--- name: "fors_extract" section: "7" platform: "linux" package: "cpl-plugin-fors-doc" version: "5.5.6+dfsg-4" release: "Debian 11 (Bullseye)" platforms: ["linux"] url: "https://new.carta.tech/fors_extract" --- # fors\_extract(7) Extraction of scientific spectra ## NAME fors\_extract - Extraction of scientific spectra ## SYNOPSIS esorex **fors\_extract** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe is used to reduce scientific spectra using the global distortion table created by the recipe fors\_calib. The spectra are bias subtracted, flat fielded (if a normalised flat field is specified) and remapped eliminating the optical distortions. The wavelength calibration can be optionally upgraded using a number of sky lines: if no sky lines catalog of wavelengths is specified, an internal one is used instead. If the alignment to the sky lines is performed, the applied dispersion coefficient table is upgraded and saved to disk, and a new CCD wavelengths map is created. This recipe accepts both FORS1 and FORS2 frames. A grism table (typically depending on the instrument mode, and in particular on the grism used) may also be specified: this table contains a default recipe parameter setting to control the way spectra are extracted for a specific instrument mode, as it is used for automatic run of the pipeline on Paranal and in Garching. If this table is specified, it will modify the default recipe parameter setting, with the exception of those parameters which have been explicitly modifyed on the command line. If a grism table is not specified, the input recipe parameters values will always be read from the command line, or from an esorex configuration file if present, or from their generic default values (that are rarely meaningful). In the table below the MXU acronym can be read alternatively as MOS and LSS, depending on the instrument mode of the input data. Either a scientific or a standard star exposure can be specified in input (not both). Input files: DO category: Type: Explanation: Required:\ SCIENCE\_MXU Raw Scientific exposure Y\ or STANDARD\_MXU Raw Standard star exposure Y\ MASTER\_BIAS Calib Master bias Y\ GRISM\_TABLE Calib Grism table . MASTER\_SKYLINECAT Calib Sky lines catalog . MASTER\_NORM\_FLAT\_MXU Calib Normalised flat field . MASTER\_DISTORTION\_TABLE Calib Global distortion model . or, in case of LSS-like MOS/MXU data, MASTER\_NORM\_FLAT\_LONG\_MXU Calib Normalised flat field . Output files: DO category: Data type: Explanation:\ REDUCED\_SCI\_MXU FITS image Extracted scientific spectra\ REDUCED\_SKY\_SCI\_MXU FITS image Extracted sky spectra\ REDUCED\_ERROR\_SCI\_MXU FITS image Errors on extracted spectra\ UNMAPPED\_SCI\_MXU FITS image Sky subtracted scientific spectra\ MAPPED\_SCI\_MXU FITS image Rectified scientific spectra\ MAPPED\_ALL\_SCI\_MXU FITS image Rectified science spectra with sky\ MAPPED\_SKY\_SCI\_MXU FITS image Rectified sky spectra\ UNMAPPED\_SKY\_SCI\_MXU FITS image Sky on CCD\ GLOBAL\_SKY\_SPECTRUM\_MXU FITS table Global sky spectrum\ OBJECT\_TABLE\_SCI\_MXU FITS table Positions of detected objects Only if the sky-alignment of the wavelength solution is requested:\ SKY\_SHIFTS\_LONG\_SCI\_MXU FITS table Sky lines offsets (LSS-like data)\ or SKY\_SHIFTS\_SLIT\_SCI\_MXU FITS table Sky lines offsets (MOS-like data)\ DISP\_COEFF\_SCI\_MXU FITS table Upgraded dispersion coefficients\ WAVELENGTH\_MAP\_SCI\_MXU FITS image Upgraded wavelength map ## OPTIONS - **--dispersion** *\* Resampling step (Angstrom/pixel) (float; default: 0.0). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.dispersion** \[default = *0.0*\]. - **--skyalign** *\* Polynomial order for sky lines alignment, or -1 to avoid alignment (int; default: 0). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.skyalign** \[default = *0*\]. - **--wcolumn** *\* Name of sky line catalog table column with wavelengths (str; default: ´WLEN´). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.wcolumn** \[default = *WLEN*\]. - **--startwavelength** *\* Start wavelength in spectral extraction (float; default: 0.0). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.startwavelength** \[default = *0.0*\]. - **--endwavelength** *\* End wavelength in spectral extraction (float; default: 0.0). