MUSE_SCIBASIC(7)

📦
version 2.8.7 · 2 versions
, in debian bookworm, ubuntu noble

💫 MUSE_SCIBASIC 💫

okay bestie, gather round, because this is the muse_scibasic recipe page — yes, that's the manual name, it's muse_scibasic from the muse recipes section 7, and it's genuinely one of the most important ones, no cap 🫶

✨ NAME ✨

muse_scibasic — strip the instrumental signature off the data of each CCD and turn those images into a pixel table. literally the glow-up stage 💅

🌸 SYNOPSIS 🌸

esorex muse_scibasic [OPTIONS] FILE.sof

🦋 DESCRIPTION 🦋

okay so here's the tea. Processing handles each raw input image separately — one at a time, main character energy only 👑

For every raw image it:

  1. trims the raw data and records the overscan statistics
  2. subtracts the bias — and yes, it takes the overscan into account unless --overscan is "none"
  3. optionally detects cosmic rays. not me warning you though 🙈 — by default cosmic ray rejection is handled in the post processing recipes while the data is reformatted into a datacube, so the default setting here is cr="none"
  4. converts the images from adu to count
  5. subtracts the dark
  6. divides by the flat-field
  7. and (optionally) propagates the integrated flux value from the twilight-sky cube

The reduced image then gets saved — that's only if --saveimage=true though, fyi.

Then the input calibrations geometry table, trace table, and wavelength calibration table get used to assign 3D coordinates to each CCD-based pixel, which is how a pixel table gets created for each exposure. iconic ✨

If --skylines contains one or more wavelengths for (bright and isolated) sky emission lines, those lines are used to correct the wavelength calibration using an offset. The data is then cut to a useful wavelength range — only if --crop=true, obviously.

If an ILLUM exposure was given as input, it's used to correct the relative illumination between all slices of one IFU. For this, the data of each slice is multiplied by the normalized median flux of that slice in the ILLUM exposure. so it's giving normalization 💖

And as the last step, the data is divided by the normalized twilight cube (if given), using the 3D coordinate of each pixel in the pixel table to interpolate the twilight correction onto the data.

This pre-reduced pixel table for each exposure is then saved to disk. slay, that's the whole pipeline 🌈

💜 OPTIONS 💜

  • --nifu <int> — which IFU to handle. Set it to 0 and all IFUs are processed serially. Set it to -1 and all IFUs are processed in parallel. (int; default: 0). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.nifu [default = 0].
  • --overscan <str> — if this is "none", stop when detecting discrepant overscan levels (see ovscsigma). For "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly. For "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant. (str; default: vpoly). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.overscan [default = vpoly].
  • --ovscreject <str> — this one decides how values get rejected when computing overscan statistics. Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit"). (str; default: dcr). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.ovscreject [default = dcr].
  • --ovscsigma <float> — if the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing. If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset". (float; default: 30.0). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.ovscsigma [default = 30.0].
  • --ovscignore <int> — the number of pixels of the overscan adjacent to the data section of the CCD that are ignored when computing statistics or fits. (int; default: 3). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.ovscignore [default = 3].
  • --crop <bool> — automatically crop the output pixel tables in wavelength, depending on the expected useful wavelength range of the active instrument mode (4750-9350 Angstrom for nominal mode and NFM, 4700-9350 Angstrom for nominal AO mode, and 4600-9350 Angstrom for the extended modes). (bool; default: True). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.crop [default = True].
  • --cr <str> — type of cosmic ray cleaning to use (for quick-look data processing). (str; default: none). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.cr [default = none].
  • --xbox <int> — search box size in x. Only used if cr=dcr. (int; default: 15). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.xbox [default = 15].
  • --ybox <int> — search box size in y. Only used if cr=dcr. (int; default: 40). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.ybox [default = 40].
  • --passes <int> — maximum number of cleaning passes. Only used if cr=dcr. (int; default: 2). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.passes [default = 2].
  • --thres <float> — threshold for detection gap in factors of standard deviation. Only used if cr=dcr. (float; default: 5.8). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.thres [default = 5.8].
  • --combine <str> — type of combination to use. > Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs! (str; default: none). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.combine [default = none].
  • --nlow <int> — number of minimum pixels to reject with minmax (int; default: 1). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.nlow [default = 1].
  • --nhigh <int> — number of maximum pixels to reject with minmax (int; default: 1). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.nhigh [default = 1].
  • --nkeep <int> — number of pixels to keep with minmax (int; default: 1). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.nkeep [default = 1].
  • --lsigma <float> — low sigma for pixel rejection with sigclip (float; default: 3.0). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.lsigma [default = 3.0].
  • --hsigma <float> — high sigma for pixel rejection with sigclip (float; default: 3.0). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.hsigma [default = 3.0].
  • --scale <bool> — scale the individual images to a common exposure time before combining them. (bool; default: True). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.scale [default = True].
  • --saveimage <bool> — save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. (bool; default: True). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.saveimage [default = True].
  • --skylines <str> — list of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit. It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate. (str; default: 5577.339,6300.304). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.skylines [default = 5577.339,6300.304].
  • --skyhalfwidth <float> — half-width of the extraction box (in Angstrom) around each sky emission line. (float; default: 5.0). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.skyhalfwidth [default = 5.0].
  • --skybinsize <float> — size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. (float; default: 0.1). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.skybinsize [default = 0.1].
  • --skyreject <str> — sigma clipping parameters for the intermediate spectrum to do the Gaussian fit to each sky emission line. Up to three comma-separated numbers can be given, which are interpreted as high sigma-clipping limit (float), low limit (float), and number of iterations (integer), respectively. (str; default: 15.,15.,1). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.skyreject [default = 15.,15.,1].
  • --resample <bool> — resample the input science data into 2D spectral images using all supplied calibrations for a visual check. > Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully! (bool; default: False). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.resample [default = False].
  • --dlambda <float> — wavelength step (in Angstrom per pixel) to use for resampling. (float; default: 1.25). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.dlambda [default = 1.25].
  • --merge <bool> — merge output products from different IFUs into a common file. (bool; default: False). The full name of this option for the EsoRex configuration file is muse.muse_scibasic.merge [default = False].

