Provided by: cpl-plugin-muse-doc_2.8.7+dfsg-3_all 
NAME
muse_scipost - Prepare reduced and combined science products.
SYNOPSIS
esorex muse_scipost [OPTIONS] FILE.sof
DESCRIPTION
Sort input pixel tables into lists of files per exposure, merge pixel tables from all IFUs of each
exposure. Correct each exposure for differential atmospheric refraction (unless --lambdaref is far
outside the MUSE wavelength range, or NFM is used which has a built-in corrector). Then the flux
calibration is carried out, if a response curve was given in the input; it includes a correction of
telluric absorption, if a telluric absorption correction file was given. If observations were done with
AO and a RAMAN_LINES file was given, a procedure is run to clean the Raman scattering emission lines from
the data. Next, the slice autocalibration is computed and the flux correction factors are applied to the
pixel table (if --autocalib="deepfield"). If user-provided autocalibration is requested
(--autocalib="user"), then the autocalibration is not computed on the input exposure but the
autocalibration factors are read from the AUTOCAL_FACTORS table and applied directly to the data. Then
the sky subtraction is carried out (unless --skymethod="none"), either directly subtracting an input sky
continuum and an input sky emission lines (for --skymethod="subtract-model"), or (--skymethod="model")
create a sky spectrum from the darkest fraction (--skymodel_fraction, after ignoring the lowest
--skymodel_ignore as artifacts) of the field of view, then fitting and subtracting sky emission lines
using an initial estimate of the input sky lines; then the continuum (residuals after subtracting the sky
lines from the sky spectrum) is subtracted as well. If --save contains "skymodel", all sky-related
products are saved for each exposure. Afterwards the data is corrected for the radial velocity of the
observer (--rvcorr), before the input (or a default) astrometric solution is applied. Now each individual
exposure is fully reduced; the pixel tables at this stage can be saved by setting "individual" in --save.
If multiple exposures were given, they are then combined. If --save contains "combined", this final
merged pixel table is saved. Finally (if --save contains "cube"), the data is resampled into a datacube,
using all parameters given to the recipe. The extent and orientation of the cube is normally computed
from the data itself, but this can be overridden by passing a file with the output world coordinate
system (OUTPUT_WCS), for example a MUSE cube. This can also be used to sample the wavelength axis
logarithmically (in that file set "CTYPE3=´AWAV-LOG´"). As a last step, the computed cube is integrated
over all filter functions given (--filter) that are also present in the input filter list table.
OPTIONS
--save <str>
Select output product(s) to save. Can contain one or more of "cube", "autocal", "skymodel",
"individual", "positioned", "combined", and "stacked". If several options are given, they have to
be comma- separated. ("cube": output cube and associated images, if this is not given, no final
resampling is done at all -- "autocal": up to two additional output products related to the slice
autocalibration -- "raman": up to four additional output products about the Raman light
distribution for AO observations -- "skymodel": up to four additional output products about the
effectively used sky that was subtracted with the "model" method -- "individual": fully reduced
pixel table for each individual exposure -- "positioned": fully reduced and positioned pixel table
for each individual exposure, the difference to "individual" is that here, the output pixel tables
have coordinates in RA and DEC, and the optional offsets were applied; this is only useful, if
both the relative exposure weighting and the final resampling are to be done externally --
"combined": fully reduced and combined pixel table for the full set of exposures, the difference
to "positioned" is that all pixel tables are combined into one, with an added weight column; this
is useful, if only the final resampling step is to be done separately -- "stacked": an additional
output file in form of a 2D column-stacked image, i.e. x direction is pseudo-spatial, y direction
is wavelength.) (str; default: ´cube,skymodel´). The full name of this option for the EsoRex
configuration file is muse.muse_scipost.save [default = cube,skymodel].
--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_scipost.resample [default =
drizzle].
--dx <float>
Horizontal step size for resampling (in arcsec or pixel). The following defaults are taken when
this value is set to 0.0: 0.2´´ for WFM, 0.025´´ for NFM, 1.0 if data is in pixel units. (float;
default: 0.0). The full name of this option for the EsoRex configuration file is
muse.muse_scipost.dx [default = 0.0].
