Provided by: cpl-plugin-muse-doc_2.8.7+dfsg-3_all 
NAME
muse_exp_align - Create a coordinate offset table to be used to align exposures during exposure
combination.
SYNOPSIS
esorex muse_exp_align [OPTIONS] FILE.sof
DESCRIPTION
Compute the coordinate offset for each input field-of-view image with respect to a reference. The created
list of coordinate offsets can then be used in muse_exp_combine as the field coordinate offsets to
properly align the exposures during their combination. The source positions used to compute the field
offsets are obtained by detecting point sources in each of the input images, unless the source detection
is overridden and an input source list is available for each input field-of-view image. In this latter
case the input source positions are used to calculate the field offsets.
OPTIONS
--rsearch <str>
Search radius (in arcsec) for each iteration of the offset computation. (str; default:
´30.,4.,2.,0.8´). The full name of this option for the EsoRex configuration file is
muse.muse_exp_align.rsearch [default = 30.,4.,2.,0.8].
--nbins <int>
Number of bins to use for 2D histogram on the first iteration of the offset computation. (int;
default: 60). The full name of this option for the EsoRex configuration file is
muse.muse_exp_align.nbins [default = 60].
--weight <bool>
Use weighting. (bool; default: True). The full name of this option for the EsoRex configuration
file is muse.muse_exp_align.weight [default = True].
--fwhm <float>
FWHM in pixels of the convolution filter. (float; default: 5.0). The full name of this option for
the EsoRex configuration file is muse.muse_exp_align.fwhm [default = 5.0].
--threshold <float>
Initial intensity threshold for detecting point sources. If the value is negative or zero the
threshold is taken as sigma above median background MAD. If it is larger than zero the threshold
is taken as absolute background level. (float; default: 15.0). The full name of this option for
the EsoRex configuration file is muse.muse_exp_align.threshold [default = 15.0].
--bkgignore <float>
Fraction of the image to be ignored. (float; default: 0.05). The full name of this option for the
EsoRex configuration file is muse.muse_exp_align.bkgignore [default = 0.05].
--bkgfraction <float>
Fraction of the image (without the ignored part) to be considered as background. (float; default:
0.1). The full name of this option for the EsoRex configuration file is
muse.muse_exp_align.bkgfraction [default = 0.1].
--step <float>
Increment/decrement of the threshold value in subsequent iterations. (float; default: 0.5). The
full name of this option for the EsoRex configuration file is muse.muse_exp_align.step [default =
0.5].
--iterations <int>
Maximum number of iterations used for detecting sources. (int; default: 100000). The full name of
this option for the EsoRex configuration file is muse.muse_exp_align.iterations [default =
100000].
--srcmin <int>
Minimum number of sources which must be found. (int; default: 5). The full name of this option for
the EsoRex configuration file is muse.muse_exp_align.srcmin [default = 5].
--srcmax <int>
Maximum number of sources which may be found. (int; default: 80). The full name of this option for
the EsoRex configuration file is muse.muse_exp_align.srcmax [default = 80].
--roundmin <float>
Lower limit of the allowed point-source roundness. (float; default: -1.0). The full name of this
option for the EsoRex configuration file is muse.muse_exp_align.roundmin [default = -1.0].
--roundmax <float>
Upper limit of the allowed point-source roundness. (float; default: 1.0). The full name of this
option for the EsoRex configuration file is muse.muse_exp_align.roundmax [default = 1.0].
--sharpmin <float>
Lower limit of the allowed point-source sharpness. (float; default: 0.2). The full name of this
option for the EsoRex configuration file is muse.muse_exp_align.sharpmin [default = 0.2].
--sharpmax <float>
Upper limit of the allowed point-source sharpness. (float; default: 1.0). The full name of this
option for the EsoRex configuration file is muse.muse_exp_align.sharpmax [default = 1.0].
--expmap <bool>
Enables the creation of a simple exposure map for the combined field- of-view. (bool; default:
False). The full name of this option for the EsoRex configuration file is
muse.muse_exp_align.expmap [default = False].
--bpixdistance <float>
Minimum allowed distance of a source to the closest bad pixel in pixel. Detected sources which are
closer to a bad pixel are not taken into account when computing the field offsets. This option has
no effect if the source positions are taken from input catalogs. (float; default: 5.0). The full
name of this option for the EsoRex configuration file is muse.muse_exp_align.bpixdistance [default
= 5.0].
--override_detection <bool>
Overrides the source detection step. If this is enabled and source catalogs are present in the
input data set, the source positions used to calculate the field offsets are read from the input
catalogs. If no catalogs are available as input data the source positions are detected on the
input images. (bool; default: False). The full name of this option for the EsoRex configuration
file is muse.muse_exp_align.override_detection [default = False].
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_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_twilight(7), muse_wavecal(7)
VERSION
muse_exp_align 2.8.7
AUTHOR
Ralf Palsa <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