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NAME

       muse_wavecal  -  Detect  arc emission lines and determine the wavelength solution for each
       slice.

SYNOPSIS

       esorex muse_wavecal [OPTIONS] FILE.sof

DESCRIPTION

       This recipe detects arc emission lines and fits a wavelength solution to each slice of the
       instrument.  The wavelength calibration table contains polynomials defining the wavelength
       solution 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 converts them from adu to count. Optionally, the dark can  be  subtracted  and
       the  data  can be divided by the flat-field, but this is not recommended. The data is then
       combined using input parameters, into separate  images  for  each  lamp.  To  compute  the
       wavelength  solution,  arc lines are detected at the center of each slice (using threshold
       detection on a S/N image) and subsequently assigned wavelengths, using pattern matching to
       identify  lines  from the input line catalog. Each line is then traced to the edges of the
       slice, using Gaussian centering in each CCD column. The Gaussians not only  yield  center,
       but also centering error, and line properties (e.g. FWHM). Deviant fits are detected using
       polynomial fits to each arc line (using the xorder parameter) and rejected. These analysis
       and  measuring  steps  are  carried  out separately on images exposed by the different arc
       lamps, reducing the amount of blending, that can otherwise influence  line  identification
       and  Gaussian  centering. The final two-dimensional fit uses all positions (of all lamps),
       their wavelengths, and the  given  polynomial  orders  to  compute  the  final  wavelength
       solution  for  each  slice,  iteratively  rejecting outliers. This final fit can be either
       unweighted (fitweighting="uniform", for fastest processing) or weighted (other  values  of
       fitweighting, for higher accuracy).

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_wavecal.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_wavecal.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_wavecal.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_wavecal.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_wavecal.ovscignore
              [default = 3].

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

       --lampwise <bool>
              Identify  and  measure  the  arc  emission lines on images separately for each lamp
              setup. (bool; default:  True).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is muse.muse_wavecal.lampwise [default = True].

       --sigma <float>
              Sigma  level used to detect arc emission lines above the median background level in
              the S/N image of the central column of each slice (float; default: 1.0).  The  full
              name  of  this  option for the EsoRex configuration file is muse.muse_wavecal.sigma
              [default = 1.0].

       --dres <float>
              The allowed range of resolutions for pattern matching (of  detected  arc  lines  to
              line  list) in fractions relative to the expected value (float; default: 0.05). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              muse.muse_wavecal.dres [default = 0.05].

       --tolerance <float>
              Tolerance  for  pattern  matching  (of  detected  arc  lines  to line list) (float;
              default: 0.1). The full name of this option for the EsoRex  configuration  file  is
              muse.muse_wavecal.tolerance [default = 0.1].

       --xorder <int>
              Order  of  the  polynomial  for  the  horizontal  curvature within each slice (int;
              default: 2). The full name of this option for  the  EsoRex  configuration  file  is
              muse.muse_wavecal.xorder [default = 2].

       --yorder <int>
              Order  of the polynomial used to fit the dispersion relation (int; default: 6). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              muse.muse_wavecal.yorder [default = 6].

       --linesigma <float>
              Sigma  level  for iterative rejection of deviant fits for each arc line within each
              slice, a negative value means to use the default (2.5).   (float;  default:  -1.0).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              muse.muse_wavecal.linesigma [default = -1.0].

       --residuals <bool>
              Create a table containing residuals of the fits to the data of all arc lines.  This
              is  useful  to  assess  the  quality  of  the wavelength solution in detail. (bool;
              default: False). The full name of this option for the EsoRex configuration file  is
              muse.muse_wavecal.residuals [default = False].

       --fitsigma <float>
              Sigma  level  for  iterative  rejection  of  deviant  datapoints  during  the final
              polynomial wavelength solution within each slice, a negative value means to use the
              default  (3.0). (float; default: -1.0). The full name of this option for the EsoRex
              configuration file is muse.muse_wavecal.fitsigma [default = -1.0].

       --fitweighting <str>
              Type of weighting to use in the final polynomial  wavelength  solution  fit,  using
              centroiding  error  estimate and/or scatter of each single line as estimates of its
              accuracy. (str; default: ´cerrscatter´). The full  name  of  this  option  for  the
              EsoRex    configuration   file   is   muse.muse_wavecal.fitweighting   [default   =
              cerrscatter].

       --saveimages <bool>
              Save (bool;  default:  False).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is muse.muse_wavecal.saveimages [default = False].

       --resample <bool>
              Resample  the  input arc images onto 2D images for a visual check using tracing and
              wavelength calibration solutions. Note that the  image  produced  will  show  small
              wiggles  even when the calibration was successful! (bool; default: False). The full
              name of this option for the EsoRex configuration file is muse.muse_wavecal.resample
              [default = False].

       --wavemap <bool>
              Create  a  wavelength map of the input images (bool; default: False). The full name
              of this option for  the  EsoRex  configuration  file  is  muse.muse_wavecal.wavemap
              [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_wavecal.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_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)

VERSION

       muse_wavecal 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