Provided by: cpl-plugin-muse-doc_2.8.7+dfsg-3build1_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