Provided by: cpl-plugin-muse-doc_2.8.7+dfsg-3_all 
NAME
muse_twilight - Combine several twilight skyflats into one cube, compute correction factors for each IFU,
and create a smooth 3D illumination correction.
SYNOPSIS
esorex muse_twilight [OPTIONS] FILE.sof
DESCRIPTION
Processing first handles each raw input image separately: it trims the raw data and records the overscan
statistics, subtracts the bias (taking account of the overscan, if --overscan is not "none"), converts
the images from adu to count, subtracts the dark, divides by the flat-field and combines all the
exposures using input parameters. The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based pixel, thereby creating a pixel
table from the master sky-flat. These pixel tables are then cut in wavelength using the --lambdamin and
--lambdamax parameters. The integrated flux in each IFU is computed as the sum of the data in the pixel
table, and saved in the header, to be used later as estimate for the relative throughput of each IFU. If
an ILLUM exposure was given as input, it is then used to correct the relative illumination between all
slices of one IFU. For this, the data of each slice within the pixel table of each IFU is multiplied by
the normalized median flux of that slice in the ILLUM exposure. The pixel tables of all IFUs are then
merged, using the integrated fluxes as inverse scaling factors, and a cube is reconstructed from the
merged dataset, using given parameters. A white-light image is created from the cube. This skyflat cube
is then saved to disk, with the white-light image as one extension. To construct a smooth 3D illumination
correction, the cube is post-processed in the following way: the white-light image is used to create a
mask of the illuminated area. From this area, the optional vignetting mask is removed. The smoothing is
then computed for each plane of the cube: the illuminated area is smoothed (by a 5x7 median filter),
normalized, fit with a 2D polynomial (of given polynomial orders), and normalized again. A smooth white
image is then created by collapsing the smooth cube. If a vignetting mask was given or NFM data is
processed, an area close to the edge of the MUSE field is used to compute a 2D correction for the
vignetted area: the original unsmoothed white-light image is corrected for large scale gradients by
dividing it with the smooth white image. The residuals in the edge area (as defined by the input mask or
hardcoded for NFM) are then smoothed using input parameters. This smoothed vignetting correction is the
multiplied onto each plane of the smooth cube, normalizing each plane again. This twilight cube is then
saved to disk.
OPTIONS
--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_twilight.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_twilight.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_twilight.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_twilight.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_twilight.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_twilight.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_twilight.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_twilight.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_twilight.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_twilight.hsigma [default = 3.0].
--scale <bool>
Scale the individual images to a common exposure time before combining them. (bool; default:
False). The full name of this option for the EsoRex configuration file is muse.muse_twilight.scale
[default = False].
--resample <str>
The resampling technique to use for the final output cube. (str; default: ´drizzle´). The full
name of this option for the EsoRex configuration file is muse.muse_twilight.resample [default =
drizzle].
--crtype <str>
Type of statistics used for detection of cosmic rays during final resampling. "iraf" uses the
variance information, "mean" uses standard (mean/stdev) statistics, "median" uses median and the
median median of the absolute median deviation. (str; default: ´median´). The full name of this
option for the EsoRex configuration file is muse.muse_twilight.crtype [default = median].
--crsigma <float>
Sigma rejection factor to use for cosmic ray rejection during final resampling. A zero or negative
value switches cosmic ray rejection off. (float; default: 50.0). The full name of this option for
the EsoRex configuration file is muse.muse_twilight.crsigma [default = 50.0].
--lambdamin <float>
Minimum wavelength for twilight reconstruction. (float; default: 5000.0). The full name of this
option for the EsoRex configuration file is muse.muse_twilight.lambdamin [default = 5000.0].
--lambdamax <float>
Maximum wavelength for twilight reconstruction. (float; default: 9000.0). The full name of this
option for the EsoRex configuration file is muse.muse_twilight.lambdamax [default = 9000.0].
--dlambda <float>
Sampling for twilight reconstruction, this should result in planes of equal wavelength coverage.
(float; default: 250.0). The full name of this option for the EsoRex configuration file is
muse.muse_twilight.dlambda [default = 250.0].
--xorder <int>
Polynomial order to use in x direction to fit the full field of view. (int; default: 2). The full
name of this option for the EsoRex configuration file is muse.muse_twilight.xorder [default = 2].
--yorder <int>
Polynomial order to use in y direction to fit the full field of view. (int; default: 2). The full
name of this option for the EsoRex configuration file is muse.muse_twilight.yorder [default = 2].
--vignmaskedges <float>
Pixels on edges stronger than this fraction in the normalized image are excluded from the fit to
the vignetted area. Set to non-positive number to include them in the fit. This has no effect for
NFM skyflats. (float; default: 0.02). The full name of this option for the EsoRex configuration
file is muse.muse_twilight.vignmaskedges [default = 0.02].
--vignsmooth <str>
Type of smoothing to use for the vignetted region given by the VIGNETTING_MASK (for WFM, or the
internal mask, for NFM); gaussian uses (vignxpar + vignypar)/2 as FWHM. (str; default: ´polyfit´).
The full name of this option for the EsoRex configuration file is muse.muse_twilight.vignsmooth
[default = polyfit].
--vignxpar <int>
Parameter used by the vignetting smoothing: x order for polyfit (default, recommended 4),
parameter that influences the FWHM for the gaussian (recommended: 10), or x dimension of median
filter (recommended 5). If a negative value is found, the default is taken. (int; default: -1).
The full name of this option for the EsoRex configuration file is muse.muse_twilight.vignxpar
[default = -1].
--vignypar <int>
Parameter used by the vignetting smoothing: y order for polyfit (default, recommended 4),
parameter that influences the FWHM for the gaussian (recommended: 10), or y dimension of median
filter (recommended 5). If a negative value is found, the default is taken. (int; default: -1).
The full name of this option for the EsoRex configuration file is muse.muse_twilight.vignypar
[default = -1].
--vignnfmmask <int>
The height of the vignetted region at the top of the MUSE field in NFM. This is the region modeled
separately (the final vignetting model might be smaller). (int; default: 22). The full name of
this option for the EsoRex configuration file is muse.muse_twilight.vignnfmmask [default = 22].
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_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_wavecal(7)
VERSION
muse_twilight 2.8.7
AUTHOR
Peter Weilbacher <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