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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-2.6.2.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 <firstname.lastname@example.org>
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This file is part of the MUSE Instrument Pipeline Copyright (C) 2005, 2018 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