Provided by: cpl-plugin-muse-doc_2.8.5+dfsg-1_all 
NAME
muse_geometry - Compute relative location of the slices within the field of view and
measure the instrumental PSF on the detectors.
SYNOPSIS
esorex muse_geometry [OPTIONS] FILE.sof
DESCRIPTION
Processing first works separately on each IFU of the raw input data (in parallel): it
trims the raw data and records the overscan statistics, subtracts the bias and converts
them from adu to count. Optionally, the dark can be subtracted and the data can be divided
by the flat-field. The data of all input mask exposures is then averaged. The averaged
image together with the trace table and wavelength calibration as well as the line catalog
are used to detect spots. The detection windows are used to measure the spots on all
images of the sequence, the result is saved, with information on the measured PSF, in the
spots tables. Then properties of all slices are computed, first separately on each IFU to
determine the peak position of the mask for each slice and its angle, subsequently the
width and horizontal position. Then, the result of all IFUs is analyzed together to
produce a refined horizontal position, applying global shifts to each IFU as needed. The
vertical position is then determined using the known slice ordering on the sky; the
relative peak positions are put into sequence, taking into account the vertical offsets of
the pinholes in the mask. The table is then cleaned up from intermediate debug data. If
the --smooth parameter is set to a positive value, it is used to do a sigma-clipped
smoothing within each slicer stack, for a more regular appearance of the output table. The
table is then saved. As a last optional step, additional raw input data is reduced using
the newly geometry to produce an image of the field of view. If these exposures contain
smooth features, they can be used as a visual check of the quality of the geometrical
calibration.
OPTIONS
--ifu1 <int>
First IFU to analyze. (int; default: 1). The full name of this option for the
EsoRex configuration file is muse.muse_geometry.ifu1 [default = 1].
--ifu2 <int>
Last IFU to analyze. (int; default: 24). The full name of this option for the
EsoRex configuration file is muse.muse_geometry.ifu2 [default = 24].
--sigma <float>
Sigma detection level for spot detection, in terms of median deviation above the
median. (float; default: 2.2). The full name of this option for the EsoRex
configuration file is muse.muse_geometry.sigma [default = 2.2].
--centroid <str>
Type of centroiding and FWHM determination to use for all spot measurements: simple
barycenter method or using a Gaussian fit. (str; default: ´gaussian´). The full
name of this option for the EsoRex configuration file is
muse.muse_geometry.centroid [default = gaussian].
--smooth <float>
Use this sigma-level cut for smoothing of the output table within each slicer
stack. Set to non-positive value to deactivate smoothing. (float; default: 1.5).
The full name of this option for the EsoRex configuration file is
muse.muse_geometry.smooth [default = 1.5].
--lambdamin <float>
When passing any MASK_CHECK frames in the input, use this lower wavelength cut
before reconstructing the image. (float; default: 6800.0). The full name of this
option for the EsoRex configuration file is muse.muse_geometry.lambdamin [default =
6800.0].
--lambdamax <float>
When passing any MASK_CHECK frames in the input, use this upper wavelength cut
before reconstructing the image. (float; default: 7200.0). The full name of this
option for the EsoRex configuration file is muse.muse_geometry.lambdamax [default =
7200.0].
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-2.8.5.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_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_geometry 2.8.5
AUTHOR
Peter Weilbacher <usd-help@eso.org>
BUG REPORTS
Please report any problems to usd-help@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