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NAME

       muse_twilight  -  Combine  several  twilight  skyflats  into  one cube, compute correction
       factors for each IFU, and create a smooth 3D illumination correction.

SYNOPSIS

       esorex muse_twilight [OPTIONS] FILE.sof

DESCRIPTION

       Processing first handles each raw input image  separately:  it  trims  the  raw  data  and
       records  the  overscan  statistics, subtracts the bias (taking account of the overscan, if
       --overscan is not "none"), converts the images from adu  to  count,  subtracts  the  dark,
       divides by the flat-field and combines all the exposures using input parameters. The input
       calibrations geometry table, trace table, and wavelength calibration  table  are  used  to
       assign  3D  coordinates  to  each CCD-based pixel, thereby creating a pixel table from the
       master sky-flat. These pixel tables are then cut in wavelength using the  --lambdamin  and
       --lambdamax parameters. The integrated flux in each IFU is computed as the sum of the data
       in the pixel table, and saved in the header, to be used later as estimate for the relative
       throughput  of  each  IFU.  If  an  ILLUM  exposure was given as input, it is then used to
       correct the relative illumination between all slices of one IFU. For  this,  the  data  of
       each  slice within the pixel table of each IFU is multiplied by the normalized median flux
       of that slice in the ILLUM exposure. The pixel tables of all IFUs are then  merged,  using
       the  integrated  fluxes  as  inverse scaling factors, and a cube is reconstructed from the
       merged dataset, using given parameters. A white-light image is created from the cube. This
       skyflat  cube  is  then  saved  to  disk,  with the white-light image as one extension. To
       construct a smooth 3D illumination correction, the cube is post-processed in the following
       way:  the  white-light  image  is used to create a mask of the illuminated area. From this
       area, the optional vignetting mask is removed. The smoothing is  then  computed  for  each
       plane  of the cube: the illuminated area is smoothed (by a 5x7 median filter), normalized,
       fit with a 2D polynomial (of given polynomial orders),  and  normalized  again.  A  smooth
       white  image is then created by collapsing the smooth cube. If a vignetting mask was given
       or NFM data is processed, an area close to the edge of the MUSE field is used to compute a
       2D  correction  for  the  vignetted  area:  the  original  unsmoothed white-light image is
       corrected for large scale gradients by dividing  it  with  the  smooth  white  image.  The
       residuals  in  the  edge area (as defined by the input mask or hardcoded for NRM) are then
       smoothed using input parameters. This smoothed vignetting  correction  is  the  multiplied
       onto  each  plane  of the smooth cube, normalizing each plane again. This twilight cube is
       then saved to disk.

OPTIONS

       --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_twilight.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_twilight.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_twilight.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_twilight.ovscignore
              [default = 3].

       --combine <str>
              Type of combination to use (str; default: ´sigclip´). The full name of this  option
              for   the  EsoRex  configuration  file  is  muse.muse_twilight.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_twilight.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_twilight.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_twilight.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_twilight.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_twilight.hsigma [default
              = 3.0].

       --scale <bool>
              Scale the individual images to a common exposure time before combining them. (bool;
              default: False). The full name of this option for the EsoRex configuration file  is
              muse.muse_twilight.scale [default = False].

       --resample <str>
              The  resampling  technique  to  use  for  the  final  output  cube.  (str; default:
              ´drizzle´). The full name of this option  for  the  EsoRex  configuration  file  is
              muse.muse_twilight.resample [default = drizzle].

       --crtype <str>
              Type  of  statistics  used  for  detection  of cosmic rays during final resampling.
              "iraf" uses the variance information, "mean" uses standard (mean/stdev) statistics,
              "median"  uses median and the median median of the absolute median deviation. (str;
              default: ´median´). The full name of this option for the EsoRex configuration  file
              is muse.muse_twilight.crtype [default = median].

       --crsigma <float>
              Sigma  rejection  factor to use for cosmic ray rejection during final resampling. A
              zero or negative value switches cosmic ray rejection off. (float;  default:  50.0).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              muse.muse_twilight.crsigma [default = 50.0].

       --lambdamin <float>
              Minimum wavelength for twilight reconstruction. (float; default: 5000.0). The  full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_twilight.lambdamin [default = 5000.0].

       --lambdamax <float>
              Maximum wavelength for twilight reconstruction. (float; default: 9000.0). The  full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_twilight.lambdamax [default = 9000.0].

       --dlambda <float>
              Sampling for twilight  reconstruction,  this  should  result  in  planes  of  equal
              wavelength  coverage. (float; default: 250.0). The full name of this option for the
              EsoRex configuration file is muse.muse_twilight.dlambda [default = 250.0].

       --xorder <int>
              Polynomial order to use in x direction to  fit  the  full  field  of  view.   (int;
              default:  2).  The  full  name  of this option for the EsoRex configuration file is
              muse.muse_twilight.xorder [default = 2].

       --yorder <int>
              Polynomial order to use in y direction to  fit  the  full  field  of  view.   (int;
              default:  2).  The  full  name  of this option for the EsoRex configuration file is
              muse.muse_twilight.yorder [default = 2].

       --vignmaskedges <float>
              Pixels on edges stronger than this fraction in the normalized  image  are  excluded
              from  the  fit to the vignetted area. Set to non-positive number to include them in
              the fit. This has no effect for NFM skyflats. (float; default: 0.02). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              muse.muse_twilight.vignmaskedges [default = 0.02].

       --vignsmooth <str>
              Type of smoothing to use for the vignetted region given by the VIGNETTING_MASK (for
              WFM, or the internal mask, for NFM); gaussian uses (vignxpar + vignypar)/2 as FWHM.
              (str;  default:  ´polyfit´).  The  full  name  of  this  option  for   the   EsoRex
              configuration file is muse.muse_twilight.vignsmooth [default = polyfit].

       --vignxpar <int>
              Parameter  used  by  the  vignetting  smoothing:  x  order  for  polyfit  (default,
              recommended 4), parameter that influences the FWHM for the  gaussian  (recommended:
              10), or x dimension of median filter (recommended 5). If a negative value is found,
              the default is taken.  (int; default: -1). The full name of  this  option  for  the
              EsoRex configuration file is muse.muse_twilight.vignxpar [default = -1].

       --vignypar <int>
              Parameter  used  by  the  vignetting  smoothing:  y  order  for  polyfit  (default,
              recommended 4), parameter that influences the FWHM for the  gaussian  (recommended:
              10), or y dimension of median filter (recommended 5). If a negative value is found,
              the default is taken.  (int; default: -1). The full name of  this  option  for  the
              EsoRex configuration file is muse.muse_twilight.vignypar [default = -1].

       --vignnfmmask <int>
              The height of the vignetted region at the top of the MUSE field in NFM. This is the
              region modeled separately (the final vignetting  model  might  be  smaller).  (int;
              default:  22).  The  full  name of this option for the EsoRex configuration file is
              muse.muse_twilight.vignnfmmask [default = 22].

       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_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_wavecal(7)

VERSION

       muse_twilight 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