--- name: "kmos_extract_spec" section: "7" platform: "linux" package: "cpl-plugin-kmos-doc" version: "2.1.0+dfsg-1" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/kmos_extract_spec" --- # kmos\_extract\_spec(7) Extract a spectrum from a cube ## NAME kmos\_extract\_spec - Extract a spectrum from a cube ## SYNOPSIS esorex **kmos\_extract\_spec** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe extracts a spectrum from a datacube. The datacube is with or without noise). The output will be a similarly formatted FITS file. Input files: DO KMOS \ category Type Explanation Required #Frames\ \-------- ----- ----------- -------- -------\ \ F3I The datacubes Y 1 \ \ F2I The mask N 0,1 Output files: DO KMOS\ category Type Explanation\ \-------- ----- -----------\ EXTRACT\_SPEC F1I Extracted spectrum \ EXTRACT\_SPEC\_MASK F2I (optional, if --save\_mask=true and \ \--mask\_method=´optimal´: The calculated mask) ## OPTIONS - **--mask\_method** *\* Method used : mask, integrated or optimal (str; default: ´integrated´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.mask\_method** \[default = *integrated*\]. - **--centre** *\* The centre of the circular mask (pixel) (str; default: ´7.5,7.5´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.centre** \[default = *7.5,7.5*\]. - **--radius** *\* The radius of the circular mask (pixel) (float; default: 3.0). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.radius** \[default = *3.0*\]. - **--save\_mask** *\* Flag to save the mask (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.save\_mask** \[default = *False*\]. - **--cmethod** *\* Apply "average", "median", "sum", "min\_max." or "ksigma". (str; default: ´ksigma´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.cmethod** \[default = *ksigma*\]. - **--cpos\_rej** *\* The positive rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.cpos\_rej** \[default = *3.0*\]. - **--cneg\_rej** *\* The negative rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.cneg\_rej** \[default = *3.0*\]. - **--citer** *\* The number of iterations for kappa-sigma-clipping. (int; default: 3). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.citer** \[default = *3*\]. - **--cmax** *\* The number of maximum pixel values to clip with min/max-clipping. (int; default: 1). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.cmax** \[default = *1*\]. - **--cmin** *\* The number of minimum pixel values to clip with min/max-clipping. (int; default: 1). The full name of this option for the EsoRex configuration file is **kmos.kmos\_extract\_spec.cmin** \[default = *1*\]. 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 kmos pipeline can be downloaded as a PDF file using the following URL: - **ftp://ftp.eso.org/pub/dfs/pipelines/kmos/kmos-pipeline-manual-2.9.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 kmos pipeline are [*kmo\_arithmetic*(7)](/kmo_arithmetic/7.md), [*kmo\_copy*(7)](/kmo_copy/7.md), [*kmo\_fit\_profile*(7)](/kmo_fit_profile/7.md), [*kmo\_fits\_strip*(7)](/kmo_fits_strip/7.md), [*kmo\_make\_image*(7)](/kmo_make_image/7.md), [*kmo\_noise\_map*(7)](/kmo_noise_map/7.md), [*kmo\_rotate*(7)](/kmo_rotate/7.md), [*kmo\_shift*(7)](/kmo_shift/7.md), [*kmo\_sky\_mask*(7)](/kmo_sky_mask/7.md), [*kmo\_stats*(7)](/kmo_stats/7.md), [*kmos\_combine*(7)](/kmos_combine/7.md), [*kmos\_dark*(7)](/kmos_dark/7.md), [*kmos\_flat*(7)](/kmos_flat/7.md), [*kmos\_gen\_reflines*(7)](/kmos_gen_reflines/7.md), [*kmos\_gen\_telluric*(7)](/kmos_gen_telluric/7.md), [*kmos\_illumination*(7)](/kmos_illumination/7.md), [*kmos\_reconstruct*(7)](/kmos_reconstruct/7.md), [*kmos\_sci\_red*(7)](/kmos_sci_red/7.md), [*kmos\_sky\_tweak*(7)](/kmos_sky_tweak/7.md), [*kmos\_std\_star*(7)](/kmos_std_star/7.md), [*kmos\_test*(7)](/kmos_test/7.md), [*kmos\_wave\_cal*(7)](/kmos_wave_cal/7.md) ## VERSION kmos\_extract\_spec 2.1.0 ## AUTHOR Alex Agudo Berbel, Y. Jung \ ## BUG REPORTS Please report any problems to usd-help@eso.org. Alternatively, you may send a report to the ESO User Support Department \. ## LICENSE This file is part of the CRIRES Instrument Pipeline Copyright (C) 2002,2003 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