--- name: "flames_cal_orderpos" section: "7" platform: "linux" package: "cpl-plugin-uves-doc" version: "6.1.8+dfsg-2" release: "Debian 12 (Bookworm)" platforms: ["linux"] url: "https://new.carta.tech/flames_cal_orderpos" --- # flames\_cal\_orderpos(7) Defines uves-echelle-simultaneous calibration fibre order positions ## 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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_mkmaster/7.md), [*flames\_cal\_predict*(7)](/flames_cal_predict/7.md), [*flames\_cal\_prep\_sff\_ofpos*(7)](/flames_cal_prep_sff_ofpos/7.md), [*flames\_cal\_wavecal*(7)](/flames_cal_wavecal/7.md), [*flames\_obs\_redchain*(7)](/flames_obs_redchain/7.md), [*flames\_obs\_scired*(7)](/flames_obs_scired/7.md), [*flames\_utl\_unpack*(7)](/flames_utl_unpack/7.md), [*uves\_cal\_cd\_align*(7)](/uves_cal_cd_align/7.md), [*uves\_cal\_mbias*(7)](/uves_cal_mbias/7.md), [*uves\_cal\_mdark*(7)](/uves_cal_mdark/7.md), [*uves\_cal\_mflat*(7)](/uves_cal_mflat/7.md), [*uves\_cal\_mflat\_combine*(7)](/uves_cal_mflat_combine/7.md), [*uves\_cal\_mkmaster*(7)](/uves_cal_mkmaster/7.md), [*uves\_cal\_orderpos*(7)](/uves_cal_orderpos/7.md), [*uves\_cal\_predict*(7)](/uves_cal_predict/7.md), [*uves\_cal\_response*(7)](/uves_cal_response/7.md), [*uves\_cal\_tflat*(7)](/uves_cal_tflat/7.md), [*uves\_cal\_wavecal*(7)](/uves_cal_wavecal/7.md), [*uves\_obs\_redchain*(7)](/uves_obs_redchain/7.md), [*uves\_obs\_scired*(7)](/uves_obs_scired/7.md), [*uves\_utl\_ima\_arith*(7)](/uves_utl_ima_arith/7.md), [*uves\_utl\_remove\_crh\_single*(7)](/uves_utl_remove_crh_single/7.md) ## VERSION flames\_cal\_orderpos 6.1.8 ## AUTHOR Jonas M. Larsen \ ## BUG REPORTS Please report any problems to cpl@eso.org. Alternatively, you may send a report to the ESO User Support Department \. ## 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