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.endwavelength** \[default = *0.0*\]. - **--flux** *\* Apply flux conservation (bool; default: True). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.flux** \[default = *True*\]. - **--flatfield** *\* Apply flat field (bool; default: False). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.flatfield** \[default = *False*\]. - **--skyglobal** *\* Subtract global sky spectrum from CCD (bool; default: False). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.skyglobal** \[default = *False*\]. - **--skymedian** *\* Sky subtraction from extracted slit spectra (bool; default: False). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.skymedian** \[default = *False*\]. - **--skylocal** *\* Sky subtraction from CCD slit spectra (bool; default: True). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.skylocal** \[default = *True*\]. - **--cosmics** *\* Eliminate cosmic rays hits (only if global sky subtraction is also requested) (bool; default: False). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.cosmics** \[default = *False*\]. - **--slit\_margin** *\* Number of pixels to exclude at each slit in object detection and extraction (int; default: 3). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.slit\_margin** \[default = *3*\]. - **--ext\_radius** *\* Maximum extraction radius for detected objects (pixel) (int; default: 6). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.ext\_radius** \[default = *6*\]. - **--cont\_radius** *\* Minimum distance at which two objects of equal luminosity do not contaminate each other (pixel) (int; default: 0). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.cont\_radius** \[default = *0*\]. - **--ext\_mode** *\* Object extraction method: 0 = aperture, 1 = Horne optimal extraction (int; default: 1). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.ext\_mode** \[default = *1*\]. - **--time\_normalise** *\* Normalise output spectra by the exposure time (bool; default: True). The full name of this option for the EsoRex configuration file is **fors.fors\_extract.time\_normalise** \[default = *True*\]. 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 fors pipeline can be downloaded as a PDF file using the following URL: - **ftp://ftp.eso.org/pub/dfs/pipelines/fors/fors-pipeline-manual-4.9.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 fors pipeline are [*fors\_align\_sky*(7)](/fors_align_sky/7.md), [*fors\_align\_sky\_lss*(7)](/fors_align_sky_lss/7.md), [*fors\_bias*(7)](/fors_bias/7.md), [*fors\_calib*(7)](/fors_calib/7.md), [*fors\_config*(7)](/fors_config/7.md), [*fors\_dark*(7)](/fors_dark/7.md), [*fors\_detect\_objects*(7)](/fors_detect_objects/7.md), [*fors\_detect\_spectra*(7)](/fors_detect_spectra/7.md), [*fors\_extract\_objects*(7)](/fors_extract_objects/7.md), [*fors\_extract\_slits*(7)](/fors_extract_slits/7.md), [*fors\_flatfield*(7)](/fors_flatfield/7.md), [*fors\_img\_science*(7)](/fors_img_science/7.md), [*fors\_img\_screen\_flat*(7)](/fors_img_screen_flat/7.md), [*fors\_img\_sky\_flat*(7)](/fors_img_sky_flat/7.md), [*fors\_normalise\_flat*(7)](/fors_normalise_flat/7.md), [*fors\_photometry*(7)](/fors_photometry/7.md), [*fors\_pmos\_calib*(7)](/fors_pmos_calib/7.md), [*fors\_pmos\_extract*(7)](/fors_pmos_extract/7.md), [*fors\_pmos\_science*(7)](/fors_pmos_science/7.md), [*fors\_remove\_bias*(7)](/fors_remove_bias/7.md), [*fors\_resample*(7)](/fors_resample/7.md), [*fors\_science*(7)](/fors_science/7.md), [*fors\_spec\_mflat*(7)](/fors_spec_mflat/7.md), [*fors\_subtract\_sky*(7)](/fors_subtract_sky/7.md), [*fors\_subtract\_sky\_lss*(7)](/fors_subtract_sky_lss/7.md), [*fors\_sumflux*(7)](/fors_sumflux/7.md), [*fors\_trace\_flat*(7)](/fors_trace_flat/7.md), [*fors\_wave\_calib*(7)](/fors_wave_calib/7.md), [*fors\_wave\_calib\_lss*(7)](/fors_wave_calib_lss/7.md), [*fors\_zeropoint*(7)](/fors_zeropoint/7.md) ## VERSION fors\_extract 5.5.6 ## AUTHOR Carlo Izzo \ ## 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 currently part of the FORS Instrument Pipeline Copyright (C) 2002-2010 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 02110-1301 USA