--- name: "xsh_cfg_recover" 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_cfg_recover" --- # xsh\_cfg\_recover(7) Optimizes a model configuration to match data taken after a major format change ## NAME xsh\_cfg\_recover - Optimizes a model configuration to match data taken after a major format change ## SYNOPSIS esorex **xsh\_cfg\_recover** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe creates a wavelength solution and an order table. Input Frames :\ \- \[UVB, VIS\] A RAW frame (Format = RAW, Tag = FMTCHK\_arm)\ \- \[NIR\] Two RAW frames (Format = RAW, Tag = FMTCHK\_arm\_ON,FMTCHK\_arm\_OFF)\ \- The old model cfg table (Format = TABLE, Tag = XSH\_MOD\_CFG\_TAB\_arm)\ \- A ref. line list. The model computes corresponding positions \ (Format = TABLE, Tag = ARC\_LINE\_LIST\_arm)\ \- \[UVB,VIS,OPTIONAL\] A master bias (Format = PRE, Tag = MASTER\_BIAS\_arm)\ \- \[UVB,VIS,OPTIONAL\] A master dark (Format = PRE, Tag = MASTER\_DARK\_arm)\ \- \[OPTIONAL-Required if method=pm,peaks\] \ An order table (Format = TABLE, Tag = ORDER\_TAB\_CENTR\_arm)\ \- \[OPTIONAL-Required if first-anneal=TRUE\] \ A table with measured line positions (Format = TABLE, Tag = XSH\_MEASCOORD\_arm)\ Products : \ \- if first-anneal=FALSE & last-step=FALSE\ nothing\ \- if first-anneal=TRUE & last-step=FALSE\ an optimized model configuration, PRO.CATG=XSH\_MOD\_CFG\_arm\ \- if last-step=TRUE\ an optimized model configuration, PRO.CATG=XSH\_MOD\_FAN\_arm\ an optimized model configuration, PRO.CATG=XSH\_MOD\_CFG\_OPT\_arm\ an quality control table, PRO.CATG=MODEL\_GUESS\_XY\_arm\ the model theoretical map corresponding to the optimized model config,\ PRO.CATG=THEO\_TAB\_MULT\_arm, THEO\_TAB\_IFU\_arm, and THEO\_TAB\_SING\_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\_cfg\_recover.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\_cfg\_recover.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\_cfg\_recover.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\_cfg\_recover.decode-bp** \[default = *2144337919*\]. - **--first-anneal** *\* Run first annealing (TRUE) or not (FALSE)See recipe man-page % Input frames (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.first-anneal** \[default = *False*\]. - **--arm** *\* Arm setting: (str; default: ´vis´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_model\_compute.arm** \[default = *vis*\]. - **--name\_i** *\* Filename with wavelength,x,y,order: (str; default: ´line\_xy\_ord.txt´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_model\_compute.name\_i** \[default = *line\_xy\_ord.txt*\]. - **--niter** *\* No of iterations for first anneal (int; default: 100000). The full name of this option for the EsoRex configuration file is **xsh.xsh\_model\_compute.niter** \[default = *100000*\]. - **--coord\_frame** *\* Co-ordinate frame for centroids (0=raw,1=pre) (int; default: 1). The full name of this option for the EsoRex configuration file is **xsh.xsh\_model\_compute.coord\_frame** \[default = *1*\]. - **--last-step** *\* Run last step (TRUE) or not (FALSE)See recipe man-page % Input frames (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.last-step** \[default = *False*\]. - **--plot** *\* Display plot (TRUE) or not (FALSE) (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.plot** \[default = *False*\]. - **--ima\_tresh\_min** *\* Min thresh raw image. (float; default: 40.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.ima\_thresh\_min** \[default = *40.0*\]. - **--cor\_prescan** *\* Correct for prescan (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.cor\_prescan** \[default = *False*\]. - **--method** *\* Model predictions correction method. safefit: safe fitgfit: 2D Gaussian line fitpeaks: line peaks detectionpm: line peaks detection & pattern match (str; default: ´safefit´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.method** \[default = *safefit*\]. - **--offx** *\* X offset to model predictions (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.offx** \[default = *0.0*\]. - **--offy** *\* Y offset to model predictions (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.offy** \[default = *0.0*\]. - **--slit** *\* Extraction slit (int; default: 5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.slit** \[default = *5*\]. - **--gfit\_box\_sy** *\* Gauss fit Y search box size for lines on actual frame (int; default: 20). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.gfit\_box\_sy** \[default = *20*\]. - **--peak\_line\_fwhm** *\* The FWHM used in line convolution, in pixel units (int; default: 4). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.peak\_line\_fwhm** \[default = *4*\]. - **--peak\_kappa** *\* The kappa value, used to identify line peaks if max\>kappa\*stdev+median, max is a valid peak where max, stdev,median are computed on the extracted spectrum (float; default: 5.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.peak\_kappa** \[default = *5.0*\]. - **--peak\_factor** *\* Relative Intensity threshold factor for line peaks detection (float; default: 10.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.peak\_factor** \[default = *10.0*\]. - **--peak\_match\_x** *\* Radii for line peaks matches (int; default: 10). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.peak\_match\_x** \[default = *10*\]. - **--peak\_match\_y** *\* Radii for line peaks matches (int; default: 20). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.peak\_match\_y** \[default = *20*\]. - **--pm\_ord\_sel** *\* From guess line and peaks positions are extracted the ones in the range \[ord\_min,ord\_min+pm\_ord\_sel\] (int; default: 1). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.pm\_ord\_sel** \[default = *1*\]. - **--pm\_radius** *\* Search radius applied in final pattern matching (data units). (float; default: 20.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.pm\_radius** \[default = *20.0*\]. - **--pm\_tolerance** *\* Max relative difference of angles and scales from their median value for match acceptance. (float; default: 0.1). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.pm\_tolerance** \[default = *0.1*\]. - **--anneal\_niter** *\* Simulated annealing iterations (int; default: 1000). The full name of this option for the EsoRex configuration file is **xsh.xsh\_cfg\_recover.anneal\_niter** \[default = *1000*\]. 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\_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\_orderpos*(7)](/xsh_orderpos/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\_cfg\_recover 3.5.0 ## AUTHOR A. Modigliani, P. Bristow \ ## 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