Provided by: cpl-plugin-uves-doc_6.1.8+dfsg-2build3_all 
NAME
flames_cal_wavecal - Performs the wavelength calibration
SYNOPSIS
esorex flames_cal_wavecal [OPTIONS] FILE.sof
DESCRIPTION
The recipe performs a wavelength calibration for each extraction window.
Conceptually, each chip contains a number of order lines, each of which contains a number of fibre
traces, each of which contains a number of extraction windows. For FLAMES/UVES data there are multiple
traces per order but only one extraction window per trace.
The number of traces is defined in the order table while the geometry of the extraction windows is
specified by recipe parameters (see below).
Expected input for this recipe is an arc lamp frame, FIB_ARC_LAMP_RED, FIB_ORDEF_TABLE_(REDL|REDU),
´guess´ line table(s) for each chip, FIB_LIN_GUE_(REDL|REDU), a wavelength catalogue table,
LINE_REFER_TABLE, and optionally a wavelength table of bright lines, LINE_INTMON_TABLE, used only for
computing Quality Control parameters.
The output line table(s), FIB_LINE_TABLE_(REDL|REDU), contains the columns X : Horizontal
position (from Gaussian fit) of detected line dX : Uncertainty (one sigma) of X Ynew :
Vertical position of detected line XWidth : Width (in pixels) of detected line from Gaussian fit
Peak : Intensity of detected line Background : Fitted background (ADU) of detected line Slope
: Linear background slope (ADU/pixel) of detected line
from Gaussian fit Intensity : Intensity of detected line scaled to unit exposure
time. (This column only present if a LINE_INTMON_TABLE
is provided.) Order : Absolute order number of detected line Y :
Relative order number of detected line
(it´s not a very descriptive column name) WaveC : Wavelength of this line (computed
using the resulting
dispersion relation) dLambdaC : Uncertainty (one sigma) of ´WaveC´.
Pixel : The width in w.l.u. of a pixel (computed locally).
Residual : Residual (in w.l.u.) of this line Residual_pix : Residual (in pixels) of this line
Lambda_candidate : Nearest line in catalogue dLambda_cat_sq : Squared distance to nearest catalogue
line dLambda_nn_sq : Squared distance to nearest neighbour multiplied by ALPHA Ident : The
wavelength associated with this emission line,
or invalid if this line was not identified dIdent : Uncertainty of catalogue
wavelength Select : 1 if the line was identified, 0 otherwise NLinSol : 1 if the line was
identified and accepted for the
polynomial fit, 0 otherwise Intensity : Intensity of detected line scaled to unit
exposure
time. (This column is present only if a LINE_INTMON_TABLE
is provided.)
The 2nd table extension contains the dispersion relation (a 2d polynomial).
The 3rd table extension contains the map from (pixel, pixel)-space to
physical order numbers (used internally by the calibration recipe; another 2d polynomial).
If there is more than one extraction window, the results of each calibration is stored in subsequent
table extensions of the same FITS file. For example, extensions 4, 5 and 6 would contain the resulting
line table (and its two associated polynomials) for the second extraction window. The results for the
calibration of the n´th extraction window is stored in extensions (3*n - 2) to 3*n.
OPTIONS
--alpha <float>
The parameter that controls the distance to the nearest neighbours (float; default: 0.1). The full
name of this option for the EsoRex configuration file is flames_cal_wavecal.identify.alpha
[default = 0.1].
--debug <bool>
Whether or not to save intermediate results to local directory (bool; default: False). The full
name of this option for the EsoRex configuration file is uves.debug [default = False].
--degree <int>
Degrees of the global 2d dispersion polynomial. If a negative number is specified, the polynomial
degrees are automatically selected by starting from (1, 1) and inreasing the degrees as long as
the RMS residual decreases significantly (int; default: 4). The full name of this option for the
EsoRex configuration file is flames_cal_wavecal.identify.degree [default = 4].
--extract.best <bool>
(optimal extraction only) If false (fastest), the spectrum is extracted only once. If true (best),
the spectrum is extracted twice, the second time using improved variance estimates based on the
first iteration. Better variance estimates slightly improve the obtained signal to noise but at
the cost of increased execution time (bool; default: True). The full name of this option for the
EsoRex configuration file is flames_cal_wavecal.extract.best [default = True].
--extract.chunk <int>
In optimal extraction mode, the chunk size (in pixels) used for fitting the analytical profile (a
fit of the analytical profile to single bins would suffer from low statistics). (int; default:
32). The full name of this option for the EsoRex configuration file is
flames_cal_wavecal.extract.chunk [default = 32].
