--- name: "fors_science" 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_science" --- # fors\_science(7) Extraction of scientific spectra ## NAME fors\_science - Extraction of scientific spectra ## SYNOPSIS esorex **fors\_science** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe is used to reduce scientific spectra using the extraction mask and the products 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 input dispersion coefficients 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. The acronym SCI on products should be read STD in case of standard stars observations A CURV\_COEFF table is not (yet) expected for LSS data. Either a scientific or a standard star exposure can be specified in input. Only in case of a standard star exposure input, the atmospheric extinction table and a table with the physical fluxes of the observed standard star must be specified in input, and a spectro-photometric table is created in output. This table can then be input again to this recipe, always with an atmospheric extinction table, and if a photometric calibration is requested then flux calibrated spectra (in units of erg/cm/cm/s/Angstrom) are also written in output. 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 . DISP\_COEFF\_MXU Calib Inverse dispersion Y\ CURV\_COEFF\_MXU Calib Spectral curvature Y\ SLIT\_LOCATION\_MXU Calib Slits positions table Y\ FLAT\_SED\_MXU Calib Slits dispersion profile . or, in case of LSS-like MOS/MXU data, MASTER\_NORM\_FLAT\_LONG\_MXU Calib Normalised flat field . DISP\_COEFF\_LONG\_MXU Calib Inverse dispersion Y\ SLIT\_LOCATION\_LONG\_MXU Calib Slits positions table Y\ GLOBAL\_DISTORTION\_TABLE Calib Global distortion . In case STANDARD\_MXU is specified in input, EXTINCT\_TABLE Calib Atmospheric extinction Y\ STD\_FLUX\_TABLE Calib Standard star flux Y\ TELLURIC\_CONTAMINATION Calib Telluric regions list . The following input files are mandatory if photometric calibrated spectra are desired: EXTINCT\_TABLE Calib Atmospheric extinction Y\ SPECPHOT\_TABLE Calib Response curves Y If requested for standard star data, the SPECPHOT\_TABLE can be dropped:\ in this case the correction is applied using the SPECPHOT\_TABLE produced\ in the same run. 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\ OBJECT\_TABLE\_SCI\_MXU FITS table Positions of detected objects Only if the global sky subtraction is requested:\ GLOBAL\_SKY\_SPECTRUM\_MXU FITS table Global sky spectrum 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 Only if a STANDARD\_MXU is specified in input:\ SPECPHOT\_TABLE FITS table Efficiency and response curves Only if a photometric calibration was requested:\ REDUCED\_FLUX\_SCI\_MXU FITS image Flux calibrated scientific spectra\ REDUCED\_FLUX\_ERROR\_SCI\_MXU FITS image Errors on flux calibrated spectra\ MAPPED\_FLUX\_SCI\_MXU FITS image Flux calibrated slit spectra ## OPTIONS - **--skyalign** *\* Polynomial order for sky lines alignment, or -1 to avoid alignment (int; default: -1). The full name of this option for the EsoRex configuration file is **fors.fors\_science.skyalign** \[default = *-1*\]. - **--flatfield** *\* Apply flat field (bool; default: True). The full name of this option for the EsoRex configuration file is **fors.fors\_science.flatfield** \[default = *True*\]. - **--skyglobal** *\* Subtract global sky spectrum from CCD (bool; default: False). The full name of this option for the EsoRex configuration file is **fors.fors\_science.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\_science.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\_science.skylocal** \[default = *True*\]. - **--cosmics** *\* Eliminate cosmic rays hits, only if either global or local (not for LSS) sky subtraction is also requested. (bool; default: False). The full name of this option for the EsoRex configuration file is **fors.fors\_science.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\_science.slit\_margin** \[default = *3*\]. - **--ext\_radius** *\* Maximum extraction radius for detected objects (unbinned pixel) (int; default: 12). The full name of this option for the EsoRex configuration file is **fors.fors\_science.ext\_radius** \[default = *12*\]. - **--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\_science.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\_science.ext\_mode** \[default = *1*\]. - **--resp\_fit\_nknots** *\* Number of knots in spline fitting of the instrument response. (-1: No fitting. -2: Read from grism table) (int; default: -2). The full name of this option for the EsoRex configuration file is **fors.fors\_science.resp\_fit\_nknots** \[default = *-2*\]. - **--resp\_fit\_degree** *\* Degree of polynomial in fitting of the instrument response. (-1: No fitting. -2: Read from grism table) (int; default: -2). The full name of this option for the EsoRex configuration file is **fors.fors\_science.resp\_fit\_degree** \[default = *-2*\]. - **--resp\_ignore\_mode** *\* Types of lines/regions to ignore in response. Valid ones are ´stellar\_absorption´, ´telluric´ and ´command\_line´ (from parameter resp\_ignore\_lines) (str; default: ´stellar\_absorption,telluric,command\_line´). The full name of this option for the EsoRex configuration file is **fors.fors\_science.resp\_ignore\_mode** \[default = *stellar\_absorption,telluric,command\_line*\]. - **--resp\_ignore\_points** *\* Extra lines/regions to ignore in response. Use a comma separated list of values. A range can be specified like 4500.0-4600.0 (str; default: ´´). The full name of this option for the EsoRex configuration file is **fors.fors\_science.resp\_ignore\_points** \[default = \]. - **--resp\_use\_flat\_sed** *\* Use the flat SED to normalise the observed spectra. Value are true, false, grism\_table. (str; default: ´grism\_table´). The full name of this option for the EsoRex configuration file is **fors.fors\_science.resp\_use\_flat\_sed** \[default = *grism\_table*\]. - **--nonlinear\_level** *\* Level above which the detector is not linear (float; default: 60000.0). The full name of this option for the EsoRex configuration file is **fors.fors\_science.nonlinear\_level** \[default = *60000.0*\]. - **--generate\_idp** *\* Set to TRUE to request IDP generation (bool; default: False). The full name of this option for the EsoRex configuration file is **fors.fors\_science.generate\_idp** \[default = *False*\]. 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*(7)](/fors_extract/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\_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\_science 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) 2002-2011 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