MUSE_DARK(7)

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

✨ MUSE_DARK 💅

okay bestie, so this is a page from the muse recipes manual, and it's all about muse_dark — the recipe that takes a bunch of separate dark images and glues them into one master dark, and also sniffs out the hot pixels. sit down, grab a strawberry 🍓, we're doing science.

NAME 🎀

muse_dark — combine several separate dark images into one master dark file and locate hot pixels.

like. that's the whole vibe. one master dark. hot pixels found. slay.

SYNOPSIS 🌸

esorex muse_dark [OPTIONS] FILE.sof

that's it, that's the invocation. a .sof file and whatever OPTIONS your heart desires. 💖

DESCRIPTION 🦋

so here's the tea, bestie. this recipe combines several separate dark images into one master dark file. the master dark holds the combined pixel values of all those raw dark exposures, and how they get combined depends on the image combination method you picked and the normalization time you specified. no cap.

here's the whole glow-up pipeline, step by step:

  1. it trims the raw data and records the overscan statistics
  2. it subtracts the bias from each raw input image — and yes, it takes the overscan into account, unless --overscan is set to "none"
  3. it converts them from adu to count
  4. it scales them according to their exposure time
  5. it combines them using the input parameters

then it finds the hot pixels using image statistics and marks them in the data quality extension. 💀 iconic behaviour honestly.

the combined image gets normalized to 1 hour exposure time. QC statistics are computed on the output master dark. and if you set --model=true, a smooth polynomial model of the combined master dark gets computed — it's built from several individual 2D polynomials so it can describe the different features you can see in MUSE dark frames.

⚠️ real talk: it is only advisable to use --model=true if the master dark is the result of at least 50 individual long dark exposures. don't come for me if you ignore this, i'm just the messenger 😭

OPTIONS ✨

okay here's the full menu, no skipping, every single one. 🫶

  • --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_dark.nifu [default = 0].
  • --overscan <str> — okay so: if this is "none", processing stops when it detects discrepant overscan levels (see ovscsigma). if it's "offset", it assumes the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly. if it's "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_dark.overscan [default = vpoly].
  • --ovscreject <str> — controls 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_dark.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|, processing stops. if overscan="vpoly", this is used as the sigma rejection level for the iterative polynomial fit (and 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_dark.ovscsigma [default = 30.0].
  • --ovscignore <int> — how many pixels of the overscan, right next to the data section of the CCD, get ignored when computing statistics or fits. (int; default: 3). the full name of this option for the EsoRex configuration file is muse.muse_dark.ovscignore [default = 3].
  • --combine <str> — type of image combination to use. (str; default: ´sigclip´). the full name of this option for the EsoRex configuration file is muse.muse_dark.combine [default = sigclip].
  • --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_dark.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_dark.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_dark.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_dark.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_dark.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_dark.scale [default = True].
  • --normalize <float> — normalize the master dark to this exposure time (in seconds). to disable normalization, set this to a negative value. (float; default: 3600.0). the full name of this option for the EsoRex configuration file is muse.muse_dark.normalize [default = 3600.0].
  • --hotsigma <float> — the sigma level, in terms of median deviation above the median dark level, above which a pixel is detected and marked as ´hot´. (float; default: 5.0). the full name of this option for the EsoRex configuration file is muse.muse_dark.hotsigma [default = 5.0].
  • --model <bool> — model the master dark using a set of polynomials. (bool; default: False). the full name of this option for the EsoRex configuration file is muse.muse_dark.model [default = False].
  • --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_dark.merge [default = False].

btw bestie 🧚 — you can create a configuration file containing these options, along with suitable default values. please refer to the details provided by the 'esorex --help' command. iykyk.

SEE ALSO 🌈

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

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

and yes, 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 muse pipeline are:

  • muse_ampl(7)
  • muse_astrometry(7)
  • muse_bias(7)
  • muse_create_sky(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_scibasic(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)

like a whole friend group fr fr. 💜

VERSION ⭐

muse_dark 2.8.7

AUTHOR 👑

Peter Weilbacher <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>.

(they're nice, i promise. don't be shy, tell them what broke 😭)

LICENSE 📜

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

no cap on that warranty disclaimer bestie, it's giving "use at your own risk" and we respect it 💅

k that's the whole page, you ate it, go build that master dark 🌸💖

muse_dark · version 2.8.7 · MUSE_DARK(7) — mwah, catch you in the next man page 🎀✨🦋

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