Provided by: cpl-plugin-uves-doc_6.1.8+dfsg-2build3_all 
NAME
flames_cal_orderpos - Defines uves-echelle-simultaneous calibration fibre order positions
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
--backsubdegx <int>
Degree (in x) of polynomial used to estimate the background (mode=poly). (int; default: 2). The
full name of this option for the EsoRex configuration file is
flames_cal_orderpos.preproc.backsubdegx [default = 2].
--backsubdegy <int>
Degree (in y) of polynomial used to estimate the background (mode=poly). (int; default: 2). The
full name of this option for the EsoRex configuration file is
flames_cal_orderpos.preproc.backsubdegy [default = 2].
--backsubgrid <int>
Number of grid points (in x- and y-direction) used to estimate the background (mode=poly). (int;
default: 50). The full name of this option for the EsoRex configuration file is
flames_cal_orderpos.preproc.backsubgrid [default = 50].
--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].
--backsubradiusy <int>
The height (in pixels) of the background sampling window is (2*radiusy + 1). This parameter is not
corrected for binning. (int; default: 2). The full name of this option for the EsoRex
configuration file is flames_cal_orderpos.preproc.backsubradiusy [default = 2].
--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].
--defpol1 <int>
The degree of the bivarite fit (cross dispersion direction). If negative, the degree is optimized
to give the best fit (int; default: -1). The full name of this option for the EsoRex configuration
file is flames_cal_orderpos.reject.defpol1 [default = -1].
--defpol2 <int>
The degree of the bivarite fit (order number). If negative, the degree is optimized to give the
best fit (int; 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].
--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].
--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].
--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].
--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].
--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].
--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].
--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].
--radx <int>
Half X size of median filtering window (int; default: 2). The full name of this option for the
EsoRex configuration file is flames_cal_orderpos.preproc.radx [default = 2].
--rady <int>
Half Y size of median filtering window (int; default: 1). The full name of this option for the
EsoRex configuration file is flames_cal_orderpos.preproc.rady [default = 1].
--samplewidth <int>
Separation of sample traces (used by Hough transform) in input image (int; default: 50). The full
name of this option for the EsoRex configuration file is flames_cal_orderpos.hough.samplewidth
[default = 50].
--sloperes <int>
Resolution (width in pixels) of Hough space (int; default: 120). The full name of this option for
the EsoRex configuration file is flames_cal_orderpos.hough.sloperes [default = 120].
--tracestep <int>
The step size used when tracing the orders (int; default: 10). The full name of this option for
the EsoRex configuration file is flames_cal_orderpos.trace.tracestep [default = 10].
--use_guess_tab <int>
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 (int;
default: 1). The full name of this option for the EsoRex configuration file is
flames_cal_orderpos.preproc.use_guess_tab [default = 1].
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_predict(7),
flames_cal_prep_sff_ofpos(7), flames_cal_wavecal(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_orderpos 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
flames_cal_orderpos 6.1.8 FLAMES_CAL_ORDERPOS(7)