Provided by: cpl-plugin-muse-doc_2.2+dfsg-2_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-2.2.0.pdf
An overview over the existing ESO pipelines can be found on the web page
http://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
http://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_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_subtract_sky(7),
muse_scipost_subtract_sky_simple(7), muse_standard(7), muse_twilight(7), muse_wavecal(7)
VERSION
muse_geometry 2.2.0
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, 2017 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