--dy <float>
Vertical step size for resampling (in arcsec or pixel). The following defaults are taken when this
value is set to 0.0: 0.2´´ for WFM, 0.025´´ for NFM, 1.0 if data is in pixel units. (float;
default: 0.0). The full name of this option for the EsoRex configuration file is
muse.muse_scipost.dy [default = 0.0].
--dlambda <float>
Wavelength step size (in Angstrom). Natural instrument sampling is used, if this is 0.0 (float;
default: 0.0). The full name of this option for the EsoRex configuration file is
muse.muse_scipost.dlambda [default = 0.0].
--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_scipost.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: 15.0). The full name of this option for
the EsoRex configuration file is muse.muse_scipost.crsigma [default = 15.0].
--rc <float>
Critical radius for the "renka" resampling method. (float; default: 1.25). The full name of this
option for the EsoRex configuration file is muse.muse_scipost.rc [default = 1.25].
--pixfrac <str>
Pixel down-scaling factor for the "drizzle" resampling method. Up to three, comma-separated,
floating-point values can be given. If only one value is given, it applies to all dimensions, two
values are interpreted as spatial and spectral direction, respectively, while three are taken as
horizontal, vertical, and spectral. (str; default: ´0.8,0.8´). The full name of this option for
the EsoRex configuration file is muse.muse_scipost.pixfrac [default = 0.8,0.8].
--ld <int>
Number of adjacent pixels to take into account during resampling in all three directions (loop
distance); this affects all resampling methods except "nearest". (int; default: 1). The full name
of this option for the EsoRex configuration file is muse.muse_scipost.ld [default = 1].
--format <str>
Type of output file format, "Cube" is a standard FITS cube with NAXIS=3 and multiple extensions
(for data and variance). The extended "x" formats include the reconstructed image(s) in FITS image
extensions within the same file. "sdpCube" does some extra calculations to create FITS keywords
for the ESO Science Data Products. (str; default: ´Cube´). The full name of this option for the
EsoRex configuration file is muse.muse_scipost.format [default = Cube].
--weight <str>
Type of weighting scheme to use when combining multiple exposures. "exptime" just uses the
exposure time to weight the exposures, "fwhm" uses the best available seeing information from the
headers as well, "none" preserves an existing weight column in the input pixel tables without
changes. (str; default: ´exptime´). The full name of this option for the EsoRex configuration file
is muse.muse_scipost.weight [default = exptime].
--filter <str>
The filter name(s) to be used for the output field-of-view image. Each name has to correspond to
an EXTNAME in an extension of the FILTER_LIST file. If an unsupported filter name is given,
creation of the respective image is omitted. If multiple filter names are given, they have to be
comma separated. (str; default: ´white´). The full name of this option for the EsoRex
configuration file is muse.muse_scipost.filter [default = white].
--autocalib <str>
The type of autocalibration to use. "none" switches it off, "deepfield" uses the revised MPDAF
method that can be used for the reduction of mostly empty "Deep Fields", "user" searches for a
user- provided table with autocalibration factors. (str; default: ´none´). The full name of this
option for the EsoRex configuration file is muse.muse_scipost.autocalib [default = none].
--raman_width <float>
Wavelength range around Raman lines [Angstrom]. (float; default: 20.0). The full name of this
option for the EsoRex configuration file is muse.muse_scipost.raman_width [default = 20.0].
--skymethod <str>
The method used to subtract the sky background (spectrum). Option "model" should work in all kinds
of science fields: it uses a global sky spectrum model with a local LSF. "model" uses fluxes
indicated in the SKY_LINES file as starting estimates, but re-fits them on the global sky spectrum
created from the science exposure. If SKY_CONTINUUM is given, it is directly subtracted, otherwise
it is created from the sky region of the science exposure. Option "subtract- model" uses the input
SKY_LINES and SKY_CONTINUUM, subtracting them directly without re-fitting the fluxes, but still
makes use of the local LSF, hence LSF_PROFILE is required. The inputs LSF_PROFILE and SKY_LINES
are necessary for these two model-based methods; SKY_CONTINUUM is required for "subtract-model"
and optional for "model"; SKY_MASK is optional for "model". Finally, option "simple" creates a sky
spectrum from the science data, and directly subtracts it, without taking the LSF into account
(LSF_PROFILE and input SKY files are ignored). It works on data that was not flux calibrated.