--extract.kappa <float>
In optimal extraction mode, this is the threshold for bad (i.e. hot/cold) pixel rejection. If a
pixel deviates more than kappa*sigma (where sigma is the uncertainty of the pixel flux) from the
inferred spatial profile, its weight is set to zero. Range: [-1,100]. If this parameter is
negative, no rejection is performed. (float; default: 10.0). The full name of this option for the
EsoRex configuration file is flames_cal_wavecal.extract.kappa [default = 10.0].
--extract.method <str>
Extraction method. (2d/optimal not supported by uves_cal_wavecal, weighted supported only by
uves_cal_wavecal, 2d not supported by uves_cal_response) (str; default: ´average´). The full name
of this option for the EsoRex configuration file is flames_cal_wavecal.extract.method [default =
average].
--extract.oversample <int>
The oversampling factor used for the virtual resampling algorithm. If negative, the value 5 is
used for S/N <=200, and the value 10 is used if the estimated S/N is > 200 (int; default: -1). The
full name of this option for the EsoRex configuration file is
flames_cal_wavecal.extract.oversample [default = -1].
--extract.profile <str>
In optimal extraction mode, the kind of profile to use. ´gauss´ gives a Gaussian profile, ´moffat´
gives a Moffat profile with beta=4 and a possible linear sky contribution. ´virtual´ uses a
virtual resampling algorithm (i.e. measures and uses the actual object profile). ´constant´
assumes a constant spatial profile and allows optimal extraction of wavelength calibration frames.
´auto´ will automatically select the best method based on the estimated S/N of the object. For low
S/N, ´moffat´ or ´gauss´ are recommended (for robustness). For high S/N, ´virtual´ is recommended
(for accuracy). In the case of virtual resampling, a precise determination of the order positions
is required; therefore the order-definition is repeated using the (assumed non-low S/N) science
frame (str; default: ´auto´). The full name of this option for the EsoRex configuration file is
flames_cal_wavecal.extract.profile [default = auto].
--extract.skymethod <str>
In optimal extraction mode, the sky subtraction method to use. ´median´ estimates the sky as the
median of pixels along the slit (ignoring pixels close to the object), whereas ´optimal´ does a
chi square minimization along the slit to obtain the best combined object and sky levels. The
optimal method gives the most accurate sky determination but is also a bit slower than the median
method (str; default: ´optimal´). The full name of this option for the EsoRex configuration file
is flames_cal_wavecal.extract.skymethod [default = optimal].
--kappa <float>
Lines with residuals more then kappa stdev are rejected from the final fit (float; default: 4.0).
The full name of this option for the EsoRex configuration file is
flames_cal_wavecal.calibrate.kappa [default = 4.0].
--length <float>
Length (in pixels) of each extraction window. This parameter is also equal to the seperation of
adjacent window centers, causing the extraction windows to always be aligned. The parameter is
automatically adjusted according to the binning of the input raw frame. If negative, the
extraction window length is determined automatically to cover the full slit (float; default: 7.0).
The full name of this option for the EsoRex configuration file is flames_cal_wavecal.length
[default = 7.0].
--maxerror <float>
This parameter controls the graceful exit of the identification loop. If the RMS of the global
fit exceeds this value (pix) the iteration stops (float; default: 20.0). The full name of this
option for the EsoRex configuration file is flames_cal_wavecal.identify.maxerror [default = 20.0].
--maxlines <int>
Maximum number of lines to detect. If zero, the default value (1600 for BLUE/REDL chip; 1400 for
REDU chip) is used. (int; default: 0). The full name of this option for the EsoRex configuration
file is flames_cal_wavecal.search.maxlines [default = 0].
--minlines <int>
Minimum number of lines to detect. If zero, the default value (1100 for BLUE/REDL chips; 1000 for
REDU chip) is used. (int; default: 0). The full name of this option for the EsoRex configuration
file is flames_cal_wavecal.search.minlines [default = 0].
--nwindows <int>
Number of extraction windows per trace. The windows will be aligned (i.e. no overlap and no
spacing between adjacent windows). Unless an offset is specified, the middle window(s) is centered
on the trace (int; default: 1). The full name of this option for the EsoRex configuration file is
flames_cal_wavecal.nwindows [default = 1].
--offset <float>
A global offset (in pixels) of all extraction windows (float; default: 0.0). The full name of this
option for the EsoRex configuration file is flames_cal_wavecal.offset [default = 0.0].
