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