FORS_SCIENCE(7)

📦 version 5.5.7, in ubuntu jammy, ubuntu noble

💖 FORS_SCIENCE 💖 — the fors recipes girlies 🎀

ok bestie sit DOWN because we're doing the scientific spectra extraction recipe and it's lowkey a whole journey. this is fors_science, one of the fors recipes, and she's the one who takes your raw science frames and turns them into actual spectra. main character energy fr.

✨ NAME ✨

fors_science — Extraction of scientific spectra 🦋

✨ SYNOPSIS ✨

esorex fors_science [OPTIONS] FILE.sof

✨ DESCRIPTION ✨

okay so this recipe reduces your scientific spectra using the extraction mask plus all the products that the recipe fors_calib made for you. the spectra get bias subtracted, flat fielded (but only if you hand over a normalised flat field, no flat no fielding 💅) and then remapped so those optical distortions are just… gone. not me eliminating distortion, it's giving glow-up.

the wavelength calibration can optionally be upgraded using a bunch of sky lines: if you don't specify a sky lines catalog of wavelengths, an internal one gets used instead. iykyk.

if the alignment to the sky lines actually happens, then the input dispersion coefficients table gets upgraded and saved to disk, and a brand new CCD wavelengths map is created. obsessed.

this recipe accepts both FORS1 and FORS2 frames, no discrimination here 🫶. you may also specify a grism table (typically it depends on the instrument mode, and especially on the grism used): this table contains a default recipe parameter setting that controls the way spectra are extracted for a specific instrument mode, as it's used for automatic runs 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, those stay yours bestie. if a grism table is NOT specified, the input recipe parameter values will always be read from the command line, or from an esorex configuration file if present, or from their generic default values (and those are rarely meaningful, ngl 💀).

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. periodt. 🌈

🌸 Input files 🌸

  • SCIENCE_MXU or STANDARD_MXU — Raw — Scientific exposure / Standard star exposure — Required: Y
  • MASTER_BIAS — Calib — Master bias — Required: Y
  • GRISM_TABLE — Calib — Grism table — Required: .
  • MASTER_SKYLINECAT — Calib — Sky lines catalog — Required: .
  • MASTER_NORM_FLAT_MXU — Calib — Normalised flat field — Required: .
  • DISP_COEFF_MXU — Calib — Inverse dispersion — Required: Y
  • CURV_COEFF_MXU — Calib — Spectral curvature — Required: Y
  • SLIT_LOCATION_MXU — Calib — Slits positions table — Required: Y
  • FLAT_SED_MXU — Calib — Slits dispersion profile — Required: .

or, in case of LSS-like MOS/MXU data,

  • MASTER_NORM_FLAT_LONG_MXU — Calib — Normalised flat field — Required: .
  • DISP_COEFF_LONG_MXU — Calib — Inverse dispersion — Required: Y
  • SLIT_LOCATION_LONG_MXU — Calib — Slits positions table — Required: Y
  • GLOBAL_DISTORTION_TABLE — Calib — Global distortion — Required: .

in case STANDARD_MXU is specified in input,

  • EXTINCT_TABLE — Calib — Atmospheric extinction — Required: Y
  • STD_FLUX_TABLE — Calib — Standard star flux — Required: Y
  • TELLURIC_CONTAMINATION — Calib — Telluric regions list — Required: .

the following input files are mandatory if photometric calibrated spectra are desired:

  • EXTINCT_TABLE — Calib — Atmospheric extinction — Required: Y
  • SPECPHOT_TABLE — Calib — Response curves — Required: 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. iconic behaviour honestly 🎀

🌸 Output files 🌸

  • 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 <int> — 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 <bool> — 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 <bool> — 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 <bool> — 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 <bool> — 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 <bool> — 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 <int> — 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 <int> — 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 <int> — 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 <int> — 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 <int> — 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 <int> — 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 <str> — 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 <str> — 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 <str> — 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 <float> — 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 <bool> — Set to TRUE to request IDP generation (bool; default: True). the full name of this option for the EsoRex configuration file is fors.fors_science.generate_idp [default = True].
🫶 heads up bestie: 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.

and that's part 1, don't go anywhere… 💅

✨ SEE ALSO ✨

okay bestie, if you want the full tea on the whole fors pipeline, you can literally download the entire manual as a PDF from this URL right here:

ftp://ftp.eso.org/pub/dfs/pipelines/fors/fors-pipeline-manual-4.9.pdf

and if you wanna see the whole family tree of ESO pipelines that already exist, the overview is living on this web page:

https://www.eso.org/sci/software/pipelines/

need the basics on EsoRex itself? it's all in the esorex(1) man page, go look 👀

and YES you can call the pipelines from python using the python-cpl package — the way that's such a slay. more info here: https://packages.python.org/python-cpl/index.html

and now, the moment you've been waiting for — the whole fors recipe squad 💅 every single sibling, no one left out:

like, that's a whole friend group fr fr 🫶

🌸 VERSION 🌸

fors_science 5.5.7

👑 AUTHOR 👑

Carlo Izzo <usd-help@eso.org> — iconic, we stan 💖

🚨 BUG REPORTS 🚨

found a problem? spill it. report it to usd-help@eso.org. alternatively, you can also send a report to the ESO User Support Department <usd-help@eso.org>.

(yeah it's the same address both times, that's just how it is bestie, no notes 😭)

💜 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

okay that's the whole page bestie, go forth and reduce some science data 💅✨

and yeah, the footer says this page is fors_science, version 5.5.7, dated FORS_SCIENCE(7) — so basically this manual is serving version 5.5.7 energy, periodt 🎀🦋

byeeee, have the best night reducing frames 💖

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