Provided by: cpl-plugin-muse-doc_2.6.2+dfsg-1_all bug

NAME

       muse_bias - Combine several separate bias images into one master bias file.

SYNOPSIS

       esorex muse_bias [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe  combines  several separate bias images into one master bias file. The master
       bias contains the combined pixel values, in adu, of the raw bias exposures,  with  respect
       to  the  image  combination  method  used.  Processing  trims the raw data and records the
       overscan statistics, corrects the data levels using  the  overscan  (if  overscan  is  not
       "none")  and combines the exposures using input parameters. The read-out noise is computed
       for each quadrant of the raw input  images  and  stored  as  QC  parameter.  The  variance
       extension  is  filled with an initial value accordingly, before image combination. Further
       QC statistics are computed on the  output  master  bias.  Additionally,  bad  columns  are
       searched for and marked in the data quality extension.

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_bias.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_bias.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_bias.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_bias.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_bias.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_bias.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_bias.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_bias.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_bias.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_bias.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_bias.hsigma  [default
              = 3.0].

       --losigmabadpix <float>
              Low  sigma  to  find  dark columns in the combined bias (float; default: 30.0). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              muse.muse_bias.losigmabadpix [default = 30.0].

       --hisigmabadpix <float>
              High  sigma  to find bright columns in the combined bias (float; default: 3.0). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              muse.muse_bias.hisigmabadpix [default = 3.0].

       --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_bias.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_create_sky(7),  muse_dark(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_bias 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