VMMOSSCIENCE(7)

📦
version 4.1.7 · 2 versions
, in debian bookworm, ubuntu noble

💖 NAME 💖

vmmosscience — extraction of scientific spectra ✨

(yes bestie, that's the whole name — this page is VMMOSSCIENCE(7) from the vimos recipes collection, iykyk 🫶)

✨ SYNOPSIS ✨

esorex vmmosscience [OPTIONS] FILE.sof

🦋 DESCRIPTION 🦋

okay so this recipe is the one that reduces your scientific spectra, and it does it using the extraction mask plus all the products that the recipe vimos_calib made for you. The spectra get bias subtracted, flat fielded (only if a normalised flat field is specified, bestie — otherwise no), and then remapped so all those optical distortions get eliminated. The wavelength calibration can optionally be upgraded using a bunch of sky lines, and here's the cute part: if you don't specify a sky lines catalog of wavelengths, an internal one gets used instead. built-in backup, we love to see it 💅

If the alignment to the sky lines is performed, then the input dispersion coefficients table gets upgraded and saved to disk, and a brand new CCD wavelengths map is created. You may also specify a configuration table (typically it depends on the grism in use): this table holds a default recipe parameter setting that controls the way spectra are extracted for a specific instrument mode, and it's literally what's used for the automatic run 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, because command line said it first, periodt. And if you don't specify a configuration table? 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 🙈 so like… specify your stuff).

Either a scientific or a standard star exposure can be specified in input — dealer's choice, both are valid 💖

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. That 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. iconic behaviour, no cap 🌈

📥 Input files 📥

the vibe check on what you're feeding it:

  • MOS_SCIENCE — Type: Raw — Scientific exposure — Required: Y
  • or MOS_STANDARD — Type: Raw — Standard star exposure — Required: Y
  • MASTER_BIAS — Type: Calib — Master bias — Required: Y
  • SKY_LINE_CATALOG — Type: Calib — Sky lines catalog — Required: . (so, not required)
  • MOS_MASTER_SCREEN_FLAT — Type: Calib — Normalised flat field — Required: . (not required)
  • MOS_DISP_COEFF — Type: Calib — Inverse dispersion — Required: Y
  • MOS_CURV_COEFF — Type: Calib — Spectral curvature — Required: Y
  • MOS_SLIT_LOCATION — Type: Calib — Slits positions table — Required: Y
  • CONFIG_TABLE — Type: Calib — Configuration table — Required: . (not required)

🌟 In case MOS_STANDARD is specified in input,

these three join the group chat:

  • EXTINCT_TABLE — Type: Calib — Atmospheric extinction — Required: Y
  • STD_FLUX_TABLE — Type: Calib — Standard star flux — Required: Y
  • TELLURIC_CONTAMINATION — Type: Calib — Telluric regions list — Required: . (not required)

🔥 In case a photometric calibration is requested for scientific data,

the following inputs are mandatory, no skipping:

  • EXTINCT_TABLE — Type: Calib — Atmospheric extinction — Required: Y
  • MOS_SPECPHOT_TABLE — Type: 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. convenient much? 💅

📤 Output files 📤

quick note before the list, because it matters: the acronym _STD_ replaces _SCI_ and _STANDARD_ replaces _SCIENCE_ in case the input is MOS_STANDARD rather than MOS_SCIENCE 🎀

  • MOS_SCIENCE_REDUCED — Data type: Image — Extracted scientific spectra
  • MOS_SCI_SKY_REDUCED — Data type: Image — Extracted sky spectra
  • MOS_SCI_ERROR_REDUCED — Data type: Image — Errors on extracted spectra
  • MOS_UNMAPPED_SCIENCE — Data type: Image — Sky subtracted scientific spectra
  • MOS_SCIENCE_EXTRACTED — Data type: Image — Rectified scientific spectra
  • MOS_SCIENCE_SKY_EXTRACTED — Data type: Image — Rectified science spectra with sky
  • MOS_SCIENCE_SKY — Data type: Image — Rectified sky spectra
  • MOS_SCI_UNMAPPED_SKY — Data type: Image — Sky on CCD
  • MOS_SCI_GLOBAL_SKY_SPECTRUM — Data type: Table — Global sky spectrum
  • OBJECT_SCI_TABLE — Data type: Table — Positions of detected objects

