--- name: "xsh_orderpos" section: "7" platform: "linux" package: "cpl-plugin-xshoo-doc" version: "3.5.0+dfsg-4" release: "Debian 11 (Bullseye)" platforms: ["linux"] url: "https://new.carta.tech/xsh_orderpos" --- # xsh\_orderpos(7) Create the orders centre traces table file ## NAME xsh\_orderpos - Create the orders centre traces table file ## SYNOPSIS esorex **xsh\_orderpos** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe creates the orders centre traces table. Input Frames for UVB and VIS:\ Raw file (Tag = ORDERDEF\_arm\_D2)\ Master Dark (Tag = MASTER\_DARK\_arm)\ Master Bias (Tag = MASTER\_BIAS\_arm) Input Frames for NIR:\ Raw file ON(Tag = ORDERDEF\_NIR\_ON)\ Raw file OFF(Tag = ORDERDEF\_NIR\_OFF) Input Frames for all arms\ Guess order table (Tag = ORDER\_TAB\_GUESS\_arm)\ Spectral format table (Tag = SPECTRAL\_FORMAT\_TAB\_arm)\ \- \[OPTIONAL\] A map of non linear bad pixels (Format=QUP, Tag = BP\_MAP\_NL\_arm)\ \- \[OPTIONAL\] A map of reference bad pixels (Format = QUP,RAW, Tag = BP\_MAP\_RP\_arm) Prepare PRE structures. For NIR, subtract NIR-OFF from NIR-ON. For UVB and NIR, Substract the master Bias and master dark. Detect Orders and calculate the order table. The final products are:\ An updated Order Table, PRO.CATG=ORDER\_TABLE\_CENTR\_arm. A order trace residuals Table, PRO.CATG=ORDERPOS\_RESID\_TAB\_arm. The order pos frame bias subtracted, PRO.CATG=ORDERDEF\_ON\_arm. ## OPTIONS - **--keep-temp** *\* If ´no´, temporary files are deleted. (str; default: ´no´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.keep-temp** \[default = *no*\]. - **--debug-level** *\* Additional xshooter debug level. One of ´none´, ´low´, ´medium´, ´high´ (str; default: ´none´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.debug-level** \[default = *none*\]. - **--time-stamp** *\* Add timestamp to product file name. (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.time-stamp** \[default = *False*\]. - **--decode-bp** *\* Integer representation of the bits to be considered bad when decoding the bad pixel mask pixel values. Most frequent codes relevant for the user: 0: good pixel, 8: pick-up noise, 16: cosmic-ray removed, 32: cosmic-ray unremoved, 128: calibration file defect, 256: hot pixel, 512: dark pixel, 4096: A/D converted saturation, 32768: non linear pixel, 1048576: extrapolated flux in NIR, 4194304: Interpolated flux during extraction. (int; default: 2144337919). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.decode-bp** \[default = *2144337919*\]. - **--pre-overscan-corr** *\* pre-overscan correction. 0: no correction 1: mean overscan correction 2: mean prescan correction 3: (mean pre+mean overscan)/2 correction (int; default: 1). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.pre-overscan-corr** \[default = *1*\]. - **--detectcontinuum-search-win-hsize** *\* Half window size in pixels for the 1D box to search for the maximum in the cross-dispersion profile (int; default: 5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-search-win-hsize** \[default = *5*\]. - **--detectcontinuum-running-win-hsize** *\* Half window size for the running median box during the search for the maximum in the cross-dispersion profile (int; default: 0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-running-win-hsize** \[default = *0*\]. - **--detectcontinuum-fit-win-hsize** *\* Half window size for the fit of the cross-dispersion profile (int; default: 5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-fit-win-hsize** \[default = *5*\]. - **--detectcontinuum-center-thresh-fac** *\* Threshold factor applied to check that the flux at the fitted peak is higher than error. (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-center-thresh-fac** \[default = *0.0*\]. - **--detectcontinuum-ordertab-step-y** *\* Step in Y for order centroid detection (int; default: 1). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-ordertab-step-y** \[default = *1*\]. - **--detectcontinuum-ordertab-deg-y** *\* Degree in Y in the polynomial order tracing X=f(Y) (int; default: 5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-ordertab-deg-y** \[default = *5*\]. - **--detectcontinuum-clip-res-max** *\* Maximum allowed residual (before kappa-sigma clip) (float; default: 0.5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-clip-res-max** \[default = *0.5*\]. - **--detectcontinuum-clip-sigma** *\* Kappa value in sigma clipping during order trace polynomial fit (float; default: 5.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-clip-sigma** \[default = *5.0*\]. - **--detectcontinuum-clip-niter** *\* Number of iterations in sigma clipping during order trace polynomial fit (int; default: 5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-clip-niter** \[default = *5*\]. - **--detectcontinuum-clip-frac** *\* Minimal fractions of points accepted / total in sigma clippingduring order trace polynomial fit (float; default: 0.4). The full name of this option for the EsoRex configuration file is **xsh.xsh\_orderpos.detectcontinuum-clip-frac** \[default = *0.4*\]. 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 xshoo pipeline can be downloaded as a PDF file using the following URL: - **ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo-pipeline-manual-12.1.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 xshoo pipeline are [*xsh\_2dmap*(7)](/xsh_2dmap/7.md), [*xsh\_cfg\_recover*(7)](/xsh_cfg_recover/7.md), [*xsh\_flexcomp*(7)](/xsh_flexcomp/7.md), [*xsh\_geom\_ifu*(7)](/xsh_geom_ifu/7.md), [*xsh\_lingain*(7)](/xsh_lingain/7.md), [*xsh\_mbias*(7)](/xsh_mbias/7.md), [*xsh\_mdark*(7)](/xsh_mdark/7.md), [*xsh\_mflat*(7)](/xsh_mflat/7.md), [*xsh\_predict*(7)](/xsh_predict/7.md), [*xsh\_respon\_slit\_nod*(7)](/xsh_respon_slit_nod/7.md), [*xsh\_respon\_slit\_offset*(7)](/xsh_respon_slit_offset/7.md), [*xsh\_respon\_slit\_stare*(7)](/xsh_respon_slit_stare/7.md), [*xsh\_scired\_ifu\_offset*(7)](/xsh_scired_ifu_offset/7.md), [*xsh\_scired\_ifu\_offset\_drl*(7)](/xsh_scired_ifu_offset_drl/7.md), [*xsh\_scired\_ifu\_stare*(7)](/xsh_scired_ifu_stare/7.md), [*xsh\_scired\_ifu\_stare\_drl*(7)](/xsh_scired_ifu_stare_drl/7.md), [*xsh\_scired\_slit\_nod*(7)](/xsh_scired_slit_nod/7.md), [*xsh\_scired\_slit\_offset*(7)](/xsh_scired_slit_offset/7.md), [*xsh\_scired\_slit\_stare*(7)](/xsh_scired_slit_stare/7.md), [*xsh\_util\_physmod*(7)](/xsh_util_physmod/7.md), [*xsh\_wavecal*(7)](/xsh_wavecal/7.md) ## VERSION xsh\_orderpos 3.5.0 ## AUTHOR L.Guglielmi,R.Haigron,P.Goldoni,F.Royer, A. Modigliani \ ## BUG REPORTS Please report any problems to amodigli@eso.org. Alternatively, you may send a report to the ESO User Support Department \. ## LICENSE This file is part of the X-shooter Instrument Pipeline Copyright (C) 2006 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA