FORS_PMOS_EXTRACT(7)

📦 version 5.5.7, in ubuntu jammy, ubuntu noble

💖 fors_pmos_extract 💖

okay bestie, welcome to the FORS recipe corner of the group chat — this one is fors_pmos_extract, a section 7 (7 = "recipes, not commands") manual page from the fors recipes collection. grab a boba, we're extracting spectra 🌈

✨ NAME ✨

fors_pmos_extract — extraction of scientific spectra 🦋

🌸 SYNOPSIS 🌸

esorex fors_pmos_extract [OPTIONS] FILE.sof

that's it, that's the whole vibe check 💅

🎀 DESCRIPTION 🎀

so this recipe is the one that reduces your scientific spectra, using the extraction mask and the products that the recipe fors_mpol_calib made for you. like, it takes those and then does the whole glow-up: the spectra get bias subtracted, flat fielded (but ONLY if a normalised flat field is specified — no flat, no flat-fielding, that's the rule ✨), and remapped so the optical distortions are gone. bye distortion 👋

and then — optional slay — the wavelength calibration can be upgraded using a bunch of sky lines. if you don't specify a sky lines catalog of wavelengths, it just uses an internal one instead. convenient 💜

if the alignment to the sky lines does happen, then the input dispersion coefficients table gets upgraded and saved to disk, AND a brand new CCD wavelengths map is created. two for one, we love to see it 🫶

this recipe accepts both FORS1 and FORS2 frames. you may also specify a grism table (which typically depends on the instrument mode, and in particular on the grism used — iykyk). that table contains a default recipe parameter setting that controls the way spectra get extracted for a specific instrument mode, exactly as it's used for automatic runs of the pipeline on Paranal and in Garching. and if you DO specify this table, it will modify the default recipe parameter setting — with the exception of those parameters which have been explicitly modified on the command line. those ones stay yours, bestie, nobody touches them. but 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 one is present, or from their generic default values (which are, and I'm quoting the lore here, rarely meaningful 💀).

either a scientific exposure or a standard star exposure can be specified in input. dealer's choice 🌟

oh and heads up: the acronym SCI on products should be read as STD in the case of standard stars observations. just a little rename, no biggie.

📥 Input files

  • SCIENCE_PMOS or STANDARD_PMOS — Raw — Scientific exposure or 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_PMOS — Calib — Normalised flat field — Required: .
  • DISP_COEFF_PMOS — Calib — Inverse dispersion — Required: Y
  • CURV_COEFF_PMOS — Calib — Spectral curvature — Required: Y
  • SLIT_LOCATION_PMOS — Calib — Slits positions table — Required: Y
  • RETARDER_WAVEPLATE_CHROMATISM — Calib — Chromatism correction — Required: .

(quick legend so you're not lost: Y = yes you need it, . = optional, she's optional, she's flexible 💅)

📤 Output files

  • REDUCED_SCI_PMOS — FITS image — Extracted scientific spectra
  • REDUCED_SKY_SCI_PMOS — FITS image — Extracted sky spectra
  • REDUCED_ERROR_SCI_PMOS — FITS image — Errors on extracted spectra
  • REDUCED_SCI_X_PMOS — FITS image — X Stokes parameter (and L)
  • REDUCED_ERROR_X_PMOS — FITS image — Error on X Stokes parameter
  • REDUCED_NUL_X_PMOS — FITS image — Null parameter for X
  • REDUCED_POL_ANGLE_PMOS — FITS image — Direction of linear polarization
  • REDUCED_POL_ANGLE_ERROR_PMOS — FITS image — Error on polarization direction
  • UNMAPPED_SCI_PMOS — FITS image — Sky subtracted scientific spectra
  • MAPPED_SCI_PMOS — FITS image — Rectified scientific spectra
  • MAPPED_ALL_SCI_PMOS — FITS image — Rectified science spectra with sky
  • MAPPED_SKY_SCI_PMOS — FITS image — Rectified sky spectra
  • UNMAPPED_SKY_SCI_PMOS — FITS image — Sky on CCD
  • GLOBAL_SKY_SPECTRUM_PMOS — FITS table — Global sky spectrum
  • OBJECT_TABLE_SCI_PMOS — FITS table — Positions of detected objects
  • OBJECT_TABLE_POL_SCI_PMOS — FITS table — Positions of real objects

and ONLY if the sky-alignment of the wavelength solution is requested, you ALSO get these two bonus icons 👑:

