SYNOPSIS

esorex flames_cal_orderpos [OPTIONS] FILE.sof

DESCRIPTION

The recipe defines the simultaneus calibration fibre order positions in a fibre-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 simultaneous calibration fibre flat fields, FIB_ORDEF_RED and optionally for each chip a DRS setup table, DRS_TABLE_(REDL|REDU), for backward compatibility, and optionally a guess order table
 FIB_ORD_GUE_(REDL|REDU) and a master bias, MASTER_BIAS_(REDL|REDU).

The recipe processes only the first raw frame found.

Output are two order tables FIB_ORD_TAB_(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) and 2 images frames FIB_ORDEF_(REDL|REDU)

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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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 flames_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.

VERSION

flames_cal_orderpos 5.7.0

AUTHOR

Jonas M. Larsen <[email protected]>

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