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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. If --model=true, a smooth polynomial model of  the
       combined  master  dark  is  computed,  created  from  several individual 2D polynomials to
       describe different features visible in MUSE dark frames. It is only advisable to use this,
       if the master dark is the result of at least 50 individual long dark exposures.

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].

       --model <bool>
              Model  the master dark using a set of polynomials. (bool; default: False). The full
              name of this option for  the  EsoRex  configuration  file  is  muse.muse_dark.model
              [default = False].

       --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-2.8.5.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 2.8.5

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,  2019  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