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NAME

       muse_exp_align  -  Create  a  coordinate offset table to be used to align exposures during
       exposure combination.

SYNOPSIS

       esorex muse_exp_align [OPTIONS] FILE.sof

DESCRIPTION

       Compute the coordinate offset for  each  input  field-of-view  image  with  respect  to  a
       reference.  The created list of coordinate offsets can then be used in muse_exp_combine as
       the field coordinate offsets to properly align the exposures during their combination. The
       source positions used to compute the field offsets are obtained by detecting point sources
       in each of the input images, unless the source detection is overridden and an input source
       list is available for each input field-of-view image. In this latter case the input source
       positions are used to calculate the field offsets.

OPTIONS

       --rsearch <str>
              Search radius (in arcsec) for each  iteration  of  the  offset  computation.  (str;
              default:   ´30.,4.,2.,0.8´).   The   full  name  of  this  option  for  the  EsoRex
              configuration file is muse.muse_exp_align.rsearch [default = 30.,4.,2.,0.8].

       --nbins <int>
              Number of bins to use for 2D  histogram  on  the  first  iteration  of  the  offset
              computation.  (int;  default:  60).  The  full  name  of this option for the EsoRex
              configuration file is muse.muse_exp_align.nbins [default = 60].

       --weight <bool>
              Use weighting. (bool; default: True). The full name of this option for  the  EsoRex
              configuration file is muse.muse_exp_align.weight [default = True].

       --fwhm <float>
              FWHM  in  pixels of the convolution filter. (float; default: 5.0). The full name of
              this option for the EsoRex configuration file is muse.muse_exp_align.fwhm  [default
              = 5.0].

       --threshold <float>
              Initial  intensity  threshold for detecting point sources. If the value is negative
              or zero the threshold is taken as sigma above  median  background  MAD.  If  it  is
              larger  than  zero  the  threshold  is  taken as absolute background level. (float;
              default: 15.0). The full name of this option for the EsoRex configuration  file  is
              muse.muse_exp_align.threshold [default = 15.0].

       --bkgignore <float>
              Fraction  of the image to be ignored. (float; default: 0.05). The full name of this
              option for the EsoRex configuration file is muse.muse_exp_align.bkgignore  [default
              = 0.05].

       --bkgfraction <float>
              Fraction  of  the  image (without the ignored part) to be considered as background.
              (float; default: 0.1). The full name of this option for  the  EsoRex  configuration
              file is muse.muse_exp_align.bkgfraction [default = 0.1].

       --step <float>
              Increment/decrement  of  the  threshold  value  in  subsequent iterations.  (float;
              default: 0.5). The full name of this option for the EsoRex  configuration  file  is
              muse.muse_exp_align.step [default = 0.5].

       --iterations <int>
              Maximum  number  of  iterations used for detecting sources. (int; default: 100000).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              muse.muse_exp_align.iterations [default = 100000].

       --srcmin <int>
              Minimum  number of sources which must be found. (int; default: 5). The full name of
              this  option  for  the  EsoRex  configuration  file  is  muse.muse_exp_align.srcmin
              [default = 5].

       --srcmax <int>
              Maximum  number of sources which may be found. (int; default: 80). The full name of
              this  option  for  the  EsoRex  configuration  file  is  muse.muse_exp_align.srcmax
              [default = 80].

       --roundmin <float>
              Lower limit of the allowed point-source roundness. (float; default: -1.0). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_exp_align.roundmin [default = -1.0].

       --roundmax <float>
              Upper  limit of the allowed point-source roundness. (float; default: 1.0). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_exp_align.roundmax [default = 1.0].

       --sharpmin <float>
              Lower  limit of the allowed point-source sharpness. (float; default: 0.2). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_exp_align.sharpmin [default = 0.2].

       --sharpmax <float>
              Upper  limit of the allowed point-source sharpness. (float; default: 1.0). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_exp_align.sharpmax [default = 1.0].

       --expmap <bool>
              Enables  the  creation  of  a  simple exposure map for the combined field- of-view.
              (bool; default: False). The full name of this option for the  EsoRex  configuration
              file is muse.muse_exp_align.expmap [default = False].

       --bpixdistance <float>
              Minimum  allowed  distance  of a source to the closest bad pixel in pixel. Detected
              sources which are closer to a bad pixel are not taken into account  when  computing
              the field offsets. This option has no effect if the source positions are taken from
              input catalogs. (float; default: 5.0). The full name of this option for the  EsoRex
              configuration file is muse.muse_exp_align.bpixdistance [default = 5.0].

       --override_detection <bool>
              Overrides  the  source  detection  step. If this is enabled and source catalogs are
              present in the input data set, the source positions used  to  calculate  the  field
              offsets  are  read  from  the input catalogs. If no catalogs are available as input
              data the source positions are detected on the input images. (bool; default: False).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              muse.muse_exp_align.override_detection [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_dark(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_exp_align 2.6.2

AUTHOR

       Ralf Palsa <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