muse_twilight - Combine several twilight skyflats into one cube,
compute correction factors for each IFU, and create a smooth 3D illumination
correction.
esorex muse_twilight [OPTIONS] FILE.sof
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.
- --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.
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)
Peter Weilbacher <https://support.eso.org>
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>.
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
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