FORS_EXTRACT(7)

📦 version 5.5.7, in ubuntu jammy, ubuntu noble

💖 FORS_EXTRACT 💖

okay bestie, this is the manual for fors_extract — the Extraction of scientific spectra recipe from the fors pipeline. yes it's a man page in section 7. yes you're gonna understand it. let's go 🦋

✨ NAME ✨

fors_extract — Extraction of scientific spectra

🎀 SYNOPSIS 🎀

esorex fors_extract [OPTIONS] FILE.sof

🌸 DESCRIPTION 🌸

So basically this recipe is the one that reduces your scientific spectra using the global distortion table that the fors_calib recipe made for you. The spectra get bias subtracted, flat fielded (but only if you specified a normalised flat field, no cap), and remapped so the optical distortions just... vanish. ✨ And the wavelength calibration can optionally get an upgrade using a bunch of sky lines — and here's the tea: if you don't specify a sky lines catalog of wavelengths, it just uses an internal one instead. iykyk.

If the alignment to the sky lines does get performed, then the applied dispersion coefficient table is upgraded and saved to disk, and a new CCD wavelengths map is created. slay.

This recipe accepts both FORS1 and FORS2 frames, iconic of it honestly. You may also specify a grism table — which typically depends on the instrument mode, and in particular on the grism used. That table contains a default recipe parameter setting to control the way spectra are extracted for a specific instrument mode, because that's how it's used for automatic runs of the pipeline on Paranal and in Garching. If you do specify this table, 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, then 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 (which are rarely meaningful, bestie, like... not it).

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, pick a lane 💅).

📥 Input files 📥

  • SCIENCE_MXU — DO category: SCIENCE_MXU, Type: Raw, Explanation: Scientific exposure, Required: Y
  • or STANDARD_MXU — DO category: STANDARD_MXU, Type: Raw, Explanation: Standard star exposure, Required: Y
  • MASTER_BIAS — DO category: MASTER_BIAS, Type: Calib, Explanation: Master bias, Required: Y
  • GRISM_TABLE — DO category: GRISM_TABLE, Type: Calib, Explanation: Grism table, Required: .
  • MASTER_SKYLINECAT — DO category: MASTER_SKYLINECAT, Type: Calib, Explanation: Sky lines catalog, Required: .
  • MASTER_NORM_FLAT_MXU — DO category: MASTER_NORM_FLAT_MXU, Type: Calib, Explanation: Normalised flat field, Required: .
  • MASTER_DISTORTION_TABLE — DO category: MASTER_DISTORTION_TABLE, Type: Calib, Explanation: Global distortion model, Required: .
  • or, in case of LSS-like MOS/MXU data: MASTER_NORM_FLAT_LONG_MXU — DO category: MASTER_NORM_FLAT_LONG_MXU, Type: Calib, Explanation: Normalised flat field, Required: .

📤 Output files 📤

  • REDUCED_SCI_MXU — Data type: FITS image, Explanation: Extracted scientific spectra
  • REDUCED_SKY_SCI_MXU — Data type: FITS image, Explanation: Extracted sky spectra
  • REDUCED_ERROR_SCI_MXU — Data type: FITS image, Explanation: Errors on extracted spectra
  • UNMAPPED_SCI_MXU — Data type: FITS image, Explanation: Sky subtracted scientific spectra
  • MAPPED_SCI_MXU — Data type: FITS image, Explanation: Rectified scientific spectra
  • MAPPED_ALL_SCI_MXU — Data type: FITS image, Explanation: Rectified science spectra with sky
  • MAPPED_SKY_SCI_MXU — Data type: FITS image, Explanation: Rectified sky spectra
  • UNMAPPED_SKY_SCI_MXU — Data type: FITS image, Explanation: Sky on CCD
  • GLOBAL_SKY_SPECTRUM_MXU — Data type: FITS table, Explanation: Global sky spectrum
  • OBJECT_TABLE_SCI_MXU — Data type: FITS table, Explanation: Positions of detected objects

Only if the sky-alignment of the wavelength solution is requested:

  • SKY_SHIFTS_LONG_SCI_MXU — Data type: FITS table, Explanation: Sky lines offsets (LSS-like data)
  • or SKY_SHIFTS_SLIT_SCI_MXU — Data type: FITS table, Explanation: Sky lines offsets (MOS-like data)
  • DISP_COEFF_SCI_MXU — Data type: FITS table, Explanation: Upgraded dispersion coefficients
  • WAVELENGTH_MAP_SCI_MXU — Data type: FITS image, Explanation: Upgraded wavelength map

💅 OPTIONS 💅

  • --dispersion <float> — 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 <int> — 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 <str> — 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 <float> — 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 <float> — 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 <bool> — 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 <bool> — 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 <bool> — 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 <bool> — 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 <bool> — 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 <bool> — 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 <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_extract.slit_margin [default = 3].
  • --ext_radius <int> — 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 <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_extract.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_extract.ext_mode [default = 1].
  • --time_normalise <bool> — 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].
heads up bestie 🫶 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 — and yes, we're listing all of them, every single one, no skipping, periodt 👑:

fors_align_sky(7), fors_align_sky_lss(7), fors_bias(7), fors_calib(7), fors_config(7), fors_dark(7), fors_detect_objects(7), fors_detect_spectra(7), fors_extract_objects(7), fors_extract_slits(7), fors_flatfield(7), fors_img_science(7), fors_img_screen_flat(7), fors_img_sky_flat(7), fors_normalise_flat(7), fors_photometry(7), fors_pmos_calib(7), fors_pmos_extract(7), fors_pmos_science(7), fors_remove_bias(7), fors_resample(7), fors_science(7), fors_spec_mflat(7), fors_subtract_sky(7), fors_subtract_sky_lss(7), fors_sumflux(7), fors_trace_flat(7), fors_wave_calib(7), fors_wave_calib_lss(7), fors_zeropoint(7)

⭐ VERSION ⭐

fors_extract 5.5.7

🌈 AUTHOR 🌈

Carlo Izzo <usd-help@eso.org>

💀 BUG REPORTS 💀

Please report any problems to usd-help@eso.org. Alternatively, you may send a report to the ESO User Support Department <usd-help@eso.org>.

📜 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

and that's the whole thing, bestie 💖 this was fors_extract, version 5.5.7, page FORS_EXTRACT(7), from the fors recipes collection — go forth and extract some spectra, you absolute main character 🧚✨

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