muse_wavecal - Detect arc emission lines and determine the
wavelength solution for each slice.
esorex muse_wavecal [OPTIONS] FILE.sof
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).
- --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.
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(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)
Peter Weilbacher <https://support.eso.org>
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>.
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