(str; default: ´model´). The full name of this option for the EsoRex configuration file is
muse.muse_scipost.skymethod [default = model].
--lambdamin <float>
Cut off the data below this wavelength after loading the pixel table(s). (float; default: 4000.0).
The full name of this option for the EsoRex configuration file is muse.muse_scipost.lambdamin
[default = 4000.0].
--lambdamax <float>
Cut off the data above this wavelength after loading the pixel table(s). (float; default:
10000.0). The full name of this option for the EsoRex configuration file is
muse.muse_scipost.lambdamax [default = 10000.0].
--lambdaref <float>
Reference wavelength used for correction of differential atmospheric refraction. The R-band (peak
wavelength ~7000 Angstrom) that is usually used for guiding, is close to the central wavelength of
MUSE, so a value of 7000.0 Angstrom should be used if nothing else is known. A value less than
zero switches DAR correction off. (float; default: 7000.0). The full name of this option for the
EsoRex configuration file is muse.muse_scipost.lambdaref [default = 7000.0].
--darcheck <str>
Carry out a check of the theoretical DAR correction using source centroiding. If "correct" it will
also apply an empirical correction. (str; default: ´none´). The full name of this option for the
EsoRex configuration file is muse.muse_scipost.darcheck [default = none].
--skymodel_fraction <float>
Fraction of the image (without the ignored part) to be considered as sky. If an input sky mask is
provided, the fraction is applied to the regions within the mask. If the whole sky mask should be
used, set this parameter to 1. (float; default: 0.1). The full name of this option for the EsoRex
configuration file is muse.muse_scipost.skymodel_fraction [default = 0.1].
--skymodel_ignore <float>
Fraction of the image to be ignored. If an input sky mask is provided, the fraction is applied to
the regions within the mask. If the whole sky mask should be used, set this parameter to 0.
(float; default: 0.05). The full name of this option for the EsoRex configuration file is
muse.muse_scipost.skymodel_ignore [default = 0.05].
--skymodel_sampling <float>
Spectral sampling of the sky spectrum [Angstrom]. (float; default: 0.3125). The full name of this
option for the EsoRex configuration file is muse.muse_scipost.skymodel_sampling [default =
0.3125].
--skymodel_csampling <float>
Spectral sampling of the continuum spectrum [Angstrom]. (float; default: 0.3125). The full name of
this option for the EsoRex configuration file is muse.muse_scipost.skymodel_csampling [default =
0.3125].
--sky_crsigma <str>
Sigma level clipping for cube-based and spectrum-based CR rejection when creating the sky
spectrum. This has to be a string of two comma- separated floating-point numbers. The first value
gives the sigma- level rejection for cube-based CR rejection (using "median"), the second value
the sigma-level for spectrum-based CR cleaning. Both can be switched off, by passing zero or a
negative value. (str; default: ´15.,15.´). The full name of this option for the EsoRex
configuration file is muse.muse_scipost.sky_crsigma [default = 15.,15.].
--rvcorr <str>
Correct the radial velocity of the telescope with reference to either the barycenter of the Solar
System (bary), the center of the Sun (helio), or to the center of the Earth (geo). (str; default:
´bary´). The full name of this option for the EsoRex configuration file is
muse.muse_scipost.rvcorr [default = bary].
--astrometry <bool>
If false, skip any astrometric calibration, even if one was passed in the input set of files. This
causes creation of an output cube with a linear WCS and may result in errors. If you want to use a
sensible default, leave this true but do not pass an ASTROMETRY_WCS. (bool; default: True). The
full name of this option for the EsoRex configuration file is muse.muse_scipost.astrometry
[default = True].
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_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_scipost 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