  • DISP_COEFF_SCI_PMOS — FITS table — Upgraded dispersion coefficients
  • WAVELENGTH_MAP_SCI_PMOS — FITS image — Upgraded wavelength map

💅 OPTIONS 💅

every single one, no skips, no cuts, we're eating the whole plate 🍓

  • --dispersion <float> — Resampling step, in Angstrom/pixel. it's a float, default is 0.0. the full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.dispersion [default = 0.0].
  • --skyalign <int> — Polynomial order for sky lines alignment, or -1 to avoid alignment entirely. int, default 0. full config name: fors.fors_pmos_extract.skyalign [default = 0].
  • --wcolumn <str> — Name of the sky line catalog table column that holds the wavelengths. str, default ´WLEN´. full config name: fors.fors_pmos_extract.wcolumn [default = WLEN].
  • --startwavelength <float> — Start wavelength in spectral extraction. float, default 0.0. full config name: fors.fors_pmos_extract.startwavelength [default = 0.0].
  • --endwavelength <float> — End wavelength in spectral extraction. float, default 0.0. full config name: fors.fors_pmos_extract.endwavelength [default = 0.0].
  • --flux <bool> — Apply flux conservation. bool, default True. full config name: fors.fors_pmos_extract.flux [default = True].
  • --flatfield <bool> — Apply flat field. bool, default False. full config name: fors.fors_pmos_extract.flatfield [default = False].
  • --skyglobal <bool> — Subtract global sky spectrum from CCD. bool, default False. full config name: fors.fors_pmos_extract.skyglobal [default = False].
  • --skymedian <bool> — Sky subtraction from extracted slit spectra. bool, default False. full config name: fors.fors_pmos_extract.skymedian [default = False].
  • --skylocal <bool> — Sky subtraction from CCD slit spectra. bool, default True. full config name: fors.fors_pmos_extract.skylocal [default = True].
  • --cosmics <bool> — Eliminate cosmic rays hits — but note: only if global sky subtraction is also requested. bool, default False. full config name: fors.fors_pmos_extract.cosmics [default = False].
  • --slit_margin <int> — Number of pixels to exclude at each slit in object detection and extraction. int, default 3. full config name: fors.fors_pmos_extract.slit_margin [default = 3].
  • --ext_radius <int> — Maximum extraction radius for detected objects, in pixels. int, default 6. full config name: fors.fors_pmos_extract.ext_radius [default = 6].
  • --cont_radius <int> — Minimum distance at which two objects of equal luminosity do not contaminate each other, in pixels. int, default 0. full config name: fors.fors_pmos_extract.cont_radius [default = 0].
  • --ext_mode <int> — Object extraction method: 0 = aperture, 1 = Horne optimal extraction. int, default 1. full config name: fors.fors_pmos_extract.ext_mode [default = 1].
  • --time_normalise <bool> — Normalise output spectra by the exposure time. bool, default True. full config name: fors.fors_pmos_extract.time_normalise [default = True].
  • --chromatism <bool> — Chromatism correction to polarization angles. bool, default True. full config name: fors.fors_pmos_extract.chromatism [default = True].
  • --check <bool> — Create intermediate products. bool, default False. full config name: fors.fors_pmos_extract.check [default = False].
📝 and psst — 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. it's giving self-care, honestly.

🦋 SEE ALSO 🦋

the full documentation for the fors pipeline can be downloaded as a PDF file using this 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's also possible to call the pipelines from python using the python-cpl package. see https://packages.python.org/python-cpl/index.html for further information.

and the other recipes of the fors pipeline — the whole friend group, honestly, they're all iconic — are:

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(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_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_pmos_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>. they will help, fr fr 🫶

📜 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 page bestie, no cap 🧚 this was fors_pmos_extract, version 5.5.7, living in section 7 of the fors recipes collection — go extract something gorgeous 🌸💜

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