Provided by: cpl-plugin-muse-doc_2.8.5+dfsg-1_all 
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. (Not yet implemented!)
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-2.8.5.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 2.8.5
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, 2019 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