Provided by: cpl-plugin-uves-doc_5.3.0+dfsg-2_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
--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].
--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].
--nwindows <long>
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 (long; default: 1). The full name of
this option for the EsoRex configuration file is flames_cal_wavecal.nwindows
[default = 1].
--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].
--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].
--range <long>
Width (pix) of search window is 2*range + 1. This parameter is automatically
adjusted according to binning. (long; default: 8). The full name of this option for
the EsoRex configuration file is flames_cal_wavecal.search.range [default = 8].
--minlines <long>
Minimum number of lines to detect. If zero, the default value (1100 for BLUE/REDL
chips; 1000 for REDU chip) is used. (long; default: 0). The full name of this
option for the EsoRex configuration file is flames_cal_wavecal.search.minlines
[default = 0].
--maxlines <long>
Maximum number of lines to detect. If zero, the default value (1600 for BLUE/REDL
chip; 1400 for REDU chip) is used. (long; default: 0). The full name of this option
for the EsoRex configuration file is flames_cal_wavecal.search.maxlines [default =
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].
--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].
--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].
--degree <long>
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 (long;
default: 4). The full name of this option for the EsoRex configuration file is
flames_cal_wavecal.identify.degree [default = 4].
--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].
--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].
--rebin.wavestep <float>
The bin size (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.scale <bool>
Whether or not to multiply by the factor dx/dlambda (pixels per wavelength) during
the rebinning. This option is disabled as default in concordance with the method
used in the MIDAS pipeline. This option should be set to true to convert the
observed flux (in pixel-space) to a flux per wavelength (in wavelength-space).
(bool; default: False). The full name of this option for the EsoRex configuration
file is flames_cal_wavecal.rebin.scale [default = False].
--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.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.chunk <long>
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). (long; default: 32). The full name of this option for the
EsoRex configuration file is flames_cal_wavecal.extract.chunk [default = 32].
--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].
--extract.oversample <long>
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 (long; default: -1). The full name of this option for the EsoRex configuration
file is flames_cal_wavecal.extract.oversample [default = -1].
--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].
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-5.3.0.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 uves pipeline are uves_cal_response(7),
uves_cal_mflat_combine(7), flames_utl_unpack(7), uves_cal_mkmaster(7),
flames_obs_redchain(7), uves_cal_wavecal(7), uves_cal_tflat(7), uves_cal_mflat(7),
flames_cal_prep_sff_ofpos(7), uves_utl_remove_crh_single(7), uves_obs_scired(7),
uves_cal_mbias(7), uves_utl_ima_arith(7), flames_obs_scired(7), uves_cal_orderpos(7),
flames_cal_mkmaster(7), flames_cal_predict(7), uves_cal_mdark(7), uves_cal_cd_align(7),
uves_obs_redchain(7), flames_cal_orderpos(7), uves_cal_predict(7)
VERSION
flames_cal_wavecal 5.3.0
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