--plotter <str>
Any plots produced by the recipe are redirected to the command specified by this parameter. The
plotting command must contain the substring ´gnuplot´ and must be able to parse gnuplot syntax on
its standard input. Valid examples of such a command may include ´gnuplot -persist´ and ´cat >
mygnuplot$$.gp´. A finer control of the plotting options can be obtained by writing an executable
script, e.g. my_gnuplot.pl, that executes gnuplot after setting the desired gnuplot options (e.g.
set terminal pslatex color). To turn off plotting, set this parameter to ´no´ (str; default:
´no´). The full name of this option for the EsoRex configuration file is uves.plotter [default =
no].
--process_chip <str>
For RED arm data process the redl, redu, or both chip(s) (str; default: ´both´). The full name of
this option for the EsoRex configuration file is uves.process_chip [default = both].
--range <int>
Width (pix) of search window is 2*range + 1. This parameter is automatically adjusted according to
binning. (int; default: 8). The full name of this option for the EsoRex configuration file is
flames_cal_wavecal.search.range [default = 8].
--rebin.scale <bool>
Whether or not to multiply by the factor dx/dlambda (pixels per wavelength) during the rebinning
to conserve the flux. This option is disabled as default because applying the flat field
correction already ensures flux conservation. Therefore this parameter should be TRUE (for
response and science data) only if reduce.ffmethd = no. (bool; default: False). The full name of
this option for the EsoRex configuration file is flames_cal_wavecal.rebin.scale [default = False].
--rebin.wavestep <float>
The bin size used for BLUE/REDL data (in w.l.u.) in wavelength space. If negative, a step size of
2/3 * ( average pixel size ) is used. (float; default: -1.0). The full name of this option for
the EsoRex configuration file is flames_cal_wavecal.rebin.wavestep [default = -1.0].
--rebin.wavestep_redu <float>
The bin size used for REDU data (in w.l.u.) in wavelength space. If negative, a step size of 2/3 *
( average pixel size ) is used. (float; default: -1.0). The full name of this option for the
EsoRex configuration file is flames_cal_wavecal.rebin.wavestep_redu [default = -1.0].
--shiftmax <float>
The maximum shift (pix) in either direction compared to guess solution. This parameter is
automatically corrected for binning (float; default: 10.0). The full name of this option for the
EsoRex configuration file is flames_cal_wavecal.first.shiftmax [default = 10.0].
--shiftstep <float>
The step size (pix) used when searching for the optimum shift. This parameter is automatically
corrected for binning (float; default: 0.1). The full name of this option for the EsoRex
configuration file is flames_cal_wavecal.first.shiftstep [default = 0.1].
--shifttoler <float>
Tolerance (pix) when matching shifted lines. This parameter is not adjusted according to binning
(float; default: 0.05). The full name of this option for the EsoRex configuration file is
flames_cal_wavecal.first.shifttoler [default = 0.05].
--tolerance <float>
Tolerance of fit. If positive, the tolerance is in pixel units. If negative, abs(tolerance) is in
wavelength units. Lines with residuals worse than the tolerance are excluded from the final fit.
Unlike in previous versions, this parameter is not corrected for CCD binning. This rejection
based on the absolute residual in pixel can be effectively disabled by setting the tolerance to a
very large number (e.g. 9999). In that case outliers will be rejected using only kappa sigma
clipping. (float; default: 0.6). The full name of this option for the EsoRex configuration file is
flames_cal_wavecal.calibrate.tolerance [default = 0.6].
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 uves pipeline can be downloaded as a PDF file using the following URL:
ftp://ftp.eso.org/pub/dfs/pipelines/uves/uves-pipeline-manual-6.1.8.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 uves pipeline are flames_cal_mkmaster(7), flames_cal_orderpos(7),
flames_cal_predict(7), flames_cal_prep_sff_ofpos(7), flames_obs_redchain(7), flames_obs_scired(7),
flames_utl_unpack(7), uves_cal_cd_align(7), uves_cal_mbias(7), uves_cal_mdark(7), uves_cal_mflat(7),
uves_cal_mflat_combine(7), uves_cal_mkmaster(7), uves_cal_orderpos(7), uves_cal_predict(7),
uves_cal_response(7), uves_cal_tflat(7), uves_cal_wavecal(7), uves_obs_redchain(7), uves_obs_scired(7),
uves_utl_ima_arith(7), uves_utl_remove_crh_single(7)
VERSION
flames_cal_wavecal 6.1.8
AUTHOR
Jonas M. Larsen <cpl@eso.org>
BUG REPORTS
Please report any problems to cpl@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 FLAMES/UVES Pipeline Copyright (C) 2004, 2005, 2006, 2007 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