okay and just so you know, 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. 🎀

…and that's not even the whole page, we're only halfway, don't go anywhere 👀

✨ SEE ALSO ✨

ok so the full documentation for the muse pipeline is a whole PDF bestie, you can download it right here:

ftp://ftp.eso.org/pub/dfs/pipelines/muse/muse-pipeline-cookbook-2.8.7.pdf

there's also a big ✨overview✨ of all the existing ESO pipelines chilling on the web at:

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

wanna know the basics of the EsoRex program? that's all in the esorex(1) man page 💅

and ooooh — you can even call the pipelines from python using the python-cpl package 🐍✨ more deets over at:

https://packages.python.org/python-cpl/index.html

and now, the other recipes of the muse pipeline, the whole friend group, no one left out 👑:

  • muse_ampl(7)
  • muse_astrometry(7)
  • muse_bias(7)
  • muse_create_sky(7)
  • muse_dark(7)
  • muse_exp_align(7)
  • muse_exp_combine(7)
  • muse_flat(7)
  • muse_geometry(7)
  • muse_illum(7)
  • muse_lingain(7)
  • muse_lsf(7)
  • muse_qi_mask(7)
  • muse_scipost(7)
  • muse_scipost_apply_astrometry(7)
  • muse_scipost_calibrate_flux(7)
  • muse_scipost_combine_pixtables(7)
  • muse_scipost_correct_dar(7)
  • muse_scipost_correct_rv(7)
  • muse_scipost_make_cube(7)
  • muse_scipost_raman(7)
  • muse_scipost_subtract_sky(7)
  • muse_scipost_subtract_sky_simple(7)
  • muse_standard(7)
  • muse_twilight(7)
  • muse_wavecal(7)

🌈 VERSION 🌈

muse_scibasic 2.8.7 — that's the one, that's the moment 💖

👑 AUTHOR 👑

Peter Weilbacher <https://support.eso.org> — icon behaviour, honestly 🫶

💀 BUG REPORTS 💀

ok so if something's acting up (and not in a cute way), please report any problems to:

https://support.eso.org

or, if you'd rather slide into the inbox instead, you can send a report straight to the ESO User Support Department:

usd-help@eso.org

no gatekeeping, they genuinely wanna know 🎀

📜 LICENSE 📜

ok so legally speaking, and this part is not a vibe, it's a fact:

this file is part of the MUSE Instrument Pipeline Copyright (C) 2005, 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., 51 Franklin St, Fifth Floor, Boston, MA 02111-1307 USA

fr fr, that warranty disclaimer is doing the most, but it's doing it on purpose. read the license, bestie 💅

and that's a wrap on muse_scibasic, version 2.8.7, living in the MUSE_SCIBASIC(7) manual page — go forth and calibrate your science data, you absolute main character 🌟💖🦋

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