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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 <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].

       --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 <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].

       --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].

       --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].

       --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 <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].

       --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].

       --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 <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.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 <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.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].

       --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].

       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-5.9.1.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 5.9.1

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