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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-2.8.7.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 2.8.7

AUTHOR

       Peter Weilbacher <https://support.eso.org>

BUG REPORTS

       Please report any problems to https://support.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