🧚 Only if fringing correction is requested (dithered exposures):

  • MOS_SCI_FRINGES — Data type: Image — Fringe map

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

  • MOS_SCI_SKYLINES_OFFSETS_SLIT — Data type: Table — Sky lines offsets
  • MOS_SCI_DISP_COEFF_SKY — Data type: Table — Upgraded dispersion coefficients
  • MOS_SCI_WAVELENGTH_MAP_SKY — Data type: Image — Upgraded wavelength map

👑 Only if a MOS_STANDARD is specified in input:

  • MOS_SPECPHOT_TABLE — Data type: Table — Efficiency and response curves

💜 Only if MOS_SPECPHOT_TABLE or MOS_MASTER_RESPONSE are specified in input:

  • MOS_SCIENCE_FLUX_REDUCED — Data type: Image — Flux calibrated scientific spectra
  • MOS_SCI_ERROR_FLUX_REDUCED — Data type: Image — Errors on flux calibrated spectra
  • MOS_SCIENCE_FLUX_EXTRACTED — Data type: Image — Flux calibrated slit spectra

✨ OPTIONS ✨

okay bestie this is the part where you customise everything, so grab a snack 🍓 every single one of these has an EsoRex config-file name too, so you can also just write it in a config file instead of typing it every time. slay.

