Provided by: cpl-plugin-muse-doc_2.8.7+dfsg-3_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-2.8.7.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 2.8.7
AUTHOR
Ralf Palsa <https://support.eso.org>
BUG REPORTS
Please report any problems to https://support.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