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NAME

       muse_flat  -  Combine  several separate flat images into one master flat file, trace slice
       locations, and locate dark pixels.

SYNOPSIS

       esorex muse_flat [OPTIONS] FILE.sof

DESCRIPTION

       This recipe combines several separate flat-field images into one  master  flat-field  file
       and  traces  the  location of the slices on the CCD. The master flat contains the combined
       pixel values of the raw flat exposures, with respect to the image combination method used,
       normalized to the mean flux. The trace table contains polynomials defining the location of
       the slices on the CCD. Processing trims the raw data and records the overscan  statistics,
       subtracts  the  bias  (taking  account  of the overscan, if --overscan is not "none"), and
       optionally, the dark from each raw input image, converts them from adu  to  count,  scales
       them  according to their exposure time, and combines the exposures using input parameters.
       To trace the position of the slices on the CCD, their edges are located using a  threshold
       method.  The  edge  detection  is  repeated at given intervals thereby tracing the central
       position (the mean of both edges) and width  of  each  slit  vertically  across  the  CCD.
       Deviant  positions of detections on CCD rows can be detected and excluded before fitting a
       polynomial to all positions measured for one slice. The  polynomial  parameters  for  each
       slice  are  saved in the output trace table. Finally, the area between the now known slice
       edges is searched for dark (and bright) pixels, using statistics in each row of the master
       flat.

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_flat.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_flat.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_flat.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_flat.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_flat.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_flat.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_flat.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_flat.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_flat.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_flat.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_flat.hsigma [default =
              3.0].

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

       --normalize <bool>
              Normalize the master flat to the average flux (bool; default: True). The full  name
              of  this  option  for  the  EsoRex  configuration  file is muse.muse_flat.normalize
              [default = True].

       --trace <bool>
              Trace the position of the slices on the master flat (bool; default: True). The full
              name  of  this  option  for  the  EsoRex configuration file is muse.muse_flat.trace
              [default = True].

       --nsum <int>
              Number of lines over which to average when tracing (int;  default:  32).  The  full
              name  of  this  option  for  the  EsoRex  configuration file is muse.muse_flat.nsum
              [default = 32].

       --order <int>
              Order of polynomial fit to the trace (int; default:  5).  The  full  name  of  this
              option for the EsoRex configuration file is muse.muse_flat.order [default = 5].

       --edgefrac <float>
              Fractional change required to identify edge when tracing (float; default: 0.5). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              muse.muse_flat.edgefrac [default = 0.5].

       --losigmabadpix <float>
              Low  sigma  to  find dark pixels in the master flat (float; default: 5.0). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_flat.losigmabadpix [default = 5.0].

       --hisigmabadpix <float>
              High sigma to find bright pixels in the master flat (float; default: 5.0). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_flat.hisigmabadpix [default = 5.0].

       --samples <bool>
              Create  a  table  containing all tracing sample points. (bool; default: False). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              muse.muse_flat.samples [default = False].

       --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_flat.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_bias(7),
       muse_create_sky(7),       muse_dark(7),       muse_exp_align(7),      muse_exp_combine(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_flat 2.6.2

AUTHOR

       Peter Weilbacher (based on Joris Gerssen's draft) <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