Provided by: cpl-plugin-muse-doc_2.8.5+dfsg-1_all 
NAME
muse_wavecal - Detect arc emission lines and determine the wavelength solution for each
slice.
SYNOPSIS
esorex muse_wavecal [OPTIONS] FILE.sof
DESCRIPTION
This recipe detects arc emission lines and fits a wavelength solution to each slice of the
instrument. The wavelength calibration table contains polynomials defining the wavelength
solution of the slices on the CCD. Processing trims the raw data and records the overscan
statistics, subtracts the bias (taking account of the overscan, if --overscan is not
"none") and converts them from adu to count. Optionally, the dark can be subtracted and
the data can be divided by the flat-field, but this is not recommended. The data is then
combined using input parameters, into separate images for each lamp. To compute the
wavelength solution, arc lines are detected at the center of each slice (using threshold
detection on a S/N image) and subsequently assigned wavelengths, using pattern matching to
identify lines from the input line catalog. Each line is then traced to the edges of the
slice, using Gaussian centering in each CCD column. The Gaussians not only yield center,
but also centering error, and line properties (e.g. FWHM). Deviant fits are detected using
polynomial fits to each arc line (using the xorder parameter) and rejected. These analysis
and measuring steps are carried out separately on images exposed by the different arc
lamps, reducing the amount of blending, that can otherwise influence line identification
and Gaussian centering. The final two-dimensional fit uses all positions (of all lamps),
their wavelengths, and the given polynomial orders to compute the final wavelength
solution for each slice, iteratively rejecting outliers. This final fit can be either
unweighted (fitweighting="uniform", for fastest processing) or weighted (other values of
fitweighting, for higher accuracy).
OPTIONS
--nifu <int>
IFU to handle. If set to 0, all IFUs are processed serially. If set to -1, all IFUs
are processed in parallel. (int; default: 0). The full name of this option for the
EsoRex configuration file is muse.muse_wavecal.nifu [default = 0].
--overscan <str>
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma),
for "offset" it assumes that the mean overscan level represents the real offset in
the bias levels of the exposures involved, and adjusts the data accordingly; for
"vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole
quadrant. (str; default: ´vpoly´). The full name of this option for the EsoRex
configuration file is muse.muse_wavecal.overscan [default = vpoly].
--ovscreject <str>
This influences how values are rejected when computing overscan statistics. Either
no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or
rejection using an iterative constant fit ("fit"). (str; default: ´dcr´). The full
name of this option for the EsoRex configuration file is
muse.muse_wavecal.ovscreject [default = dcr].
--ovscsigma <float>
If the deviation of mean overscan levels between a raw input image and the
reference image is higher than |ovscsigma x stdev|, stop the processing. If
overscan="vpoly", this is used as sigma rejection level for the iterative
polynomial fit (the level comparison is then done afterwards with |100 x stdev| to
guard against incompatible settings). Has no effect for overscan="offset". (float;
default: 30.0). The full name of this option for the EsoRex configuration file is
muse.muse_wavecal.ovscsigma [default = 30.0].
--ovscignore <int>
The number of pixels of the overscan adjacent to the data section of the CCD that
are ignored when computing statistics or fits. (int; default: 3). The full name of
this option for the EsoRex configuration file is muse.muse_wavecal.ovscignore
[default = 3].
--combine <str>
Type of lampwise image combination to use. (str; default: ´sigclip´). The full name
of this option for the EsoRex configuration file is muse.muse_wavecal.combine
[default = sigclip].
--lampwise <bool>
Identify and measure the arc emission lines on images separately for each lamp
setup. (bool; default: True). The full name of this option for the EsoRex
configuration file is muse.muse_wavecal.lampwise [default = True].
--sigma <float>
Sigma level used to detect arc emission lines above the median background level in
the S/N image of the central column of each slice (float; default: 1.0). The full
name of this option for the EsoRex configuration file is muse.muse_wavecal.sigma
[default = 1.0].
--dres <float>
The allowed range of resolutions for pattern matching (of detected arc lines to
line list) in fractions relative to the expected value (float; default: 0.05). The
full name of this option for the EsoRex configuration file is
muse.muse_wavecal.dres [default = 0.05].
--tolerance <float>
Tolerance for pattern matching (of detected arc lines to line list) (float;
default: 0.1). The full name of this option for the EsoRex configuration file is
muse.muse_wavecal.tolerance [default = 0.1].
--xorder <int>
Order of the polynomial for the horizontal curvature within each slice (int;
default: 2). The full name of this option for the EsoRex configuration file is
muse.muse_wavecal.xorder [default = 2].
--yorder <int>
Order of the polynomial used to fit the dispersion relation (int; default: 6). The
full name of this option for the EsoRex configuration file is
muse.muse_wavecal.yorder [default = 6].
--linesigma <float>
Sigma level for iterative rejection of deviant fits for each arc line within each
slice, a negative value means to use the default (2.5). (float; default: -1.0).
The full name of this option for the EsoRex configuration file is
muse.muse_wavecal.linesigma [default = -1.0].
--residuals <bool>
Create a table containing residuals of the fits to the data of all arc lines. This
is useful to assess the quality of the wavelength solution in detail. (bool;
default: False). The full name of this option for the EsoRex configuration file is
muse.muse_wavecal.residuals [default = False].
--fitsigma <float>
Sigma level for iterative rejection of deviant datapoints during the final
polynomial wavelength solution within each slice, a negative value means to use the
default (3.0). (float; default: -1.0). The full name of this option for the EsoRex
configuration file is muse.muse_wavecal.fitsigma [default = -1.0].
--fitweighting <str>
Type of weighting to use in the final polynomial wavelength solution fit, using
centroiding error estimate and/or scatter of each single line as estimates of its
accuracy. (str; default: ´cerrscatter´). The full name of this option for the
EsoRex configuration file is muse.muse_wavecal.fitweighting [default =
cerrscatter].
--saveimages <bool>
Save (bool; default: False). The full name of this option for the EsoRex
configuration file is muse.muse_wavecal.saveimages [default = False].
--resample <bool>
Resample the input arc images onto 2D images for a visual check using tracing and
wavelength calibration solutions. Note that the image produced will show small
wiggles even when the calibration was successful! (bool; default: False). The full
name of this option for the EsoRex configuration file is muse.muse_wavecal.resample
[default = False].
--wavemap <bool>
Create a wavelength map of the input images (bool; default: False). The full name
of this option for the EsoRex configuration file is muse.muse_wavecal.wavemap
[default = False].
--merge <bool>
Merge output products from different IFUs into a common file. (bool; default:
False). The full name of this option for the EsoRex configuration file is
muse.muse_wavecal.merge [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-2.8.5.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_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)
VERSION
muse_wavecal 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