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NAME

       muse_ampl   -  Determine  the  instrumental  throughput  from  exposures  taken  with  the
       pico-amplifier / photo diode readings.

SYNOPSIS

       esorex muse_ampl [OPTIONS] FILE.sof

DESCRIPTION

       This recipe combines several separate amplifier  images  (flat-fields  with  special  FITS
       headers  containing  pico  amplifier measurements) into one master image file and computes
       the instrumental throughput per IFU (and slice). 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 them using input
       parameters. To compute the throughput the image is converted into a pixel table, the  flux
       is  then  integrated  over the given filter band, and the ratio of the expected flux (FITS
       header INS.AMPL2.CURR) to measured flux is taken, in the same units. If a  geometry  table
       was given as input, the relative area of the IFUs is taken into account when computing the
       flux per unit area. The resulting ratio is  the  instrument  efficiency  (throughput)  and
       saved as QC parameters for the whole input image and per slice in the output pixel table.

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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.hsigma [default =
              3.0].

       --fbeam <float>
              Factor to describe the widening of the beam from the focal plane to photo diode  2.
              (float;  default:  1.1).  The full name of this option for the EsoRex configuration
              file is muse.muse_ampl.fbeam [default = 1.1].

       --temp <float>
              Lamp temperature [K] used to create  the  black  body  function.  (float;  default:
              3200.0).  The  full  name  of  this  option  for  the  EsoRex configuration file is
              muse.muse_ampl.temp [default = 3200.0].

       --savemaster <bool>
              Save the processed and combined master image before any concolution is done. (bool;
              default:  False). The full name of this option for the EsoRex configuration file is
              muse.muse_ampl.savemaster [default = False].

       --savetable <bool>
              Save the table with all the processed pixel values.  (bool;  default:  False).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              muse.muse_ampl.savetable [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_ampl.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_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), muse_wavecal(7)

VERSION

       muse_ampl 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