Provided by: cpl-plugin-uves-doc_5.3.0+dfsg-2_all bug

NAME

       uves_cal_orderpos - Defines echelle order positions

SYNOPSIS

       esorex uves_cal_orderpos [OPTIONS] FILE.sof

DESCRIPTION

       The recipe defines the order positions in an echelle image. The orders are initially
       detected by means of a Hough transformation, the orders are then traced, and the positions
       are finally fitted with a global polynomial.

       Expected input frames are narrow flat fields, ORDER_FLAT_xxx, or standard stars,
       STANDARD_xxx, where xxx is ´BLUE´ or ´RED´, and optionally for each chip a DRS setup table
       (DRS_TABLE_BLUE, DRS_TABLE_REDL, DRS_TABLE_REDU) or guess order table
       (ORDER_GUESS_TAB_BLUE, ORDER_GUESS_TAB_REDL, ORDER_GUESS_TAB_REDU, or, for backward
       compatibility, ORDER_TABLE_BLUE, ORDER_TABLE_REDL, ORDER_TABLE_REDU). The recipe processes
       only the first raw frame found.

       Output is one (or two if input is a red frame) order table(s) (UVES:
       ORDER_TABLE_(BLUE|REDL|REDU); FLAMES: FIB_ORDEF_(REDL|REDU) contaning the columns: X
       : Position along x Order            : Relative order number Y                : Order line
       centroid location Yfit             : The fitted order location dY               :
       Uncertainty of Y dYfit_Square     : Variance of Yfit Residual         : Y - Yfit
       Residual_Square  : Residual^2 OrderRMS         : Root mean squared residual of initial
                          one-dimensional linear fit of order

       The bivariate fit polynomial itself is stored in table extension no. 2.

       The 3rd table extension contains a table that defines the active fibre traces and their
       positions (for support of FLAMES/UVES)

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].

       --use_guess_tab <long>
              If a Guess order table is provided this parameter set how it is used:0: No usage,
              1: use it to set lower/upper Y raws where order are searched 2: the order table try
              to fully match the guess (long; default: 1). The full name of this option for the
              EsoRex configuration file is uves_cal_orderpos.preproc.use_guess_tab [default = 1].

       --radx <long>
              Half X size of median filtering window (long; default: 2). The full name of this
              option for the EsoRex configuration file is uves_cal_orderpos.preproc.radx [default
              = 2].

       --rady <long>
              Half Y size of median filtering window (long; default: 1). The full name of this
              option for the EsoRex configuration file is uves_cal_orderpos.preproc.rady [default
              = 1].

       --mmethod <str>
              Background subtraction method. If equal to ´median´ the background is sampled using
              the median of a sub-window. If ´minimum´, the minimum sub-window value is used. If
              ´no´, no background subtraction is done.  (str; default: ´median´). The full name
              of this option for the EsoRex configuration file is
              uves_cal_orderpos.preproc.mmethod [default = median].

       --backsubgrid <long>
              Number of grid points (in x- and y-direction) used to estimate the background
              (mode=poly). (long; default: 50). The full name of this option for the EsoRex
              configuration file is uves_cal_orderpos.preproc.backsubgrid [default = 50].

       --backsubradiusy <long>
              The height (in pixels) of the background sampling window is (2*radiusy + 1). This
              parameter is not corrected for binning. (long; default: 2). The full name of this
              option for the EsoRex configuration file is
              uves_cal_orderpos.preproc.backsubradiusy [default = 2].

       --backsubkappa <float>
              The value of kappa in the one-sided kappa-sigma clipping used to estimate the
              background (mode=poly). (float; default: 4.0). The full name of this option for the
              EsoRex configuration file is uves_cal_orderpos.preproc.backsubkappa [default =
              4.0].

       --backsubdegx <long>
              Degree (in x) of polynomial used to estimate the background (mode=poly). (long;
              default: 2). The full name of this option for the EsoRex configuration file is
              uves_cal_orderpos.preproc.backsubdegx [default = 2].

       --backsubdegy <long>
              Degree (in y) of polynomial used to estimate the background (mode=poly). (long;
              default: 2). The full name of this option for the EsoRex configuration file is
              uves_cal_orderpos.preproc.backsubdegy [default = 2].

       --samplewidth <long>
              Separation of sample traces (used by Hough transform) in input image (long;
              default: 50). The full name of this option for the EsoRex configuration file is
              uves_cal_orderpos.hough.samplewidth [default = 50].

       --minslope <float>
              Minimum possible line slope. This should be the ´physical´ slope on the chip, i.e.
              not taking binning factors into account, which is handled by the recipe (float;
              default: 0.0). The full name of this option for the EsoRex configuration file is
              uves_cal_orderpos.hough.minslope [default = 0.0].

       --maxslope <float>
              Maximum possible line slope (float; default: 0.2). The full name of this option for
              the EsoRex configuration file is uves_cal_orderpos.hough.maxslope [default = 0.2].

       --sloperes <long>
              Resolution (width in pixels) of Hough space (long; default: 120). The full name of
              this option for the EsoRex configuration file is uves_cal_orderpos.hough.sloperes
              [default = 120].

       --pthres <float>
              In automatic mode, or if the number of orders to detect is read from a guess table,
              the detection of new lines stops when the intensity of a candidate line drops to
              less than ´pthres´ times the intensity of the previous detection.  (float; default:
              0.2). The full name of this option for the EsoRex configuration file is
              uves_cal_orderpos.hough.pthres [default = 0.2].

       --tracestep <long>
              The step size used when tracing the orders (long; default: 10). The full name of
              this option for the EsoRex configuration file is uves_cal_orderpos.trace.tracestep
              [default = 10].

       --minthresh <float>
              The minimum threshold value is (min + minthres*(max - min)). Here ´min´ and ´max´
              are the lowest and highest pixel values in the central bin of the order (float;
              default: 0.2). The full name of this option for the EsoRex configuration file is
              uves_cal_orderpos.trace.minthresh [default = 0.2].

       --maxgap <float>
              If the order line drops below detection threshold, the order tracing algorithm will
              try to jump a gap of maximum size ´maxgap´ multiplied by the image width (float;
              default: 0.2). The full name of this option for the EsoRex configuration file is
              uves_cal_orderpos.trace.maxgap [default = 0.2].

       --maxrms <float>
              When fitting the orders with straight lines, this is the maximum allowed RMS
              relative to the median RMS of all orders (float; default: 100.0). The full name of
              this option for the EsoRex configuration file is uves_cal_orderpos.reject.maxrms
              [default = 100.0].

       --defpol1 <long>
              The degree of the bivarite fit (cross dispersion direction). If negative, the
              degree is optimized to give the best fit (long; default: -1). The full name of this
              option for the EsoRex configuration file is uves_cal_orderpos.reject.defpol1
              [default = -1].

       --defpol2 <long>
              The degree of the bivarite fit (order number). If negative, the degree is optimized
              to give the best fit (long; default: -1). The full name of this option for the
              EsoRex configuration file is uves_cal_orderpos.reject.defpol2 [default = -1].

       --kappa <float>
              Used for kappa-sigma clipping of the final polynomial fit. If negative, no clipping
              is done (float; default: 4.0). The full name of this option for the EsoRex
              configuration file is uves_cal_orderpos.reject.kappa [default = 4.0].

       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), flames_cal_wavecal(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),
       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

       uves_cal_orderpos 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