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NAME

       muse_geometry  -  Compute  relative  location  of  the slices within the field of view and
       measure the instrumental PSF on the detectors.

SYNOPSIS

       esorex muse_geometry [OPTIONS] FILE.sof

DESCRIPTION

       Processing first works separately on each IFU of the raw  input  data  (in  parallel):  it
       trims  the  raw  data and records the overscan statistics, subtracts the bias and converts
       them from adu to count. Optionally, the dark can be subtracted and the data can be divided
       by  the  flat-field.  The  data of all input mask exposures is then averaged. The averaged
       image together with the trace mask and wavelength calibration as well as the line  catalog
       are  used  to  detect  spots.  The  detection windows are used to measure the spots on all
       images of the sequence, the result is saved, with information on the measured PSF, in  the
       spots  tables. Then properties of all slices are computed, first separately on each IFU to
       determine the peak position of the mask for each slice and  its  angle,  subsequently  the
       width  and  horizontal  position.  Then,  the  result  of all IFUs is analyzed together to
       produce a refined horizontal position, applying global shifts to each IFU as  needed.  The
       vertical  position  is  then  determined  using  the  known slice ordering on the sky; the
       relative peak positions are put into sequence, taking into account the vertical offsets of
       the  pinholes  in  the mask. The table is then cleaned up from intermediate debug data. If
       the --smooth parameter is set to a positive value,  it  is  used  to  do  a  sigma-clipped
       smoothing within each slicer stack, for a more regular appearance of the output table. The
       table is then saved. As a last optional step, additional raw input data is  reduced  using
       the  newly  geometry  to produce an image of the field of view. If these exposures contain
       smooth features, they can be used as a visual check of  the  quality  of  the  geometrical
       calibration.

OPTIONS

       --ifu1 <long>
              First  IFU  to  analyze.  (long;  default: 1). The full name of this option for the
              EsoRex configuration file is muse.muse_geometry.ifu1 [default = 1].

       --ifu2 <long>
              Last IFU to analyze. (long; default: 24). The full name  of  this  option  for  the
              EsoRex configuration file is muse.muse_geometry.ifu2 [default = 24].

       --sigma <float>
              Sigma  detection  level  for spot detection, in terms of median deviation above the
              median. (float; default: 2.2).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is muse.muse_geometry.sigma [default = 2.2].

       --centroid <str>
              Type of centroiding and FWHM determination to use for all spot measurements: simple
              barycenter method or using a Gaussian fit. (str;  default:  ┬┤gaussian┬┤).  The  full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_geometry.centroid [default = gaussian].

       --smooth <float>
              Use this sigma-level cut for smoothing of  the  output  table  within  each  slicer
              stack.  Set  to non-positive value to deactivate smoothing.  (float; default: 1.5).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              muse.muse_geometry.smooth [default = 1.5].

       --lambdamin <float>
              When  passing  any  MASK_CHECK  frames  in the input, use this lower wavelength cut
              before reconstructing the image. (float; default: 6800.0). The full  name  of  this
              option for the EsoRex configuration file is muse.muse_geometry.lambdamin [default =
              6800.0].

       --lambdamax <float>
              When passing any MASK_CHECK frames in the input,  use  this  upper  wavelength  cut
              before  reconstructing  the  image. (float; default: 7200.0). The full name of this
              option for the EsoRex configuration file is muse.muse_geometry.lambdamax [default =
              7200.0].

       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-1.2.1.pdf

       An  overview  over  the  existing  ESO  pipelines  can  be   found   on   the   web   page
       http://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
       http://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_align(7),  muse_exp_combine(7), muse_flat(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_subtract_sky(7),
       muse_scipost_subtract_sky_simple(7), muse_standard(7), muse_twilight(7), muse_wavecal(7)

VERSION

       muse_geometry 1.2.1

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, 2015 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