  • --skyalign <int> — polynomial order for aligning those sky lines, or -1 to just... not align them at all (int; default: -1). EsoRex config name: vimos.vmmosscience.skyalign [default = -1].
  • --flatfield <bool> — apply flat field (bool; default: True). EsoRex config name: vimos.vmmosscience.flatfield [default = True].
  • --skyglobal <bool> — subtract the global sky spectrum from the CCD (bool; default: False). EsoRex config name: vimos.vmmosscience.skyglobal [default = False].
  • --skymedian <bool> — sky subtraction from the extracted slit spectra (bool; default: False). EsoRex config name: vimos.vmmosscience.skymedian [default = False].
  • --skylocal <bool> — sky subtraction from the CCD slit spectra (bool; default: True). EsoRex config name: vimos.vmmosscience.skylocal [default = True].
  • --cosmics <bool> — eliminate cosmic ray hits, and heads up: this only works if global or local sky subtraction is also requested (bool; default: True). EsoRex config name: vimos.vmmosscience.cosmics [default = True].
  • --slit_margin <int> — number of pixels to exclude at each slit when doing object detection and extraction (int; default: 3). EsoRex config name: vimos.vmmosscience.slit_margin [default = 3].
  • --ext_radius <int> — maximum extraction radius for detected objects, in pixels (int; default: 6). EsoRex config name: vimos.vmmosscience.ext_radius [default = 6].
  • --cont_radius <int> — the minimum distance at which two objects of equal luminosity stop contaminating each other, in pixels (int; default: 0). EsoRex config name: vimos.vmmosscience.cont_radius [default = 0].
  • --ext_mode <int> — which object extraction method you want: 0 = aperture, 1 = Horne optimal extraction (int; default: 1). EsoRex config name: vimos.vmmosscience.ext_mode [default = 1].
  • --detection <float> — object detection threshold, in ADU (float; default: 2.0). EsoRex config name: vimos.vmmosscience.detection [default = 2.0].
  • --resp_fit_nknots <int> — number of knots in the spline fitting of the instrument response. (-1: no fitting. -2: read from the grism table) (int; default: -2). EsoRex config name: vimos.vmmosscience.resp_fit_nknots [default = -2].
  • --resp_fit_degree <int> — degree of the polynomial when fitting the instrument response. (-1: no fitting. -2: read from the grism table) (int; default: -2). EsoRex config name: vimos.vmmosscience.resp_fit_degree [default = -2].
  • --resp_ignore_mode <str> — which types of lines/regions to ignore in the response. Valid ones are ´stellar_absorption´, ´telluric´ and ´command_line´ (from the parameter resp_ignore_lines) (str; default: ´stellar_absorption,telluric,command_line´). EsoRex config name: vimos.vmmosscience.resp_ignore_mode [default = stellar_absorption,telluric,command_line].
  • --resp_ignore_points <str> — extra lines/regions to ignore in the response. Give it a comma separated list of values. You can also specify a range like 4500.0-4600.0 (str; default: ´´). EsoRex config name: vimos.vmmosscience.resp_ignore_points [default = ].
  • --resp_use_flat_sed <str> — use the flat SED to normalise the observed spectra. Values are true, false, grism_table. (str; default: ´grism_table´). EsoRex config name: vimos.vmmosscience.resp_use_flat_sed [default = grism_table].
  • --resp_shift <float> — the extracted standard star gets shifted by this many angstroms before it's used to compute the response. this one's for when your observed std stars aren't centered in the slits, we've all been there 🙈 positive values shift the spectrum to the red. The shift is given in Angstroms but no fraction of pixels will be shifted (float; default: 0.0). EsoRex config name: vimos.vmmosscience.resp_shift [default = 0.0].
  • --time_normalise <bool> — normalise the output spectra by the exposure time (bool; default: True). EsoRex config name: vimos.vmmosscience.time_normalise [default = True].
  • --anyframe <bool> — look for a standard star in any frame classified as MOS_STANDARD (bool; default: False). EsoRex config name: vimos.vmmosscience.anyframe [default = False].
  • --alignment <str> — type of alignment of dithered frames, either to the nearest neighbour pixel or to fractions of pixel (str; default: ´integer´). EsoRex config name: vimos.vmmosscience.alignment [default = integer].
  • --stack_method <str> — frames combination method (str; default: ´average´). EsoRex config name: vimos.vmmosscience.stack_method [default = average].
  • --minrejection <int> — number of lowest values to be rejected (int; default: 1). EsoRex config name: vimos.vmmosscience.minrejection [default = 1].
  • --maxrejection <int> — number of highest values to be rejected (int; default: 1). EsoRex config name: vimos.vmmosscience.maxrejection [default = 1].
  • --klow <float> — low threshold in the ksigma method (float; default: 3.0). EsoRex config name: vimos.vmmosscience.klow [default = 3.0].
  • --khigh <float> — high threshold in the ksigma method (float; default: 3.0). EsoRex config name: vimos.vmmosscience.khigh [default = 3.0].
  • --kiter <int> — max number of iterations in the ksigma method (int; default: 999). EsoRex config name: vimos.vmmosscience.kiter [default = 999].
  • --dither <bool> — align dithered frames before stacking (for multiple input frames) (bool; default: True). EsoRex config name: vimos.vmmosscience.dither [default = True].
  • --compute <bool> — compute offsets of dithered images from detected objects (true), or read the offsets from the header (false) (bool; default: False). EsoRex config name: vimos.vmmosscience.dither.compute [default = False].
  • --fringing <bool> — apply fringing correction, and no cap this one is only for dithered observations (bool; default: True). EsoRex config name: vimos.vmmosscience.fringing [default = True].
  • --offset <float> — minimum required offset between exposures for applying the sky fringing correction (float; default: 3.0). EsoRex config name: vimos.vmmosscience.fringing.offset [default = 3.0].
  • --generate_idp <bool> — generate IDP products (bool; default: False). EsoRex config name: vimos.vmmosscience.generate_idp [default = False].
💡 psst — you can totally make a configuration file holding all of these options plus suitable default values, so you never have to type them again. go check the details from the esorex --help command. iykyk.

👀 SEE ALSO 👀

The full documentation for the vimos pipeline can be downloaded as a PDF file using the following URL:

ftp://ftp.eso.org/pub/dfs/pipelines/vimos/vimos-pipeline-manual-6.9.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 vimos pipeline are vimos_ima_bias(7), vimos_ima_dark(7), vimos_ima_det_noise(7), vimos_ima_fringe(7), vimos_ima_science(7), vimos_ima_standard(7), vimos_ima_twilight_flat(7), vmbias(7), vmdark(7), vmdet(7), vmifucalib(7), vmifucombine(7), vmifucombinecube(7), vmifuscience(7), vmifustandard(7), vmmoscalib(7), vmspphot(7) — the whole friend group fr fr 💖

🌈 VERSION 🌈

vmmosscience 4.1.7

🫶 AUTHOR 🫶

Carlo Izzo <https://support.eso.org>

😭 BUG REPORTS 😭

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

👑 LICENSE 👑

This file is part of the VIMOS Instrument Pipeline Copyright (C) 2019 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

and that's the whole thing bestie 💅 this is vmmosscience version 4.1.7, living its life as the VMMOSSCIENCE(7) page — go forth and reduce some spectra, you absolute icon ✨🦋

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