the bias levels of the exposures involved, and adjusts the  data  accordingly;  for
              "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole
              quadrant. (str; default: ´vpoly´). The full name of  this  option  for  the  EsoRex
              configuration file is muse.muse_dark.overscan [default = vpoly].

       --ovscreject <str>
              This  influences how values are rejected when computing overscan statistics. Either
              no rejection at all  ("none"),  rejection  using  the  DCR  algorithm  ("dcr"),  or
              rejection  using an iterative constant fit ("fit"). (str; default: ´dcr´). The full
              name of this option for the EsoRex configuration file is  muse.muse_dark.ovscreject
              [default = dcr].

       --ovscsigma <float>
              If  the  deviation  of  mean  overscan  levels  between  a  raw input image and the
              reference image is higher  than  |ovscsigma  x  stdev|,  stop  the  processing.  If
              overscan="vpoly",  this  is  used  as  sigma  rejection  level  for  the  iterative
              polynomial fit (the level comparison is then done afterwards with |100 x stdev|  to
              guard against incompatible settings).  Has no effect for overscan="offset". (float;
              default: 30.0). The full name of this option for the EsoRex configuration  file  is
              muse.muse_dark.ovscsigma [default = 30.0].

       --ovscignore <int>
              The  number  of pixels of the overscan adjacent to the data section of the CCD that
              are ignored when computing statistics or fits. (int; default: 3). The full name  of
              this option for the EsoRex configuration file is muse.muse_dark.ovscignore [default
              = 3].

       --combine <str>
              Type of image combination to use. (str; default: ´sigclip´). The full name of  this
              option  for  the  EsoRex  configuration  file  is muse.muse_dark.combine [default =
              sigclip].

       --nlow <int>
              Number of minimum pixels to reject with minmax. (int; default: 1). The full name of
              this option for the EsoRex configuration file is muse.muse_dark.nlow [default = 1].

       --nhigh <int>
              Number of maximum pixels to reject with minmax. (int; default: 1). The full name of
              this option for the EsoRex configuration file is  muse.muse_dark.nhigh  [default  =
              1].

       --nkeep <int>
              Number  of  pixels  to  keep  with minmax. (int; default: 1). The full name of this
              option for the EsoRex configuration file is muse.muse_dark.nkeep [default = 1].

       --lsigma <float>
              Low sigma for pixel rejection with sigclip. (float; default: 3.0). The full name of
              this  option  for the EsoRex configuration file is muse.muse_dark.lsigma [default =
              3.0].

       --hsigma <float>
              High sigma for pixel rejection with sigclip. (float; default: 3.0). The  full  name
              of  this option for the EsoRex configuration file is muse.muse_dark.hsigma [default
              = 3.0].

       --scale <bool>
              Scale the individual images to a common exposure time before combining them. (bool;
              default:  True).  The full name of this option for the EsoRex configuration file is
              muse.muse_dark.scale [default = True].

       --normalize <float>
              Normalize  the  master  dark  to  this  exposure  time  (in  seconds).  To  disable
              normalization,  set  this  to  a negative value. (float; default: 3600.0). The full
              name of this option for the EsoRex configuration file  is  muse.muse_dark.normalize
              [default = 3600.0].

       --hotsigma <float>
              Sigma  level, in terms of median deviation above the median dark level, above which
              a pixel is detected and marked as ´hot´. (float; default: 5.0). The  full  name  of
              this option for the EsoRex configuration file is muse.muse_dark.hotsigma [default =
              5.0].

       --merge <bool>
              Merge output products from different IFUs  into  a  common  file.  (bool;  default:
              False).  The  full  name  of  this  option  for  the  EsoRex  configuration file is
              muse.muse_dark.merge [default = False].

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

              ftp://ftp.eso.org/pub/dfs/pipelines/muse/muse-pipeline-cookbook-2.6.2.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 muse pipeline are muse_ampl(7), muse_astrometry(7), muse_bias(7),
       muse_create_sky(7),      muse_exp_align(7),       muse_exp_combine(7),       muse_flat(7),
       muse_geometry(7),    muse_illum(7),    muse_lingain(7),    muse_lsf(7),   muse_qi_mask(7),
       muse_scibasic(7),            muse_scipost(7),            muse_scipost_apply_astrometry(7),
       muse_scipost_calibrate_flux(7),                         muse_scipost_combine_pixtables(7),
       muse_scipost_correct_dar(7),    muse_scipost_correct_rv(7),     muse_scipost_make_cube(7),
       muse_scipost_raman(7),  muse_scipost_subtract_sky(7), muse_scipost_subtract_sky_simple(7),
       muse_standard(7), muse_twilight(7), muse_wavecal(7)

VERSION

       muse_dark 2.6.2

AUTHOR

       Peter Weilbacher <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  MUSE  Instrument Pipeline Copyright (C) 2005, 2018 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., 51 Franklin St, Fifth Floor, Boston,
       MA  02111-1307  USA