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NAME

       muse_lingain  -  Compute  the  gain  and  a  model  of the residual non-linearity for each
       detector quadrant

SYNOPSIS

       esorex muse_lingain [OPTIONS] FILE.sof

DESCRIPTION

       The recipe uses the bias and flat field images of a detector monitoring exposure  sequence
       to  determine  the detector gain in counts/ADU and to model the residual non-linearity for
       each of the four detector quadrants of all IFUs. All measurements done by the  recipe  are
       done  on  the  illuminated  parts of the detector, i.e. on the slices. The location of the
       slices is taken from the given trace table, which is a mandatory input. Using  the  traces
       of  the  slices on the detector a set of measurement windows is placed along these traces.
       The data used for the determination of the gain and  the  residual  non-linearity  is  the
       taken  from  these  windows.  Bad  pixels  indicated by an, optionally, provided bad pixel
       table, or flagged during the preprocessing  (bias  subtraction)  of  the  input  data  are
       excluded  from  the measurements. Local measurements of the read-out-noise, the signal and
       the gain are calculated for each of the measurement windows. Using these measurements  the
       gain  for  each detector quadrant is computed as the zero-order coefficient of a 1st order
       polynomial fitted to the binned gain measurements as a function of the signal  level.  The
       residual  non-linearity  is  modelled  by a (high) order polynomial which is fitted to the
       fractional percentage deviation of the count rate from an  expected  constant  count  rate
       (the linear case) as function of the signal level.

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_lingain.nifu [default = 0].

       --ybox <int>
              Size  of  windows along the traces of the slices. (int; default: 50). The full name
              of this option for the EsoRex configuration file is muse.muse_lingain.ybox [default
              = 50].

       --xgap <int>
              Extra offset from tracing edge. (int; default: 3). The full name of this option for
              the EsoRex configuration file is muse.muse_lingain.xgap [default = 3].

       --xborder <int>
              Extra offset from the detector edge  used  for  the  selection  of  slices.   (int;
              default:  10).  The  full  name of this option for the EsoRex configuration file is
              muse.muse_lingain.xborder [default = 10].

       --order <int>
              Order of the polynomial used to fit the  non-linearity  residuals.  (int;  default:
              12).   The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              muse.muse_lingain.order [default = 12].

       --toffset <float>
              Exposure time offset in  seconds  to  apply  to  linearity  flat  fields.   (float;
              default:  0.018). The full name of this option for the EsoRex configuration file is
              muse.muse_lingain.toffset [default = 0.018].

       --fluxtol <float>
              Tolerance value for the overall flux consistency check of a pair  of  flat  fields.
              The  value is the maximum relative offset. (float; default: 0.01). The full name of
              this option for the EsoRex configuration file is muse.muse_lingain.fluxtol [default
              = 0.01].

       --sigma <float>
              Sigma value used for signal value clipping. (float; default: 3.0). The full name of
              this option for the EsoRex configuration file is muse.muse_lingain.sigma [default =
              3.0].

       --signalmin <float>
              Minimum  signal  value in log(ADU) used for the gain analysis and the non-linearity
              polynomial model. (float; default: 0.0). The full  name  of  this  option  for  the
              EsoRex configuration file is muse.muse_lingain.signalmin [default = 0.0].

       --signalmax <float>
              Maximum  signal  value in log(ADU) used for the gain analysis and the non-linearity
              polynomial model. (float; default: 4.9). The full  name  of  this  option  for  the
              EsoRex configuration file is muse.muse_lingain.signalmax [default = 4.9].

       --signalbin <float>
              Size of a signal bin in log10(ADU) used for the gain analysis and the non-linearity
              polynomial model. (float; default: 0.1). The full  name  of  this  option  for  the
              EsoRex configuration file is muse.muse_lingain.signalbin [default = 0.1].

       --gainlimit <float>
              Minimum  signal  value  [ADU]  used for fitting the gain relation. (float; default:
              100.0). The full  name  of  this  option  for  the  EsoRex  configuration  file  is
              muse.muse_lingain.gainlimit [default = 100.0].

       --gainsigma <float>
              Sigma  value  for gain value clipping. (float; default: 3.0). The full name of this
              option for the EsoRex configuration file is muse.muse_lingain.gainsigma [default  =
              3.0].

       --ctsmin <float>
              Minimum  signal  value  in  log(counts) to consider for the non-linearity analysis.
              (float; default: 3.0). The full name of this option for  the  EsoRex  configuration
              file is muse.muse_lingain.ctsmin [default = 3.0].

       --ctsmax <float>
              Maximum  signal  value  in  log(counts) to consider for the non-linearity analysis.
              (float; default: 4.9). The full name of this option for  the  EsoRex  configuration
              file is muse.muse_lingain.ctsmax [default = 4.9].

       --ctsbin <float>
              Size  of a signal bin in log10(counts) used for the non-linearity analysis. (float;
              default: 0.1). The full name of this option for the EsoRex  configuration  file  is
              muse.muse_lingain.ctsbin [default = 0.1].

       --linearmin <float>
              Lower  limit  of  desired linear range in log10(counts). (float; default: 2.5). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              muse.muse_lingain.linearmin [default = 2.5].

       --linearmax <float>
              Upper  limit  of  desired linear range in log10(counts). (float; default: 3.0). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              muse.muse_lingain.linearmax [default = 3.0].

       --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_lingain.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_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_lingain 2.6.2

AUTHOR

       Ralf Palsa <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